Programmatic interface to Synapse services for Python
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README.md

Python Synapse Client

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Get the synapseclient from PyPI Supported Python Versions Monthly downloads of synapseclient from PyPI

A Python client for Sage Bionetwork's Synapse, a collaborative compute space that allows scientists to share and analyze data together. The Python client can be used as a library for development of software that communicates with Synapse or as a command-line utility.

There is also a Synapse client for R.

Documentation

For more information about the Python client, see:

For more information about interacting with Synapse, see:

Installation

The Python Synapse client has been tested on Python 2.7, 3.4 and 3.5 on Mac OS X, Ubuntu Linux and Windows.

Install using pip

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

(sudo) pip install synapseclient[pandas,pysftp]

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

(sudo) pip install --upgrade synapseclient

The dependencies on pandas and pysftp are optional. Synapse Tables integrate with Pandas. The library pysftp is required for users of SFTP file storage. Both libraries require native code to be compiled or installed separately from prebuilt binaries.

Install from source

Clone the source code repository.

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

Install develop branch

Installing the develop branch can be useful for testing or for access to the latest features, with the acceptance of an increased risk of experiencing bugs. Using virtualenv to create an isolated test environment is a good idea.

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

Replace python setup.py install with python setup.py develop to make the installation follow the head without having to reinstall.

Installing a tagged version

Checking out a tagged version will ensure that JIRA issues are validated on the correct version of the client code. Instead of checking out the develop branch, check out the tag instead, for example:

git checkout v1.0.dev2

Command line usage

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.

querying for entities that are part of the Synapse Commons Repository

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

querying for a test entity

The test entity is tagged with an annotation 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"'

downloading test data from synapse

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

getting help

synapse -h

Note that a synapse account is required.

Usage as a library

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

Example

import synapseclient

syn = synapseclient.Synapse()

## log in using cached API key
syn.login('joeuser')

## 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)

querying for my projects

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

querying for entities that are part of the Synapse Commons Repository

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

querying for entities that are part of TCGA pancancer that are also RNA-Seq data

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

Authentication

Authentication toward synapse can be accomplished in a few different ways. One is by passing username and password to the syn.login function.

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

It is much more convenient to use an API key, which can be generated and cached locally by doing the following once:

syn.login('me@nowhere.com', 'secret', rememberMe=True)

Then, in subsequent interactions, specifying username and password is optional and only needed to login as a different user. Calling login with no arguments uses cached credentials when they are available.

syn.login('me@nowhere.com')

As a short-cut, creating the Synapse object and logging in can be done in one step:

import synapseclient
syn = synapseclient.login()

Caching credentials can also be done from the command line client:

synapse login -u me@nowhere.com -p secret --rememberMe

Synapse Utilities (synapseutils)

The purpose of synapseutils is to create a space filled with convenience functions that includes traversing through large projects, copying entities, recursively downloading files and many more.

Example

import synapseutils
import synapseclient
syn = synapseclient.login()

#COPY: copies all synapse entities to a destination location
synapseutils.copy(syn, "syn1234", destinationId = "syn2345")

#COPY WIKI: copies the wiki from the entity to a destionation entity. Only a project can have subwikipages.
synapseutils.copyWiki(syn, "syn1234", destinationId = "syn2345")


#WALK: Traverses through synapse directories, behaves exactly like os.walk()
walkedPath = synapseutils.walk(syn, "syn1234")

for dirpath, dirname, filename in walkedPath:
    print(dirpath)
    print(dirname)
    print(filename)

License and Copyright

© Copyright 2013-15 Sage Bionetworks

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