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ome / ome-zarr-py

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
https://pypi.org/project/ome-zarr
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Validate data #102

Open will-moore opened 2 years ago

will-moore commented 2 years ago

See https://github.com/ome/ome_zarr_test_suite/pull/11

Currently ome-zarr-py doesn't validate data, e.g. checking that essential metadata is present or that data is expected dimensions.

Maybe add this functionality to the info command by default (perhaps with a --no-validate option)?

joshmoore commented 2 years ago

cc: @glyg

will-moore commented 2 years ago

As discussed on https://github.com/ome/ngff/issues/58 - assigning this to @glyg for the code-based validation of the zarr data that can't be covered by JSON schema validation. Thanks!

dstansby commented 2 months ago

Would be great to have an ome_zarr validate command 😄

glyg commented 2 months ago

Hi @dstansby Apologies for the stale issue. I do not have the bandwidth to look into that, and won't before several months. Integration of ome-zarr in our projects is in the pipe though so if you can wait that long I'll be happy to address it :).

I think a request to https://ome.github.io/ome-ngff-validator/ would do a lot of the work