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XNAT Web Application

This is the XNAT Web application build. The latest release version of XNAT is 1.7.0 Build #775 (Sep 22, 2016 12:34:05 PM). The source for the release version can be found at the 1.7.0 tag in the xnat-web source repository.

Installing

If you just want to install the latest release version of XNAT, you can download it from the XNAT bintray repository:

Download

You will also need to download the latest release version of the XNAT pipeline engine:

Download

If you would like to build a virtual machine that can run XNAT, you can use the XNAT Vagrant project.

Building

Configuring

Gradle

In order for the build to work at the moment (and to be able to import the Gradle project into an IDE), you need to set up some properties in a file named gradle.properties. This can be placed in your global properties file, which is located in the folder .gradle under your home folder, or in the same folder as the build.gradle file.

This properties file must contain values for the following properties:

repoUsername=xxx
repoPassword=xxx
deployHost=xxx
deployPort=xxx
deployContext=xxx
deployUser=xxx
deployPassword=xxx

The repo properties are used when deploying build artifacts to the Maven repository. The deploy properties are used when deploying to a remote Tomcat server. Note that the values for these properties don't need to be valid! If you're not going to deploy to the Maven repository and you're not going to deploy to a remote Tomcat server, you can use the values shown up above (i.e. "xxx" for everything) and be totally fine. Gradle will pitch a fit if there's not a value for these properties though, so you need to have something in there. We'll try to fix this so that you don't have to have junk values just to make it feel better about itself, but until that time just keep the placekeeper values in there.

There are a lot of other useful properties you can set in gradle.properties, so it's worth spending a little time reading about the various properties Gradle recognizes in this file.

XNAT Configuration

You also need to add another initial configuration file in your home directory. Create a directory path xnat/config in your home directory and a file named xnat-conf.properties there. In this file, define the following properties:

datasource.driver=org.postgresql.Driver
datasource.url=jdbc:postgresql://localhost/<XNAT Instance Name>
datasource.username=<database username>
datasource.password=<database password>

hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
hibernate.hbm2ddl.auto=update
hibernate.show_sql=false
hibernate.cache.use_second_level_cache=true
hibernate.cache.use_query_cache=true

IMPORTANT NOTE: You'll definitely want to fill in the three <placeholders> above! ...<XNAT Instance Name>, <database username> and <database password>

Building

You can build with a simple Gradle command:

gradle clean war

You may need to build the XDAT Data Builder Gradle plugin and XNAT Data Models library first, although it should be available on the XNAT Maven repository.

This will create your deployable web application in the location:

build/libs/xnat-web-1.7.0.war

You can perform a build to your local Maven repository for development purposes like this:

gradle clean jar publishToMavenLocal

You can perform a build deploying to the XNAT Maven repository like this:

gradle clean jar publishToMavenLocal publish

For this last one, the values set for repoUsername and repoPassword must be valid credentials for pushing artifacts to the Maven server. The publish task actually comprises a number of other tasks, which will publish all available artifacts to each repository defined in the repositories configuration in the build.gradle file. Practically speaking this means that publish is an alias for the publishMavenJavaPublicationToMavenRepository task.

You can specify the name of the generated WAR file (and thus the application context of the application within the Tomcat server) from the command line or a properties file.

On the command line, add the flag -ParchiveName=name[.war] to your Gradle command (.war will be appended if it’s not specified). This may look something like this:

./gradlew -ParchiveName=ROOT.war war

You can also set the archiveName value in the gradle.properties file. gradle.properties can be in your repository folder, thus affecting only the local build, or in ~/.gradle/gradle.properties, which will affect any build that uses the archiveName property. To set this value in gradle.properties, just add the line:

archiveName=ROOT

If you don’t explicitly set archiveName, the build uses the naming scheme xnat-web-version.war.

Note that gradle.properties is in this repository's .gitignore file, so if you create a local version you won’t get the annoying “Untracked files” message from git.

Configuring

You must perform a couple of configuration steps in your run-time environment (e.g. your local development workstation, a Vagrant VM, etc.) in order for XNAT to run properly:

  • In your Tomcat start-up configuration, add -Dxnat.home=<path> where <path> is some writeable location. This is where XNAT will look for its configuration and logs folders, e.g. ${xnat.home}/config and ${xnat.home}/logs.
  • Copy xnat-conf.properties into the config folder underneath the path you specified for xnat.home. For example, I set xnat.home to ~/xnat. Under that I have the folder config, which contains xnat-conf.properties (you don't have to create logs: log4j will create it if it doesn't exist).

Running XNAT

From Gradle

You can deploy your generated war file to a local Tomcat instance with the deployToTomcat task. Unlike the Cargo tasks described below, this task doesn't go through the Tomcat manager or transfer the war via network connection. Instead, it copies the physical war file to a local folder named webapps. The key is that you need to specify the location of your Tomcat instance with the property tomcatHome. As with archiveName above, you can specify this on the command line or in the gradle.properties file:

./gradlew -PtomcatHome=/var/lib/tomcat7
tomcatHome=/var/lib/tomcat7

tomcatHome defaults to ‘.’, so if you don’t specify a value for it, you’ll end up with a folder named webapps in your local repository folder. That folder is also in .gitignore so you won’t get bugged by git. You probably didn't intend to have another copy of the war file somewhere in your development folder, but it’s better than copying files off to random locations or pitching a fit.

Note that deployToTomcat depends on the war task, so there’s no need to specify the war task explicitly.

This provides an efficient workflow for development on a VM or server: set the two values in gradle.properties and you can quickly redeploy:

./gradlew deployToTomcat

Gradle will compile or package any changes since the last build as necessary, re-package your application into a war if needed, and copy the resulting war file into the Tomcat webapps folder. It’s worth noting if nothing has changed the war won’t be regenerated or copied.

You can deploy the built war to a remote Tomcat using the Cargo plugin.

gradle cargoDeployRemote
gradle cargoRedeployRemote
gradle cargoUndeployRemote

As you can probably guess, the first task deploys the application to the remote Tomcat. If there is already an application deployed at the specified context, this task will fail. In that case you can use the second task to redeploy. The third task undeploys the remote application, clearing the context.

You'll need to have installed the Tomcat manager application onto the Tomcat server. You'll also need to configure the tomcat-users.xml file appropriately. This is described in the Tomcat Manager How-to page, but a sample tomcat-users.xml might look like this:

<?xml version='1.0' encoding='utf-8'?>
<tomcat-users>
    <role rolename="manager-gui"/>
    <role rolename="manager-script"/>
    <role rolename="manager-jmx"/>
    <user username="admin" password="s3cret" roles="manager-gui"/>
    <user username="deploy" password="s3cret" roles="manager-script,manager-jmx"/>
</tomcat-users>

You need to pass in a few values when you run the Gradle build with any of the Cargo remote tasks:

  • deployHost is the address for the VM hosting the remote Tomcat.
  • deployPort is the port the Tomcat is running on. Note that this should be the Tomcat port, not the proxy server, e.g. nginx or httpd.
  • deployContext is the context, i.e. application path, to which you want to deploy XNAT. This can be / or /xnat or whatever.
  • deployUser is the username configured in the Tomcat manager.
  • deployPassword is the password for the user.

The easiest way to specify these values is to put them in your gradle.properties file, usually located in ~/.gradle but you can also have it in the root of the build folder.

deployHost=xnat17dev.xnat.org
deployPort=8080
deployContext=/
deployUser=deploy
deployPassword=s3cret

You can also specify these on the Gradle command line. Just take each setting and preface it with -D.

In the IDE

You can run XNAT from within your IDE. You need to set the appropriate values for the VM to configure available heap and permgen space, as well as setting xnat.home appropriately. For example, in IntelliJ, I have the following line for the VM options in my local Tomcat debug configuration:

Xms512m -Xmx1g -XX:MaxPermSize=256m -Dxnat.home=/Users/xxx/xnat