[libur-perl] annotated tag upstream/0.450 created (now 3060100)
gregor herrmann
gregoa at debian.org
Mon Oct 31 23:18:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
gregoa pushed a change to annotated tag upstream/0.450
in repository libur-perl.
at 3060100 (tag)
tagging d3bf5cbe92fba108710dd86301d159fd2897a6df (commit)
replaces upstream/0.440
tagged by gregor herrmann
on Mon Oct 31 23:40:18 2016 +0100
- Log -----------------------------------------------------------------
Upstream version 0.450
APipe Tester (53):
Updated class browser cache.
Updated `ur` tab completion.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated `ur` tab completion.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Merge pull request #17 from tmooney/master
Merge pull request #37 from nnutter/master
Merge pull request #38 from amb43790/perl5.8-fix
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Updated class browser cache.
Adam Coffman (4):
Make boolean a subclass of Text
add text view for boolean type
Make AND and OR case insensitive in boolean expressions.
Change _message methods to only run sprintf if multiple args are passed
Adam Dukes (16):
test for INSERT(null)/UPDATE nullable foreign keys, and UPDATE(null)/DELETE
test update
adding nullable fk constraint checks
update
update
setting nullable foreign keys to null on delete works
half ass update, need to remove fks that are in primary key
nulling nullable foreign keys pre insert and delete, and updating fk_column values post insert complete
numbered test, added a check for empty get after deletion, removed a test that looked for sql that correctly is not produced when no_commit is on
Merge branch 'master' of git at github.com:sakoht/UR into null_fk
restoring meta.sqlite3-dump and schema to original ur versions
adjusted cleanup files method to use the namespace base directory when removing files. Previously it assumed you were in the base namespace dir if 'URT' appeared in your path
Merge branch 'null_fk'
new branch
fixed bug in recursively generating names in command_name() in Command.pm
reverted an edition to filter_by_string that allowed 'and's in the
Anthony Brummett (2211):
Initial copy from svn r31720 on 13 Jan 2008 when UR was moved from
Made YAML::Syck optional. It's only used in debugging dumps, where performance isn't a requirement, and breaks our ability to run on perl5.6.
From svn r31965 on 2008-01-24 12:02:49 -0600 (Thu, 24 Jan 2008)
From svn r33612 on 2008-04-10 15:39:57 -0500 (Thu, 10 Apr 2008)
From svn r33671 on 2008-04-14 22:13:49 -0500 (Mon, 14 Apr 2008)
From svn r35285 on 2008-06-05 15:32:18 -0500 (Thu, 05 Jun 2008)
From svn r35748 on 2008-06-20 11:25:05 -0500 (Fri, 20 Jun 2008)
From svn r35760 on 2008-06-20 13:42:47 -0500 (Fri, 20 Jun 2008)
From svn r35952 on 2008-06-26 11:10:29 -0500 (Thu, 26 Jun 2008)
From svn r38012 on 2008-08-29 09:33:26 -0500 (Fri, 29 Aug 2008)
From svn r38307 on 2008-09-04 15:55:28 -0500 (Thu, 04 Sep 2008)
From svn r38465 on 2008-09-09 16:23:37 -0500 (Tue, 09 Sep 2008)
From svn r38543 on 2008-09-11 14:30:52 -0500 (Thu, 11 Sep 2008)
From svn r39094 on 2008-09-25 17:01:04 -0500 (Thu, 25 Sep 2008)
From svn r39297 on 2008-10-02 13:23:16 -0500 (Thu, 02 Oct 2008)
From svn r39481 on 2008-10-07 13:52:12 -0500 (Tue, 07 Oct 2008)
From svn r41360 on 2008-11-25 14:50:40 -0600 (Tue, 25 Nov 2008)
From svn r41421 on 2008-11-26 16:45:10 -0600 (Wed, 26 Nov 2008)
From svn r41422 on 2008-11-26 16:57:12 -0600 (Wed, 26 Nov 2008)
Now supports the create_from_inline_class_data() API
From svn r42803 on 2009-01-20 10:09:47 -0600 (Tue, 20 Jan 2009)
From svn r43039 on 2009-01-27 11:08:48 -0600 (Tue, 27 Jan 2009)
From svn r43731 on 2009-02-18 15:17:48 -0600 (Wed, 18 Feb 2009)
From svn r45356 on 2009-04-03 08:43:33 -0500 (Fri, 03 Apr 2009)
From svn r46107 on 2009-04-22 10:51:27 -0500 (Wed, 22 Apr 2009)
From svn r46180 on 2009-04-23 15:48:19 -0500 (Thu, 23 Apr 2009)
From svn r46660 on 2009-05-07 16:02:57 -0500 (Thu, 07 May 2009)
From svn r46713 on 2009-05-09 13:53:03 -0500 (Sat, 09 May 2009)
Relocated the URT namespaces under UR/t for easier distribution.
From svn r46729 on 2009-05-11 09:03:56 -0500 (Mon, 11 May 2009)
From svn r46730 on 2009-05-11 09:04:50 -0500 (Mon, 11 May 2009)
From svn r46825 on 2009-05-13 15:29:11 -0500 (Wed, 13 May 2009)
From svn r46839 on 2009-05-14 02:39:03 -0500 (Thu, 14 May 2009)
From svn r46862 on 2009-05-14 12:17:09 -0500 (Thu, 14 May 2009)
From svn r47001 on 2009-05-20 05:34:35 -0500 (Wed, 20 May 2009)
From svn r47004 on 2009-05-20 09:34:18 -0500 (Wed, 20 May 2009)
From svn r47134 on 2009-05-21 21:40:04 -0500 (Thu, 21 May 2009)
From svn r47150 on 2009-05-22 09:03:32 -0500 (Fri, 22 May 2009)
From svn r47151 on 2009-05-22 09:15:53 -0500 (Fri, 22 May 2009)
From svn r47349 on 2009-05-28 17:19:23 -0500 (Thu, 28 May 2009)
'ur update dbic-classes' is renamed to 'ur export dbic classes'
Some final adjustments to get us current with svn 50717 on 3 Sep 2009
Forgot to include Devel::callcount
First commit for branch to manage CPAN releases where everything is layed out properly
A fre more files for a proper CPAN release dir
Finally a link to the doc dir
Importing the CPAN release 0.10 of UR
Imported CPAN release 0.11
Merge branch 'CPAN-releases-0.11' into merge-11-and-master
Further cleanup after merging 0.11 and master
Updated version numbers and Changes file in preparation for 0.12 release
Remove UR/Object/Property/Compressable.pm
Getopt::Long does now support processing opts from an arbitrary list.
Don't install the singular accessor sub when the property name is not plural
Add -I and --inc options to 'ur test run' to add paths to perl's -I
Remove UR/Object/Property/Compressable.pm from MANIFEST
Revert a previous change in Command.pm with GetOptions()
make the iterator merge test pass on Ubuntu 9.04
Forgot to change the call to GetOptionsFromList back to GetOptions
Corrected typos in Context.pod
Make sure UR_USE_DUMMY_AUTOGENERATED_IDS is 0 instead of undef
Merge branch 'master' of /gscuser/mjohnson/git/UR
Remove some debugging stuff
Croak with an error message if the metadata for PK cols is wrong
Made some umlet diagrammer class properties is_optional so commit() no longer complains
'ur update class-diagram' now excludes UR::Object and UR::Entity by default
Correct handling for MetaDB ghost objects, and what metaDB they belong to
Better parsing during _resolve_fk_name and table definitions spanning multiple lines
Better handling for a get() involving some classes with datasource and others without
Allow calling commit() and rollback as a function - but print a warning
Fixed an error message for when you get class objects in scalar context
Merge commit 'origin/master'
Merge branch 'master' of git at github.com:sakoht/UR
In UR::DataSource::RDBMS::_id_values_for_primary_key(), check that the primary key columns
Fix a bug involving filters on delegated properties with overlapping classes/tables.
Merge branch 'master' of git at github.com:sakoht/UR
Got the 'not in' operator working with a test case
Improved message when moving a deleted file
Print the SQL params as part of the failure message
Add more test cases for default values
Merge branch 'master' of git at github.com:sakoht/UR
Better error msgs when using a via property and the remote class didn't load
Merge branch 'master' of github.com:sakoht/UR
ur update classes test now wipes out any metaDB data
Fix for my previous fix/commit "Better error msgs"
fixed the synopsis help
Copied deployed versions of UR::Contest and UR::Object
Remove breakpoint
Update UR::Context's POD to document reload() and data concurrency ideas
Change the rules for data-change conflicts when loading data
Remove breakpoints
Removed a commented-out line that was messing up vi's bracket matching
Fixes for whitespace/intenting that were introduced in commit
nullable_hangoff_data.t test works
Eliminate unnecessary method call
Final fix for the nulalble hangoff data test
Complain if we weren't able to find a TableColumn while processing the FK data
Fixed the error message about missing foreigh key metadata
Only breakpoint when there are any keys in %$extra
Improve msg when objects are invalid during commit()
Command params with default values now show those values in the help text
More help text improvments for Command.pm
Teach the modulewriter about 'id_class_by' property properties
Teach the modulewriter about more complicated 'where'
Comment ouit a breakpoint
Another fix for the conflicting data problem
Remove old, commented-out code that was refactored/replaced in the last commit
Simplified the data merging code.
Changed some of the class/table names in the data merge test to make them more clear
Change some dies to Carp::croak and improve messages
added "require Test::MockObject"
Fixed some POD errors with =back
Typo on the variable name in a message
Error message for missing required command args improved
Improve error message when there's @extra stuff after resolving rule
You can get query stats from the Context
Change for SQL where clause building where property exists in parent and child classes
Cache the results of $self->monitor_query to improve speed
Remove MONITOR_QUERY messages about calling the db_iterator
Change the MONITOR_QUERY messages to include a running elapsed time for each rule
Change accounting of applicable filters during SQL generation
Improve error message when an unknown property is used to filter
Improve SQL performance when querying a subclass and the parent class has subclassify_by
Further tweaking to the monitor query output
Some monitor_query things commented out for performance testing
Some small performace tweaks
Make the monitor query messages more consistent
Add documentation about UR_CONTEXT_MONITOR_QUERY
Get rid of a warning
For undocumented command module properties, try getting documentation from parent classes
Rearrange autogenerated help text for object lister commands
Get rid of a warning when checking data_type for '::'
Remove unnecessary checks for the monitor_query flag
Fix a bug where turning monitor_sql programmaticaly causes logging in UR::DataSource::File to die
Make Sys::Hostname import nothing, and call Sys::Hostname::hostname using the fully-qualified name
Rename UR::Object::Viewer::create_viewer() to create()
Rename UR::Object::Viewer::create_viewer() to just create().
a Viewer's subject_id is technically is_optional, since you might create a viewer and never assign a subject
Setting indirect properties at object creation time works
Setting indirect properties through their default_values now works
Test an indirect property's default value refering to something that already exists
Update the class initializer documentation about default_value
Refactoring the UR namespace commands describe, browser and info to the new View system
'ur describe <class>' is now working
'ur info <thing' now works
Be more user-friendly when figuring out default aspects for a view
Object listers with the newtext style is now working with the new View system
Attempts at getting the View system cleaned up and ready to merge
Fixed the recursive View problem
Got the Default text view test to verify the text is correct
Moved the default text test to the appropriate place under URT
Get rid of some warnings
Further refactor for moving from the old Viewer system to the new View system
Be smarter when finding the encompassing view
Fix bug in the file DataSource with 'like' operator
Merge branch 'master' of github.com:sakoht/UR
Give a name to UR::Object::Type::InternalAPI's composite_id_decomposer and composite_id_resolver closures
Fix cut-and-paste error in the last commit with an incorrectly named variable
Check $! after reading a line from the file. If a real error occurred, throw an exception
Merge branch 'master' of github.com:sakoht/UR
Use Carp::shortmess to show where a query originates from when UR_CONTEXT_MONITOR_QUERY=1
Fix for spurious exception about: Can't locate object method "class"
Attempt to mitigate slowness in UR::BoolExpr by making query() smarter
Remove all the classes/methods involved in the old Viewer system
Fix for 'ur describe' failing after commit 2e47287c
Remove a warning about printing undefined value in the error message printed after queries in _sync_database
with --lsf and --jobs, actually limit the number of lsf jobs to what the user specified
Gracefully handle control-C while tests are running.
Cosmetic fixups for the test runner
On advice from our DBA, stop doing '_hash_join_enabled"=FALSE' after connecting
Hack to get around a problem with OSX 10.5 and getline()/<FH>.
use Sub::Name::subname() to give the data source iterators names
use File::Temp to create temp filenames/directories instead of assumming /tmp/
Get rid of a warning on perl 5.12
use Sub::Name::subname() to give the FileMux data source iterator a name
Show the last param of DBI connect as a hashref with keys/values instead of the string 'HASH(0x1234)'
Removed a warning about exists() with an undefined key
Fix a bug with loading and saving objects where the table_name included the schema/owner
First commit for commit() using map-reduce-ish stuff
File to enable the UR_NR_CPU env var
Move the dbh disconnect to before the fork()s to get around oracle errors
parallel_grep() now works on lists that might not contain objects
Moved UR::Context::_parallel_grep() to UR::Util::mapreduce_grep()
Make UR::Context::_sync_databases _not_ use mapreduce_grep()
Test case for command help text
Save a function call by saving the return value from cmd->doc the first time
Don't show duplicated params in Command help text
Better error message while processing an indirect property
'ur test run' will now return exit code 1 if one or more tests fail, and code 0 if they all passed
Added a 'product' built-in calculation property
Don't write out metaDB info for namespaces without filesystem representation
Remove the fake 'is_indirect' meta-property. It was used as an alias for is_delegated or is_calculate or is_legacy_eav.
Support properties that are calculated and not is_mutable.
Add another test to the calculated_accessor test to ensure that calculated+is_constant proprties only call the calculation sub when the value is needed, and not before
Improve error messages during subclassify_by automagic subclassing
Testcase for automagic subclassification via subclassify_by
Improve error messages that happen around subclassify_by magic
Added test cases for subclassify_by and they all pass now
Add method UR::Util->display_string_for_params_list()
Calculated subclassify_by is working
Initial code for subclassify_by being an indirect property. Doesn't work correctly yet
Revert Tom's change in f4f640... that was put in to revert part of ef68b5... that included code that wasn't ready to go in yet
Refactor the UR::Context::create_entity() code about subclassify_by into new method _create_entity_from_abstract_class()
When a property is calculate+immutable, pass the known creation params in as a list instead of a hashref
Misc cleanup for the subclassify_by refactoring
Change the implementation for cached, calculated properties
Calculated accessors can now specify 'self' in the calculate_from, and have it passed in as an arg
A calculated subclassify_by now works for objects loaded from the DB.
Alter control-C behavior while running tests
Add --color option to 'ur test run' to product color output
Fix a (mostly cosmetic issue) where 'ur test run' could insert an empty path to $PERL5LIB
Fix a problem where multiple "-I"s to 'ur test run' would not do what you expected
Fixed a bug where tests ran in an exec-ed perl would not load modules from the namespace your cwd was under
The test harness (ur test run) can again be run when you're not in a namespace dir
Add a __self__ method to UR::Object
Updated the indirect accessor test for things which already worked but were not tested properly
UR::Datasource::RDBMS::PendingDDL tried to refer to ::Table using 4 ID properties, but it only has 3
Improve the error message you get when you mess up the id_by metadata in an object accessor
simple comment/doc addition for UR::Object::__self__
The Accessorwriter now supports calculate properties having a column_name
Comment out the part in the class Initializer where it croaks if you have a delegated subclassify_by
More changes to subclassify_by final subclass resolution
Test cases for the new calculated/subclassify proeprties
More support for subclassify_by being an indirect property
Even more support for subclassify_by being an indirect property
Cosmetic changes to error messages
Yet more support for subclassify_by being an indirect property
Fix for indirect property value handling in create_entity
Merge branch 'master' into calculated_subclassify_by
Go back to older behavior for some automagic subclassing
Revert an earlier change when we needed to keep around %extra params after rule creation on an abstract parent class
Go back to older behavior in create_entity() where we're binning properties of the creation class
Add a test for a class that overrides the default_value of a parent class
Final cleanup of the subclassify_by refactoring
'ur test run' can now detect when lsf-ed jobs aren't starting up properly.
Removing unnecessary modules.
First pass at internal functions to load/save SQLite databases when the sqlite3 executable isn't available
Add a --junit command line option to the test runner
Merge branch 'junit'
Reformat a comment so it doens't run off the edge of the terminal
Rename UR::DataSource::RDBMS::disconnect_default_dbh() to disconnect_default_handle()
UR::DataSource::SQLite::_init_database() is now called from within create_dbh() instead of server()
Change URT::DataSource::SomeSQLite to use File::Temp to make temp DB files and clean them up automatically afterward
Update t/URT/t/98_ur_update.t to create the DB file before accessing it
Give the test a plan
Better handling of the internal dump/restore of the DB file when the sqlite3 binary isn't available
A test case for the internal dump/restore of sqlite databases
server() (rather than _database_file_path) is again the canonical way to specify the DB file path for SQLite datasources
Make the Vending machine datasource fab up a new, independent DB file with File::Temp for every execution
Merge branch 'master' into sqlitefix
All these namespace-oriented command modules did not have a call to $self->_init and weren't working
Update version number to 0.14
Update Changes file for 0.14 release
Update MANIFEST in preparation for 0.14
One more change message about SQLite internal initialization
Remove warnings about redeclared temporary variables
One more redefined temporary variable in the test
Remove warnings generated by Text::Wrap if any of the passed-in strings are undef
Fixes for 'ur update classes' on a mysql database
Keep better track of table names during resolve_attribute_name_for_column_name() used by 'ur update classes'
Remove an 'uninitialized value' warning that happens when the user has no PERL5LIB env var set
Forgot a closing paren from the last commit
Refuse to load a class where there are multiple ID properties and one of them is called "id"
Update the documentation to more clearly state that you shouldn't name a table "type" and shouldn't use a column named "id"
If 'ur update classes' comes across a table named "type", make the generated class named TypeTable to avoid a conflict with the class metadata
Point to the new SchemaDesign pod
Remove more occurances of "type_name" and "parent_type_name"
If a Namespace command has problems loading a module, print out the failure message
Print out a warning when it comes across a table called 'type' that it is renaming the resulting class/module to TypeTable
UR::DataSource::Mysql override for get_foreign_key_details_from_data_dictionary.
Some DBD drivers return foreign_key_info() data in different key names
Merge branch 'master' into mysqlfix
Added XML::LibXML to the required module list
Bumped up the version number to 0.15
Updated MANIFEST
Remove reference to 'Genome' namespace
When creating a completion spec file, print a warning and continue if a module doesn't load
Require Getopt::Complete v0.13 for the new bash completion functionality
Updated Changes file for 0.15
META.yml still had an old version number mentioned
Remove some uninitialized value warnings
Typo fix in the Changes file
Merge branch 'master' of github.com:sakoht/UR
Improve error message when a module gets loaded outside the namespace dir
Fix an error in SQL generation involving indirect properties with tree-like (rather than linear) inheritance
More fixes for the indirect property bug(s).
Fix the number of declared tests
More indirect property bug fixes
The new RDBMS join changes were breaking when the indirect property join had to go through an inline view
Doc updates for UR::Datasource::File
Implement disconnect_default_handle for UR::Datasource::File
UR::Datasource::File->_invalidate_cache returns true, now
Rename internal variables to better reflect their use
More variable renaming in create_iterator_closure_for_rule
Comment out all the old caching code in advance of making new caching behavior
First pass at the new caching/seeking implementation
Better tracking of the cache data file offsets
Add properties to UR::DataSource::File for specifying the filehandle class and whether to close the filehandle
Correct behavior for the file offset cache when the rule contains no sorted columns - don't use it
Better tracking of the read fingerprint during overlapping reads.
Tweaks to File datasource properties. Tests are passing now
Remove old/obsolete/commented-out code from UR::DataSource::File.
Bump up $MAX_CACHE_SIZE to 1000 temporarily for testing
Improve the error message for when the property data in a class desc is something other than a hashref
When the number of cache slots is exhausted, print a warning and extend the cache rather than dying
Improve error message when you try to make a rule with params the subject class doesn't recognize
Give a reasonable error message if the user tries to use '-hints' and didn't give a listref
Speed things up by remembering the value of monitor_query
Merge branch 'master' into file_ds_handle
Improve the warning message when the File datasource runs out of offset cache slots
Fix a bug where the file offset cache could be used incorrectly
Improve file datasource seeking behavior
Fix a bug in UR::Context object cache pruner
The last File datasource patch for file seeking makes seek position change in the test
Try to be smarter about guessing the command name in the autogenerated help
Require Getopt::Complete version 0.14
Preparation for 0.16 release
Make the test skip_all if XML::LibXSLT is not loadable
Updating another version number 0.15 to 0.16
Documentation updates
MySQL datasource checks the setting lower_case_table_names on init
MySQL does not support an 'escape' clause in the 'like' operator
Fix some problems with the 'between' operator
Pre-create iterators and fetch rows from them for each underlying data source
Fix the FileMux data source iterator to properly merge sort the underlying datasource data coming in
File datasource now saves new offset into in its offset cache every 1000 lines read
Fix a bug in the save-position-every-1000-lines code
Make the File datasource more speed efficient
Type/bugfixes from the previous commit
File datasource seeking behavior chagnes
Got the order of string/numeric comparison wrong
Fix a bug involving an object accessor with an id_by that's delegated
Cosmetic
Fixes for some of the null/undef value inconsistancies between items loaded from the DB and object cache
Added a --csv-delimiter option to the object lister command
Be more consistent with multiple-value and string/numeric handling when evaluating rules
Use Scalar::Util::looks_like_number instead of my homemade check for numberness
generate_schema_for_class_meta() now properly generated table metadata when the 'table_name' is an owner+table like DB_OWNER.TABLE_NAME
Be consistent about undef/NULL handling w.r.t. a query that hits a database, or already cached data
testcase for the NULL/undef handling against an SQL datasource
Merge branch 'master' into null_handling_bug
Fixes after merging the null_handling_bug with master
When SQL fails to execute, not all the params passed to execute() were being printed out
XSL views weren't working properly. Fix from Joshua McMichael
When it can't find a suitable class for a view, make the error message more clear
Added env var UR_DEBUG_OBJECT_PRUNING to print out class/object counts whenever the object pruner is done
Documentation for the UR_DEBUG_OBJECT_PRUNING env var
Merge branch 'master' into annotator_improvements
Remove debugger breakpoint
Put in a default value for the max command name width if it wouldn't figure out one
Remove debugging prints
Update version numbers and changelog info
Update MANIFEST for 0.17
Remove mention of removed file in the MANIFEST
Add debian package builder files to the repository
Fix formatting in the debian changelog file
Make XML::XSLT and Getopt::Complete optional in Makefile.PL
remove unnecessary diag()s in the test
Remove more unnecessary diag()s in the test
More changes to get debian packages built correctly by making XML::XSLT and Getopt::Complete::Cache optional
removed execute bit
Change the name of the object fabricator closure
Replace the operator named '[]' with the operator named 'in'
Be more consistent about the 'in' operator naming
Testcase for the new standardized rule construction
When resolving a boolexpr, @non_ur_object_refs should only have non-ur-object refs
UR::BoolExpr::values() should not return values for keys starting with '-'
Merge branch 'rule-bug'
Merge branch 'master' into in-operator
Change docs for 'in' operator to mention that it does intersection
Bug fixes for 'not in' operator
Bugfix for Index handling indirect properties with undef or missing values
remove whitespace
$comparison_values was being reused by mistake, causing it to not iterate properly over the list
Handle comparisons with is-many properties against undef value with the in and not-in operators
Fix for looking up cached objects by is-many properties
More tests with in and not-in filters including missing optional properties and undef
Remove regexes from UR::Object::Index to speed things up
'not in' operator with an index was failing
Only use Getopt::Complete::Cache if it's trying to tab-complete
Switch to Carp::carp instead of warn
Remove a warning about redefinition of the file open constants like O_CREAT
Remove debugger breakpoint
Prepare for release 0.18
Remove some use of UR::Object::Reference and ::Reference::Property
Continued from prior commit. Remove commented-out code from code removal
Remove more UR::Object::Reference and ::Property
Remove mention of UR::Object::Reference and ::Property from Metadata docs
Remove UR::Object::Reference from the 'ur describe' command
Work toward removing UR::Object::Property::ID
Remove some UR::Object::Reference::Property
Be more methodical about metaDB data wrt. table names and owners
Cosmetic: whitespace
Merge branch 'master' into insert_ordering_bug
Reverts change in 8e6877 for URT/DataSource/MetaDB.sqlite3-dump
Fix for MetaDB data mistakenly being committed
Fix for the 'pretty' output style in cases where the value is nothing
Fixed the number of tests this testcase runs
Remove UR::Object::Reference from UR::Context
Axed UR::ModuleBase::_smart_can()
Remove UR::Object::Reference from UR::Object::Property
Remove UR::Object::Reference from the accessorwriter
Merge branch 'master' into remove-reference
Remove UR::Object::Reference from 'ur update classes'
Remove UR::Object::Reference from UR::Object::Type::View::Default::Xml
Remove UR::Object::Reference from UR::Object::Type::InternalAPI
Remove UR::Object::Reference stuff from the class metadata docs
Remove UR::Object::Reference from 'ur update class-diagram'
Remove the properties for UR::Object::References from UR::Object::Type's class definition
Remove UR::Object::Reference from the class initializer
Update the name of the 'update classes' command module
Extra termina output for 'ur update classes-from-db'
Use hashes to check property names instead of sorted lists for better diagnostics when the test fails
Final removal of UR::Object::Reference and UR::Object::Reference::Property
Properly invalidate the _all_property_names cached data when a property is added/removed
Merge branch 'remove-reference'
Remove UR::Object::Property::ID
Fixed the update classes test after removing UR::Object::Property::ID
Remove a warning about undef value when resolveing reverse_as properties
Found another place where it was being sloppy about table owner and table name
_id_property_change_callback wasn't getting called at the right time
Remove use of UR::Object::Property::Unique from runtime
Finish removing UR::Object::Property::Unique
Cosmetic whitespace
Remove UR::Object::Inheritance metadata objects
Fixes to the umlet class diagrammer after removing metadata classes
This metadb binary file shouldn't have been part of commit a267c746
Merge branch 'master' into remove-inheritance-unique
Added is_subset_of() to UR::BoolExpr and UR::BoolExpr::Template
Add some pod to UR::BoolExpr
Remove unnecessary diag() messages in the test
Change the exception message when FileMux can't figure things out
Typo fix
Added method get_rule_for_value_id() to UR::BoolExpr::Template
Refactor the query cache to hash by template IDs and rule IDs
Merge branch 'master' into all-params-loaded-refactor
Avoid using up offset cache entries when there's no data
Helpful warning message if it couldn't find a property for any of the column names
Fix for custom column names in properties with file data sources
Be more consistent with null/undef/empty-string handling with File data sources
Merge branch 'master' into file-null-handling
foreign key pragma got put in by mistake
Properly handle autogenerating foreign key metadata between schemas
Add a warning message for metadata problem
Added a testcase for the bug fixed back in da174c (messy handling of tables with/without schema names)
Removed a breakpoint
Fix a problem with the Tk debugger running away
Remove old, commented-out code
Remove old methods dealing with the previously-removed DBIC class writer
Fix other places that it does 'eval "use $class"' and replace with use_module_with_namespace_constraints()
Merge branch 'runaway-debugger'
Remove redundant statements
Rename a variable to make its use clearer
Improve error message when there's a problem generating support classes
The _all_property_type_names cached data needs to be invalidated when properties change
Merge branch 'master' into cleanup
Remove commented-out/obsolete code. Finish removing _create_object and _delete_object
cache data for property_meta_for_name() and direct_id_property_metas()
Remove unnecessary call to get property metadata
Remove debuggung code
Remove more old debugging code
rules with in-clauses now note in all_params_loaded the values that matched nothing
Merge branch 'in-clause'
Remove typo comment
memoize the answer for is_subset_of in UR::BoolExpr::Template
Fixes for boolexpr memoizing is_subset_of
Make the MetaDB for the URT namespace write itself in a temp dir
48_inline_datasources.t now uses File::Temp for temp dir creation for automatic cleanup
Renamed test to be more descriptive
Only try removing the metaDB file if it exists to avoid a warning
Test was a duplicate of create_get_simple and did not test calculated properties at all
Remove a warning about undefined hash keys
Be more clear about how the temp file for the database gets created
minor test cleanup - tests shouldn't leave anythign in /tmp anymore
above.t removes its own temp directory now
Merge branch 'master' into urt-tmp-metadb
Typo fix in the POD
Couple more POD typo fixes
Update MANIFEST after rearranging a few tests
re-enable these tests when running in the build environment
Tell Build.PL to include MetaDB files
Clean up the 98_ur_update.t test
Toggle the AutoCommit flag instad of commit/begin
Better error message for problem delegated property definitions
Better error message when it can't find property metadata while resolving delegated properties
When using -hints, the query cache will remember which ones matched 0 items
infer_property_value_from_rule needed to use specifies_value_for in case the value is undef
Wrap a SKIP block around a test that doesn't work yet
Merge branch 'master' into dont-reload
Improve error message from context_return() to include the method's name
Additional test for -hints and avoiding loading from the DB
Merge branch 'master' into dont-reload
Improve error messages
Improve the indirect read-only accessor in certain cases
is_loaded() can give up earlier if the asked-for class has no loaded subclasses
Improve speed of _loading_was_done_before_with_a_superset_of_this_rule()
Avoid a call to use_module_with_namespace_constraints()
If an is_many object accessor has a where clause, fold it into the templated used for the query
Bugfix for the previous where-clause change
generate_schema_for_class_meta() now correctly creates PkConstraintColumn metadata
Remove breakpoint
speed up _loading_was_done_before_with_a_superset_of_this_rule
Fix bug and efficiency issue in hint handling with query cache
Avoid BoolExpr stringification in UR::Context::query and UR::Object::Command::List::execute
Make properties referenced by 'id_class_by' metadata auto-define themselves
More efficient queries for infdirect properties though id_class_by object accessors
First refactor of indirect ro accessor for more reusability
Pull out the bridge resolve logic to its own method
Fix bug in new indirect property handler with where-clauses
The indirect rw accessors now use the smarter bridging logic
Merge branch 'indirect-accessor-speedup'
Avoid an 'uninitialized value' warning
to_property_meta() needs to bail out if there's no $remote_class
Add additional restriction for the new indirect property resolver
break out return values for is_many and not is_many
Add additional test for query with a missing indirect property value
Merge branch 'master' of github.com:sakoht/UR
Merge branch 'master' into indirect-accessor-speedup
A test case for a delegated property where the final class has many ID properties
Fix typo on the call to sort
Fixed 'ur update classes-from-db' from throwing bad exceptions
Refactor the underlying context iterator to load ancillary objects before returning the primary object
The new behavior or incirect property bridges wasn't behaving well with UR::Values
Merge branch 'master' of github.com:genome/UR
Refactorization to move the object fabricator tracking into its own package
moved UR::Context::__create_object_fabricator_for_loading_template to UR::Context::ObjectFabricator::create_for_loading_template()
Accessors detect value changes by wrapping the comparison in an eval {}
Remove commented-out calls to the old object fabricator
Move code to apply local all_params_loaded to UR::Context to its own function
Some docs for the new object fabricator class
get() with via property will record info in all_params_loaded about the linked-to class
remove commented-out lines
Merge branch 'master' into buffered-loading
Remove a warning
Remove old, commented-out lines
Fix for when $needs_further_boolexpr_evaluation is true
Remove more comment-out code
Refactor object fabricator where it deals with delegation and/or hints
Fixed a broken 'skip' line in the test
Move pod about object fabricators from UR::Context to UR::Context::ObjectFabricator
Merge branch 'master' into buffered-loading
Improve error messages
Remove empty keys in join data for source_class_meta and foreign_class_meta
Added comment about when to go to the next join
Remove breakpoint
Fixes a bug with property definitions
Catch an error in class definitions which can generate junk SQL
Merge branch 'master' into buffered-loading
Import iterators for ancillary objects apply their all_params_loaded sooner
Added testcase for efficiently loading for a 5-table join with several is_many properties
Update the number of tests
Merge branch 'master' into buffered-loading
Improve error messages
in_clause_values needs to be initialized to a hashref, not listref
__self__ is the right nomenclature, not 'self'
Error message improvements
Fix for when member-methods are called on a set object rather than a set class
Remove unused variable
Add function combinarions_of_values() to UR::Util
group_by with UR::Object::Set instances should work now
Tests for some UR::Object::Set operations
Merge branch 'set-tests'
Forgot to update the expected number of queries
count() on Sets now properly does a group-by and count(*) in SQL
use context_return() for group_by to alert the user if more than one subset is getting returned
UR::Context::_get_objects_for_class_and_rule_from_cache() now works properly got Set objects (queries with -group_by)
overload the eq test to use display_name just like ==
Update comment to be correct
Add CARP_NOT so errors don't appear to come from the accessor writer
Avoid stringification for rules during Set processing
Throw an exception if a rule has -order_by and -group_by that aren't consistent
Fix for RDBMS where the same column name can appear multiple times in a select
Add Set test for queries including both -group_by and -order_by
count() on Sets is now correct, even when there are added/deleted/changed objects
Fixed problem where cached results are returned in the wrong order with -order_by
More correct fix for the order_by problem with cached objects
Clearer error message
Merge branch 'set-tests'
Trim error message for invalid objects during commit()
For Ghost classes, don't blindly make properties is_optional
Typo in the data_type
__errors_ on Ghosts always returns no errors.
Stricter checking of is/data_type for property metadata
Better error message when an autoloaded class fails to load
Changed output for UR_USED_LIBS and UR_USED_MODS env vars
Changed 'use UR::Object::Type' at the top to 'use UR'
Fix a problem where the 98_ur_update.t test can fail
Fix a bug in namespace command _init() about munging @INC
Merge branch 'master' of github.com:genome/UR
Fix type. BLOB should be Blob
'ur update classes-from-db' creates UR-ish data types based on DB types
Change Carp::confess to Carp::croak and improve error messages
Improve error message when it can't find a schema or dump file
Merge branch 'master' into update-types
changed the is_class_wide property metadata to is_classwide
PostgreSQL requires single quotes around the sequence name
Command::V1 needs to be able to call is_sub_command_delegator on Command::V2 classes
First pass at purging calls to uc() when dealign with database metadata like tables/columns/etc
Convert tables/columns to lower case in UR's MetaDB
use a regex instead of string eq when looking for date-type data types
whitespace changes to conform to standard
Make the test emit the excpetions if there are any unexpected exceptions
Remove breakpoint
Improve error message when an object requiring subclassing has problems
Change the begavior of 'load' observers with autosubclassing objects
Better error message when a File datasource can't connect a column to a property
whitespace changes
Remove useless line
Add exception to diagnostic output if the test fails
Remove old, fake accessors for the column_names of properties
Get the last 2 tests passing with lower-case table/column names
Remove old, commented-out code
change Carp::confess to Carp::croak
When it looks for the sqlite3 executable, send the output of 'which' to /dev/null
Added method table_and_column_names_are_upper_case() to UR::DataSource
When resolving the sequence name for a table, keep upper-case if the column_name is upper-case
When generating SQL, be more careful matching columns with values
If the data source is table_and_column_names_are_upper_case, force upper-case for the internal cache of column names
Found a place in UR::DS::RDBMS where it was callign a column name as if it were a method
Rewrite a multi-statement map as a more readable foreach loop
Merge branch 'master' into remove-uc
Take out the check for lower_case_table_names at handle init time
cosmetic fixes for observers
Improve error message when primary keys don't match up with ID properties
Fixed typos in docs for UR::Util
Change Carp::cluck to carp and remove uninitialized value warning
New class definition for UR::Namespace::Command::Base
Refactor UR::Namespace::Command::Base to resolve namespace_name in create()
Refactor UR::Namespace::Command::Base::_modules_in_tree
Subclasses of UR::Namespace::Command::Base no longer need to call _init()
Add function UR::Util::path_relative_to()
Added test for methods in UR::Namespace::Command::Base
Cosmetic changes to the docs
Avoid a warning about an undefined ID when writing a class with no data source
Remove duplicate comments/docs
'ur describe' will now show info for calculated properties instead of (no column)
UR::Namespace::Command::Base's properties aren't is_transient anymore with the new layout
update classes from db doesn't need to call _init() anymore
correct the number of tests run
UR::Namespace::get_data_sources searches in @INC instead of just under namespace directory
Whitespace changes for the test runner class definition
'ur test run' can autodetect what namespace you're in
Fixes to (maybe) allow --cover-git-changes to work
Allow the TabCompletionSpec command to auto-discover it's namespace
Change prints to status/error_message()
Remove an error message that appears when you run the test
Remove wierd uninitialized value warning with DBD::Pg
Need to remove trailing slashes after adding in $ENV{PERL_USED_ABOVE} paths
Go back to the old way of loading the namespace module
Get rid of uninitialized value warning
Merge branch 'master' into command-base
Testcase for SQLite using mixed-case table and column names and commit()
Merge branch 'master' into command-base
Test case for 'ur define namespace'
more tests for checking output of 'ur define namespace'
Test case for 'ur describe' command
Force the namespace to URT so the test runs from any directory
UR::Namespace::get_material_classes works when the modules aren't all in one subdir
Make a simple DB with a couple of tables for the test
After running 'ur update classes' with the initial simple DB
ur update classes now works when the directory tree is broken up
One more module (Car.pm) in the directory tree
Tell Devel::Callcount not to make a file in the current directory
whitespace
Changed a grep to foreach loop so it can end early if it finds what you're looking for
Remove breakpoint
check the whole list of supplied aggregates for "count", not just the first one
Bugfix for a template improperly thinking it's is_id_only
Testcase for the previous commit
Fix for the limit_cache_size test caused by the previous fix to BoolExpr/Template.pm
With properly handle is_id_only when the operator is "in"
Add UR::Context to @CARP_NOT
Re-apply a patch that was removed by mistake in a4a8ef
Fix for properly recognizing real ID properties named 'id'
More tests about rule/template construction
Get the is_id_only flag correct when there is both real properties and -group_by
Git the matches_all flag correct when there's a mix of real property names and -group_by
Merge branch 'master' into template
Merge branch 'master' into command-base
Do a better job splicing in the namespace's lib path
Changes for the alternate layout update classes test
Merge branch 'master' into command-base
Added Changes details for UR::NS::Command::Base refactoring
Fixed a bug in unload() when no objects were present
Fix the test count
Turn a die into Carp::croak to better reflect where the error happens
Remove duplicate 'require UR::Object::Type'
Rename the class metadata id_sequence_generator_name to id_generator
Easier way to override aitogenerating IDs for a class
The Modulewriter preserves the value for id_generator
A bit more documentation about ID generation
Move the check for id_generator
Avoid uninitialized value warning
Fix a bug in internal ID autogeneration
Fix bug in *_set accessors
Fix renaming of id_generator
Add query_underlying_context property to UR::Context
Add test for clear_cache.
Refactor out the loading iterator from UR::Context into its own module
Object lister validates 'show' items as valid properties
Fix object lister handling of expressions in the show list
Add method object_exists_in_underlying_context() to UR::Context
UR::Context::__merge_db_data_with_existing_object() handles deleted DB data
Added _remove_object_from_other_loading_iterators() to UR::Context::LoadingIterator
More accurate counting of an object's changes in _change_count
Add a while loop around the iterator core so we can get rid of goto
Back out prior change to lister show param checking
Added UR::Object::_changed_property_names()
Fix crash in __merge_db_data_with_existing_object
Better detection of changing DB data
LoadingIterator's deletion detection requires the underlying context iterator to return already cached things
When undo()ing a delete, decrement _change_count to account for undoing the delete
Hack to make object_exists_in_underlying_context report false for objects instantiated with __define__
Improvements to the DB-deletion-detection code in the LoadingIterator
Test case for detecting DB deletions
Remove a breakpoint
Hack to firce an object's _change_count to never go below 0 after undo
Hack to fix _change_count accounting around software transactions
object_exists_in_underlying_context() now handles objects instantiated with __define__
Remove breakpoint
Fix test to account for the LoadingIterator handling object deletions differently
Fix the test to detecting DB deleted objects
Fix "not in" operator
Added comment to test
Add comment to test
Discard next DB object earlier if it has changes to order-by columns
Merge branch 'master' into detect-db-delete4
__defined is another key that needs to be removed from the hash for UR::Object::Join
Revert 4f3902 'Fix "not in" operator';
Don't run one of the tests; it's actually broken.
whitespace
Merge branch 'master' into detect-db-delete4
The new deletion detection code changes iterator behavior
Remove debugging prints and crufty/commented-out code
Remove old code
For bx Templates, force order_by, recurse, hints, etc to listrefs if scalars are supplied
Additional tests for handling changing objects
If the next underlying object is deleted in the current cx, skip and pick again
Fix comments in the LoadingIterator about changing objects
Remove redundant check for changed $next_obj_underlying_context
More complete testcase for observers on DB entities
Observer aspects are is_optional
Merge branch 'master' into detect-db-delete4
Get the number of tests right
Add line to Changes about DB deletion detection code
Fix some inefficient SQL joins
speculative code to handle joins because of an indirect id_by
Start counting query time sooner
Fix subclassify_by with DB queries
Improve error messages
First attempt at efficientizing left joins that matched nothing
Some (most) joins have no where clause
updated test since left joins matching nothing is now correctly tracked
Refactor code from the object fabricator into its own method
add column_index_for_class_and_property() to QueryPlan
Fix for loading objects from DB that have changes unrelated to the BX
ObjectFabricators store their hints_or_delegation as a property of the object
Added destination_is_all_id_properties() to UR::Object::Join
column_index_for_class_and_property renamed to column_index_for_class_property_and_object_num()
Add method column_index_for_class_and_property_before_object_num to QueryPlan
Object fabricator using column_index_for_class_and_property_before_object_num
Allow _resolve_delegation_data to return false
QueryPlan _get_alias_join() checks data more strictly to avoid crashing
Object fabricator's _resolve_delegation_data() efficiency improvement
hints_or_delegation data is now a list instead of a hash
If one of the properties in a join has no table/column, set the needs_further_boolexpr_evaluation_after_loading flag
Separate data in @hints_or_delegations between matching objects and missing objects
delegation_data isn't stored in the object fabricator obj any more
Unify handling of source data between the hints_or_delegation and delegations_with_no_objects data
Remove original, commented-out code for _resolve_delegation_data
Remove special code for handling missing delegated data
New test cases for different kinds of delegated properties
comment
Improve error messages
Merge branch 'master' into null-hangoff-data2
Comment
Make the test for methodness in commit() more clear
make the names of tables/columns in the test more consistent
Better parsing of foreign key constraints with SQLite
Make get_column_details_from_data_dictionary() API compliant
Parse out the column size data from the data type in SQLite
replace occurances of get_default_dbh with get_default_handle
0 is a valid value for is_id on Property metadata
Detect when a non-object is passed into an id_by accessor and throw a useful exception
Improve error messages
Add id_properties() method/accessor for class metadata
all_property_names will now return properties named 'id'
Simple test for the object lister command
Add --order-by option to object lister command
Add _post_module_written_* methods
Merge branch 'master' of github.com:genome/UR
Fix UR::Context error messages during display_invalid_data_for_save()
et the number of tests to run
typo
Simplify if-condition
Fix implied property bug
Add comment
typo
Re-fix implied property bug
comments
Update Changes for 0.32
Change occurrences of 'genome center' to 'genome institute'
update debian package changelog
Update $VERSION to 0.32
Update MANIFEST for 0.32
Update META.yml for 0.32
The reported pathanme can be different if the tempdir path contains a symlink
Add tarball for test namespace
To work with systems that use 'sqlite3n' suffixes with their SQLite DBs
Data::UUID compatability
Merge branch 'master' into 0.32-prepare
_concrete_property_meta_for_class_and_name() returns a list sometimes
move _concrete_property_meta_for_class_and_name() from UR::DataSource::QueryPlan to UR::Object::Type
use _concrete_property_meta_for_class_and_name to get the right property metadata
Merge branch 'master' into resolve-id-props
Update $VERSION to 0.33
Code and pod for the implementation of the UR_DBI_SUMMARIZE_SQL env var
Update Changelog for 0.33
Update MANIFEST for 0.33
Update META.tml for 0.33
Another update for META.yml
Add gmt-web subdirectory
remove pre and post-amble stuff added by pod2html
icon is a png, not jpg
fix markdown syntax
Remove debugging print
Make the encoding options for JSON strings a property of the view class
Better error message when resolving joins and a property's metadata can't be found
Avoid an error message during global destruction
Move Slimspace test into the URT test directory
Make the test work with a temp directory
Remove redundant line
Remove an undefined hash key warning
URT::DataSource::SomeSQLite now uses a temp file for its _data_dump_path
change diag() into note() so the output doesn't show up when run from the test harness
Don't need "use above"
Remove restriction of not running in the Build harness
Change diag() to note() so the test is more quiet in the test harness
Avoid warning about non-numberic value in addition
Don't emit test errors to the console
Suppress warnings for SQLite-like datasources when running in the test harness
Turn off status/warning/error messages to the terminal for the command objects under test
Turn on the PERL_ABOVE_QUIET env var when running in the test harness
Change the warn about "Null in-clause" into a warning_message
Suppress the warnings about null in-clauses, since that's what we're actually testing for
Avoid an uninitialized value warning with unlink()
Set value for a required property to avoid a warning about the 'product' property
Change more diag() to note() to keep test harness output clean
Keep the Vending test data source from printing warnings inside the test harness
Remove print statement
If the flock fails because it's not supported, don't die
During _sync_database, be more careful about flock()
Move the RemoteCache datasource to the attic
Typo
Finish moving UR::DataSource::RemoteCache and UR::Service::DataSourceProxy to the attic
Avoid uninitialized value warning
Change owner to 'main' in UR's metadb and remove the *3n SQLite files
After import of the updated meta DB dump
More SQLite 3/3n database and dump updates
Make the default owner 'main' for all SQLite databases and remove references to *3n* files
fix ur_update test because metadb data has "main" as the schema owner, now
Add comment about a (probably) inconsequential bug in older DBD::SQLite::table_info()
Get the test working with newer versions of DBD::SQLite
Add is_connected property to datasources to flag whether it is connected
Remove comment that was not true anymore
When looking up column info, we're only interested in tables, not every kind of entity
Support loading/saving the foreign_keys enforcement setting in SQLite DB dumps
Merge branch 'master' into sqlite-compat
Change confess() to croak() in UR::DataSource::SQLite
Fixed a string concat
Propogate DBI's return value of disconnect() back to the caller
Fix another string concat
Move the call to disconnect until after we know there's an object
Always use the internal dumping method instead of relying on the sqlite3 executable
Merge branch 'master' into sqlite-compat
Make UR::All load even if some optional modules aren't available
Update version numbers to 0.34
Update changelogs for 0.34
Remove Slimspace.pm test namespace
Update MANIFEST for 0.34
Add Command/DynamicTree.pm to META.yml
Remove dependancy on File::Slurp
Don't import functions into our namespace
Revert "Remove Slimspace.pm test namespace"
Check for writable-ness of the dump file before trying to write to it
Add mention of Command::DynamicTree to the changelog
Finish rename of Command::DynamicTree to SubCommandFactory
Improve error message when BoolExpr cannot resolve an object's value
Bugfix for BoolExprs containing a via/to property
Improve exception message when an id_class_by accessor has problems
Add a comment to the top of the test describing what it's for
Better exception message in _first_class_in_inheritance_with_a_table()
Allow queries that include is_transient properties in the filters
Allow undef as values in a class' property definition
Simple test case for querying by a calculated property
Add the class inheritance list to 'ur describe' output
renamed the test to reflect what it's testing
Test hinting by a transient property (which should have no effect)
Test hinting by a calculated property (which should have no effect
Allow via/to properties where the 'via' is a method name
Improve error messages
Correct the number of tests
remove short_name from class metadata
Remove type_name from class metadata
remove attribute_name from Property metadata
Add another XML-related module to the optional list
Make property_meta_for_name() more consistent
Fix command-line arg handling for is_optional properties
Exception message improvements
Fix parsing of command-line values
rename variable $template_data to $query_plan
improve error/exception messages
recurse_property_on_this_row is needed
Switch to a regex from a chain of eq
Only an exception if there's really a problem
Add a method does_support_recursive_queries() to datasources to indicate support for -recurse in get()
Fix handling of --script-opts
Fix the regex so it only matches whole things, not partial matches
The exception message changed. Change what the test looks for to match
Fix for mutating a property that required delete-create to accomplish
Merge branch 'master' into via-fix
Merge branch 'master' into remove_type_name
Remove old, commented-out line
avoid undefined value warning
Check for errors while processing the recursion description
Support -recurse queries in the Context if the DataSource doesn't support them
Merge branch 'master' into recurse-queries
Change behavior of 'like' operator with object listers
Add method _object_cache_pruning_report to UR::Context
Avoid a crash when generating delegate views
More command line arg processing changes
Object cache pruner improvements
Clean up pruned objects more correctly in DESTROY
A DataSource is_connected changing shouldn't be counted as a "change"
Add tests for pruning the dependant File data sources
Fix problem with context rollback()
Move the remaining XML-related modules into the conditionally used section in UR::All
Merge branch 'all' into rem
Make messages about resolving command line params into status_message() instead of print STDERR
Fix error message generation for hybrid command parentage
Fix for Set aggregates when the set includes a filter not expressable in the database
Fix dumping SQLite datasources
Merge branch 'master' of github.com:genome/UR
Fix test to match change from last commit
Add UR::DataSource::QueryPlan to the CARP_NOT list
Use a different scheme to make join IDs unique (fix for prior commit)
Implement -offset and -page for BoolExprs
Added -offset meta-option for BoolExprs and changed -page
Merge branch 'master' into limit-offset
Remove unnecessary joins in-place instead of making a new list and copying it over
Fix a bug where a filter was applied to the wrong alias
Merge branch 'master' of github.com:genome/UR
Another double-join test
Fix typo
Added a test for a prior fix
Refactor to move import iterator code into its own file for readability
Refactor Object Fabricator for clarity
Extract the ObjectFabricators' closures into a list for speed
Merge branch 'refactor-import'
Improve speed of 'in' and 'not in' comparisons by using a binary search instead of linear
Call the comparison function less often
Ensure that undef/null values sort at the end of in-clause values in BoolExprs
Speed up 'in' and 'not in' comparisons even more
Remove the distinction between lists of numbers and strings
Save some time during automagic subclassing by not calling $obj->id more than once
Merge branch 'faster-in-clause'
Testcase for the prior commit about "skip making indexes on delegated properties"
Add another test to make sure the data is right
Query efficiency improvement
Improve query efficiency by limiting the number of times a loaded object gets evaluated against the rule
We should only need to re-evaluate against the rule if $needs_further_boolexpr_evaluation is true
Avoid setting the $needs_further_boolexpr_eval flag unnecessarily
Update comment to remove a lie
Fix queries that hit the data source and order by calculated properties
Improve query efficiency with calculated properties
Merge branch 'master' into query-efficiency
Avoid a call to get() during is_many property resolution by going right to query()
Speed up UR::Context::_loading_was_done_before_with_a_superset_of_this_rule()
Merge branch 'query-efficiency'
DeletedRefs are turned back into objects after rollback
Fix the params for UR::DataSource::RDBMS::validate_subscription
Change exception message when multiple objects match in scalar context
Make the test work properly with no-commit on
Merge branch 'rollback-delete'
Fix entries in the query cache for individual items loaded from in-clause filters
Update changelogs for 0.35
Update version numbers to 0.35
Update MANIFEST and META.yml for 0.35
Update documentation
Merge branch 'in-clause-fixes' into 035
Include an additional chage related to in-clauses to the 0.35 release
includes a 'version' for above.pm
Skip test on systems without libxslt
Improve speed of property normalization at class definition time
Fill in the cache for property_meta_for_name() at class definition time
Fix for PostgreSQL's like operator excape clause format being different than Oracle's
Split the sql 'like' escape process into the char and a formatter
Workaround for a bug in Perl 5.8 involving custom sorts
Merge branch 'speedup-class-init'
Fix exception message
Add method UR::Object::remove_observers() to go with the already-existing add_observers()
Refactor __signal_change__ to split up change recording from observer notification
Merge branch 'master' into observer-improvement
Make command subclass resolution faster by being smarter about guessing the right subclass name
Add the 'valid_signals' metaproperty to UR::Object::Type
Lean on the 'valid_signals' metadata for approving observer creation
Refactor the observer API
Move the _load() method from UR::Value into UR::DataSource::QueryPlan
Change UR::Value to load from UR::DataSource::Default instead of the old custom _load() behavior
quick efficiency improvement for UR::Value::__display_name__
Things loading from UR::DataSource::Default shouldn't have to supply values for delegated or calculated properties
Fixup the loading template's final_class_name for Value and Set subclasses
Allow UR::DataSource::Default to save for some classes and discard changes for others
Allow UR::Value::__load__() to provide data for all properties, not just id properites
Improve exception message in __load__ when ID properties aren't all provided
Improve exception message when there's problems mapping fields between what's requested and what's returned by __load__
De-hackify the initialzation of QueryPlans for Default datasources a bit
Allow queries on UR::Values using an in-filter on id proprties
Improve exception message when not all the ID properties are present in the query
Add more UR::Value tests
Merge branch 'master' into deprecate-old-observer-api2
Remove a warning at commit() time if this module is used
Avoid a warning message
Change some calls to Carp::confess() to croak()
Add rollback() and commit() methods to UR::DataSource::Default to avoid warnings during commit and rollback
Check for DeletedRefs before deleting them
During rollback, UR::Observers need to run their overridden delete(), not just the basic UR::Object::Delete
Make the ok message true
Bail out early if there were no Observers found
Pass the method from the old API into the aspect to the new API
UR::Observer needs to hook into both create() and __define__
Fix the test
Make the test work after the Observer API refactoring
Make the param parsing more efficient with hash slices
Remove commented-out code
Fix for prior commit that switched to hash slices for param parsing
Merge branch 'master' into deprecate-old-observer-api2
Fix the case where classes have a validate_subscription() method instead of 'valid_signals' metadata
More docs for 'ur test run'
Allow order-by metadata in a BoolExpr to have + or - to indicate ascending or descending sort
Refactor the "order by" clause generation to be a method
Typo in the regex for order by parsing
Implement descending order-by in the object sorter closures
Implement descending order-by in SQL data sources
Refactor to remove unnecessary loop to connect order-by properties with db property data
Refactor to remove a redundant loop over order-by properties
comment + whitespace
Fix bug where descending order-by would fil if it wasn't the first item
Merge branch 'master' into orderby
Refactor sorter sub to be more compact
Fix for order-by on an RDBMS column with NULLs
Fix for order-by on cached data with NULL/undef values
Additional tests for the new NULL/undef sorting behavior
Fix the shell exit code when using the --lsf switch
Sort the observers by priority
Remove old, commented-out code for observers
Don't need to pre-validate params for observer creation
Handle the situation when an observer's priority changes
Testcase for the priority of observers
Additional documentation for Observers
Change algorithm for finding tests to run
Refactor the messaging API (error_message, queue_error_messages, etc)
Add code in the old-message-api adaptor to handle clearning the callback
Fix the tests to use the new location for stderr filehandle
move the method message_callback() into ObjectDeprecated.pm
Move the UR::ModuleBase::Message class into ObjectDeprecated, too
Fix a bug where multiple instances with the same ID (different classes) overwrite each other's message flags
Change the key used for storing instance msg data
Make the msg settings do some rudimentary inheriting from parents
Better error message when the class name isn't a valid class name
Move the location of __signal_change__ "query"
Fix bug with loading Set objects with a -group_by clause
Fix for messaging functions on non-UR classes
Allow a messaging callback to skip printing the message by throwing an exception
Allow a messaging callback using the old API to rewrite the message text
Change the mechanism used to avoid printing messages
Add some deprecated messaging methdos back in
Better compatability with the deprecated messaging api
Merge branch 'master' into message_refactor
Fix the default values for dump status,error,etc messages
update changelog for 0.36
Update version numbers to 0.36
Command-type modules need to turn on dump_usage_messages(1) to get help displayed on the terminal
Merge branch 'master' into 0.36
Update MANIFEST for 0.36
Update META.yml for 0.36
update debual changelog for 0.36
Fix the data source to avoid deep recursion
Fix for printing compile error messages when a module fails to autoload
First attempt at using Parse::YAPP to make a parser for text description Rules
Fixed the shift/reduce conflicts in the grammar
Added a more complete _error method from Travis Abbot
Add bx string parsing test from the recdescent-bx branch
Comment out one test using '=>' meaning equal
Switch resolve_for_string() to use the new BxParser instead of simple regexes
Make the BxParser code go in the UR::BoolExpr::BxParser namespace
Put the tokens into a list instead of a hash
When it matches 'AND', flatten the two sublists into a single return list
Allow the words 'and' and 'or' to match in the 'value' position
Debugging print statements to be removed later
Set the LOADED_BXPARSE flag to true after it's loaded
Add separate tokens for '=' and '=>' so they both match for the equal rule
The token '-' now always tokenizes as MINUS instead of either NEGATIVE or BETWEEN_RANGE
Typo
Add additional keywords that can also be values
Break up the like, in and between operators into their words ("in") and char equivalents (":")
Needed a rule to match in-values with just two items
Force number-types to be numeric context
The NEGATIVE token was renamed MINUS
Change the recognition order of 'between', 'in', and 'like' to get them to match as tokens
Comment out debugging prints
Attempt to get ':' to work as either a 'in' or 'between'
Put the debugging prints back in, but with a debug flag to control it
Allow ':' to work as either IN or BETWEEN
Remove second arg to debug_message() from UR::ModuleConfig
Simplify parsing of the hints,order and page
Simplify rule for an_operator
Move the the precedence of the NOT_WORD token
The parser can now distinguish "," being used as either AND or SET_SEPARATOR
Parser returns the right data structure for "expr or expr"
Typo
Allow a rule with multiple ORs by pulling up the sub exprs if the second one starts with -or
Allow rules that mix ANDs and ORs
The flattener not handles multiple levels of OR correctly
Fix bug with resolve() on or-type rules
Typo
Refactored the way conjunctionas and disjunctions are combined
Added comments
Remove debugging prints
Move the code that post-processes the parse tree into resolve() args into the grammar
Teach the grammar about 'order by' and 'group by'
Backward compatability with LIKE values
Tell yapp to put the generated parser code into package UR::BoolExpr::BxParse
The Indexer now handles the case where the operator is explicitly '='
BoolExpr grammar now handles en empty string to mean no filters
cosmetic
Add another test with empty filter but with order by
Fix the number of tests
Refactor to move the code that simplifies the final parse tree into a method
Refactor the code that handles combining ANDed and ORed exprs into their own methods
Name the variables better in _and() and _or()
When an error occurs, also print the whole expression it was asked to parse
Make the tokenizer states encoded in the %token_states data structure
Chance to logging for UR_CONTEXT_MONITOR_QUERY
Avoid an exception about dereferencing undef as a hashref
Clarify the error message
State machine changes for the tokenizer
Change the single/double quote string regexes to have non-capturing groups
Allow '/' as a starting character for the WORD token
Disallow the old syntax for in-values when using the new syntax 'in' operator
Cleanup: remove old commented out lines
Merge branch 'master' into yapp-bx
Simplify tokenizer's tracking of current and next state
Simple implementation of an OR-type rule iterator
Better implementation of an OR-type rule iterator
Remove breakpoints
Update test count
Support -order with OR-type rules
Refactor to move code for handling OR-type rules from get_objects_for_class_and_rule into its own method
Remove commented out lines
Change the OR-rule iterator to avoid returning duplicate objects
Allow 'desc' or 'asc' as a keyword in an order-by clause
Whitespace
Change the parser's error message to show the problem characters, not just the token name
Add negative test cases for bad order-by clauses
Changes to BxParser.pm (derived from BxParser.yp) over the last few commits
Update comment
Remove 2 module 'use's that weren't necessary
Add help test for the Lister command about the new syntax for filters
Update POD for UR::BoolExpr to show an example of resolve_for_string() with the new syntax
Merge branch 'master' into yapp-bx
Forgot a newline on a log message for UR_CONTEXT_MONITOR_QUERY
Fix an issue with unnecessarly querying the DB with certain order-by queries
For error_messages related to bad IDs, have the message originate from the class the caller tried to create, not from the Context
Change the symantics for messages getting printed
Autovivicate the message queue when error_message_arrayref() is called
Change the test data sources to use the newer messaging API when avoiding printing messages in the test harness
Change tests to avoid printing errors/warnings when they're expected with the new messaging API
Allow debug flags for both the tokenizer and the parser
Allow dashes in the value for the 'like' operator
Go back to the old code for parsing strings into boolexprs
Skip tests when loading XML::LibXSLT fails for any reason
Make the Vending datasources quiet about re-initializing the DBs when run under the test harness
Have the lister command try the old syntax perser if the new one fails, but issue a warning instead of running
Allow dots '.' as a legal char in values and like-values
Allow bare lists of words as values
For bare word lists, allow anything except 'and' and 'or' as the not-first words.
For bare word lists, allow multiple spaces between the words in the list
whitespace
Change the non-terminal "first_value_part" to "single_value"
Revert "Go back to the old code for parsing strings into boolexprs"
Merge branch 'keep-yapp' into reinstate-yapp
Go ahead and run the query if it's parsable by the old parser
error_message, warning_message(), etc always return the last message as a string
Fix the documentation for the messaging methods
Rearrange the messaging tests
Merge branch 'message_fixes'
Fix a problem where if a UR::Value-related property is in the hints list, it would crash
Merge branch 'joins'
Fix crashes on Solaris when saving File datasource data
Merge branch 'master' into test-cleanup
Fix the messaging test for the case where the msg is undef
Convert to new messaging API to suppress expected error/warning messages during tests
Suppress expected messages
Suppress expected warning messages
Make a warning message more clear
Don't need to exlicitly commit/begin, maipulating the AutoCommit flag does all the work
Suppress warning_message during clear_cache, since it complains about QueryPlan objects
Improve error message for Lister command when a filter or show isn't one of the properties of the class you're trying to list
Use socketpair instead of creating TCP sockets for communication
Try to get more info about one kind of failure in the installation tests
Merge branch 'master' into test-cleanup
When the new BoolExpr parser fails and the old one succeeds, include the error from the new parser in the warning message
Parse::Yapp is now a dependancy
More documetation for resolve_for_string()
More docs for resolve_for_string() about "group by" and "order by".
Update changelog for 0.37
Update version numbers to 0.37
Update MANIFEST for 0.37
Run yapp on BxParse.yp with the -s flag so Parse::Yapp::Driver is no longer required
Update META.yml for 0.37
Remove libparse-yapp-perl from debian dependancies
Better error messages when there is a problem creating an Observer
Make non-UR objects valid values in BoolExprs
Merge branch 'master' into access-as
Value class for coderefs
Allow colons ':' in WORD character values
Allow keywords like "like" and "desc" to be property names
Merge branch 'filter'
UR::BoolExpr::value_for() now behaves properly when the value is a hashref
Test case for the prior commit "Make non-UR objects valid values in BoolExprs"
Merge branch 'access-as'
Refactor to move Oracle specific code into UR::DataSource::Oracle
Refactor to move variable declaration inside the blocks that use them
Continue searching up the inheritance got table/column info if it didn't find it on the first try
whitespace
Better error when database metadata has malformed data_source info
Fix finding the proper table name for a given property name
Faster lookup of column names in FK constraints
Remove commented out line
When updating a DB row, infer the table structure from the class metadata
Test case for committing when the metaDB info is not current
Fix crash due to bad SQL for inserts for some cases of out-of-date metaDB info
Merge branch 'master' into missing_metadata
Refactor to change calls to sort as a workaround for a bug in Perl 5.8
Add a 'original_command_line' property to Command::V1 and Command::V2
Better exception message when there's a problem following the chain of delegated properties
Avoid an exception in QueryPlan for certain queries
Move the values we're printing into the value list for printf()
Fixed issue with Tree commands not printing usage text when run with no parameters
Add 'original_command_line' to the list of params it will not generate help for
If a query's in-clause has more than 100 items, don't put the rule in the query cache
Merge branch 'master' into large-in-clause
Avoid stringifying rules by calling id
Better fix for the more-than-100-in-clause-list
Fix bug in QueryPlan where it would not handle property names with "." in them in some cases
Speed: take a hash slice instead of looping through keys
Speed: use __meta__ to get class meta instead of UR::Object::Class->get()
Speed: make __errors__ faster by pre-getting values directly from the object as a hash slice
Speed: check common case first
Speed: get at the class/r_class metas by going directly to __meta__ instead of going through get()
Speed: cache the results from get_property_name_pairs_for_join()
Speed: cache the results from id_property_names()
Need to remove a few new keys from the objects before comparing
Avoid an uninitialized value warning
fix a bug where it would die when calling create_entity() with a rule
Improve speed by doing the common and cheap comparisons first
Refactor autogenerate_new_object_id_datasource() remember the generator function
Fix a coupld of bugs related to hard refs in rules
Refactor to move common code up
Comment-out code dealing with hard refs in get_rule_for_values()
Merge branch 'large-in-clause'
Improve error message when 'to' property metadata is not resolvable
Fail a little earlier if a property meta is missing
Remove commented-out line
remove unnecessary call to class()
Make the warning message better
Add a comment about why a previous commit commented a line out
Merge commit '231f9331acd8f8b9e9b502039a06e303898ce674' into fix-object-hints
Re-word warning message for clarity
Change the parent of UR::Value::Number to UR::Value::Text
Re-throw the exception in most cases
Always try getting by ID first
Allow a child class to define a columned property even if it does not directly have a table_name
Better error message when a class' "is" is invalid
Work even if the # of linking properties is different
Rewrite to make more functional
Be more careful with "truth" while loading objects
Change several Carp::confess() to Carp::croak()
Collapse a bunch of single my() into two
Support making one property an alias for another
When unalasing properties, work when the operator is more than one word
Fix for unalising logic
Fix for unaliasing logic
Cleanup
Update class initializer docs to talk about alias properties
Make the test pass
typo
Don't re-get data we already have
Alias property fix
Merge branch 'master' into alias-fix
Another alias property fix.
Allow 'offset' and 'limit' in the BoolExpr syntax parser
Add 'true' and 'false' operators to the BoolExpr string parser
add 'is null' and 'is not null' to the BoolExpr text parser
Fix BoolExpr bug recognizing >= and <=
Fix docs
Fix bug involving turning a forward join into a reverse join
Fix for joins involving UR::Value classes and where clauses
Test for previous commit b8c4868 (where clause fix)
Improve error message
Allow + as a character matching the WORD roken in the BoolExpr text parser
BoolExpr string parser can now detect a partially parsed string
Make the SQL prepare error better
Put the var in the proper scope
Make queries via 'sql' more efficient
Throw an exception if the SQL supplied does not have all the pk columns
Allow the raw sql filter to have placeholders
Throw an exception if the params supplied doesn't match the number of placeholders
Be more efficient when fetching IDs in a get() with sql
Be a bit more efficient when figuring out if all the ID columns are present
More tests around missing ID columns
Merge branch 'raw-sql-fix'
Make is_many accessors more efficient
Fix for previous commit 'Make is_many accessors more efficient'
rename the test to reflect what it does now
Exception message improvements
_concrete_property_meta_for_class_and_name() now handles property names with dots
Handle handle an odd many-to-many relationship
whitespace
Experiment with a new indirect accessor implementation
Fix $UR::Context::initialized
Improve error message
whitespace
Changes to the experimental indirect accessor code
Fix indirect property value resolution for another corner case
Expand the use of the same optimization in 9846be
Merge branch 'indirect-ro-refactor'
Fix for bug introduced in 1416f2
First commit for UR::DataSource::Filesystem
Fix regex matching method calls in path spec
Change scheme for recording where we've added pathname globs
whitespace
Added method for resolving values for properties in path spec without values in the rule
Add test for properties with an in-clause
More examples of path specs
Allow glob wildcards hard-coded into the path spec
Refactor to make the regex construction for glob matching functional instead of procedural
The glob positions list needs to be updated when known variables are filled in
Update comments and remove commented-out lines
Refactor to move common code out of if/else branches
whitespace
Refactor to move the glob position fixer up so it dosen't need to be passed in as an arg to the resolver sub
Need a minimal match for chars preceeding the '*' to work when there are more than one glob in the same path part
Add method resolve_file_info_for_rule_and_path_spec() which calls the var, sub and glob resolver
Get things working to reolve paths when a method name is in the path spec
Better name for a sub
Change property names from server and sort_order to path and sorted_columns
The Filesystem data source can actually read and return data
Change debugging print to match the format of the others
Added a test for getting multiple rows from the same file
dded a test for a get() matching nothing
Add newlines to logging prints to make things more readable
Test reading from multiple files to find matching data
re-use the null sub to avoid making a new one
update comment to match reality
Bugfix for when a property has a column name different than the property name
Add a test got getting by ID
Support classses having 'tables' with the Filesystem datasource
Be explicit in the debugging messages when there are no filters
Fix bug about printing 'first match' messages too much
The 'server' property for UR::DS::Filesystem is now 'path'
Update the number of tests
Add support for getting the column names out of the top of the file
Test having different column order in different files
Remove commented out lines
Allow the file contents to be not sorted by ID, but still return data to the loading iterator by ID
Variable rename @next_record -> @next_record_for_each_file
Change comments
Add more info to the TODO list
Need to use a string comparison, not numeric
Forgot to pass in the rule
_add_join() didn't need $order_by
Refactor to pull the order-by column resolution into its own method
Change a die into Carp::croak()
Give classes a __default__ table_name where appropriate
Initial support for -order-by with the file Filesystem data source
get() with order-by as well as arbitrary sorting now works with the Filesystem data source
Added support for -order-by descending and having the file sorted descending
Allow the path property to be an arrayref
Avoid a memory leak when reading a file bails out early
Teach the Filesystem data source to stop reading early if the file is sorted properly
Pass a reference to the comparison data to the comparator functions instead of the raw data
Avoid an uninitialized value warning if a file is sorted by a column that isn't in the rule
Sort the resultsets in the right order for descending
Add another test using the 'between' operator and multiple sorted columns
Cleanup
Behave properly after a fork()
Be more precise when sorting string or numeric properties/columns
Refactor to have a common method for getting a sort sub
Make the API for committed/saved/rolled-back status tracking more consistent
Added File::Temp and File::Path to the prerequisites list
UR::DataSource::Filesystem saving works
Prepend "FILE:" to the logger output during saves, to match the other logger output
After a fork(), and it notices there's been a fork, remember the new PID as the primary pid
Removed the 'quick_disconnect' property from UR::DS::Filesystem
Added pod to the Filesystem data source
Mention in the POD that you can put braces around property and method names in the path spec
You can now use $. and __FILE__ as column names in class metadata that uses the new Filesystem datasource
Fix the case where some property values are determined from pathname resolution
Remove breakpoints
Merge branch 'master' into newfileds
cleanup
Allow "undef" as a value in the data source's "columns" list
Check for eof when a read returns nothing
Allow handle_class to be something that inherits from IO::File to override some of its methods
Fix a bug with multi-char record_separators
doc updates
Now that UR::DataSource::Filesystem is working, File and FileMux are deprecated.
Improve server response when getting foreign key info
Do the same trick for removing the hint for table_info(), column_info() and pk_info()
Don't change the error callback unnecessarily
Avoid losing $@ while looking for class ancestors
Add a test case for query hints
Add new class metadata called join_hint
Allow both query_hints and join_hints as part of the same query
Make select_hint the key to specify hints
Some documentation about select_hint and join_hint
Don't visit the same class more than once
Don't add the same class' join hint more than once
Changed args for UR::BoolExpr::Template::Or::_compose() now
UR::BoolExpr::resolve() now accepts meta-params for or-type rules
Hack to support splitting apart composite rules with meta-params
Test for or-type rules with meta-params
Refactor from assigning globs to using Sub::Install and Sub::Name
Refactor the messaging system (again)
Add a check for retrieving the callback
Change the way messages settings are stored and retrieved
typo
Fix to pass the basic messaging test
messaging methods now trigger observers after UR is initialized
Change the test in line with the new messaging settings behavior
Fix format of messages
use the right args when setting a message callback
Fix for classes that inherit from UR::ModuleBase but not UR::Object
Fix for users of the original old, old, old messaging system
Additional checks that signals propagate up to parents, but not down to children
Tests for the new signaling behavior of the messaging system
Refactor to move subclasses_loaded() to UR::Object::Type
Merge branch 'messaging'
Use a module for detecting when we're in global destruction mode
Small improvements to the class browser (ur sys class-browser)
Env var UR_DUMP_type_MESSAGES now has precedence over the entity/class/parent setting
Merge branch 'master' of github.com:genome/UR
Don't leave files laying around in /tmp
Add 'tsv' style to the object lister command
Fix File and FileMux datasource logging when UR_DBI_MONITOR_SQL is on
Add Class::AUtoloadCan to the CARP_NOT list for better logging during UR_CONTEXT_MONITOR_QUERY
Merge branch 'master' of github.com:genome/UR
Change the name of the Yapp driver package name to avoid CPAN "unauthorized release" warnings
update debian changelog for 0.391
update META.{yml,json} for 0.391
Update changelog for 0.391
update version numbers to 0.391
Remove mention of providing Parse::Yapp::Driver
re-generated by Build.PL
Update version numbers to 0.392
update changelog for 0.392
update META.{yml,json} for 0.392
update debian changelog for 0.392
A few stragglers updating their version numbers
Add dist_author section
META.yml updated from Build
typo in comment
Avoid a list assignment
Factor out the conversion template for date and timestamp
Make 2 my()s into 1
Add cast_for_data_conversion() to use when SQL needs to compare dissimilar types
Add left/right coercion info for joins
Use the coercion information to build the where clause
Reverse a previous commit where we made UR::Value::Number isa Text
whitespace
prime the class_alias cache with the source class' table name
refactor intersect_lists() into UR::Util
test case for joining text-type columns with non-text columns in Oracle
remove empty 'has' section from the test
Some undeclared prerequsites
Better implementation of super_can()
Clean up broken or chatty tests
Improve error message
Merge branch 'master' of github.com:genome/UR
Switch $TIMESTAMP_FORMAT and $DATE_FORMAT
Fix the Timestamp format for SQL generation.
Merge branch 'master' of github.com:genome/UR
Update changes for version 0.40
Update version numbers to 0.40
Remove Class::Inspector from the list of prerequsites
Update META.{yml,json} for 0.40
After running ./Build dist
update debian changelog for 0.40
Fixed typo/spelling errors in pod
Remove breakpoint
Fix typo in comment
Remove duplicate variable
Combine several ||= into one assignment
Fix a bug when joining two child classes that don't have tables but their parents do
Fix bug with inherited implied property data_type
Add additional diag messages to figure out why the test fails
Update version numbers to 0.41_01
Update META.{json,yml} for 0.41_01
Update Changes for 0.41_01
Try to get the test to pass on CPAN again
Update version numbers to 0.41_02
exec-ing these commands should be done with the same perl as is running the test, not /usr/bin/perl
Update version numbers to 0.41_03
Turn off ANSI coloring during this test
Test the XML view renderer only if we can load the required XML modules
Let the system pick a TCP port for us
Update version numbers to 0.41_04
Fix comment about how to generate the module from the grammar
Avoid an uninitialized value warning when calling colored() with no color
Update version numbers to 0.41_05
Merge branch 'master' of github.com:genome/UR
Fixes for pod errors from Olivier Sallou (http://osallou.myopenid.com/)
Always remove double //
Ensure we're comparing things in the same order, not random hash key order
Try getting some feedback when the test fails
Merge branch '041_01'
Update module version numbers to 0.41
Updates Changes for 0.41
update META.{yml,json} for 0.41
update debian changelog for 0.41
Avoid an uninitialized value warning
Merge branch 'master' of github.com:genome/UR
Command properties with example_values shows them in the help output
Change UR_COMMAND_DUMP_STATUS_MESSAGES env var initializing
Avoid an uninitialized value warning, since undef is a valid value in the constraint list
Refactor out a method to get the SQL for a BoolExpr
Merge branch 'master' of github.com:genome/UR
reverts a94be9d4d7a6cc13509daa5c145a2f0f7d80de69
Better handling of negation operators; should be clearer and more complete.
Expanded the basic get() test to cover the old operator/value syntax
Better handling of negated operators in SQL
Expand the test to cover all three means of handling operators
bx Property comparison for not between
First commit for a WebServer service
This module's name changed
Cleanup
host and port are lazily autogenerated
Test connecting and running a handler
Allow the WebServer to store its callback as an attribute
Class and tests for a UrlRouter service
Add method to make a file/directory serving closure
Test directory/file handling in streaming mode
add method module_data_subdirectory()
First commit of a new Class Browser web-app
Add in jQuery 2.0.0
Add in Twitter Bootstrap 2.3.1
Test namespace for the class browser tests
Add option to log route results
remove testing code
Basic class-browser page comes up
Clean up in preparation for actually rendering a web page
It will render a treeview by path name
Refactor to have a method to run a template
Web-app is minimally functional
Refactor to have a method to return 404
Links in the Paths list now refer to class names, not path names
allow render_perl_module to work even if the module isn't loaded yet
The Classes, Inheritance and Paths tabs are all populated now
The inheritance inserter uses class names instead of a hashref
Class detail now shows inheritance tree
Class detail shows major class metadata and property info
Hovering on a property table row pops up more info about that property
Change presentation of property metadata
Print an error to the terminal when the template has an error
Make ID properties stand out
Refactor how modal windows come up
Change the rendering of class properties
Class detail pane shows methods
class methods are now shown sorted by alpha
Class' method overrides are now shown as a list
Make the button links to other classes smaller
Show private methods, too
Moved template partials into their own subdirectory
function names now link back to where they were defined
Show the class' table name in the class metadata
Saving/loading class info cache files is now working
Long class names render better in the treeview
Refactor main script
Refactor to mave methods to get/set the cached data for inheritance/classes/files
Be more rigorous about passing around the right namespace name
Tests for the internal tree structures used by the HTML templates
Search input in the navbar is working
Switching to another namespace works
Fix the number of tests
Merge branch 'master' into class-browser
class browser cache file
Move the class browser tests to a top-level test directory
Pass along the command's verbose setting to the UrlRouter
Remove the $does_streaming option
Make announce() a public method
Return immediately if there's no callback function to run
Add documentation
Fix test for latest changes
Remove old class browser views
Search box now looks for partial matches on class names
Tables in the class-detail are now sortable when the column headers are clicked
Switch to using merge sort
Allow listening on connections other than localhost
Make the class browser cache changes more deterministic
Test should not look at the absolute paths
Improve efficiency of some set aggregates
Fix a bug with unloaded UR::Object::Join instances
An object's class must be is_uncachable in order to be unload()ed
Move all the set's cached values into a common key
Set's cached aggregate values are removed when the members change
Set aggregates always trust the cached value when it exists
Test that cached aggregate values are expired when member values change
Sets track changes in membership with a flag
Update the deps cache anytime we've calculated an aggregate
Only set the __members_have_changes flag when a create/delete was to a set member
Clear the __members_have_changes flag when the Context commits
Rename variable
Check for dependant aggregates before evaluating the object against the rule
More comments to explain recent set changes
whitespace
Add 'isa' operator
Avoid a 'used once' warning
Cached/calculated properties (memoized) now have a method to clear a previous calculation
Add a function to always return an object
Refactor to harmonize data source methods around handles
Implement disconnect() for UR::DataSource::FileMux
Refactor to add a method to get the current file's position
whitespace
Speed up the test by not sleeping before exiting
Don't double-call init_created_handle()
Add a test for the new signals sent by UR::DataSource
Set an error message if one of the initialization SQL statements fails
typo
Merge branch 'master' of github.com:genome/UR
exit() is ineffectual during 'ur test use'
Combine duplicate code
Change handling of id_generator for class metadata
RDBMS data sources signal observers when a query or commit fails
Merge branch 'db-faults'
Better error reporting when there's a problem loading modules we depend on
Move the fake DBI wrapping code to its own module
Initial import of RDBMSRetriableOperations from the Genome tree
Make the retry times configurable
Send a 'retry' signal when the operation is to be retried
Make retriable wrappers for the basic retriable operations
Add do_sql() to UR::DataSource::RDBMS
Add method for datasources to indicate the DBI handle class
get_default_handle/connect is a retriable operation
do_sql() should get the err string from the handle object, not the DBI package
Improve readability of the ok()s in the test
Set the error_message on prepare to the object instead of the class
Add test for retriable commit
Move Oracle date format setting to its own method
Hack to avoid infinite recursion - see the comment in the code
Merge branch 'retry-db'
Make sure we're dealing with an object and not a class name
Merge branch 'master' of github.com:genome/UR
Don't commit or rollback when autocommit is on
Remove old, commented-out code
Sync/commit properly when AutoCommit is on
Improve error message when a parent module fails to load
Change message type for "Ineffective commit/rollback" messages
Be more strict when getting related Table/Column/etc objects
Merge branch 'master' of github.com:genome/UR
Change the function signature for cast_for_data_conversion()
cast_for_data_conversion() now takes an additional arg to specify what SQL clause it's working on
Allow using 'like' to filter on a datelike column on Postgres
Extract method to get the table name for a class
Extract method to get a sequence name from a class' ID properties
extract a method to get the sequence name for a class name
RDBMS data sources now send a signal when they're getting the value for a sequence
RDBMS data sources now send a signal when retrieving the next value from a sequence fails
Speed up the test by allowing fractional sleep times
Improve variable scoping
Cache an Index's indexed_property_names instead of splitting them every time
Simplify double negative
Indexes now cache which properties are numeric/non-numeric
Do proper numeric/string comparison for 'not ='
Add method to retrieve all the objects in a UR::Object::Index
comment out useless debugging code
Fix a bug in the test
Be more precise about data types
Do proper numeric/string comparison for >
Do proper numeric/string comparison for <
Do proper numeric/string comparison for >= and <=
Do proper numeric/string comparison for between
UR::Value subclasses can have custom serializers
refactor to make each class' loader into a cached closure
Use each_arrayref to avoid nested loops in perl-space
use map to avoid a loop in perl-space
condense the single/multi loaders into one loader to save a function call
Improve Command::V2's autogenerated docs for boolean params
error_message et al. now works like sprintf by accepting a format string and list
class browser cache node IDs are now consistent
remove commented-out lines
Merge branch 'master' of github.com:genome/UR
value_id_to_values_frozen() can correctly thaw data structures containing UR objects
Work for the case the embedded data structure has multiple references to the same object
Correctly handle self referential data structures when thawing data
Handle the case of a reference to a reference to the data
Avoid a warnings about undef used as a hash key
Forgot to bump up the number of tests
Be more strict about property names in class definitions
rename variables to make it more clear
Move is_valid_class_name() into UR::Util and make it a public function
extract function to get the class suffix for a given BoolExpr operator
Use the Oracle/Pg version of _value_is_null() for all RDBMS data source
replace conditional with polymorphism for operator SQL generation
add function to do a require at run-time
Allow RDBMS subclasses to have custom implementations for SQL operators
Postgres-specific implementations of true and false
Context fires signal "sync_databases_ after _sync_databases runs but before committing them
add method to return what UR datasource class is appropriate for the given DBI connect string
add function to touch a file
Move method to make a DB table from class metadata
avoid error messages when the table already exists in the alternate database
When the UR data_type is missing, assume varchar
Make sure the schema exists in the alternate DB before creating the table
Working version of UR_TEST_FILLDB
sqlite now supports a directory of DB files
Extract method for creating the handle for the alternate save DB
Creating an alternate dbh in sqlite needs additional handling for a directory of schema files
extract method to determine whether a "server" pathname represents a directory of schema files
Improve functionality of UR_TEST_FILLDB with table inheritance
Fix SQLite emulation of DBI's foreign_key_info()
remove commented-out code
Avoid unnecessary data copying when emulating foreign_key_info
Eliminate more unnecessary data copying
Extract method to handle the foreign key info for one table
Improve SQLIte's implementation of foreign_key_info
Explicity set the FK actions in the test
avoid an uninitialized value warning in the test and in general
Improve Singleton accessors
remove unnecessary lines
fire observers for classwide properties
Fix for older Perls that use depth-first method resolution
change var names to better reflect their purpose
extract function to save rows to the alternate DB from a loading template
Move table creation up one scope - now the insert-creator doesn't need to know about $ds_type
Support passing the username and password in the alternate DB connect string
Handle data with foreign key dependancies
ensure we always have an up-to-date picture of the schema
more effective way of determining column order - based on column names instead of property names
extract method to turn one FK into a prerequsite loading closure
whitespace
Method to return a data source appropriate type given a UR data type
use the appropriate data type for the column when constructing the SQL table
Filling alternate DB now controlled with property on the datasource
Use raw DB info for foreign keys instead of MetaDB info
avoid uninitialized value warnings
Alternate DB loading works properly with classes having multiple ID properties/columns
spelling
Normalize schema/table/column names in foreign key data
Handle the case when a table's FK points back to the same table
extract method to get the foreign key data for a class's table
Handle the case where a class' PKs point to another table's PKs, but not because of inheritance
Fix a bug involving inserting dummy ID data to the alternate DB
avoid an uninitialized value warning
$class_name was never actually supplied when the column data was built
whitespace
Work for the case where a join does not produce a loading template
Add another heuristic to know when it's working with a new FK
fig bug in _is_dummy_autogenerated_id() should fixup with another commit
Add method to return the cannonical order by list
resolve_order_by_clause() now takes the query plan as its only arg
Refactor order_by clause generation
Refactor how order_by columns are managed
add method to get the table and column name for a column like table_name.column_name
Fallback for classes with non-RDBMS data sources
avoid an uninitialized value warning
UR::Object::Type::property_for_column() now supports an argument like table_name.column_name
add method to tell if a property is a text type
PostgreSQL now uses the "C" collation for ordering on text fields to match how UR sorts using cmp
typo
additional documentation for negation
We only need to be testing for a - in order by column lists
Revert portion of 162dc
Don't count saved objects as prerequisites in the alternate DB
give names to the alternate DB inserter subrefs
Merge pull request #4 from amb43790/cmiller
Merge pull request #3 from amb43790/postgres_collation
Merge pull request #5 from amb43790/alternate-db
avoid warnings when a blank property_name is passed in
move the check for $table_name up one scope
Handle the case where a class' table_name is an inline view
Use the same mechanism for finding a column's property_meta as the UR::DS::Pg
Extract the code to resolve the column's property_meta to the caller
be more tollerant of case mismatches
When resolving the order by property metas, defer to the query plan
escape any strange characters in the table name
Make a method to extract the SQL alias for an inline view
support optional "as" in inline views
combine the two loops into one
always ask that class' data source instead of the top-level class' data source
Use the same condition as the "next" right after.
Merge pull request #6 from amb43790/rt99411
avoid an uninitialized value warning
Merge pull request #7 from amb43790/warning
_get_foreign_key_setting() takes an optional DB handle
Add XML::Dumper as an optional prerequisite
avoid an uninitialized value warning from $type
avoid an uninitialized value warning with $value->{operator}
avoid uninitialized value warning with members of @$val
extract function to tell whether an element of the list is a null value
use the default handle instead of making a new one
put quotes around empty strings, too
Don't overwrite URT's metaDB dump file in the repo when 98_ur_update.t runs
avoid an uninitialized value warning later when $constraint_name is used as a hash key
avoid a warning about re-declared my variables $class and $params
remove warning "test_hashref() called too early to check prototype"
fixup with 552c8ad0b21f61ef3e97d95eb9689d1754d58af3
suppress expected error message about datasource failing to sync
avoid uninitialized value warnings in 04_rdbms_retriable_operation.t
Sort the BoolExpr's param keys when displaying
avoid an uninitialized value warning inside _create_data_file
Extract function to return the proper order property definition keys should be processed in
Switch to id comparison instead of stringify for more reliable results
Remove unnecessary cruft
Merge pull request #1 from nnutter/ur-test-fixes
Notable changes since the last release
remove broken tests that do not get run with the test suite
POD fixes
Checking in changes prior to tagging of version 0.41_01.
Checking in changes prior to tagging of version 0.42_01.
missing requirement from UR::Util
Use version objects to compare versions
"return" has a higher precedence than "or"
Attempt to avoid running XML view test when it's not available
Make the test quieter by using warning_message instead of Carp
Checking in changes prior to tagging of version 0.42_02.
03k_rule_for_property_meta_no_properties.t needs Test::Exception
Checking in changes prior to tagging of version 0.42_03.
Checking in changes prior to tagging of version 0.43.
Merge pull request #19 from amb43790/release2
Implement an automatic unloading mechanism
Add docs for UR::Context::AutoUnloadPool
Mention AutoUnloadPool in the docs where it talks about unloading
typo
Forgot to use Scalar::Util
Don't add meta objects to the pool
After the pool is drained, invalidate yourself
Report what happens when memory debugging is turned on
Merge branch 'master' into autounload
Move is_prunable() to UR::Object and use accessors
Use the new is_prunable() as the test for adding to the pool
Avoid false-positive by checking if is loaded first
Use a hash slice on the object cache instead of is_loaded()
Merge pull request #23 from amb43790/autounload
Extract method to get the singular name for an is_many accessor
extract method to get the iterator name for an is_many accessor
extract method to get the set name for an is_many accessor
extract method to get the rule name for an is_many accessor
extract method to get the arrayref name for an is_many accessor
extract method to get the adder name for an is_many accessor
extract method to get the remover name for an is_many accessor
Spelling patches submitted from Debian
Link to relevent parts of the documentation
Clarify the documentation
Be consistent with calling the adders/removers methods and not accessors
Merge pull request #26 from amb43790/spelling
Merge pull request #25 from amb43790/is_many_property_names
Remove redundant check
Modify lists in-place instead of making new lists
remove unused hash
both names refer to the same function
$property_set is always a ref from 2 lines above
Fix bug
Turn these subs in UR::Util into functions from methods
Merge pull request #32 from amb43790/boolexpr
remove comment that is a lie
Be more efficient
Remove duplicate variable $data_source -> $self
Extract method to get or create the table object during metadata refresh
Extract method to update column metadata during metadata refresh
remove unused code for detecting bitmap indexes
Extract method to update foreign key metadata during refresh
Extract method to update primary key metadata during refresh
Extract method to update unique constraint metadata during refresh
Use fetchrow_hashref() instead of fetch() with var bindings
_get_table_names_from_data_dictionary() can return qualified table names
extract method to determine what table name to use for DB metadata objects
Remove ancient commented-out code
Remove owner from the primary key of all the MetaDB tables
SQLite now returns schema info when querying for foreign keys
'owner' is no longer tracked in the MetaDB or its objects
Forgot use strict/warnings
Avoid an uninitialized warning in _table_name_to_use_for_metadata_objects()
Allow constructs like schema.table as an argument
SQLite dumps shouldn't include schemas other than 'main'
Remove owner from the PK of the MetaDB tables
the backup MetaDB changed
Was only ever called with one arg
Remove backup DB that was added by mistake
Add more PostgreSQL data types
Use the already existing method to find table metas or ghosts
match column names when the case differs
Try appending an underscore if there's a problem creating a new property meta
avoid dying while updating classes - see comment in code
Avoid dying while updating classes
extract functions to pretty-print single and multi-line parts of a class definition
Change class rewriter field formatter
Merge pull request #36 from genome/remove-owner-with-recent
Fix for older versions of SQLite
Fix for unitialized value warnings
typo
Merge pull request #39 from amb43790/undef-owner
Perl 5.21.1 and later have a different warning message
Test with 5.20 and 5.21 on Travis
Merge pull request #41 from brummett/5.21-fix
Allow UR::Bx::Template->resolve() to accept meta-params like -order_by
Allow meta-params like -order in a property's where clause
remove debugging prints
properly local-ize $@
Merge pull request #50 from brummett/eval
Don't select the same columns multiple times with diamond inheritance
move is_meta_param to UR::BX::Util and use it
make the error easier to read
typo
Collect the template meta-params separately
whitespace
WIP - normal doubly indirect case is sorting properly now
Store the where-clause meta keys as a hash for faster lookup
For the default -order_by case we can avoid the sort
-order_by works in where clauses of id_class_by properites
Move the "default" sorter down where it is used
Extract common code from the -order_by results ordering subs
Change how the order-by sorter is created
Get the resolver once instead of each time through the loop
Fix the id-by doubly delegated case
Merge pull request #46 from brummett/order-by
Combine the id-class-by and id-by cases for doubly delegated properties
bring up $bridging_identifiers in preparation for combining via-to section
combine the via case with both id-by cases for doubly delegated properties
Rename variable
Use the via-via case only when there's a single property linking the bridge to the result
Don't use the double-delegated speedup for reverse-as properties
Rename variable
Add a handler for via-reverseas double delegations
Add a comment about what we're doing in this section
Only use this efficiency when there's a single linking property.
Use the efficient query code only if we didn't fall through
Extract functions
Add test case for doubly delegated via/via with multiple FK properties
Remove redundant else branch
convert to subtests
add test for creating a multi-ID object using its composite ID
add test for getting a multi-ID object using its composite ID from the DB
Merge pull request #53 from brummett/doubly-delegated-refactor
convert to subtests
Properly handle the case where an already composite id-by links to a class with multiple ID properties
Hhandle the reverse_as case where an already composite id-by links to a class with multiple ID properties
Let the class construct it's own composite id instead of assuming the separator is \t
Merge pull request #55 from brummett/composite-id
commentary/doc addition
Add 'once' parameter to UR::Observer
Remove 'once' observer before running its callback
Bugfix when List::MoreUtils::PP is used
Merge pull request #61 from brummett/travis-ci-fix
Merge pull request #58 from brummett/observe-once
Add "role" keyword support to the moduleloader
Extract method for converting old names in class definitions to the new name
Extract function to process has, has_constant, has_optional, etc sections of the class definition
Extract function to force a class def property is an arrayref
Split the prop list into class-only and class-and-role props
function to return a hashref of subname => coderef for a package
minimal implementation for Roles
Don't include the "roles" key if there are no roles
Convert to subtests
Extract methods to access a role's property data
Role initialization will want to use this, too
Roles' properties sourced from class metas aren't required and don't have defaults
Support a class consuming more than one role
Support 'requires' metadata for roles
Throw an exception if the named role does not exist
Detect property conflicts when composing roles
Add tests for roles and classes with conflicting method names.
Move the Default data source test alongside the other data source tests
add test for loader returning resultset
add test for saving objects
Add test for detecting failure during sync_database
use error_message() instead of a bare print to STDERR
commit() is now a separate phase of saving
Extract method to determine order for saving data sources
initial docs for roles
Allow roles to be dynamically loaded
Allow parent classes to fulfill requirements of roles
improve error message
Report the correct error location under certain conditions
Properly localize $@ while loading a class/module
Extract method to normalize property descriptions during class initialization
Allow a Role's properties to get column_name metadata when composed into a class
remove unnecessary variable
Remove dead code
Roles can have an __import__ method that gets called when a class composes them
Merge pull request #67 from brummett/error_loc
Re-enable property normalization in its former location
extract method to load Role modules during role composition
Extract methods to collect properties and meta-properties from roles during class initialization
Move role-related code out of UR::Object::Type::Initializer and into UR::Role
Allow classes with overloads to load without 'bool' overloading
Roles now have an 'excludes' property
Roles' overloads are composed into classes
Add tests to ensure you can't get() or create() from a Roll's class
Don't report exceptions as coming from the class initializer
Improve error message
Handle 'fallback' overloading specially in Roles
Remove double call to get Role's methods
Add test for Roles having class meta params like doc.
Move the 'role' keyword implementation to UR::Role
Compose roles before subclass preprocessing happens
Alter test to ensure "valid_signals" values are combined together
Role definitions can have DeferredValue objects
more documentation for Roles
typo
Add links to other docs
Fix bug in object cache pruner
Merge pull request #69 from brummett/pruner-bug
Extract method to apply extra params from a class definition
Role definition throws exception for unrecognized params
Autogenerated ghost classes don't get roles from the live class
Skip over constant declarations in the target package
Basic support for UR attributes
Assign params as a list instead of shift
The attribute is now called Overload
If a class method overrides one of the roles, it must declare that intention
refactor to move override validation to its own method
typo
extract functions to apply role properties and meta-properties to a class description
Use croak instead of die in AccessorWriter
Improve some error messages involving lists
Merge pull request #76 from brummett/croak
UR::Role is now known as UR::Role::Prototype
Role instances are created when composing role prototypes into classes
Basic support for assigning parameters to roles
Extract function to check common things between loading classes and roles
Support real dynamic loading of Roles
Add an attribute handler for RoleParam
Role params are working as 'our' variables
Make sure all role params have values when they're composed
add docs for parameterized roles
Remove old DeferredValue implementation
not needed anymore
UR::Role provides a define() method
Basic documentation for the new role classes
convert to subtests
Fix a bug with the -limit option to get()
Add test for the -offset being larger than the result list
Some version of perl put a period at the end of the warning message
Merge pull request #80 from brummett/limit
Merge pull request #66 from brummett/default-ds
Fix test
switch to throws_ok in test
Bug fix with class-wide mutator method
Class-wide calculated default properties now work
Delay calling a calculated default sub until needed
Merge pull request #81 from brummett/travis-failures
Merge branch 'master' into classwide-calculated_default
unneeded variable
remove breakpoint
typo
make the docs tell the truth
rename variable
Make is_subset_of() aware of -limit and -offset
Handle the case where a bx has more filters, but includes a limit or offset
SQL for limit and offset appear in the SQL
convert to subtests
Better determine id_only and matches_all BoolExprs
Extract methods to get the limit and offset values when constructing SQL
Properly handle -limit and -offset when there are changed objects
Handle limit/offset queries where the data source does not support it
back-out Oracle support for limit
Remove duplicate pod from UR/Object/Type.pm
Merge pull request #89 from brummett/type-pod
Add debian changelog entries for older versions
Genome Institute => McDonnell Genome Institute
update copyright date
changes since the last release
Don't pollute the Test:: namespace with our test module
Changes from running 'minil release'
run_tests() function now runs the test directly instead of returning a subref
Some versions of Test::Builder require subtests to have a plan
Get tests passing on perl 5.8
Move UR::Test to URT::Test
extract function to unload a single object
Merge pull request #90 from brummett/release
Fix test
Extract getting $class and $id to the encompassing scope
rename $UR::Context::destroy_should_clean_up_all_objects_loaded
Fix a bug involving the AutoUnloadPool and iterators
Extract common object weakening code to common method
remove unused function
Merge branch 'master' into limit-offset-in-db
Merge pull request #85 from brummett/limit-offset-in-db
typo
Change the name of the test to reflect what it does
Weakened objects with changes shouldn't get removed from the object cache
extract method to save an object from being removed from the object cache
using refaddr() will be more reliable, in case objects have string overloading
fix message printing condition
Merge pull request #92 from brummett/iter-autounload-bug2
Mask exceptions when $ds isn't something we can call get() on
Fix a bug involving classes with the Default data source and unloading.
remove commented-out lines
remove unused variables
Catch the case where a property chain includes a non-existent property
Fix a bug with the cross-datasource joiner
Merge pull request #94 from brummett/value-autounloadpool
Merge pull request #95 from brummett/multi-datasource-join
Merge branch 'master' into roles
add $VERSION to new files in this branch
Give a useful exception when a RoleParam attribute is missing its name
More subs to not pass on to composing classes
Improve exception messages with autogenerated classes
Merge pull request #98 from brummett/exceptions
Add fatal message type
convert to subtests
Fix a problem when creating an object with multiple of the same coderef as attribute values
Merge pull request #99 from brummett/thaw-coderefs
Add implementation for fatal message type
convert to subtests
doc updates for fatal messages
Extract sub to test sending a message
test fatal messages
Extract top-level Context commit code to where it belongs
base transaction now deleted Change objects after committing
improve error messages
add test for double rollback
Put lowest-level commit code back into UR::Context::commit()
Merge pull request #103 from brummett/change-objects
Fix an error in the test matching a fatal message
Eliminate a warning when sorting by a chain property (prop.other_prop)
Restrict the types of warnings we're masking while sorting
Resolve the right properties to sort by
Remove TODOs that are already true
convert to subtests
Fix a bug in the test
Merge pull request #105 from brummett/fix-set-test
Merge pull request #104 from brummett/sorter-error
Merge pull request #101 from brummett/fatal-message
rename variable
fix typo
Retrieving *_messages() includes subclasses and instances
refactor to eliminate common code
Merge branch 'master' into roles
Merge pull request #63 from brummett/roles
update docs for error_messages() to match new behavior
convert to subtests
remove commented-out code
Move __errors__ sub outside the subtest
Use constants for the transaction state instead of strings
use croak instead of die
A software transaction's validator can be changed
docs for the new commit validator function
Localize $@ in accessors
localize $@ in BoolExprs and PropertyComparisons, too
Merge pull request #108 from brummett/evals-in-accessors
Merge pull request #107 from brummett/transaction-validity
Give these role properties default values
Check for parent class method name conflicts when composing a role
add method modifiers to roles: before, after, around
documentation for method modifiers
Merge pull request #109 from brummett/role-fixes
Merge branch 'master' into method-modifiers
Don't copy method modifier subs into consuming classes
Merge pull request #110 from brummett/method-modifiers
extract function to turn a hash field into an arrayref
Extract function for normalizing ID property data in class descriptions
Rename method property_names => has_property_names
add method to return the names of ID properties
id_by Role properties are now transferred to consuming classes
Refuse to apply a role when the class redefines a property from ID to non-ID
add docs for id_by in roles
bugfix in the docs for method modifiers
Add method to determine if the class directly has table data
Classes using 'subclassify_by' can now use the Default data source
Rename variable
Throw exception if class method Overrides a method that doesn't exist in the role
Throw exception if a method declares Override for a role the class doesn't consume
Allow a class method to 'Overrides' a role property
Merge pull request #114 from brummett/detect-role-override-error
method should return a class name instead of true/false
Merge pull request #112 from brummett/id-by-in-roles
convert to subtests
iterators now have a peek() method to non-destructively return the next object
remove old, commented-out code
add remaining() method to iterators
Iterators can now be constructed from a list of prepared values
Add map() method to UR::Object::Iterator
Extract non-object-ness from UR::Object::Iterator
Merge pull request #116 from brummett/iterator-enhancements
Allow sets to be sorted with cmp
extract method to determine the "show" columns
extract method to create the iterator
extract method to print the results from the iterator
Merge pull request #117 from brummett/set-lister
Merge pull request #119 from yanick/silence-warnings
Ref addresses can be re-used, use a serial number instead
Merge pull request #127 from brummett/file_ds_bug
major changes since 0.44
Tell TravisCI to test on 5.24
Update copyright date
fix pod errors
Try extracting more info from a failed test.
Results of 'minil release'
Ben Oberkfell (29):
modify to work smarter w/ Protytpe library
pretty update
default_aspects is an arrayref, shouldn't be defined is_many
Add safe fork() functionality
More things than just UR::DataSource::RDBMS should be doing preparation prior to fork, so break this out into something generic.
there should not have been a die in the superclass
Merge branch 'master' of github.com:genome/UR
preserve filehandle positions on fork
fix test case test count
Merge branch 'master' of github.com:genome/UR
fix on forking and properly disconnecting database handles.
remove superfluous get() call in finish_up_after_fork
Detect bad use of select() in modules.
escape bytea output so storable doesnt barf.
Merge branch 'master' of github.com:genome/UR
comma-separate the class id property columns in this error message
changes to facilitate workflow interaction with postgres/oracle testing
break out table meta gets into a separate method, so the data source name can be easily overridden for internal postgres/oracle sync testing
Merge branch 'master' of github.com:genome/UR
fix local variable
remove debug message left in
ignore case when looking for large object columns
treat null values like we do oracle
break this out so that code in our internal postgres testing repo can override it.
fix for properly closing the db handle out after a fork.
more places to swap data source ID so that postgres testing datasources work as they should
do not disconnect parent database handles prior to forking. set InactiveDestroy and let the children forget the handles ever existed.
Only commit if there are changed objects at the end of execution that are associated with a data source.
only rollback on disconnect if autocommit is off and we risk committing automatically
Brian Derickson (31):
duplicate values in an in-clause are now removed properly
added is_sub_command_delegator method to Command::Tree and Command::V2
Revert "added is_sub_command_delegator method to Command::Tree and Command::V2"
removed breakpoint
Merge branch 'master' of github.com:genome/UR
removed debugging code from datasource
fixed compile error
removed breakpoints
added no warnings to prevent harmless warning messages that are
added is_direct, which returns true if a property is "direct", ie it is
removed breakpoint
added Command::DynamicTree, which is a fusion of
removed a bunch of comments and breakpoints used for development
Merge branch 'dynamic_tree'
added _ask_user_question method to Dispatch/Shell.pm, since there were
Merge branch 'master' of github.com:genome/UR
commands that use Command::DynamicTree can now override the
Merge branch 'master' of github.com:genome/UR
renamed DynamicTree to SubCommandFactory
improved error messages when figuring out delegated properties in query
fixed uninitialized value warning by adding defined check
added methods to Command/V2 for handling errors when multiple commands are executed
removed breakpoint
Merge branch 'master' of github.com:genome/UR
removed breakpoint
fixed bug where Command::Tree would emit an error if given --help
changed timing of commit signal on changed objects
fixed a few sorts due to perl 5.8 bug
fixed more sorts to get around perl bug
created new environment variable UR_RUN_LONG_TESTS
fixed bug in sub command factory where some subclasses were not getting correct _target_class_name
Chris Oliver (13):
Added icon_16 for gmt-web
Cleaned up a little html for gmt-web
Added some formatting to gmt-web
Use templates for install page
Merge branch 'master' of github.com:genome/UR
Unnested pre tags
Added links in nav to examples
Updated gmt package name in gmt-web
Added introduction to gmt-web
Added documentation link
Added header to documentation
Made install page consistent
Added exe_name for install page
David Morton (6):
Add 'ur show subclasses' command
updated indirect accessor to take filters
updated test 47b to support filtering parameters on indirect accessors which are more than one step away from the primary class
Remove unused option to ur show subclasses
Don't let Term::ANSIColor polute our namespace
Merge pull request #43 from davidlmorton/imports
Eddie Belter (21):
CHANGELOG: Added '_resolve_boolexpr in list command
List command now has a sort position
CHANGELOG: Comman/V1 croaks is get opt has errors
Merge branch 'master' of github.com:genome/UR
Command Tree: if help requested, do not display error
Fixed problem where indirect accessors bridging over a missing has-one entity would get an undef bridge item instead of an empty list, causing an exception during indirect accessor usage
SubCommandFactory: added target base class; moved target class overloading to method
Command Tree: get meta before using class when building the sub command mapping
Command Tree: get class instead of meta
Merge branch 'master' of github.com:genome/UR
Command View Doc Methods: update to give "..." for command tree
Move methods from Genome::Utility::Text to UR::Value::Text/HASH and create CamelCase class
UR::Value - rm camel case class, move methods to text
UR Object View: make _xml_doc optinal transient
Ur Object View: make xsl_path optional
XML View: is_transient is implied in has_optional_transient
Merge pull request #87 from ebelter/view
SubCommandFactory: Skip sub commands that do not build
SubCommandFactory: test and test classes
Remove unused use statements
Merge pull request #111 from ebelter/sub-command-factory
Edward Belter (7):
corrected test count
Merge branch 'idclass2' of git at github.com:sakoht/UR into idclass2
corrected test count
updated UR::Context to better handle multi-id property classes
Merge branch 'master' of git at github.com:sakoht/UR
added if block in UR.pm to avoid compiation error when only compiling UR.pm by itself.
UR::BoolExpr: removed old app thing: previously able to get w/ property id given an array ref of objects, that would then remap the arrayref to the id from the objects; UR/Object/Type/AccessorWriter: clarify warn message when getting directly with UR::Object.
Eric Clark (2):
Fixed manifest and perl version format for 5.10
added a couple missing dependencies
Feiyu Du (2):
Updated to handle views in the inheritance hierarchy at save time by ignoring them. All persistent properties will need to be implemented in physical tables.
Now, when inferring database table/column structure for classes w/o data dictionary information, we will also infer foreign key constraints.
Gabriel Sanderson (1):
Revert commit that caused the workflow server to immediately shut down, causing builds to hang indefinitely.
Ian Ferguson (2):
Set status messages to print by default
Fixed broken dump message inheritance test
James Koval (13):
Tracking caller's line and file when calling *_message
Eliminate need to call V1.t with a specific working dir
Recording caller's subroutine
Added method accessors for call-stack info on error_message
Fix whitespace and braces formatting
Override signal validation to allow error_die signals
Catch command errors and emit signals with metrics about failure
Remove brace in comment, which breaks auto-indenting
Call super validate_subscription with correct params
Require build ids to be 9 digits
Leave bjobs and error message parsing to the observer
Only use one observer
Only die if the evaled command died
Jason Walker (2):
Added property example_values.
Respect camel case table names and column names in RDBMS data sources.
Jim Eldred (2):
Merge pull request #106 from brummett/messages
Merge pull request #113 from brummett/default-datasource-counts-as-a-table
Jim Weible (1):
Allow subsecond oracle timestamps
Joshua McMichael (6):
XSL views now include a /common.xsl, if it exists, that should include common templates used by all perspectives
added GENOME_DEV_MODE variable to xsl vars
added display name and label name var elements to base XSL; added regex to remove invalid XML entities before transformation
fixed another invalid XML entity parsing issue
fixed merge conflict, fixed another vector for invalid XML entities being parsed
instantiate global XSL variables using parameters instead of variables. This change allows overriding globals at runtime
Justin Lolofie (10):
_generate_content passes on additional params, e.g. solr_doc => $xml_solr_gave_me
methods to store program name and user in oracle variable
set_env doesnt require module/action
trying to use aggregate function "count" in a JSON set view,
UR_DBI_SUMMARIZE_SQL prints a count of times queries had to be executed
UR_DBI_SUMMARIZE_SQL was counting every query twice when UR_DBI_MONITOR_SQL was turned on
static html view doesnt apply xsl
store username in default xsl variable
removing the 2 breakpoints I hit most often
fixed the last line of help for 'genome tools'...
Kyung Kim (2):
corrected scalar comparison not in quotes
made comparision is to is_deeply for comparing in
Mark Burnett (3):
add UR::Util::ArrayRefIterator
Value::Iterator copies instead of modifies its input
add UR::Value::JSON
Mark Johnson (1):
Filter @INC through UR::Util::used_libs_perl5lib_prefix() before setting PERL5LIB.
Matt Callaway (15):
Generate the .pod file at the same location as the .pm if no output path is given
Add dependency on libjson-perl
Add Provides: ur so one can apt-get install ur
Check the time on an sqlite schema file and move an older dump or db file to .bak
Add dependency on libclass-autoloadcan-perl
Remove the restriction that submodules live under the module that defines the namespace.
Update version in debian packaging
Add requirement on libossp-uuid-perl
Alter _show_item_is_property_name to allow dots in property names. Alter Style to use __get_attr__ to resolve attributes with dots, eg. foo.bar. This allows Listers to display indirect attributes.
Use spaces to join lists so we don't mess up CSV format.
Remove pollution from the SYSTEM namespace. It looks like nothing else could be using this since it would be broken if they did. Change SYSTEM to UR.
Add new env var in support of Shell.pm.
Merge branch 'master' of github.com:genome/UR
replace *all* :: with / to go from mod to path
input_path is optional, handle the case where it is undef
Nathan Nutter (187):
added support for creating an opts_spec file for the Command class; fixed class_name<->command_name asymmetry; updated bin/ur to Bash complete itself
renamed my new tests to better reflect what they are testing
updated my tests to be more thorough
updated lib/UR/Namespace/Command/CreateCompletionSpecFile.pm to handle a output file parameter to override default location
fixed miscalled method (non-Complete method called in Complete method)
updated opts file after fixing improperly returned options values
Merge branch 'master' of github.com:sakoht/UR
fixed loading of external namespaces for CreateCompletionSpecFile
fixed bug when an is_many property had default_values
Merge branch 'master' of github.com:sakoht/UR
fixed add_change_to_transaction_log would treat and id of zero as non-existant and improperly skip property
updates to allow transactions to work in a broader range of scenarios
changed text output, e.g. five to 5
fixed typo
Merge branch 'master' of github.com:sakoht/UR
moved rollback signal to before changes are undone and deleted for transaction rollbacks
fixed observers not removing their subscriptions when deleted
Merge branch 'master' of github.com:sakoht/UR
fixed loop that was exceeding array index
fixed typo, mispelling 'commited'
Merge branch 'master' of github.com:sakoht/UR
updated opts file for ur command
UR::Change::undo now unloads created transactions rather than ignoring them
UR::Context::Transaction validates that first change was the creation of itself during rollback
Merge branch 'master' of github.com:sakoht/UR
added an 'external_change' aspect to UR::Change::undo
undefined table_name's len in UR.pm so it will support greated than 256 bytes
updated Command to identify more data types as files for getopt complete
Merge branch 'master' of github.com:sakoht/UR
changed help text to not refere to Genome::*
updated ur create-completion-spec-file to be more concise and to fix bug
updated to be more GNU standard in how output is displayed to terminal
updated .opts file
Merge branch 'master' of github.com:sakoht/UR
changed output of error when command missing sub-command is run
Merge branch 'master' of github.com:sakoht/UR
enable various messages just a few lines earlier in _execute_delegate_class_with_params
show error for cmd with sub-cmds that has no params and process command that has any params
exit on failure tab completion
Merge branch 'master' of github.com:sakoht/UR
updated tab completion spec file
restored lib/UR/Time.pm from prior to 1dfe655
UR now also updated PERL5LIB with abs_path as it does @INC
better method for resolving INC/PERL5LIB; does not use regex
still support undefined PERL5LIB but don't duplicate loop
hopefully made used_libs more robust and added test case for it
used_libs now compares to abs_path since UR.pm does that to @INC
push PERL_USED_ABOVE onto used_libs
unshift above libs instead of push
use original path when Cwd::abs_path returns undef (a directory does not exist)
UR::Util::used_libs returns unique list now
backup tab completion file and restore if failed to generate new one
use Clone::PP to deep_copy instead of Data::Dumper to reseolve CODE ref warnings
only try to use sqlite3 bin to load/dump if 'which' can find it
return empty string instead of undef for abstract help_synopsis
improve error message when class has sub_class but no sub_tree
update opts file
only do numeric comparison of version if looks numeric
renamed debian -> ubuntu-lucid and updates to packaging config
no longer use sqlite3 bin to load db
open Meta DB for namespace so tests don't have to generate new Meta.sqlite3
fix lower_case_table_names check for MySQL data sources
resolve symlinks in %INC just like we do for @INC
added a slim namespace and test to catch bug fixed by '[master 62a2001] resolve symlinks in %INC just like we do for @INC'
unlink and ln instead of just 'ln -sfT' for Mac compatability
refactored comparison_value_and_escape_character_to_regex
prevent 'fake' UR::Objects that are recreated during from undo from triggering UR::Object::DESTROY
fix "Can't bless non-reference value" error
do not reverse constant properties
add the command line list operator \!: for 'not in'
refactor filter regex into its own sub so it's programatically accessible
Commands that fail to commit will now rollback and exit non-zero
refactor display of invalid data for save for re-use
Transacation commit now checks for invalid data for save and rollsback if invalid
add test to check that Transacation commit now checks for invalid data for save and rollsback if invalid
don't force rollback if Transaction commit fails
fix Vending tests that had missing machine_id or non-integer ID
commit always resolves self to an object
fix bad logic from previous commit
add test for checking that UR::Context->commit triggers commit observer
tweak UR::Object::Tag __display_name__ to be like how they are displayed in UR::Context commit
use __display_name__ when displaying error tags in UR::Context commit
add process accessor on UR::Context
add test to make sure process and current differ within transaction
fix not signaling on property (index not updated)
add test for fix not signaling on property (index not updated)
fix boolexpr filter change causing exception
add test for fix boolexpr filter change causing exception
Getopt::Complete changed from being COMP_LINE based to COMP_WORDS based so this param changed to comp_cword
Getopt::Complete changed from being COMP_LINE based to COMP_WORDS based so this param changed to comp_cword
add trailing commas
make filter shell_args_position => 1
UR::BoolExpr no longer assumes a ref is a param list for UR::Value::PerlReferences
refactor _generate_content to split out the generation of the xml_doc
refactor addition of perldata to XML node so it can be used elsewhere
PerlReference's XML view will now generate XML including the perldata (XML representation of the Perl data)
SCALAR is a PerlReference
add a basic expected output test for UR::Value::PerlReference XML views
refactor common map/grep into map_column_name_to_column_meta to allow override in Oracle
override map_column_name_to_column_meta for better case insensitivity
Revert "override map_column_name_to_column_meta for better case insensitivity"
Revert "refactor common map/grep into map_column_name_to_column_meta to allow override in Oracle"
fix warning about using shift
whitespace
fix for create_iterator not accepting a BoolExpr as argument
fix for not removing trailing slashes in final list (PERL_USED_ABOVE had one)
reformat test so each "sub-test" is in its own scope and add test for trailing slash on PERL_USED_ABOVE
resolve . instead of leaving it to be resolved later
add test to catch case where used_libs changed after a chdir
switch several create_iterator calls to current syntax
fix for not finding URT in lib path
typo
typo
whitespace
add ability to specify a Command::Tree's source(s) instead of assuming children of it
class method to UR::Object::Set are called to it rather than to members
Merge branch 'feature/command_tree'
Merge branch 'master' of github.com:genome/UR
change die to warn because previous implementation didn't even try to use
should only be validating properties that are also from Command classes
fix for recursive loop in UR::Object::Set->can
Revert "fix for recursive loop in UR::Object::Set->can"
Revert "class method to UR::Object::Set are called to it rather than to members"
add _init_subclass to Set so that it is not handled by the member aggregating accessors
unimplemented class methods on Sets are now delegated to member class (with arguments passed through)
fix for incorrect 1:1 between key index and values index (due to non-contant values)
delete should return deletedref object like SUPER does
ID needs to be a class because isa is called on it
typo? worked in DFS MRO but revealed in C3 MRO
allow setting MRO for Namespace
whitespace & typos
add test for method resolution order
Merge branch 'c3' into gb_master
allow UR::Value::Text to act more like strings
add file test methods to UR::Filesystem::Path and inherit from Text
Merge branch 'filesystem_path_methods' into gb_master
fix for change in mro behavior on newer Perls
add line_count to UR::Value::FilePath
fix bug introduced in 2e4b1aa
fix for case where die was not re-thrown
remove debugging output
validate param string before assuming it is an ID
only set bytea_output for PG >= 9
revert bytea output escaping changes
show more debugging info if fail to connect to DB
add do_after_fork_in_child and consolidate the comments
base class implements methods so can is not needed
fix a couple warnings
disconnect dbh before fork instead of giving up after
using default handle in closure is risky since it may get disconnected
rename person_set to cool_person_set
add overload operators for != and ne like == and eq
do local aggregates iff members have changes
return 1 at end so command exits 0
fix for $sub_class being undefined
fix infinite loop in GetOptions error message passing
Unset UR_COMMAND_DUMP_STATUS_MESSAGES.
pass class name to observer callbacks
make date template accessible
whitespace
show relational properties in listers
refactor so subclasses can somewhat control formatting
change =cut to comments for more stable syntax highlighting
show data source in message for context/clarify
fix issue when data sources shared a table name
filter invalid class names
probably only supposed to die on error
fix '0 but true' being flagged as invalid integer
refactor column property translations
update formatting of module writer
improve the format of valid_values
whitespace
improve normalization of vendor data type
cleanup attributes_have output to match other sections
remove and ignore binary SQLite files
move comment
whitespace
whitespace
remove commented out code
make sub curly braces consistent
remove execute and execute_and_rollback
add UR::Context::Transaction eval and do
test eval and do
fix returning error string on die
add semicolons on final statement of block
throw an exception if commit/rollback fail
catch exceptions in (overridden) __display_name__
Nathaniel Nutter (87):
whitespace
Merge pull request #1 from nnutter/add_remove_accessors
Merge pull request #2 from susannasiebert/master
close file so that's it's not locked
Merge pull request #9 from amb43790/ur-test-fixes
remove alt directory
Merge pull request #10 from nnutter/alt
add minil.toml
generate cpanfile with `mymeta-cpanfile --no-configure`
sort perl to top
add Test::More as a testing dependency
migrate Build.PL to Minilla
remove "boilerplate"
update .gitignore
add next version placeholder to Changes
move Test::Fork to test dependecy
add Minilla as develop dependency
add Minilla's auto-generated boilerplate
update .gitignore for Carton
update .gitignore for Build script
add missing dependencies
auto-generated update
add Version::Next as develop dependency
add CPAN::Uploader as develop dependency
Merge pull request #11 from nnutter/minilla
add Travis CI config file
set minimum version of Minilla to 1.1.0
add 'No BumpVersion' "annotations" where needed
Merge pull request #13 from nnutter/minilla
Merge pull request #12 from nnutter/travis-ci
enable Travis CI badge in README.md
auto-generated from `minil build`
Merge pull request #14 from nnutter/master
add member_iterator to UR::Object::Set
refactor to limit scope of variable (@members)
refactor: extract $cool_names
add test for member_iterator
remove do blocks
compare members against member_iterator
Merge pull request #15 from nnutter/member_iterator
Merge pull request #16 from tmooney/master
Merge pull request #22 from nnutter/master
Merge pull request #24 from nnutter/master
add failing test exposing issue with transaction change ordering
record object creation prior to using object
Merge pull request #28 from nnutter/master
Merge pull request #29 from nnutter/master
Merge pull request #31 from nnutter/reverse_as
remove comments
remove no-longer-accurate comment
normalize set rules
add test case to prevent regression
remove breakpoint
whitespace
flatten_hard_refs should not silently allow nonsense UR::Object refs
Merge pull request #33 from nnutter/set
rename variables to clarify intent of code
Merge pull request #34 from nnutter/flatten_hard_refs
revert the context_return change to is_many accessors
convert test to use subtests
add primitive copy method to UR::Object
prevent accidental infinite recursion
extract to subtest
allow overrides to be passed to copy
add doc about %overrides
add txtest test helper
use txtest to minimize shared state between subtests
fix incorrect behavior for is_many properties
try to clarify docs
Merge pull request #42 from nnutter/copy
check if schema exists in backwards compatible way
Merge pull request #47 from nnutter/pg
Merge pull request #49 from nnutter/above
Merge pull request #59 from nnutter/master
Merge pull request #64 from sebokopter/added_use_strict_everywhere
Merge pull request #68 from nnutter/tab-completion
Merge pull request #70 from nnutter/default
Merge pull request #72 from nnutter/master
Merge pull request #74 from nnutter/master
Merge pull request #77 from nnutter/try
Merge pull request #75 from nnutter/help
add __saved_value_for_property__
Merge pull request #78 from nnutter/rollback
Merge pull request #1 from brummett/classwide-calculated_default
Merge pull request #83 from nnutter/transaction-unload
Merge pull request #82 from nnutter/classwide-calculated_default
Merge pull request #84 from nnutter/master
Neil Bowers (1):
Symbols weren't being imported into the calling package
Philip Kimmey (1):
Limited module test to .pm modules (not .pm*)
Rob Long (1):
Fixed BoolExpr.pm to correctly parse '_key operator' => value type expressions which start with an underscore, added a test, 82, to verify.
Robert Long (2):
Updated UR::DataSource::RDBMS to handle classes with a view in the inheritance hierarchy, but with a concrete table above and below the view, which have constraints between their primary keys, and where constraints must be inferred from the class structure.
Moved the POD for UR::Context back to the bottom of the module instead of a separate file.
Scott Smith (497):
Made the id_class_by meta-property work, and test them in the most complicated situation so far: being behind a has-many indirect mutable property. Properties which are indirect which wrap has-many properties still have an insufficient number of accessors (add_*, and now remove_*) directly available. We test the case in which the bridge must have items added/removed when a property changes, but not the case in which the bridge might update because the property is not part of the i [...]
fix to ensure the id_class_name is set when using add_* wrappers for adding related objects through has-many relationships.
added a test case to demonstrate the problem of missing values in the id_class_by field
Merge branch 'master' into webdispatch
Josh M's latest changes.
New xsl.
Merge branch 'webdispatch' into web-josh2
Merge branch 'master' into web-j1
Merge branch 'web-j1' into web-j2
updated the #! line to use a non-site-specific interpreter
restored executability
new view tree based on a cleanup of the old UR::Object::Viewer
Merge branch 'new-view' of git at github.com:sakoht/UR into new-view
Now infers subject/perspective/toolkit from class name if not in params. Removed debug code
merged from trunk
Merge branch 'new-view' into new-view-plus-test-path
made test 62_nullable_foreign_key_handling_on_insert_delete use a different test db than that of 98_update
made test 62_nullable_foreign_key_handling_on_insert_delete use a different test db than that of 98_update
renamed test 62 to test 64, since another test 62 and 63 were added in parallel.
Fixed hole in command naming update.
revereted UR::ModuleLoader because of odd DBI behavior.
Renamed generate_support_class to __extend_namespace__, and pulled it out of the deprecated list.
Updated version number to 0.13 in prep for next release. Updated Changes.
Don't try to load classes when you're in the middle of defining them. Classes which are built by __extend_namespace__ will pre-empt explicitly defined ones.
Removed debug code where a command module does not have a file. Commands defined in-line, or dynamically are generating garbage in the terminal.
Command::DynamicSubCommands makes auto-generating a command list based on another group of classes easy.
Updated changes for the 0.13 release.
Moved UR::Object POD to the bottom of the module.
Ensure dynamic commands are overridden by real commands on the filesystem.
Updated MANIFEST
Added default _target_class_name method to be overridden in subclasses.
Handle the case in which the class from which dynamic commands are built is not loaded when the command compiles.
Eliminate warning when comparing undef values on objects during reload.
Ensure that we resolve the boolean expression for the subclass of view, not the view base class, when delegating.
Added sub_command_category as an optional field for grouping sub-commands.
New Xsl default view for auto-converting XML to a specified format.
Views: auto infer parameters more completely from the class name. Better error messages when params are missing.
Added an error message when a property is described with an arrayref instead of a hashref.
Install a subname for calculated properties so that call stacks are more readable.
fixed bug causing modules which override automatic commands to not appear in help lists
Updated how Command.pm resolves its name.
Indirect accessors may create an object or assign an existing object.
Fixed omission in logic for inserting into NAMESPACE.TABLE_NAME w/o metadata
Updated mk_indirect_rw_accessor to handle is_many and not correctly
Fix the "between" operator to work again
handle nullable fk ordering issue
Merge branch 'rdbms'
help now returns non-success exit code
handle regular references correctly when normalizing a rule
removed circular fk in umlet view class
added datasource for classes to do custom loading
test for custom loader
added XML::LibXSLT to deps.
typo fix in comment
optimized key-value to just id
allow op in where clause in class property definition
cleanup UR::Value classes
added a test to make sure normalized rules return real references instead of clones of the original reference
CHANGELOG: The dummy-ids formula now includes hosname AND pid.
remove warnings from xsl creation where values are undefined
updated the Getopt::Complete version to 0.15
removed comment
fixed warning in Command module
removed the last thing which called preprocess_params
Updated version to 0.17 for the next release.
Removed dumping of debug info.
updated developer list
added __display_name__ to tags
major cleanup of command tree
new "ur define db" has a simpler interface to making datasources.
made the namespace name non-optional
cosmetic cleanup
hid old datasource command tree
the new "ur init" is a one-command starter for using UR
added transaction around init logic
renamed mods
removed old Gtk and Gtk2 toolkit modules with old App deps
removed old Gtk and Gtk2 toolkit modules with old App deps
updated the tutorial to use the new command tree, and a Music namespace
Merge branch 'master' of github.com:sakoht/UR
updated the default "owner" for SQLite databases to go from undef to main on and after v1.26
cleanup cruft
added precision to the version number for API changes
Removed Date::Calc, and use Date::Format which is all Perl. Code is faster overall
removed accidental file copy commit
updated version to 0.19 in prep for next release. removed Storable from deps
removed old UserOperation module
added deps to Makefile.PL
Merge branch 'master' of github.com:sakoht/UR
removed accidental commit of a Cmd.pm. Updated the lister to not depend on XML::LibXML
make XML::LibXML optional for UR. It's only needed by certain optional parts of the view system.
Merge branch 'master' of github.com:sakoht/UR
cleanup makefile
updated Makefile.PL
added a test to ensure all UR modules compile. cosmetic cleanup. ensure we do not attempt to use XML::LibXSL unless needed
updated Getopt::Complete version to 0.18
Updated Changes
updated MANIFEST and tutorial
updated MANIFEST
Merge branch 'master' of github.com:sakoht/UR
restore changes for 0.19
Updated versions and manifest.
cleanup boolexpr, and contect core construct/destruct
restored old version module to match prior releases
updated deps for packaging
updated manifest
updated changelog for 0.19
updated manifest
initial v0.20 code fixes META.yml
typo fix in README
doc updates
Merge branch 'master' of github.com:sakoht/UR
handle the case where there is no PERL5LIB setting
added a method to detect the default owner for sqlite
handle old vs. new sqlite owner undef => main
removed debug code
remove warning for undef value on old versions of sqlite
updated to handle sqlite changes present in DBD::SQLite > 1.26_04. still some test failures on t98
added new sqlite schema and dump for use with newer sqlite
new dump for the vending machine tests using new sqlite APIs
Updates to be aware of sqlite API changes during
on perl 5.12 ->isa() might return true even if @ISA has been emptied, now accounted for
ensure DBD::SQLite has been used before we check the version
skip test 83 for newer sqlite until fixed
the owner on fk constraint coluns was non-nullable, even though everything else supports null values for owner (reqd for DBD::SQLite < 1.26_04)
Huge speedup on the core constructor by caching metadata.
Correctly merged the fix too do deep copies for default_values which are
updated version to 0.20 for the next release
add logic to ensure that Class::Autouse plays nicely with Class::Autouse_1_99_02.
CHANGELOG: revamp object constructor and bx for 35%-60% time reduction
Merge branch 'master' of github.com:sakoht/UR
Merge branch 'master' of github.com:sakoht/UR
change to support unset PERL5LIB
switch from Module::Install Makefile.PL to Module::Build Build.PL
Disbled test 99 during installation. Polished install.
Run install tests in parallel. Disable tests during install which must write to sqlite databases.
running 8 tests in parallel is actually faster than 16
added the vending db to the repo for tests to work
updated manifest
updated META.yml
removed old META.yml file
removed META.yml from the MANIFEST
restored META.yml since "./Build dist" puts it in the MANIFEST
restored META.yml since "./Build dist" puts it in the MANIFEST
updated to not use the version module
removed v from the docs on version number
revered change to generate a temp file inside of the server() method
removed inc
removed old UR::DBIx::ContextualFetch
ensure modules have a VERSION
updated META.yml
updated manifest for removed modules
added Date::Pcalc as a dep
use $^X instead of "perl" as the interpreter path
remove UR::DBIx::ContextualFetch
added JSON to the dep list
disable test 98 on OS X
updated Build.PL to fix parallelization issue on test 42. also include Test::Fork
disable test 98 during install because of file issues and speed
updated pod
updated Changelog missed on 0.24. initialized changelog for 0.25
update to version 0.25
built 0.25
removed old moose modules
updated all versions to 0.26
build version 0.26
Merge branch 'master' of github.com:sakoht/UR
use the base view class early, and cleanup test 78 so it fully skips
relocated old CGIs
added the base view to the pre-loaded class list
removed moose stuff from manifest
fixed ::View usage
reset the test count
relocated speculative code under alt
updated version to 0.27
removed umlet from the UR::All module. prev commit relocated the modules
switch UR to Class::Autouse 1.99_04
ensure _02 and _04 play nicely together
added more doc lines to UR.pm
removed old source => "data dictionary" cruft
classes which implement __load__ get a UR::DataSource::Default which works in a basic way
Updated the object lister to pre-query results.
Merge branch 'master' of github.com:sakoht/UR
speed test script
removed files from MANIFEST moved to alt/
updated deps to Class::Autouse 2.0, Clone::PP
updated to use Class::Autouse 2.0
updated meta for pending 0.27 release
added UR::ModuleBuild which has all of the extra doc generation
disabled tests 63 and 63b on machiens without XML::LibXML
updated version to 0.28 for next release
updated logic for POD creation to handle sub-commands, version, and correct base bin naming
Broke out UR::Namespace::Command::Base from UR::Namespace::Command to give them distict docs
document creation creates a temporary object, and it now also deletes it
updated version to 0.28
updated changelog
added new tests
restored callcount lister
updated changelog
removed old Class::Autouse overrides
explicit POD for UR to prevent bootstrapping problems
explicit POD for UR to prevent bootstrapping problems
updated meta to 0.28
updated build and manifest files. fixed bug with UR::Namespace::Command needing to use ::Base
updated META.yml
added an environment variable to control loading under parent namespaces
updated authors list
updated to correctly create man page names for commands
added dir of scripts used to get UR read for release
added code to correctly update the version number in the modules plus in any manually generated POD
updated to try to ensure test 42 doen't run in parallel
Merge branch 'master' of github.com:sakoht/UR
disable warning where undef is suppose to be treated as an empty string
updated tests cases to be more agnostic about their error message when a method is missing, in prep for dropping AUTOSUB
updated version to 0.29
CHANGELOG: the attributes_have declaration in a class now results in property meta with real additional accessors (rw)
Merge branch 'master' of github.com:genome/UR into mm
Merge branch 'master' of github.com:sakoht/UR
updated pod generator
recurse targets
set a version number on Class::AutoloadCAN
when property meta objects have additional properties custom to a subclass, the Class::AutoloadCAN logic is now more thorough/correct in inferring this and providing an accessor.
cosmetic/whitespace
cosmetic: remove commented-out code, add comments about methods which need to move
cosmetic: removed commented-out code, fix indenting
Ensure that subclass descriptions are preprocessed by parent classes before normalizing property descriptions. This allows parent classes to shift inheritance around, then have additional meta attributes applied to the final subclass indirectly by newly introduced ancestors
Command now auto subclassifies into either ::V1 or ::V2
Merge branch 'master' of github.com:genome/UR
tests
updated
fix typo
ensure we preprocess class descriptions before normalizing properties. fix bug with setting the subclassify_by property when it already exists, and losing information
Classes which have multiple versions usable in-parallel express this with a use_parallel_versions boolean flag in the base class definition
Fix to handle indirect properties with and without via/to.
handle "ur init" when there is no data source specified
fixed warning message when via/to only has via set
Merge branch 'master' of github.com:genome/UR
cosmetic cleanup of Command::V2
new Command::Tree is a subclass of Command::V2 for sub-comand delegation
removed UR::Time
removed $DB::single
redo namespace controls to not just work from the root namespace
use correct entry point name for command pod (manual pages)
Merge branch 'master' of github.com:sakoht/UR
updated manifest
updated manifest
updated META.yml
removed any build tarballs from manifest
made the base class for namespace commands abstract
Merge branch 'master' of github.com:genome/UR
updated UR::All. added URI::Escape to Build.PL
updated doc generation
updated pod for commands
updated Changes for 0.29
updated manifest
updated version 0.30 for next release
add VERSION back to Command, and to new modules
updated how build date is presented
Updated Changes (late) for 0.30
removed Getopt::Complete dependency to prevent an internal bug. Will restore before 0.31 release.
Restore origin commits.
repair UR::BoolExpr::Template::Or. -or => [\@p1, \@p2, ..., \@pN] now works
updated set ->count() to do a null group
queries with group_by do not add filters to get extra values for sub-classification (kills lovely laziness)
modified Command::Tree to look for sub-trees under modules related to the command target
Merge branch 'master' of github.com:genome/UR
ignore non-perl files as possible sub-commands
restore support for OO params
Fixed bugs in Command::V2 handling OO params. Divided out the code for documentation and shell args parsing into separate modules.
updated how errors are shown for unprocessable OO cmdline args
Merge branch 'master' of github.com:sakoht/UR
updated version to 0.31 for next release
Added -aggregate to the bx template, with matching support in the
fixed problem with boolean expressions which have more than one constant value, in which the keys are sorted but not the values at certain points in the code
normalized test names to use _ instaed of -
normalized test name
restored shortened versions of order_by group_by, and hints
fixed issue with ::Or and _constant_values being an arrayref while _underlying_keys returns a list
working code
Merge branch 'master' into ag3
set relaying
set version to 0.31 for next release
Merge branch 'master' into ag3
updated test count
normalized test names
whitespace cleanup
initial set-relay logic
Merge branch 'ag3'
stringified bx now uses the abbreviated form of alternate operators
property chains are now usable in boolean expressions and queries
debug code
remove breakpoint
Merge branch 'master' into chain
When a newly loaded abstract object is found to already exist in its concrete subclass, the abstract object is destroyed. We require that the abstract object which is discarded to be re-blessed to avoid the DESTROY handler from believing it is the "real" object, and wiping out indexes.
Merge branch 'master' of https://github.com/genome/UR
Merge branch 'master' into chain
broke out pv extraction
Property comparisons now just implement the _compare class method.
allow sets to come back from the db even if they are already cached since cache reading doesn't work yet
reverted last change
Merge branch 'master' of github.com:genome/UR
cleanup and additions to value space
added __get_attr__ to get property values which are singular or chained
updated property_meta_for_name to handle property chains
The boolean expression resolver handles chained properties.
prevent breakage on chain delegates ...no support for non-RDBMS queries yet
remove old hard-coded information about data types. is_numeric is still implemented here.
support for chained properties in queries
new data types
Merge branch 'pc'
updated changelog
Squashed commit of the following:
Merge branch 'master' of github.com:genome/UR
restore testing of unloading select data
cosmetic
added error message to bx is_subset_of()
added a method for terse data dumper
Cosmetic cleanup. Initial support for "to" without "via" for properties returning sets which are reductions of properties returning larger sets. Initial code to note final accessor on join data.
cleanup of _generate_template_data_for_loading
simplified test case for readability
cosmetic cleanup
added UR::DataSource::QueryPlan to break out the get/generate_template_data_for_loading structure
the last refactor broke some logic into the query plan class, but it was accidentally not committed
made Data::UUID optional since it's binary
added back Data::UUID to Build.PL
relocated _fast_construct_and to the ::And template, and removed the _and from the method name
Merge branch 'master' of github.com:genome/UR
added a parameter to turn on/off sloppy primitive types
new module for slopy primitive types
cosmetic
Support for flatten and reframe on UR::BoolExpr.
Set relaying is now lazy. Sets stringify readbly.
tests for set relaying, flatten and reframe, and a _params_list fix
The bx reframe() now works for primitive/value properties.
test case to show joining custom data sources
renamed some tests to group them around rule examination
renamed some tests to group them around rule examination
Merge branch 'master' of github.com:genome/UR
Broke out join calculation logic for properties into its own module.
Changed UR::Object ids back into type Scalar instead of UR::Value. Logic to ensure we don't use the OO version of primitives where we previously didn't is not in place yet.
flatten() and reframe() for bx now handle -* keys
Merge branch 'master' of github.com:genome/UR
The bx flatten() and reframe() handle intermediate "where" ..mostly.
In a step toward refactoring aways _init_core, in ::QueryPlan,
Improvements to flatten() and reframe().
commented-out $DB::single in tests
fixed typo in test commenting out $DB::single
Broke out _add_join in ::QueryPlan to improve readability, allow
Fixed a join bug in the last commit.
x
x
Restore the resetting of the prev table name in joins to outside the
Merge branch 'on17' into on18
x
x
Old code did "next LABEL" even after being broken out into a sub.
Merge branch 'on18'
Merge branch 'master' of github.com:genome/UR
Replaces $meta->properties() with a method which
Merge branch 'master' of github.com:genome/UR
cosmetic cleanup
Merge branch 'master' of github.com:genome/UR
Fixed a bug in the id_by accessor where, if the
removed debug line
added a more comprehensive test for text-based views
added more comprehensive tests for text-based views
updated comments
fixed regex test to work on versions of Perl & Data::Dumper which quote numbers _and_ which do not.
removed "use Data::Dump" since it is not used and adds a dependency to UR
commetns/cosmetic
skip UR::Value in _reverse_all_changes
updated error message
cosmetic/whitespace
added display name for values which simply returns the id
added explicit data types to rule_display and member_class_name
updated the object sorters to pivot on a meta-property's is_numeric() return value
updated is_numeric to avoid infinite loops and to operate during bootstrapping
updated to handle sorting things with values starting with "inf", which confound old sorting logic but not new
updated to work with new sorting and is_numeric logic in core internal iterators
ensure view _observer_data is set when binding subjects to prevent issues during view deletion
add a test for deleting views, tracking via/to w/o type
support "." and "-" in command-line expressions
Merge branch 'master' of github.com:genome/UR
--help now gives an exit code of zero instead of 1
Merge primitive-view branch.
Either Command::V1 & 2 can be an entry point and still produce correct command-names in documentation for commands written on the other.
updated test case to match the fixed logic for generating command names from classes with numbers in the name
added a test script to test caching
skip making indexes on delegated properties, and when doing queries vs an index skip using those properties (ssmith)
Renamed UR::Report to UR::DBI::Report. This is a legacy component which does sqlrun-like tablification of query results. It should be refactored into a command from which other tools can subclass.
command properties are now is_input, unless explicitly set to is_output, is_param, or calculated or transient. doc generation how doesn't put out error messages when using --help
added a version to above.pm
updated comment
upgraded the minimum version of Getopt::Complete, since we now depend on comp_word instead of comp_line
fixed Command::V2 to return params even when there are known errors, so that failure can be handled further down-stream in the cmdline processing
listers will now use the __display_name__ when showing UR objects
Merge branch 'master' of github.com:genome/UR
Eliminate warnings.
Only show arguments on V2 commands for properties which are is_input or is_param. Show them in the help in order in which they appear in the command. Do not show the class name for the param in the docs.
let the hints list include methods, not just properties
Merge branch 'master' of github.com:genome/UR
Merge branch 'master' of github.com:genome/UR
Merge branch 'master' of github.com:genome/UR
prevent warnings on _pad_string
x
support id_class_by properties with an access_as => "auto" param which will automatically handle both objects and primitives and return the later as such case-by-case
remove debug code emitting warning
removed debug code
Merge branch 'master' into all2.m
Merge branch 'master' into access-as
presumes any class with a colon is not a "sloppy primitive". fixes a warning
Merge branch 'master' into access-as
support for basic queries of extended meta-properties
updated UR version to 0.38
updated UR::BoolExpr::BxParser to use a different package name for Parse::Yapp's embedded parser module to prevent 'unauthorized release' messages on CPAN.
handle different wc output on Mac OS X
made test more verbose
made warning message more verbose
updated changelog for UR 0.38
updated META.yml for 0.38
updated Changes list for 0.38
updated META.yml for 0.38
updated UR debian/control file to include librmo-compat-perl
only check sub_command_names when the method exists: even though the error is trapped, avoids junk on the screen
Merge branch 'master' of github.com:sakoht/UR
made the XML default generator faster on primitive data
Merge branch 'xml-lighter'
XML now does not use display names for data ...XML is data not display
x
When calculating joins, ensure that we look-up a datasource for parent classes now that ds lookup is outside of the _add_join method
updated query plan to work optimally where the join target is generic and has no data source but the next join has a concreate data source (ie. software results where an input has a specific type but inputs in general do not
Merge branch 'master' of github.com:genome/UR
Test case for feature in the last commit which merges two joins into one when the first goes to something too abstract to have a data source, but the initial class in the next table is more concrete. This allows queries on remotething.id => $r->id to work.
updated test 87e to have value_class_name and value_id instead of just value
Merge branch 'master' into join-fix
Merge branch 'master' into join-fix
Added a method to bx flatten_hard_refs which will turn key=>$obj into key.id=>$obj->id where $obj can be gotten by its id given the data_type of the property. Updated UR::Context to call this method before doing a query. This change was not made during the default resolve() or normalize() because they are used during object construction and the effort to back out into the original data in the constructor was greater.
cosmetic cleanup of warnings in test 87e
Updated the QueryPlan to not complain about joining to things via UR::Object id, even when there are no id_properties mapping to explicit database columns. In this case queries are merely inefficient instead of impossible.
ensure that joins to table with LOB columns get correct LOB handling
UR::Object::Join now recognizes increased type specificity on a
QueryPlan now handles hints to object properties correctly.
fixed warning message
UR::DataSource::RDBMS now caches its belief as to the correct sequence generator on a per-class basis, saving considerable time when constructing large sets of objects.
Don't check objects for errors until after verifying that they have a datasource. This saves a lot of time on no-op commits from Command objects.
Revert "Don't check objects for errors until after verifying that they have a datasource. This saves a lot of time on no-op commits from Command objects."
make is_transactional optional on classes since the core meta-data needs seens to need those to be undef
added support for optionally dumping all DDL for a table, not just a delta
mad "ur show schema" and renamed "ur describe" as "ur show properties"
renamed "ur describe" to "ur show properties" in the docs
updated "ur show schema" to drive on class names
fixed old occurances of UR::Namespace::Command::Describe > ::Show::Properties
moved a _get_class_data_for_loading in queryplan up to before table/column mapping is examined since some subclasses rewrite that mapping in that method
add "use Clone::PP" to UR::Util so it will break at compile time instead of run-time if not installed
added comment
Updated help input/param grouping, new shell entry.
initial wrapper to take over the shell-specific methods on general methods
Merge branch 'master' into cmdshell
added new test modules for testing commands
added help detail to test class
fixed help_detail broken in the last doc update
error in parsing property flags was resulting in inverted inputs/params in documentation
no longer show Boolean flags twice in documentation
added better error message for odd keys in boolexpr
fixed error checking for indirect properties to correctly recognize when a required property is being specified because another specified property is "via" it, and will set it implicitly (already supported in the UR::Object constructor, just not in Command::V2 cmdline parsing)
removed old test file
added UR::Util::on_destroy to allow more cleanly organized cleanup routines
UR::Util::on_destroy correctly handles callbacks which reset $@
Merge branch 'master' of github.com:genome/UR
removed debug print statement
updated to handle a missing DBS::Oracle::db::ora_server_version when running in the debugger
make database tests conditional on the installation of the related DBD::* driver
updated to 0.39
cleaned cruft from MANIFEST
final packaging updates for 0.39
default_value can now be an ID or a query in hash form
fix warning message
make Command::V2 more tolerant of odd default_value meta properties as objects
updated the object lister params and docs
updated --show logic to handle the +/-/^ prefix more flexibly
removed $DB::single from boolexpr
Merge pull request #1 from neilbowers/master
added _wrapper_has to Command::V2 to support auto-generating wrapper commands
remove $DB::single
handle that UR::Value can have objects which are subclasses of each other with the same ID
allow dispatch for a command defined in code (don't require "use" to work)
Fix __self__ with params, and define_boolexpr() as obj method.
update alias accessors for complete symmetry with the property being aliased
disable test 93 on OS X
respect a custom ID separator when decomposing a list of IDs as well as a single ID
Fix bugs with multi-part IDs and in-clauses.
Updated loading for UR::Value subclasses with multi-part IDs.
remove print statement from UR::ModuleBuild
remove $DB::single
Merge branch 'master' of github.com:genome/UR
remove TODO from a test that is now passing: multi-value IDs with UR::Value
Command::V2 is_output now settable from the command line
Scott Smith X (1):
removed junk bak file which ended up in the manifest
Sebastian Heil (2):
added 'use strict;' to every .pm and .pl file where it's missing
added 'use warnings;' to every .pm and .pl file where it's missing
Steven Wallace (14):
Taught is_numeric that NUMBERs are numeric.
Made the case guessing of names the last resort.
Made tags more robust about the property format.
Fixed some issues with can() misreporting.
Made gets across bridge tables faster.
Fixed getting delegated properties with 'in'.
Cleaned up some whitespace.
Added a test for the in operator on join queries.
Made join ids unique when resolving joins.
Fixed performance bug when joining onto a table with an id not named "id".
Fixed bugs in joins.
Merge branch 'master' of github.com:genome/UR
Committed the changes I talked about last commit.
Removed an unused variable.
Susanna Siebert (3):
outputs that are calculated don't need to be required to be specified on the command line
added test coverage for calculated properties
move caluclated property tests into the foreach loop
Thomas B. Mooney (17):
Merge pull request #44 from tmooney/propagate_gcb_changes
Merge pull request #48 from tmooney/verify_lister_properties
Merge pull request #51 from tmooney/remove_deprecated_parser
Merge pull request #52 from tmooney/duplicate_table_declaration
Merge pull request #54 from tmooney/duplicate_insert_columns
Merge pull request #56 from tmooney/faster_invalid_save_error
Merge pull request #71 from tmooney/disable_sqlite_use_immediate_transaction
Merge pull request #86 from tmooney/no_verify_infinite_loop
Merge pull request #96 from tmooney/external_changes_undo_on_context_rollback
Merge pull request #100 from tmooney/default_last_not_first
Merge pull request #115 from tmooney/role_instances_are_not_transactional
PG: The COLLATE must come before the DESC in the ORDER BY.
Merge pull request #122 from tmooney/datasource_pg_collates_desc_orders_properly
Remove breakpoint.
Merge pull request #123 from tmooney/remove_create_entity_breakpoint
Use the _object_property_to_string helper in the XML style.
Merge pull request #125 from tmooney/xml_lister_supports_dot_syntax
Thomas Mooney (108):
Better Command generated POD formatting
Eliminate warning 'uninitialized value in pattern match' if the definer of a Command did not specify a type for a property
Spaces interact poorly with the HTML views--they're considered invalid URI characters by XML::LibXSLT--so change them to hyphens.
Escape string values for aspects within the view XML
Quiet warnings caused by trying to indent an undefined value.
Remove duplicate definition of member_class_name that prevented members() from seeing the value it expects.
Refactor default XML view to use XML::LibXML--this handles any and all escaping that might be necessary (unless delegating to a non-XML view); add a convenience accessor to avoid needing to include the BoolExpr in a view of a Set
Use the LibXML doc created by the XML view if available rather than reparsing the resulting string.
Allow calling UR::Object::Set->get() to get a set with properties. (This works like UR::Object->define_set() does.)
Merge branch 'master' of github.com:sakoht/UR
Comment out tag-along change in AccessorWriter for now.
Fixes courtesy of Scott Smith:
Hyphenate the auto-generated expected perspective so that it will be properly converted back to CamelCase later.
revert change in d50c1e04108c246af4f8ea7ed36b7a12aa4e80ae; is causing issues with 'use above'.
Better implementation of removing trailing slashes--cut them off at the source in _use_safe.
Reset the @INC in the event that the module was not found in the expected directory.
Merge branch 'master' of github.com:sakoht/UR
Remove extraneous "d" from error message.
Use the default value 1 for numberless hostnames in dummy autogenerated ids.
Limit the dummy ids to fit within 11 characters (including the "-").
Silence uninitialized value warnings when no default value for parameter.
Include parameter types in POD and HTML versions of help text.
A simple command for generating POD for a command and all its subcommands.
Include the required --output-path parameter in the synposis examples.
Fix typo data_tye => data_type
Don't load all the sub-subcommands just to find if there are any for help text.
Make owner column nullable to match other tables in schema.
Defer loading subcommands until they are needed.
Reapply overwritten commit bad30a82c3a041a3004c949f2412bd84caeaa5e4.
A fix for UR::Values in the case of id_class_by bucketing.
Remove stray $DB::single = 1;
Remove $DB::single line.
Update in anticipation of a new version of Getopt::Complete.
Make `ur update classes-from-db` work to update a single class.
Now that there are UR::Value subclasses, cast a wider net finding them.
New bridge crosser case: id_by with a known property data_type.
Testcase demonstrating effectiveness of new bridge crosser rule.
Implement shortcut() similarly to execute() so that result is properly set.
Extract some of the XSL logic into subroutines for subclass overriding.
Return the XML view we're getting.
Set the perspective and toolkit appropriately in view class defintions.
Don't match an earlier part of the path if it contains the namespace name.
Include subdirectory searching anywhere in @INC, not just in namespace dir.
New view to enumerate available views for a class in a namespace.
Need to check for the namespace directory even without a subdir specified.
Specify toolkit in HTML views.
Also include a classname XSL variable for the object.
Add a json perspective for avaialble views.
Save $@ into a variable in case intervening lines affect its value.
Use DBI's quote mechanism for IN queries to escape things like single quotes.
Fix for some missing results using OR queries in lister/iterators.
Allow is_many bare args in positions other than the last for V2.
Don't throw "multiple results" error when OR boolexpr used in a void context.
Extract property stringification logic; use this in Pretty format as well.
Remove initialization of getopt for is_many properties to empty arrayref.
Extend namespace so that auto-generated classes are found when asked for.
Basic support for --order-by using dot-syntax in listers.
Search a little more thoroughly for matching values evaluating in-clauses.
Remove breakpoint.
Allow empty strings for values (i.e., allow name='') so null can be entered.
Quiet warning in middle of join resolution.
return instead of dying to eliminate extra error message when nothing found.
Fix typo s/sue/use/.
Typo fix: Test for the existence of the object we just created.
Use __meta__ instead of UR::Object::Type->get().
Confess if fork()ing the process fails.
whitespace.
Remove input & param checks from lister properties to document.
Don't split up valid boolean expressions as parameters.
Don't crash when meta-options used in "where" for delegated properties.
Take the schema into account when looking up Pg unique constraints.
Update other RDBMS types to take schema into account.
Test for sqlite unique index lookups across schemata.
Auto-box single values for is_many properties in creation.
Revert "Auto-box single values for is_many properties in creation."
Don't recycle a join when joining for a different property.
Auto-box single values for is_many properties in creation.
Use context return for simple is_many accessors.
Allow updating is_many with single value.
Test for getting/setting is_many with one or many values.
Update test to also test indirect creation.
Verify our results belong to the desired class.
Handle missing statuses.
Replace _unique_elements with List::MoreUtils::uniq.
Always read from the terminal when getting user input.
Remove commented-out breakpoint.
Whitespace.
Die on bad properties.
Check the front of dot-properties for validity as well.
Allow callers to handle @extra if they wish.
Croak instead of dying.
Remove extraneous 'g' modifier.
Stop calling the old parser.
Remove old query parser.
Don't process the same class for joins twice.
New test for diamond inheritance to the same table.
Uniquely get table and column names.
Regular expression that matches more quickly on large dumps.
More accurate comment.
Set sqlite_use_immediate_transaction = 0 for newer DBD::SQLite.
Die if the user asked to not verify but they selected too many items.
UR::Context->rollback() fires undo() for UR::Change with external_change
Test both within and without a transaction.
Sort the Default datasource last instead of first.
Add a datasource ordering sanity test with the URT DataSources.
Shuffle the initial set to better test sorting.
Get the objects to fix tests under 5.8
Indicate that Role Instances are not transactional.
Travis Abbott (25):
New test for caching of queries with subclass specific params
updated to test calculated params as well, +cleanup.
Query caching fix for tableless subclasses.
fix errors related to preprocessing and normalization of properties
improve error message for redundant property meta properties
flatten extra properties and property attributes back into objects
Add auto-generation of html docs in addition to pod
documentation generator now has the concept of "navigation links"
add parent_command_class method to Command::V1
added index generation for html doc generator
added links to generated index files in navigation menus
Merge branch 'master' of https://github.com/genome/UR into docgen
Merge branch 'docgen'
remove warnings about untitled doc sections
make output dirs (i.e., mkdir -p) for output dirs while generating docs
update command --help generator to translate pod => txt
doc generator respects _is_hidden_in_docs
new _additional_help_sections for commands
Merge branch 'normalize'
add option to doc generator to exclude certain modules
updated dependency list to add the following:
add option to document generator to filter out sections based on name
during command doc generation, make sure parent_class is set
update pod2html formatting to appease ie9
Command::Vx::entry_point... changes
Yanick Champoux (1):
silence warnings for perl 5.22+
abrummet (320):
From svn r31809 on 2008-01-16 09:41:49 -0600 (Wed, 16 Jan 2008)
From svn r31834 on 2008-01-16 15:24:38 -0600 (Wed, 16 Jan 2008)
From svn r31836 on 2008-01-16 16:12:40 -0600 (Wed, 16 Jan 2008)
From svn r31873 on 2008-01-17 17:02:08 -0600 (Thu, 17 Jan 2008)
From svn r31883 on 2008-01-18 09:01:25 -0600 (Fri, 18 Jan 2008)
From svn r31894 on 2008-01-18 14:43:17 -0600 (Fri, 18 Jan 2008)
From svn r31935 on 2008-01-23 09:07:59 -0600 (Wed, 23 Jan 2008)
From svn r31936 on 2008-01-23 09:09:24 -0600 (Wed, 23 Jan 2008)
From svn r31939 on 2008-01-23 10:00:26 -0600 (Wed, 23 Jan 2008)
From svn r31940 on 2008-01-23 10:05:34 -0600 (Wed, 23 Jan 2008)
From svn r31941 on 2008-01-23 10:07:55 -0600 (Wed, 23 Jan 2008)
From svn r31964 on 2008-01-24 12:01:34 -0600 (Thu, 24 Jan 2008)
From svn r32013 on 2008-01-25 16:42:15 -0600 (Fri, 25 Jan 2008)
From svn r32014 on 2008-01-25 16:44:31 -0600 (Fri, 25 Jan 2008)
From svn r32015 on 2008-01-25 16:45:04 -0600 (Fri, 25 Jan 2008)
From svn r32036 on 2008-01-28 16:07:51 -0600 (Mon, 28 Jan 2008)
From svn r32093 on 2008-01-30 17:48:43 -0600 (Wed, 30 Jan 2008)
From svn r32158 on 2008-02-04 14:20:38 -0600 (Mon, 04 Feb 2008)
From svn r32226 on 2008-02-08 10:39:49 -0600 (Fri, 08 Feb 2008)
From svn r32227 on 2008-02-08 10:40:29 -0600 (Fri, 08 Feb 2008)
From svn r32376 on 2008-02-18 14:33:49 -0600 (Mon, 18 Feb 2008)
From svn r32377 on 2008-02-18 14:38:57 -0600 (Mon, 18 Feb 2008)
From svn r32378 on 2008-02-18 14:43:04 -0600 (Mon, 18 Feb 2008)
From svn r32528 on 2008-02-22 08:27:50 -0600 (Fri, 22 Feb 2008)
From svn r32649 on 2008-02-28 08:53:44 -0600 (Thu, 28 Feb 2008)
From svn r32679 on 2008-02-28 16:43:04 -0600 (Thu, 28 Feb 2008)
From svn r32683 on 2008-02-28 18:48:06 -0600 (Thu, 28 Feb 2008)
From svn r32788 on 2008-03-06 09:10:14 -0600 (Thu, 06 Mar 2008)
From svn r32833 on 2008-03-08 16:57:59 -0600 (Sat, 08 Mar 2008)
From svn r32834 on 2008-03-08 17:00:26 -0600 (Sat, 08 Mar 2008)
From svn r32835 on 2008-03-08 17:01:02 -0600 (Sat, 08 Mar 2008)
From svn r32918 on 2008-03-11 17:14:53 -0500 (Tue, 11 Mar 2008)
From svn r34066 on 2008-04-28 13:57:26 -0500 (Mon, 28 Apr 2008)
From svn r35082 on 2008-05-29 09:33:35 -0500 (Thu, 29 May 2008)
From svn r35083 on 2008-05-29 09:35:31 -0500 (Thu, 29 May 2008)
From svn r35084 on 2008-05-29 09:36:31 -0500 (Thu, 29 May 2008)
From svn r35085 on 2008-05-29 09:39:20 -0500 (Thu, 29 May 2008)
From svn r35111 on 2008-05-29 14:24:23 -0500 (Thu, 29 May 2008)
From svn r35668 on 2008-06-18 13:48:48 -0500 (Wed, 18 Jun 2008)
From svn r35670 on 2008-06-18 13:49:57 -0500 (Wed, 18 Jun 2008)
From svn r35711 on 2008-06-19 10:23:26 -0500 (Thu, 19 Jun 2008)
From svn r35744 on 2008-06-20 11:06:01 -0500 (Fri, 20 Jun 2008)
From svn r35745 on 2008-06-20 11:07:48 -0500 (Fri, 20 Jun 2008)
From svn r35821 on 2008-06-23 15:52:37 -0500 (Mon, 23 Jun 2008)
From svn r35834 on 2008-06-24 10:36:03 -0500 (Tue, 24 Jun 2008)
From svn r35847 on 2008-06-24 13:52:45 -0500 (Tue, 24 Jun 2008)
From svn r35871 on 2008-06-24 16:44:58 -0500 (Tue, 24 Jun 2008)
From svn r35954 on 2008-06-26 11:24:30 -0500 (Thu, 26 Jun 2008)
From svn r36107 on 2008-07-01 10:55:35 -0500 (Tue, 01 Jul 2008)
From svn r36108 on 2008-07-01 10:57:02 -0500 (Tue, 01 Jul 2008)
From svn r36159 on 2008-07-02 14:02:41 -0500 (Wed, 02 Jul 2008)
From svn r36160 on 2008-07-02 14:06:57 -0500 (Wed, 02 Jul 2008)
From svn r36170 on 2008-07-02 15:19:06 -0500 (Wed, 02 Jul 2008)
From svn r36182 on 2008-07-02 17:01:30 -0500 (Wed, 02 Jul 2008)
From svn r36183 on 2008-07-02 17:06:48 -0500 (Wed, 02 Jul 2008)
From svn r36217 on 2008-07-03 11:45:50 -0500 (Thu, 03 Jul 2008)
From svn r36245 on 2008-07-07 13:42:02 -0500 (Mon, 07 Jul 2008)
From svn r36247 on 2008-07-07 13:46:56 -0500 (Mon, 07 Jul 2008)
From svn r36249 on 2008-07-07 14:37:18 -0500 (Mon, 07 Jul 2008)
From svn r36251 on 2008-07-07 14:40:59 -0500 (Mon, 07 Jul 2008)
From svn r36296 on 2008-07-08 12:56:37 -0500 (Tue, 08 Jul 2008)
From svn r36346 on 2008-07-09 09:39:56 -0500 (Wed, 09 Jul 2008)
From svn r36349 on 2008-07-09 10:28:24 -0500 (Wed, 09 Jul 2008)
From svn r36395 on 2008-07-09 16:18:52 -0500 (Wed, 09 Jul 2008)
From svn r36397 on 2008-07-09 16:30:19 -0500 (Wed, 09 Jul 2008)
From svn r36398 on 2008-07-09 16:31:13 -0500 (Wed, 09 Jul 2008)
From svn r36399 on 2008-07-09 16:32:21 -0500 (Wed, 09 Jul 2008)
From svn r36400 on 2008-07-09 16:39:10 -0500 (Wed, 09 Jul 2008)
From svn r37120 on 2008-07-31 09:50:36 -0500 (Thu, 31 Jul 2008)
From svn r37121 on 2008-07-31 09:54:01 -0500 (Thu, 31 Jul 2008)
From svn r37122 on 2008-07-31 09:55:34 -0500 (Thu, 31 Jul 2008)
From svn r37125 on 2008-07-31 10:31:22 -0500 (Thu, 31 Jul 2008)
From svn r37214 on 2008-08-04 10:33:54 -0500 (Mon, 04 Aug 2008)
From svn r37215 on 2008-08-04 10:34:28 -0500 (Mon, 04 Aug 2008)
From svn r37216 on 2008-08-04 10:35:20 -0500 (Mon, 04 Aug 2008)
From svn r37421 on 2008-08-11 15:59:00 -0500 (Mon, 11 Aug 2008)
From svn r37438 on 2008-08-12 10:50:11 -0500 (Tue, 12 Aug 2008)
From svn r37488 on 2008-08-12 16:11:37 -0500 (Tue, 12 Aug 2008)
From svn r37489 on 2008-08-12 16:12:31 -0500 (Tue, 12 Aug 2008)
From svn r37703 on 2008-08-19 16:22:46 -0500 (Tue, 19 Aug 2008)
From svn r37704 on 2008-08-19 16:25:19 -0500 (Tue, 19 Aug 2008)
From svn r37706 on 2008-08-19 16:57:07 -0500 (Tue, 19 Aug 2008)
From svn r37771 on 2008-08-21 13:10:17 -0500 (Thu, 21 Aug 2008)
From svn r37839 on 2008-08-25 09:44:47 -0500 (Mon, 25 Aug 2008)
From svn r37840 on 2008-08-25 09:57:35 -0500 (Mon, 25 Aug 2008)
From svn r37844 on 2008-08-25 11:01:37 -0500 (Mon, 25 Aug 2008)
From svn r37880 on 2008-08-26 10:22:02 -0500 (Tue, 26 Aug 2008)
From svn r37881 on 2008-08-26 10:25:23 -0500 (Tue, 26 Aug 2008)
From svn r37884 on 2008-08-26 11:03:57 -0500 (Tue, 26 Aug 2008)
From svn r37888 on 2008-08-26 11:15:22 -0500 (Tue, 26 Aug 2008)
From svn r37897 on 2008-08-26 12:37:12 -0500 (Tue, 26 Aug 2008)
From svn r38122 on 2008-09-04 09:44:47 -0500 (Thu, 04 Sep 2008)
From svn r38274 on 2008-09-04 12:08:00 -0500 (Thu, 04 Sep 2008)
From svn r38303 on 2008-09-04 15:50:43 -0500 (Thu, 04 Sep 2008)
From svn r38305 on 2008-09-04 15:53:31 -0500 (Thu, 04 Sep 2008)
From svn r38306 on 2008-09-04 15:54:43 -0500 (Thu, 04 Sep 2008)
From svn r38460 on 2008-09-09 15:58:28 -0500 (Tue, 09 Sep 2008)
From svn r38461 on 2008-09-09 16:06:09 -0500 (Tue, 09 Sep 2008)
From svn r38462 on 2008-09-09 16:19:12 -0500 (Tue, 09 Sep 2008)
From svn r38463 on 2008-09-09 16:21:06 -0500 (Tue, 09 Sep 2008)
From svn r38464 on 2008-09-09 16:21:50 -0500 (Tue, 09 Sep 2008)
From svn r38466 on 2008-09-09 16:33:41 -0500 (Tue, 09 Sep 2008)
From svn r38499 on 2008-09-10 15:03:20 -0500 (Wed, 10 Sep 2008)
From svn r38512 on 2008-09-10 16:28:35 -0500 (Wed, 10 Sep 2008)
From svn r38541 on 2008-09-11 14:28:27 -0500 (Thu, 11 Sep 2008)
From svn r38957 on 2008-09-23 11:01:52 -0500 (Tue, 23 Sep 2008)
From svn r39095 on 2008-09-25 17:02:14 -0500 (Thu, 25 Sep 2008)
From svn r39295 on 2008-10-02 13:20:29 -0500 (Thu, 02 Oct 2008)
From svn r39296 on 2008-10-02 13:22:24 -0500 (Thu, 02 Oct 2008)
From svn r39298 on 2008-10-02 13:25:07 -0500 (Thu, 02 Oct 2008)
From svn r39502 on 2008-10-07 16:50:39 -0500 (Tue, 07 Oct 2008)
From svn r39503 on 2008-10-07 16:53:43 -0500 (Tue, 07 Oct 2008)
From svn r39504 on 2008-10-07 16:54:49 -0500 (Tue, 07 Oct 2008)
From svn r39546 on 2008-10-08 15:14:03 -0500 (Wed, 08 Oct 2008)
From svn r39766 on 2008-10-14 15:53:46 -0500 (Tue, 14 Oct 2008)
From svn r39909 on 2008-10-17 09:04:56 -0500 (Fri, 17 Oct 2008)
From svn r39910 on 2008-10-17 09:38:05 -0500 (Fri, 17 Oct 2008)
From svn r39911 on 2008-10-17 09:38:35 -0500 (Fri, 17 Oct 2008)
From svn r39923 on 2008-10-17 13:23:38 -0500 (Fri, 17 Oct 2008)
From svn r40022 on 2008-10-21 11:33:05 -0500 (Tue, 21 Oct 2008)
From svn r40099 on 2008-10-22 13:23:11 -0500 (Wed, 22 Oct 2008)
From svn r40165 on 2008-10-23 15:23:09 -0500 (Thu, 23 Oct 2008)
From svn r40493 on 2008-10-30 16:49:28 -0500 (Thu, 30 Oct 2008)
From svn r40494 on 2008-10-30 16:51:20 -0500 (Thu, 30 Oct 2008)
From svn r40496 on 2008-10-30 16:52:52 -0500 (Thu, 30 Oct 2008)
From svn r40585 on 2008-11-03 16:11:28 -0600 (Mon, 03 Nov 2008)
From svn r40586 on 2008-11-03 16:12:07 -0600 (Mon, 03 Nov 2008)
From svn r40607 on 2008-11-04 13:55:33 -0600 (Tue, 04 Nov 2008)
From svn r40608 on 2008-11-04 13:56:46 -0600 (Tue, 04 Nov 2008)
From svn r40757 on 2008-11-10 14:09:02 -0600 (Mon, 10 Nov 2008)
From svn r40758 on 2008-11-10 14:10:13 -0600 (Mon, 10 Nov 2008)
From svn r40771 on 2008-11-10 16:09:18 -0600 (Mon, 10 Nov 2008)
From svn r40941 on 2008-11-12 18:46:05 -0600 (Wed, 12 Nov 2008)
From svn r40942 on 2008-11-12 18:46:22 -0600 (Wed, 12 Nov 2008)
From svn r40943 on 2008-11-12 18:46:46 -0600 (Wed, 12 Nov 2008)
From svn r40944 on 2008-11-12 18:47:03 -0600 (Wed, 12 Nov 2008)
From svn r40950 on 2008-11-13 10:14:08 -0600 (Thu, 13 Nov 2008)
From svn r40974 on 2008-11-13 14:08:53 -0600 (Thu, 13 Nov 2008)
From svn r41054 on 2008-11-17 14:13:39 -0600 (Mon, 17 Nov 2008)
From svn r41055 on 2008-11-17 14:13:58 -0600 (Mon, 17 Nov 2008)
From svn r41127 on 2008-11-18 15:49:31 -0600 (Tue, 18 Nov 2008)
From svn r41131 on 2008-11-18 16:18:06 -0600 (Tue, 18 Nov 2008)
From svn r41137 on 2008-11-18 17:04:29 -0600 (Tue, 18 Nov 2008)
From svn r42757 on 2009-01-15 17:33:50 -0600 (Thu, 15 Jan 2009)
From svn r42781 on 2009-01-16 17:10:53 -0600 (Fri, 16 Jan 2009)
From svn r42783 on 2009-01-16 17:12:30 -0600 (Fri, 16 Jan 2009)
From svn r42784 on 2009-01-16 17:16:48 -0600 (Fri, 16 Jan 2009)
From svn r42804 on 2009-01-20 10:12:24 -0600 (Tue, 20 Jan 2009)
From svn r42806 on 2009-01-20 10:18:42 -0600 (Tue, 20 Jan 2009)
From svn r42807 on 2009-01-20 10:19:17 -0600 (Tue, 20 Jan 2009)
From svn r42809 on 2009-01-20 10:21:44 -0600 (Tue, 20 Jan 2009)
From svn r42811 on 2009-01-20 10:29:45 -0600 (Tue, 20 Jan 2009)
From svn r42835 on 2009-01-20 13:54:15 -0600 (Tue, 20 Jan 2009)
From svn r42841 on 2009-01-20 15:23:11 -0600 (Tue, 20 Jan 2009)
From svn r42964 on 2009-01-23 14:02:01 -0600 (Fri, 23 Jan 2009)
From svn r42965 on 2009-01-23 14:03:00 -0600 (Fri, 23 Jan 2009)
From svn r42966 on 2009-01-23 14:03:17 -0600 (Fri, 23 Jan 2009)
From svn r42967 on 2009-01-23 14:03:40 -0600 (Fri, 23 Jan 2009)
From svn r42968 on 2009-01-23 14:04:04 -0600 (Fri, 23 Jan 2009)
From svn r43003 on 2009-01-26 15:18:52 -0600 (Mon, 26 Jan 2009)
From svn r43040 on 2009-01-27 11:12:22 -0600 (Tue, 27 Jan 2009)
From svn r43042 on 2009-01-27 11:44:28 -0600 (Tue, 27 Jan 2009)
From svn r43043 on 2009-01-27 11:44:53 -0600 (Tue, 27 Jan 2009)
From svn r43044 on 2009-01-27 11:45:11 -0600 (Tue, 27 Jan 2009)
From svn r43045 on 2009-01-27 11:45:37 -0600 (Tue, 27 Jan 2009)
From svn r43046 on 2009-01-27 11:47:22 -0600 (Tue, 27 Jan 2009)
From svn r43047 on 2009-01-27 11:47:53 -0600 (Tue, 27 Jan 2009)
From svn r43048 on 2009-01-27 11:48:43 -0600 (Tue, 27 Jan 2009)
From svn r43049 on 2009-01-27 11:50:17 -0600 (Tue, 27 Jan 2009)
From svn r43087 on 2009-01-27 14:19:04 -0600 (Tue, 27 Jan 2009)
From svn r43259 on 2009-02-04 11:39:49 -0600 (Wed, 04 Feb 2009)
From svn r43261 on 2009-02-04 11:59:01 -0600 (Wed, 04 Feb 2009)
From svn r43270 on 2009-02-04 13:35:22 -0600 (Wed, 04 Feb 2009)
From svn r43339 on 2009-02-05 17:43:13 -0600 (Thu, 05 Feb 2009)
From svn r43349 on 2009-02-06 09:05:42 -0600 (Fri, 06 Feb 2009)
From svn r43364 on 2009-02-06 13:53:56 -0600 (Fri, 06 Feb 2009)
From svn r43365 on 2009-02-06 13:54:44 -0600 (Fri, 06 Feb 2009)
From svn r43406 on 2009-02-10 08:59:11 -0600 (Tue, 10 Feb 2009)
From svn r43407 on 2009-02-10 09:00:04 -0600 (Tue, 10 Feb 2009)
From svn r43408 on 2009-02-10 09:03:36 -0600 (Tue, 10 Feb 2009)
From svn r43413 on 2009-02-10 12:37:31 -0600 (Tue, 10 Feb 2009)
From svn r43733 on 2009-02-18 15:41:01 -0600 (Wed, 18 Feb 2009)
From svn r43774 on 2009-02-19 14:49:21 -0600 (Thu, 19 Feb 2009)
From svn r43786 on 2009-02-20 10:26:16 -0600 (Fri, 20 Feb 2009)
From svn r43837 on 2009-02-23 13:09:39 -0600 (Mon, 23 Feb 2009)
From svn r43857 on 2009-02-24 09:20:11 -0600 (Tue, 24 Feb 2009)
From svn r43866 on 2009-02-24 12:47:05 -0600 (Tue, 24 Feb 2009)
From svn r43882 on 2009-02-24 16:03:37 -0600 (Tue, 24 Feb 2009)
From svn r43883 on 2009-02-24 16:04:39 -0600 (Tue, 24 Feb 2009)
From svn r43930 on 2009-02-26 09:33:25 -0600 (Thu, 26 Feb 2009)
From svn r43938 on 2009-02-26 11:31:21 -0600 (Thu, 26 Feb 2009)
From svn r44311 on 2009-03-06 10:27:50 -0600 (Fri, 06 Mar 2009)
From svn r44686 on 2009-03-16 14:09:17 -0500 (Mon, 16 Mar 2009)
From svn r44945 on 2009-03-24 10:19:39 -0500 (Tue, 24 Mar 2009)
From svn r44946 on 2009-03-24 10:23:21 -0500 (Tue, 24 Mar 2009)
From svn r44997 on 2009-03-24 17:19:40 -0500 (Tue, 24 Mar 2009)
From svn r45039 on 2009-03-25 13:00:40 -0500 (Wed, 25 Mar 2009)
From svn r45184 on 2009-03-30 09:49:15 -0500 (Mon, 30 Mar 2009)
From svn r45185 on 2009-03-30 09:51:06 -0500 (Mon, 30 Mar 2009)
From svn r45320 on 2009-04-02 11:26:29 -0500 (Thu, 02 Apr 2009)
From svn r45353 on 2009-04-02 16:52:51 -0500 (Thu, 02 Apr 2009)
From svn r45428 on 2009-04-06 13:31:00 -0500 (Mon, 06 Apr 2009)
From svn r45429 on 2009-04-06 13:34:14 -0500 (Mon, 06 Apr 2009)
From svn r45430 on 2009-04-06 13:35:28 -0500 (Mon, 06 Apr 2009)
From svn r45431 on 2009-04-06 13:36:03 -0500 (Mon, 06 Apr 2009)
From svn r45630 on 2009-04-10 09:23:04 -0500 (Fri, 10 Apr 2009)
From svn r45654 on 2009-04-10 14:37:50 -0500 (Fri, 10 Apr 2009)
From svn r45655 on 2009-04-10 14:38:51 -0500 (Fri, 10 Apr 2009)
From svn r45656 on 2009-04-10 14:40:39 -0500 (Fri, 10 Apr 2009)
From svn r45675 on 2009-04-13 08:48:08 -0500 (Mon, 13 Apr 2009)
From svn r45707 on 2009-04-13 16:24:55 -0500 (Mon, 13 Apr 2009)
From svn r45825 on 2009-04-15 10:37:10 -0500 (Wed, 15 Apr 2009)
From svn r46101 on 2009-04-22 09:31:31 -0500 (Wed, 22 Apr 2009)
From svn r46117 on 2009-04-22 12:37:03 -0500 (Wed, 22 Apr 2009)
From svn r46118 on 2009-04-22 12:37:46 -0500 (Wed, 22 Apr 2009)
From svn r46161 on 2009-04-23 14:12:08 -0500 (Thu, 23 Apr 2009)
From svn r46187 on 2009-04-23 16:59:12 -0500 (Thu, 23 Apr 2009)
From svn r46190 on 2009-04-23 18:03:49 -0500 (Thu, 23 Apr 2009)
From svn r46191 on 2009-04-23 18:12:13 -0500 (Thu, 23 Apr 2009)
From svn r46193 on 2009-04-23 18:27:16 -0500 (Thu, 23 Apr 2009)
From svn r46194 on 2009-04-23 18:29:31 -0500 (Thu, 23 Apr 2009)
From svn r46205 on 2009-04-24 10:49:31 -0500 (Fri, 24 Apr 2009)
From svn r46521 on 2009-05-04 20:05:18 -0500 (Mon, 04 May 2009)
From svn r46522 on 2009-05-04 21:52:42 -0500 (Mon, 04 May 2009)
From svn r46523 on 2009-05-04 21:54:46 -0500 (Mon, 04 May 2009)
From svn r46525 on 2009-05-05 08:20:42 -0500 (Tue, 05 May 2009)
From svn r46528 on 2009-05-05 09:46:13 -0500 (Tue, 05 May 2009)
From svn r46529 on 2009-05-05 09:46:39 -0500 (Tue, 05 May 2009)
From svn r46530 on 2009-05-05 09:46:53 -0500 (Tue, 05 May 2009)
From svn r46531 on 2009-05-05 09:47:07 -0500 (Tue, 05 May 2009)
From svn r46568 on 2009-05-06 09:47:05 -0500 (Wed, 06 May 2009)
From svn r46569 on 2009-05-06 09:53:22 -0500 (Wed, 06 May 2009)
From svn r46570 on 2009-05-06 09:54:45 -0500 (Wed, 06 May 2009)
From svn r46572 on 2009-05-06 11:04:54 -0500 (Wed, 06 May 2009)
From svn r46618 on 2009-05-07 11:08:18 -0500 (Thu, 07 May 2009)
From svn r46830 on 2009-05-13 16:33:45 -0500 (Wed, 13 May 2009)
From svn r46874 on 2009-05-14 13:52:41 -0500 (Thu, 14 May 2009)
From svn r46946 on 2009-05-18 16:01:30 -0500 (Mon, 18 May 2009)
From svn r46963 on 2009-05-19 11:22:55 -0500 (Tue, 19 May 2009)
From svn r46979 on 2009-05-19 13:35:44 -0500 (Tue, 19 May 2009)
From svn r47003 on 2009-05-20 09:33:21 -0500 (Wed, 20 May 2009)
From svn r47030 on 2009-05-20 13:07:57 -0500 (Wed, 20 May 2009)
From svn r47046 on 2009-05-20 16:19:40 -0500 (Wed, 20 May 2009)
From svn r47163 on 2009-05-22 13:14:48 -0500 (Fri, 22 May 2009)
From svn r47164 on 2009-05-22 13:21:50 -0500 (Fri, 22 May 2009)
From svn r47173 on 2009-05-22 14:34:35 -0500 (Fri, 22 May 2009)
From svn r47174 on 2009-05-22 14:36:01 -0500 (Fri, 22 May 2009)
From svn r47212 on 2009-05-26 12:36:54 -0500 (Tue, 26 May 2009)
From svn r47273 on 2009-05-27 14:30:49 -0500 (Wed, 27 May 2009)
From svn r47350 on 2009-05-28 17:27:39 -0500 (Thu, 28 May 2009)
From svn r47353 on 2009-05-28 17:34:23 -0500 (Thu, 28 May 2009)
From svn r47367 on 2009-05-29 13:08:52 -0500 (Fri, 29 May 2009)
From svn r47373 on 2009-05-29 14:48:46 -0500 (Fri, 29 May 2009)
From svn r47375 on 2009-05-29 15:29:47 -0500 (Fri, 29 May 2009)
From svn r47377 on 2009-05-29 15:35:05 -0500 (Fri, 29 May 2009)
From svn r47379 on 2009-05-29 15:37:03 -0500 (Fri, 29 May 2009)
From svn r47380 on 2009-05-29 15:53:59 -0500 (Fri, 29 May 2009)
From svn r47391 on 2009-05-29 16:50:42 -0500 (Fri, 29 May 2009)
From svn r47526 on 2009-06-02 16:51:26 -0500 (Tue, 02 Jun 2009)
From svn r47584 on 2009-06-04 09:57:51 -0500 (Thu, 04 Jun 2009)
From svn r47706 on 2009-06-08 15:36:56 -0500 (Mon, 08 Jun 2009)
From svn r47786 on 2009-06-10 16:00:01 -0500 (Wed, 10 Jun 2009)
From svn r47847 on 2009-06-11 15:40:14 -0500 (Thu, 11 Jun 2009)
From svn r47872 on 2009-06-12 16:27:34 -0500 (Fri, 12 Jun 2009)
From svn r47881 on 2009-06-15 11:50:21 -0500 (Mon, 15 Jun 2009)
From svn r47882 on 2009-06-15 11:51:12 -0500 (Mon, 15 Jun 2009)
From svn r47883 on 2009-06-15 11:52:18 -0500 (Mon, 15 Jun 2009)
From svn r48004 on 2009-06-18 11:40:24 -0500 (Thu, 18 Jun 2009)
From svn r48005 on 2009-06-18 11:41:19 -0500 (Thu, 18 Jun 2009)
From svn r48006 on 2009-06-18 11:41:54 -0500 (Thu, 18 Jun 2009)
From svn r48007 on 2009-06-18 11:42:35 -0500 (Thu, 18 Jun 2009)
From svn r48008 on 2009-06-18 11:43:51 -0500 (Thu, 18 Jun 2009)
From svn r48219 on 2009-06-24 10:45:37 -0500 (Wed, 24 Jun 2009)
From svn r48220 on 2009-06-24 10:46:04 -0500 (Wed, 24 Jun 2009)
From svn r48489 on 2009-07-02 11:21:03 -0500 (Thu, 02 Jul 2009)
From svn r48601 on 2009-07-07 11:57:52 -0500 (Tue, 07 Jul 2009)
From svn r48792 on 2009-07-10 15:00:09 -0500 (Fri, 10 Jul 2009)
From svn r48798 on 2009-07-10 16:07:06 -0500 (Fri, 10 Jul 2009)
From svn r48934 on 2009-07-15 11:43:31 -0500 (Wed, 15 Jul 2009)
From svn r49116 on 2009-07-21 17:26:40 -0500 (Tue, 21 Jul 2009)
From svn r49336 on 2009-07-28 16:14:42 -0500 (Tue, 28 Jul 2009)
From svn r49376 on 2009-07-29 14:49:16 -0500 (Wed, 29 Jul 2009)
From svn r49425 on 2009-07-30 16:27:39 -0500 (Thu, 30 Jul 2009)
From svn r49426 on 2009-07-30 16:30:54 -0500 (Thu, 30 Jul 2009)
From svn r49441 on 2009-07-31 14:05:06 -0500 (Fri, 31 Jul 2009)
From svn r49442 on 2009-07-31 14:30:07 -0500 (Fri, 31 Jul 2009)
From svn r49443 on 2009-07-31 14:31:47 -0500 (Fri, 31 Jul 2009)
From svn r49516 on 2009-08-04 11:21:14 -0500 (Tue, 04 Aug 2009)
From svn r49517 on 2009-08-04 11:24:45 -0500 (Tue, 04 Aug 2009)
From svn r49518 on 2009-08-04 11:25:36 -0500 (Tue, 04 Aug 2009)
From svn r49546 on 2009-08-04 16:27:27 -0500 (Tue, 04 Aug 2009)
From svn r49576 on 2009-08-05 11:22:19 -0500 (Wed, 05 Aug 2009)
From svn r49577 on 2009-08-05 11:22:44 -0500 (Wed, 05 Aug 2009)
From svn r49614 on 2009-08-05 15:35:55 -0500 (Wed, 05 Aug 2009)
From svn r49681 on 2009-08-06 16:40:39 -0500 (Thu, 06 Aug 2009)
From svn r49682 on 2009-08-06 16:41:07 -0500 (Thu, 06 Aug 2009)
From svn r49683 on 2009-08-06 16:41:20 -0500 (Thu, 06 Aug 2009)
From svn r49992 on 2009-08-17 09:44:24 -0500 (Mon, 17 Aug 2009)
From svn r50047 on 2009-08-18 11:02:59 -0500 (Tue, 18 Aug 2009)
From svn r50051 on 2009-08-18 11:23:34 -0500 (Tue, 18 Aug 2009)
From svn r50057 on 2009-08-18 12:39:22 -0500 (Tue, 18 Aug 2009)
From svn r50218 on 2009-08-21 15:34:10 -0500 (Fri, 21 Aug 2009)
From svn r50225 on 2009-08-21 16:52:38 -0500 (Fri, 21 Aug 2009)
From svn r50226 on 2009-08-21 16:58:48 -0500 (Fri, 21 Aug 2009)
From svn r50227 on 2009-08-21 17:01:34 -0500 (Fri, 21 Aug 2009)
From svn r50250 on 2009-08-24 11:30:09 -0500 (Mon, 24 Aug 2009)
From svn r50251 on 2009-08-24 11:30:35 -0500 (Mon, 24 Aug 2009)
From svn r50253 on 2009-08-24 11:30:53 -0500 (Mon, 24 Aug 2009)
From svn r50254 on 2009-08-24 11:31:07 -0500 (Mon, 24 Aug 2009)
From svn r50303 on 2009-08-25 10:41:15 -0500 (Tue, 25 Aug 2009)
From svn r50323 on 2009-08-25 14:36:35 -0500 (Tue, 25 Aug 2009)
From svn r50324 on 2009-08-25 14:37:21 -0500 (Tue, 25 Aug 2009)
From svn r50327 on 2009-08-25 15:08:36 -0500 (Tue, 25 Aug 2009)
From svn r50328 on 2009-08-25 15:09:45 -0500 (Tue, 25 Aug 2009)
From svn r50329 on 2009-08-25 15:10:00 -0500 (Tue, 25 Aug 2009)
From svn r50375 on 2009-08-25 16:24:13 -0500 (Tue, 25 Aug 2009)
From svn r50412 on 2009-08-26 17:06:24 -0500 (Wed, 26 Aug 2009)
From svn r50426 on 2009-08-27 11:11:35 -0500 (Thu, 27 Aug 2009)
From svn r50593 on 2009-08-31 15:37:39 -0500 (Mon, 31 Aug 2009)
From svn r50635 on 2009-09-01 16:55:54 -0500 (Tue, 01 Sep 2009)
adukes (18):
From svn r33559 on 2008-04-09 16:02:52 -0500 (Wed, 09 Apr 2008)
From svn r34731 on 2008-05-15 16:35:54 -0500 (Thu, 15 May 2008)
From svn r34732 on 2008-05-15 16:41:43 -0500 (Thu, 15 May 2008)
From svn r36677 on 2008-07-16 15:17:30 -0500 (Wed, 16 Jul 2008)
From svn r36683 on 2008-07-16 16:56:05 -0500 (Wed, 16 Jul 2008)
From svn r36974 on 2008-07-25 12:13:58 -0500 (Fri, 25 Jul 2008)
From svn r36975 on 2008-07-25 12:15:12 -0500 (Fri, 25 Jul 2008)
From svn r36976 on 2008-07-25 12:18:12 -0500 (Fri, 25 Jul 2008)
From svn r36979 on 2008-07-25 12:50:17 -0500 (Fri, 25 Jul 2008)
From svn r37541 on 2008-08-13 17:20:24 -0500 (Wed, 13 Aug 2008)
From svn r38672 on 2008-09-17 10:15:06 -0500 (Wed, 17 Sep 2008)
From svn r39019 on 2008-09-23 17:37:58 -0500 (Tue, 23 Sep 2008)
From svn r44621 on 2009-03-12 16:17:57 -0500 (Thu, 12 Mar 2009)
From svn r45050 on 2009-03-25 13:56:51 -0500 (Wed, 25 Mar 2009)
From svn r45466 on 2009-04-07 14:20:59 -0500 (Tue, 07 Apr 2009)
From svn r46863 on 2009-05-14 12:20:07 -0500 (Thu, 14 May 2009)
From svn r47866 on 2009-06-12 15:18:21 -0500 (Fri, 12 Jun 2009)
From svn r47867 on 2009-06-12 15:32:08 -0500 (Fri, 12 Jun 2009)
apregier (8):
Remove check for set params during error message
Remove breakpoint
Use isa instead of string comparison to determine type of id_by property
Explicitly check whether the meta-attribute name is valid
Add a test for failure case
Line no longer needed
$self is class_name->__meta__
Merge pull request #8 from apregier/master
boberkfe (1):
From svn r49666 on 2009-08-06 14:21:47 -0500 (Thu, 06 Aug 2009)
charris (5):
From svn r34302 on 2008-05-07 11:27:08 -0500 (Wed, 07 May 2008)
From svn r35124 on 2008-05-30 09:20:15 -0500 (Fri, 30 May 2008)
From svn r36002 on 2008-06-27 12:48:31 -0500 (Fri, 27 Jun 2008)
From svn r36003 on 2008-06-27 12:49:18 -0500 (Fri, 27 Jun 2008)
From svn r36290 on 2008-07-08 12:11:46 -0500 (Tue, 08 Jul 2008)
ebelter (14):
From svn r36253 on 2008-07-07 15:10:33 -0500 (Mon, 07 Jul 2008)
From svn r36254 on 2008-07-07 15:14:28 -0500 (Mon, 07 Jul 2008)
From svn r36255 on 2008-07-07 15:15:50 -0500 (Mon, 07 Jul 2008)
From svn r36319 on 2008-07-08 15:13:36 -0500 (Tue, 08 Jul 2008)
From svn r36320 on 2008-07-08 15:18:09 -0500 (Tue, 08 Jul 2008)
From svn r36321 on 2008-07-08 15:19:48 -0500 (Tue, 08 Jul 2008)
From svn r36327 on 2008-07-08 15:59:29 -0500 (Tue, 08 Jul 2008)
From svn r36329 on 2008-07-08 16:09:07 -0500 (Tue, 08 Jul 2008)
From svn r36330 on 2008-07-08 16:11:53 -0500 (Tue, 08 Jul 2008)
From svn r36331 on 2008-07-08 16:12:57 -0500 (Tue, 08 Jul 2008)
From svn r38974 on 2008-09-23 12:23:56 -0500 (Tue, 23 Sep 2008)
From svn r38975 on 2008-09-23 12:24:31 -0500 (Tue, 23 Sep 2008)
From svn r41122 on 2008-11-18 14:50:23 -0600 (Tue, 18 Nov 2008)
From svn r41156 on 2008-11-19 12:30:30 -0600 (Wed, 19 Nov 2008)
eclark (78):
From svn r33426 on 2008-04-03 16:08:05 -0500 (Thu, 03 Apr 2008)
From svn r33427 on 2008-04-03 16:08:42 -0500 (Thu, 03 Apr 2008)
From svn r34348 on 2008-05-08 12:22:05 -0500 (Thu, 08 May 2008)
From svn r34755 on 2008-05-16 11:52:14 -0500 (Fri, 16 May 2008)
From svn r35308 on 2008-06-06 13:13:03 -0500 (Fri, 06 Jun 2008)
From svn r35309 on 2008-06-06 13:14:17 -0500 (Fri, 06 Jun 2008)
From svn r35692 on 2008-06-18 17:12:11 -0500 (Wed, 18 Jun 2008)
From svn r35693 on 2008-06-18 17:26:45 -0500 (Wed, 18 Jun 2008)
From svn r35723 on 2008-06-19 14:50:15 -0500 (Thu, 19 Jun 2008)
From svn r35747 on 2008-06-20 11:16:53 -0500 (Fri, 20 Jun 2008)
From svn r35761 on 2008-06-20 13:46:23 -0500 (Fri, 20 Jun 2008)
From svn r35762 on 2008-06-20 13:51:32 -0500 (Fri, 20 Jun 2008)
From svn r35856 on 2008-06-24 15:25:16 -0500 (Tue, 24 Jun 2008)
From svn r35906 on 2008-06-25 11:43:46 -0500 (Wed, 25 Jun 2008)
From svn r36363 on 2008-07-09 11:49:57 -0500 (Wed, 09 Jul 2008)
From svn r38919 on 2008-09-22 14:56:28 -0500 (Mon, 22 Sep 2008)
From svn r38929 on 2008-09-22 15:39:23 -0500 (Mon, 22 Sep 2008)
From svn r39730 on 2008-10-14 13:15:48 -0500 (Tue, 14 Oct 2008)
From svn r39742 on 2008-10-14 13:35:26 -0500 (Tue, 14 Oct 2008)
From svn r39849 on 2008-10-16 10:46:25 -0500 (Thu, 16 Oct 2008)
From svn r40078 on 2008-10-21 23:12:00 -0500 (Tue, 21 Oct 2008)
From svn r40891 on 2008-11-12 12:06:17 -0600 (Wed, 12 Nov 2008)
From svn r40906 on 2008-11-12 13:47:28 -0600 (Wed, 12 Nov 2008)
From svn r40916 on 2008-11-12 15:14:43 -0600 (Wed, 12 Nov 2008)
From svn r44969 on 2009-03-24 14:42:24 -0500 (Tue, 24 Mar 2009)
From svn r44988 on 2009-03-24 16:44:39 -0500 (Tue, 24 Mar 2009)
From svn r45260 on 2009-03-31 14:41:21 -0500 (Tue, 31 Mar 2009)
From svn r46008 on 2009-04-20 15:56:35 -0500 (Mon, 20 Apr 2009)
From svn r46009 on 2009-04-20 16:01:26 -0500 (Mon, 20 Apr 2009)
From svn r46818 on 2009-05-13 12:19:14 -0500 (Wed, 13 May 2009)
From svn r47776 on 2009-06-10 12:02:38 -0500 (Wed, 10 Jun 2009)
Fixed UR::Object::Type::Initializer::_preprocess_subclass_description to recurse on parent_class_names()
Fix for rt55121 - Objects with composite id cannot be set in property that has single value id_by.
Small fixes
When walking through the properties to find the final_property_meta. Sometimes a via points to a property thats undefined. final_property_meta now returns nothing when this happens (instead of dieing with an undefined value error.)
Added two new methods. all_subject_classes returns a list of all classes viewed by this view. all_subject_classes_ancestry augments this list with all the ancesters of these classes.
Discover the aspect_type through 'via' if the property is delegated.
No longer needed
Changed the default aspects for text views so that if a view has no parent, all aspects are used, otherwise none.
Complete rewrite of the Default Xml view. Now returns a document using generic element <object> and defers to XML::Dumper when it renders a perl data structure.
Merge branch 'generic-web-view'
Moved the override of default aspects into the Xml view, since it breaks one of the tests when its part of the text view.
convert generate_delegate_view exceptions to warnings, since we'd rather return something than nothing.
Changed UR::Exit::death so it does not show itself in the stack track printed by Carp::confess
Fixes for creating an Xsl view without a transform (simply generates the primary xsl file with all the imports).
Xsl now allows both a perspective and a desired_perspective.
Fixed some problems with extra slashes in paths to xsl files
Merge branch 'master' of github.com:sakoht/UR
Should exit with an error code when the delegate class object cannot be created.
Removed bare_args from Command.pm
added default values for is_many, and moved shell_args_position options to the end in the help description
Fixed commands that use ' ' to get bare_args.
Allow the view to take a hash of xsl variables that you want set in the resulting transform. rest_variable is deprecated and will be removed soon.
Previous commit was squashing false, but defined values in the xml view.
Fixed some bugs with clearing the subject of a view during UR::Context->clear_cache
Memoize view class resolving to save a lot of filesystem access. Also fixed a warning when cancelling a change subscription.
Calling UR::Value wasn't returning existing objects from the context, it was trying to create them again. Bugfix and test case.
above.pm now prefers the PERL_USED_ABOVE paths over paths it discovers based on cwd(). Added a test to make sure this is always true.
Default set view that works
Moved xsl hook functions into the base UR class so they are available to everything.
Changed the return code to be based on !has_problems instead of all_passed. all_passed fails when a test is skipped.
default resource requirement should have double equals, not single.
Allow modules that are loaded under _use_safe to call use lib themselves and preserve their changes.
Change to UR::Util::used_libs
First draft default json view.
Allow changing the default value for dump_status_messages. Since it is off by default, sometimes we want it on (for all classes, not just a specific one).
Change dump_status_default global to environment variable for easy access.
Changed property() to use ancestry_class_names instead of {_ordered_inherited_class_names} because auto-vivication was breaking everything.
Merge branch 'master' of github.com:sakoht/UR
Add url_to_type/type_to_url test that is being deleted from Genome repo.
Add currentTime magic variable to root.xsl.
Suppress undefined warning for GENOME_DEV_MODE
Rewrite this expression so that undef values dont appear when the is_many property neither has a param or a default value. Fixes workflow test failures.
Revert is_many change on views, and is_many default values.
is_many bug: When a property is given a value during ->create(), remove it from the %default_values hash that will be used to fabricate the object.
Enable Json set views.
Rewrite Xsl.pm to generate its transform using dom objects, rather than badly hand crafted xml.
Remove GENOME_DEV_MODE from the xsl
edemello (1):
From svn r39782 on 2008-10-14 17:42:51 -0500 (Tue, 14 Oct 2008)
gregor herrmann (1):
New upstream version 0.450
gsanders (18):
From svn r35121 on 2008-05-29 16:59:50 -0500 (Thu, 29 May 2008)
From svn r35347 on 2008-06-09 16:03:28 -0500 (Mon, 09 Jun 2008)
From svn r35349 on 2008-06-09 16:04:46 -0500 (Mon, 09 Jun 2008)
From svn r35350 on 2008-06-09 16:05:48 -0500 (Mon, 09 Jun 2008)
From svn r35356 on 2008-06-09 16:40:03 -0500 (Mon, 09 Jun 2008)
From svn r35733 on 2008-06-19 16:48:39 -0500 (Thu, 19 Jun 2008)
From svn r35968 on 2008-06-26 13:39:36 -0500 (Thu, 26 Jun 2008)
From svn r35970 on 2008-06-26 13:50:01 -0500 (Thu, 26 Jun 2008)
From svn r37156 on 2008-07-31 15:27:02 -0500 (Thu, 31 Jul 2008)
From svn r37380 on 2008-08-08 15:52:47 -0500 (Fri, 08 Aug 2008)
From svn r39999 on 2008-10-20 16:44:34 -0500 (Mon, 20 Oct 2008)
From svn r41209 on 2008-11-20 13:48:47 -0600 (Thu, 20 Nov 2008)
From svn r42779 on 2009-01-16 16:36:31 -0600 (Fri, 16 Jan 2009)
From svn r42780 on 2009-01-16 16:43:03 -0600 (Fri, 16 Jan 2009)
From svn r45604 on 2009-04-09 14:29:28 -0500 (Thu, 09 Apr 2009)
From svn r47614 on 2009-06-04 17:02:30 -0500 (Thu, 04 Jun 2009)
From svn r47658 on 2009-06-05 16:03:58 -0500 (Fri, 05 Jun 2009)
From svn r47717 on 2009-06-08 18:20:10 -0500 (Mon, 08 Jun 2009)
iferguso (1):
From svn r49373 on 2009-07-29 14:08:47 -0500 (Wed, 29 Jul 2009)
josborne (1):
From svn r33891 on 2008-04-21 15:15:34 -0500 (Mon, 21 Apr 2008)
jschindl (1):
From svn r41026 on 2008-11-14 15:50:57 -0600 (Fri, 14 Nov 2008)
jwalker (15):
From svn r34364 on 2008-05-08 15:19:46 -0500 (Thu, 08 May 2008)
From svn r34365 on 2008-05-08 15:20:40 -0500 (Thu, 08 May 2008)
From svn r38337 on 2008-09-05 12:51:24 -0500 (Fri, 05 Sep 2008)
From svn r38341 on 2008-09-05 13:47:08 -0500 (Fri, 05 Sep 2008)
From svn r39483 on 2008-10-07 14:08:39 -0500 (Tue, 07 Oct 2008)
From svn r39497 on 2008-10-07 16:17:49 -0500 (Tue, 07 Oct 2008)
From svn r39513 on 2008-10-08 08:56:21 -0500 (Wed, 08 Oct 2008)
From svn r40055 on 2008-10-21 14:49:51 -0500 (Tue, 21 Oct 2008)
From svn r41005 on 2008-11-14 12:46:05 -0600 (Fri, 14 Nov 2008)
From svn r44456 on 2009-03-10 15:14:20 -0500 (Tue, 10 Mar 2009)
From svn r44636 on 2009-03-13 11:25:22 -0500 (Fri, 13 Mar 2009)
From svn r45847 on 2009-04-15 14:57:22 -0500 (Wed, 15 Apr 2009)
From svn r46086 on 2009-04-21 15:58:20 -0500 (Tue, 21 Apr 2009)
From svn r47107 on 2009-05-21 14:05:52 -0500 (Thu, 21 May 2009)
From svn r47218 on 2009-05-26 13:24:57 -0500 (Tue, 26 May 2009)
jweible (6):
From svn r35622 on 2008-06-17 10:53:50 -0500 (Tue, 17 Jun 2008)
From svn r36559 on 2008-07-14 14:01:40 -0500 (Mon, 14 Jul 2008)
From svn r36660 on 2008-07-16 13:54:27 -0500 (Wed, 16 Jul 2008)
From svn r37018 on 2008-07-28 14:44:01 -0500 (Mon, 28 Jul 2008)
From svn r37021 on 2008-07-28 14:56:29 -0500 (Mon, 28 Jul 2008)
From svn r37208 on 2008-08-04 08:48:17 -0500 (Mon, 04 Aug 2008)
lcarmich (1):
From svn r41415 on 2008-11-26 15:51:20 -0600 (Wed, 26 Nov 2008)
mjohnson (1):
From svn r41027 on 2008-11-14 16:10:57 -0600 (Fri, 14 Nov 2008)
nnutter (163):
remove broken feature, support for multiple data types
support new style BoolExpr which may not contain commas
whitespace
minor cleanup
fix space being gobbled from 'name~%foo 123%'
remove noise and put diff in diag
support properties declared by type_has
refactor multiple arrayref printing into pprint_arrayref
add support for array ref values to where operators
wrap doc strings in q() when needed
do not assume a specified class has a data_source
class initializer should die if a property has id_by and reverse_as
ModuleWriter should not create id_by fields for reverse_as properties
brackets are not needed for single is
handle arrayref in type has
use pprint_arrayref for 'is' section
preserve is_many if it differs from via
preserve is_mutable on reverse_as
fix for via => '__self__' properties
implied_by should not be used in class definitions
remove unused hash
fix for data_length check when using dummy IDs
optional direct properties are not required
remove commented code
more refactoring of common code
Merge branch 'update_classes'
delegate id to UR::Singleton
better solution to id "conflic"
Revert "better solution to id "conflic""
send a subclass_loaded signal
cleanup/refactor
stop crawling at device boundary by default
Revert "Only commit if there are changed objects at the end of execution that are associated with a data source."
initial class browser cache
remove breakpoint and comment
make test more resilient
support --debug option to enable all debug messages
allow UR_DUMP_STATUS_MESSAGES, UR_DUMP_DEBUG_MESSAGES, and UR_COMMAND_DUMP_DEBUG_MESSAGES
feature merge: support for --debug option on commands
add another exception to used_libs
add lib boilerplate
specify test count
add observer test for multiple inheritance
add an error message so it can be tracked
whitespace
use strict/warnings
add test for multiple data sources using RDBMSRetriableOperations
remove unused variable declaration
make deep recursion fatal
search for datasource method recursively
cache results to avoid repeated recursive calls
add test for infinite recursion bug
support intermediate classes inheriting RDBMSRetriableOperations
whitespace
use a plan instead of done_testing
fix spelling
use "$type" instead of "it" for test name
do not dump message to STDERR
fix spelling
carp sprintf warnings instead of just warn
whitespace
remove commented out code
whitespace
whitespace
trailing whitespace
whitespace to trigger change
replace load_class_or_file internals with Module::Runtime
rename load_class_or_file to use_package_optimistically (but alias old name)
remove load_class_or_file alias
do not override existing add/remove subs
rename test
remove use of join labels in Join objects
remove commented code
remove unused label
remove unused code
%data_source_for_class doesn't need to be checked
%classes_to_prune is not even needed
revert to stepping through object cache in 10 chronological passes
add is_prunable
add is_weakened
add is_strengthened
use is_prunable
filter out objects from report that won't be prunable
record object load prior to using object
whitespace
move singular accessor to beginning of accessor creation
add support for singular reverse_as properties
fix typo
improved test using an RDBMS data source
add alternate admin schema that has an implicit constraint
add test covering dot notation
check for cwd() failures
use getcwd() instead of cwd()
add missing dependency
add Test::Fatal as test dependency
whitespace
catch exceptions so we can restore file
localize $@ earlier
remove unnecessary conditional
switch to two argument form
die if rename failed for reasons other than ENOENT
show errors if various cleanup failed
add support for default_from (method) attribute
collapse for loop
add documentation for `default_from`
support code refs for `default_from`
document code ref and 1 values for `default_from`
replace default_from with calculated_default
rename test from default_from to calculated_default
fix UR::Value::Text->get('') failing once cached
prevent calculated_default properties from being set is_calculated
properly limit scope when using `local $@`
should tell user to see --help only before _execute_body
trivial refactor
copy over error_die signalling for Command::V2
delegate execute to Command::V1
copy comment from V2
delegate create to V1
delegate shortcut to V1
copy comment from V2
delegate _execute_body to V1
delegate exit_code_for_return_value to V1
extract common V1/V2 code into Command::Common
remove unused lines
convert to not use BoolExpr
pull defaults up into class description
prevent auto-vivification of keys in a type's `has` block
remove unused accessor
minor doc change
add `register_callback` API, e.g. an observer with an Observer
refactor: replace conditional with polymorphism
remove binning of object by class name since it isn't needed
convert to lower level observer API
replace validate_subscription with valid_signals in Command
remove validate_subscription previously superseded by valid_signals
replace default implementation of validate_subscription
fix logic mistake
default subject_class_name is UR::Object
have to have loaded prototype to use bare curly braces
fix parameter validation after (sloppy) refactor
add test coverage for UR::Observer defaults and validation
install observers on instances so that aspects are valid (valid_signals)
add valid_signals to UR::Context
allow UR::ModuleBase to "register" signals for each message type
Parent must define signal as part of its interface
only check objects that changed during the transaction
extract `__rollback_property__` method so it can be overridden
rename variable for grammar
call _make_retriable_operation_observer as a method
fix typo
use class method to get defaults instead of keeping %defaults in scope
update docs to reflect that aspects are now strictly validated
add `unregister_callback` by extracting from `delete`
add test for `register_callback` and `unregister_callback`
move method to UR::Context
remove expectation that all properties have keys in saved values
disable log_all_changes if last transaction
add failing test for classide + calculated_default property
add failing test case showing unexpected behaviour due to unload
extract method: changed_object
do not presume to get the changed object directly
show calculated default value in docs
use same message and formatting for calculated_default as default_value
ssmith (247):
Cleanup to play nicely w/ App.
From svn r31769 on 2008-01-14 21:19:12 -0600 (Mon, 14 Jan 2008)
From svn r31770 on 2008-01-14 21:20:48 -0600 (Mon, 14 Jan 2008)
From svn r31773 on 2008-01-14 21:32:02 -0600 (Mon, 14 Jan 2008)
From svn r31778 on 2008-01-15 08:40:20 -0600 (Tue, 15 Jan 2008)
From svn r32041 on 2008-01-28 18:44:41 -0600 (Mon, 28 Jan 2008)
From svn r32104 on 2008-01-30 21:52:23 -0600 (Wed, 30 Jan 2008)
From svn r32120 on 2008-01-31 22:51:28 -0600 (Thu, 31 Jan 2008)
From svn r32286 on 2008-02-12 23:03:46 -0600 (Tue, 12 Feb 2008)
From svn r32288 on 2008-02-12 23:07:10 -0600 (Tue, 12 Feb 2008)
From svn r33610 on 2008-04-10 15:32:04 -0500 (Thu, 10 Apr 2008)
From svn r33614 on 2008-04-10 19:10:34 -0500 (Thu, 10 Apr 2008)
From svn r33615 on 2008-04-10 20:04:10 -0500 (Thu, 10 Apr 2008)
From svn r33616 on 2008-04-10 20:04:58 -0500 (Thu, 10 Apr 2008)
From svn r33617 on 2008-04-10 20:08:25 -0500 (Thu, 10 Apr 2008)
From svn r33669 on 2008-04-14 21:40:00 -0500 (Mon, 14 Apr 2008)
From svn r33670 on 2008-04-14 21:40:47 -0500 (Mon, 14 Apr 2008)
From svn r33908 on 2008-04-22 05:00:36 -0500 (Tue, 22 Apr 2008)
From svn r34002 on 2008-04-24 17:08:52 -0500 (Thu, 24 Apr 2008)
From svn r34006 on 2008-04-24 23:49:41 -0500 (Thu, 24 Apr 2008)
From svn r34009 on 2008-04-24 23:58:11 -0500 (Thu, 24 Apr 2008)
From svn r34222 on 2008-05-04 19:05:03 -0500 (Sun, 04 May 2008)
From svn r34223 on 2008-05-04 19:11:41 -0500 (Sun, 04 May 2008)
From svn r34256 on 2008-05-05 20:59:21 -0500 (Mon, 05 May 2008)
From svn r34265 on 2008-05-06 12:31:49 -0500 (Tue, 06 May 2008)
From svn r34272 on 2008-05-06 13:33:22 -0500 (Tue, 06 May 2008)
From svn r34327 on 2008-05-08 07:29:55 -0500 (Thu, 08 May 2008)
From svn r34328 on 2008-05-08 08:23:17 -0500 (Thu, 08 May 2008)
From svn r34329 on 2008-05-08 08:24:01 -0500 (Thu, 08 May 2008)
From svn r34336 on 2008-05-08 09:30:46 -0500 (Thu, 08 May 2008)
From svn r34339 on 2008-05-08 10:29:14 -0500 (Thu, 08 May 2008)
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Base version of the http dispatcher does the real work in a child process, while the parent returns a key to be used later to poll for the status of results.
Base version of the http dispatcher does the real work in a child process, while the parent returns a key to be used later to poll for the status of results.
Dispatch logic is now out of the command module, but is just directly in the cgi script. Now we have status checking and job cleanup. Just need the form.
moved logic out to the command-dispatch.cgi
added command-ui.cgi and some mods in the Command.pm documentation generator.
updated URLs to work wherever checked-out
cgi to return command results from an execution. currently does not do polling, just must be refreshed.
ajax requests works, but we're faking w/ hard-coded params
added job id to results header. added comment to indicate where a hack is still in place. cosmetic changes
Added test modules.
renamed stage to status in cgi
updated title logic
Merge branch 'foo' into webdispatch
cosmetic updates to output
testing using stdout/stderr side-by-side in overlapping opaque divs.
Added logic to make parts of the title clickable to "go up". Show small doc line with each command.
added comments
added comments
reverted changes in-progress to test fix to UR::Object::Set
reverted changes in-progress to test fix to UR::Object::Set
updated test cases to actually use the checkout tree lib
Updated the "use lib" in the test cases to work on the lib in the checkout. They currently use the URT/Vendor modules, but not the checkout UR modules
fixed problem with missing test on transactions
Restored the transaction test to position 99 because it ends up in the beginning during "make test". Ideally it would be at the beginning when running "ur test run", but we need to optimize for the person installing, not the person developing.
Added order_by and specify_by to has-many meta properties. Updated new UR::Object::View module and POD.
Cleanup in main ::View module. Initial attempt at refactoring UR::Object::View::Default::Text.
Die when using a module inside of an accesor, and the use fails. We must make sure this isn't in an eval to prevent inappropriate failure.
updated method names from old Viewer names.
The text view now works. Test case and modules need cleanup. The aspect-hasa/isa-view issue needs further simplification. We cheat on has-many relationships and reuse the same sub-view.
text and xml viewers working
Fixed typo
Relocated the view test to be URT/t/63_view_text.t
Merge branch 'master' of git at github.com:sakoht/UR
whitespace/cosmetic
Class to represent the value of a hypothetical entity.
switching a "true" check to a defined() check shaves off .5s of compile time for UR.pm
thepler (3):
From svn r35178 on 2008-06-03 11:53:08 -0500 (Tue, 03 Jun 2008)
From svn r35196 on 2008-06-03 13:14:13 -0500 (Tue, 03 Jun 2008)
From svn r35199 on 2008-06-03 13:52:27 -0500 (Tue, 03 Jun 2008)
-----------------------------------------------------------------------
No new revisions were added by this update.
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-perl/packages/libur-perl.git
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