| """Filter the small catalog first; downloads require --download and a byte budget.""" |
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| from concurrent.futures import ThreadPoolExecutor |
| from pathlib import Path |
|
|
| from hesrt_io import RELEASE_TAG, download_sample, load_catalog |
|
|
|
|
| def main() -> None: |
| parser = argparse.ArgumentParser(description=__doc__) |
| for field in ["organism", "technology", "gse", "gsm", "tissue", "disease"]: |
| parser.add_argument("--" + field) |
| parser.add_argument("--limit", type=int) |
| parser.add_argument("--download", action="store_true") |
| parser.add_argument("--max-gb", type=float, default=2.0) |
| parser.add_argument("--workers", type=int, default=4) |
| parser.add_argument("--revision", default=RELEASE_TAG) |
| parser.add_argument("--output", type=Path, default=Path("hesrt_subset")) |
| parser.add_argument("--cache-dir") |
| args = parser.parse_args() |
| if not 1 <= args.workers <= 8 or args.max_gb <= 0 or (args.limit is not None and args.limit < 1): |
| parser.error("Use 1-8 workers, a positive byte budget and a positive limit") |
| frame, revision = load_catalog(args.revision, args.cache_dir) |
| for argument, field in [("organism", "organism"), ("technology", "technology"), ("gse", "gse_id"), ("gsm", "gsm_id")]: |
| value = getattr(args, argument) |
| if value: |
| frame = frame.loc[frame[field].eq(value)] |
| for field in ["tissue", "disease"]: |
| value = getattr(args, field) |
| if value: |
| frame = frame.loc[frame[field].str.contains(value, case=False, regex=False, na=False)] |
| frame = frame.sort_values(["archive_bytes", "gsm_id"]) |
| if args.limit is not None: |
| frame = frame.head(args.limit) |
| args.output.mkdir(parents=True, exist_ok=True) |
| frame.to_csv(args.output / "selection.csv", index=False) |
| summary = {"revision": revision, "samples": len(frame), "studies": int(frame.gse_id.nunique()), |
| "compressed_gb": float(frame.archive_bytes.sum()) / 1e9, |
| "uncompressed_gb": float(frame.uncompressed_bytes.sum()) / 1e9, |
| "mode": "download" if args.download else "dry_run"} |
| (args.output / "selection.json").write_text(json.dumps(summary, indent=2) + "\n") |
| print(json.dumps(summary, indent=2), flush=True) |
| if not len(frame): |
| parser.error("No matching samples; inspect available labels in the catalog") |
| if not args.download: |
| print("No sample packages downloaded. Add --download after reviewing selection.csv.") |
| return |
| if summary["compressed_gb"] > args.max_gb: |
| parser.error("Selection exceeds --max-gb; narrow it or explicitly raise the budget") |
| def fetch(row: dict) -> str: |
| return str(download_sample(row, args.output, revision, args.cache_dir)) |
| with ThreadPoolExecutor(max_workers=args.workers) as pool: |
| for folder in pool.map(fetch, frame.to_dict("records")): |
| print(folder, flush=True) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
