A python client for Sage Synapse, a collaborative compute space that allows scientists to share and analyze data together. Please visit these pages for more information: Getting Started Guide to Synapse and Getting started with the Synapse python client.

The Python client can be used as a library for development of software that communicates with Synapse or as a command-line utility. See also the Synapse R client.

Note: The January 25th, 2013 release of the Synapse platform made changes that are incompatible with older versions of the Python Client. If you have a version prior to 0.2.1, you'll need to upgrade to use the latest features of the Synapse platform.

The python synapse client has been tested on python 2.7 on Mac OS X, Ubuntu Linux and Windows 2008.

The Python Synapse Client is on PyPI and can be installed with pip:

pip install synapseclient

...or to upgrade an existing installation of the Synapse client:

pip install --upgrade synapseclient

Clone the source code repository.

git clone git://github.com/Sage-Bionetworks/synapsePythonClient.git
cd synapsePythonClient
python setup.py install

The synapse client can be used from the shell command prompt. Valid commands include: query, get, cat, add, update, delete, and onweb. A few examples are shown.

synapse -u me@nowhere.com -p secret query 'select id, name from entity where parentId=="syn150935"'

The test entity is tagged with an attribute test_data whose value is "bogus". We'll use the ID of this entity in the next example.

synapse -u me@nowhere.com -p secret query 'select id, name, parentId from entity where test_data=="bogus"'

synapse -u me@nowhere.com -p secret get syn1528299

synapse -h

Note that a synapse account is required.

The synapse client can be used to write software that interacts with the Sage Synapse repository.

import synapseclient

syn = synapseclient.Synapse()
syn.login('me@nowhere.com', 'secret')

## credentials may also be specified in .synapseConfig,
## in which case you can do:
# syn.login()

## retrieve a 100 by 4 matrix
matrix = syn.get('syn1901033')

## inspect its properties
print matrix.name
print matrix.description
print matrix.path

## load the data matrix into a dictionary with an entry for each column
with open(matrix.path, 'r') as f:
    labels = f.readline().strip().split('\t')
    data = {label: [] for label in labels}
    for line in f:
        values = [float(x) for x in line.strip().split('\t')]
        for i in range(len(labels)):
            data[labels[i]].append(values[i])

## load the data matrix into a numpy array
import numpy as np
np.loadtxt(fname=matrix.path, skiprows=1)

profile = syn.getUserProfile()
query_results = syn.query('select id,name from projects where project.createdByPrincipleId==%s' % profile['ownerId'])

syn.query('select id, name from entity where parentId=="syn150935"')

syn.query('select id, name from entity where freeze=="tcga_pancancer_v4" and platform=="IlluminaHiSeq_RNASeqV2"')

Authentication toward synapse can be specified in three ways:

1. By passing username and password to the login function (or using the -u and -p parameters on the command line)

2. Creating a configuration file in the home directory called .synapseConfig that contains the username and password. See example below.

3. Using cached authentication. Everytime the client authenticates the credentials are cached for 24 hours. Meaning that subsequent interactions do not need the username and password credentials.

###Example config file stored in ~/.synapseConfig [authentication] username: me@nowhere.com password: secret

© Copyright 2013 Sage Bionetworks

This software is licensed under the Apache License, Version 2.0.