Refactor ChEBI models to ignore extra fields #95
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Updated ChEBI-related Pydantic models to use ConfigDict(extra="ignore") for better compatibility with API responses containing unexpected fields. Removed unused fields and simplified model definitions. Added an integration test for fetching ChEBI entries without a definition.
JR-1991
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94-fetch-rhea-for-23-butanediol-dehydrogenase-fails
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This pull request refactors the ChEBI fetcher data models to be more robust against unexpected fields in the API response, as has been reported in #94, and simplifies their structure. It also introduces a new integration test for fetching ChEBI entries without a definition. The most important changes are grouped below:
Data Model Simplification and Robustness
ChEBIName,ChEBINames,ChEBIChemicalData, and many fields fromChEBIStructure,ChEBIEntryData, andChEBIEntryResult), streamlining the models to only include fields used by the codebase.model_config = ConfigDict(extra="ignore")to the main ChEBI data models (ChEBIStructure,ChEBIEntryData,ChEBIEntryResult, andChebiSearchResult) to ignore any unexpected fields returned by the ChEBI API, making the fetcher more robust to upstream changes. [1] [2]pyenzyme/fetcher/chebi.py.Testing Improvements
test_fetch_chebi_wo_defintionto ensure the fetcher can handle ChEBI entries that lack a definition.This change is