File size: 4,704 Bytes
7e1f9af | 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 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | #!/usr/bin/env python3
import argparse
import gzip
import hashlib
import sys
from pathlib import Path
REQUIRED_FASTA = [
"chr20.fa",
"chr21.fa",
"chr22.fa",
"chr20_21_22.fa",
"chr20.fa.gz",
"chr21.fa.gz",
"chr22.fa.gz",
]
REQUIRED_PREPROCESSED_PREFIXES = [
"chr20_21_22_uint8_distinct_byte-level_train",
"chr20_21_22_uint8_distinct_byte-level_val",
"chr20_21_22_uint8_distinct_byte-level_test",
]
def sha256(path: Path) -> str:
h = hashlib.sha256()
with path.open("rb") as f:
for block in iter(lambda: f.read(1024 * 1024), b""):
h.update(block)
return h.hexdigest()
def read_sha_manifest(path: Path) -> dict[str, str]:
result = {}
for line in path.read_text().splitlines():
if not line.strip():
continue
digest, filename = line.split(None, 1)
result[filename.strip()] = digest
return result
def read_sizes(path: Path) -> dict[str, int]:
result = {}
for line in path.read_text().splitlines():
if not line.strip():
continue
filename, size = line.split("\t", 1)
result[filename] = int(size)
return result
def check_fasta_head(path: Path) -> bool:
opener = gzip.open if path.suffix == ".gz" else open
with opener(path, "rt", encoding="utf-8", errors="replace") as f:
for line in f:
line = line.strip()
if line:
return line.startswith(">")
return False
def main() -> int:
parser = argparse.ArgumentParser(description="Validate the OneScience Evo2 mini genome dataset.")
parser.add_argument("--dataset-root", default="data_mini", help="Dataset root in the dataset repository.")
parser.add_argument("--package-root", default=".", help="Dataset package root. Default: current directory.")
parser.add_argument("--skip-sha256", action="store_true", help="Skip SHA256 checks.")
args = parser.parse_args()
root = Path(args.package_root).resolve()
dataset_root = (root / args.dataset_root).resolve() if not Path(args.dataset_root).is_absolute() else Path(args.dataset_root)
genome_root = dataset_root / "genome_data"
preprocessed = genome_root / "preprocessed_data"
errors: list[str] = []
if not genome_root.is_dir():
errors.append(f"missing genome_data directory: {genome_root}")
for rel in REQUIRED_FASTA:
path = genome_root / rel
if not path.is_file():
errors.append(f"missing FASTA file: genome_data/{rel}")
else:
try:
if not check_fasta_head(path):
errors.append(f"FASTA header not found in first record: genome_data/{rel}")
except Exception as exc:
errors.append(f"cannot read FASTA file genome_data/{rel}: {exc}")
for prefix in REQUIRED_PREPROCESSED_PREFIXES:
bin_path = preprocessed / f"{prefix}.bin"
idx_path = preprocessed / f"{prefix}.idx"
if not bin_path.is_file():
errors.append(f"missing preprocessed bin: {bin_path}")
elif bin_path.stat().st_size <= 0:
errors.append(f"empty preprocessed bin: {bin_path}")
if not idx_path.is_file():
errors.append(f"missing preprocessed idx: {idx_path}")
elif idx_path.stat().st_size <= 0:
errors.append(f"empty preprocessed idx: {idx_path}")
size_manifest = root / "metadata" / "data_mini.files.tsv"
if size_manifest.is_file():
for rel, expected_size in read_sizes(size_manifest).items():
path = dataset_root / rel
if not path.is_file():
errors.append(f"file listed in size manifest is missing: {rel}")
elif path.stat().st_size != expected_size:
errors.append(f"size mismatch for {rel}: {path.stat().st_size} != {expected_size}")
else:
errors.append("missing metadata/data_mini.files.tsv")
if not args.skip_sha256:
sha_manifest = root / "metadata" / "data_mini.sha256"
if sha_manifest.is_file():
for rel, expected_digest in read_sha_manifest(sha_manifest).items():
path = dataset_root / rel
if path.is_file() and sha256(path) != expected_digest:
errors.append(f"sha256 mismatch for {rel}")
else:
errors.append("missing metadata/data_mini.sha256")
if errors:
for error in errors:
print(f"[FAIL] {error}", file=sys.stderr)
return 1
print("[OK] Evo2 mini dataset files, FASTA readability, preprocessed splits, sizes and hashes passed validation.")
return 0
if __name__ == "__main__":
raise SystemExit(main())
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