r34602 - in /branches/upstream/libbio-primerdesigner-perl/current: ./ lib/Bio/ lib/Bio/PrimerDesigner/ scripts/ t/

gregoa at users.alioth.debian.org gregoa at users.alioth.debian.org
Fri May 1 23:30:20 UTC 2009 

Author: gregoa
Date: Fri May  1 23:30:15 2009
New Revision: 34602

URL: http://svn.debian.org/wsvn/pkg-perl/?sc=1&rev=34602
Log:
[svn-upgrade] Integrating new upstream version, libbio-primerdesigner-perl (0.06)

Modified:
    branches/upstream/libbio-primerdesigner-perl/current/META.yml
    branches/upstream/libbio-primerdesigner-perl/current/README
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner.pm
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Remote.pm
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Result.pm
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Tables.pm
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/epcr.pm
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/ispcr.pm
    branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/primer3.pm
    branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer
    branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer.cgi
    branches/upstream/libbio-primerdesigner-perl/current/t/remote.t

Modified: branches/upstream/libbio-primerdesigner-perl/current/META.yml
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/META.yml?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/META.yml (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/META.yml Fri May  1 23:30:15 2009
@@ -1,6 +1,6 @@
 ---
 name: Bio-PrimerDesigner
-version: 0.04
+version: 0.06
 author:
   - 'Sheldon McKay <mckays at cshl.edu>; Ken Youens-Clark <kclark at cshl.edu>'
 abstract: Design PCR primers using primer3 and epcr

Modified: branches/upstream/libbio-primerdesigner-perl/current/README
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/README?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/README (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/README Fri May  1 23:30:15 2009
@@ -108,7 +108,7 @@
     working properly.
 
 AUTHORS
-    Copyright (C) 2003-2008 Sheldon McKay <mckays at cshl.edu>, Ken
+    Copyright (C) 2003-2009 Sheldon McKay <mckays at cshl.edu>, Ken
     Youens-Clark <kclark at cpan.org>.
 
 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner.pm Fri May  1 23:30:15 2009
@@ -397,7 +397,7 @@
 
 =head1 AUTHORS
 
-Copyright (C) 2003-2008 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Remote.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Remote.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Remote.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Remote.pm Fri May  1 23:30:15 2009
@@ -96,13 +96,14 @@
     my $request  = HTTP::Request->new( 'POST', $url );
     $request->content( $content );
     my $response = $ua->request( $request );
-    my $output   = $response->content;
 
     return $self->error("No reponse from host $url")
         unless $response;
 
+    my $output   = $response->content;
+
     return $self->error("Incorrect response from host $url")
-        unless $response->content =~ /$program OK/m;
+        unless $output =~ /$program OK/m;
 
     return 1;
 }
@@ -115,7 +116,7 @@
 
 =head1 AUTHOR
 
-Copyright (C) 2003-2008 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Result.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Result.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Result.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Result.pm Fri May  1 23:30:15 2009
@@ -207,7 +207,7 @@
 
 =head1 AUTHOR
 
-Copyright (c) 2003-2008 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
+Copyright (c) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Tables.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Tables.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Tables.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/Tables.pm Fri May  1 23:30:15 2009
@@ -334,7 +334,7 @@
 
 =head1 AUTHOR
 
-Copyright (C) 2003-2008 Sheldon McKay E<lt>mckays at cshl.eduE<gt>.
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>.
 
 =head1 LICENSE
 

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/epcr.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/epcr.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/epcr.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/epcr.pm Fri May  1 23:30:15 2009
@@ -290,7 +290,7 @@
 
 =head1 AUTHOR
 
-Copyright (C) 2003-2008 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/ispcr.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/ispcr.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/ispcr.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/ispcr.pm Fri May  1 23:30:15 2009
@@ -301,7 +301,7 @@
 
 =head1 AUTHOR
 
-Copyright (C) 2003-2008 Sheldon McKay E<lt>mckays at cshl.edu<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.edu<gt>,
                      Ken Y. Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/primer3.pm
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/primer3.pm?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/primer3.pm (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/lib/Bio/PrimerDesigner/primer3.pm Fri May  1 23:30:15 2009
@@ -28,6 +28,9 @@
 
 Readonly our 
     $VERSION => sprintf "%s", q$Revision: 24 $ =~ /(\d+)/;
+
+Readonly our
+    $REMOTE_URL => 'mckay.cshl.edu/cgi-bin/primer_designer.cgi';
 
 use base 'Class::Base';
 
@@ -487,7 +490,7 @@
     my $length     =  length $dna;
     my $result     =  $self->design(
         'remote',
-        'dev.wormbase.org/db/seq/primer_designer.cgi',
+        $REMOTE_URL,
         { 
             num        => 1,
             seq        => $dna,
@@ -533,7 +536,7 @@
 
 =head1 AUTHOR
 
-Copyright (C) 2003-2008 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer Fri May  1 23:30:15 2009
@@ -194,7 +194,7 @@
 
 =head1 AUTHOR
 
-Copyright (C) 2003-8 Sheldon McKay E<lt>smckay at cshl.eduE<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 SEE ALSO

Modified: branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer.cgi
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer.cgi?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer.cgi (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/scripts/primer_designer.cgi Fri May  1 23:30:15 2009
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
 
 # $Id: primer_designer.cgi 6 2008-11-06 21:34:01Z kyclark $
 
@@ -15,6 +15,8 @@
 );
 
 print header;
+
+check(param('check'));
 
 #
 # Get remote config info and re-hashify it.
@@ -64,6 +66,28 @@
 
 # -------------------------------------------------------------------
 
+#
+# Pass the request and parameters to the local Bio::PrimerDesigner.
+#
+$binary eq 'primer3' ? primer3( %config ) : ePCR( %config );
+
+# -------------------------------------------------------------------
+sub check{
+
+=head2 check
+
+Verifies that this CGI is active and supports the requested binary.
+
+=cut
+
+my $program = shift;
+  if ($program) {
+    print "$program OK\n" if $program =~ /e-PCR|primer3/;
+    exit;
+  }
+}
+
+
 =pod
 
 =head1 NAME
@@ -95,7 +119,7 @@
 
 =head1 AUTHORS
 
-Copyright (C) 2003-8 Sheldon McKay E<lt>smckay at cshl.eduE<gt>,
+Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays at cshl.eduE<gt>,
 Ken Youens-Clark E<lt>kclark at cpan.orgE<gt>.
 
 =head1 LICENSE

Modified: branches/upstream/libbio-primerdesigner-perl/current/t/remote.t
URL: http://svn.debian.org/wsvn/pkg-perl/branches/upstream/libbio-primerdesigner-perl/current/t/remote.t?rev=34602&op=diff
==============================================================================
--- branches/upstream/libbio-primerdesigner-perl/current/t/remote.t (original)
+++ branches/upstream/libbio-primerdesigner-perl/current/t/remote.t Fri May  1 23:30:15 2009
@@ -19,7 +19,7 @@
 
 ok(
     $rem->CGI_request( 
-        'dev.wormbase.org/db/seq/primer_designer.cgi',
+        'mckay.cshl.edu/cgi-bin/primer_designer.cgi',
     	{ program => 'primer3' }
 	),
     'Call to remote server'

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