Python Synapse Client
A python client for Sage 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's 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 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 acceptence 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.
Synapse Commons Repository
querying for entities that are part of thesynapse -u me@nowhere.com -p secret query 'select id, name from entity where parentId=="syn150935"'
entity
querying for a testThe 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'])
Synapse Commons Repository
querying for entities that are part of thesyn.query('select id, name from entity where parentId=="syn150935"')
TCGA pancancer that are also RNA-Seq data
querying for entities that are part ofsyn.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
License and Copyright
© Copyright 2013 Sage Bionetworks
This software is licensed under the Apache License, Version 2.0.