Add offline WURCS-to-SMILES glycan translator and wire it into both pipelines - #10
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…ipelines Replaces the currently-broken live GlyTouCan glycoct chain (confirmed 0% success, GlyTouCan's API stopped returning glycoct) with an offline glypy -> IUPAC-condensed -> GlyLES route for the cognate-ligand master set (get_ec_information.py), added as a fallback after the existing live chain. For PDB bound-entity glycans (process_all_pdb_contacts.py), where the live chain still works but carries real reliability risk (unthrottled, no retry, HTML-scraped CSDB endpoint), the offline route is used as the primary path instead, falling back to the live chain only on failure. Benchmarked (see docs/iupac_translator_plan.md for full methodology): - cognate-ligand master set: 0% live chain -> 89.1% offline (of glycans with a GlyTouCan ID at all) - PDB-deposited glycans: 96% offline vs. a working-but-fragile live chain Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
nextflow/bin/wurcs_to_iupac.py: an offline translator from WURCS glycan notation to GlyLES-compatible IUPAC-condensed notation, built onglypy's structured WURCS parse.get_smiles_from_wurcs_offline()toutils.py, wrapping the translator +glylesconversion with a timeout guard (GlyLES is known to hang on malformed input instead of failing fast).get_ec_information.py(cognate-ligand master set, GlyTouCan-sourced): added as a fallback after the existing live glycoct/CSDB chain — that live chain is confirmed dead (0% success, GlyTouCan's API stopped returningglycoct).process_all_pdb_contacts.py(PDB bound-entity glycans): made the primary path, live chain now only runs as fallback — the live chain still works here but carries real reliability risk (unthrottled, no retry, HTML-scraped CSDB endpoint).glypy/glylestonextflow/envs/procoggraph.yaml.Benchmarked against real data (see
docs/iupac_translator_plan.mdfor full methodology): 0% → 89.1% on the real cognate-ligand master set glycans with a GlyTouCan ID; 96% on a real sample of PDB-deposited glycan structures.Stacked on #9 (feature/kegg-bulk-source-priority) — this PR's diff is scoped to just the glycan translation work.
Test plan
nextflow/bin/tests/test_wurcs_to_iupac.py— translator regression tests (13 assertions across known-good structures, furanose-suffix handling, undefined-anomer handling, and confirmed-unsupported substituents)nextflow/bin/tests/test_utils_glycan_offline.py— offline helper + Context B fallback-wiring tests (mocked, no live network calls)nextflow/bin/tests/test_get_ec_information_glycan_fallback.py— Context A backfill-masking logic validated in isolation🤖 Generated with Claude Code