Use utility function for safeguards

lib/galaxy/managers/workflows.py

@@ -35,7 +35,6 @@
 from sqlalchemy.orm import (
     aliased,
     joinedload,
-    object_session,
     Query,
     subqueryload,
 )
@@ -67,6 +66,7 @@
     WorkflowInvocationStep,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.index_filter_util import (
     append_user_filter,
     raw_text_column_filter,
@@ -822,8 +822,7 @@ def _workflow_from_raw_description(
         # Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
         # when AT LEAST ONE step in steps belonged to a session.
         for step in steps:
-            if step and object_session(step):
-                object_session(step).add(workflow)
+            if ensure_object_added_to_session(workflow, object_in_session=step):
                 break
 
         comments: List[model.WorkflowComment] = []

lib/galaxy/model/__init__.py

@@ -129,6 +129,7 @@
     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,
@@ -2471,9 +2472,7 @@ def __init__(self, action_type, workflow_step=None, output_name=None, action_arg
         self.output_name = output_name
         self.action_arguments = action_arguments
         self.workflow_step = workflow_step
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if workflow_step and object_session(workflow_step):
-            object_session(workflow_step).add(self)
+        ensure_object_added_to_session(self, object_in_session=workflow_step)
 
 
 class PostJobActionAssociation(Base, RepresentById):
@@ -2488,9 +2487,7 @@ class PostJobActionAssociation(Base, RepresentById):
     def __init__(self, pja, job=None, job_id=None):
         if job is not None:
             self.job = job
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if job and object_session(job):
-                object_session(job).add(self)
+            ensure_object_added_to_session(self, object_in_session=job)
         elif job_id is not None:
             self.job_id = job_id
         else:
@@ -2861,9 +2858,7 @@ class UserNotificationAssociation(Base, RepresentById):
 
     def __init__(self, user, notification):
         self.user = user
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if user and object_session(user):
-            object_session(user).add(self)
+        ensure_object_added_to_session(self, object_in_session=user)
         self.notification = notification
 
 
@@ -3517,9 +3512,7 @@ class GroupRoleAssociation(Base, RepresentById):
 
     def __init__(self, group, role):
         self.group = group
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if group and object_session(group):
-            object_session(group).add(self)
+        ensure_object_added_to_session(self, object_in_session=group)
         self.role = role
 
 
@@ -3690,9 +3683,7 @@ def __init__(self, type, quota):
         assert type in self.types.__members__.values(), "Invalid type"
         self.type = type
         self.quota = quota
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if quota and object_session(quota):
-            object_session(quota).add(self)
+        ensure_object_added_to_session(self, object_in_session=quota)
 
 
 class DatasetPermissions(Base, RepresentById):
@@ -3733,9 +3724,7 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, Library):
             self.library = library_item
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if library_item and object_session(library_item):
-                object_session(library_item).add(self)
+            ensure_object_added_to_session(self, object_in_session=library_item)
         else:
             raise Exception(f"Invalid Library specified: {library_item.__class__.__name__}")
         self.role = role
@@ -3757,9 +3746,7 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, LibraryFolder):
             self.folder = library_item
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if library_item and object_session(library_item):
-                object_session(library_item).add(self)
+            ensure_object_added_to_session(self, object_in_session=library_item)
         else:
             raise Exception(f"Invalid LibraryFolder specified: {library_item.__class__.__name__}")
         self.role = role
@@ -3781,9 +3768,7 @@ def __init__(self, action, library_item, role):
         self.action = action
         if isinstance(library_item, LibraryDataset):
             self.library_dataset = library_item
-            # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if library_item and object_session(library_item):
-                object_session(library_item).add(self)
+            ensure_object_added_to_session(self, object_in_session=library_item)
         else:
             raise Exception(f"Invalid LibraryDataset specified: {library_item.__class__.__name__}")
         self.role = role
@@ -4405,11 +4390,7 @@ def __init__(
         elif dataset:
             add_object_to_object_session(self, dataset)
         self.dataset = dataset
-
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if dataset and object_session(dataset):
-            object_session(dataset).add(self)
-
+        ensure_object_added_to_session(self, object_in_session=dataset)
         self.parent_id = parent_id
 
     @property
@@ -7279,9 +7260,7 @@ class GalaxySessionToHistoryAssociation(Base, RepresentById):
 
     def __init__(self, galaxy_session, history):
         self.galaxy_session = galaxy_session
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if galaxy_session and object_session(galaxy_session):
-            object_session(galaxy_session).add(self)
+        ensure_object_added_to_session(self, object_in_session=galaxy_session)
         add_object_to_object_session(self, history)
         self.history = history
 
@@ -7793,9 +7772,7 @@ def add_connection(self, input_name, output_name, output_step, input_subworkflow
 
         conn = WorkflowStepConnection()
         conn.input_step_input = step_input
-        # Safeguard: conn was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if step_input and object_session(step_input):
-            object_session(step_input).add(conn)
+        ensure_object_added_to_session(conn, object_in_session=step_input)
         conn.output_name = output_name
         add_object_to_object_session(conn, output_step)
         conn.output_step = output_step
@@ -8077,9 +8054,7 @@ class WorkflowOutput(Base, Serializable):
 
     def __init__(self, workflow_step, output_name=None, label=None, uuid=None):
         self.workflow_step = workflow_step
-        # Safeguard: self was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if object_session(workflow_step):
-            object_session(workflow_step).add(self)
+        ensure_object_added_to_session(self, object_in_session=workflow_step)
         self.output_name = output_name
         self.label = label
         self.uuid = get_uuid(uuid)
@@ -8468,28 +8443,23 @@ def add_output(self, workflow_output, step, output_object):
             # dispatch on actual object and not step type.
             output_assoc = WorkflowInvocationOutputValue()
             output_assoc.workflow_invocation = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.value = output_object
             self.output_values.append(output_assoc)
         elif output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationOutputDatasetAssociation()
             output_assoc.workflow_invocation = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.dataset = output_object
             self.output_datasets.append(output_assoc)
         elif output_object.history_content_type == "dataset_collection":
             output_assoc = WorkflowInvocationOutputDatasetCollectionAssociation()
             output_assoc.workflow_invocation = self
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.workflow_output = workflow_output
             output_assoc.workflow_step = step
             output_assoc.dataset_collection = output_object
@@ -8943,18 +8913,14 @@ def add_output(self, output_name, output_object):
         if output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationStepOutputDatasetAssociation()
             output_assoc.workflow_invocation_step = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.dataset = output_object
             output_assoc.output_name = output_name
             self.output_datasets.append(output_assoc)
         elif output_object.history_content_type == "dataset_collection":
             output_assoc = WorkflowInvocationStepOutputDatasetCollectionAssociation()
             output_assoc.workflow_invocation_step = self
-            # Safeguard: output_assoc was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if object_session(self):
-                object_session(self).add(output_assoc)
+            ensure_object_added_to_session(output_assoc, object_in_session=self)
             output_assoc.dataset_collection = output_object
             output_assoc.output_name = output_name
             self.output_dataset_collections.append(output_assoc)

lib/galaxy/model/store/__init__.py

@@ -40,10 +40,7 @@
 )
 from rocrate.rocrate import ROCrate
 from sqlalchemy import select
-from sqlalchemy.orm import (
-    joinedload,
-    object_session,
-)
+from sqlalchemy.orm import joinedload
 from sqlalchemy.orm.scoping import scoped_session
 from sqlalchemy.sql import expression
 from typing_extensions import Protocol
@@ -60,6 +57,7 @@
 )
 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.mapping import GalaxyModelMapping
 from galaxy.model.metadata import MetadataCollection
 from galaxy.model.orm.util import (
@@ -1027,9 +1025,7 @@ def _import_workflow_invocations(
             imported_invocation = model.WorkflowInvocation()
             imported_invocation.user = self.user
             imported_invocation.history = history
-            # Safeguard: imported_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
-            if history and object_session(history):
-                object_session(history).add(imported_invocation)
+            ensure_object_added_to_session(imported_invocation, object_in_session=history)
             workflow_key = invocation_attrs["workflow"]
             if workflow_key not in object_import_tracker.workflows_by_key:
                 raise Exception(f"Failed to find key {workflow_key} in {object_import_tracker.workflows_by_key.keys()}")
@@ -1051,8 +1047,7 @@ def attach_workflow_step(imported_object, attrs):
             for step_attrs in invocation_attrs["steps"]:
                 imported_invocation_step = model.WorkflowInvocationStep()
                 imported_invocation_step.workflow_invocation = imported_invocation
-                # Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                self.sa_session.add(imported_invocation_step)
+                ensure_object_added_to_session(imported_invocation, session=self.sa_session)
                 attach_workflow_step(imported_invocation_step, step_attrs)
                 restore_times(imported_invocation_step, step_attrs)
                 imported_invocation_step.action = step_attrs["action"]

lib/galaxy/webapps/base/webapp.py

@@ -24,7 +24,6 @@
     select,
     true,
 )
-from sqlalchemy.orm import object_session
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import util
@@ -39,6 +38,7 @@
 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.structured_app import (
     BasicSharedApp,
     MinimalApp,
@@ -1120,9 +1120,7 @@ def create_new_session(trans, prev_galaxy_session=None, user_for_new_session=Non
     if user_for_new_session:
         # The new session should be associated with the user
         galaxy_session.user = user_for_new_session
-        # Safeguard: galaxy_session was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if user_for_new_session and object_session(user_for_new_session):
-            object_session(user_for_new_session).add(galaxy_session)
+        ensure_object_added_to_session(galaxy_session, object_in_session=user_for_new_session)
     return galaxy_session
 
 

lib/galaxy/workflow/extract.py

@@ -9,6 +9,7 @@
     model,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
@@ -71,8 +72,7 @@ def extract_workflow(
     workflow.stored_workflow = stored
     stored.latest_workflow = workflow
     trans.sa_session.add(stored)
-    # Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
-    trans.sa_session.add(workflow)
+    ensure_object_added_to_session(workflow, session=trans.sa_session)
     with transaction(trans.sa_session):
         trans.sa_session.commit()
     return stored

lib/galaxy/workflow/modules.py

@@ -18,7 +18,6 @@
 )
 
 from cwl_utils.expression import do_eval
-from sqlalchemy.orm import object_session
 from typing_extensions import TypedDict
 
 from galaxy import (
@@ -36,6 +35,7 @@
     WorkflowStep,
     WorkflowStepConnection,
 )
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.model.dataset_collections import matching
 from galaxy.schema.invocation import (
     CancelReason,
@@ -645,9 +645,7 @@ def from_workflow_step(Class, trans, step, **kwds):
     def save_to_step(self, step, **kwd):
         step.type = self.type
         step.subworkflow = self.subworkflow
-        # Safeguard: step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-        if self.subworkflow and object_session(self.subworkflow):
-            object_session(self.subworkflow).add(step)
+        ensure_object_added_to_session(step, object_in_session=self.subworkflow)
 
     def get_name(self):
         if hasattr(self.subworkflow, "name"):

lib/galaxy/workflow/run.py

@@ -10,7 +10,6 @@
     Union,
 )
 
-from sqlalchemy.orm import object_session
 from typing_extensions import Protocol
 
 from galaxy import model
@@ -20,6 +19,7 @@
     WorkflowInvocationStep,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.schema.invocation import (
     CancelReason,
     FailureReason,
@@ -226,9 +226,7 @@ def invoke(self) -> Dict[int, Any]:
                     workflow_invocation_step = WorkflowInvocationStep()
                     assert workflow_invocation_step
                     workflow_invocation_step.workflow_invocation = workflow_invocation
-                    # Safeguard: workflow_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
-                    if workflow_invocation and object_session(workflow_invocation):
-                        object_session(workflow_invocation).add(workflow_invocation_step)
+                    ensure_object_added_to_session(workflow_invocation_step, object_in_session=workflow_invocation)
                     workflow_invocation_step.workflow_step = step
                     workflow_invocation_step.state = "new"
 

lib/galaxy/workflow/run_request.py

@@ -9,8 +9,6 @@
     TYPE_CHECKING,
 )
 
-from sqlalchemy.orm import object_session
-
 from galaxy import exceptions
 from galaxy.model import (
     EffectiveOutput,
@@ -24,6 +22,7 @@
     WorkflowRequestStepState,
 )
 from galaxy.model.base import transaction
+from galaxy.model.database_utils import ensure_object_added_to_session
 from galaxy.tools.parameters.meta import expand_workflow_inputs
 from galaxy.workflow.resources import get_resource_mapper_function
 
@@ -488,9 +487,7 @@ def workflow_run_config_to_request(
     workflow_invocation = WorkflowInvocation()
     workflow_invocation.uuid = uuid.uuid1()
     workflow_invocation.history = run_config.target_history
-    # Safeguard: workflow_invocation was implicitly merged into this Session prior to SQLAlchemy 2.0.
-    if run_config.target_history and object_session(run_config.target_history):
-        object_session(run_config.target_history).add(workflow_invocation)
+    ensure_object_added_to_session(workflow_invocation, object_in_session=run_config.target_history)
 
     def add_parameter(name: str, value: str, type: WorkflowRequestInputParameter.types) -> None:
         parameter = WorkflowRequestInputParameter(