ome_zarr download on hcs data doesn't bring down data

[tlambert03]

Not sure if I'm using it wrong... but tried to do:

uvx ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0010/76-45.ome.zarr --output .

and after a long while, it eventually finished, but had only downloaded the top level (26KB) zarr.json file. I had been expecting it to download the actual data as well, similar to image data. is that how it should behave? Or do I need to do something different with hcs data?

[will-moore]

Hi, I'm afraid I just don't think that download ever worked with HCS data.

Looking at the code, it iterates through the nodes...

    location = parse_url(input_path)
    reader = Reader(location)
    for node in reader():
        // download .zattrs or zarr.json
        // if Multiscales, download array

That iteration logic was originally designed to feed layers to napari.
The plate is considered a single node, and since it isn't a Multiscales then no arrays are downloaded.

I am considering deprecating parse_url and nodes iteration logic in ome-zarr-py (#476) and moving it to napari-ome-zarr (ome/napari-ome-zarr#123), so then the download logic here would need updating anyway.

[tlambert03]

Ok, I can download it other ways… just thought I’d let you know, but if it’s a known issue that won’t be fixed, feel free to close!