just-dna-enricher

The network tier of the just-dna workspace. It fills the source-independent resolution table (resolution.csv) that just-dna-compiler consumes — Ensembl cache → HuggingFace snapshot → ClinVar cache → live Ensembl (V2 GraphQL, with a V1 REST fallback on 500/503, and tenacity retries) — then hands off to a deterministic, offline compile. The ClinVar link sits after the Ensembl cache so a variant both references know keeps its Ensembl alts/source and no already-compiled module's digest moves; it is a complementary reference that makes an offline clinical enrich possible without the 14 GB dbSNP cache.

It is the only package in the workspace allowed to fetch: just-dna-format and just-dna-compiler stay strictly inject-only (CONSTITUTION Goal 2 + the 0.5 amendment). The dependency arrow points inward — enricher → compiler → format — so httpx / huggingface_hub never enter the compile path.

just-dna-enricher enrich spec/ --strict            # write spec/resolution.csv
just-dna-enricher enrich spec/ --offline           # cache-only, zero egress
just-dna-enricher enrich-and-compile spec/ out/    # enrich, then compile from resolution.csv
just-dna-enricher upload out/coronary --dry-run    # publisher surface ([dev]): plan an HF upload
just-dna-enricher upload out/coronary              # upload compiled artifacts to the HF collection
just-dna-enricher clinvar build --vcf clinvar.vcf.gz --out cv/   # build the ClinVar snapshot ([dev])
just-dna-enricher clinvar publish cv/              # create-or-update datasets/just-dna-seq/clinvar

Publisher / [dev] surface. Snapshot download is part of the runtime enrich chain; the publisher half is upload — pushing a compiled module (parquet + manifest) or a built ClinVar reference snapshot (data/*.parquet + release.json) to a HuggingFace dataset repo — plus the ClinVar builder (clinvar build, which needs polars). Install it explicitly:

pip install 'just-dna-enricher[dev]'
# or, in this workspace:
uv sync --package just-dna-enricher --group dev

Downstream repos (ensembl-mcp, just-dna-lite/pipelines) adopt this package as the single source of truth for variant resolution instead of maintaining their own query/download code. Lite's pipelines v1-port publish still has a local copy until it adopts the 0.5 enricher tier; the canonical publisher API is just_dna_enricher.upload.