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just-dna-format

The declarative schema + integrity contract for just-dna annotation modules: both the authored input DSL and the compiled manifest.json. Dependency-light (Pydantic + cryptography, for Ed25519 signature verification) so it can be shared as the single source of truth by:

  • just-dna-compiler — the reference transform (spec → parquet artifact + manifest);
  • just-dna-pipelinesemits manifest.json when it compiles a module;
  • just-dna-marketplaceindexes, serves, and verifies those manifests;
  • just-dna-agents — authoring support (renders reference.authoring_reference()).

Keeping the contract in one small package prevents the sides from drifting.

What's here

Module Contents
just_dna_format.spec The authored DSL: ModuleSpecConfig, VariantRow, StudyRow, ModuleInfo, Defaults (+ extract_pmids).
just_dna_format.binning The measure→phenotype primitive: MeasureBinRow + Activity/CopyNumber/RepeatAllele/Heteroplasmy rows and validate_bins (0.4).
just_dna_format.pgx PGx star-allele model: HaplotypeRow, AlleleFunctionRow, DiplotypeRow, PharmVariantRow (0.4).
just_dna_format.pgs PgsRow — a curated PGS-Catalog interface with ancestry-validity fields (0.4).
just_dna_format.vocab Shared constrained vocabularies, identifier grammars, and validator helpers.
just_dna_format.derive Legacy state/ClinVar-boolean → 0.3-axis derivations (total, idempotent).
just_dna_format.manifest ModuleManifest + sub-models (Identity, Display, Stats, Compilation, FileEntry, Artifact, Provenance, Signature, GenePanelSpec); read_manifest / write_manifest. SPEC §4.
just_dna_format.integrity sha256_file, artifact_digest (canonical Merkle root), build_artifact, verify_manifest, verify_signature, IntegrityError. SPEC §5.
just_dna_format.signing Ed25519 signing over artifact.digest (key management side).
just_dna_format.aggregate Cross-version log / provenance union helpers.
just_dna_format.reference authoring_reference() / json_schemas() — drift-proof DSL description generated from the live models.
just_dna_format.identity Name/namespace rules, canonical_id, SemVer Version + parse_version, version_from_legacy (vN → N.0.0), latest. SPEC §6.

Usage

from just_dna_format.manifest import ModuleManifest, read_manifest
from just_dna_format.integrity import build_artifact, verify_manifest

# Compiler side: hash outputs and record the digest.
artifact = build_artifact(output_dir, ["weights.parquet", "annotations.parquet", "studies.parquet"])

# Downloader side: verify before installing (raises IntegrityError on any mismatch).
verify_manifest(module_dir, read_manifest(module_dir / "manifest.json"))

All hashes are SHA-256, lowercase hex, prefixed sha256:. The artifact.digest is a Merkle-style root over the canonical file listing — verifying it verifies the whole set and is the version's immutable content identity.

Develop

uv sync
uv run pytest -vvv

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