Fix typing error: session type

lib/galaxy/celery/base_task.py

@@ -11,7 +11,6 @@ from sqlalchemy import (
 )
 from sqlalchemy.dialects.postgresql import insert as ps_insert
 from sqlalchemy.exc import IntegrityError
-from sqlalchemy.orm import Session
 
 from galaxy.model import CeleryUserRateLimit
 from galaxy.model.base import transaction
@@ -70,7 +69,7 @@ class GalaxyTaskBeforeStartUserRateLimit(GalaxyTaskBeforeStart):
 
     @abstractmethod
     def calculate_task_start_time(
-        self, user_id: int, sa_session: Session, task_interval_secs: float, now: datetime.datetime
+        self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         return now
 
@@ -99,7 +98,7 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     )
 
     def calculate_task_start_time(  # type: ignore
-        self, user_id: int, sa_session: Session, task_interval_secs: float, now: datetime.datetime
+        self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         with transaction(sa_session):
             result = sa_session.execute(
@@ -138,7 +137,7 @@ class GalaxyTaskBeforeStartUserRateLimitStandard(GalaxyTaskBeforeStartUserRateLi
     )
 
     def calculate_task_start_time(
-        self, user_id: int, sa_session: Session, task_interval_secs: float, now: datetime.datetime
+        self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         last_scheduled_time = None
         with transaction(sa_session):

lib/galaxy/managers/dbkeys.py

@@ -14,9 +14,9 @@ from typing import (
 )
 
 from sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy.model import HistoryDatasetAssociation
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.util import (
     galaxy_directory,
     sanitize_lists_to_string,
@@ -166,6 +166,6 @@ class GenomeBuilds:
         return (chrom_info, db_dataset)
 
 
-def get_len_files_by_history(session: Session, history_id: int):
+def get_len_files_by_history(session: galaxy_scoped_session, history_id: int):
     stmt = select(HistoryDatasetAssociation).filter_by(history_id=history_id, extension="len", deleted=False)
     return session.scalars(stmt)

lib/galaxy/managers/group_roles.py

@@ -5,13 +5,13 @@ from typing import (
 )
 
 from sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.model import GroupRoleAssociation
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.structured_app import MinimalManagerApp
 
 log = logging.getLogger(__name__)
@@ -93,7 +93,7 @@ class GroupRolesManager:
             trans.sa_session.commit()
 
 
-def get_group_role(session: Session, group, role) -> Optional[GroupRoleAssociation]:
+def get_group_role(session: galaxy_scoped_session, group, role) -> Optional[GroupRoleAssociation]:
     stmt = (
         select(GroupRoleAssociation).where(GroupRoleAssociation.group == group).where(GroupRoleAssociation.role == role)
     )

lib/galaxy/managers/group_users.py

@@ -5,7 +5,6 @@ from typing import (
 )
 
 from sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import ObjectNotFound
@@ -15,6 +14,7 @@ from galaxy.model import (
     UserGroupAssociation,
 )
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.structured_app import MinimalManagerApp
 
 log = logging.getLogger(__name__)
@@ -96,7 +96,7 @@ class GroupUsersManager:
             trans.sa_session.commit()
 
 
-def get_group_user(session: Session, user, group) -> Optional[UserGroupAssociation]:
+def get_group_user(session: galaxy_scoped_session, user, group) -> Optional[UserGroupAssociation]:
     stmt = (
         select(UserGroupAssociation).where(UserGroupAssociation.user == user).where(UserGroupAssociation.group == group)
     )

lib/galaxy/managers/groups.py

@@ -2,7 +2,6 @@ from sqlalchemy import (
     false,
     select,
 )
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import (
@@ -152,11 +151,11 @@ class GroupsManager:
         return group
 
 
-def get_group_by_name(session: Session, name: str):
+def get_group_by_name(session: galaxy_scoped_session, name: str):
     stmt = select(Group).filter(Group.name == name).limit(1)
     return session.scalars(stmt).first()
 
 
-def get_not_deleted_groups(session: Session):
+def get_not_deleted_groups(session: galaxy_scoped_session):
     stmt = select(Group).where(Group.deleted == false())
     return session.scalars(stmt)

lib/galaxy/managers/jobs.py

@@ -20,10 +20,7 @@ from sqlalchemy import (
     or_,
     true,
 )
-from sqlalchemy.orm import (
-    aliased,
-    Session,
-)
+from sqlalchemy.orm import aliased
 from sqlalchemy.sql import select
 
 from galaxy import model
@@ -1069,7 +1066,7 @@ def summarize_job_outputs(job: model.Job, tool, params):
     return outputs
 
 
-def get_jobs_to_check_at_startup(session: Session, track_jobs_in_database: bool, config):
+def get_jobs_to_check_at_startup(session: galaxy_scoped_session, track_jobs_in_database: bool, config):
     if track_jobs_in_database:
         in_list = (Job.states.QUEUED, Job.states.RUNNING, Job.states.STOPPED)
     else:

lib/galaxy/managers/pages.py

@@ -24,10 +24,7 @@ from sqlalchemy import (
     select,
     true,
 )
-from sqlalchemy.orm import (
-    aliased,
-    Session,
-)
+from sqlalchemy.orm import aliased
 
 from galaxy import (
     exceptions,
@@ -64,6 +61,7 @@ from galaxy.model.index_filter_util import (
     text_column_filter,
 )
 from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.schema import (
     CreatePagePayload,
     PageContentFormat,
@@ -644,12 +642,12 @@ def placeholderRenderForSave(trans: ProvidesHistoryContext, item_class, item_id,
     )
 
 
-def get_page_revision(session: Session, page_id: int):
+def get_page_revision(session: galaxy_scoped_session, page_id: int):
     stmt = select(PageRevision).filter_by(page_id=page_id)
     return session.scalars(stmt)
 
 
-def get_shared_pages(session: Session, user: User):
+def get_shared_pages(session: galaxy_scoped_session, user: User):
     stmt = (
         select(PageUserShareAssociation)
         .where(PageUserShareAssociation.user == user)
@@ -660,12 +658,12 @@ def get_shared_pages(session: Session, user: User):
     return session.scalars(stmt)
 
 
-def get_page(session: Session, user: User, slug: str):
+def get_page(session: galaxy_scoped_session, user: User, slug: str):
     stmt = _build_page_query(select(Page), user, slug)
     return session.scalars(stmt).first()
 
 
-def page_exists(session: Session, user: User, slug: str) -> bool:
+def page_exists(session: galaxy_scoped_session, user: User, slug: str) -> bool:
     stmt = _build_page_query(select(Page.id), user, slug)
     return session.scalars(stmt).first() is not None
 

lib/galaxy/managers/roles.py

@@ -9,10 +9,7 @@ from sqlalchemy import (
     false,
     select,
 )
-from sqlalchemy.orm import (
-    exc as sqlalchemy_exceptions,
-    Session,
-)
+from sqlalchemy.orm import exc as sqlalchemy_exceptions
 
 from galaxy import model
 from galaxy.exceptions import (
@@ -26,6 +23,7 @@ from galaxy.managers import base
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import Role
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.schema import RoleDefinitionModel
 from galaxy.util import unicodify
 
@@ -162,6 +160,6 @@ class RoleManager(base.ModelManager[model.Role]):
         return role
 
 
-def get_roles_by_ids(session: Session, role_ids):
+def get_roles_by_ids(session: galaxy_scoped_session, role_ids):
     stmt = select(Role).where(Role.id.in_(role_ids))
     return session.scalars(stmt).all()

lib/galaxy/managers/users.py

@@ -24,7 +24,6 @@ from sqlalchemy import (
     select,
     true,
 )
-from sqlalchemy.orm import Session
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import (
@@ -46,6 +45,7 @@ from galaxy.model import (
     UserQuotaUsage,
 )
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.security.validate_user_input import (
     VALID_EMAIL_RE,
     validate_email,
@@ -873,7 +873,7 @@ class AdminUserFilterParser(base.ModelFilterParser, deletable.PurgableFiltersMix
         self.fn_filter_parsers.update({})
 
 
-def get_users_by_ids(session: Session, user_ids):
+def get_users_by_ids(session: galaxy_scoped_session, user_ids):
     stmt = select(User).where(User.id.in_(user_ids))
     return session.scalars(stmt).all()
 

lib/galaxy/webapps/galaxy/services/histories.py

@@ -20,7 +20,6 @@ from sqlalchemy import (
     select,
     true,
 )
-from sqlalchemy.orm import Session
 
 from galaxy import (
     exceptions as glx_exceptions,
@@ -45,6 +44,7 @@ from galaxy.managers.notification import NotificationManager
 from galaxy.managers.users import UserManager
 from galaxy.model import HistoryDatasetAssociation
 from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.model.store import payload_to_source_uri
 from galaxy.schema import (
     FilterQueryParams,
@@ -820,7 +820,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
         return None
 
 
-def get_fasta_hdas_by_history(session: Session, history_id: int):
+def get_fasta_hdas_by_history(session: galaxy_scoped_session, history_id: int):
     stmt = (
         select(HistoryDatasetAssociation)
         .filter_by(history_id=history_id, extension="fasta", deleted=False)

lib/galaxy/webapps/galaxy/services/quotas.py

@@ -6,7 +6,6 @@ from sqlalchemy import (
     select,
     true,
 )
-from sqlalchemy.orm import Session
 
 from galaxy import util
 from galaxy.managers.context import ProvidesUserContext
@@ -14,6 +13,7 @@ from galaxy.managers.groups import get_group_by_name
 from galaxy.managers.quotas import QuotaManager
 from galaxy.managers.users import get_user_by_email
 from galaxy.model import Quota
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.quota._schema import (
     CreateQuotaParams,
     CreateQuotaResult,
@@ -161,7 +161,7 @@ class QuotasService(ServiceBase):
         payload["in_groups"] = list(map(str, new_in_groups))
 
 
-def get_quotas(session: Session, deleted: bool = False):
+def get_quotas(session: galaxy_scoped_session, deleted: bool = False):
     is_deleted = true()
     if not deleted:
         is_deleted = false()