File size: 4,836 Bytes
d8cc85c | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 | #!/usr/bin/env python3
"""Validate the standardized PDENNEval dataset package."""
from __future__ import annotations
import argparse
import hashlib
import json
import math
import sys
from pathlib import Path
import h5py
import numpy as np
REPO_ROOT = Path(__file__).resolve().parents[1]
DATA_ROOT = REPO_ROOT / "data"
CHECKSUM_PATH = REPO_ROOT / "files_sha256.jsonl"
EXPECTED_FILES = {
"1D_Burgers_Sols_Nu0.001.hdf5": {
"datasets": {
"tensor": {"ndim": 3, "dtype": "float32"},
"x-coordinate": {"ndim": 1, "dtype": "float32"},
"t-coordinate": {"ndim": 1, "dtype": "float32"},
},
"attrs": {"Nu": 0.001},
},
"2D_DarcyFlow_beta0.1_Train.hdf5": {
"datasets": {
"tensor": {"ndim": 4, "dtype": "float32"},
"nu": {"ndim": 3, "dtype": "float32"},
"x-coordinate": {"ndim": 1, "dtype": "float32"},
"y-coordinate": {"ndim": 1, "dtype": "float32"},
},
"attrs": {"beta": 0.1},
},
"1D_Advection_Sols_beta1.0.hdf5": {
"datasets": {
"tensor": {"ndim": 3, "dtype": "float32"},
"x-coordinate": {"ndim": 1, "dtype": "float32"},
"t-coordinate": {"ndim": 1, "dtype": "float32"},
},
"attrs": {},
},
}
def fail(message: str) -> None:
print(f"[FAIL] {message}")
raise SystemExit(1)
def ok(message: str) -> None:
print(f"[OK] {message}")
def warn(message: str) -> None:
print(f"[WARN] {message}")
def sha256_file(path: Path) -> str:
digest = hashlib.sha256()
with path.open("rb") as handle:
for chunk in iter(lambda: handle.read(1024 * 1024), b""):
digest.update(chunk)
return digest.hexdigest()
def as_float(value: object) -> float | None:
try:
return float(value)
except (TypeError, ValueError):
return None
def validate_hdf5_file(path: Path, spec: dict[str, object]) -> None:
if not path.is_file():
fail(f"missing expected HDF5 file: {path}")
with h5py.File(path, "r") as handle:
for attr_name, expected in spec.get("attrs", {}).items():
actual = as_float(handle.attrs.get(attr_name))
if actual is None or not math.isclose(actual, float(expected), rel_tol=1e-6, abs_tol=1e-12):
fail(f"{path.name} attr {attr_name!r} expected {expected}, got {handle.attrs.get(attr_name)!r}")
for dataset_name, dataset_spec in spec["datasets"].items():
if dataset_name not in handle:
fail(f"{path.name} missing dataset {dataset_name!r}")
dataset = handle[dataset_name]
if dataset.ndim != dataset_spec["ndim"]:
fail(f"{path.name}/{dataset_name} ndim expected {dataset_spec['ndim']}, got {dataset.ndim}")
if str(dataset.dtype) != dataset_spec["dtype"]:
fail(f"{path.name}/{dataset_name} dtype expected {dataset_spec['dtype']}, got {dataset.dtype}")
if any(dim <= 0 for dim in dataset.shape):
fail(f"{path.name}/{dataset_name} has invalid shape {dataset.shape}")
probe = np.asarray(dataset[0])
if not np.isfinite(probe).all():
fail(f"{path.name}/{dataset_name} first slice contains non-finite values")
ok(f"{path.name} HDF5 schema is readable")
def verify_checksums(full_hash: bool) -> None:
if not CHECKSUM_PATH.exists():
warn(f"checksum manifest is not present: {CHECKSUM_PATH}")
return
records = [json.loads(line) for line in CHECKSUM_PATH.read_text(encoding="utf-8").splitlines() if line.strip()]
if not records:
fail("checksum manifest is empty")
for record in records:
path = REPO_ROOT / record["path"]
if not path.is_file():
fail(f"checksum entry points to missing file: {path}")
size = path.stat().st_size
if size != record["size"]:
fail(f"size mismatch for {path}: expected {record['size']}, got {size}")
if full_hash:
digest = sha256_file(path)
if digest != record["sha256"]:
fail(f"sha256 mismatch for {path}")
mode = "size+sha256" if full_hash else "size"
ok(f"checksum manifest verified in {mode} mode: {len(records)} files")
def main() -> int:
parser = argparse.ArgumentParser()
parser.add_argument("--full-hash", action="store_true", help="verify SHA256 for all large HDF5 files")
args = parser.parse_args()
if not DATA_ROOT.is_dir():
fail(f"dataset data root does not exist: {DATA_ROOT}")
for filename, spec in EXPECTED_FILES.items():
validate_hdf5_file(DATA_ROOT / filename, spec)
verify_checksums(args.full_hash)
ok("dataset validation completed")
return 0
if __name__ == "__main__":
sys.exit(main())
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