History contents manager: improve contents query

Serializers in the index_v2 of history_contents were re-
querying the database for mapped model attributes.

- eagerload collection on hdcas
- undefer _metadata on hdas
- eaglerload tags and annotations for both
- rework annotatable manager mixin to cycle through annotations
bypassing the get_item_annotation_str call (which would bypass
item.annotations even if already loaded)

Anecdotally provides significant speed up.

lib/galaxy/managers/annotatable.py

@@ -6,6 +6,18 @@ import logging
 log = logging.getLogger( __name__ )
 
 
+# needed to extract this for use in manager *and* serializer, ideally, would use self.manager.annotation
+# from serializer, but history_contents has no self.manager
+# TODO: fix
+def _match_by_user( item, user ):
+    if not user:
+        return None
+    for annotation in item.annotations:
+        if annotation.user_id == user.id:
+            return annotation.annotation
+    return None
+
+
 class AnnotatableManagerMixin( object ):
     #: class of AnnotationAssociation (e.g. HistoryAnnotationAssociation)
     annotation_assoc = None
@@ -36,7 +48,7 @@ class AnnotatableManagerMixin( object ):
         return annotation_obj
 
     def _user_annotation( self, item, user ):
-        return item.get_item_annotation_str( self.session(), user, item )
+        return _match_by_user( item, user )
 
     def _delete_annotation( self, item, user, flush=True ):
         returned = item.delete_item_annotation( self.session(), user, item )
@@ -54,10 +66,8 @@ class AnnotatableSerializerMixin( object ):
         """
         Get and serialize an `item`'s annotation.
         """
-        # user = item.user
-        sa_session = self.app.model.context
-        returned = item.get_item_annotation_str( sa_session, user, item )
-        return returned
+        annotation = _match_by_user( item, user )
+        return annotation.strip() if annotation else None
 
 
 class AnnotatableDeserializerMixin( object ):
@@ -81,12 +91,7 @@ class AnnotatableFilterMixin( object ):
         """
         Get the annotation by the item's owner.
         """
-        if not item.user:
-            return None
-        for annotation in item.annotations:
-            if annotation.user == item.user:
-                return annotation.annotation
-        return None
+        return _match_by_user( item, item.user )
 
     def filter_annotation_contains( self, item, val ):
         """

lib/galaxy/managers/history_contents.py

@@ -8,6 +8,8 @@ from sqlalchemy import sql
 from sqlalchemy import asc, desc
 from sqlalchemy import true, false
 from sqlalchemy import func
+from sqlalchemy.orm import eagerload
+from sqlalchemy.orm import undefer
 
 from galaxy import model
 from galaxy import exceptions as glx_exceptions
@@ -207,8 +209,10 @@ class HistoryContentsManager( containers.ContainerManagerMixin ):
                 raise TypeError( 'Unknown contents type:', result_type )
 
         # query 2 & 3: use the ids to query each component_class, returning an id->full component model map
-        id_map[ self.contained_class_type_name ] = self._by_ids( self.contained_class, id_map[ self.contained_class_type_name ] )
-        id_map[ self.subcontainer_class_type_name ] = self._by_ids( self.subcontainer_class, id_map[ self.subcontainer_class_type_name ] )
+        contained_ids = id_map[ self.contained_class_type_name ]
+        id_map[ self.contained_class_type_name ] = self._contained_id_map( contained_ids )
+        subcontainer_ids = id_map[ self.subcontainer_class_type_name ]
+        id_map[ self.subcontainer_class_type_name ] = self._subcontainer_id_map( subcontainer_ids )
 
         # cycle back over the union query to create an ordered list of the objects returned in queries 2 & 3 above
         contents = []
@@ -310,10 +314,28 @@ class HistoryContentsManager( containers.ContainerManagerMixin ):
         """Return the id for this row in the union results"""
         return union[ 2 ]
 
-    def _by_ids( self, component_class, id_list ):
+    def _contained_id_map( self, id_list ):
+        """Return an id to model map of all contained-type models in the id_list."""
         if not id_list:
             return []
-        query = self._session().query( component_class ).filter( component_class.id.in_( id_list ) )
+        component_class = self.contained_class
+        query = ( self._session().query( component_class )
+            .filter( component_class.id.in_( id_list ) )
+            .options( undefer( '_metadata' ) )
+            .options( eagerload( 'tags' ) )
+            .options( eagerload( 'annotations' ) ) )
+        return dict( ( row.id, row ) for row in query.all() )
+
+    def _subcontainer_id_map( self, id_list ):
+        """Return an id to model map of all subcontainer-type models in the id_list."""
+        if not id_list:
+            return []
+        component_class = self.subcontainer_class
+        query = ( self._session().query( component_class )
+            .filter( component_class.id.in_( id_list ) )
+            .options( eagerload( 'collection' ) )
+            .options( eagerload( 'tags' ) )
+            .options( eagerload( 'annotations' ) ) )
         return dict( ( row.id, row ) for row in query.all() )