Move function to model.base to avoid circular import

lib/galaxy/managers/workflows.py

@@ -65,8 +65,10 @@
     WorkflowInvocation,
     WorkflowInvocationStep,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.model.index_filter_util import (
     append_user_filter,
     raw_text_column_filter,

lib/galaxy/model/__init__.py

@@ -119,7 +119,10 @@
 import galaxy.model.tags
 import galaxy.security.passwords
 import galaxy.util
-from galaxy.model.base import transaction
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.model.custom_types import (
     DoubleEncodedJsonType,
     JSONType,
@@ -129,7 +132,6 @@
     UUIDType,
 )
 from galaxy.model.database_object_names import NAMING_CONVENTION
-from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.item_attrs import (
     get_item_annotation_str,
     UsesAnnotations,

lib/galaxy/model/base.py

@@ -20,6 +20,7 @@
 
 from sqlalchemy import event
 from sqlalchemy.orm import (
+    object_session,
     scoped_session,
     Session,
     sessionmaker,
@@ -167,3 +168,22 @@ def before_flush(session, flush_context, instances):
             obj.__create_version__(session)
         for obj in versioned_objects(session.deleted):
             obj.__create_version__(session, deleted=True)
+
+
+def ensure_object_added_to_session(object_to_add, *, object_in_session=None, session=None) -> bool:
+    """
+    This function is intended as a safeguard to mimic pre-SQLAlchemy 2.0 behavior.
+    `object_to_add` was implicitly merged into a Session prior to SQLAlchemy 2.0, which was indicated
+    by `RemovedIn20Warning` warnings logged while running Galaxy's tests. (See https://github.com/galaxyproject/galaxy/issues/12541)
+    As part of the upgrade to 2.0, the `cascade_backrefs=False` argument was added to the relevant relationships that turned off this behavior.
+    This function is called from the code that triggered these warnings, thus emulating the cascading behavior.
+    The intention is to remove all such calls, as well as this function definition, after the move to SQLAlchemy 2.0.
+    # Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0
+    """
+    if session:
+        session.add(object_to_add)
+        return True
+    if object_in_session and object_session(object_in_session):
+        object_session(object_in_session).add(object_to_add)
+        return True
+    return False

lib/galaxy/model/store/__init__.py

@@ -56,8 +56,10 @@
     ProvidesUserFileSourcesUserContext,
 )
 from galaxy.files.uris import stream_url_to_file
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.metadata import MetadataCollection
 from galaxy.model.orm.util import (

lib/galaxy/webapps/base/webapp.py

@@ -37,8 +37,10 @@
 from galaxy.managers import context
 from galaxy.managers.session import GalaxySessionManager
 from galaxy.managers.users import UserManager
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.structured_app import (
     BasicSharedApp,
     MinimalApp,

lib/galaxy/workflow/extract.py

@@ -8,8 +8,10 @@
     exceptions,
     model,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,

lib/galaxy/workflow/modules.py

@@ -35,7 +35,7 @@
     WorkflowStep,
     WorkflowStepConnection,
 )
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import ensure_object_added_to_session
 from galaxy.model.dataset_collections import matching
 from galaxy.schema.invocation import (
     CancelReason,

lib/galaxy/workflow/run.py

@@ -18,8 +18,10 @@
     WorkflowInvocation,
     WorkflowInvocationStep,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.schema.invocation import (
     CancelReason,
     FailureReason,

lib/galaxy/workflow/run_request.py

@@ -21,8 +21,10 @@
     WorkflowRequestInputParameter,
     WorkflowRequestStepState,
 )
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy.tools.parameters.meta import expand_workflow_inputs
 from galaxy.workflow.resources import get_resource_mapper_function
 

test/integration/test_job_files.py

@@ -22,8 +22,10 @@
 from sqlalchemy import select
 
 from galaxy import model
-from galaxy.model.base import transaction
-from galaxy.model.database_utils import ensure_object_added_to_session
+from galaxy.model.base import (
+    ensure_object_added_to_session,
+    transaction,
+)
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util