feat: VRS Correctness#106
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Add `vrs_utils.identify_allele` and `normalize_and_identify`, and switch `vrs_map._construct_vrs_allele` to use them in place of direct `ga4gh_identify` calls. The GA4GH Merkle-tree caches sub-object digests on the object after first identification, so any subsequent mutation (notably the pre-map `refgetAccession` swap, normalization, or state coercion) leaves a stale id unless the cached digests are cleared first. Clearing both the location and allele digests before identification ensures the id always reflects current content. - vrs_utils: new module centralizing the digest-correctness invariant - vrs_map: route both the ref-identical and SNV/delins branches through the new helpers; the ref-identical branch also gains a reassigned `normalize` return value as a side-effect - tests/test_vrs_utils: offline coverage for content-addressing, the stale-digest clearing invariant, the normalize+identify pairing, and the malformed-input error path - align: incidental formatter-driven whitespace tweak
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coverage: 0.0%. remained the same — feature/bencap/vrs-correctness into mavedb-dev |
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This pull request introduces a new utility module to centralize and enforce correct GA4GH VRS allele identification, addressing a subtle bug where cached digests could result in stale or incorrect identifiers after object mutation or normalization. All allele identification is now routed through new helper functions to guarantee digest correctness. The change also includes comprehensive tests for these helpers and updates existing code to use them.
VRS allele identification and normalization improvements:
vrs_utils.pywithidentify_alleleandnormalize_and_identifyhelpers, ensuring that all GA4GH VRS allele identifiers are recomputed from current object content and not affected by stale cached digests._construct_vrs_alleleinvrs_map.pyto usenormalize_and_identifyandidentify_alleleinstead of callingga4gh_identifydirectly, enforcing the new digest-correctness invariant. [1] [2]ga4gh_identifyfromvrs_map.py, further centralizing identification logic in the new utility.vrs_map.pyfor use in allele construction.Testing:
test_vrs_utils.pywith thorough tests covering digest correctness, mutation safety, normalization pairing, and error handling in the new helper functions.Other:
_run_blatfor readability (no functional change).