girder_jupyter

The Jupyter Notebook web application provides a graphical interface for creating, opening, renaming, and deleting files in a virtual filesystem. girder_jupyter is a python package that implements a contents manager to allow Girder to become a backend for this virtual filesystem. This allows notebooks and files to be stored in a Girder server from within Jupyter.

Getting Started

Install the package in the Python environment you are running your Jupyter server in:

pip install girder-jupyter

Add the following options to your jupyter_notebook_config.py

c.NotebookApp.contents_manager_class = 'girder_jupyter.contents.manager.GirderContentsManager'
c.GirderContentsManager.api_key = '<api key>'
c.GirderContentsManager.api_url = '<api url>'

Where <api key> is replaced with a Girder API key for the Girder server and <api url> is the URL to Girder instance you want to use for example http://localhost:8080/api/v1.

Configuration Parameters

• api_url - An API URL for the Girder server. Defaults to 'http://localhost:8080/api/v1'
• api_key -A Girder API key key for the Girder server at api_url. The key should have read and write permission scope.
• token - A Girder token for the Girder server at api_url. This parameter is particularly useful when running instances from JupyterHub.
• root - The root in the Girder hierarchy to use as the content managers root. This path can include {login} which will be replace with the current users login. Defaults to 'user/{login}'

Note that either api_key or token must be provided for the contents manager to be able to authenticate with the Girder server.