Allow DCE as outer input to to_cwl

ahmedhamidawan · Jun 7, 2024 · dff6307 · dff6307
1 parent bd4a529
commit dff6307
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Showing 2 changed files with 14 additions and 2 deletions.
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -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.

diff --git a/test/unit/workflows/test_modules.py b/test/unit/workflows/test_modules.py
@@ -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]]