From 0e4df328e21f52e61f7dc698ac408215ba97292d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 20 Sep 2023 15:25:28 -0400
Subject: [PATCH] Fix SA2.0 ORM usage in managers.groups

Move data access method to managers.users
---
 lib/galaxy/managers/groups.py | 34 ++++++++++++++++++++++++++--------
 lib/galaxy/managers/users.py  | 11 ++++++++++-
 2 files changed, 36 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index 2fc03d42738a..374428c979f1 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -4,7 +4,11 @@
     List,
 )
 
-from sqlalchemy import false
+from sqlalchemy import (
+    false,
+    select,
+)
+from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import (
@@ -14,6 +18,11 @@
 )
 from galaxy.managers.base import decode_id
 from galaxy.managers.context import ProvidesAppContext
+from galaxy.managers.users import get_users_by_ids
+from galaxy.model import (
+    Group,
+    Role,
+)
 from galaxy.model.base import transaction
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.fields import (
@@ -35,7 +44,7 @@ def index(self, trans: ProvidesAppContext):
         Displays a collection (list) of groups.
         """
         rval = []
-        for group in trans.sa_session.query(model.Group).filter(model.Group.deleted == false()):
+        for group in get_not_deleted_groups(trans.sa_session):
             item = group.to_dict(value_mapper={"id": DecodedDatabaseIdField.encode})
             encoded_id = DecodedDatabaseIdField.encode(group.id)
             item["url"] = url_for("group", id=encoded_id)
@@ -101,11 +110,11 @@ def update(self, trans: ProvidesAppContext, group_id: int, payload: Dict[str, An
             sa_session.commit()
 
     def _check_duplicated_group_name(self, sa_session: galaxy_scoped_session, group_name: str) -> None:
-        if sa_session.query(model.Group).filter(model.Group.name == group_name).first():
+        if get_group_by_name(sa_session, group_name):
             raise Conflict(f"A group with name '{group_name}' already exists")
 
     def _get_group(self, sa_session: galaxy_scoped_session, group_id: int) -> model.Group:
-        group = sa_session.query(model.Group).get(group_id)
+        group = sa_session.get(model.Group, group_id)
         if group is None:
             raise ObjectNotFound("Group with the provided id was not found.")
         return group
@@ -114,18 +123,27 @@ def _get_users_by_encoded_ids(
         self, sa_session: galaxy_scoped_session, encoded_user_ids: List[EncodedDatabaseIdField]
     ) -> List[model.User]:
         user_ids = self._decode_ids(encoded_user_ids)
-        users = sa_session.query(model.User).filter(model.User.table.c.id.in_(user_ids)).all()
-        return users
+        return get_users_by_ids(sa_session, user_ids)
 
     def _get_roles_by_encoded_ids(
         self, sa_session: galaxy_scoped_session, encoded_role_ids: List[EncodedDatabaseIdField]
     ) -> List[model.Role]:
         role_ids = self._decode_ids(encoded_role_ids)
-        roles = sa_session.query(model.Role).filter(model.Role.id.in_(role_ids)).all()
-        return roles
+        stmt = select(Role).where(Role.id.in_(role_ids))
+        return sa_session.scalars(stmt).all()
 
     def _decode_id(self, encoded_id: EncodedDatabaseIdField) -> int:
         return decode_id(self._app, encoded_id)
 
     def _decode_ids(self, encoded_ids: List[EncodedDatabaseIdField]) -> List[int]:
         return [self._decode_id(encoded_id) for encoded_id in encoded_ids]
+
+
+def get_group_by_name(session: Session, name: str):
+    stmt = select(Group).filter(Group.name == name).limit(1)
+    return session.scalars(stmt).first()
+
+
+def get_not_deleted_groups(session: Session):
+    stmt = select(Group).where(Group.deleted == false())
+    return session.scalars(stmt)
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 4489a00689e6..dedc1d5ef90d 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -23,6 +23,7 @@
     select,
     true,
 )
+from sqlalchemy.orm import Session
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import (
@@ -36,7 +37,10 @@
     base,
     deletable,
 )
-from galaxy.model import UserQuotaUsage
+from galaxy.model import (
+    User,
+    UserQuotaUsage,
+)
 from galaxy.model.base import transaction
 from galaxy.security.validate_user_input import (
     VALID_EMAIL_RE,
@@ -850,3 +854,8 @@ def get_user_by_username(session, user_class, username):
         return session.execute(stmt).scalar_one()
     except Exception:
         return None
+
+
+def get_users_by_ids(session: Session, user_ids):
+    stmt = select(User).where(User.id.in_(user_ids))
+    return session.scalars(stmt).all()