vitessce-python "Exception opening new comm"

Describe the bug In a notebook environment, Vitessce fails to render, and Exception opening new comm is printed to the log.

I first noticed this in the workspace environment PSC is providing, and filed an issue there, but Juan has reproduced it in a plain Jupyter, and Ilan says he has also seen it.

To Reproduce We do not have a reliable reproducer. Possibly a race condition?

Expected behavior Vitessce renders

Screenshots

Environment:

Release or git hash:
Browser:
Browser version:

Aug 02 '22 19:08 mccalluc

@mccalluc have you made any progress in reliably reproducing it? Would you be able to provide information about the versions of Python and Jupyter / JupyterLab? If you are able to, !pip freeze > requirements.txt from within the remote notebook would also be useful

Aug 16 '22 19:08 keller-mark

We do not have a reliable reproducer.

Does this mean the exception does not occur reliably, so the widget renders some of the time? Or do you see the exception consistently?

Aug 16 '22 19:08 keller-mark

I see it very often, but not 100% of the time. I'll try again in a bit and post to Slack. (Maybe frequency is related to characteristics of datasets?)

Aug 16 '22 19:08 mccalluc

When I open a workspace for HBM989.VVXT.224 by adding .ws.ipynb, the top notebook cell contains the line

!pip install vitessce[all]==1.0.9

For me, this line fails because all includes jupyter-server-proxy which fails to install in the workspace in isolation:

!pip install jupyter-server-proxy

Both lines result in ERROR: Failed building wheel for cffi

Are you also seeing this error?

jupyter-server-proxy is required when the client (in this case, the notebook widget running in the browser) is not local to the python process (in this case, the python process is running on a server at PSC)

Aug 24 '22 19:08 keller-mark

No, I haven't see that error before, and I just ran it in a new notebook, and it seemed to work:

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Installing collected packages: simpervisor, negspy, mypy-extensions, asciitree, widgetsnbextension, ujson, typing-extensions, tomli, toml, starlette, priority, platformdirs, pathspec, numpy, multidict, jupyterlab-widgets, hyperframe, hpack, h11, frozenlist, fasteners, click, async-timeout, aiofiles, yarl, wsproto, tifffile, scipy, pandas, numcodecs, h2, black, aiosignal, zarr, hypercorn, generate-tiff-offsets, aiohttp, vitessce, ipywidgets, jupyter-server-proxy
Successfully installed aiofiles-0.8.0 aiohttp-3.8.1 aiosignal-1.2.0 asciitree-0.3.3 async-timeout-4.0.2 black-22.8.0 click-8.1.3 fasteners-0.17.3 frozenlist-1.3.1 generate-tiff-offsets-0.1.7 h11-0.13.0 h2-4.1.0 hpack-4.0.0 hypercorn-0.14.1 hyperframe-6.0.1 ipywidgets-8.0.1 jupyter-server-proxy-3.2.1 jupyterlab-widgets-3.0.2 multidict-6.0.2 mypy-extensions-0.4.3 negspy-0.2.24 numcodecs-0.10.2 numpy-1.23.2 pandas-1.4.4 pathspec-0.10.0 platformdirs-2.5.2 priority-2.0.0 scipy-1.9.1 simpervisor-0.4 starlette-0.14.0 tifffile-2020.10.1 toml-0.10.2 tomli-2.0.1 typing-extensions-4.3.0 ujson-5.4.0 vitessce-1.0.9 widgetsnbextension-4.0.2 wsproto-1.2.0 yarl-1.8.1 zarr-2.12.0

Sep 01 '22 19:09 mccalluc

There seems to be an underlying issue with the workspace, in that it cannot communicate with any ipywidget in the same notebook execution where the ipywidgets package is installed.

I just tried the following in a HuBMAP workspace notebook:

!pip install ipywidgets==7.7.2

import ipywidgets
slider = ipywidgets.IntSlider(value=40)
slider

And it also throws Exception opening new comm (see slack message).

Sep 02 '22 21:09 keller-mark

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"Exception opening new comm"

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