From 194f5ad5df3e606a01addf7d8de249f1d51ef2eb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 14 Nov 2023 09:56:13 +0100
Subject: [PATCH] Use sqlalchemy 2.0 query syntax

---
 lib/galaxy/jobs/handler.py   | 14 ++++++--------
 lib/galaxy/model/__init__.py | 11 ++++++-----
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 977293cb2117..359fdeddfc89 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -125,22 +125,20 @@ def __init__(
 
     def setup_query(self):
         if self.grab_model is model.Job:
-            grab_condition = self.grab_model.table.c.state == self.grab_model.states.NEW
+            grab_condition = self.grab_model.state == self.grab_model.states.NEW
         elif self.grab_model is model.WorkflowInvocation:
-            grab_condition = self.grab_model.table.c.state.in_(
-                (self.grab_model.states.NEW, self.grab_model.states.CANCELLING)
-            )
+            grab_condition = self.grab_model.state.in_((self.grab_model.states.NEW, self.grab_model.states.CANCELLING))
         else:
             raise NotImplementedError(f"Grabbing {self.grab_model.__name__} not implemented")
         subq = (
             select(self.grab_model.id)
             .where(
                 and_(
-                    self.grab_model.table.c.handler.in_(self.self_handler_tags),
+                    self.grab_model.handler.in_(self.self_handler_tags),
                     grab_condition,
                 )
             )
-            .order_by(self.grab_model.table.c.id)
+            .order_by(self.grab_model.id)
         )
         if self.max_grab:
             subq = subq.limit(self.max_grab)
@@ -148,11 +146,11 @@ def setup_query(self):
             subq = subq.with_for_update(skip_locked=True)
         self._grab_query = (
             self.grab_model.table.update()
-            .where(self.grab_model.table.c.id.in_(subq))
+            .where(self.grab_model.id.in_(subq))
             .values(handler=self.app.config.server_name)
         )
         if self._supports_returning:
-            self._grab_query = self._grab_query.returning(self.grab_model.table.c.id)
+            self._grab_query = self._grab_query.returning(self.grab_model.id)
         if self.handler_assignment_method == HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION:
             self._grab_conn_opts["isolation_level"] = "SERIALIZABLE"
         log.info(
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index ac2abf82df32..3c19fe0384a6 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1644,7 +1644,7 @@ def set_state(self, state: JobState) -> bool:
             # generate statement that will not revert DELETING or DELETED back to anything non-terminal
             rval = session.execute(
                 update(Job.table)
-                .where(Job.table.c.id == self.id, ~Job.table.c.state.in_((Job.states.DELETING, Job.states.DELETED)))
+                .where(Job.id == self.id, ~Job.state.in_((Job.states.DELETING, Job.states.DELETED)))
                 .values(state=state)
             )
             if rval.rowcount == 1:
@@ -8226,25 +8226,26 @@ def cancel(self):
 
     def cancel_invocation_steps(self):
         sa_session = object_session(self)
+        assert sa_session
         job_subq = (
-            sa_session.query(Job.id)
+            select(Job.id)
             .join(WorkflowInvocationStep)
             .filter(WorkflowInvocationStep.workflow_invocation_id == self.id)
-            .filter(~Job.table.c.state.in_(Job.finished_states))
+            .filter(~Job.state.in_(Job.finished_states))
             .with_for_update()
             .scalar_subquery()
         )
         sa_session.execute(update(Job.table).where(Job.id == job_subq).values({"state": Job.states.DELETING}))
 
         job_collection_subq = (
-            sa_session.query(Job.id)
+            select(Job.id)
             .join(ImplicitCollectionJobsJobAssociation)
             .join(ImplicitCollectionJobs)
             .join(
                 WorkflowInvocationStep, WorkflowInvocationStep.implicit_collection_jobs_id == ImplicitCollectionJobs.id
             )
             .filter(WorkflowInvocationStep.workflow_invocation_id == self.id)
-            .filter(~Job.table.c.state.in_(Job.finished_states))
+            .filter(~Job.state.in_(Job.finished_states))
             .with_for_update()
             .subquery()
         )