File size: 2,887 Bytes
fcbea81 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 | #!/usr/bin/env python3
"""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())
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