openvax / datacache / 27786378336

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github

Committed by web-flow

Commit Message

Make test_download.py hermetic; remove dead wget path; harden zip/gz decompress (closes #42) (#56)

* Make test_download.py hermetic; remove dead wget download path (closes #42)

test_fetch_decompress hit a live Ensembl FTP server and looped over
use_wget_if_available/timeout while the file was only downloaded once — so the
result depended on iteration order (the flakiness in #42), and CI was noisy.

- Rewrite the tests to serve a local .gz over file:// with the cache redirected
  to a tmp dir (the pattern test_streaming_download.py already uses): no network,
  no cross-run cached state. Adds deterministic cache-reuse + force coverage.
- Remove the wget download path: subprocess.call's non-zero exit was ignored
  (silent partial downloads), and the modernization's streaming Python
  downloader (_stream_to_file, #49) already handles http(s) and ftp. Drops the
  subprocess/errno imports and the wget threading through the private helpers.
- Keep use_wget_if_available on the public fetch_file / Cache.fetch as a
  deprecated, ignored no-op (warns when explicitly passed) so callers don't break.

No version bump — leaving the release/version decision to the maintainer.

* Harden zip/gz decompression; add zip test + tighten deprecation test

Addressing review of #42:
- Stream the chosen zip member straight to the destination via z.open() +
  copyfileobj, replacing ZipFile.extract() which wrote into the current working
  directory and recreated the member's stored path (cwd-pollution + a "../"
  path-traversal footgun). Member selection (named match, else biggest) is
  unchanged.
- Stream the gunzip to disk instead of reading the whole decompressed file into
  memory — consistent with the streaming download goal (#49).
- Add a .zip decompression test (previously only .gz was covered) that also
  asserts nothing leaks into the cwd, and pin the deprecation warning message
  with pytest.warns(match=...).

* Decompress atomically (sibling temp + move) so corrupt a... (continued)

Coverage Stats

23 of 23 new or added lines in 2 files covered. (100.0%)

1 existing line in 1 file now uncovered.

347 of 439 relevant lines covered (79.04%)

2.37 hits per line