Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
js
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Geppetto logo

Geppetto Jupyter Notebook Extension

This is an experimental repo for a Jupyter notebook extension. This extension enables the Jupyter Python server based on tornado that allows the client to establish a websocket connection and serve static resources.

Other than serving the application as a Geppetto backend, Jupyter Geppetto allows, by embedding a notebook in the page, to interact with the notebook and synchronize frontend features with the notebook.

How to install

Before installing, it is recommended to activate a Python 3 virtual environment:

python3 -m venv jupyter-geppetto
source jupyter-geppetto/bin/activate

Or, with conda

conda create -n jupyter-geppetto python=3.7
conda activate jupyter-geppetto

Install with pip

pip install jupyter_geppetto
jupyter nbextension enable --py --sys-prefix jupyter_geppetto

Install extension from sources

git clone --recursive https://github.com/openworm/org.geppetto.frontend.jupyter.git
pip install .

jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
jupyter nbextension enable --py --sys-prefix jupyter_geppetto
jupyter serverextension enable --py --sys-prefix jupyter_geppetto

Overwrite the local install

pip install . --upgrade --no-deps --force-reinstall

Notice: old installs made without --sys-prefix (so )

How to run

After the extension is installed the Jupyter notebook must be run with the parameter --library, which specifies the Python libraries to be loaded together with the extension:

exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=my_geppetto_application_lib

To connect go to the URL: http://localhost:8888/geppetto assuming the default Jupyter configuration, otherwise change the port accordingly.

Note if you get a 404 and you have a custom configuration of Jupyter notebook you will have to add the following to your jupyter_notebook_config.py:

c.NotebookApp.nbserver_extensions = {'jupyter_geppetto':True}

Development

Jupyter Geppetto serves In order to use the synchronization capability,

Geppetto websocket api

Jupyter Geppetto implements the websocket api through a Tornado handler. It supports the messages coming from a geppetto-application frontend. See geppetto-client for the available messages and implementation.

Currently, only a subset of the messages is supported. For further information, see the current release of pygeppetto.

Web api

Allows to add own custom routes and handlers from inside the application. The dependencies must be added from within the libraries specified in the parameter --library

In the file root of your module (init.py of your package), call the RouteManager methods to add your custom routes:

from jupyter_geppetto.webapi import RouteManager

RouteManager.add_controller(MyController) # Add a controller (preferred way for http requests)
RouteManager.add_route('/my/path', MyTornadoHandler) # for more custom control

A controller class is a standard class with webapi annotations on methods. Methods return the response as a string. The RouteManager creates a handler for each method and binds the method with the handler.

Example:

from jupyter_geppetto.webapi import get, post

class MyController:

    @get('/my/simple/path')
    def simple_action(handler):
        return "My response payload" # Simple text response

    @get('/myresource/(.*)')
    def action_with_url_param(handler, param):
        import json
        return json.dumps({'param':param}) # JSON response
    
    @get('/myresource')
    def action_with_query_string_params(handler, param1, param2=None):
        '''Handles 
            /myresource?param1=something&param2=somethingelse
            /myresource?param1=something
        '''
        return ...   
    
    @get('/myresource1')
    def alt_action_with_query_string_params(handler, **kwargs):
        '''Handles any query string parameter'''
        return ...   
        
    @get('/myresource1/(.*)')
    def action_with_url_and_query_string_params(handler, param, param1, param2):
        '''Handles /myresource?param1=comething&param2=somethingelse'''
        return ... 
        
    @post('/myresource2')
    def simple_post_action(handler, payload, param1, param2):
        '''Handles /myresource and body param1=something&param2=somethingelse'''
        return ... 
        
    @get('/myresource3', {'Content-type': 'image/png', 'Cache-Control': 'max-age=600'})
    def get_action_with_headers(handler):
        '''Sets headers'''
        return ... 
        
    @get('/myresource3')
    def get_action_use_handler(handler):
        '''The first parameter is the tornado handler'''
        handler.write('Whatever')
        return ... 

Iframe embedding

In the frontend, it is required to embed an iframe with a jupyter notebook.

Example

import PythonConsole from 'geppetto-client/js/components/interface/pythonConsole/PythonConsole';

// Inside your React component render:
<PythonConsole key="console" pythonNotebookPath="notebooks/notebook.ipynb" />

Synchronization

This feature allows to synchronize backend and frontend objects. In order to use synchronization, it is required to have the iframe embed enabled and initialized. It's implemented through a IPython/Jupyter widget. On the JS side, the connection is achieved through the PythonControlledCapability of the Geppetto client.

Usage

from jupyter_geppetto import synchronization
class MyClass:
    def a(self):
        ...
    def b(self):
        ...
synchronization.startSynchronization(MyClass().__dict__)

Deployment

An application based on Jupyter Geppetto can be deployed as a standard jupyter notebook application. It is recommended a dockerized setup with JupyterHub (e.g. on Kubernetes).