Export mapped variants and add README for public data dump#728
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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 - Gate dump annotation files on the presence of current mapped variants, so score sets whose mappings are all superseded no longer emit empty or stale annotation files.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.
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Coverage Report for CI Build 27652871621Coverage decreased (-0.2%) to 88.96%Details
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Coverage Regressions25 previously-covered lines in 4 files lost coverage.
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Reopens the erroneously closed #711.