pyBIS is a Python module for interacting with openBIS. It can be used completely independent from Jupyter or JupyterHub. However, in combination with Jupyter it offers a sort of IDE for openBIS, making the life of a normal user with moderate programming skills very easy.
pyBIS uses the openBIS API v3. Because of some compatibility problems, openBIS version 16.05.1 is the minimal requirement. On the Python side, pyBIS uses Python 3.5 and pandas.
pyBIS is devided in several parts:
- the pyBIS module which holds all the method to interact with openBIS
- the JupyterHub authenticator which uses pyBIS for authenticating against openBIS, validating and storing the session token
- the Vagrantfile to set up a complete virtual machine, based on Cent OS 7, including JupyterHub
- the dataset-uploader-api.py, an ingestion plug-in for openBIS, allowing people to upload new datasets