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Fix UniProt TrEMBL parsing, fetcher error chaining and id_mapping - #102
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- fetch_uniprot: parse unreviewed (TrEMBL) entries that only carry
submissionNames; fall back to the first submission name for name, id
and EC number. Optional model fields now have real defaults.
- fetch_uniprot: report 4xx responses as ValueError (invalid/unknown ID)
instead of ConnectionError, give a clear message for inactive
(deleted/merged) entries, and strip surrounding whitespace.
- compose: chain the last fetcher exception so the real cause shows up
in the traceback.
- compose: id_mapping now also updates species_id in reaction
reactants/products/modifiers, so mapped reactions no longer refer to
undeclared species.
- compose: id_mapping keys match whole IDs, case-insensitively
("CHEBI:1" no longer renames CHEBI:15377), and mappings that give two
species the same ID raise a ValueError.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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The lint workflow installed the latest ruff, which reports hundreds of pre-existing issues across the codebase. Pin it to 0.15.22, the version .pre-commit-config.yaml already uses. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
UniProt fetcher
fetch_uniprot("Q7DDU0")failed withrecommendedName Field required: unreviewed (TrEMBL) entries only havesubmissionNames. The name, ID and EC number now fall back to the first submission name. TheOptionalmodel fields had no default, so Pydantic v2 still required them; they now default toNone.ValueError("invalid or not found"), not a misleadingConnectionError. Inactive (deleted/merged) entries get a clear message instead of a parse error. Surrounding whitespace in the ID is stripped.Composer
_fetch_with_fetcherschains the last fetcher exception (raise ... from), so the real cause shows up in the traceback.id_mappingnow also renamesspecies_idin reaction reactants/products/modifiers. Before,compose(reactions=["RHEA:19273"], id_mapping={"CHEBI:63153": "ManNAc"})produced a reaction referring to an undeclared species.id_mappingkeys match whole IDs, case-insensitively, instead of by substring:"CHEBI:1"used to rename water (CHEBI:15377)."CHEBI:63153","chebi:63153","63153"and"OBO:CHEBI_63153"all work.ValueErrorinstead of producing duplicate IDs.Behaviour change: a mapping key that only matched as a substring of an ID no longer matches.
Tests
tests/unit/test_uniprot.pyandtests/unit/test_composer.py; each fails against the previous code.Q7DDU0and the RHEA:19273 mapping intests/integration/.-m remotefetcher/composer tests pass locally.🤖 Generated with Claude Code
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