From 248b8bb90e2fcfca6abb19768da645383257dd0d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 6 Oct 2023 10:17:58 -0400
Subject: [PATCH] SA2.0: Replacde flush with commit

---
 lib/tool_shed/webapp/api2/__init__.py     |  4 +++-
 lib/tool_shed/webapp/api2/repositories.py | 13 +++++++++----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/lib/tool_shed/webapp/api2/__init__.py b/lib/tool_shed/webapp/api2/__init__.py
index 6961c8407b93..3630038280f3 100644
--- a/lib/tool_shed/webapp/api2/__init__.py
+++ b/lib/tool_shed/webapp/api2/__init__.py
@@ -29,6 +29,7 @@
 from galaxy.exceptions import AdminRequiredException
 from galaxy.managers.session import GalaxySessionManager
 from galaxy.managers.users import UserManager
+from galaxy.model.base import transaction
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import unicodify
 from galaxy.web.framework.decorators import require_admin_message
@@ -331,7 +332,8 @@ def ensure_valid_session(trans: SessionRequestContext) -> None:
         #        be needed.
         if prev_galaxy_session:
             sa_session.add(prev_galaxy_session)
-        sa_session.flush()
+        with transaction(sa_session):
+            sa_session.commit()
 
 
 def set_auth_cookie(trans: SessionRequestContext, session):
diff --git a/lib/tool_shed/webapp/api2/repositories.py b/lib/tool_shed/webapp/api2/repositories.py
index 776e4064a7ab..4c809e2c1cec 100644
--- a/lib/tool_shed/webapp/api2/repositories.py
+++ b/lib/tool_shed/webapp/api2/repositories.py
@@ -20,6 +20,7 @@
 from starlette.datastructures import UploadFile as StarletteUploadFile
 
 from galaxy.exceptions import InsufficientPermissionsException
+from galaxy.model.base import transaction
 from galaxy.webapps.galaxy.api import as_form
 from tool_shed.context import SessionRequestContext
 from tool_shed.managers.repositories import (
@@ -357,7 +358,8 @@ def set_malicious(
         repository_metadata = get_repository_metadata_for_management(trans, encoded_repository_id, changeset_revision)
         repository_metadata.malicious = True
         trans.sa_session.add(repository_metadata)
-        trans.sa_session.flush()
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.delete(
@@ -374,7 +376,8 @@ def unset_malicious(
         repository_metadata = get_repository_metadata_for_management(trans, encoded_repository_id, changeset_revision)
         repository_metadata.malicious = False
         trans.sa_session.add(repository_metadata)
-        trans.sa_session.flush()
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.put(
@@ -392,7 +395,8 @@ def set_deprecated(
             raise InsufficientPermissionsException("You do not have permission to update this repository.")
         repository.deprecated = True
         trans.sa_session.add(repository)
-        trans.sa_session.flush()
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.delete(
@@ -410,7 +414,8 @@ def unset_deprecated(
             raise InsufficientPermissionsException("You do not have permission to update this repository.")
         repository.deprecated = False
         trans.sa_session.add(repository)
-        trans.sa_session.flush()
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.delete(