Unverified Commit 01502917 authored by mvdbeek's avatar mvdbeek
Browse files

Fix ``to_cwl`` for nested collections 

Fixes
```
TypeError
Object of type DatasetCollection is not JSON serializable
```
seen when running https://github.com/galaxyproject/iwc/pull/315
parent c3e53c49

lib/galaxy/workflow/modules.py

+6 −5
Original line number Diff line number Diff line
@@ -123,6 +123,8 @@ class ConditionalStepWhen(BooleanToolParameter): 


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:

        element_identifier = value.element_identifier

        value = value.hda
@@ -152,14 +154,13 @@ def to_cwl(value, hda_references, step): 
                properties, value.dataset.created_from_basename or element_identifier or value.name

            )

            return properties

    elif hasattr(value, "collection"):

        collection = value.collection

        if collection.collection_type == "list":

            return [to_cwl(dce, hda_references=hda_references, step=step) for dce in collection.dataset_elements]

    elif isinstance(value, model.DatasetCollection):

        if value.collection_type == "list":

            return [to_cwl(dce, hda_references=hda_references, step=step) for dce in value.dataset_elements]

        else:

            # Could be record or nested lists

            rval = {}

            for element in collection.elements:

            for element in value.elements:

                rval[element.element_identifier] = to_cwl(

                    element.element_object, hda_references=hda_references, step=step

                )

test/unit/workflows/test_modules.py

+13 −0
Original line number Diff line number Diff line
@@ -261,6 +261,19 @@ def test_to_cwl(): 
    assert hda_references == hdas





def test_to_cwl_nested_collection():

    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")

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

    hdca = model.HistoryDatasetCollectionAssociation(name="the collection", collection=dc_outer)

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

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

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





class MapOverTestCase(NamedTuple):

    data_input: str

    step_input_def: Union[str, List[str]]