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Update mapping check to allow pure annotation #500

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Merged
BSnelling merged 1 commit into from
Jul 1, 2026
Merged

Update mapping check to allow pure annotation #500

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4 changes: 2 additions & 2 deletions petab/v2/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -945,8 +945,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
new_petab_ids = {
m.petab_id
for m in problem.mappings
# Ignore identity mappings used for annotation
if m.petab_id != m.model_id
# Ignore identity mappings and annotation-only rows
if m.model_id and m.petab_id != m.model_id
}
old_petab_ids = (
{c.id for c in problem.conditions}
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8 changes: 8 additions & 0 deletions tests/v2/test_lint.py
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Expand Up @@ -146,6 +146,14 @@ def test_check_mapping_table(uses_pysb):
check = CheckMappingTable()
assert check.run(problem) is None

# Valid: mapping table is used purely for annotation
# petabEntityId appears elsewhere in the problem
problem.add_mapping(petab_id="c1", model_id=None, name="Condition 1")
problem.add_condition("c1", p2="1")

check = CheckMappingTable()
assert check.run(problem) is None

# Invalid: petabEntityId is referenced in the model
pysb.SelfExporter.cleanup()
pysb_model_invalid = pysb.Model("test_model_invalid")
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