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Server Extension for Jupyter notebooks to connect to openBIS and download/upload datasets, inluding the notebook itself

Project description

Jupyter openBIS Server

The server part of the jupyter-openbis-extension and jupyterlab-openbis notebook extension. Uses the pyBIS module internally to communicate with openBIS. Communicates with the notebook extensions via the tornado webserver.

Install the server extension

The server extension will be automatically installed when you install the Jupyter Notebook Extension (the «classic» Jupyter Notebook):

pip install --upgrade jupyter-openbis-extension

If you need to install or upgrade the server extension alone, you can do so by:

pip install --upgrade jupyter-openbis-server

install Jupyter extension manually

In most cases, a simple pip install --upgrade jupyter-openbis-server will install the server extension. However, in some cases (e.g. when installing via pip install -e .) you need to issue the following command to register the extension:

**In the library path, e.g. etc/jupyter/

$ jupyter serverextension enable --py jupyter-openbis-server --sys-prefix

This will create a file ~/.jupyter/jupyter_notebook_config.json with the following content:

  "NotebookApp": {
    "nbserver_extensions": {
      "jupyter-openbis-server.main": true

Uninstall Jupyter openBIS Server

Unfortunately, pip doesn't automatically clean up the Jupyter configuration when uninstalling. You have to do it yourself:

$ jupyter serverextension disable --py jupyter-openbis-server
$ pip uninstall jupyter-openbis-server

Project details

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