Extension for Jupyter notebooks to connect to openBIS and download/upload datasets, inluding the notebook itself
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
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
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
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
Development with Vagrant
If you want to use a predefined development environment, follow these steps:
Install latest version of VirtualBox (https://www.virtualbox.org)
Install latest version of Vagrant (https://www.vagrantup.com/downloads.html)
vagrant plugin install vagrant-vbguest vagrant-notify-forwarder vagrant-disksize
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:
- vagrant ssh
- screen -r
You can escape from the screen by typing ^A followed by ^D.
clone repository and install extension for development
$ git clone firstname.lastname@example.org:sispub/jupyter-openbis-extension.git $ cd jupyter-openbis-extension $ virtualenv venv $ source venv/bin/activate (venv) $ pip install -e .
-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.
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