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fix: clean-up error message if only 1 ancestor is valid for ontology term #637

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merged 1 commit into from
Sep 20, 2023
Merged

fix: clean-up error message if only 1 ancestor is valid for ontology term #637

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7 changes: 5 additions & 2 deletions cellxgene_schema_cli/cellxgene_schema/validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -147,8 +147,11 @@ def _validate_curie_ancestors(

if True not in checks:
if errors:
all_ancestors = list(allowed_ancestors.values())
self.errors.append(f"'{term_id}' in '{column_name}' is not a child term id of '{all_ancestors}'.")
all_ancestors = [ancestor for ancestors in allowed_ancestors.values() for ancestor in ancestors]
# print ancestor as string with single-quotes if only 1 entry
if len(all_ancestors) == 1:
all_ancestors = f"'{all_ancestors[0]}'"
self.errors.append(f"'{term_id}' in '{column_name}' is not a child term id of {all_ancestors}.")
return False
return True

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6 changes: 3 additions & 3 deletions cellxgene_schema_cli/tests/test_schema_compliance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,7 +264,7 @@ def test_assay_ontology_term_id(self):
self.validator.errors,
[
"ERROR: 'EFO:0000001' in 'assay_ontology_term_id' is not a "
"child term id of '[['EFO:0002772', 'EFO:0010183']]'."
"child term id of ['EFO:0002772', 'EFO:0010183']."
],
)

Expand Down Expand Up @@ -603,7 +603,7 @@ def test_tissue_ontology_term_id_child_of_anatomical_entity(self):
self.validator.errors,
[
"ERROR: 'UBERON:0001062' in 'tissue_ontology_term_id' is not a child term id of "
"'[['UBERON:0001062']]'. When 'tissue_type' is 'tissue' or 'organoid', 'tissue_ontology_term_id' "
"'UBERON:0001062'. When 'tissue_type' is 'tissue' or 'organoid', 'tissue_ontology_term_id' "
"MUST be a child term id of 'UBERON:0001062' (anatomical entity)."
],
)
Expand All @@ -616,7 +616,7 @@ def test_tissue_ontology_term_id_child_of_anatomical_entity(self):
self.validator.errors,
[
"ERROR: 'UBERON:0001062' in 'tissue_ontology_term_id' is not a child term id of "
"'[['UBERON:0001062']]'. When 'tissue_type' is 'tissue' or 'organoid', 'tissue_ontology_term_id' "
"'UBERON:0001062'. When 'tissue_type' is 'tissue' or 'organoid', 'tissue_ontology_term_id' "
"MUST be a child term id of 'UBERON:0001062' (anatomical entity)."
],
)
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