jupyter-openbis-extension 0.6.0

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

Jupyter-OpenBIS-Extension

Requirements

The jupyter-openbis-extension needs at least Python 3.3 in order to run. The Jupyter notebook server starts this extension during startup and must therefore run under the same Python version. The kernel can be anything (Python 2.7, Julia, R, Perl...)

This extension has been successfully tested with Safari 12.0.3, Chrome 72.0 and Firefox 66.0. There is a known incompatibility before Firefox 61.0b13 with Tornado > 6.x (the webserver used by Jupyter). If you encounter such incompatibilities, try to downgrade to Tornado 5.1.1. However, Tornado 5.1.1 will not work with Jupyter Lab 3.

Install the extension

If you haven't done yet: download the latest jupyter-openbis-extension from pip. It will automatically install the various dependencies, e.g. Pandas and NumPy.

pip install --upgrade jupyter-openbis-extension

Create a configuration file

This step is not really necessary, as you can define openBIS connections within the Jupyter notebook. However, if you need to connect to the same openBIS connections many times, this will become convenient. Create a file openbis-connections.yaml. It should contain connection information to your server(s), for example:

connections:
    - name                : TEST local openBIS instance
      url                 : https://localhost:8443
      verify_certificates : false
      username            : username
      password            : password
    - name                : PRODUCTION openBIS instance
      url                 : https://openbis.example.com
      verify_certificates : true
      username            : username

Note 1: You do not need neither username nor password. With the current version, you are able to enter username and password directly from within a Jupyter notebook.

Note 2: Place this file in any of these directories (on Mac OS X):

/Users/your_username/jupyter-openbis-extension/notebooks
/Users/your_username/.jupyter
/Users/your_username/.pyenv/versions/3.6.0/etc/jupyter  # or wherever your jupyter installation is located
/usr/local/etc/jupyter
/etc/jupyter

These directories can be found by invoking

$ jupyter --paths

The config section from the output lists the directories where your openbis-connections.yaml file should be placed.

install Jupyter extension manually

In most cases, a simple pip install --upgrade jupyter-openbis-extension will do. However, in some cases you need to issue the following commands to get the extension running correctly:

$ jupyter serverextension enable --py jupyter-openbis-extension
$ jupyter nbextension install --py jupyter-openbis-extension --user
$ jupyter nbextension enable --py jupyter-openbis-extension --user

If you want to install the extension globally, use --system instead of --user.

Launching Jupyter notebook

Now you are ready to launch Jupyter notebook:

$ jupyter notebook --no-browser

Observe the terminal. It should tell you which server(s) have been registered. If you provided a password, it will try to connect:

$ jupyter notebook
Registered: https://localhost:8443
Successfully connected to: https://localhost:8443
Registered: https://openbis.example.com

Congratulations! You can retry non-successful connections later, directly from the GUI. Copy the the URL given in the output and paste it in your browser. You might also just start Jupyter without the --no-browser option.

Uninstall Jupyter extension

$ jupyter serverextension disable --py jupyter-openbis-extension
$ jupyter nbextension disable --py jupyter-openbis-extension --user
$ jupyter nbextension uninstall --py jupyter-openbis-extension --user

This should remove the registrations in the paths listed by the

$ jupyter --paths

command.

Development with Vagrant

If you want to use a predefined development environment, follow these steps:

1. Install latest version of VirtualBox (https://www.virtualbox.org)

2. Install latest version of Vagrant (https://www.vagrantup.com/downloads.html)

3. vagrant plugin install vagrant-vbguest vagrant-notify-forwarder vagrant-disksize

4. cd vagrant

5. vagrant up

After the setup is complete, you'll have

• Jupyter with openBIS extension running at http://localhost:8888.
• openBIS running at https://localhost:8122/openbis/, with credentials admin/password.
• Object /DEFAULT/DEFAULT with a lot of datasets for testing.

Hint: Jupyter creates no log file. Everything is printed onto the console. In order to see this output do the following:

1. vagrant ssh
2. screen -r

You can escape from the screen by typing ^A followed by ^D.

clone repository and install extension for development

$ git clone [e-mail]:sispub/jupyter-openbis-extension.git
$ cd jupyter-openbis-extension
$ virtualenv venv
$ source venv/bin/activate
(venv) $ pip install -e .

The -e is a shortcut for --editable. This means, it will only establish a link to your source folder instead of copying the files. When you do any modifications on the jupyter server extension (the Python files) you need to restart Jupyter notebook in order to see the changes.

If you make modifications on the UI (the Javascript files) you only need to reload the page in order the see the effect.

How to extend Jupyter Notebooks is described here. To distribute Jupyter Extensions, read this documentation carefully.