Scripts to create a XNAT virtual machine http://nrg.wikispaces.com/XNAT+Virtual+Machine

build.properties

#WINDOWS USERS: The '\' character is not supported by Maven.  Do not use the '\' character in your file paths.  Replace any '\' characters with the '/'.  The '/' works as a file path separator on UNIX and WINDOWS.

maven.appserver.home=/home/xnat/tomcat/
#maven.appserver.home=/var/lib/tomcat6/

xdat.project.name=xnat
xdat.project.template=xnat
xdat.project.db.name=xnat
xdat.project.db.driver=org.postgresql.Driver
xdat.project.db.connection.string=jdbc:postgresql://localhost/xnat
xdat.project.db.user=xnat
xdat.project.db.password=xnat

#IMAGE FILE LOCATION (FOR USE WITH THE xnat TEMPLATE)
#Location where image data will be stored.
xdat.archive.location=/home/xnat/xnat_data/archive

#Location where image data may be stored temporarily before it is stored into the archive.
xdat.prearchive.location=/home/xnat/xnat_data/prearchive

#Location where cached image data should be stored
xdat.cache.location=/home/xnat/xnat_data/cache

#Location where thumbnails should be cached
xdat.project.image.thumbnail.location=/home/xnat/xnat_data/archive/cache/Thumbnails

#Location where Lo-Res images should be cached
xdat.project.image.lo_res.location=/home/xnat/xnat_data/archive/LoRes

xdat.smtp.server=localhost

xdat.admin_email=admin@your-place.org
xdat.url=http://localhost:8080/xnat

#  'xdat.require_login' must be set to 'true' or 'false'.  It governs whether or not users will be 
#  prompted to login when visiting the site.  If true, users will be required to login.  If false,
#  users will be automatically logged in using an XNAT guest account.
xdat.require_login=true


#  'xdat.enable_new_registrations' must be set to 'true' or 'false'.  Users are provided with a 
#  link on the Login.vm page to register for a new account.  If this variable is true, that newly
#  registered account will be automatically enabled and the user will be allowed to immediately login.
#  If this is false, then an email will be sent to the admin (xdat.admin_email) requesting that the 
#  account be enabled, and the user will be unable to login until the account is enabled.
xdat.enable_new_registrations=false

create-virtualbox-vm.sh

## Create a VirtualBox virtual machine.
## 
## Allows access to XNAT via port 8080 of the host machine
##
## Currently requires manually clicking through the guest OS installation 
##
## Requires 32-bit Ubuntu Desktop 9.04 ISO
##
## Tested on Ubuntu 9.04 guest and Ubuntu 9.04 host, VirtualBox (2.1.4 OSE)
##
## This script is run on the host machine.
##
## John Paulett (jpaulett _at_ wustl.edu)

# http://blog.arextech.net/index.php/tag/virtualbox/
VMNAME=xnat-demo
BASE_DIR=$HOMEvbox
DISTRO=ubuntu-9.04-desktop-i386.iso

HD=$BASE_DIR/$VMNAME/$VMNAME.vdi

VBoxManage createvm -name $VMNAME -ostype Ubuntu -register -basefolder $BASE_DIR
VBoxManage createhd -filename $HD -size 50000 -register #| awk '/UUID/ { print $5 }'
VBoxManage modifyvm $VMNAME -memory 512 -bioslogoimagepath $BASE_DIR/logo-xnat.bmp -hda $HD

## Port forward through VirtualBox's NAT to Tomcat
## http://mydebian.blogdns.org/?p=148
# SSH 8080 -> 8080
VBoxManage setextradata $VMNAME "VBoxInternal/Devices/pcnet/0/LUN#0/Config/tomcat/HostPort" 8080
VBoxManage setextradata $VMNAME "VBoxInternal/Devices/pcnet/0/LUN#0/Config/tomcat/GuestPort" 8080
VBoxManage setextradata $VMNAME "VBoxInternal/Devices/pcnet/0/LUN#0/Config/tomcat/Protocol" TCP

## Setup the Ubuntu install CD
VBoxManage openmedium dvd $BASE_DIR/$DISTRO
VBoxManage modifyvm $VMNAME -dvd $BASE_DIR/$DISTRO
VBoxManage startvm $VMNAME


################################################################################
########################### Manual Step: Install OS ############################
################################################################################


VBoxManage controlvm $VMNAME poweroff
# wait for it to shutdown
VBoxManage modifyvm $VMNAME -dvd none
VBoxManage unregisterimage dvd $BASE_DIR/$DISTRO

## First Step Install
VBoxManage startvm $VMNAME

#VBoxManage getextradata xnat enumerate

DicomServer.xml

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
<properties>
<comment>
	configuration file for DicomServer, by karchie@npg.wustl.edu
</comment>

<entry key="arcspec">/home/xnat/xnat_data/cache/archive_specification.xml</entry>
<entry key="xnat_url">http://localhost:8080/xnat</entry>
<entry key="user">admin</entry>
<entry key="password">admin</entry>

<entry key="xnat_public_url">http://localhost:8080/xnat</entry>


<entry key="http_port">8180</entry>
<entry key="scp_public_host">localhost</entry>
<entry key="scp_public_port">8104</entry>
<entry key="sessions_url">http://localhost:8180/session</entry>
<entry key="project_spec">(0008,1030):Project:\s*(\w+)</entry>

<entry key="log4j.rootLogger">WARN,R</entry>

<entry key="log4j.appender.R">org.apache.log4j.RollingFileAppender</entry>
<entry key="log4j.appender.R.File">/home/xnat/xnat_data/dicom_log/DicomServer.log</entry>
<entry key="log4j.appender.R.MaxFileSize">100KB</entry>
<entry key="log4j.appender.R.MaxBackupIndex">4</entry>
<entry key="log4j.appender.R.layout">org.apache.log4j.PatternLayout</entry>
<entry key="log4j.appender.R.layout.ConversionPattern">%d %5p [%t] %c - %m%n</entry>

<entry key="log4j.logger.org.dcm4che2">WARN</entry>
<entry key="log4j.logger.org.nrg">INFO</entry>
	
<entry key="log4j.additivity.org.nrg.xnat.received">false</entry>
<entry key="log4j.logger.org.nrg.xnat.received">INFO,RECEIVED</entry>

<entry key="log4j.appender.RECEIVED">org.apache.log4j.DailyRollingFileAppender</entry>
<entry key="log4j.appender.RECEIVED.File">/home/xnat/xnat_data/dicom_log/DicomServer-received.log</entry>
<entry key="log4j.appender.RECEIVED.DatePattern">'.'yyyy-MM-dd</entry>
<entry key="log4j.appender.RECEIVED.layout">org.apache.log4j.PatternLayout</entry>
<entry key="log4j.appender.RECEIVED.layout.ConversionPattern">%d %m%n</entry>
	
</properties>

guest-setup.sh

## Setup the Ubuntu Virtual Machine
## 
## Currently the commands require some manual intervention (e.g. entering sudo 
## password, rebooting), so this script can not be run as a single bash script.
##
## Tested on Ubuntu 9.04 guest and Ubuntu 9.04 host, VirtualBox (2.1.4 OSE)
## Tested on Ubuntu 9.10 guest and Ubuntu 9.10 host, VMWare Server (2.0.2)
## Tested on Ubuntu 9.10 guest and Ubuntu 9.10 host, VirtualBox (3.0.8 OSE)
## Tested on Ubuntu 9.10 guest and Ubuntu 9.10 host, VMWare Player (3.0.0)
##
## VMWare Specifics
##   To ssh in
##     ssh xnat@192.168.277.129
##
## Virtualbox Specifics
##   To Open Ports:
##     VBoxManage setextradata xnat-demo "VBoxInternal/Devices/pcnet/0/LUN#0/Config/ssh/HostPort" 2222
##     VBoxManage setextradata xnat-demo "VBoxInternal/Devices/pcnet/0/LUN#0/Config/ssh/GuestPort" 22
##     VBoxManage setextradata xnat-demo "VBoxInternal/Devices/pcnet/0/LUN#0/Config/ssh/Protocol" TCP
##   Which can then be used like
##     ssh -p 2222 xnat@localhost
##   The host has an IP of 10.0.2.2
##
## This script and the required supporting files are available at 
## http://gist.github.com/gists/206346
## The script assumes that build.properties and DicomServer.xml have 
## been downloaded to /home/xnat/
##
##
## John Paulett (jpaulett _at_ wustl.edu)

## VirtualBox Guest Additions for mouse integration, requires reboot
## Mount via menu with "Devices > Install guest additions".
#sudo /media/cdrom/VBoxLinuxAdditions-x86.run
#sudo reboot

## Upgrade
sudo apt-get update && sudo apt-get -y upgrade && sudo apt-get -y dist-upgrade
## Install dependencies
sudo apt-get -y install openssh-server mercurial openjdk-6-jdk postgresql tomcat6 tomcat6-user postfix mailx ntp
## If installed from server install and you want a desktop
#sudo apt-get install ubuntu-desktop
## A few additional dependencies to make using XNAT with Ubuntu easier
sudo apt-get -y install icedtea6-plugin 

## Clean the apt cache to save diskspace
sudo apt-get -y autoremove && sudo apt-get clean

## Modify configuration files
echo "localhost:*:xnat:xnat:xnat" >> ~/.pgpass
chmod 600 ~/.pgpass
echo "export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/" >> ~/.bashrc
source ~/.bashrc

## Setup database
sudo -u postgres createuser -D -A -R xnat
sudo -u postgres psql -c "ALTER USER xnat WITH PASSWORD 'xnat'"

## Remove primary Tomcat init script
## http://www.debuntu.org/how-to-manage-services-with-update-rc.d
sudo update-rc.d -f tomcat6 remove

## Reboot (to apply changes from upgrade)
sudo reboot

################################################################################
############################# Part 2: After Reboot ############################# 
################################################################################

## Install Tomcat local instance
cd ~
tomcat6-instance-create tomcat

## Get Tomcat to start on boot
CRONFILE=/tmp/xnat-cron
echo "JAVA_HOME=/usr/lib/jvm/java-6-openjdk/" > $CRONFILE
echo "@reboot /home/xnat/tomcat/bin/startup.sh" >> $CRONFILE
echo "@reboot cd /home/xnat/DicomServer && bin/arc-dcmstore start" >> $CRONFILE
crontab $CRONFILE

## Setup database
sudo -u postgres createdb -O xnat xnat
sudo -u postgres createlang plpgsql xnat

## Checkout code
hg clone http://bitbucket.org/nrg/xdat_release xnat
cd xnat/
REV=`hg log --rev tip --template "{latesttag} ({rev}:{node|short})"`
hg clone http://bitbucket.org/nrg/pipeline_1_4 pipeline

## Need build.properties (available at http://gist.github.com/gists/206346)
cp ~/build.properties ~/xnat

## Run the build
./bin/setup.sh -Ddeploy=true
psql -h localhost -U xnat -f deployments/xnat/sql/xnat.sql 
cd deployments/xnat/
../../bin/StoreXML -location security/security.xml -allowDataDeletion true
cd ../..

## Customize the deployment
SITEVM=projects/xnat/src/templates/screens/site_description.vm
echo "<b>XNAT Virtual Machine Demo</b><br />" > $SITEVM
echo "Login: admin/admin<br />" >> $SITEVM
echo "HG Revision: $REV <br />" >> $SITEVM
bin/quick-deploy-templates.sh

## Install DicomServer
## http://nrg.wustl.edu/projects/DICOM/DicomServer-1.4RC3.html
cd ~
DICOMSERVER=DicomServer-xnat-1.4-r702
wget http://nrg.wustl.edu/projects/DICOM/$DICOMSERVER.tgz
tar xzvf $DICOMSERVER.tgz
mv DicomServer-xnat-1.4 DicomServer
rm $DICOMSERVER.tgz

## Need DicomServer.xml (available at http://gist.github.com/gists/206346)
mv DicomServer.xml DicomServer/etc/

## Optional: Install XNAT Desktop
cd ~
XNATDESKTOP=xnd_v0.92_linux_gtk_x86.zip
wget http://nrg.wustl.edu/xnd/download/$XNATDESKTOP
unzip $XNATDESKTOP
mv linux.gtk.x86/ xnd
chmod u+x xnd/xnd
rm $XNATDESKTOP

## Start tomcat (only need to do it once, cron will start on boot)
~/tomcat/bin/startup.sh

## Go to http://localhost:8080/xnat and configure
## wget http://nrg.wustl.edu/1.4/sample1.zip
## wget http://nrg.wustl.edu/1.4/sample2.zip
## When configuring the Dicom Server section of XNAT:
##    DICOM host: localhost
##    DICOM port: 8104
##    DICOM AE Title: XNAT
##    DICOM Server HTTP URL: http://localhost:8180/session
##    Applet Link: true


## Start DicomServer
cd DicomServer
bin/arc-dcmstore start