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MolecularAI / aizynthfinder

A tool for retrosynthetic planning
https://molecularai.github.io/aizynthfinder/
MIT License
583 stars 134 forks source link

Using Voila to run the notebook #78

Closed DocMinus closed 1 year ago

DocMinus commented 2 years ago

This is not really an issue related to AIZynthfinder, rather a Voila issue. Thought I'd ask here anyway:

Running a notebook via Voila aizynthfinder.ipynb works rather well, except - there is a problem with the generated images, they don't seem to be generated (in the correct path?) and can thus not be read, therefor the generated synthesis tree is displayed empty with only arrows (but with the starting materials). I attempted the whitelisting suggestion from the Voila docs, but there must be more to it than that.

Anyone who hangs out here has experience with Voila? Maybe even used it with AIZynthfinder?

SGenheden commented 1 year ago

In the latest release we have implemented a python-native route for drawing routes. Please try this.

DocMinus commented 1 year ago

Thanks for this. Doesn't work though. Now one can't even get as far as to enter any string. But I think its a Voila issue. Here are the error message I get, if you car/have time.
....\path.conda\envs\aizynth-env\lib\site-packages\jupyter_server\base\handlers.py:197: UserWarning: The Tornado web application does not have an 'authorizer' defined in its settings. In future releases of jupyter_server, this will be a required key for all subclasses of JupyterHandler. For an example, see the jupyter_server source code for how to add an authorizer to the tornado settings: https://github.com/jupyter-server/jupyter_server/blob/653740cbad7ce0c8a8752ce83e4d3c2c754b13cb/jupyter_server/serverapp.py#L234-L256 warnings.warn( 403 GET /voila/files/favicon.ico (::1): File not whitelisted 403 GET /voila/files/favicon.ico (::1) 1.00ms

There are other ways to make the app available to non-python users, so perhaps not a big deal. I will go ahead and close this issue, unless anyone wants to reopen it.