Release 2026.2.5#777
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Add and modified related tests.
Add an alembic file.
…seded score set now.
…onstraintToReplacesId Bugfix/estelle/706/unique constraint to replaces
Emit a va/{urn}.va.ndjson file per mapped score set in the public data
export, one record per current mapped variant carrying its highest
materialized VA-Spec layer.
- add variant_highest_level_annotation to resolve the highest available
layer (pathogenicity > functional statement > study result), returning
None for variants without a post-mapped allele
- extract get_current_mapped_variants_for_annotation as the shared
eager-load source of truth for the annotated-variant endpoints and the
export, and route the three streaming routers through it
- document the va/ output, layer ladder, and the functional-evidence-only
caveat in the dump README
- cover the resolver with unit tests across the uncalibrated, functional,
pathogenicity, and unmapped cases
- Omit the score-calibration "Baseline score" extension when no baseline score exists. Extension.value is required, so a null value was stripped by model_dump(exclude_none=True) and the object no longer re-parsed through the VA-Spec models. This also corrects the API's VA-Spec streaming endpoints, which share the builder. - Gate dump annotation files on the presence of current mapped variants, so score sets whose mappings are all superseded no longer emit empty or stale annotation files. - Newline-terminate every NDJSON record to match the API streams and keep line-based consumers happy. - Add regression tests covering the baseline-score extension round-trip.
…-mapped-variants-in-dump Export mapped variants and add README for public data dump
Coverage Report for CI Build 28065435907Coverage decreased (-0.06%) to 89.135%Details
Uncovered Changes
Coverage RegressionsNo coverage regressions found. Coverage Stats
💛 - Coveralls |
Relocks python-multipart 0.0.27 -> 0.0.32 and idna 3.13 -> 3.18 within existing pyproject constraints to clear Dependabot alerts. Major bumps required for starlette/fastapi and cryptography are tracked in #778; ecdsa has no patched version available.
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Features
Bug Fixes
replaces_idshould have a unique constraint #706 via Bugfix/estelle/706/unique constraint to replaces #738Maintenance
N/A