Transforms support

[will-moore]

Adding support for ome/ngff#138

Since that PR isn't merged yet, we need custom URL for loading schemas from that branch.

This PR build is deployed at https://deploy-preview-32--ome-ngff-validator.netlify.app - but I don't know of good sample data to test with.

To test a sample file containing various example snippets from the PR above see https://deploy-preview-32--ome-ngff-validator.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/v0.5/idr0050/4995115.zarr

NB: this is valid according to the proposed schemas, but won't make any sense to a viewer client.

I'm not loading some schemas, such as coordinate_systems_and_transforms.schema and coordinateTransformations.schema. I'm don't see that they are needed by any validation yet, but I've not tried much.
Also the strict schemas aren't used (same as before).

[netlify]

✅ Deploy Preview for ome-ngff-validator ready!

Name	Link
🔨 Latest commit	2408246
🔍 Latest deploy log	https://app.netlify.com/sites/ome-ngff-validator/deploys/65c25dd7e7511a00088ef8b0
😎 Deploy Preview	https://deploy-preview-32--ome-ngff-validator.netlify.app/
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

---

To edit notification comments on pull requests, go to your Netlify site configuration.

[will-moore]

cc @joshmoore - know any good samples for testing?

[joshmoore]

I'd probably start from https://github.com/scverse/spatialdata-notebooks/tree/main/notebooks/developers_resources/storage_format

cc: @LucaMarconato

[LucaMarconato]

Thanks @joshmoore for tagging. Unfortunately the datasets linked could be some good starting points (and especially the code to generate variations of them), but they don't agree 100% to the current specs. As discussed here: scverse/spatialdata#35 we wanted to wait until the transformation PR got merged, but unfortunately it didn't happen.

[will-moore]

Testing a bunch of invalid sample files, validation is working but I find the errors can be a bit verbose.
E.g. "affine": [[1, 2, 3, 4], [5, 6, 7, 8, 9], 1],
gives me 21 Errors!

The useful ones are:

{
  "instancePath": "/multiscales/0/coordinateTransformations/0/affine/0",
  "schemaPath": "#/$defs/mtxFlatOrNested/oneOf/0/items/type",
  "keyword": "type",
  "params": {
    "type": "number"
  },
  "message": "must be number"
}
{
  "instancePath": "/multiscales/0/coordinateTransformations/0/affine/2",
  "schemaPath": "#/$defs/mtxFlatOrNested/oneOf/1/items/type",
  "keyword": "type",
  "params": {
    "type": "array"
  },
  "message": "must be array"
}

[will-moore]

I tried adding an invalid arrayCoordinateSystem block (without axes element) but this doesn't fail validation

{
"multiscales": [
      {
          "version": "0.5-dev",
          "name": "example",
          "arrayCoordinateSystem" : {
            "name" : "myDataArray",
            "missing_axes" : []
          },

The schema that contains arrayCoordinateSystem spec is coordinate_systems_and_transforms.schema but that schema isn't referenced by the image.schema or any other schemas that I can see, so I haven't loaded it in this PR.

[joshmoore]

LucaMarconato commented 2 weeks ago
scverse/spatialdata#35 we wanted to wait until the transformation PR got merged...

cc: @bogovicj but I think, @LucaMarconato, that it would now be a good time to tackle this.

[joshmoore]

@will-moore: I've updated the title to be "Transforms supports" rather than v0.5. I leave it up to you whether to change the usages internally or if we just close for the moment.

[will-moore]

I'll close for now, thx