sevenbridges-python 0.7.2

SBG API python client bindings

CHANGESETS

sevenbridges-python is a Python library that provides an interface for the Seven Bridges Platform and Cancer Genomics Cloud public APIs. It works with Python versions 2.6+ and supports Python 3.

The Seven Bridges Platform is a cloud-based environment for conducting bioinformatic analyses. It is a central hub for teams to store, analyze, and jointly interpret their bioinformatic data. The Platform co-locates analysis pipelines alongside the largest genomic datasets to optimize processing, allocating storage and compute resources on demand.

The The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is also a cloud-based computation environment. It was built as one of three pilot systems funded by the National Cancer Institute to explore the paradigm of colocalizing massive genomics datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources to analyze them. The CGC makes more than a petabyte of multi-dimensional data available immediately to authorized researchers. You can add your own data to analyze alongside TCGA using predefined analytical workflows or your own tools.

Installation

The easiest way to install sevenbridges-python is using pip. :

$ pip install sevenbridges-python

Get the Code

sevenbridges-python is actively developed on GitHub, where the code is always available.

The easiest way to obtain the source is to clone the public repository :

$ git clone git://github.com/sbg/sevenbridges-python.git

Once you have a copy of the source, you can embed it in your Python package, or install it into your site-packages by invoking: :

$ python setup.py install

If you are interested in reviewing this documentation locally, clone this repository, position yourself in the docs directory and after installing requirements-dev.txt, invoke: :

$ make html

Run Tests

In order to run tests clone this repository, position yourself in the root of the cloned project and after installing requirements-dev.txt, invoke: :

py.test

Authentication and Configuration

In order to authenticate with the API, sevenbridges-python library requires that you pass in your authentication token and the URL endpoint for the environment you are working in: either the Seven Bridges Platform or the Cancer Genomics Cloud.

You can find your authentication token on the respective platform pages:

• https://igor.sbgenomics.com/developers - for the Seven Bridges Platform

• https://cgc.sbgenomics.com/developers - for the CGC

  The API endpoints for the platforms are:

• https://api.sbgenomics.com/v2 for the Seven Bridges Platform

• https://cgc-api.sbgenomics.com/v2 for the CGC

The API documentation is available:

• http://docs.sevenbridges.com/docs/the-api for the Seven Bridges Platform.

• http://docs.cancergenomicscloud.org/docs/the-cgc-api for the CGC

Initialize configuration using the configuration file

Once you obtain your authentication token you can pass it to the Config object. You can instantiate your API object by passing the appropriate configuration. There are three ways you can pass configure the library:

1. Pass parameters url and token explicitly when initializing the config object.

2. Put the API endpoint and token in the environment variables API_URL and AUTH_TOKEN respectively.

3. Use the configuration file $HOME/.sbgrc with defined parameters.

Explicit initialization

import sevenbridges as sbg
api_config = sbg.Config(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>')

Initialization via environment variables

import sevenbridges as sbg

import os

# Usually these would be set in the shell beforehand
os.environ['SB_API_ENDPOINT'] = 'https://api.sbgenomics.com/v2'
os.environ['SB_AUTH_TOKEN'] = '<TOKEN_HERE>'

api = sbg.Api()

Initialization via config file

import sevenbridges as sbg
config = sbg.Config(profile='my-profile-cgc')

Notes on config file format

The $HOME/.sevenbridges/credentials file has a simple .ini file format, for example:

[default]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = <TOKEN_HERE>

[my-profile-cgc]
api_endpoint = https://cgc-api.sbgenomics.com/v2
auth_token = <TOKEN_HERE>

Initializing the sevenbridges-python library

The API object represents the central resource for querying, saving and performing all other actions on your resources. Once you have instantiated the configuration class, pass it to the API class constructor.

import sevenbridges as sbg
api_config = sbg.Config()  # Or any other choice of initialization method
api = sbg.Api(config=api_config)

Examples

The following code illustrates the way the library should be used. For more detailed examples consult the documentation, hosted on readthedocs.

import sevenbridges as sbg

api_config = sbg.Config()  # Or any other choice of initialization method
api = sbg.Api(config=api_config)

# Get current user
user = api.users.me()

# Query your projects
projects = api.projects.query(limit=100)

# Fetch project files
project = projects[0]
files = project.get_files()