Open will-moore opened 2 months ago
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@will-moore @manzt: I've also hard-coded the URL for https://github.com/hms-dbmi/vizarr/pull/172 here as well :+1:
ome_zarr view idr0001-2551.zarr
.../idr0001-2551.zarr $ http-server --cors
:+1: from my side on the additional column:
@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.
Sorry, I just wanted to get a screenshot in place. No complaints :smile:
Initial RO-Crate validation! π
cc: @sherwoodf
@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!
@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)
@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.
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.
@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?
The dataset is sparse indeed. Data starts at 3072,3072,512. Unfortunately, OME-Zarr or Zarr don't have metadata for storing data offsets like this.
That last commit attempts to look-up Organism and Imaging method. E.g. https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/0.0.5/idr0010/76-45.zarr
Only quick thought is if we can have two more levels of "not there":
[ ]
or just omit (name / description)
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 loadingversion
schema from https://raw.githubusercontent.com/normanrz/ngff/spec-rfc2/latest/schemas/version.schemaPreview 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: