Fix for installing a repository from the tool shed that includes a repository dependency defintion where the required repository is owned by a user other than the dependent repository.

lib/galaxy/util/shed_util.py

@@ -720,7 +720,11 @@ def get_installed_and_missing_repository_dependencies_for_new_install( trans, re
             for rd_tup in rd_tups:
                 tool_shed, name, owner, changeset_revision = rd_tup
                 # Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists.
-                repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, repo_info_tuple )
+                # We need to create a temporary repo_info_tuple that includes the correct repository owner which we get from the current rd_tup.  The current
+                # tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td )
+                tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup )
+                tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None )
+                repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple )
                 if repository:
                     new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ]
                     if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED:

lib/galaxy/util/shed_util_common.py

@@ -1068,6 +1068,12 @@ def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
         return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name )
     else:
         return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name )
+def generate_clone_url_from_repo_info_tup( repo_info_tup ):
+    """Generate teh URL for cloning a repositoyr given a tuple of toolshed, name, owner, changeset_revision."""
+    # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab']
+    toolshed, name, owner, changeset_revision = repo_info_tup
+    # Don't include the changeset_revision in clone urls.
+    return url_join( toolshed, 'repos', owner, name )
 def generate_data_manager_metadata( app, repository, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ):
     """Update the received metadata_dict with information from the parsed data_manager_config_filename."""
     if data_manager_config_filename is None:

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

@@ -1472,12 +1472,15 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
             repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
             repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
             metadata = repository_metadata.metadata
-            if not includes_tools and 'tools' in metadata:
-                includes_tools = True
-            if not has_repository_dependencies and 'repository_dependencies' in metadata:
-                has_repository_dependencies = True
-            if not includes_tool_dependencies and 'tool_dependencies' in metadata:
-                includes_tool_dependencies = True
+            if not includes_tools:
+                if 'tools' in metadata:
+                    includes_tools = True
+            if not has_repository_dependencies:
+                if 'repository_dependencies' in metadata:
+                    has_repository_dependencies = True
+            if not includes_tool_dependencies:
+                if 'tool_dependencies' in metadata:
+                    includes_tool_dependencies = True
             repo_dir = repository.repo_path( trans.app )
             repo = hg.repository( suc.get_configured_ui(), repo_dir )
             ctx = suc.get_changectx_for_changeset( repo, changeset_revision )