[WIP] Fix SA2.0 (query->select) in webapps.galaxy.services

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

@@ -2,7 +2,10 @@
 
 from dateutil.parser import isoparse
 from markupsafe import escape
-from sqlalchemy import false
+from sqlalchemy import (
+    false,
+    select,
+)
 from sqlalchemy.orm import undefer
 
 from galaxy import (
@@ -372,11 +375,12 @@ def _list_switch(self, trans, histories):
         new_history = histories[0]
         galaxy_session = trans.get_galaxy_session()
         try:
-            association = (
-                trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation)
+            stmt = (
+                select(trans.app.model.GalaxySessionToHistoryAssociation)
                 .filter_by(session_id=galaxy_session.id, history_id=new_history.id)
-                .first()
+                .limit(1)
             )
+            association = trans.sa_session.scalars(stmt).first()
         except Exception:
             association = None
         new_history.add_galaxy_session(galaxy_session, association=association)
@@ -405,11 +409,10 @@ def list_shared(self, trans, **kwargs):
                     # hit if this user isn't having the history shared with her.
                     history = self.history_manager.by_id(self.decode_id(id))
                     # Current user is the user with which the histories were shared
-                    association = (
-                        trans.sa_session.query(trans.app.model.HistoryUserShareAssociation)
-                        .filter_by(user=trans.user, history=history)
-                        .one()
+                    stmt = select(trans.app.model.HistoryUserShareAssociation).filter_by(
+                        user=trans.user, history=history
                     )
+                    association = trans.sa_session.execute(select(stmt)).scalar_one()
                     trans.sa_session.delete(association)
                     with transaction(trans.sa_session):
                         trans.sa_session.commit()
@@ -483,8 +486,13 @@ def display_by_username_and_slug(self, trans, username, slug, **kwargs):
         """
         # Get history.
         session = trans.sa_session
-        user = session.query(model.User).filter_by(username=username).first()
-        history = trans.sa_session.query(model.History).filter_by(user=user, slug=slug, deleted=False).first()
+
+        stmt = select(model.User).filter_by(username=username).limit(1)
+        user = session.scalars(stmt).first()
+
+        stmt = select(model.History).filter_by(user=user, slug=slug, deleted=False).limit(1)
+        history = session.scalars(stmt).first()
+
         if history is None:
             raise web.httpexceptions.HTTPNotFound()
 
@@ -541,9 +549,7 @@ def permissions(self, trans, payload=None, **kwd):
             permissions = {}
             for action_key, action in trans.app.model.Dataset.permitted_actions.items():
                 in_roles = payload.get(action_key) or []
-                in_roles = [
-                    trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in in_roles
-                ]
+                in_roles = [trans.sa_session.get(trans.app.model.Role, trans.security.decode_id(x)) for x in in_roles]
                 permissions[trans.app.security_agent.get_action(action.action)] = in_roles
             trans.app.security_agent.history_set_default_permissions(history, permissions)
             return {"message": "Default history '%s' dataset permissions have been changed." % history.name}