Unverified Commit 539441dd authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #20485 from mvdbeek/fix_workflow_invocation_import_link_outputs 

[24.2] Link workflow invocation outputs upon importing invocation
parents 876fdf0b 6d0a0b53

lib/galaxy/model/store/__init__.py

+10 −0
Original line number Diff line number Diff line
@@ -1194,6 +1194,11 @@ class ModelImportStore(metaclass=abc.ABCMeta): 
                label = workflow_output.get("label")

                workflow_output = workflow.workflow_output_for(label)

                output_dataset_collection.workflow_output = workflow_output

                output_dataset_collection_attrs = output_dataset_collection_attrs.get("dataset_collection") or {}

                if hdca_id := output_dataset_collection_attrs.get(object_key):

                    hdca = object_import_tracker.find_hdca(hdca_id)

                    if hdca:

                        output_dataset_collection.dataset_collection = hdca

                self._session_add(output_dataset_collection)

                output_dataset_collections.append(output_dataset_collection)
@@ -1206,6 +1211,11 @@ class ModelImportStore(metaclass=abc.ABCMeta): 
                label = workflow_output.get("label")

                workflow_output = workflow.workflow_output_for(label)

                output_dataset.workflow_output = workflow_output

                output_dataset_dataset_attrs = output_dataset_attrs.get("dataset") or {}

                if dataset_id := output_dataset_dataset_attrs.get(object_key):

                    dataset = object_import_tracker.find_hda(dataset_id)

                    if dataset:

                        output_dataset.dataset = dataset

                self._session_add(output_dataset)

                output_datasets.append(output_dataset)

test/integration/test_workflow_tasks.py

+6 −0
Original line number Diff line number Diff line
@@ -99,6 +99,7 @@ class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, Us 
            assert "wf_output_1" in output_collections

            out = output_collections["wf_output_1"]

            assert out["src"] == "hdca"

            assert out["id"]



            inputs = invocation_details["inputs"]

            assert inputs["0"]["src"] == "hdca"
@@ -144,6 +145,9 @@ steps: 
    in:

      input:

        source: input

outputs:

  extracted_dataset:

    outputSource: extract_dataset/output

"""

            )

            inputs = {"input": {"src": "hdca", "id": copied_collection["id"]}}
@@ -164,6 +168,8 @@ steps: 
                workflow_request=workflow_request,

            )

            imported_invocation_details = self._export_and_import_workflow_invocation(summary)

            assert imported_invocation_details["outputs"]["extracted_dataset"]["src"] == "hda"

            assert imported_invocation_details["outputs"]["extracted_dataset"]["id"]

            original_contents = self.dataset_populator.get_history_contents(new_history["id"])

            contents = self.dataset_populator.get_history_contents(imported_invocation_details["history_id"])

            assert len(contents) == len(original_contents) == 5