Unverified Commit 0f77df79 authored by mvdbeek's avatar mvdbeek
Browse files

Fix extract workflow from history with empty mapped over collections 

Fixes https://github.com/galaxyproject/galaxy/issues/18484.

It's not ideal on the one hand, but better to have a workflow with gaps
than an internal server error IMO. We do the same for datasets in some
non-terminal states.
parent 5ae13639

lib/galaxy/webapps/galaxy/controllers/workflow.py

+1 −0
Original line number Diff line number Diff line
@@ -320,6 +320,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi 
            # Optionally target a different history than the current one.

            history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=history)

        if not user:

            trans.response.status = 403

            return trans.show_error_message("Must be logged in to create workflows")

        if (job_ids is None and dataset_ids is None) or workflow_name is None:

            jobs, warnings = summarize(trans, history)

lib/galaxy/workflow/extract.py

+9 −1
Original line number Diff line number Diff line
@@ -321,7 +321,15 @@ class WorkflowSummary: 
        # tracking with creating_job_associations. Will delete at some point.

        elif dataset_collection.implicit_output_name:

            # TODO: Optimize db call

            dataset_instance = dataset_collection.collection.dataset_instances[0]

            element = dataset_collection.collection.first_dataset_element

            if not element:

                # Got no dataset instance to walk back up to creating job.

                # TODO track this via tool request model

                job = DatasetCollectionCreationJob(dataset_collection)

                self.jobs[job] = [(None, dataset_collection)]

                return

            else:

                dataset_instance = element.hda

            if not self.__check_state(dataset_instance):

                # Just checking the state of one instance, don't need more but

                # makes me wonder if even need this check at all?