#!/usr/bin/env python3 """Select CryoAtlas release archives, download them, and verify SHA-256.""" import argparse import hashlib import json from pathlib import Path from huggingface_hub import HfApi, hf_hub_download REPO = 'markfaa/CryoAtlas' def select_archives(manifest, args, entry_map=None): if args.part: parts = {f'train_part{n:02d}' for n in args.part} return [r for r in manifest if r['component'] in parts] if args.test: components = {'test_benchmark_618', 'test_remaining_534'} if args.test == 'all' else { 'test_benchmark_618' if args.test == 'benchmark' else 'test_remaining_534'} return [r for r in manifest if r['component'] in components] if args.resources: return [r for r in manifest if r['component'] == 'benchmark_resources'] emd = args.emd.upper() if not emd.startswith('EMD-'): emd = 'EMD-' + emd if emd not in entry_map: raise ValueError(f'{emd} is not in the fixed v1.0 release.') return [r for r in manifest if r['path'] == entry_map[emd]] def main(): parser = argparse.ArgumentParser(description=__doc__) group = parser.add_mutually_exclusive_group(required=True) group.add_argument('--part', type=int, choices=(1, 2, 3, 4), nargs='+') group.add_argument('--test', choices=('benchmark', 'remaining', 'all')) group.add_argument('--resources', action='store_true') group.add_argument('--emd', help='Find and download the complete archive containing this EMD ID.') parser.add_argument('--destination', type=Path, default=Path('CryoAtlas-downloads')) parser.add_argument('--revision', default='main') parser.add_argument('--dry-run', action='store_true', help='Show selected archives and sizes without downloading them.') args = parser.parse_args() # Pin all reads and downloads to one repository revision. revision = HfApi().dataset_info(REPO, revision=args.revision).sha def read_json(name): return json.loads(Path(hf_hub_download(REPO, name, repo_type='dataset', revision=revision)).read_text()) manifest = read_json('resources/metadata/catalog/archives.json') entry_map = read_json('resources/metadata/catalog/entry_archives.json') if args.emd else None try: selected = select_archives(manifest, args, entry_map) except ValueError as exc: parser.error(str(exc)) if not selected: parser.error('No matching archives.') print(f'Revision: {revision}') for row in selected: print(f"{row['bytes']/1e9:8.3f} GB {row['path']}") print(f"Total: {sum(r['bytes'] for r in selected)/1e9:.3f} GB") if args.emd: print('Selection is an entire archive containing this entry, not an individual-entry download.') if args.dry_run: return for row in selected: path = Path(hf_hub_download(REPO, row['path'], repo_type='dataset', revision=revision, local_dir=args.destination)) if path.stat().st_size != row['bytes']: raise RuntimeError(f'Size mismatch: {row["path"]}') sha = hashlib.sha256() with path.open('rb') as stream: for block in iter(lambda: stream.read(8 * 1024 * 1024), b''): sha.update(block) if sha.hexdigest() != row['sha256']: raise RuntimeError(f'SHA-256 mismatch: {row["path"]}') print(f'Verified: {row["path"]}') if __name__ == '__main__': main()