Handle sub-collection DCE dereference during mapped job rerun

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: guerler

lib/galaxy/managers/jobs.py

@@ -2178,15 +2178,16 @@ def dereference_callback(data_request: DataRequestUri) -> DataRequestInternalHda
             new_hdas.append(DereferencedDatasetPair(hda, data_request))
             return DataRequestInternalHda(id=hda.id, src="hda")
 
-        def dereference_dce_callback(data_request: DataRequestInternalDce) -> DataRequestInternalHda:
+        def dereference_dce_callback(
+            data_request: DataRequestInternalDce,
+        ) -> Optional[DataRequestInternalHda]:
             dce = trans.sa_session.get(model.DatasetCollectionElement, data_request.id)
             if dce is None:
                 raise RequestParameterInvalidException(f"Dataset collection element {data_request.id} not found")
             hda = dce.hda
             if hda is None:
-                raise RequestParameterInvalidException(
-                    f"Dataset collection element {data_request.id} does not reference a dataset"
-                )
+                # Sub-collection DCE, pass through for collection parameter expansion
+                return None
             return DataRequestInternalHda(id=hda.id, src="hda")
 
         tool_state = RequestInternalToolState(tool_request.request)

lib/galaxy/tool_util/parameters/convert.py

@@ -71,7 +71,7 @@
 EncodeFunctionT = Callable[[int], str]
 DereferenceCallable = Callable[[DataRequestUri], DataRequestInternalHda]
 DereferenceCollectionCallable = Callable[[DataRequestCollectionUri], DataRequestInternalHdca]
-DereferenceDceCallable = Callable[[DataRequestInternalDce], DataRequestInternalHda]
+DereferenceDceCallable = Callable[[DataRequestInternalDce], Optional[DataRequestInternalHda]]
 # interfaces for adapting test data dictionaries to tool request dictionaries
 # e.g. {class: File, path: foo.bed} => {src: hda, id: ab1235cdfea3}
 AdaptDatasets = Callable[[JsonTestDatasetDefDict], DataRequestHda]
@@ -244,8 +244,10 @@ def dereference_dict(src_dict: dict):
             return data_request_hdca.model_dump()
         elif src == "dce" and dereference_dce is not None:
             data_request_dce: DataRequestInternalDce = DataRequestInternalDce.model_validate(src_dict)
-            data_request_hda_from_dce: DataRequestInternalHda = dereference_dce(data_request_dce)
-            return data_request_hda_from_dce.model_dump()
+            data_request_hda_from_dce = dereference_dce(data_request_dce)
+            if data_request_hda_from_dce is not None:
+                return data_request_hda_from_dce.model_dump()
+            return src_dict
         else:
             return src_dict