martelogan / tapioca-cbrain

Simple Python wrapper for CBrain (https://portal.cbrain.mcgill.ca) implemented as a flavor of tapioca (https://tapioca-wrapper.readthedocs.io/)

Tapioca cbrain

Installation

Note: pending stable deployment on pypi, we recommend the following developer install.

git clone https://github.com/martelogan/tapioca-cbrain.git
cd tapioca-cbrain
python setup.py install

Ideally, it is advised to manage Python virtual environments via conda in order to safely segregate module dependencies. In this case, it is recommended to locallize pip installations during conda environment creation, to avoid dependency conflicts, by instantiating the environment with its own pip setup, à la conda create --name custom_venv_name pip then activating it (linux example: source activate custom_venv_name)

Getting Started

from tapioca_cbrain import Cbrain

# assuming credentials known in advance:
api = Cbrain(cbrain_api_token="<your_api_token_string>")

# get user profile details as response object
user_response_obj = api.users(id='<your_user_id>').get()

# print user profile dict
user_data = user_response_obj().data
print user_data

# post to create a new CBrain session, and store response (with credentials)
session_payload = {'login': '<your_username_string>', 'password': '<your_password_string>'}
session_response_obj = api.session(id='').post(data=session_payload)
session_data = session_response_obj().data

# credential print statements
print session_data['cbrain_api_token']
print session_data['user_id']

Jupyter Notebook

Through this simple (minimalist) wrapper, our workflow can readily take advantage of Jupyter Notebook.

For example, listing available endpoints by typing api. + pressing tab

>>> api.
api.bourreaux                    api.data_providers               api.data_providers_browse
api.data_providers_delete        api.data_providers_isalive       api.data_providers_register
...

Or typing api.users? + presssing enter to get

>>> api.users?
Docstring:
Automatic generated __doc__ from resource_mapping.
Resource: {id}/
Docs: https://portal.cbrain.mcgill.ca/swagger#!/Users
...

Disclaimer

Significant work remains to ensure complete api support, but this should suffice to get up & running.

A quick demo CLI gist demonstrates how we could automate session creation and apply this wrapper to easily expose our api to end-users.

Note also, for the sake of this project, a simple (presently unmaintained) swagger2tapioca utility gist was written to convert generic OpenAPI/Swagger v2.0(JSON) to tapioca resource_mapping.py files (ie. effectively automate tapioca wrapper creation)