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removed dangling entry from manifest

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1 parent f7561a8 commit 00cff1b02391ec65635dd2382096010720c12cc0 @lstein lstein committed Jun 1, 2011
Showing with 18 additions and 75 deletions.
  1. +8 −3 Changes
  2. +2 −1 MANIFEST
  3. +6 −69 META.yml
  4. +1 −1 Makefile.PL
  5. +1 −1 lib/Bio/Graphics/Browser2.pm
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11 Changes
@@ -1,7 +1,12 @@
2.34
- * Fixed broken https:// links in karyotype summary table; patch courtesy Dan Bolser
- * Fixed behavior of "q" parameter to match the documented behavior.
- * Fixed RemoteSet to avoid failures due to nonexistence of download directory.
+ * Fix broken https:// links in karyotype summary table; patch courtesy Dan Bolser
+ * Fix behavior of "q" parameter to match the documented behavior.
+ * Fix RemoteSet to avoid failures due to nonexistence of download directory.
+ * Fix bug that allowed unauthorized users to view restricted tracks under
+ following circumstances: FastCGI activated, track configuration changed, server
+ not restarted.
+ * Added an LDAP authentication plugin (LDAPAuthenticate).
+ * Clean up appearance of favorite stars and checkboxes to deconfuse users.
2.33
* Fixed plugin authentication system to prevent an all-dark screen during authentication
View
@@ -70,6 +70,7 @@ conf/plugins/FastaDumper.pm
conf/plugins/FBTableDumper.pm
conf/plugins/FilterTest.pm
conf/plugins/GeneFinder.pm
+conf/plugins/LDAPAuthenticate.pm
conf/plugins/OligoFinder.pm
conf/plugins/PamAuthenticate.pm
conf/plugins/PrimerDesigner.pm
@@ -84,7 +85,6 @@ conf/plugins/Spectrogram.pm
conf/plugins/Submitter.pm
conf/plugins/test.pm
conf/plugins/TestAuthenticator.pm
-conf/plugins/TestAuthorizer.pm
conf/plugins/TestFinder.pm
conf/plugins/TrackDumper.pm
conf/plugins/TrackFinder.pm
@@ -648,3 +648,4 @@ t/testdata/phylo_align/species.tre
t/testdata/phylo_align/volvox_alignment.conf
t/testdata/phylo_align/volvox_phyloalign.gff
t/testdata/TemplateCopy.pm
+META.yml
View
@@ -6,9 +6,8 @@ build_requires:
Capture::Tiny: 0
ExtUtils::CBuilder: 0
configure_requires:
- Module::Build: 0.38
-dynamic_config: 1
-generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.110930'
+ Module::Build: 0.36
+generated_by: 'Module::Build version 0.3607'
license: perl
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -17,7 +16,6 @@ name: GBrowse
provides:
Bio::DB::GFF::Aggregator::match_gap:
file: lib/Bio/DB/GFF/Aggregator/match_gap.pm
- version: 0
Bio::DB::GFF::Aggregator::reftranscript:
file: lib/Bio/DB/GFF/Aggregator/reftranscript.pm
version: 0.10
@@ -29,193 +27,136 @@ provides:
version: 0.30
Bio::DB::SeqFeature::Store::BedLoader:
file: lib/Bio/DB/SeqFeature/Store/BedLoader.pm
- version: 0
Bio::DB::Tagger:
file: lib/Bio/DB/Tagger.pm
version: 1.00
Bio::DB::Tagger::Iterator:
file: lib/Bio/DB/Tagger.pm
- version: 0
Bio::DB::Tagger::Tag:
file: lib/Bio/DB/Tagger/Tag.pm
- version: 0
Bio::DB::Tagger::mysql:
file: lib/Bio/DB/Tagger/mysql.pm
- version: 0
Bio::Graphics::Browser2:
file: lib/Bio/Graphics/Browser2.pm
- version: 2.33
+ version: 2.34
Bio::Graphics::Browser2::Action:
file: lib/Bio/Graphics/Browser2/Action.pm
- version: 0
Bio::Graphics::Browser2::AdminTracks:
file: lib/Bio/Graphics/Browser2/UserTracks.pm
- version: 0
Bio::Graphics::Browser2::AuthorizedFeatureFile:
file: lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
- version: 0
Bio::Graphics::Browser2::CAlign:
file: lib/Bio/Graphics/Browser2/CAlign.pm
- version: 0
Bio::Graphics::Browser2::CachedTrack:
file: lib/Bio/Graphics/Browser2/CachedTrack.pm
- version: 0
Bio::Graphics::Browser2::DataBase:
file: lib/Bio/Graphics/Browser2/DataBase.pm
- version: 0
Bio::Graphics::Browser2::DataLoader:
file: lib/Bio/Graphics/Browser2/DataLoader.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::bam:
file: lib/Bio/Graphics/Browser2/DataLoader/bam.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::bed:
file: lib/Bio/Graphics/Browser2/DataLoader/bed.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::bigwig:
file: lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::featurefile:
file: lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::generic:
file: lib/Bio/Graphics/Browser2/DataLoader/generic.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::gff:
file: lib/Bio/Graphics/Browser2/DataLoader/gff.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::gff3:
file: lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::sam:
file: lib/Bio/Graphics/Browser2/DataLoader/sam.pm
- version: 0
Bio::Graphics::Browser2::DataLoader::wiggle:
file: lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
- version: 0
Bio::Graphics::Browser2::DataSource:
file: lib/Bio/Graphics/Browser2/DataSource.pm
- version: 0
Bio::Graphics::Browser2::ExternalData:
file: lib/Bio/Graphics/Browser2/ExternalData.pm
- version: 0
Bio::Graphics::Browser2::GFFhelper:
file: lib/Bio/Graphics/Browser2/GFFhelper.pm
- version: 0
Bio::Graphics::Browser2::I18n:
file: lib/Bio/Graphics/Browser2/I18n.pm
- version: 0
Bio::Graphics::Browser2::Markup:
file: lib/Bio/Graphics/Browser2/Markup.pm
- version: 0
Bio::Graphics::Browser2::MetaDB:
file: lib/Bio/Graphics/Browser2/RegionSearch.pm
- version: 0
Bio::Graphics::Browser2::MetaSegment:
file: lib/Bio/Graphics/Browser2/RegionSearch.pm
- version: 0
Bio::Graphics::Browser2::MetaSegment::Iterator:
file: lib/Bio/Graphics/Browser2/RegionSearch.pm
- version: 0
Bio::Graphics::Browser2::OptionPick:
file: lib/Bio/Graphics/Browser2/OptionPick.pm
- version: 0
Bio::Graphics::Browser2::PadAlignment:
file: lib/Bio/Graphics/Browser2/PadAlignment.pm
- version: 0
Bio::Graphics::Browser2::Plugin:
file: lib/Bio/Graphics/Browser2/Plugin.pm
version: 0.30
Bio::Graphics::Browser2::Plugin::AuthPlugin:
file: lib/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm
- version: 0
Bio::Graphics::Browser2::PluginSet:
file: lib/Bio/Graphics/Browser2/PluginSet.pm
- version: 0
Bio::Graphics::Browser2::Realign:
file: lib/Bio/Graphics/Browser2/Realign.pm
- version: 0
Bio::Graphics::Browser2::Region:
file: lib/Bio/Graphics/Browser2/Region.pm
- version: 0
Bio::Graphics::Browser2::RegionSearch:
file: lib/Bio/Graphics/Browser2/RegionSearch.pm
- version: 0
Bio::Graphics::Browser2::RemoteSet:
file: lib/Bio/Graphics/Browser2/RemoteSet.pm
- version: 0
Bio::Graphics::Browser2::Render:
file: lib/Bio/Graphics/Browser2/Render.pm
- version: 0
Bio::Graphics::Browser2::Render::HTML:
file: lib/Bio/Graphics/Browser2/Render/HTML.pm
- version: 0
Bio::Graphics::Browser2::Render::Login:
file: lib/Bio/Graphics/Browser2/Render/Login.pm
- version: 0
Bio::Graphics::Browser2::Render::Slave:
file: lib/Bio/Graphics/Browser2/Render/Slave.pm
- version: 0
Bio::Graphics::Browser2::Render::Slave::Status:
file: lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
- version: 0
+ Bio::Graphics::Browser2::Render::TrackConfig:
+ file: lib/Bio/Graphics/Browser2/Render/TrackConfig.pm
Bio::Graphics::Browser2::RenderPanels:
file: lib/Bio/Graphics/Browser2/RenderPanels.pm
- version: 0
Bio::Graphics::Browser2::Session:
file: lib/Bio/Graphics/Browser2/Session.pm
- version: 0
Bio::Graphics::Browser2::Shellwords:
file: lib/Bio/Graphics/Browser2/Shellwords.pm
- version: 0
Bio::Graphics::Browser2::SubtrackTable:
file: lib/Bio/Graphics/Browser2/SubtrackTable.pm
- version: 0
Bio::Graphics::Browser2::TrackDumper:
file: lib/Bio/Graphics/Browser2/TrackDumper.pm
- version: 0
Bio::Graphics::Browser2::UserConf:
file: lib/Bio/Graphics/Browser2/UserTracks.pm
- version: 0
Bio::Graphics::Browser2::UserDB:
file: lib/Bio/Graphics/Browser2/UserDB.pm
version: 0.5
Bio::Graphics::Browser2::UserTracks:
file: lib/Bio/Graphics/Browser2/UserTracks.pm
- version: 0
Bio::Graphics::Browser2::UserTracks::Database:
file: lib/Bio/Graphics/Browser2/UserTracks/Database.pm
- version: 0
Bio::Graphics::Browser2::UserTracks::Filesystem:
file: lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
- version: 0
Bio::Graphics::Browser2::Util:
file: lib/Bio/Graphics/Browser2/Util.pm
- version: 0
Bio::Graphics::GBrowseFeature:
file: lib/Bio/Graphics/GBrowseFeature.pm
- version: 0
Bio::Graphics::Karyotype:
file: lib/Bio/Graphics/Karyotype.pm
- version: 0
Bio::Graphics::Wiggle::Loader::Nosample:
file: lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
- version: 0
CGI::Toggle:
file: lib/CGI/Toggle.pm
- version: 0
FakeHomol:
file: lib/Bio/Graphics/Browser2/GFFhelper.pm
- version: 0
LRUCache:
file: lib/Bio/Graphics/Browser2/DataBase.pm
- version: 0
Legacy::DB::SyntenyBlock:
file: lib/Legacy/DB/SyntenyBlock.pm
- version: 0
Legacy::DB::SyntenyIO:
file: lib/Legacy/DB/SyntenyIO.pm
- version: 0
Legacy::Graphics::Browser:
file: lib/Legacy/Graphics/Browser.pm
version: 1.17
@@ -224,19 +165,15 @@ provides:
version: 1.01
Legacy::Graphics::Browser::PageSettings:
file: lib/Legacy/Graphics/Browser/PageSettings.pm
- version: 0
Legacy::Graphics::Browser::Synteny:
file: lib/Legacy/Graphics/Browser/Synteny.pm
version: 0.01
Legacy::Graphics::Browser::Util:
file: lib/Legacy/Graphics/Browser/Util.pm
- version: 0
Legacy::Graphics::BrowserConfig:
file: lib/Legacy/Graphics/Browser.pm
- version: 0
MyFeatureFileLoader:
file: lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
- version: 0
recommends:
Bio::DB::BigFile: 1
Bio::DB::Sam: 1.2
@@ -272,4 +209,4 @@ requires:
perl: 5.008
resources:
license: http://dev.perl.org/licenses/
-version: 2.33
+version: 2.34
View
@@ -1,4 +1,4 @@
-# Note: this file was auto-generated by Module::Build::Compat version 0.3800
+# Note: this file was auto-generated by Module::Build::Compat version 0.3607
require 5.008;
unless (eval "use Module::Build::Compat 0.02; 1" ) {
@@ -2,7 +2,7 @@ package Bio::Graphics::Browser2;
# $Id$
# Globals and utilities for GBrowse and friends
-our $VERSION = '2.33';
+our $VERSION = '2.34';
use strict;
use warnings;

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