tools/validate_dataset.py

#!/usr/bin/env python3
import argparse
import csv
import hashlib
from pathlib import Path

try:
    import yaml
except Exception as exc:
    raise SystemExit(f"PyYAML is required to parse manifest.yaml: {exc}")


def count_lines(path: Path) -> int:
    with path.open("r", encoding="utf-8") as handle:
        return sum(1 for line in handle if line.strip())


def sha256_file(path: Path) -> str:
    h = hashlib.sha256()
    with path.open("rb") as handle:
        for chunk in iter(lambda: handle.read(1024 * 1024), b""):
            h.update(chunk)
    return h.hexdigest()


parser = argparse.ArgumentParser()
parser.add_argument("--data-root", default=".")
parser.add_argument("--sample-pt", type=int, default=3)
parser.add_argument("--require-checksums", action="store_true")
args = parser.parse_args()

root = Path(args.data_root).resolve()
manifest_path = root / "manifest.yaml"
if not manifest_path.is_file():
    raise SystemExit(f"missing manifest: {manifest_path}")

data = yaml.safe_load(manifest_path.read_text(encoding="utf-8"))
required_keys = [
    "resource",
    "platform_resource",
    "website_integration",
    "runtime",
    "onescience",
    "runtime_package",
    "files",
    "relations",
    "run_matrix",
    "capabilities",
    "commands",
    "expected_outputs",
    "diagnostics",
    "domain_extension",
]
missing = [k for k in required_keys if k not in data]
if missing:
    raise SystemExit(f"missing manifest keys: {missing}")
if data["resource"]["id"] != "OneScience/proteinmpnn":
    raise SystemExit(f"unexpected resource id: {data['resource']['id']}")
if data["platform_resource"]["primary"]["repo_id"] != "OneScience/proteinmpnn":
    raise SystemExit("platform_resource.primary.repo_id mismatch")

ds = root / "pdb_2021aug02_sample"
for rel in ["README", "list.csv", "valid_clusters.txt", "test_clusters.txt"]:
    p = ds / rel
    if not p.is_file() or p.stat().st_size == 0:
        raise SystemExit(f"missing or empty file: {p}")

pdb_dir = ds / "pdb"
if not pdb_dir.is_dir():
    raise SystemExit(f"missing pdb dir: {pdb_dir}")

pt_files = sorted(pdb_dir.rglob("*.pt"))
if len(pt_files) != 870:
    raise SystemExit(f"unexpected pt file count: {len(pt_files)}")

with (ds / "list.csv").open("r", encoding="utf-8", newline="") as handle:
    reader = csv.DictReader(handle)
    expected = ["CHAINID", "DEPOSITION", "RESOLUTION", "HASH", "CLUSTER", "SEQUENCE"]
    if reader.fieldnames != expected:
        raise SystemExit(f"unexpected list.csv columns: {reader.fieldnames}")
    rows = 0
    for row in reader:
        rows += 1
        if rows <= 5 and not row["SEQUENCE"]:
            raise SystemExit("empty sequence in list.csv sample")
if rows <= 0:
    raise SystemExit("list.csv has no data rows")

valid_lines = count_lines(ds / "valid_clusters.txt")
test_lines = count_lines(ds / "test_clusters.txt")
if valid_lines <= 0 or test_lines <= 0:
    raise SystemExit("cluster split files must be non-empty")

checksum_path = root / "checksums.sha256"
if args.require_checksums and not checksum_path.is_file():
    raise SystemExit(f"missing checksum manifest: {checksum_path}")
if checksum_path.is_file():
    checksum_lines = count_lines(checksum_path)
    if checksum_lines < 874:
        raise SystemExit(f"checksum manifest has too few entries: {checksum_lines}")

sample = []
for path in pt_files[: max(args.sample_pt, 0)]:
    if path.stat().st_size <= 0:
        raise SystemExit(f"empty pt file: {path}")
    sample.append(f"{path.relative_to(root)}:{path.stat().st_size}:{sha256_file(path)[:16]}")

print("DATASET_VALIDATION_OK")
print(f"manifest_resource={data['resource']['id']}")
print(f"data_files={sum(1 for p in ds.rglob('*') if p.is_file())}")
print(f"pt_files={len(pt_files)}")
print(f"list_rows={rows}")
print(f"valid_clusters={valid_lines}")
print(f"test_clusters={test_lines}")
if sample:
    print("sample_pt=" + ",".join(sample))