Validate (.ome).zarr against ngff schema

[yarikoptic]

A part inspired from

• 1281

  and current problem of presumably having LOTS of non-compliant zarrs in the archive:

• https://github.com/dandisets/000108/issues/14

For any .zarr we encounter we should

• check if it is actually an OME .zarr. I think we can do that by looking for .omero top level key in .zattrs
• NB if that is the best way was asked:
  • https://github.com/ome/ngff/issues/228

For any OME .zarr (be either detected through above or having .ome.zarr extension), validate that zarr against the specified version (if no version -- validation error)

❯ jq '.omero.version' .zattrs
"0.4"

of schema as provided on https://github.com/ome/ngff under {schema_version}/schemas/ folder in .schema json files and issue corresponding validation errors to the users trying to upload non-compliant OME .ngffs.

[yarikoptic]

following advice in https://github.com/ome/ngff/issues/228#issuecomment-1957119902 let's :

• consider versions from .multiscales[].version and .omero.version.
• if more than 1 found -- issue a validation error on inconsistency of OME/NGFF version, stop validation
• if 1 version found -- load that schema and validate against
• if no version found -- not OME/NGFF, no OME specific validation

[yarikoptic]

here is stats across zarrs on S3 - first one for .ome.version, 2nd for .multiscales[].version:

dandi@drogon:~$ sort /tmp/ome-versions.out | uniq -c
     20 [0.2,0.2]
   4303 ["0.4","0.4"]
    572 [null,"0.4"]

where that file was created using for d in *-*-*; do git -C $d annex whereis .zattrs | awk '/versionId=/{print $2;}' | xargs curl --silent | jq -c '[.omero.version, .multiscales[].version]'; done | tee /tmp/ome-versions.out

note that some had it (incorrectly) as floats I think. Might be worth making code robust there and explicitly test for it being a string and otherwise issue validation error

[jwodder]

@yarikoptic

• So should dandi-cli just download the OME schemata on the fly when needed?
• Could you link me to an example valid (or nearly-valid) OME Zarr?

[yarikoptic]

well -- ideally cache locally. I thought we already do something similar to dandi schema or used to do for bids at some point.

"nearly-valid" I think most of zarrs in 000108 according to e.g. https://ome.github.io/ome-ngff-validator/?source=https://dandiarchive.s3.amazonaws.com/zarr/e41844a2-dad0-4b1c-9c53-d55883e0553f which errors with

{
  "instancePath": "/omero/channels/0/window",
  "schemaPath": "#/properties/omero/properties/channels/items/properties/window/required",
  "keyword": "required",
  "params": {
    "missingProperty": "start"
  },
  "message": "must have required property 'start'"
}

but then otherwise is happy to report 7 Datasets checked ✓.

I also found one in https://dandiarchive.org/dandiset/000243/draft/files?location=sub-S01%2Fanat&page=1 which fully valid https://ome.github.io/ome-ngff-validator/?source=https://dandiarchive.s3.amazonaws.com/zarr/7723d02f-1f71-4553-a7b0-47bda1ae8b42

also those in 000026 seems to be good: https://dandiarchive.org/dandiset/000026/draft/files?location=sub-I45%2Fses-SPIM%2Fmicr&page=1