Release 2026.2.2#731
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bencap
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May 12, 2026
bencap
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- Fixes a bug where normalized HGVS was not being recognized as submitted succesfully to ClinGen
- Fixes a bug where variant recoder outputs were not being properly parsed and used in phase 3 of VEP lookup
…AR responses CAR's batch API guarantees responses are returned in the same order as submitted HGVS strings (per API docs). The previous HGVS string-matching approach failed when CAR normalized expressions (e.g. "delinsA" → "del"), because the submitted string never appeared in the returned allele's hgvs lists, silently dropping valid registrations into the failure path. - Replace `get_allele_registry_associations` with a direct `zip` of submitted HGVS strings and CAR responses in the job; positional correspondence is the documented contract - Remove `get_allele_registry_associations` from services.py and `is_car_submission_error` TypeGuard helper (replaced by inline `"errorType" in response` key check which pyright narrows correctly) - Write `MISSING_IDENTIFIER` failure annotations for variants that cannot produce a valid HGVS string before submission, rather than silently skipping them - Handle truncated CAR responses (network drop / service-side omission) via `hgvs_list[len(registered_alleles):]` with `EXTERNAL_API_ERROR` - Update tests: rename `no_linked_alleles` → `all_car_errors` with proper error-response mocks; remove tests for deleted function
…ocessing
- request_with_backoff: re-raise 4xx errors immediately (except 429,
which is retried); avoids ~10 min hang from exhausting retry sleeps
on unretryable client errors
- run_variant_recoder: catch HTTPError and return {} so a 400 from
Ensembl marks affected variants FAILED instead of aborting the job
- get_functional_consequence: same HTTPError handling; a 4xx on Phase 1
routes all variants to Recoder, a 4xx on Phase 3 marks them FAILED
- Phase 1: filter None consequences before storing; VEP returning a
None most_severe_consequence is now treated as a miss and routed
through Recoder rather than falling into the UNKNOWN outcome branch
- Phase 3: flatten hgvs_to_genomic.values() (list-of-lists) to a
deduplicated set of strings before batching; the previous code sent
nested lists to VEP which returned nothing
- Remove dead missing_hgvs_to_variant_ids variable
Add unit tests covering:
- None consequence routing to Recoder
- Most-severe priority selection across multiple genomic HGVS strings
- Multiple mapped variants sharing an HGVS all receiving the consequence
- Realistic Variant Recoder and VEP response format parsing (new file
tests/lib/test_vep.py)
Restore E2E network test for the Recoder fallback path with a protein
HGVS fixture (NP_009225.1:p.Val1696His).
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