Example output missing row group metadata

[ziw-liu]

The row level in the HCS samples don't have zarr.json. Therefore they are not recognized as zarr groups (e.g. by zarr-python):

aws s3 ls --endpoint-url https://uk1s3.embassy.ebi.ac.uk --no-sign-request s3://idr/share/ome2024-ngff-challenge/idr0035/Week9_090907.zarr/B/ | grep json
aws s3 ls --endpoint-url https://uk1s3.embassy.ebi.ac.uk --no-sign-request s3://idr/zarr/v0.5/idr0010/76-45.ome.zarr/A/ | grep json

Example tree from the spec:

.
│
└── 5966.zarr                 # One OME-Zarr plate (id=5966)
    ├── zarr.json             # Implements "plate" specification
    ├── A                     # First row of the plate
    │   ├── zarr.json
    │   │
    │   ├── 1                 # First column of row A
    │   │   ├── zarr.json     # Implements "well" specification
    │   │   │
    │   │   ├── 0             # First field of view of well A1
    │   │   │   │
    │   │   │   ├── zarr.json # Implements "multiscales", "omero"
    │   │   │   ├── 0         # Resolution levels          
    │   │   │   ├── ...
    │   │   │   └── labels    # Labels (optional)
    │   │   └── ...           # Other fields of view
    │   └── ...               # Other columns
    └── ...                   # Other rows

[will-moore]

Thanks for the report. I'm not sure if we are going to be able to update all those plates, but I'll check on the code that created them and on other plate generation code we have....

It looks like we are creating the Well groups directly without first creating row groups at

ome2024-ngff-challenge/src/ome2024_ngff_challenge/resave.py

Line 467 in 92e19d1

well_input_config = input_config.sub_config(well_path)

I also checked v0.4 plates from bioformats2raw e.g. (https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0056B/7361.zarr). This does have e.g. 7361.zarr/A/.zgroup and same for those from omero-cli-zarr e.g. https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0013A/3451.zarr/