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-pipelines— emitsmanifest.jsonwhen it compiles a module;just-dna-marketplace— indexes, serves, and verifies those manifests;just-dna-agents— authoring support (rendersreference.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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