validate_preview.py

#!/usr/bin/env python3
"""Smoke-test PERMANOVA/MMD on preview_dataset.jsonl vs Chinese reference."""

from __future__ import annotations

import json
import sys
from pathlib import Path

ROOT = Path(__file__).resolve().parents[2]
sys.path.insert(0, str(ROOT.parent))

from bio_factory.config import CHINESE_CLINICAL_REF
from bio_factory.validation.fidelity_validator import FidelityValidator


def main() -> None:
    preview = Path(__file__).parent / "preview_dataset.jsonl"
    if not preview.exists():
        raise SystemExit(f"Missing {preview}")

    n = sum(1 for ln in preview.read_text().splitlines() if ln.strip())
    print(f"Preview records: {n}")

    validator = FidelityValidator(permanova_permutations=99)
    audit = validator.audit_chinese_cohort(preview, CHINESE_CLINICAL_REF)
    print(json.dumps({
        "overall_passed": audit["overall_passed"],
        "permanova_p": audit["permanova_p"],
        "mmd": audit["mmd"],
        "clinical_triplet_p": audit.get("clinical_triplet_p"),
    }, indent=2))


if __name__ == "__main__":
    main()