Getting TypeError: e.store.get is not a function

[fercer]

Hi vizarr team, thanks for this amazing work!

I just started getting the following error early this week when trying to visualize Zarr files (stored localy or even remotely e.g. from IDR).

ERROR:RPC:Error in method Error: TypeError: e.store.get is not a function
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/imjoy_rpc/rpc.py", line 404, in _wait
    result = await result
  File "/content/vizarr/example/imjoy_plugin.py", line 23, in run
    await viewer.add_image(img)
Exception: Error: TypeError: e.store.get is not a function

The viewer shows, but the image is not being loaded.

I've reproduced the error by cloning the most recent version of vizarr from this repository and following the steps from the IDR example (vizarr/example/IDR_example.ipynb).

Here are the versions of the packages that I'm using:

python: 3.10.12
imjoy: 0.11.20
imjoy_rpc: 0.5.57
zarr: 2.18.2
fsspec: 2023.6.0

[manzt]

Hi there, thanks for trying out vizarr. I need to update the examples but the preferred way to use vizarr is through the custom Widget (not imJoy) https://github.com/hms-dbmi/vizarr/issues/174#issuecomment-1771739245

[manzt]

I'll work on updating the examples. In the meantime, you should be able to get started with the following (no need to clone this repo, just pip install vizarr)

from fsspec import get_mapper
import zarr

# Create a remote mapping to the data
url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/"
store = get_mapper(url)
z_grp = zarr.open(store, mode='r')
z_grp

import vizarr # make sure to pip install vizarr
viewer = vizarr.Viewer()
viewer.add_image(source=z_grp)
viewer

[fercer]

Thanks for the prompt answer @manzt!

I installed vizarr from pip and used it as normal python package as you suggested, and it works nicely without issues on my PC.

For some reason it is still not loading when used on colab; however, that might be related to a different reason. Unfortunately the colab notebook does not display any errors, so I can't elaborate on what is failing in the environment.

Thank you!

[manzt]

hmm, I just tried with the link in the readme. I'm not sure what's happen in google colab:

[manzt]

I installed vizarr from pip and used it as normal python package as you suggested, and it works nicely without issues on my PC.

Glad it's working for you! I needed a kick to update the notebook materials :) #186

[fercer]

I just tested again in colab and now is working completely. Probably some issue on the environment not related to vizarr.

For completeness, I tested with zarr images stored remotely from IDR, and stored locally, both worked without issues.

Thanks again for your help!

[manzt]

great!