remote zarr require `s3` to be in the URI

[psobolewskiPhD]

First reported on image.sc, see https://forum.image.sc/t/qupath-0-6-0rc1-unable-to-read-remote-ome-zarr-by-url/101605/19

When trying to load a remote zarr, the URI needs to have s3 in it, which is annoying when using e.g. google buckets.
It looks like due to this code:

ZarrReader/src/loci/formats/services/JZarrServiceImpl.java

Line 83 in 31d6d95

if (root != null && (root.toLowerCase().contains("s3:") || root.toLowerCase().contains("s3."))) {

Could this be relaxed to allow other buckets? For example we use google, which provides an s3-interoperable XML Api:
https://cloud.google.com/storage/docs/interoperability#xml_api

Example zarr:
https://ome.github.io/ome-ngff-validator/?source=https://storage.googleapis.com/jax-public-ngff/example_v2/LacZ_ctrl.zarr

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/qupath-0-6-0rc1-unable-to-read-remote-ome-zarr-by-url/101605/29

[JensWendt]

*Bump

This also excludes a lot of self hosted S3 storage solutions, e.g. my institution uses https://radosgw.public.os2.xxxx

[dominikl]

Thanks. I will have a look if this is doable with a small fix. There also seems to be a problem with / and \ mentioned by @JensWendt on the image.sc thread. FYI: We're are focussing our efforts on utilising the https://github.com/glencoesoftware/omero-zarr-pixel-buffer for zarr in OMERO. There probably won't be much further development happen on the ZarrReader. Don't expect that it'll will keep up with zarr versions and ngff spec versions evolving.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/qupath-0-6-0rc1-unable-to-read-remote-ome-zarr-by-url/101605/36

[dominikl]

PR open, still trying to figure out a way to actually test it...