Reuse clean_taxon_name in metatraits_gtdb CURIE construction#576
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metatraits_gtdb built its GTDB CURIEs with an inline `.replace(" ", "_")`
at both construction sites (synthetic node id and subClassOf target),
duplicating the canonical logic in gtdb/utils.clean_taxon_name. Import and
reuse it so the two transforms cannot drift if the canonical cleaner ever
changes. Behaviour is identical (clean_taxon_name is the same space->
underscore replacement); the prefix-stripping lookup-map code is unchanged.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Summary
Tidy-up:
metatraits_gtdbbuilt its GTDB CURIEs with an inline.replace(" ", "_")at both construction sites, duplicating the canonical logic ingtdb/utils.clean_taxon_name. This imports and reusesclean_taxon_nameso the two GTDB-emitting transforms (gtdbandmetatraits_gtdb) can't drift if the canonical cleaner ever changes.Change
clean_taxon_nameinmetatraits_gtdb.search_name.replace(" ", "_")→clean_taxon_name(search_name).current_species.replace(' ', '_')→clean_taxon_name(current_species).Behaviour-identical —
clean_taxon_nameis the same space→underscore replacement. The prefix-stripping lookup-map code (replace("s__", "")) is unrelated and left unchanged.Verification
ruff+codespellclean.tests/test_gtdb.py+tests/test_metatraits.py: 45 passed.gtdb/utils.pyhas no imports).🤖 Generated with Claude Code