Unverified Commit cf211c12 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #18661 from mvdbeek/fix_extract_workflow_from_history 

[24.1] Fix extract workflow from history when implicit collection has no jobs
parents dfea749b b30fed83

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?

lib/galaxy_test/api/test_workflow_extraction.py

+40 −0
Original line number Diff line number Diff line
@@ -224,6 +224,46 @@ test_data: 
        collection_step_state = loads(collection_step["tool_state"])

        assert collection_step_state["collection_type"] == "paired"



    def test_empty_collection_map_over_extract_workflow(self):

        with self.dataset_populator.test_history() as history_id:

            self._run_workflow(

                """class: GalaxyWorkflow

inputs:

  input: collection

  filter_file: data

steps:

  filter_collection:

    tool_id: __FILTER_FROM_FILE__

    in:

       input: input

       how|filter_source: filter_file

    state:

       how:

         how_filter: remove_if_present

  concat:

    tool_id: cat1

    in:

      input1: filter_collection/output_filtered

test_data:

  input:

    collection_type: list

    elements:

      - identifier: i1

        content: "0"

  filter_file: i1""",

                history_id,

                wait=True,

            )

            response = self._post(

                "workflows", data={"from_history_id": history_id, "workflow_name": "extract with empty collection test"}

            )

            assert response.status_code == 200

            workflow_id = response.json()["id"]

            workflow = self.workflow_populator.download_workflow(workflow_id)

            assert workflow

            # TODO: after adding request models we should be able to recover implicit collection job requests.

            # assert len(workflow["steps"]) == 4



    @skip_without_tool("cat_collection")

    def test_subcollection_mapping(self, history_id):

        jobs_summary = self._run_workflow(