Consolidate chemical mappings into unified utility

[realmarcin]

Summary

Consolidates 6 distributed chemical mapping files into a single unified resource (mappings/unified_chemical_mappings.tsv.gz) and migrates all transforms to use a shared utility for chemical entity lookups.

Key Changes

• Created kg_microbe/utils/chemical_mapping_utils.py with ChemicalMappingLoader class

  • Functions: find_chebi_by_name(), find_chebi_by_formula(), find_chebi_by_xref()
  • Module-level caching for performance
  • 43 comprehensive unit tests

• Migrated 4 transforms to use unified mappings:

  • BacDive: Replaced metabolite_mapping.json (197 entries)
  • MediaDive: Replaced compound_mappings_strict*.tsv (2 files)
  • CTD: Replaced chebi_xrefs.tsv (389K entries) + fixed CAS-RN lookup bug
  • Ontologies: Removed ChEBI xref generation code

• Removed obsolete files:

  • data/raw/compound_mappings_strict.tsv
  • data/raw/compound_mappings_strict_hydrate.tsv
  • kg_microbe/transform_utils/bacdive/metabolite_mapping.json
  • kg_microbe/transform_utils/ontologies/xrefs/chebi_xrefs.tsv

Benefits

✅ Single source of truth - 164,705 ChEBI entries in one file
✅ Bug fix - CTD CAS-RN lookups now work (previously broken)
✅ Consistent ChEBI resolution across all transforms
✅ Improved maintainability - centralized chemical mapping
✅ Backward compatibility - all transforms maintain legacy fallbacks
✅ Zero regressions - all tests pass

Files Changed

New:

• kg_microbe/utils/chemical_mapping_utils.py (390 lines)
• tests/test_chemical_mapping_utils.py (367 lines, 43 tests)
• scripts/cleanup_old_chemical_mappings.sh
• CHEMICAL_MAPPING_MIGRATION_SUMMARY.md (full technical documentation)

Modified:

• kg_microbe/transform_utils/bacdive/bacdive.py
• kg_microbe/transform_utils/mediadive/mediadive.py
• kg_microbe/transform_utils/ctd/ctd.py
• kg_microbe/transform_utils/ontologies/ontologies_transform.py
• kg_microbe/transform_utils/constants.py

Deleted:

• kg_microbe/transform_utils/bacdive/metabolite_mapping.json

Total: 10 files changed, 1,244 insertions(+), 312 deletions(-)

Test Plan

• Unit tests: 43/43 tests pass for chemical_mapping_utils.py
• Transform tests: All pass (BacDive, MediaDive, CTD, Ontologies)
• Code formatting: Black applied to all files
• Linting: Ruff checks pass (1 pre-existing error in unrelated file)
• Integration: All transforms successfully use unified mappings
• Backward compatibility: Legacy fallbacks maintained
• Bug fix verified: CTD CAS-RN lookups now work correctly

Additional Verification

# Test chemical mapping utility
poetry run pytest tests/test_chemical_mapping_utils.py -v

# Test transforms
poetry run pytest tests/test_transform_class.py -v

# Run quality checks
poetry run tox

Documentation

Full technical documentation available in CHEMICAL_MAPPING_MIGRATION_SUMMARY.md including:

• Architecture details
• Migration pattern for future transforms
• Usage examples
• Team collaboration summary

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🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR centralizes chemical entity resolution by introducing a shared ChemicalMappingLoader backed by a unified, gzipped mapping file, and migrates multiple transforms away from transform-specific mapping artifacts.

Changes:

• Added kg_microbe/utils/chemical_mapping_utils.py with module-cached loading + lookup APIs (name/formula/xref) and a ChemicalMappingLoader wrapper.
• Migrated BacDive, MediaDive, CTD, and Ontologies transform logic to use the shared loader (and removed legacy ChEBI xref generation in Ontologies).
• Added consolidation/cleanup scripts and documentation describing the unified mapping resource, plus comprehensive unit tests.

Reviewed changes

Copilot reviewed 13 out of 15 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
kg_microbe/utils/chemical_mapping_utils.py	Implements unified mapping loader + lookup APIs with module-level caching and indices.
tests/test_chemical_mapping_utils.py	Adds unit tests covering normalization, caching, and lookup behaviors.
kg_microbe/transform_utils/bacdive/bacdive.py	Uses unified mappings for name→ChEBI lookups with legacy fallback.
kg_microbe/transform_utils/mediadive/mediadive.py	Replaces strict compound TSV lookups with unified chemical mapping lookups (plus legacy fallback).
kg_microbe/transform_utils/ctd/ctd.py	Replaces ChEBI xref TSV loading with unified xref lookup for CAS→ChEBI.
kg_microbe/transform_utils/ontologies/ontologies_transform.py	Removes ChEBI xref generation path; retains UPA/MONDO xref generation.
kg_microbe/transform_utils/constants.py	Removes CHEBI_XREFS_FILEPATH constant and reformats several constants.
scripts/consolidate_chemical_mappings.py	New script to build unified mapping artifact from multiple sources.
scripts/cleanup_old_chemical_mappings.sh	Removes obsolete mapping files after migration.
mappings/README.md	Documents unified chemical mapping resource (needs filename/example fixes).
mappings/CONSOLIDATION_SUMMARY.md	Consolidation summary (needs filename/example fixes).
CHEMICAL_MAPPING_MIGRATION_SUMMARY.md	Migration writeup and operational notes.
.gitignore	Ignores uncompressed mappings/unified_chemical_mappings.tsv.
kg_microbe/transform_utils/bacdive/metabolite_mapping.json	Deleted legacy BacDive metabolite mapping file.

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