[16.07] Fix tool dependencies handling in Tool Shed model (#2950)

* Fix the cause of toolshed test 1400 failing.

* Fix handling of repositories without tool dependencies.

* Fix tool dependency retrieval.

In some cases, a process might attempt to fetch tool dependencies for revision
1:7334f6d0ac17, but the repository has been updated, and tool dependency
metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves
that issue.

* Correct the logic that returns an empty string for an empty dict.

* Fix getting latest revision with tool dependencies.

* Use self.app instead of trans.app

Conflicts:
	lib/galaxy/webapps/tool_shed/controllers/repository.py

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -782,7 +782,7 @@ 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:

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -1713,8 +1713,8 @@ def get_tool_dependencies( self, trans, **kwd ):
         owner = kwd.get( 'owner', None )
         changeset_revision = kwd.get( 'changeset_revision', None )
         repository = suc.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

@@ -244,11 +244,13 @@ 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 suc.get_metadata_revisions( self,

lib/tool_shed/util/metadata_util.py

@@ -26,7 +26,7 @@ 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: