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Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements

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The list:paired_or_unpaired branch in produce_outputs used
history_content_type == "dataset" to distinguish paired from unpaired
elements. This check is always False because even singletons are
wrapped in sub-collections, so all elements were routed to
_handle_paired which crashes on elements[1] for 1-element collections.

Replace the history_content_type check with element count inspection
on the sub-collection. Also unwrap singletons in _handle_unpaired
since the assert there fails for the same reason.

Fixes #22204
This commit is contained in:
Ernest Provo
2026-04-07 17:34:20 +02:00
committed by mvdbeek
parent a7ea5a5b80
commit 040918f766
1 changed files with 8 additions and 3 deletions
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lib/galaxy/tools/__init__.py
+8 -3
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@@ -4036,8 +4036,12 @@ class SplitPairedAndUnpairedTool(DatabaseOperationTool):
def _handle_unpaired(dce):
element_identifier = dce.element_identifier
assert getattr(dce.element_object, "history_content_type", None) == "dataset"
copied_value = dce.element_object.copy(copy_tags=dce.element_object.tags, flush=False)
element_object = dce.element_object
# In list:paired_or_unpaired collections, unpaired elements are
# wrapped in a 1-element sub-collection. Unwrap to get the dataset.
if getattr(element_object, "history_content_type", None) != "dataset":
element_object = element_object.elements[0].element_object
copied_value = element_object.copy(copy_tags=element_object.tags, flush=False)
unpaired_dce_copies[element_identifier] = copied_value
unpaired_dce_columns[element_identifier] = dce.columns
@@ -4057,7 +4061,8 @@ class SplitPairedAndUnpairedTool(DatabaseOperationTool):
_handle_paired(element)
elif collection_type == "list:paired_or_unpaired":
for element in collection.elements:
if getattr(element.element_object, "history_content_type", None) == "dataset":
sub_collection = element.element_object
if len(sub_collection.elements) == 1:
_handle_unpaired(element)
else:
_handle_paired(element)