Fix SA2.0 (query->select) in galaxy.workflow

jdavcs · Aug 10, 2023 · 8f063d3 · 8f063d3
1 parent 39c5465
commit 8f063d3
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Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
@@ -370,26 +370,22 @@ def build_workflow_run_configs(
             input_id = input_dict["id"]
             try:
                 if input_source == "ldda":
-                    ldda = trans.sa_session.query(LibraryDatasetDatasetAssociation).get(
-                        trans.security.decode_id(input_id)
-                    )
+                    ldda = trans.sa_session.get(LibraryDatasetDatasetAssociation, trans.security.decode_id(input_id))
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                         trans.get_current_user_roles(), ldda.dataset
                     )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
                 elif input_source == "ld":
-                    ldda = (
-                        trans.sa_session.query(LibraryDataset)
-                        .get(trans.security.decode_id(input_id))
-                        .library_dataset_dataset_association
-                    )
+                    ldda = trans.sa_session.get(
+                        LibraryDataset, trans.security.decode_id(input_id)
+                    ).library_dataset_dataset_association
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                         trans.get_current_user_roles(), ldda.dataset
                     )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
                 elif input_source == "hda":
                     # Get dataset handle, add to dict and history if necessary
-                    content = trans.sa_session.query(HistoryDatasetAssociation).get(trans.security.decode_id(input_id))
+                    content = trans.sa_session.get(HistoryDatasetAssociation, trans.security.decode_id(input_id))
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                         trans.get_current_user_roles(), content.dataset
                     )

diff --git a/lib/galaxy/workflow/scheduling_manager.py b/lib/galaxy/workflow/scheduling_manager.py
@@ -79,12 +79,12 @@ def __startup_recovery(self):
             log.info(
                 "(%s) Handler unassigned at startup, resubmitting workflow invocation for assignment", invocation_id
             )
-            workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id)
+            workflow_invocation = sa_session.get(model.WorkflowInvocation, invocation_id)
             self._assign_handler(workflow_invocation)
 
     def _handle_setup_msg(self, workflow_invocation_id=None):
         sa_session = self.app.model.context
-        workflow_invocation = sa_session.query(model.WorkflowInvocation).get(workflow_invocation_id)
+        workflow_invocation = sa_session.get(model.WorkflowInvocation, workflow_invocation_id)
         if workflow_invocation.handler is None:
             workflow_invocation.handler = self.app.config.server_name
             sa_session.add(workflow_invocation)