SQLAlchemy 2.0

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -125,7 +125,7 @@ def __init__(self, config=None, **kwargs) -> None:
         self[ShortTermStorageMonitor] = sts_manager  # type: ignore[type-abstract]
         self[galaxy_scoped_session] = self.model.context
         self.visualizations_registry = MockVisualizationsRegistry()
-        self.tag_handler = tags.GalaxyTagHandler(self.model.context)
+        self.tag_handler = tags.GalaxyTagHandler(self.model.session)
         self[tags.GalaxyTagHandler] = self.tag_handler
         self.quota_agent = quota.DatabaseQuotaAgent(self.model)
         self.job_config = Bunch(

lib/galaxy/celery/base_task.py

@@ -11,7 +11,6 @@
 )
 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 @@ def __call__(self, task: Task, task_id, args, kwargs):
 
     @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
 
@@ -81,38 +80,28 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     We take advantage of efficiencies in its dialect.
     """
 
-    _update_stmt = (
-        update(CeleryUserRateLimit)
-        .where(CeleryUserRateLimit.user_id == bindparam("userid"))
-        .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
-        .returning(CeleryUserRateLimit.last_scheduled_time)
-    )
-
-    _insert_stmt = (
-        ps_insert(CeleryUserRateLimit)
-        .values(user_id=bindparam("userid"), last_scheduled_time=bindparam("now"))
-        .returning(CeleryUserRateLimit.last_scheduled_time)
-    )
-
-    _upsert_stmt = _insert_stmt.on_conflict_do_update(
-        index_elements=["user_id"], set_=dict(last_scheduled_time=bindparam("sched_time"))
-    )
-
     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(
-                self._update_stmt, {"userid": user_id, "interval": task_interval_secs, "now": now}
+            update_stmt = (
+                update(CeleryUserRateLimit)
+                .where(CeleryUserRateLimit.user_id == user_id)
+                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
+                .returning(CeleryUserRateLimit.last_scheduled_time)
             )
-            if result.rowcount == 0:
+            result = sa_session.execute(update_stmt, {"interval": task_interval_secs, "now": now}).all()
+            if not result:
                 sched_time = now + datetime.timedelta(seconds=task_interval_secs)
-                result = sa_session.execute(
-                    self._upsert_stmt, {"userid": user_id, "now": now, "sched_time": sched_time}
+                upsert_stmt = (
+                    ps_insert(CeleryUserRateLimit)  # type:ignore[attr-defined]
+                    .values(user_id=user_id, last_scheduled_time=now)
+                    .returning(CeleryUserRateLimit.last_scheduled_time)
+                    .on_conflict_do_update(index_elements=["user_id"], set_=dict(last_scheduled_time=sched_time))
                 )
-            for row in result:
-                return row[0]
+                result = sa_session.execute(upsert_stmt).all()
             sa_session.commit()
+            return result[0][0]
 
 
 class GalaxyTaskBeforeStartUserRateLimitStandard(GalaxyTaskBeforeStartUserRateLimit):
@@ -138,7 +127,7 @@ 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/celery/tasks.py

@@ -195,7 +195,7 @@ def set_metadata(
     try:
         if overwrite:
             hda_manager.overwrite_metadata(dataset_instance)
-        dataset_instance.datatype.set_meta(dataset_instance)
+        dataset_instance.datatype.set_meta(dataset_instance)  # type:ignore [arg-type]
         dataset_instance.set_peek()
         # Reset SETTING_METADATA state so the dataset instance getter picks the dataset state
         dataset_instance.set_metadata_success_state()
@@ -228,6 +228,7 @@ def setup_fetch_data(
 ):
     tool = cached_create_tool_from_representation(app=app, raw_tool_source=raw_tool_source)
     job = sa_session.get(Job, job_id)
+    assert job
     # self.request.hostname is the actual worker name given by the `-n` argument, not the hostname as you might think.
     job.handler = self.request.hostname
     job.job_runner_name = "celery"
@@ -260,6 +261,7 @@ def finish_job(
 ):
     tool = cached_create_tool_from_representation(app=app, raw_tool_source=raw_tool_source)
     job = sa_session.get(Job, job_id)
+    assert job
     # TODO: assert state ?
     mini_job_wrapper = MinimalJobWrapper(job=job, app=app, tool=tool)
     mini_job_wrapper.finish("", "")
@@ -320,6 +322,7 @@ def fetch_data(
     task_user_id: Optional[int] = None,
 ) -> str:
     job = sa_session.get(Job, job_id)
+    assert job
     mini_job_wrapper = MinimalJobWrapper(job=job, app=app)
     mini_job_wrapper.change_state(model.Job.states.RUNNING, flush=True, job=job)
     return abort_when_job_stops(_fetch_data, session=sa_session, job_id=job_id, setup_return=setup_return)

lib/galaxy/config/__init__.py

@@ -747,7 +747,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self._override_tempdir(kwargs)
-        self._configure_sqlalchemy20_warnings(kwargs)
         self._process_config(kwargs)
         self._set_dependent_defaults()
 
@@ -764,36 +763,6 @@ def _set_dependent_defaults(self):
                     f"{dependent_config_param}, {config_param}"
                 )
 
-    def _configure_sqlalchemy20_warnings(self, kwargs):
-        """
-        This method should be deleted after migration to SQLAlchemy 2.0 is complete.
-        To enable warnings, set `GALAXY_CONFIG_SQLALCHEMY_WARN_20=1`,
-        """
-        warn = string_as_bool(kwargs.get("sqlalchemy_warn_20", False))
-        if warn:
-            import sqlalchemy
-
-            sqlalchemy.util.deprecations.SQLALCHEMY_WARN_20 = True
-            self._setup_sqlalchemy20_warnings_filters()
-
-    def _setup_sqlalchemy20_warnings_filters(self):
-        import warnings
-
-        from sqlalchemy.exc import RemovedIn20Warning
-
-        # Always display RemovedIn20Warning warnings.
-        warnings.filterwarnings("always", category=RemovedIn20Warning)
-        # Optionally, enable filters for specific warnings (raise error, or log, etc.)
-        # messages = [
-        #     r"replace with warning text to match",
-        # ]
-        # for msg in messages:
-        #     warnings.filterwarnings('error', message=msg, category=RemovedIn20Warning)
-        #
-        # See documentation:
-        # https://docs.python.org/3.7/library/warnings.html#the-warnings-filter
-        # https://docs.sqlalchemy.org/en/14/changelog/migration_20.html#migration-to-2-0-step-three-resolve-all-removedin20warnings
-
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 

lib/galaxy/dependencies/pinned-requirements.txt

@@ -182,7 +182,7 @@ sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==1.4.52 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.25 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/jobs/__init__.py

@@ -1182,7 +1182,9 @@ def galaxy_url(self):
         return self.get_destination_configuration("galaxy_infrastructure_url")
 
     def get_job(self) -> model.Job:
-        return self.sa_session.get(Job, self.job_id)
+        job = self.sa_session.get(Job, self.job_id)
+        assert job
+        return job
 
     def get_id_tag(self):
         # For compatibility with drmaa, which uses job_id right now, and TaskWrapper
@@ -1552,7 +1554,7 @@ def change_state(self, state, info=False, flush=True, job=None):
     def get_state(self) -> str:
         job = self.get_job()
         self.sa_session.refresh(job)
-        return job.state
+        return job.state  # type:ignore[return-value]
 
     def set_runner(self, runner_url, external_id):
         log.warning("set_runner() is deprecated, use set_job_destination()")

lib/galaxy/managers/base.py

@@ -318,9 +318,9 @@ def _one_with_recast_errors(self, query: Query) -> U:
         # overridden to raise serializable errors
         try:
             return query.one()
-        except sqlalchemy.orm.exc.NoResultFound:
+        except sqlalchemy.exc.NoResultFound:
             raise exceptions.ObjectNotFound(f"{self.model_class.__name__} not found")
-        except sqlalchemy.orm.exc.MultipleResultsFound:
+        except sqlalchemy.exc.MultipleResultsFound:
             raise exceptions.InconsistentDatabase(f"found more than one {self.model_class.__name__}")
 
     # NOTE: at this layer, all ids are expected to be decoded and in int form

lib/galaxy/managers/collections.py

@@ -839,7 +839,7 @@ def get_collection_contents(self, trans: ProvidesAppContext, parent_id, limit=No
     def _get_collection_contents_qry(self, parent_id, limit=None, offset=None):
         """Build query to find first level of collection contents by containing collection parent_id"""
         DCE = model.DatasetCollectionElement
-        qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)
+        qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)  # type:ignore[var-annotated]
         qry = qry.order_by(DCE.element_index)
         qry = qry.options(
             joinedload(model.DatasetCollectionElement.child_collection), joinedload(model.DatasetCollectionElement.hda)

lib/galaxy/managers/datasets.py

@@ -112,8 +112,8 @@ def purge_datasets(self, request: PurgeDatasetsTaskRequest):
         self.error_unless_dataset_purge_allowed()
         with self.session().begin():
             for dataset_id in request.dataset_ids:
-                dataset: Dataset = self.session().get(Dataset, dataset_id)
-                if dataset.user_can_purge:
+                dataset: Optional[Dataset] = self.session().get(Dataset, dataset_id)
+                if dataset and dataset.user_can_purge:
                     try:
                         dataset.full_delete()
                     except Exception:

lib/galaxy/managers/dbkeys.py

@@ -14,9 +14,9 @@
 )
 
 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 @@ def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta
         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/export_tracker.py

@@ -8,7 +8,7 @@
     and_,
     select,
 )
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.exc import NoResultFound
 from sqlalchemy.orm.scoping import scoped_session
 
 from galaxy.exceptions import ObjectNotFound
@@ -44,7 +44,7 @@ def set_export_association_metadata(self, export_association_id: int, export_met
             export_association: StoreExportAssociation = self.session.execute(stmt).scalars().one()
         except NoResultFound:
             raise ObjectNotFound("Cannot set export metadata. Reason: Export association not found")
-        export_association.export_metadata = export_metadata.json()
+        export_association.export_metadata = export_metadata.model_dump_json()  # type:ignore[assignment]
         with transaction(self.session):
             self.session.commit()
 
@@ -76,4 +76,4 @@ def get_object_exports(
             stmt = stmt.offset(offset)
         if limit:
             stmt = stmt.limit(limit)
-        return self.session.execute(stmt).scalars()
+        return self.session.execute(stmt).scalars()  # type:ignore[return-value]

lib/galaxy/managers/folders.py

@@ -20,11 +20,11 @@
     or_,
     select,
 )
-from sqlalchemy.orm import aliased
-from sqlalchemy.orm.exc import (
+from sqlalchemy.exc import (
     MultipleResultsFound,
     NoResultFound,
 )
+from sqlalchemy.orm import aliased
 
 from galaxy import (
     model,
@@ -505,7 +505,7 @@ def _get_contained_datasets_statement(
             stmt = stmt.where(
                 or_(
                     func.lower(ldda.name).contains(search_text, autoescape=True),
-                    func.lower(ldda.message).contains(search_text, autoescape=True),
+                    func.lower(ldda.message).contains(search_text, autoescape=True),  # type:ignore[attr-defined]
                 )
             )
         sort_column = LDDA_SORT_COLUMN_MAP[payload.order_by](ldda, associated_dataset)
@@ -536,7 +536,7 @@ def _filter_by_include_deleted(
 
     def build_folder_path(
         self, sa_session: galaxy_scoped_session, folder: model.LibraryFolder
-    ) -> List[Tuple[str, str]]:
+    ) -> List[Tuple[int, Optional[str]]]:
         """
         Returns the folder path from root to the given folder.
 
@@ -546,6 +546,7 @@ def build_folder_path(
         path_to_root = [(current_folder.id, current_folder.name)]
         while current_folder.parent_id is not None:
             parent_folder = sa_session.get(LibraryFolder, current_folder.parent_id)
+            assert parent_folder
             current_folder = parent_folder
             path_to_root.insert(0, (current_folder.id, current_folder.name))
         return path_to_root

lib/galaxy/managers/forms.py

@@ -1,5 +1,8 @@
 from sqlalchemy import select
-from sqlalchemy.orm import exc as sqlalchemy_exceptions
+from sqlalchemy.exc import (
+    MultipleResultsFound,
+    NoResultFound,
+)
 
 from galaxy.exceptions import (
     InconsistentDatabase,
@@ -59,9 +62,9 @@ def get(self, trans: ProvidesUserContext, form_id: int) -> FormDefinitionCurrent
         try:
             stmt = select(FormDefinitionCurrent).where(FormDefinitionCurrent.id == form_id)
             form = self.session().execute(stmt).scalar_one()
-        except sqlalchemy_exceptions.MultipleResultsFound:
+        except MultipleResultsFound:
             raise InconsistentDatabase("Multiple forms found with the same id.")
-        except sqlalchemy_exceptions.NoResultFound:
+        except NoResultFound:
             raise RequestParameterInvalidException("No accessible form found with the id provided.")
         except Exception as e:
             raise InternalServerError(f"Error loading from the database.{unicodify(e)}")

lib/galaxy/managers/genomes.py

@@ -95,7 +95,7 @@ def _create_genome_filter(model_class=None):
             if self.database_connection.startswith("postgres"):
                 column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")
             else:
-                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")
+                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")  # type:ignore[assignment]
             lower_val = val.lower()  # Ignore case
             # dbkey can either be "hg38" or '["hg38"]', so we need to check both
             if op == "eq":

lib/galaxy/managers/group_roles.py

@@ -5,13 +5,13 @@
 )
 
 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 @@ def _remove_role_from_group(self, trans: ProvidesAppContext, group_role: model.G
             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 sqlalchemy import select
-from sqlalchemy.orm import Session
 
 from galaxy import model
 from galaxy.exceptions import ObjectNotFound
@@ -15,6 +14,7 @@
     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 @@ def _remove_user_from_group(self, trans: ProvidesAppContext, group_user: model.U
             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)
     )