Unverified Commit dff6307e authored by mvdbeek's avatar mvdbeek
Browse files

Allow DCE as outer input to to_cwl

parent bd4a5293

lib/galaxy/workflow/modules.py

+2 −2
Original line number Diff line number Diff line
@@ -128,9 +128,9 @@ def to_cwl(value, hda_references, step): 
    element_identifier = None

    if isinstance(value, model.HistoryDatasetCollectionAssociation):

        value = value.collection

    if isinstance(value, model.DatasetCollectionElement) and value.hda:

    if isinstance(value, model.DatasetCollectionElement):

        element_identifier = value.element_identifier

        value = value.hda

        value = value.element_object

    if isinstance(value, model.HistoryDatasetAssociation):

        # I think the following two checks are needed but they may

        # not be needed.

test/unit/workflows/test_modules.py

+12 −0
Original line number Diff line number Diff line
@@ -274,6 +274,18 @@ def test_to_cwl_nested_collection(): 
    assert result["outer"][0]["basename"] == "inner"





def test_to_cwl_dataset_collection_element():

    hda = model.HistoryDatasetAssociation(create_dataset=True, flush=False)

    hda.dataset.state = model.Dataset.states.OK

    dc_inner = model.DatasetCollection(collection_type="list")

    model.DatasetCollectionElement(collection=dc_inner, element_identifier="inner", element=hda)

    dc_outer = model.DatasetCollection(collection_type="list:list")

    dce_outer = model.DatasetCollectionElement(collection=dc_outer, element_identifier="outer", element=dc_inner)

    result = modules.to_cwl(dce_outer, [], model.WorkflowStep())

    assert result[0]["class"] == "File"

    assert result[0]["basename"] == "inner"





class MapOverTestCase(NamedTuple):

    data_input: str

    step_input_def: Union[str, List[str]]