Merge branch 'release_16.07' into dev

galaxyproject · Sep 23, 2016 · 317fb47 · 317fb47
2 parents 51a6d84 + 3b3e2e3
commit 317fb47
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 8 deletions.
diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -853,7 +853,7 @@ def metadata( self, trans, id, **kwd ):
             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:

diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1465,8 +1465,8 @@ def get_tool_dependencies( self, trans, **kwd ):
         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 ''
 

diff --git a/lib/galaxy/webapps/tool_shed/model/__init__.py b/lib/galaxy/webapps/tool_shed/model/__init__.py
@@ -245,11 +245,13 @@ def get_repository_dependencies( self, app, changeset, toolshed_url ):
     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,

diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
@@ -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:

diff --git a/test/shed_functional/functional/test_1400_review_migration_stages.py b/test/shed_functional/functional/test_1400_review_migration_stages.py
@@ -29,7 +29,7 @@ def test_0005_load_migration_stages_page( self ):
                                       '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',