XNAT 1.6 Workshop Virtual Machine

This virtual machine is provided by the Neuroinformatics Research Group at the
Washington University School of Medicine for testing, development, and educational
purposes ONLY. You shouldn't store any protected health information (PHI) or other
sensitive data in this server.

This test XNAT instance comprises the following:

 * XNAT 1.6 Workshop Beta
 * Ubuntu 11.10
 * Apache Tomcat 6.0.32
 * PostgreSQL 9.0.7
 * OpenJDK 1.6.0_23

Note that PostgreSQL was installed from binary installer packages and NOT using
the Ubuntu package manager. This was done so that version 9.0 of PostgreSQL--which
is not easily available through the standard Ubuntu software repositories could be
used. The net effect of this is that this package will not be managed and updated
through the standard Ubuntu package manager process.

In addition, a number of other helpful tools are included with this image:

 * The Ubuntu package manager is configured to access the NeuroDebian software
   repository. See http://neuro.debian.net/ for more information.
 * Version 0.9.3 of pyxnat is installed, along with the most up-to-date version
   of Python available at the time of this release.
 * Mercurial 1.9.1 is installed for updating packages from the XNAT source
   repository on bitbucket.org.

The default login credentials are:

User: xnat
Password: xnat2012

The default PostgreSQL credentials are:

User: xnat
Password: xnat

The xnat user has trust privileges to the database from the local machine, meaning
that all you need to do is type 'psql' when logged in as xnat to access the xnat
database.

The default login on the XNAT application itself is:

User: admin
Password: admin

Starting and stopping XNAT/Tomcat

sudo service tomcat6 start
sudo service tomcat6 stop

Accessing the database

psql

You can also run pgadmin3 from the command line or the desktop launcher.

Locations

All of the main working folders on the VM are located under /opt/xnat:

 * XNAT builder code is located in /opt/xnat/xnat_builder_1_6
 * The pipeline installation is in /opt/xnat/pipeline_1_6
 * The data folders for the XNAT installation are in /opt/xnat/data
 * Scripts, data, and other information specific to the workshop are located in
   /opt/xnat/workshop2012.

The installed XNAT web application can be easily accessed in ~xnat/deploy, which
is a symbolic link to /var/lib/tomcat6/webapps/xnat.

The XNAT virtual machine is built and configured in a default state. The only
changes you should need to make are to set the system SMTP server for mailing
purposes as well as the default administrator email address. To make this easier,
a script named configure.sh is provided in the ~xnat/bin folder:

  sudo configure.sh myemail@myschool.edu smtp.myschool.edu

This will stop Tomcat, update the relevant configuration files and database
entries for the mail settings, then restart Tomcat. Note the use of sudo to allow
the proper permissions for stopping and starting Tomcat.

Once you've done this, you can start using XNAT by starting a browser and going
to http://localhost:8080/xnat. You can log in with the admin credentials from
above. 

Updating and Building Code

You can update the main source-controlled folders using the updateAll.sh script.
This updates the XNAT builder, pipeline, and workshop code from the NRG repositories
on Bitbucket.

Once you've updated, you can rebuild your code by calling the rebuild.sh script.
This shuts down Tomcat, updates your XNAT application, imports database changes,
and restarts Tomcat.

These scripts are located in the ~xnat/bin folder and are available whenever you're
logged into the VM as the xnat user.