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Merge branch 'release_16.07' into dev

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This commit is contained in:
Nicola Soranzo
2016-09-23 17:54:04 +01:00
parent 51a6d84934 3b3e2e3358
commit 317fb472c9
5 changed files with 10 additions and 8 deletions
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lib/galaxy/webapps/tool_shed/api/repositories.py
+1 -1
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@@ -853,7 +853,7 @@ class RepositoriesController( BaseAPIController ):
else:
metadata_dict[ 'repository_dependencies' ] = []
if metadata.includes_tool_dependencies and recursive:
metadata_dict[ 'tool_dependencies' ] = repository.get_tool_dependencies( changehash )
metadata_dict[ 'tool_dependencies' ] = repository.get_tool_dependencies( self.app, changehash )
else:
metadata_dict[ 'tool_dependencies' ] = {}
if metadata.includes_tools:
lib/galaxy/webapps/tool_shed/controllers/repository.py
+2 -2
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@@ -1465,8 +1465,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
dependencies = repository.get_tool_dependencies( changeset_revision )
if dependencies is not None:
dependencies = repository.get_tool_dependencies( trans.app, changeset_revision )
if len( dependencies ) > 0:
return encoding_util.tool_shed_encode( dependencies )
return ''
lib/galaxy/webapps/tool_shed/model/__init__.py
+5 -3
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@@ -245,11 +245,13 @@ class Repository( object, Dictifiable ):
def get_type_class( self, app ):
return app.repository_types_registry.get_class_by_label( self.type )
def get_tool_dependencies( self, changeset_revision ):
def get_tool_dependencies( self, app, changeset_revision ):
repo = hg.repository( ui.ui(), self.repo_path( app ) )
changeset_revision = metadata_util.get_next_downloadable_changeset_revision( self, repo, changeset_revision )
for downloadable_revision in self.downloadable_revisions:
if downloadable_revision.changeset_revision == changeset_revision:
return downloadable_revision.metadata.get( 'tool_dependencies', [] )
return []
return downloadable_revision.metadata.get( 'tool_dependencies', {} )
return {}
def installable_revisions( self, app, sort_revisions=True ):
return metadata_util.get_metadata_revisions( self,
lib/tool_shed/util/metadata_util.py
+1 -1
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@@ -32,7 +32,7 @@ def get_all_dependencies( app, metadata_entry, processed_dependency_links=[] ):
dependency_dict[ 'tools' ] = dependency_metadata.metadata[ 'tools' ]
dependency_dict[ 'repository_dependencies' ] = []
if dependency_dict['includes_tool_dependencies']:
dependency_dict['tool_dependencies'] = repository.get_tool_dependencies( dependency_dict['changeset_revision'] )
dependency_dict['tool_dependencies'] = repository.get_tool_dependencies( app, dependency_dict['changeset_revision'] )
if dependency_dict['has_repository_dependencies']:
dependency_dict['repository_dependencies'] = get_all_dependencies( app, dependency_metadata, processed_dependency_links )
else:
test/shed_functional/functional/test_1400_review_migration_stages.py
+1 -1
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@@ -29,7 +29,7 @@ class TestToolMigrationStages( ShedTwillTestCase ):
'blast_datatypes', 'bwa_wrappers', 'picard', 'lastz',
'lastz_paired_reads', 'bowtie_color_wrappers', 'bowtie_wrappers',
'xy_plot', 'bam_to_sam' ]
migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8',
migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_a46483351fd0196637614121868fb5c386612b55',
'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0',
'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib',
'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', 'samtools', '0.1.16', 'cufflinks',