| |
| """Smoke-test generated STRING Parquet configs with the Hugging Face datasets API.""" |
|
|
| import argparse |
| import glob |
| import sys |
| from pathlib import Path |
| from typing import Dict, List |
|
|
|
|
| CONFIGS = ( |
| "species", |
| "protein_info", |
| "protein_aliases", |
| "protein_sequences", |
| "protein_links", |
| ) |
|
|
| SPLITS = ("train", "validation", "test") |
|
|
|
|
| def parse_args() -> argparse.Namespace: |
| parser = argparse.ArgumentParser(description="Validate local or uploaded STRING HF dataset configs.") |
| parser.add_argument( |
| "--repo-id", |
| default=None, |
| help="Optional HF dataset repo id, for example LiteFold/STRING. If omitted, validates local Parquet.", |
| ) |
| parser.add_argument("--data-dir", type=Path, default=Path("data")) |
| parser.add_argument("--config", choices=CONFIGS, default="protein_links") |
| parser.add_argument("--split", default="train") |
| parser.add_argument("--streaming", action="store_true") |
| parser.add_argument("--preview-rows", type=int, default=3) |
| return parser.parse_args() |
|
|
|
|
| def local_data_files(data_dir: Path, config: str) -> Dict[str, List[str]]: |
| files: Dict[str, List[str]] = {} |
| for split in SPLITS: |
| pattern = str(data_dir / config / ("%s-*.parquet" % split)) |
| matches = sorted(glob.glob(pattern)) |
| if matches: |
| files[split] = matches |
| if not files: |
| raise SystemExit("No local Parquet files found for config %s under %s" % (config, data_dir)) |
| return files |
|
|
|
|
| def main() -> int: |
| args = parse_args() |
| try: |
| from datasets import load_dataset |
| except ImportError as exc: |
| raise SystemExit( |
| "datasets is required. Install dependencies with: python -m pip install -r requirements.txt" |
| ) from exc |
|
|
| if args.repo_id: |
| dataset = load_dataset(args.repo_id, args.config, split=args.split, streaming=args.streaming) |
| else: |
| files = local_data_files(args.data_dir, args.config) |
| if args.split not in files: |
| raise SystemExit( |
| "Split %s is not present locally for config %s. Available splits: %s" |
| % (args.split, args.config, ", ".join(sorted(files))) |
| ) |
| dataset = load_dataset("parquet", data_files=files, split=args.split, streaming=args.streaming) |
|
|
| print("config:", args.config) |
| print("split:", args.split) |
| print("features:", dataset.features) |
|
|
| if args.streaming: |
| iterator = iter(dataset) |
| for index in range(args.preview_rows): |
| try: |
| print("row[%d]:" % index, next(iterator)) |
| except StopIteration: |
| break |
| else: |
| print("num_rows:", len(dataset)) |
| for index in range(min(args.preview_rows, len(dataset))): |
| print("row[%d]:" % index, dataset[index]) |
|
|
| return 0 |
|
|
|
|
| if __name__ == "__main__": |
| sys.exit(main()) |
|
|
