n5: prevent failure on missing group metadata #651
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In the N5 spec, https://github.com/saalfeldlab/n5#file-system-specification point 3, the `{"n5": "$version"}` metadata is only expected at the root level. Datasets missing the metadata on inner groups fail to load: ``` In [43]: list(zarr.hierarchy.Group(store=zarr.n5.N5Store("ex.n5")).groups()) ... ValueError: group not found at path 'setup0' ``` This changes the group parsing logic to not fail if the metadata is missing. Suggestions welcome on how to detect the top group/array in order to special case the parsing.
jakirkham
reviewed
Nov 12, 2020
Co-authored-by: jakirkham <jakirkham@gmail.com>
Codecov Report
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Files 27 27
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+ Hits 10066 10084 +18
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Carreau
approved these changes
Nov 18, 2020
6 tasks
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In the N5 spec, https://github.com/saalfeldlab/n5#file-system-specification
point 3, the
{"n5": "$version"}metadata is only expected at the root level.Datasets missing the metadata on inner groups fail to load:
This changes the group parsing logic to not fail if the metadata is
missing. Suggestions welcome on how to detect the top group/array in
order to special case the parsing.
see tischi/i2k-2020-s3-zarr-workshop#1 (comment) for the original report
TODO: