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84a242a | 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 | #!/usr/bin/env python3
"""Check saved-output archive integrity without running scientific analysis."""
from __future__ import annotations
import argparse
import csv
import gzip
import hashlib
import json
from pathlib import Path
import zipfile
def require(condition: bool, message: str) -> None:
if not condition:
raise ValueError(message)
def sha256(path: Path) -> str:
digest = hashlib.sha256()
with path.open("rb") as handle:
for block in iter(lambda: handle.read(1024 * 1024), b""):
digest.update(block)
return digest.hexdigest()
def validate(root: Path, original_archive_manifest: Path | None = None) -> dict:
root = root.resolve()
def local_path(name: str) -> Path:
candidate = (root / name).resolve()
require(candidate.is_relative_to(root), f"Manifest path escapes archive root: {name}")
return candidate
summary = json.loads((root / "archive_summary.json").read_text())
with gzip.open(root / "file_manifest.csv.gz", "rt", newline="") as handle:
rows = list(csv.DictReader(handle))
packaged = [row for row in rows if row["status"] == "packaged_byte_for_byte"]
verified = 0
expected_archive_names = {policy["archive"] for policy in summary["policies"]}
require({path.name for path in root.glob("*.zip")} == expected_archive_names,
"ZIP files differ from the archive summary")
for policy in summary["policies"]:
archive_name = policy["archive"]
archive_path = local_path(archive_name)
matching = [row for row in packaged if row["archive"] == archive_name]
expected = {row["archive_member"]: row for row in matching}
require(len(expected) == len(matching), f"Duplicate manifest members: {archive_name}")
require(len(expected) == policy["packaged_files"], f"Incorrect packaged count: {archive_name}")
require(archive_path.stat().st_size == policy["archive_bytes"], f"Archive size mismatch: {archive_name}")
require(sha256(archive_path) == policy["archive_sha256"], f"Archive hash mismatch: {archive_name}")
with zipfile.ZipFile(archive_path) as archive:
names = archive.namelist()
require(len(names) == len(set(names)), f"Duplicate ZIP members: {archive_name}")
require(set(names) == set(expected), f"ZIP member set mismatch: {archive_name}")
for name in names:
# Reading the entire member also invokes ZipFile's CRC check.
payload = archive.read(name)
row = expected[name]
require(len(payload) == int(row["source_bytes"]), f"Payload size mismatch: {name}")
require(hashlib.sha256(payload).hexdigest() == row["sha256"], f"Payload hash mismatch: {name}")
verified += 1
require(verified == len(packaged), "Some packaged manifest rows were not verified")
mirrors = [row for row in packaged if row["summary_mirror"]]
expected_mirrors = {row["summary_mirror"] for row in mirrors}
require(len(expected_mirrors) == len(mirrors), "Duplicate mirror paths in manifest")
actual_mirrors = {path.relative_to(root).as_posix() for path in (root / "summary_tables").rglob("*.csv")}
require(actual_mirrors == expected_mirrors, "Missing or stale generated summary mirrors")
for row in mirrors:
require(sha256(local_path(row["summary_mirror"])) == row["sha256"],
f"Summary mirror hash mismatch: {row['summary_mirror']}")
require(sum(policy["source_files"] for policy in summary["policies"]) == len(rows),
"Original file count differs between summary and manifest")
missing = len(rows) - verified
require(sum(policy["missing_files"] for policy in summary["policies"]) == missing,
"Missing file count differs between summary and manifest")
require(summary["all_saved_files_packaged"] == (missing == 0), "Incorrect completeness flag")
original_members_verified = None
if original_archive_manifest is not None:
original = json.loads(original_archive_manifest.read_text())
source_members = {item["member"]: item for item in original["files"]}
require(len(source_members) == len(original["files"]), "Duplicate original archive members")
prefix = summary["source_directory_name"] + "/"
require({prefix + row["archive_member"] for row in rows} == set(source_members),
"Original archive and packaged inventory describe different source CSVs")
for row in packaged:
member = prefix + row["archive_member"]
source = source_members[member]
require(row["sha256"] == source["sha256"] and int(row["source_bytes"]) == source["bytes"],
f"Original archive member identity mismatch: {member}")
original_members_verified = len(packaged)
return {
"scope": "release_archive_integrity_only_not_scientific_reproduction",
"original_csv_files_in_manifest": len(rows),
"verified_zip_members": verified,
"verified_summary_mirrors": len(mirrors),
"zip_crc_ok": True,
"all_packaged_member_sha256_matches": True,
"archive_sha256_matches": True,
"stale_summary_mirrors": 0,
"missing_original_csv_payloads": missing,
"all_original_csv_payloads_packaged": missing == 0,
"verified_original_archive_member_hashes": original_members_verified,
"new_scientific_experiments": False,
}
def main() -> None:
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--output-dir", type=Path,
default=Path(__file__).resolve().parents[2] / "results/downstream")
parser.add_argument("--write-report", action="store_true",
help="Write verification.json after successful integrity checks")
parser.add_argument("--require-complete", action="store_true",
help="Return nonzero if any original CSV payload remains unavailable")
parser.add_argument("--original-archive-manifest", type=Path,
help="Also compare member identities to the original archive recovery manifest")
args = parser.parse_args()
report = validate(args.output_dir, args.original_archive_manifest)
if args.write_report:
(args.output_dir / "verification.json").write_text(json.dumps(report, indent=2) + "\n")
print(json.dumps(report, indent=2))
if args.require_complete and not report["all_original_csv_payloads_packaged"]:
raise SystemExit(1)
if __name__ == "__main__":
main()
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