Missing dependency for .zarr files

[jo-mueller]

Hi all,

following up some discussions on image.sc about the upload and use of .zarr files to OMERO, I have also discovered, that the problem in the latter of those issues (blosc dependency missing for "proper" zarr usage) persists in the container-based setup.

Error I observed

1. I uploaded a ZARR file to our OMERO instance as discussed in this thread and the image cannot be displayed there.

2. When I download (parts of) the image via ezomero like this:

metadata, data = ezomero.get_image(conn, image_id=some_id, no_pixels=False, dim_order='tczyx', start_coords=(2000, 2000, 5, 0, 0), axis_lengths=(512, 512, 1, 1, 1))

I receive the following error:

WARNING:omero.gateway:InternalException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <aaaa9577-994e-4bad-a45a-ac6aa8c1a7a7omero.api.RawPixelsStore> getTile((5, 0, 0, 2000, 2000, 512, 512), {})
Traceback (most recent call last):
File "/home/pol_haase/johamuel/miniforge3/envs/microwells/lib/python3.9/site-packages/omero/gateway/__init__.py", line 4856, in __call__
  return self.f(*args, **kwargs)
File "/home/pol_haase/johamuel/miniforge3/envs/microwells/lib/python3.9/site-packages/omero_api_RawPixelsStore_ice.py", line 998, in getTile
  return _M_omero.api.RawPixelsStore._op_getTile.invoke(self, ((z, c, t, x, y, w, h), _ctx))
omero.InternalException: exception ::omero::InternalException
{
  serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (java.lang.NoClassDefFoundError):
Could not initialize class org.blosc.IBloscDll
  at com.bc.zarr.CompressorFactory$BloscCompressor.cbufferSizes(CompressorFactory.java:352)
  at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:338)
  at com.bc.zarr.chunk.ChunkReaderWriterImpl_Short.read(ChunkReaderWriterImpl_Short.java:55)
  at com.bc.zarr.ZarrArray.read(ZarrArray.java:278)
  at com.bc.zarr.ZarrArray.read(ZarrArray.java:255)
  at loci.formats.services.JZarrServiceImpl.readBytes(JZarrServiceImpl.java:266)
  at loci.formats.in.ZarrReader.openBytes(ZarrReader.java:362)
  at loci.formats.ImageReader.openBytes(ImageReader.java:465)
  at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:167)
  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
  at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:350)
  at ome.io.bioformats.BfPixelBuffer.getTileDirect(BfPixelBuffer.java:518)
  at ome.services.RawPixelsBean.getTile(RawPixelsBean.java:961)
  at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
...
  serverExceptionClass = ome.conditions.InternalException
  message =  Wrapped Exception: (java.lang.NoClassDefFoundError):
Could not initialize class org.blosc.IBloscDll
}

Possible solution

As discussed in this image-sc thread, the problem is likely just a missing dependency (e.g., libblosc). To fix it, I could probably simply build my own container based on the omero containers and fix it, but including the dependency here would probably be the more sustainable solution.

I would be happy to send a PR to fix it if you can point me to the correct place where to add it. That being said, I am not sure whether this is a missing dependency of the webserver or the other involved containers.

[jburel]

The blosc library is not installed. This is a server dependency. Are you using omero-server-docker? or another server.

[jo-mueller]

Hi @jburel ,

thanks for the quick reply. I have essentially used the docker-example-omero which led to the error.

[jburel]

Thanks.
I have opened a PR ome/omero-server-docker#89
this is the first step to upgrade docker-example-omero.

[imagesc-bot]

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

https://forum.image.sc/t/images-batch-import-into-a-dataset-in-omero-using-ezomero-2-1-0/89529/22

[jo-mueller]

Thanks for the lightning-fast fix @jburel . How often are docker containers released? I.e., how long would it take for this change to take effect in production?

[pwalczysko]

Thanks for the lightning-fast fix @jburel . How often are docker containers released? I.e., how long would it take for this change to take effect in production?

@jo-mueller please see https://hub.docker.com/r/openmicroscopy/omero-server/tags for the de-facto release frequency. In short, it is a manual process, so please bear with us, thank you :)

[jo-mueller]

Will keep my eyes peeled then :) Your work is very appreciated, thanks!

[jburel]

@jo-mueller A new version of the omero-server-docker has been pushed to dockerhub. It should include blosc

[jo-mueller]

Thanks big time! 👍