Skip to content

Resolve CodeQL code-quality findings + metpo-edit.owl whitespace #453

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
turbomam merged 1 commit into from
Jun 1, 2026
Merged

Resolve CodeQL code-quality findings + metpo-edit.owl whitespace #453

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion metpo/analysis/analyze_ontology_value.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,6 @@ def main(input):
removal_candidates = []
for _, row in only_imported.iterrows():
ont_file = row["ontology_file"]
df[df["object_source"] == ont_file]

# Check if ALL terms are available natively elsewhere
all_redundant = True
Expand Down
1 change: 1 addition & 0 deletions metpo/database/filter_ols_chromadb.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ def main(input_path, input_collection, output_path, output_collection, batch_siz
output_client.delete_collection(name=output_collection)
print(f" Deleted existing collection: {output_collection}")
except Exception:
# Collection may not exist yet (e.g. first run); nothing to delete.
pass

output_coll = output_client.create_collection(
Expand Down
1 change: 1 addition & 0 deletions metpo/literature_mining/analysis/metpo_assessor.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1023,6 +1023,7 @@ def _extract_content_text(self, input_text: Any) -> str:
if isinstance(data, dict) and "content" in data:
return data["content"]
except yaml.YAMLError:
# Not valid YAML either; fall through and return the raw input text.
pass
return input_text
elif isinstance(input_text, dict):
Expand Down
2 changes: 1 addition & 1 deletion metpo/presentations/analyze_ontogpt_grounding.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,4 +132,4 @@ def main():


if __name__ == "__main__":
totals, per_file = main()
main()
16 changes: 4 additions & 12 deletions metpo/scripts/audit_metatraits_substrate_curies.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -330,18 +330,10 @@ def _report_sections(rows: list[AuditRow]) -> list[str]:
[
"## Related Files\n",
"\n",
"- [`docs/casamino_acids_curie_mapping_case_study.md`]"
"(../../docs/casamino_acids_curie_mapping_case_study.md) "
"-- CHEBI:78020 error case study\n",
"- [`docs/linkml_embedding_and_validation_tools.md`]"
"(../../docs/linkml_embedding_and_validation_tools.md) "
"-- OAK/linkml-store tooling research\n",
"- [`data/mappings/metatraits_in_sheet_resolution.tsv`]"
"(metatraits_in_sheet_resolution.tsv) "
"-- in-sheet resolution table\n",
"- [`data/mappings/metatraits_external_curie_coverage.tsv`]"
"(metatraits_external_curie_coverage.tsv) "
"-- external CURIE coverage\n",
"- [`docs/casamino_acids_curie_mapping_case_study.md`](../../docs/casamino_acids_curie_mapping_case_study.md) -- CHEBI:78020 error case study\n",
"- [`docs/linkml_embedding_and_validation_tools.md`](../../docs/linkml_embedding_and_validation_tools.md) -- OAK/linkml-store tooling research\n",
"- [`data/mappings/metatraits_in_sheet_resolution.tsv`](metatraits_in_sheet_resolution.tsv) -- in-sheet resolution table\n",
"- [`data/mappings/metatraits_external_curie_coverage.tsv`](metatraits_external_curie_coverage.tsv) -- external CURIE coverage\n",
]
)

Expand Down
16 changes: 0 additions & 16 deletions metpo/tools/make_bacdive_utilization_enum.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -140,22 +140,6 @@ def convert_tsv_to_linkml_enum(
"meaning": id_uri
}

# # Add description if we have bacdive key info
# if pd.notna(row['bacdive key']) and row['bacdive key']:
# bacdive_key = row['bacdive key']
# description_parts = [f"Relationship type: {bacdive_key}"]
#
# # Add count if available
# if pd.notna(row['bacdive count']) and str(row['bacdive count']).isdigit():
# count = int(row['bacdive count'])
# description_parts.append(f"BacDive occurrences: {count:,}")
#
# # Add notes if available
# if pd.notna(row['notes']) and row['notes']:
# description_parts.append(f"Notes: {row['notes']}")
#
# pv_entry['description'] = '; '.join(description_parts)

# Add to permissible values
linkml_enum["enums"][enum_name]["permissible_values"][key] = pv_entry

Expand Down
6 changes: 3 additions & 3 deletions src/ontology/metpo-edit.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ AnnotationAssertion(rdfs:label dcterms:title "title")

# Annotation Property: IAO:0000117 (term editor)

AnnotationAssertion(rdfs:label IAO:0000117 "term editor")
AnnotationAssertion(rdfs:label IAO:0000117 "term editor")


############################
Expand All @@ -71,8 +71,8 @@ AnnotationAssertion(rdfs:label dcterms:title "title")

# Annotation Property: <http://qudt.org/schema/qudt/ucumCode> (UCUM code)

AnnotationAssertion(rdfs:label <http://qudt.org/schema/qudt/ucumCode> "UCUM code")
AnnotationAssertion(rdfs:comment <http://qudt.org/schema/qudt/ucumCode> "A UCUM code that identifies a unit of measure.")
AnnotationAssertion(rdfs:label <http://qudt.org/schema/qudt/ucumCode> "UCUM code")
AnnotationAssertion(rdfs:comment <http://qudt.org/schema/qudt/ucumCode> "A UCUM code that identifies a unit of measure.")


)
Loading