DAX Installation

Table of Contents:

  1. Requirements
  2. For Linux user
  3. For Mac user
  4. Warnings
  5. Install dax
  6. For Linux user
  7. For Mac user
  8. No Sudo Access
  9. Verify the installation
  10. Programming in python

Requirements

Requirements for DAX: * Linux or MacOS operating system (has not been tested on windows yet). * Python installed with version 2.7.X * git or pip installed

To check that your python version is 2.7.X:

python --version

For Linux user

To install pip if you want/don’t have it (optional):

easy_install pip

To install git if you don’t have it:

apt-get install git

For Mac user

If svn command doesn’t exist on you mac, install xcode from the Apple Store. Run it and go to Xcode -> Preferences -> Downloads -> Command Line Tools -> Install. Now, you can use svn.

A quick way to check the installation of Xcode and command line developer is to run:

xcode-select --install

If it asks: “install requested for command line developer tools”, do the install.

To install pip, run:

sudo easy_install pip

If you don’t have easy_install, follow the instructions on this link https://pypi.python.org/pypi/setuptools .

To Install git: on this link http://git-scm.com/downloads , click on the Mac Os X button to download the package and install it.

Warnings

Before starting with the different steps, if you see a ‘Permission denied’ while trying to install the libraries, add sudo in front of the command line. It will ask for your password. This will use the sudo access (http://en.wikipedia.org/wiki/Sudo) when running the command line and you will have the permission to install packages everywhere on your computer.

If you don’t have sudo access on your computer, follow the section No Sudo access.

Previously all of the commonly used CLI tools (XnatSwitchProcessStatus, Xnatupload, Xnatdownload, and Xnatinfo etc) were stored under masimatlab. These versions are no longer maintained and the new versions are part of DAX. If you get errors that your versions don’t work, you should check your PATH variable

echo $PATH

If you see a reference to masimatlab/trunk/xnatspiders/Xnat_tools, you should remove this from your path so versions do not conflict. When you install DAX, your environement is set for the new versions (but does not make any changes to the old versions so you need to do this manually).

If you get any nasty traceback errors, you may be missing a required module package. Below is an example:

Traceback (most recent call last):
File "/usr/local/bin/fsdownload", line 14, in <module>
  from dax import XnatUtils
File "/Library/Python/2.7/site-packages/dax/__init__.py", line 3, in <module>
  from .launcher import Launcher
File "/Library/Python/2.7/site-packages/dax/launcher.py", line 12, in <module>
  import processors
File "/Library/Python/2.7/site-packages/dax/processors.py", line 4, in <module>
  import task
File "/Library/Python/2.7/site-packages/dax/task.py", line 9, in <module>
  import XnatUtils, bin
File "/Library/Python/2.7/site-packages/dax/bin.py", line 8, in <module>
  import redcap
File "/Library/Python/2.7/site-packages/redcap/__init__.py", line 19, in <module>
  from .project import Project
File "/Library/Python/2.7/site-packages/redcap/project.py", line 10, in <module>
  from .request import RCRequest, RedcapError, RequestException
File "/Library/Python/2.7/site-packages/redcap/request.py", line 18, in <module>
  from requests import post, RequestException
ImportError: No module named requests

In this case, the “requests” package is missing. To install, just run “sudo pip install requests”. If you get other import errors, they can generally be fixed by running sudo pip install where package name is the last word in the ImportError line.

Install DAX

Install for Linux user

  • Install dax (Distributed Automation for XNAT) package:

With pip:

sudo pip install dax
#or
pip install https://github.com/VUIIS/dax/archive/master.zip --upgrade
#to get the last version of dax and not the version on pip

OR with git:

git clone git://github.com/VUIIS/dax
cd dax
sudo python setup.py install
  • add the XNAT variables to your file ~/.xnat_profile:

Run these commands:

echo "export XNAT_USER=XXXXXXXX" >> ~/.xnat_profile
echo "export XNAT_PASS=XXXXXXXX" >> ~/.xnat_profile
echo "export XNAT_HOST=http://XXXXXXXXXXX" >> ~/.xnat_profile

Replace the XXXXX by your personal information.

  • Last step, you need to check that the file .xnat_profile is called in your .bash_profile.

To do so, use the following command to see the content of your file .bash_profile:

cat ~/.bash_profile

If you don’t see the line “source ~/.xnat_profile” or “. ~/.xnat_profile”, your configuration file is not linked to your bash_profile.

To do so, run:

echo "source ~/.xnat_profile" >> ~/.bash_profile
  • Apply the changes:

Run this command:

. ~/.xnat_profile

You are ready to go.

Install for Mac user

  • Install dax (Distributed Automation for XNAT) package:

With pip:

sudo pip install dax
# or
pip install https://github.com/VUIIS/dax/archive/master.zip --upgrade
#to get the last version of dax and not the version on pip

OR with git:

git clone git://github.com/VUIIS/dax
cd dax
sudo python setup.py install
  • add the XNAT variables to your file ~/.xnat_profile:

Run these commands:

echo "export XNAT_USER=XXXXXXXX" >> ~/.xnat_profile
echo "export XNAT_PASS=XXXXXXXX" >> ~/.xnat_profile
echo "export XNAT_HOST=http://xnat.vanderbilt.edu:8080/xnat" >> ~/.xnat_profile

Replace the XXXXX by your personal information.

  • Last step, you need to check that the file .xnat_profile is called in your .bash_profile.

To do so, use the following command to see the content of your file .bash_profile:

cat ~/.bash_profile

If you don’t see the line “source ~/.xnat_profile” or “. ~/.xnat_profile”, your configuration file is not linked to your bash_profile.

To do so, run:

echo "source ~/.xnat_profile" >> ~/.bash_profile
  • Apply the changes:

Run this command:

. ~/.xnat_profile

You are ready to go.

No Sudo access

If you are not a sudoer on your computer (Linux or MacOS), you can still install dax locally. You need to use git to clone the dax repository and install it locally. Follow the steps below to process with the installation:

git clone git://github.com/VUIIS/dax
cd dax
python setup.py install --user

You will need to add the local folder of dax/Xnat_tools executables to your PATH:

  • For Linux: echo “export PATH=/.local/bin:$PATH”>>/.bashrc
  • For MacOS: echo “export PATH=~/Library/Python/2.7/bin/:$PATH” >> ~/.profile

If you don’t see a line like “source ~/.profile” or “. ~/.profile” (same for .bashrc), your configuration file is not linked to your bash_profile. To do so, run:

echo "source ~/.profile" >> ~/.bash_profile
# or for bashrc
echo "source ~/.bashrc" >> ~/.bash_profile

Run your configuration file to apply the changes:

. ~/.profile
#or for bashrc
. ~/.bashrc

Verify the installation

If you want to be sure everything is installed, you can check running those commands:

XXXXXXXXX$ python
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>import httplib2
>>>import lxml
>>>import pyxnat
>>>import redcap
>>>import dax

If you don’t have any error, the python packages are all installed properly.

Now you can verify your logins by running:

XnatCheckLogin

If you see ‘–>Good login’, you are good to go.

You are ready to use the Xnat_tools, dax executables or the spiders.

Programming in python

All the Spiders/DAX package/Xnat_tools are written in python.

‘’‘Where can I learn how to program in python?’‘’ If you want to learn how to program in python, here are several links that could help you: * http://www.learnpython.org * https://www.python.org * http://stackoverflow.com * http://google.com

‘’‘Where can I program in python?’‘’