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Reuse clean_taxon_name in metatraits_gtdb CURIE construction #576

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Merged
realmarcin merged 1 commit into from
Jun 16, 2026
Merged

Reuse clean_taxon_name in metatraits_gtdb CURIE construction #576

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5 changes: 3 additions & 2 deletions kg_microbe/transform_utils/metatraits_gtdb/metatraits_gtdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
from typing import Dict, Optional, Set, Union

from kg_microbe.transform_utils.constants import METATRAITS_GTDB, RAW_DATA_DIR
from kg_microbe.transform_utils.gtdb.utils import clean_taxon_name
from kg_microbe.transform_utils.metatraits.metatraits import MetaTraitsTransform
from kg_microbe.transform_utils.transform import Transform
from kg_microbe.utils.chemical_mapping_utils import ChemicalMappingLoader
Expand Down Expand Up @@ -295,7 +296,7 @@ def _search_ncbitaxon_by_label(self, search_name: str) -> Optional[str]:
# because they must match the prefix-free metatraits input labels;
# only the emitted CURIE carries s__. Input is species-level only
# (gtdb_species_summary.jsonl.gz; genus/family summaries disabled).
gtdb_id = search_name.replace(" ", "_")
gtdb_id = clean_taxon_name(search_name)
synthetic_node_id = f"GTDB:s__{gtdb_id}"

# Extract accession for hierarchical linking
Expand Down Expand Up @@ -393,7 +394,7 @@ def _create_hierarchical_edges(self) -> None:
# s__ prefix matches the canonical gtdb-transform CURIE
# scheme (GTDB:s__<species>) so this subClassOf edge lands
# on a real GTDB taxonomy node in the merged graph.
OBJECT_COLUMN: f"GTDB:s__{current_species.replace(' ', '_')}",
OBJECT_COLUMN: f"GTDB:s__{clean_taxon_name(current_species)}",
RELATION_COLUMN: RDFS_SUBCLASS_OF,
PRIMARY_KNOWLEDGE_SOURCE_COLUMN: "infores:gtdb-metatraits",
}
Expand Down
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