Refactor: improve archive handling in LinkedData::Utils::FileHelpers #256
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- Switch from shelling out to `file --mime` to checking magic bytes
(PK for ZIP, 1F 8B for GZIP). Improves portability and removes
external dependency.
- Add `safe_join` guard to block path traversal.
- Normalize gzip names via `resolve_gzip_name` (strip control chars,
collapse to basename, ensure non-empty).
- Explicitly exclude .tar.gz and .tgz files (not supported yet).
- align with RubyZip v3+ semantics:
- enforce explicit destination_directory (no implicit cwd writes),
- block path traversal (`../` entries skipped).
- use streaming writes (`IO.copy_stream`) to reduce memory usage.
- Rename `files_from_zip` to `filenames_in_archive` for clarity
(returns entry names, not extracted files
- add rubyzip gem as dependency to gemspec
- pin thin gem to v1 for compatibility reasons
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #256 +/- ##
===========================================
+ Coverage 80.21% 80.23% +0.01%
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Files 84 84
Lines 5843 5874 +31
===========================================
+ Hits 4687 4713 +26
- Misses 1156 1161 +5
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alexskr
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alexskr
changed the title
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Summary
This PR refactors
LinkedData::Utils::FileHelpersto improve archive handling.Motivation
Zip/Gzip functionality silently broke after the rubyzip gem was updated to v3.0 in ncbo_cron:
RubyZip v3 changed extraction behavior (destination_directory: required).
Needed stronger protections against Zip Slip (path traversal).
.gz extraction previously buffered the whole file into memory.
Changes
files_from_ziptofilenames_from_archivefor clarity (returns entry names, not extracted fileszip?/gzip?now act as pure predicates (returning true/false) instead of raising on missing files.model/test_ontology_submissiontoutils/test_filehelpersontologies_linked_datagem