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V05 dev2 #36
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V05 dev2 #36
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✅ Deploy Preview for ome-ngff-validator ready!
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@will-moore @manzt: I've also hard-coded the URL for hms-dbmi/vizarr#172 here as well 👍 |
vizarr PR is now merged This reverts commit 3a1ecfb.
@joshmoore Not exactly sure what you're doing there....
https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=http://127.0.0.1:8080/plates/4403.zarr Also e.g.
Works at https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=http://127.0.0.1:8080/4403.zarr |
Sorry, I just wanted to get a screenshot in place. No complaints 😄 |
Initial RO-Crate validation! 🎉 cc: @sherwoodf |
@sherwoodf - I noticed you had key NB: for |
@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 |
That last commit attempts to look-up Organism and Imaging method. E.g. |
Only quick thought is if we can have two more levels of "not there":
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<div class="rocrate"> | ||
<h1>Ro-crate metadata</h1> |
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<h1>Ro-crate metadata</h1> | |
<h1>RO-Crate metadata</h1> |
could potentially have a info (I) with a link to what RO-Crate is.
Last commit handles series metadata as in https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://radosgw.public.os.wwu.de/n4bi-goe/Platynereis-H2B-TL.ome.zarr/ |
This updates the validator to support
v0.5-dev2
data, as specified at ome/ngff#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://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0044/4007801.zarr
cc @normanrz
TODO: