FIX skip .git directories in submodules #3740
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Previously, the upload command only skipped files starting with "." which correctly skipped root hidden files (.git/, .datalad/, etc.) but not hidden files/dirs in submodules (e.g., derivatives/.git/annex/objects/ or derivatives/.datalad/config). This could cause the CLI to upload duplicate annex objects or internal datalad files when uploading datasets containing submodules. The fix adds a check for any hidden path component (starting with .) anywhere in the relative path, while still correctly following symlinks that point to .git/annex/objects/. Also adds unit tests for the new shouldIncludeFile() function. Co-Authored-By: Claude Opus 4.5 <[email protected]>
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Pull request overview
This PR fixes a bug where the OpenNeuro CLI was not skipping .git directories in submodules (e.g., derivatives/.git), which could cause duplicate git-annex objects to be uploaded as regular files. The fix extracts file filtering logic into a new shouldIncludeFile() function that checks for hidden files/directories anywhere in the relative path, not just at the root level.
Changes:
- Added
hiddenPathPatternregex andshouldIncludeFile()function to properly filter hidden files in subdirectories - Refactored
addGitFiles()to use the new filtering function - Added comprehensive unit tests covering various scenarios including root-level hidden files, submodule hidden files, and edge cases
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| cli/src/commands/upload.ts | Added hiddenPathPattern regex and shouldIncludeFile() function to detect and exclude hidden files/directories in submodules; refactored addGitFiles() to use new filtering logic |
| cli/src/commands/upload.test.ts | Added comprehensive unit tests for hiddenPathPattern regex and shouldIncludeFile() function covering regular files, hidden files at root, hidden files in submodules, and edge cases |
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I typically save derivatives as nested submodules/datalad datasets. I was uploading a dataset and noticed that the openneuro CLI was correctly skipping the parent
.gitfolder but not thederivatives/.git. This could cause the CLI to upload duplicate annex objects as regular files when uploading datasets containing git-annex submodules.This fix creates a new
shouldIncludeFile()function to extract the inclusion logic, adding a check for dot files anywhere in the relative path. It also adds unit tests for the new shouldIncludeFile() function.