V05 dev2 - Githubissues

will-moore commented 2 months ago

This updates the validator to support v0.5-dev2 data, as specified at https://github.com/ome/ngff/pull/242.

Validating against image schema at https://raw.githubusercontent.com/normanrz/ngff/spec-rfc2/latest/schemas/image.schema and also loading version schema from https://raw.githubusercontent.com/normanrz/ngff/spec-rfc2/latest/schemas/version.schema

Preview build viewing sample data: https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/v0.5-dev2/6001240.zarr

cc @normanrz

TODO:

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joshmoore commented 1 month ago

@will-moore @manzt: I've also hard-coded the URL for https://github.com/hms-dbmi/vizarr/pull/172 here as well :+1:

joshmoore commented 1 month ago

When using `ome_zarr view idr0001-2551.zarr`

When using `.../idr0001-2551.zarr $ http-server --cors`

joshmoore commented 3 weeks ago

:+1: from my side on the additional column:

will-moore commented 3 weeks ago

@joshmoore Not exactly sure what you're doing there....

$ ls plates/
2783928.zarr    4403.zarr   51.zarr
$ http-server --cors

https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=http://127.0.0.1:8080/plates/4403.zarr Looks good.

Also e.g.

$ $ http-server plates --cors

Works at https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=http://127.0.0.1:8080/4403.zarr etc.

joshmoore commented 3 weeks ago

Sorry, I just wanted to get a screenshot in place. No complaints :smile:

joshmoore commented 3 weeks ago

Initial RO-Crate validation! 🎉

cc: @sherwoodf

will-moore commented 3 weeks ago

@sherwoodf - I noticed you had key licence at https://github.com/ome/ome2024-ngff-challenge/blob/53cdf2b73dec2a8341998b7a114a16dea3e5424f/dev3/zarr-crate/example_usage/example_ro_crate/ro-crate-metadata.json#L26C7-L26C65 and Josh had the same in the sample above. But we think this should be license as at https://schema.org/license. So the validator is checking for license.

NB: for name, description and license I'm just looking for the first "@graph" item that has those attributes, which is very simplistic. Any suggestions on improvements to this validation logic would be appreciated!

sherwoodf commented 3 weeks ago

@will-moore On license vs licence - you're definitely correct it should be licen_s_e

I think looking for objects with those fields works for the basic ro-crates that we're expecting to get.

If you wanted to invest in something longer term right now (which might be over the top), I would recommend using some sort of ro-crate/linked data tooling instead because the flattened data structure isn't wonderful for parsing, and we can probably update rules we go.

I've only used the python one, but there is a javascript package that might work with svelte: https://www.npmjs.com/package/ro-crate - it mentions an 'in development' validation promises.

We could write shacl shapes and run on the rdf graph that gets produced (https://github.com/zazuko/rdf-validate-shacl) - again, probably over engineering a solution for what we need right now. I could write us some shapes if we wanted to go down that route (if you're not familiar with them they're essentially schema descriptions for validating rdf graphs)

sherwoodf commented 3 weeks ago

@will-moore ignore the bit about shacl - i've just remembered that we don't have terms for the fbbi_id yet so it gets dropped from the RDF graph.

joshmoore commented 3 weeks ago

See https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://data-humerus.webknossos.org/data/zarr3_experimental/scalable_minds/l4_sample/color for a webknossos dataset that is currently erroring because sharding isn't used.

will-moore commented 2 weeks ago

@joshmoore @normanrz That non-sharded image is fixed now: https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://data-humerus.webknossos.org/data/zarr3_experimental/scalable_minds/l4_sample/color But I don't see any chunks being loaded. I'm getting 404s when I try to load any chunk, and I'm not seeing anything in vizarr either. It is mostly a sparse image or is something broken?

Screenshot 2024-08-22 at 08 51 14