Merge pull request #20863 from mvdbeek/undo_eager_joinedload (81f9e6da) · Commits · NDIP / Galaxy

lib/galaxy/managers/workflows.py

+3 −14

Original line number	Diff line number	Diff line
		@@ -66,9 +66,6 @@ from galaxy.managers.context import ProvidesUserContext
		from galaxy.managers.executables import artifact_class
		from galaxy.model import (
		History,
		ImplicitCollectionJobs,
		ImplicitCollectionJobsJobAssociation,
		Job,
		StoredWorkflow,
		StoredWorkflowTagAssociation,
		StoredWorkflowUserShareAssociation,
		@@ -422,9 +419,9 @@ class WorkflowsManager(sharable.SharableModelManager[model.StoredWorkflow], dele
		return workflow_canvas.finish(for_embed=for_embed)

		def get_invocation(
		self, trans, decoded_invocation_id: int, eager=False, check_ownership=True, check_accessible=True
		self, trans, decoded_invocation_id: int, check_ownership=True, check_accessible=True
		) -> WorkflowInvocation:
		workflow_invocation = _get_invocation(trans.sa_session, eager, decoded_invocation_id)
		workflow_invocation = _get_invocation(trans.sa_session, decoded_invocation_id)
		if not workflow_invocation:
		encoded_wfi_id = trans.security.encode_id(decoded_invocation_id)
		message = f"'{encoded_wfi_id}' is not a valid workflow invocation id"
		@@ -2259,16 +2256,8 @@ def _get_stored_workflow(session, workflow_uuid, workflow_id, by_stored_id):
		return session.scalars(stmt).first()


		def _get_invocation(session, eager, invocation_id):
		def _get_invocation(session, invocation_id):
		stmt = select(WorkflowInvocation)
		if eager:
		stmt = stmt.options(
		subqueryload(WorkflowInvocation.steps)
		.joinedload(WorkflowInvocationStep.implicit_collection_jobs)
		.joinedload(ImplicitCollectionJobs.jobs)
		.joinedload(ImplicitCollectionJobsJobAssociation.job)
		.joinedload(Job.input_datasets)
		)
		stmt = stmt.where(WorkflowInvocation.id == invocation_id).limit(1)
		return session.scalars(stmt).first()

lib/galaxy/model/init.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -8964,7 +8964,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
		back_populates="parent_workflow_invocation",
		uselist=True,
		)
		steps = relationship(
		steps: Mapped[list["WorkflowInvocationStep"]] = relationship(
		"WorkflowInvocationStep",
		back_populates="workflow_invocation",
		order_by=lambda: WorkflowInvocationStep.order_index,

lib/galaxy/model/store/init.py

+7 −5

Original line number	Diff line number	Diff line
		@@ -2848,10 +2848,12 @@ class BcoModelExportStore(FileSourceModelExportStore, WorkflowInvocationOnlyExpo
		parametric_domain_items: List[ParametricDomainItem] = []
		for inv_step in workflow_invocation.steps:
		try:
		for k, v in inv_step.workflow_step.tool_inputs.items():
		param, value, step = k, v, inv_step.workflow_step.order_index
		tool_inputs = inv_step.workflow_step.tool_inputs
		if tool_inputs:
		for k, v in tool_inputs.items():
		param, value, step_index = k, v, inv_step.workflow_step.order_index
		parametric_domain_items.append(
		ParametricDomainItem(param=str(param), value=str(value), step=str(step))
		ParametricDomainItem(param=str(param), value=str(value), step=str(step_index))
		)
		except Exception:
		continue

lib/galaxy/webapps/galaxy/api/workflows.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -1459,7 +1459,7 @@ class FastAPIInvocations:
		serialization_params = InvocationSerializationParams(
		step_details=step_details, legacy_job_state=legacy_job_state
		)
		return self.invocations_service.show(trans, invocation_id, serialization_params, eager=True)
		return self.invocations_service.show(trans, invocation_id, serialization_params)

		@router.get(
		"/api/invocations/{invocation_id}/request",

lib/galaxy/webapps/galaxy/services/invocations.py

+5 −9

Original line number	Diff line number	Diff line
		@@ -138,16 +138,12 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
		invocation_dict = self.serialize_workflow_invocations(invocations, serialization_params)
		return invocation_dict, total_matches

		def show(self, trans, invocation_id, serialization_params, eager=False):
		wfi = self._workflows_manager.get_invocation(
		trans, invocation_id, eager, check_ownership=False, check_accessible=True
		)
		def show(self, trans, invocation_id, serialization_params):
		wfi = self._workflows_manager.get_invocation(trans, invocation_id, check_ownership=False, check_accessible=True)
		return self.serialize_workflow_invocation(wfi, serialization_params)

		def as_request(self, trans: ProvidesUserContext, invocation_id) -> WorkflowInvocationRequestModel:
		wfi = self._workflows_manager.get_invocation(
		trans, invocation_id, True, check_ownership=True, check_accessible=True
		)
		wfi = self._workflows_manager.get_invocation(trans, invocation_id, check_ownership=True, check_accessible=True)
		return self.serialize_workflow_invocation_to_request(trans, wfi)

		def cancel(self, trans, invocation_id, serialization_params):
		@@ -210,7 +206,7 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
		ensure_celery_tasks_enabled(trans.app.config)
		model_store_format = payload.model_store_format
		workflow_invocation = self._workflows_manager.get_invocation(
		trans, invocation_id, eager=True, check_ownership=False, check_accessible=True
		trans, invocation_id, check_ownership=False, check_accessible=True
		)
		if not workflow_invocation:
		raise ObjectNotFound()
		@@ -238,7 +234,7 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
		) -> AsyncTaskResultSummary:
		ensure_celery_tasks_enabled(trans.app.config)
		workflow_invocation = self._workflows_manager.get_invocation(
		trans, invocation_id, eager=True, check_ownership=False, check_accessible=True
		trans, invocation_id, check_ownership=False, check_accessible=True
		)
		if not workflow_invocation:
		raise ObjectNotFound()