Merge pull request #5514 from jmchilton/optimize_public_grids

[18.01] Optimize public grid database interactions.

lib/galaxy/model/mapping.py

@@ -1570,7 +1570,11 @@ def simple_mapping(model, **kwds):
         backref="histories"),
     ratings=relation(model.HistoryRatingAssociation,
         order_by=model.HistoryRatingAssociation.table.c.id,
-        backref="histories")
+        backref="histories"),
+    average_rating=column_property(
+        select([func.avg(model.HistoryRatingAssociation.table.c.rating)]).where(model.HistoryRatingAssociation.table.c.history_id == model.History.table.c.id),
+        deferred=True
+    )
 ))
 
 # Set up proxy so that
@@ -2184,7 +2188,11 @@ def simple_mapping(model, **kwds):
         backref="stored_workflows"),
     ratings=relation(model.StoredWorkflowRatingAssociation,
         order_by=model.StoredWorkflowRatingAssociation.table.c.id,
-        backref="stored_workflows")
+        backref="stored_workflows"),
+    average_rating=column_property(
+        select([func.avg(model.StoredWorkflowRatingAssociation.table.c.rating)]).where(model.StoredWorkflowRatingAssociation.table.c.stored_workflow_id == model.StoredWorkflow.table.c.id),
+        deferred=True
+    )
 ))
 
 # Set up proxy so that
@@ -2316,7 +2324,11 @@ def simple_mapping(model, **kwds):
         backref="pages"),
     ratings=relation(model.PageRatingAssociation,
         order_by=model.PageRatingAssociation.table.c.id,
-        backref="pages")
+        backref="pages"),
+    average_rating=column_property(
+        select([func.avg(model.PageRatingAssociation.table.c.rating)]).where(model.PageRatingAssociation.table.c.page_id == model.Page.table.c.id),
+        deferred=True
+    )
 ))
 
 # Set up proxy so that
@@ -2348,7 +2360,11 @@ def simple_mapping(model, **kwds):
         backref="visualizations"),
     ratings=relation(model.VisualizationRatingAssociation,
         order_by=model.VisualizationRatingAssociation.table.c.id,
-        backref="visualizations")
+        backref="visualizations"),
+    average_rating=column_property(
+        select([func.avg(model.VisualizationRatingAssociation.table.c.rating)]).where(model.VisualizationRatingAssociation.table.c.visualization_id == model.Visualization.table.c.id),
+        deferred=True
+    )
 ))
 
 # Set up proxy so that

lib/galaxy/web/framework/helpers/grids.py

@@ -573,7 +573,12 @@ class CommunityRatingColumn(GridColumn, UsesItemRatings):
     """ Column that displays community ratings for an item. """
 
     def get_value(self, trans, grid, item):
-        ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, item, webapp_model=trans.model)
+        if not hasattr(item, "average_rating"):
+            # No prefetched column property, generate it on the fly.
+            ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, item, webapp_model=trans.model)
+        else:
+            ave_item_rating = item.average_rating
+            num_ratings = 2  # just used for pluralization
         return trans.fill_template("tool_shed_rating.mako",
                                    ave_item_rating=ave_item_rating,
                                    num_ratings=num_ratings,

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -5,7 +5,7 @@
 from six import string_types
 from six.moves.urllib.parse import unquote_plus
 from sqlalchemy import and_, false, func, null, true
-from sqlalchemy.orm import eagerload, eagerload_all
+from sqlalchemy.orm import eagerload, eagerload_all, undefer
 
 import galaxy.util
 from galaxy import exceptions
@@ -209,8 +209,20 @@ class NameURLColumn(grids.PublicURLColumn, NameColumn):
     operations = []
 
     def build_initial_query(self, trans, **kwargs):
-        # Join so that searching history.user makes sense.
-        return trans.sa_session.query(self.model_class).join(model.User.table)
+        # TODO: Tags are still loaded one at a time, consider doing this all at once:
+        # - eagerload would keep everything in one query but would explode the number of rows and potentially
+        #   result in unneeded info transferred over the wire.
+        # - subqueryload("tags").subqueryload("tag") would probably be better under postgres but I'd
+        #   like some performance data against a big database first - might cause problems?
+
+        # - Pull down only username from associated User table since that is all that is used
+        #   (can be used during search). Need join in addition to the eagerload since it is used in
+        #   the .count() query which doesn't respect the eagerload options  (could eliminate this with #5523).
+        # - Undefer average_rating column to prevent loading individual ratings per-history.
+        # - Eager load annotations - this causes a left join which might be inefficient if there were
+        #   potentially many items per history (like if joining HDAs for instance) but there should only
+        #   be at most one so this is fine.
+        return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
 
     def apply_query_filter(self, trans, query, **kwargs):
         # A public history is published, has a slug, and is not deleted.

lib/galaxy/webapps/galaxy/controllers/page.py

@@ -2,6 +2,7 @@
 
 from markupsafe import escape
 from sqlalchemy import and_, desc, false, true
+from sqlalchemy.orm import eagerload, undefer
 
 from galaxy import managers, model, util, web
 from galaxy.model.item_attrs import UsesItemRatings
@@ -82,8 +83,8 @@ class PageAllPublishedGrid(grids.Grid):
     )
 
     def build_initial_query(self, trans, **kwargs):
-        # Join so that searching history.user makes sense.
-        return trans.sa_session.query(self.model_class).join(model.User.table)
+        # See optimization description comments and TODO for tags in matching public histories query.
+        return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
 
     def apply_query_filter(self, trans, query, **kwargs):
         return query.filter(self.model_class.deleted == false()).filter(self.model_class.published == true())

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -12,6 +12,7 @@
 )
 from six import string_types
 from sqlalchemy import and_, desc, false, or_, true
+from sqlalchemy.orm import eagerload, undefer
 
 from galaxy import managers, model, util, web
 from galaxy.datatypes.interval import Bed
@@ -212,8 +213,8 @@ class VisualizationAllPublishedGrid(grids.Grid):
     )
 
     def build_initial_query(self, trans, **kwargs):
-        # Join so that searching history.user makes sense.
-        return trans.sa_session.query(self.model_class).join(model.User.table)
+        # See optimization description comments and TODO for tags in matching public histories query.
+        return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
 
     def apply_query_filter(self, trans, query, **kwargs):
         return query.filter(self.model_class.deleted == false()).filter(self.model_class.published == true())

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -10,7 +10,7 @@
 from markupsafe import escape
 from six.moves.http_client import HTTPConnection
 from sqlalchemy import and_
-from sqlalchemy.orm import joinedload
+from sqlalchemy.orm import eagerload, joinedload, lazyload, undefer
 from sqlalchemy.sql import expression
 
 from galaxy import (
@@ -138,8 +138,10 @@ class StoredWorkflowAllPublishedGrid(grids.Grid):
     ]
 
     def build_initial_query(self, trans, **kwargs):
-        # Join so that searching stored_workflow.user makes sense.
-        return trans.sa_session.query(self.model_class).join(model.User.table)
+        # See optimization description comments and TODO for tags in matching public histories query.
+        # In addition to that - be sure to lazyload the latest_workflow - it isn't needed and it causes all
+        # of its steps to be eagerly loaded.
+        return trans.sa_session.query(self.model_class).join("user").options(lazyload("latest_workflow"), eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
 
     def apply_query_filter(self, trans, query, **kwargs):
         # A public workflow is published, has a slug, and is not deleted.