Merge pull request #1193 from mvdbeek/gvk_ts_fixes

Add enhancements to the Galaxy repository install process

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -1294,6 +1294,21 @@ class AdminToolshed( AdminGalaxy ):
                 # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't...
                 tool_panel_section_id = str( tool_section.id )
         if tool_shed_repository.status == trans.install_model.ToolShedRepository.installation_status.UNINSTALLED:
+            repository_type = suc.get_repository_type_from_tool_shed(trans.app,
+                                                                     tool_shed_url,
+                                                                     tool_shed_repository.name,
+                                                                     tool_shed_repository.owner)
+            if repository_type == rt_util.TOOL_DEPENDENCY_DEFINITION:
+                # Repositories of type tool_dependency_definition must get the latest
+                # metadata from the Tool Shed since they have only a single installable
+                # revision.
+                raw_text = suc.get_tool_dependency_definition_metadata_from_tool_shed(trans.app,
+                                                                                      tool_shed_url,
+                                                                                      tool_shed_repository.name,
+                                                                                      tool_shed_repository.owner)
+                new_meta = json.loads(raw_text)
+                # Clean up old repository dependency and tool dependency relationships.
+                suc.clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url)
             # The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall
             # so the repository_installation_updater will function.
             tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app,

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

@@ -1681,6 +1681,14 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                      includes_tool_dependencies=includes_tool_dependencies,
                      repo_info_dicts=repo_info_dicts )
 
+    @web.expose
+    def get_repository_type( self, trans, **kwd ):
+        """Given a repository name and owner, return the type."""
+        repository_name = kwd[ 'name' ]
+        repository_owner = kwd[ 'owner' ]
+        repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
+        return str( repository.type )
+
     @web.json
     def get_required_repo_info_dict( self, trans, encoded_str=None ):
         """
@@ -1748,6 +1756,22 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
             return contents
         return ''
 
+    @web.json
+    def get_tool_dependency_definition_metadata( self, trans, **kwd ):
+        """
+        Given a repository name and ownerof a repository whose type is
+        tool_dependency_definition, return the current metadata.
+        """
+        repository_name = kwd[ 'name' ]
+        repository_owner = kwd[ 'owner' ]
+        repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
+        encoded_id = trans.app.security.encode_id( repository.id )
+        repository_tip = repository.tip( trans.app )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
+                                                                                 encoded_id,
+                                                                                 repository_tip )
+        return repository_metadata.metadata
+
     @web.expose
     def get_tool_versions( self, trans, **kwd ):
         """

lib/tool_shed/util/shed_util_common.py

@@ -81,6 +81,59 @@ This message was sent from the Galaxy Tool Shed instance hosted on the server
 """
 
 
+def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owner):
+    """
+    Determine if the relationship between a repository_dependency record
+    associated with a tool_shed_repository record on the Galaxy side
+    can be eliminated.
+    """
+    rd_dict = metadata_dict.get('repository_dependencies', {})
+    rd_tups = rd_dict.get( 'repository_dependencies', [] )
+    for rd_tup in rd_tups:
+        tsu, n, o, none1, none2, none3 = common_util.parse_repository_dependency_tuple(rd_tup)
+        if tsu == tool_shed_url and n == name and o == owner:
+            # The repository dependency is current, so keep it.
+            return False
+    return True
+
+
+def can_eliminate_tool_dependency(metadata_dict, name, type, version):
+    """
+    Determine if the relationship between a tool_dependency record
+    associated with a tool_shed_repository record on the Galaxy side
+    can be eliminated.
+    """
+    td_dict = metadata_dict.get('tool_dependencies', {})
+    for td_key, td_val in td_dict.items():
+        n = td_val.get('name', None)
+        t = td_val.get('type', None)
+        v = td_val.get('version', None)
+        if n == name and t == type and v == version:
+            # The tool dependency is current, so keep it.
+            return False
+    return True
+
+
+def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, tool_shed_url):
+    """
+    Repositories of type tool_dependency_definition allow for defining a
+    package dependency at some point in the change log and then removing the
+    dependency later in the change log.  This function keeps the dependency
+    relationships on the Galaxy side current by deleting database records
+    that defined the now-broken relationships.
+    """
+    for rrda in tool_shed_repository.required_repositories:
+        rd = rrda.repository_dependency
+        r = rd.repository
+        if can_eliminate_repository_dependency(metadata_dict, tool_shed_url, r.name, r.owner):
+            trans.install_model.context.delete(rrda)
+            trans.install_model.context.flush()
+    for td in tool_shed_repository.tool_dependencies:
+        if can_eliminate_tool_dependency(metadata_dict, td.name, td.type, td.version):
+            trans.install_model.context.delete(td)
+            trans.install_model.context.flush()
+
+
 def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url,
                                            metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ):
     """
@@ -298,6 +351,19 @@ def get_latest_downloadable_changeset_revision( app, repository, repo ):
     return hg_util.INITIAL_CHANGELOG_HASH
 
 
+def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url, name, owner ):
+    """
+    Send a request to the tool shed to retrieve the current metadata for a
+    repository of type tool_dependency_definition defined by the combination
+    of a name and owner.
+    """
+    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+    params = dict( name=name, owner=owner )
+    pathspec = [ 'repository', 'get_tool_dependency_definition_metadata' ]
+    metadata = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    return metadata
+
+
 def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ):
     """
     Return the installable changeset_revision in the repository changelog after the changeset to which
@@ -711,6 +777,18 @@ def get_repository_query( app ):
     return query
 
 
+def get_repository_type_from_tool_shed( app, tool_shed_url, name, owner ):
+    """
+    Send a request to the tool shed to retrieve the type for a repository defined by the
+    combination of a name and owner.
+    """
+    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+    params = dict( name=name, owner=owner )
+    pathspec = [ 'repository', 'get_repository_type' ]
+    repository_type = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    return repository_type
+
+
 def get_tool_panel_config_tool_path_install_dir( app, repository ):
     """
     Return shed-related tool panel config, the tool_path configured in it, and the relative path to