UsesHDA: fix new-style display apps; documentation

lib/galaxy/web/base/controller.py

@@ -332,6 +332,8 @@ class UsesHistoryDatasetAssociationMixin:
         return None
 
     def get_hda_dict( self, trans, hda ):
+        """Return full details of this HDA in dictionary form.
+        """
         hda_dict = hda.get_api_value( view='element' )
         history = hda.history
         hda_dict[ 'api_type' ] = "file"
@@ -341,9 +343,10 @@ class UsesHistoryDatasetAssociationMixin:
         can_access_hda = ( trans.user_is_admin() or can_access_hda )
         hda_dict[ 'accessible' ] = can_access_hda
 
-        # return here if deleted and purged or can't access
+        # ---- return here if deleted AND purged OR can't access
         purged = ( hda.purged or hda.dataset.purged )
         if ( hda.deleted and purged ) or not can_access_hda:
+            #TODO: get_api_value should really go AFTER this - only summary data
             return trans.security.encode_dict_ids( hda_dict )
 
         if trans.user_is_admin() or trans.app.config.expose_dataset_path:
@@ -353,6 +356,7 @@ class UsesHistoryDatasetAssociationMixin:
             history_id = trans.security.encode_id( history.id ),
             history_content_id = trans.security.encode_id( hda.id ) )
 
+        # indeces, assoc. metadata files, etc.
         meta_files = []
         for meta_type in hda.metadata.spec.keys():
             if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ):
@@ -361,13 +365,15 @@ class UsesHistoryDatasetAssociationMixin:
             hda_dict[ 'meta_files' ] = meta_files
 
         hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda )
-        #hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
+        hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
         hda_dict[ 'visualizations' ] = hda.get_visualizations()
 
-        # return here if deleted
+        # ---- return here if deleted
         if hda.deleted and not purged:
             return trans.security.encode_dict_ids( hda_dict )
 
+        # if a tool declares 'force_history_refresh' in its xml, when the hda -> ready, reload the history panel
+        # expensive
         if( ( hda.state in [ 'running', 'queued' ] )
         and ( hda.creating_job and hda.creating_job.tool_id ) ):
             tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id )
@@ -383,7 +389,6 @@ class UsesHistoryDatasetAssociationMixin:
         def get_display_app_url( display_app_link, hda, trans ):
             web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ )
             dataset_hash, user_hash = da_util.encode_dataset_user( trans, hda, None )
-            return ''
             return web_url_for( controller='dataset',
                             action="display_application",
                             dataset_id=dataset_hash,