| |
| """Validate the standardized OneScience MatPL dataset package.""" |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| import hashlib |
| import sys |
| from pathlib import Path |
|
|
| import numpy as np |
|
|
|
|
| EXPECTED_TOP_LEVEL = ["AuAg", "Cu", "HfO2", "LiSiC"] |
|
|
|
|
| def sha256_file(path: Path) -> str: |
| digest = hashlib.sha256() |
| with path.open("rb") as handle: |
| for chunk in iter(lambda: handle.read(1024 * 1024), b""): |
| digest.update(chunk) |
| return digest.hexdigest() |
|
|
|
|
| def require_file(path: Path) -> None: |
| if not path.is_file(): |
| raise FileNotFoundError(f"missing file: {path}") |
|
|
|
|
| def require_dir(path: Path) -> None: |
| if not path.is_dir(): |
| raise FileNotFoundError(f"missing directory: {path}") |
|
|
|
|
| def check_movement(path: Path) -> None: |
| require_file(path) |
| with path.open(encoding="utf-8", errors="replace") as handle: |
| text = handle.read(4096) |
| if not text.strip(): |
| raise ValueError(f"empty MOVEMENT file: {path}") |
| if "Iteration" not in text and "atoms" not in text.lower() and "lattice" not in text.lower(): |
| raise ValueError(f"unexpected MOVEMENT header: {path}") |
|
|
|
|
| def check_xyz(path: Path) -> None: |
| require_file(path) |
| with path.open(encoding="utf-8", errors="replace") as handle: |
| first = handle.readline().strip() |
| second = handle.readline() |
| atoms = int(first) |
| if atoms <= 0: |
| raise ValueError(f"invalid xyz atom count in {path}") |
| if not second: |
| raise ValueError(f"missing xyz comment line in {path}") |
|
|
|
|
| def check_npy(path: Path) -> None: |
| require_file(path) |
| arr = np.load(path, allow_pickle=False) |
| if arr.size == 0: |
| raise ValueError(f"empty npy array: {path}") |
|
|
|
|
| def read_checksum_manifest(path: Path) -> list[tuple[str, str]]: |
| require_file(path) |
| entries: list[tuple[str, str]] = [] |
| with path.open(encoding="utf-8") as handle: |
| for line_no, raw in enumerate(handle, start=1): |
| line = raw.strip() |
| if not line: |
| continue |
| parts = line.split(None, 1) |
| if len(parts) != 2: |
| raise ValueError(f"invalid checksum line {line_no}: {raw!r}") |
| entries.append((parts[0], parts[1])) |
| return entries |
|
|
|
|
| def validate_checksums(package_root: Path, manifest_path: Path) -> int: |
| entries = read_checksum_manifest(manifest_path) |
| for expected_hash, rel_path in entries: |
| target = package_root / rel_path |
| require_file(target) |
| if sha256_file(target) != expected_hash: |
| raise ValueError(f"checksum mismatch: {rel_path}") |
| return len(entries) |
|
|
|
|
| def main() -> int: |
| parser = argparse.ArgumentParser(description=__doc__) |
| parser.add_argument("--dataset-root", default="data/MatPL") |
| parser.add_argument("--checksum-manifest", default="metadata/sha256_manifest.txt") |
| parser.add_argument("--skip-checksum", action="store_true") |
| args = parser.parse_args() |
|
|
| package_root = Path.cwd() |
| dataset_root = Path(args.dataset_root) |
| for name in EXPECTED_TOP_LEVEL: |
| require_dir(dataset_root / name) |
|
|
| check_movement(dataset_root / "Cu/pwdata/0_300_MOVEMENT") |
| check_movement(dataset_root / "Cu/pwdata/1_500_MOVEMENT") |
| check_movement(dataset_root / "Cu/pwdata/valid_movement") |
| check_xyz(dataset_root / "AuAg/AuAg-5762.xyz") |
|
|
| npy_files = sorted(dataset_root.glob("**/*.npy")) |
| if len(npy_files) < 100: |
| raise ValueError(f"too few npy files: {len(npy_files)}") |
| for sample in npy_files[:8]: |
| check_npy(sample) |
|
|
| checksum_count = 0 |
| if not args.skip_checksum: |
| checksum_count = validate_checksums(package_root, Path(args.checksum_manifest)) |
|
|
| print("MatPL dataset validation passed") |
| print(f"top-level systems: {', '.join(EXPECTED_TOP_LEVEL)}") |
| print(f"npy files: {len(npy_files)}") |
| print(f"checksum entries verified: {checksum_count}") |
| return 0 |
|
|
|
|
| if __name__ == "__main__": |
| try: |
| raise SystemExit(main()) |
| except Exception as exc: |
| print(f"MatPL dataset validation failed: {exc}", file=sys.stderr) |
| raise SystemExit(1) |
|
|
