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Guillaume Meyer (The Opinionated Man)andGitHub 6df80e77a4 fix: correctness and security hardening of the cleaning scripts (#122) (#126)
* fix: rewrite ODT/EPUB manifests and measure real zip bytes (#122)

Two container correctness/security fixes from issue #122:

- clean_odt dropped marker-bearing parts while leaving their entries in
  META-INF/manifest.xml, so readers flagged the package as damaged. It is
  now two-pass: compute the dropped set, then rewrite the manifest
  attribute-order-independently, and write each part exactly once. The same
  bug class in clean_epub (dropped parts left in the OPF manifest, plus
  dangling spine itemrefs) gets the same two-pass treatment.
- The zip budget trusted ZipInfo.file_size from the archive's own central
  directory, so a crafted DOCX/ODT could declare a tiny size and still
  expand via zf.read. Budgets are now charged on actual decompressed bytes
  via _read_zip_member (streaming, cap enforced mid-read), with the declared
  size kept only as a fast-path pre-reject.

* fix: classify unrecognized bytes as "unknown", not text (#122)

Two classification defects from issue #122:

- format_dispatch.classify_bytes fell back to "text" for any unrecognized
  file, so a binary with valid UTF-8 runs could be decoded and written back
  mangled (corrupted with --in-place) in clean_file auto mode. Unrecognized
  bytes now classify as "unknown"; clean_file refuses them in auto mode
  (exit 2, no write, router advice) and --as text / --force-text are the
  explicit opt-ins. inspect_file reports kind "unknown" (exit 0), audit_lib
  records a non-actionable item, and the HTTP server answers /inspect with
  kind "unknown" but rejects /clean of unknown formats (400).
- classify(path) read the whole file to sniff a header, and only a full read
  could detect zip containers. It now routes known extensions without
  reading, sniffs a 4096-byte header once for images and prefix-based
  containers, and reads the whole file only when the header is a zip local
  header (PK), where the container signature lives in the central directory.

* feat: distinct exit code for partial audits (#122)

audit_dir and audit_website reported success (0) even when some files or
URLs could not be scanned; the exit status was computed only over the items
that succeeded. A scan that is missing items is not a clean scan.

- common.EXIT_PARTIAL = 3, with precedence: partial (3) > actionable (1)
  > clean (0) — an incomplete audit is the more important CI signal.
- audit_dir returns 3 when any file was skipped/failed; audit_website
  returns 3 when any URL failed to fetch or inspect. Both are independent
  of the output format (human/json/sarif already share one return).

* fix: verify the pinned upstream ref on existing checkouts (#122)

setup_ctrlregen.sh/setup_synthid.sh (and their .ps1 twins) only verified
the pinned commit in the fresh-clone branch; an existing checkout at an
unknown or drifted revision was silently reused, defeating the commit pin.

All four scripts now check HEAD against the pinned ref in the
existing-checkout branch too, and repair by fetch + detach checkout
(re-applying the sparse-checkout set), failing hard if the ref cannot be
reached or the re-pin does not land on it.

* docs: unknown-format behavior, audit exit codes, backend isolation (#122)

- README: clean_file no longer auto-cleans unrecognized formats (--as text
  / --force-text are the opt-ins), and the CtrlRegen bootstrap documents the
  isolation expectation for its research-era dependency pins plus the new
  re-pin check on existing checkouts.
- SKILL.md: audit exit codes (0/1/2/3, partial=3) and a note that /clean
  requires a name with a known extension.
- audit_website: document why stdlib ElementTree is used (stdlib-first) and
  that defusedxml is the fallback if that policy changes (DTD rejection stays).
- requirements-ctrlregen.txt: advisory/isolation note for the pinned research
  dependencies.

* test: ODT manifest and EPUB OPF dangling-ref regressions (#122)

- clean_odt: dropped marker-bearing parts remove their META-INF/manifest.xml
  file-entry (attribute-order-independent), exactly one manifest entry, root
  and surviving entries kept, and the manifest is byte-identical when nothing
  is dropped.
- clean_epub: dropped non-content parts lose their <item> entry in the OPF
  manifest, so the book no longer references removed members.
2026-08-17 17:15:35 -07:00

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"""Tests for the binary-input guard on the text-only tools."""
from __future__ import annotations
import io
import os
import subprocess
import sys
import zipfile
from pathlib import Path
import pytest
ROOT = Path(__file__).resolve().parents[1]
SCRIPTS = ROOT / "service" / "scripts"
sys.path.insert(0, str(SCRIPTS))
from common import guard_binary, looks_binary
DOCX_XML = (
'<?xml version="1.0" encoding="UTF-8" standalone="yes"?>'
'<w:document xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main">'
"<w:body><w:p><w:r><w:t>Table 1 holds the results.</w:t></w:r></w:p></w:body>"
"</w:document>"
)
def make_docx(path: Path) -> Path:
with zipfile.ZipFile(path, "w", zipfile.ZIP_DEFLATED) as zf:
zf.writestr("[Content_Types].xml", "<Types/>")
zf.writestr("word/document.xml", DOCX_XML)
return path
def run(script: str, *args: str) -> subprocess.CompletedProcess:
return subprocess.run(
[sys.executable, str(SCRIPTS / script), *args],
capture_output=True,
text=True,
timeout=60,
check=False,
)
# --- looks_binary ----------------------------------------------------------
@pytest.mark.parametrize(
"data,expected_fragment",
[
(b"PK\x03\x04rest", "ZIP"),
(b"%PDF-1.7\n", "PDF"),
(b"\x89PNG\r\n\x1a\nrest", "PNG"),
(b"\xff\xd8\xff\xe0rest", "JPEG"),
(b"\x7fELF\x02\x01", "ELF"),
(b"SQLite format 3\x00", "SQLite"),
(b"plain text\x00with a nul", "NUL"),
],
)
def test_flags_binary(data, expected_fragment):
kind = looks_binary(data)
assert kind is not None
assert expected_fragment.lower() in kind.lower()
@pytest.mark.parametrize(
"data",
[
b"",
b"Just some prose.\n",
b"# Markdown\n\n- bullet\n",
"Accented prose: naïve café résumé\n".encode(),
"Zero width and nbsp here\n".encode(),
b"Latin-1 bytes: caf\xe9 na\xefve\n", # not UTF-8, still text
b"a\tb\r\nc\x0cd\x1b[0m\n", # tabs, CRLF, form feed, ANSI escape
],
)
def test_allows_text(data):
assert looks_binary(data) is None
def test_compressed_bytes_are_flagged(tmp_path):
data = make_docx(tmp_path / "x.docx").read_bytes()
assert looks_binary(data) is not None
def test_guard_binary_can_be_overridden():
guard_binary(b"PK\x03\x04", "x.docx", allow_binary=True) # must not raise
with pytest.raises(SystemExit) as exc:
guard_binary(b"PK\x03\x04", "x.docx")
assert exc.value.code == 2
# --- CLI behaviour ---------------------------------------------------------
def test_inspect_text_refuses_docx(tmp_path):
docx = make_docx(tmp_path / "doc.docx")
r = run("inspect_text.py", str(docx))
assert r.returncode == 2
assert "looks like" in r.stderr
assert "inspect_file.py" in r.stderr
assert "Suspicious:" not in r.stdout
def test_inspect_text_force_text_still_works(tmp_path):
docx = make_docx(tmp_path / "doc.docx")
r = run("inspect_text.py", str(docx), "--force-text")
assert r.returncode in (0, 1)
assert "Length:" in r.stdout
def test_clean_text_refuses_docx_and_writes_nothing(tmp_path):
docx = make_docx(tmp_path / "doc.docx")
before = docx.read_bytes()
out = tmp_path / "doc.cleaned.docx"
r = run("clean_text.py", str(docx), "-o", str(out))
assert r.returncode == 2
assert not out.exists()
assert docx.read_bytes() == before
def test_clean_text_in_place_leaves_docx_intact(tmp_path):
docx = make_docx(tmp_path / "doc.docx")
before = docx.read_bytes()
r = run("clean_text.py", str(docx), "--in-place")
assert r.returncode == 2
assert docx.read_bytes() == before
assert not (tmp_path / "doc.docx.bak").exists()
def test_clean_file_still_routes_docx_to_container(tmp_path):
docx = make_docx(tmp_path / "doc.docx")
out = tmp_path / "out.docx"
r = run("clean_file.py", str(docx), "-o", str(out), "--json")
assert r.returncode == 0, r.stderr
assert out.exists()
with zipfile.ZipFile(out) as zf:
assert zf.testzip() is None
assert "word/document.xml" in zf.namelist()
def test_clean_file_refuses_unknown_binary(tmp_path):
blob = tmp_path / "mystery.bin"
blob.write_bytes(b"\x00\x01\x02\x03" * 64)
out = tmp_path / "out.bin"
r = run("clean_file.py", str(blob), "-o", str(out))
assert r.returncode == 2
assert not out.exists()
def test_clean_file_in_place_refuses_before_taking_a_backup(tmp_path):
"""The refusal must land before backup_path(), not after.
Sniffing after the backup left a .bak sidecar for a file the run never
touches, which is exactly what clean_text.py avoids.
"""
blob = tmp_path / "mystery.bin"
blob.write_bytes(b"\x00\x01\x02\x03" * 64)
before = blob.read_bytes()
r = run("clean_file.py", str(blob), "--in-place")
assert r.returncode == 2
assert blob.read_bytes() == before
assert not (tmp_path / "mystery.bin.bak").exists()
assert list(tmp_path.iterdir()) == [blob]
def test_clean_file_in_place_as_text_on_docx_leaves_no_backup(tmp_path):
"""--as text bypasses classify(), so the guard is the only thing left."""
docx = make_docx(tmp_path / "doc.docx")
before = docx.read_bytes()
r = run("clean_file.py", str(docx), "--in-place", "--as", "text")
assert r.returncode == 2
assert docx.read_bytes() == before
assert not (tmp_path / "doc.docx.bak").exists()
def test_clean_file_auto_refuses_unknown_text_like_bytes(tmp_path):
"""Extension-less bytes with no magic classify as "unknown" and are
refused in auto mode — even when they look like plain text, because
"text" is no longer the catch-all for unrecognized files."""
blob = tmp_path / "no_extension"
blob.write_text("just plain text, no extension, no magic\n", encoding="utf-8")
before = blob.read_bytes()
r = run("clean_file.py", str(blob), "--in-place")
assert r.returncode == 2
assert blob.read_bytes() == before
assert not (tmp_path / "no_extension.bak").exists()
def test_clean_file_as_text_opt_in_cleans_unknown(tmp_path):
"""--as text is the explicit opt-in that turns an unknown file into a
text clean."""
blob = tmp_path / "no_extension"
blob.write_text("Hidden\u200bmark here.\n", encoding="utf-8")
out = tmp_path / "out.txt"
r = run("clean_file.py", str(blob), "-o", str(out), "--as", "text")
assert r.returncode == 0, r.stderr
assert out.read_text(encoding="utf-8") == "Hiddenmark here.\n"
def test_clean_file_force_text_opt_in_on_unknown_binary(tmp_path):
"""--force-text also opts in, bypassing both the unknown refusal and
the binary guard (explicit override)."""
blob = tmp_path / "mystery.bin"
blob.write_bytes(b"\x00\x01\x02\x03" * 64)
out = tmp_path / "out.bin"
r = run("clean_file.py", str(blob), "-o", str(out), "--force-text")
assert r.returncode == 0, r.stderr
assert out.exists()
def test_inspect_file_json_reports_unknown_kind(tmp_path):
blob = tmp_path / "no_extension"
blob.write_text("no magic, no extension\n", encoding="utf-8")
r = run("inspect_file.py", str(blob), "--json")
assert r.returncode == 0
import json
payload = json.loads(r.stdout)
assert payload["kind"] == "unknown"
assert "note" in payload
def test_router_advice_is_not_circular(tmp_path):
"""clean_file.py refuses unknown bytes with router advice (never a pointer
back at itself); inspect_file.py reports the file as unknown instead."""
blob = tmp_path / "mystery.bin"
blob.write_bytes(b"\x00\x01\x02\x03" * 64)
r = run("clean_file.py", str(blob))
assert r.returncode == 2
assert "no supported text, image or container format" in r.stderr
assert "Use inspect_file.py / clean_file.py" not in r.stderr
assert "--force-text" in r.stderr
r = run("inspect_file.py", str(blob))
assert r.returncode == 0
assert "Kind: unknown" in r.stdout
assert "--as text|image|container" in r.stdout
def test_text_only_scripts_keep_the_pointer_to_the_routers(tmp_path):
docx = make_docx(tmp_path / "doc.docx")
r = run("clean_text.py", str(docx))
assert r.returncode == 2
assert "Use inspect_file.py / clean_file.py" in r.stderr
def test_text_files_are_unaffected(tmp_path):
src = tmp_path / "note.txt"
src.write_text("Hiddenmark here.\n", encoding="utf-8")
out = tmp_path / "note.cleaned.txt"
r = run("clean_text.py", str(src), "-o", str(out))
assert r.returncode == 0, r.stderr
assert out.read_text(encoding="utf-8") == "Hiddenmark here.\n"
def test_stdin_binary_is_refused():
docx = io.BytesIO()
with zipfile.ZipFile(docx, "w") as zf:
zf.writestr("word/document.xml", DOCX_XML)
r = subprocess.run(
[sys.executable, str(SCRIPTS / "inspect_text.py")],
input=docx.getvalue(),
capture_output=True,
timeout=60,
check=False,
)
assert r.returncode == 2
assert b"looks like" in r.stderr
PNG_HEADER = b"\x89PNG\r\n\x1a\n" + b"\x00\x00\x00\rIHDR" + b"\x00" * 32
JPEG_HEADER = b"\xff\xd8\xff\xe0\x00\x10JFIF\x00" + b"A" * 64
@pytest.mark.parametrize("data,label", [(PNG_HEADER, "PNG"), (JPEG_HEADER, "JPEG")])
@pytest.mark.parametrize("io_encoding", [None, "cp1252", "latin-1"])
def test_stdin_non_ascii_magic_is_refused_whatever_the_codec(data, label, io_encoding):
"""The ZIP test alone could not catch this: 'PK' is ASCII.
PNG's 0x89 and JPEG's 0xff only survive to the sniff if stdin is read as
bytes. Decoding first makes detection depend on the console codec.
"""
env = dict(os.environ)
if io_encoding is None:
env.pop("PYTHONIOENCODING", None)
else:
env["PYTHONIOENCODING"] = io_encoding
r = subprocess.run(
[sys.executable, str(SCRIPTS / "inspect_text.py")],
input=data,
capture_output=True,
timeout=60,
env=env,
check=False,
)
assert r.returncode == 2, (label, io_encoding, r.stderr)
assert label.encode() in r.stderr, (label, io_encoding, r.stderr)
def test_stdin_text_still_flows_through():
r = subprocess.run(
[sys.executable, str(SCRIPTS / "clean_text.py")],
input="plaintext\n".encode(),
capture_output=True,
timeout=60,
check=False,
)
assert r.returncode == 0, r.stderr
assert r.stdout.replace(b"\r\n", b"\n") == b"plaintext\n"