Fix SA2.0 (query->select) in galaxy.webapps.base (note)

Also drop unused parameters and logic from select methods in legacy
controller.

lib/galaxy/webapps/base/controller.py

@@ -8,7 +8,10 @@
     Optional,
 )
 
-from sqlalchemy import true
+from sqlalchemy import (
+    select,
+    true,
+)
 from webob.exc import (
     HTTPBadRequest,
     HTTPInternalServerError,
@@ -447,7 +450,7 @@ def _copy_hdca_to_library_folder(self, trans, hda_manager, from_hdca_id: int, fo
         Fetches the collection identified by `from_hcda_id` and dispatches individual collection elements to
         _copy_hda_to_library_folder
         """
-        hdca = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(from_hdca_id)
+        hdca = trans.sa_session.get(trans.app.model.HistoryDatasetCollectionAssociation, from_hdca_id)
         if hdca.collection.collection_type != "list":
             raise exceptions.NotImplemented(
                 "Cannot add nested collections to library. Please flatten your collection first."
@@ -614,85 +617,40 @@ def get_visualization(self, trans, id, check_ownership=True, check_accessible=Fa
         """
         # Load workflow from database
         try:
-            visualization = trans.sa_session.query(trans.model.Visualization).get(trans.security.decode_id(id))
+            visualization = trans.sa_session.get(trans.model.Visualization, trans.security.decode_id(id))
         except TypeError:
             visualization = None
         if not visualization:
             error("Visualization not found")
         else:
             return self.security_check(trans, visualization, check_ownership, check_accessible)
 
-    def get_visualizations_by_user(self, trans, user, order_by=None, query_only=False):
-        """
-        Return query or query results of visualizations filtered by a user.
-
-        Set `order_by` to a column or list of columns to change the order
-        returned. Defaults to `DEFAULT_ORDER_BY`.
-        Set `query_only` to return just the query for further filtering or
-        processing.
-        """
-        # TODO: move into model (as class attr)
-        DEFAULT_ORDER_BY = [model.Visualization.title]
-        if not order_by:
-            order_by = DEFAULT_ORDER_BY
-        if not isinstance(order_by, list):
-            order_by = [order_by]
-        query = trans.sa_session.query(model.Visualization)
-        query = query.filter(model.Visualization.user == user)
-        if order_by:
-            query = query.order_by(*order_by)
-        if query_only:
-            return query
-        return query.all()
-
-    def get_visualizations_shared_with_user(self, trans, user, order_by=None, query_only=False):
-        """
-        Return query or query results for visualizations shared with the given user.
+    def get_visualizations_by_user(self, trans, user):
+        """Return query results of visualizations filtered by a user."""
+        stmt = select(model.Visualization).filter(model.Visualization.user == user).order_by(model.Visualization.title)
+        return trans.sa_session.scalars(stmt).all()
+
+    def get_visualizations_shared_with_user(self, trans, user):
+        """Return query results for visualizations shared with the given user."""
+        # The second `where` clause removes duplicates when a user shares with themselves.
+        stmt = (
+            select(model.Visualization)
+            .join(model.VisualizationUserShareAssociation)
+            .where(model.VisualizationUserShareAssociation.user_id == user.id)
+            .where(model.Visualization.user_id != user.id)
+            .order_by(model.Visualization.title)
+        )
+        return trans.sa_session.scalars(stmt).all()
 
-        Set `order_by` to a column or list of columns to change the order
-        returned. Defaults to `DEFAULT_ORDER_BY`.
-        Set `query_only` to return just the query for further filtering or
-        processing.
+    def get_published_visualizations(self, trans, exclude_user=None):
         """
-        DEFAULT_ORDER_BY = [model.Visualization.title]
-        if not order_by:
-            order_by = DEFAULT_ORDER_BY
-        if not isinstance(order_by, list):
-            order_by = [order_by]
-        query = trans.sa_session.query(model.Visualization).join(model.VisualizationUserShareAssociation)
-        query = query.filter(model.VisualizationUserShareAssociation.user_id == user.id)
-        # remove duplicates when a user shares with themselves?
-        query = query.filter(model.Visualization.user_id != user.id)
-        if order_by:
-            query = query.order_by(*order_by)
-        if query_only:
-            return query
-        return query.all()
-
-    def get_published_visualizations(self, trans, exclude_user=None, order_by=None, query_only=False):
-        """
-        Return query or query results for published visualizations optionally excluding
-        the user in `exclude_user`.
-
-        Set `order_by` to a column or list of columns to change the order
-        returned. Defaults to `DEFAULT_ORDER_BY`.
-        Set `query_only` to return just the query for further filtering or
-        processing.
+        Return query results for published visualizations optionally excluding the user in `exclude_user`.
         """
-        DEFAULT_ORDER_BY = [model.Visualization.title]
-        if not order_by:
-            order_by = DEFAULT_ORDER_BY
-        if not isinstance(order_by, list):
-            order_by = [order_by]
-        query = trans.sa_session.query(model.Visualization)
-        query = query.filter(model.Visualization.published == true())
+        stmt = select(model.Visualization).filter(model.Visualization.published == true())
         if exclude_user:
-            query = query.filter(model.Visualization.user != exclude_user)
-        if order_by:
-            query = query.order_by(*order_by)
-        if query_only:
-            return query
-        return query.all()
+            stmt = stmt.filter(model.Visualization.user != exclude_user)
+        stmt = stmt.order_by(model.Visualization.title)
+        return trans.sa_session.scalars(stmt).all()
 
     # TODO: move into model (to_dict)
     def get_visualization_summary_dict(self, visualization):
@@ -837,7 +795,7 @@ def save_visualization(self, trans, config, type, id=None, title=None, dbkey=Non
             vis = self._create_visualization(trans, title, type, dbkey, slug, annotation)
         else:
             decoded_id = trans.security.decode_id(id)
-            vis = session.query(trans.model.Visualization).get(decoded_id)
+            vis = session.get(trans.model.Visualization, decoded_id)
             # TODO: security check?
 
         # Create new VisualizationRevision that will be attached to the viz
@@ -1071,7 +1029,7 @@ def get_hda(self, trans, dataset_id, check_ownership=True, check_accessible=Fals
             raise HTTPBadRequest(f"Invalid dataset id: {str(dataset_id)}.")
 
         try:
-            data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(int(dataset_id))
+            data = trans.sa_session.get(trans.app.model.HistoryDatasetAssociation, int(dataset_id))
         except Exception:
             raise HTTPBadRequest(f"Invalid dataset id: {str(dataset_id)}.")
 

lib/galaxy/webapps/base/webapp.py

@@ -21,6 +21,7 @@
 from paste.urlmap import URLMap
 from sqlalchemy import (
     and_,
+    select,
     true,
 )
 from sqlalchemy.orm.exc import NoResultFound
@@ -866,13 +867,14 @@ def handle_user_logout(self, logout_all=False):
         self.sa_session.add_all((prev_galaxy_session, self.galaxy_session))
         galaxy_user_id = prev_galaxy_session.user_id
         if logout_all and galaxy_user_id is not None:
-            for other_galaxy_session in self.sa_session.query(self.app.model.GalaxySession).filter(
+            stmt = select(self.app.model.GalaxySession).filter(
                 and_(
-                    self.app.model.GalaxySession.table.c.user_id == galaxy_user_id,
-                    self.app.model.GalaxySession.table.c.is_valid == true(),
-                    self.app.model.GalaxySession.table.c.id != prev_galaxy_session.id,
+                    self.app.model.GalaxySession.user_id == galaxy_user_id,
+                    self.app.model.GalaxySession.is_valid == true(),
+                    self.app.model.GalaxySession.id != prev_galaxy_session.id,
                 )
-            ):
+            )
+            for other_galaxy_session in self.sa_session.scalars(stmt):
                 other_galaxy_session.is_valid = False
                 self.sa_session.add(other_galaxy_session)
         with transaction(self.sa_session):
@@ -933,9 +935,10 @@ def get_or_create_default_history(self):
         # Look for default history that (a) has default name + is not deleted and
         # (b) has no datasets. If suitable history found, use it; otherwise, create
         # new history.
-        unnamed_histories = self.sa_session.query(self.app.model.History).filter_by(
+        stmt = select(self.app.model.History).filter_by(
             user=self.galaxy_session.user, name=self.app.model.History.default_name, deleted=False
         )
+        unnamed_histories = self.sa_session.scalars(stmt)
         default_history = None
         for history in unnamed_histories:
             if history.empty:
@@ -962,12 +965,13 @@ def get_most_recent_history(self):
         if not user:
             return None
         try:
-            recent_history = (
-                self.sa_session.query(self.app.model.History)
+            stmt = (
+                select(self.app.model.History)
                 .filter_by(user=user, deleted=False)
                 .order_by(self.app.model.History.update_time.desc())
-                .first()
+                .limit(1)
             )
+            recent_history = self.sa_session.scalars(stmt).first()
         except NoResultFound:
             return None
         self.set_history(recent_history)