Verifying a Genomarker Receipt

How to verify

1. Download the receipt's JSON: add .json to its public link, /r/<token>.json.
2. Copy the provenance hash from the Verify section of the receipt's public page.
3. Run one of the reference verifiers below with two arguments: the path to the JSON file and the provenance hash. It prints PASS and exits 0 when the hashes match, prints FAIL and exits 1 when they do not, and exits 2 if an argument is missing.
4. Optionally, ask Genomarker to confirm the hash. On the same site that serves the receipt page, request GET /api/receipts/by-hash/<provenance hash> — with or without the sha256: prefix. A published hash returns found: true, the receipt's public_url and its status (published, unpublished or revoked); an unknown hash returns 404 with found: false. Do not rely on a receipt whose status is unpublished or revoked.

What this proves

• Byte-equivalence: the receipt JSON you hold is canonically identical to the receipt Genomarker published at that link.
• Integrity of metadata: its parameters, software environment, dataset fingerprint and result hashes are unmodified.

What this does not prove

• Bit-replay: the receipt does not by itself let a third party re-run the analysis. Replay requires Genomarker's independent replay engine and its CLI — in development, mid-2027.
• Identity: the hash alone does not prove who issued a receipt. Genomarker's public lookup confirms that Genomarker published a receipt with exactly that hash, and its current status. Receipts from schema 1.8.0 onward also carry a detached ES256 signature over the rigor verdict (integrity.signing); the verify.py and verify.mjs in the receipt's .zip bundle check it offline against the keys published at /.well-known/genomarker-signing-jwks.json. Earlier receipts carry none.

Reference verifier — Python

pip install rfc8785

import hashlib
import json
import sys

import rfc8785

if len(sys.argv) != 3:
    print("usage: python3 verify_receipt.py RECEIPT_JSON PROVENANCE_HASH", file=sys.stderr)
    sys.exit(2)

with open(sys.argv[1], "rb") as f:
    payload = json.loads(f.read())

expected = sys.argv[2].strip().lower()
if not expected.startswith("sha256:"):
    expected = "sha256:" + expected

subject = {k: v for k, v in payload.items() if k != "integrity"}
recomputed = "sha256:" + hashlib.sha256(rfc8785.dumps(subject)).hexdigest()

print("PASS" if expected == recomputed else "FAIL")
print(f"expected={expected}")
print(f"recomputed={recomputed}")
sys.exit(0 if expected == recomputed else 1)

python3 verify_receipt.py receipt.json sha256:<provenance hash>

Reference verifier — Node

npm install canonicalize

import { readFileSync } from "node:fs";
import { createHash } from "node:crypto";
import canonicalize from "canonicalize";

if (process.argv.length !== 4) {
  console.error("usage: node verify-receipt.mjs RECEIPT_JSON PROVENANCE_HASH");
  process.exit(2);
}

const payload = JSON.parse(readFileSync(process.argv[2], "utf8"));

let expected = process.argv[3].trim().toLowerCase();
if (!expected.startsWith("sha256:")) expected = "sha256:" + expected;

const subject = { ...payload };
delete subject.integrity;
const recomputed = "sha256:" + createHash("sha256").update(canonicalize(subject)).digest("hex");

console.log(expected === recomputed ? "PASS" : "FAIL");
console.log("expected=" + expected);
console.log("recomputed=" + recomputed);
process.exit(expected === recomputed ? 0 : 1);

node verify-receipt.mjs receipt.json sha256:<provenance hash>

JSON Schema

The full schema for the receipt 1.x family (1.0.0, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0, 1.6.0, 1.7.0, 1.8.0, 1.9.0, 1.10.0, and 1.11.0) is published at https://genomarker.com/schemas/receipt-1.0.0.json. Minor bumps add optional fields only and keep this URL — 1.1.0 adds the optional method.handler_specific keys calibration_metrics, decision_curve_analysis, and subgroup_performance (emitted by model-training receipts). 1.2.0 adds the optional method.handler_specific.data_quality confounder pre-flight block (emitted by differential-expression receipts). 1.3.0 adds the optional method.handler_specific.analysis_classification field (one of "pre-specified", "post-hoc", or "exploratory") and the optional method.handler_specific.sap provenance block ({id, payload_sha256, zenodo_doi, locked_at, amendment_chain_depth}) — pre-registered analysis plan support. 1.4.0 adds the optional method.handler_specific.reporting_checklists block (TRIPOD+AI / REMARK / STARD-AI checklists, emitted by every inferential handler with applicable checklists) and the optional method.handler_specific.reporting_supplements block (frozen prose snapshot at publish-time). 1.5.0 adds the optional method.handler_specific.repro_score block (Reproducibility Score emission — composite 0-100 + letter A/B/C/D/F + 12 per-axis grades + evidence- link map). 1.6.0 adds the optional method.handler_specific.ingest_quality block (robust ingest — upload-time gene-ID harmonization + Excel repair + PHI screen + colData alignment + TPM rejection, with the tiered verdict hard-refuse / block-with-override / warn / ok). 1.7.0 adds the optional method.handler_specific.gate block (tiered gate and signed record — the composite severity-tiered gate verdict across confounder / colData / PHI / high-unmappable / ML-leakage / plan-amendment surfaces, plus the signed-override attribution when a block-with-override was waived). 1.8.0 fills the previously-reserved integrity.signing slot (RO-Crate / PROV emission — a detached ES256 JWS over the count-only rigor verdict, verdict_status "origin-signed-replay-pending" — PHI-free and offline-verifiable; null on legacy receipts). 1.9.0 adds the optional method.handler_specific.methods_parse block (Methods-Diff — the reproducibility-relevant metadata of the Claude Sonnet 4.6 LLM call that parsed external paper Methods prose into a typed MethodsCandidate — source + prose/system-prompt/parsed-candidate SHA-256s + parser provider/model/version + target handler type + user-confirm timestamp + token counts; emitted only by the methods_parse handler). 1.10.0 adds the optional method.handler_specific.sc_aggregation block (PHI-safe counts-only pseudobulk reduction, emitted by the sc_pseudobulk handler) and the optional method.handler_specific.mast block (MAST mixed-model method, emitted by the sc_mast handler) — single-cell differential expression. 1.11.0 adds the optional method.handler_specific.evidence_sources_used block (version-only evidence provenance — bundle_version + per-source {version, license} + bundle sha256, no gene list; embedded only at export time when a gene-evidence reference is included) — the gene evidence card. The schema URL is forever-stable; future major versions get new URLs.

Scope notes

The stdlib-only verifiers shipped inside receipt.zip use a hand-rolled canonicalization that is correct for typical payloads but does not cover every RFC 8785 edge case (exotic floats, surrogate-pair keys, U+2028/U+2029). For production verification or audit, prefer the reference snippets above.