OneScience-Group/AlphaFold3_dataset

1#!/usr/bin/env python32from __future__ import annotations3 4import argparse5import hashlib6import json7from pathlib import Path8 9try:10    import yaml11except ImportError as exc:12    raise SystemExit("PyYAML is required for dataset validation: pip install pyyaml") from exc13 14 15def sha256(path: Path) -> str:16    h = hashlib.sha256()17    with path.open("rb") as f:18        for chunk in iter(lambda: f.read(1024 * 1024), b""):19            h.update(chunk)20    return h.hexdigest()21 22 23def check_json(path: Path) -> None:24    data = json.loads(path.read_text(encoding="utf-8"))25    if data.get("dialect") != "alphafold3":26        raise AssertionError(f"{path} dialect is not alphafold3")27    if "sequences" not in data or not data["sequences"]:28        raise AssertionError(f"{path} has no sequences")29 30 31def main() -> None:32    parser = argparse.ArgumentParser()33    parser.add_argument("--root", default=".")34    parser.add_argument("--skip-hash", action="store_true")35    args = parser.parse_args()36 37    root = Path(args.root).resolve()38    manifest = yaml.safe_load((root / "metadata" / "file_manifest.yaml").read_text(encoding="utf-8"))39 40    for entry in manifest["dataset_directories"]:41        path = root / entry["path"]42        if not path.exists():43            raise AssertionError(f"missing linked dataset directory: {entry['path']}")44 45    for entry in manifest["files"]:46        path = root / entry["path"]47        if not path.is_file():48            raise AssertionError(f"missing verified data file: {entry['path']}")49        if path.name != Path(entry["source_path"]).name:50            raise AssertionError(f"filename mismatch: {entry['path']}")51        if path.stat().st_size != entry["size_bytes"]:52            raise AssertionError(f"size mismatch: {entry['path']}")53        if not args.skip_hash and sha256(path) != entry["sha256"]:54            raise AssertionError(f"sha256 mismatch: {entry['path']}")55 56    check_json(root / "data" / "infer_input_data" / "all_data" / "7r6r_data.json")57    check_json(root / "data" / "infer_input_data" / "all_data" / "t1119_data.json")58    print("dataset_validation_ok: true")59 60 61if __name__ == "__main__":62    main()63