Re: How to load an extension into every notebook on a server

Looking at the Genepattern code [1], it's using display() to publish data.
The notebook interface will only actually use the Javascript that sends if
it's coming from code run in a cell, so that part of the loading can't work
at startup.

I think we'd probably encourage you to keep putting the command to load the
extension at the top of every notebook, by analogy with a similar situation
we had with pylab. It used to be possible to run "ipython notebook
--pylab", and have a lot of numpy & matplotlib functions pre-loaded into
the namespace. But this produces notebooks which can only be run by someone
starting the notebook server in the same way. We found it better to use a
'%pylab' magic inside the notebook when we want the namespace set up like
that. I think loading the genepattern extension is a similar thing: it's
clearer what's going on when that lives inside the notebook, rather than
hidden in your config.

[1]
https://github.com/genepattern/genepattern-notebook/blob/master/profile/extensions/genepattern.py

Thomas

On 23 December 2015 at 22:06, Ted Liefeld <[email protected]>
wrote:

> I am building a Docker image to have a Jupyter server with the GenePattern
> notebook extension in it.  So far so good except that in every notebook I
> have to enter
>
>      %reload_ext genepattern
>
> into the first cell to make the extension active.  I have been prowling
> through the docs and have tried putting this command in lots of places,
> none of which have worked (e.g. ~/.jupyter/jupyter_notebook_config.py,
>  ~/.ipython/profile_default/startup/ipython_notebook_config.py) both
> normally (ie as above) and also as a config setting
>         c.InteractiveShellApp.exec_lines = ['%reload_ext genepattern']
>
> It seems with all the layers of config I am not finding the right one to
> insert this at. Can anyone point me in the right direction?  My current
> container is using Jupyter 4.0.6, IPython 4.0.1 and Python 3.4.3.
>
> Thanks
>
> Ted
>
>
> --
> Ted Liefeld                                      UC San Diego
> Mesirov Lab                                    [email protected]
>
> Office 2A24, BRF-II                        858-534-2010
>
>
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