Comments (2)
Symlinks are resolved by the container kernel, not the host kernel. A relative path that doesn't go outside the mount would work as expected, but an absolute path to a location that does not exist in the container will just be a dangling symlink inside the container.
❯ mkdir -p /tmp/datasetA/sub-123/anat/
❯ mkdir -p /tmp/datasetB
❯ ln -s /tmp/datasetA/sub-123 /tmp/datasetB/
❯ echo "This exists" > /tmp/datasetA/sub-123/anat/sub-123_T1w.nii.gz
❯ cat /tmp/datasetB/sub-123/anat/sub-123_T1w.nii.gz
This exists
❯ docker run --rm -it -v /tmp/datasetA:/data:ro busybox cat /data/sub-123/anat/sub-123_T1w.nii.gz
This exists
❯ docker run --rm -it -v /tmp/datasetB:/data:ro busybox cat /data/sub-123/anat/sub-123_T1w.nii.gz
cat: can't open '/data/sub-123/anat/sub-123_T1w.nii.gz': No such file or directory
❯ docker run --rm -it -v /tmp/datasetB:/data:ro busybox ls -lR /data
/data:
total 0
lrwxrwxrwx 1 1000 1000 21 Oct 23 19:44 sub-123 -> /tmp/datasetA/sub-123
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Oh wow I did not know that thanks!
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Related Issues (20)
- github action to run bids-validator on bids-examples
- Validator requires echo entity to be immediately before "_bold.nii.gz" HOT 4
- deno 101: how to ship/run the "build"? HOT 7
- deno testing 101: deno_tests.yml is chronically red, "on purpose"? HOT 4
- deno: lost --config option? HOT 1
- deno run on a built bids-validator.js: Attempted to load JSON module without specifying "type" HOT 2
- Tests for some reason expect `/tmp/$USER` to exist? HOT 1
- deno: could --schema be made to take `src/schema` yaml tree as input? HOT 5
- IntendedFor links pointing into `derivatives/` directory fail HOT 2
- Update evalInitialColumns to account for recommended columns.
- Should we be relaxed about initial `/` for dataset-relative paths?
- [BUG] Validator isn't screaming when PET image files are lacking sidecar files HOT 1
- IntendedFor links pointing at `_meg.ds/` directories fail
- CITATION.cff support
- Bundle deno validator into bids-validator BIDS-app
- Legacy validator permitting (i)EEG files without sidecars HOT 3
- New phenotype filename rule messes with filename rule suggestion heuristic.
- Implement allequal in expression language. HOT 2
- TSV column type check overhaul HOT 2
- No error/warning when IDs in `participant.tsv` do not match directory names HOT 5
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