Metadata-Version: 1.2
Name: blackfynn
Version: 1.7.2
Summary: Python client for the Blackfynn Platform
Home-page: http://app.blackfynn.io
Author: Blackfynn, Inc.
Author-email: mark@blackfynn.com
License: UNKNOWN
Description: blackfynn-py
        ============
        
        Python client and command line tool for Blackfynn.
        
        Installation
        ------------
        
        Note: we currently only support *Python v2.7*.
        
        .. code:: python
        
            pip install blackfynn
        
        Credentials Setup
        -----------------
        
        Connection credentials to Blackfynn can sourced from environment
        variables. In your ``~/.bashrc`` or ``~/.bash_profile``, set the
        following variables. Before using the client library or command line
        tool, ensure these environment variables are set.
        
        .. code:: bash
        
            export BLACKFYNN_USER=you@company.com
            export BLACKFYNN_PASS=<your-password>
        
        Client Library
        --------------
        
        Basic Usage: examples
        ~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            # imports
            from blackfynn import Blackfynn
        
            # client
            bf = Blackfynn()
        
            # If you belong to more than one organization, explicitly set your context, otherwise, ignore.
            bf.set_context('my organization name')
        
            # print your available datasets
            datasets = bf.datasets()
            print datasets
        
            # grab some dataset (e.g. first one)
            ds = datasets[0]
        
            # list items inside dataset (first level)
            print ds.items
        
        Upload data
        ~~~~~~~~~~~
        
        Upload files
        ^^^^^^^^^^^^
        
        You must upload files into a ``Dataset`` or ``Collection``.
        
        .. code:: python
        
            # upload a file into a dataset (ds)
            ds.upload_files('/path/to/my_data.nii.gz')
        
        Retrieve data
        ~~~~~~~~~~~~~
        
        Retrieve timeseries data
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        .. code:: python
        
            ts = bf.get('N:package:your-timeseries-id')
        
            # get first minute of data in 1-second chunks
            for chunk in ts.get_data_iter(chunk_size='1s', length='1m'):
                # do something with data (pandas Dataframe)
                print "Mean values =", chunk.mean()
        
            # you can do the same thing for a single channel
            channel = ts.channels[0]
            for chunk in channel.get_data_iter(chunk_size='5s', length='10m'):
                # do something with data (pandas Series)
                print "Max value =", chunk.max()
        
        Command Line Tool
        -----------------
        
        Usage
        ~~~~~
        
        .. code:: bash
        
            >> bf --help
            Blackfynn Client
        
            Usage:
              bf upload [options] <destination> <file> [<file>...]
              bf append [options] <destination> <file> [<file>...]
              bf search [options] <term> [<term>...]
              bf datasets [options]
              bf dataset [options] <dataset> [<command>] [<action>] [<action-args>...]
              bf create [options] collection <destination> <name>
              bf create [options] dataset <name>
              bf delete [options] <item>
              bf show [options] <item>
              bf orgs [options]
              bf env [options]
              bf version
        
            Options
              -h --help       Show help.
              --user=<user>   Email/username
              --pass=<pass>   Password
              --host=<host>   Blackfynn host
              --org=<org>     Set organization context
        
        Basic examples
        ~~~~~~~~~~~~~~
        
        Show your setup
        
        .. code:: bash
        
            bf env
        
        Show your datasets
        
        ::
        
            >> bf datasets --org blackfynn
            Datasets:
             - Studies (id: N:dataset:12aba9af-650c-4fd5-b150-ae77a60a92a0)
             - NICU (id: N:dataset:4fb54fdf-aafb-4746-96bc-25b9f6588254)
             - Blackfynn (id: N:dataset:5a6779a4-e3d8-473f-91d0-0a99f144dc44)
             - Streaming (id: N:dataset:79627c2f-cd6c-4095-8f15-4114c80290ec)
             - Patients (id: N:dataset:967ff102-d2d1-4e11-a8c8-a72c99d70b48)
             - Subjects (id: N:dataset:e4189eb0-6e66-47e6-8a23-80d81f4a0095)
        
        Search for things
        
        ::
        
            >> bf search Fred
             * <TimeSeries name='Fred Tugwell' id='N:package:5385f12f-879e-4d9e-a3c2-b7ff798972d8'>
             * <TimeSeries name='Fred Heard' id='N:package:a3e6f016-f9b7-44f3-bb74-0a027935fba6'>
        
        Show specific item
        
        .. code:: bash
        
            >> bf show 'N:package:1234-1234-1234-1234'
        
        File uploads
        ~~~~~~~~~~~~
        
        Upload a file into a Dataset.
        
        .. code:: bash
        
            bf upload 'N:dataset:1234-1234-1234-1234' /path/to/my_data.nii.gz
        
        Upload all files and directories into a dataset. This action will create
        a collection named 'folder', and recursively upload all contents into
        this collection.
        
        .. code:: bash
        
            bf upload 'N:dataset:1234-1234-1234-1234' /path/to/folder
        
        If your environment variables are not set, you can also enter
        credentials
        
        .. code:: bash
        
            bf upload --user=<email> --pass=<pass> 'N:dataset:1234-1234-1234-1234' /path/to/data_i_want_to_upload.mef
        
        Append data into an existing TimeSeries object (note: append process
        currently only supports timeseries data)
        
        .. code:: bash
        
            bf append 'N:package:1234-1234-1234-1234' /path/to/data_i_want_to_append.mef
        
Keywords: blackfynn client rest api
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Utilities
Requires-Python: <3
