Utilities to interact with the SciTran API from the client side for search, get, put, and compute
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README.md

Scitran client software

This repository includes Matlab and Python utilities to interact with the SciTran API from the client side for search, get, and put. See the project wiki page for a general introduction and links to specific manual pages.

Matlab Client Setup

  • Even when using the Matlab version, you must have python on your path to enable authorization. The key Python module is oauth2client. If you use, say, anaconda to manage your python method than pip is included and you can do the install this way from your terminal

    pip install oauth2client
    

    There are many ways to do the install for other systems, and we will add other examples here later.

  • The python executable must be in the path environment variable in Matlab. You can find your path by typing

    getenv('PATH')
    

    If the path to python is not in this list, then you set add it, say be

    setenv('PATH',['/Users/wandell/anaconda/bin/:',getenv('PATH')]);
    

    You might verify that you succeeded by trying from within your Matlab command window

    system('which python')
    
  • If your terminal environment is set up properly, the best way to initiate scitran client is to start matlab from a terminal. In that case, the Matlab program inherits your shell ENV. Many people start Matlab from an icon, however. This sets up Matlab's own idiosyncratic environment. In that case, you may have to set your ENV (PATH) to include paths to python & required libs manually from within Matlab. See XXX for instructions on how to do this.

Docker requirements

For certain applications, you will want to run docker containers. This will require that you have Docker installed on your local machine. To do that visit the docker website for OSX and Linux instructions. If you have Homebrew on OSX, you can install the toolbox from the command line with brew cask install dockertoolbox.

Once you have Docker installed you can invoke any docker machine and container you set up on your computer.

If you're using docker-machine on OSX there are a couple more steps required. First you will need to first create a 'machine'. To create a machine you should issue the create command (below we use 'default' for the machine name):

   docker-machine create --driver virtualbox default

To get the machine started, issue the start command followed by the machine name:

  docker-machine start default

Now you're ready to issue docker commands through Matlab or Python. See matlab/stDockerConfig.m for Matlab implementation details.

Scitran client dependencies

  • The purpose of the software is to access a Flywheel instance. You will need an authorization token. On first access, you will be prompted for the client ID and secret. This secret can only be given by an administrator of the instance you wish to connect to. So, speak to your administrator about the client ID and secret.

  • JSONlab The MATLAB SciTran client uses JSONlab to load, save, and parse json objects. Hence, JSONlab must be on your MATLAB path. Version XXX is included in this distribution.

Python Client

Check out the docs!