File size: 4,978 Bytes
dc0b89d | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 | #!/usr/bin/env python3
"""Report and validate SUMI OpenCT collection readiness without network I/O."""
from __future__ import annotations
import argparse
import csv
import json
from pathlib import Path
EXPECTED_DATASETS = {
"DSB17",
"LIDC-IDRI",
"LNDb19",
"LTRC",
"LUNA16",
"MIDRC",
"NLST",
"RSNA-STR",
}
MIRROR_ALLOWED = {
"mirror_allowed_with_attribution",
"mirror_selected_public_ct_with_attribution",
}
def read_jsonl(path: Path) -> list[dict]:
if not path.exists():
return []
rows: list[dict] = []
with path.open(encoding="utf-8") as f:
for line_number, line in enumerate(f, start=1):
if not line.strip():
continue
try:
value = json.loads(line)
except json.JSONDecodeError as exc:
raise RuntimeError(f"Invalid JSON at {path}:{line_number}: {exc}") from exc
if not isinstance(value, dict):
raise RuntimeError(f"Expected an object at {path}:{line_number}")
rows.append(value)
return rows
def count_csv_rows(path: Path) -> int:
if not path.exists():
return 0
with path.open(newline="", encoding="utf-8") as f:
return sum(1 for _ in csv.DictReader(f))
def collect_status(root: Path) -> tuple[list[dict], list[str]]:
registry_path = root / "manifests/source_datasets.csv"
with registry_path.open(newline="", encoding="utf-8") as f:
registry = list(csv.DictReader(f))
errors: list[str] = []
names = {row.get("dataset", "") for row in registry}
if names != EXPECTED_DATASETS:
errors.append(
f"registry datasets differ: missing={sorted(EXPECTED_DATASETS - names)}, "
f"unexpected={sorted(names - EXPECTED_DATASETS)}"
)
status: list[dict] = []
for source in registry:
dataset = source["dataset"]
planned = int(source["planned_scans"])
manifest_path = root / f"manifests/{dataset}.jsonl"
manifest = read_jsonl(manifest_path)
folders = [str(row.get("folder", "")) for row in manifest]
source_uids = [str(row.get("source_series_uid", "")) for row in manifest]
if len(folders) != len(set(folders)):
errors.append(f"{dataset}: duplicate folder in {manifest_path}")
if any(not value for value in folders):
errors.append(f"{dataset}: manifest row missing folder")
if len(source_uids) != len(set(source_uids)):
errors.append(f"{dataset}: duplicate source_series_uid in {manifest_path}")
if any(not value for value in source_uids):
errors.append(f"{dataset}: manifest row missing source_series_uid")
if len(manifest) > planned:
errors.append(f"{dataset}: {len(manifest)} uploads exceed planned count {planned}")
collector = source.get("collector", "")
if collector and collector != "none" and not (root / collector).is_file():
errors.append(f"{dataset}: collector does not exist: {collector}")
policy = source.get("mirror_policy", "")
if policy not in MIRROR_ALLOWED and manifest:
errors.append(f"{dataset}: restricted source has {len(manifest)} uploaded manifest rows")
selection_path = source.get("required_selection", "")
selection_rows = count_csv_rows(root / selection_path) if selection_path else None
status.append(
{
"dataset": dataset,
"planned": planned,
"uploaded": len(manifest),
"preparation_status": source.get("preparation_status", ""),
"mirror_policy": policy,
"selection_rows": selection_rows,
}
)
return status, errors
def main() -> None:
parser = argparse.ArgumentParser()
parser.add_argument("--root", type=Path, default=Path("."))
parser.add_argument("--json", action="store_true")
args = parser.parse_args()
root = args.root.resolve()
status, errors = collect_status(root)
if args.json:
print(json.dumps({"sources": status, "errors": errors}, indent=2, sort_keys=True))
else:
print(f"{'dataset':<12} {'planned':>8} {'uploaded':>8} preparation")
for row in status:
selection = row["selection_rows"]
suffix = f" (selection rows: {selection})" if selection is not None else ""
print(
f"{row['dataset']:<12} {row['planned']:>8} {row['uploaded']:>8} "
f"{row['preparation_status']}{suffix}"
)
print(
f"{'TOTAL':<12} {sum(row['planned'] for row in status):>8} "
f"{sum(row['uploaded'] for row in status):>8}"
)
print("validation: " + ("OK" if not errors else "FAILED"))
for error in errors:
print(f"- {error}")
if errors:
raise SystemExit(1)
if __name__ == "__main__":
main()
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