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A client for Synapse, a collaborative compute space that allows scientists to share and analyze data together.

Project description

Python Synapse Client

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Get the synapseclient from PyPI Supported Python Versions

A Python client for Sage Bionetworks' 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.

Python 2 Support

The sun is setting on Python 2. Many major open source Python packages are moving to require Python 3.

The Synapse engineering team will step down Python 2.7 support to only bug fixes, and require Python 3 on new feature releases. Starting with Synapse Python client version 2.0 (will be released in Q1 2019), Synapse Python client will require Python 3.

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, 3.5 and 3.6 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 release candidate branch

For validation, validators would install a release candidate branch to verify that a bug has been fix or a new feature/ an improvement works as expected. To prevent overwriting your working environment, 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 v1.8.2-rc
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

After a version is release, a tag will be created for the released version. To install a specific release, instead of checking out the release candidate branch, check out the tag instead, for example:

git checkout v1.8.2

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.

downloading test data from synapse

synapse -u my_username -p my_password 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 username and password
syn.login('my_username', 'my_password')

## 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)

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('my_username', 'my_password')

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

syn.login('my_username', 'my_password', 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('my_username')

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 my_username -p my_password --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 destination entity. Only a project can have sub wiki pages.
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 2013-18 Sage Bionetworks

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

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