Omero and jupyterhub

Hi, @j.burel mentioned at the community meeting that you were looking into launching containers from omero web client to separate the analysis environment from the database server, with a system à la mybinder. I developed some simple notebooks to run analysis or explore data (sorry for the hard-coded paths there). For now the jupyterhub instance and omero are separated, but I was wondering if you found a way to integrate both a bit more (I was thinking maybe jupyterhub API could help). I’m happy to beta-test or help in anyway you can think of work in that direction.

Best,

Guillaume

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Hi @glyg

We’ve got several proof of concepts spread across several experimental repositories and gists, including:

  • Running python code on a remote JupyterHub/BinderHub from the command line
  • Passing parameters to a python notebook as HTML query parameters on JupyterHub/BinderHub
  • Authenticating JupyterHub using OMERO login credentials and passing an OMERO session token to a notebook
  • Probably other things I’ve forgotten about :grinning:

Alongside the above we’re looking at replacing the IDR Virtual Analysis Environment with our own BinderHub as it provides more flexibility.

None of the above is close to production yet, and will have to be scheduled alongside all our other development priorities. Is there anything you’re particularly interested in?

Thanks @manics for the answer. Well, I’d say that all of them or interesting :sweat_smile: but I think I’d be happy with the 2nd one, I think I can come up with the first one and I have not yet started to struggle with centralized authentication. We are still on a prototyping stage so production readiness is not an issue.

Best

G.

Hi Guillaume

I have updated an initial gist from @manics showing the idea of passing parameters to the notebook via the url. See https://gist.github.com/jburel/3068c253073da6df07381fec84f8a9ee
Obviously it will be more suitable to pass sessionID but it will get you a sense of what we are thinking.
It uses https://github.com/manics/jupyter-urlparams.

Cheers

Jmarie

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Thanks a lot @j.burel, I’ll have a close look into this

This is another option https://github.com/manics/jupyter-notebookparams
See this thread for more background: https://discourse.jupyter.org/t/pass-parameters-to-a-notebook-on-jupyterhub-binderhub/1973