Metadata-Version: 1.1
Name: sevenbridges-python
Version: 0.9.6
Summary: SBG API python client bindings
Home-page: https://github.com/sbg/sevenbridges-python
Author: Seven Bridges Genomics Inc.
Author-email: senad.ibraimoski@sbgenomics.com
License: Apache Software License 2.0
Description: sevenbridges-python
        ===================
        
        
        |Travis| |PyPI version| |Documentation| |Licence|
        
        `CHANGESETS <CHANGES.md>`__
        
        sevenbridges-python is a `Python <http://www.python.org/>`__ library
        that provides an interface for `the Seven Bridges
        Platform <https://www.sbgenomics.com/>`__ and `Cancer Genomics
        Cloud <http://www.cancergenomicscloud.org/>`__ public APIs. It works
        with Python versions 2.6+ and supports Python 3.
        
        The `Seven Bridges Platform <https://www.sbgenomics.com/>`__ 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) <http://www.cancergenomicscloud.org/>`__, powered by `Seven
        Bridges <https://www.sbgenomics.com/>`__, is also a cloud-based
        computation environment. It was built as one of three pilot systems
        funded by the `National Cancer Institute <http://www.cancer.gov/>`__ to
        explore the paradigm of colocalizing massive genomics datasets, like The
        `Cancer Genomics Atlas (TCGA) <http://cancergenome.nih.gov/>`__,
        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, you should pass the following items to sevenbridges-python:
        
        (a) Your authentication token
        
        (b) The API endpoint you will be interacting with. This is either the endpoint for the Seven Bridges Platform or for the Seven Bridges Cancer Genomics Cloud (CGC) or for CAVATICA.
        
        You can find your authentication token on the respective pages:
        
        -  https://igor.sbgenomics.com/developer for the Seven Bridges Platform
        -  https://cgc.sbgenomics.com/developer for the CGC
        -  https://cavatica.sbgenomics.com/developer for Cavatica
        
        The API endpoints for each environment are:
        
        -  https://api.sbgenomics.com/v2 for the Seven Bridges Platform
        -  https://cgc-api.sbgenomics.com/v2 for the CGC.
        -  https://cavatica-api.sbgenomics.com/v2 for CAVATICA
        
        
        For more information about the API, including details of the available parameters for each API call, you should check 
        the API documentation before using this library:
        
        -  http://docs.sevenbridges.com/docs/the-api for the Seven Bridges Platform.
        -  http://docs.cancergenomicscloud.org/docs/the-cgc-api for the CGC.
        -  http://docs.cavatica.org/docs/the-api for CAVATICA
        
        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/.sevenbridges/credentials`` with defined parameters.
        
        Explicit initialization
        ~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            import sevenbridges as sbg
            api_config = sbg.Config(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>')
        
        Initialization via environment variables
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            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
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            import sevenbridges as sbg
            config = sbg.Config(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>
        
            [cgc]
            api_endpoint = https://cgc-api.sbgenomics.com/v2
            auth_token = <TOKEN_HERE>
            
            [cavatica]
            api_endpoint = https://cavatica-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.
        
        .. code:: python
        
            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.
        
        .. code:: python
        
            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()
        
        .. |PyPI version| image:: https://badge.fury.io/py/sevenbridges-python.svg
           :target: https://pypi.python.org/pypi/sevenbridges-python
        .. |Documentation| image:: https://readthedocs.org/projects/sevenbridges-python/badge/?version=latest
           :target: http://sevenbridges-python.readthedocs.org/en/latest/
        .. |Licence| image:: https://img.shields.io/badge/licence-Apache-orange.svg
           :target: https://github.com/sbg/sevenbridges-python/blob/master/LICENCE
        .. |Travis| image:: https://travis-ci.org/sbg/sevenbridges-python.svg
           :target: https://travis-ci.org/sbg/sevenbridges-python
        
        
        Contributing
        ------------
        
        Contributions, bug reports and issues are very welcome.
        
        You can make your own contributions by forking the develop branch of this repository, 
        making your changes, and issuing pull request on the develop branch.
        Contributors should read the `Seven Bridges Notice to Contributors <CONTRIBUTORS_NOTICE.md>`_ and 
        sign the `Seven Bridges Contributor Agreement <https://secure.na1.echosign.com/public/esignWidget?wid=CBFCIBAA3AAABLblqZhAqt_9rHEqy2MggS0uWRmKHUN2HYi8DWNjkgg5N68iKAhRFTy7k2AOEpRHMMorxc_0*>`_ before submitting a pull request.
        
        Copyright
        ---------
        
        Copyright (c) 2016-2017 Seven Bridges Genomics, Inc. All rights reserved.
        
        This project is open-source via the `Apache 2.0 License <http://www.apache.org/licenses/LICENSE-2.0>`_.
        
Keywords: sevenbridges,sbg,api,cgc,cancer,genomics,cloud
Platform: Windows
Platform: POSIX
Platform: MacOS
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
