r34604 - in /trunk/libbio-primerdesigner-perl: ./ debian/ lib/Bio/ lib/Bio/PrimerDesigner/ scripts/ t/
gregoa at users.alioth.debian.org
gregoa at users.alioth.debian.org
Fri May 1 23:31:58 UTC 2009
Author: gregoa
Date: Fri May 1 23:31:53 2009
New Revision: 34604
URL: http://svn.debian.org/wsvn/pkg-perl/?sc=1&rev=34604
Log:
New upstream release.
Modified:
trunk/libbio-primerdesigner-perl/META.yml
trunk/libbio-primerdesigner-perl/README
trunk/libbio-primerdesigner-perl/debian/changelog
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner.pm
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Remote.pm
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Result.pm
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Tables.pm
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/epcr.pm
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/ispcr.pm
trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/primer3.pm
trunk/libbio-primerdesigner-perl/scripts/primer_designer
trunk/libbio-primerdesigner-perl/scripts/primer_designer.cgi
trunk/libbio-primerdesigner-perl/t/remote.t
Modified: trunk/libbio-primerdesigner-perl/META.yml
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/META.yml?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/META.yml (original)
+++ trunk/libbio-primerdesigner-perl/META.yml Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/README
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/README?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/README (original)
+++ trunk/libbio-primerdesigner-perl/README Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/debian/changelog
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/debian/changelog?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/debian/changelog (original)
+++ trunk/libbio-primerdesigner-perl/debian/changelog Fri May 1 23:31:53 2009
@@ -1,4 +1,4 @@
-libbio-primerdesigner-perl (0.05-2) UNRELEASED; urgency=low
+libbio-primerdesigner-perl (0.06-1) UNRELEASED; urgency=low
[ Charles Plessy ]
* debian/copyright: show the way to GPLv3, not GPLv2.
@@ -7,6 +7,8 @@
* debian/rules: skip test t/remote.t which tries to connect to somewhere and
causes a FBTFS; thanks to Daniel Schepler for the bug report
(closes: #526566)
+
+ * New upstream release.
-- Charles Plessy <plessy at debian.org> Sun, 08 Mar 2009 14:25:54 +0900
Modified: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Remote.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Remote.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Remote.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Remote.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Result.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Result.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Result.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Result.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Tables.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Tables.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Tables.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/Tables.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/epcr.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/epcr.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/epcr.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/epcr.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/ispcr.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/ispcr.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/ispcr.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/ispcr.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/primer3.pm
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/primer3.pm?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/primer3.pm (original)
+++ trunk/libbio-primerdesigner-perl/lib/Bio/PrimerDesigner/primer3.pm Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/scripts/primer_designer
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/scripts/primer_designer?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/scripts/primer_designer (original)
+++ trunk/libbio-primerdesigner-perl/scripts/primer_designer Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/scripts/primer_designer.cgi
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/scripts/primer_designer.cgi?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/scripts/primer_designer.cgi (original)
+++ trunk/libbio-primerdesigner-perl/scripts/primer_designer.cgi Fri May 1 23:31:53 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: trunk/libbio-primerdesigner-perl/t/remote.t
URL: http://svn.debian.org/wsvn/pkg-perl/trunk/libbio-primerdesigner-perl/t/remote.t?rev=34604&op=diff
==============================================================================
--- trunk/libbio-primerdesigner-perl/t/remote.t (original)
+++ trunk/libbio-primerdesigner-perl/t/remote.t Fri May 1 23:31:53 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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