Customizing Data Types

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Tutorial Video (from 2010 XNAT Workshop)

This page describes how to create a custom data type to support your particular research requirements. This includes:

  • Defining your new data type, including custom attributes
  • Creating user interface elements and custom code
  • Creating REST API functions
  • Packaging your data type for distribution
  • Installing the data type into your XNAT deployment

Defining Custom Data Types

The XNAT application is built around the core xnat.xsd XML schema. This schema defines the basic data types which are expected to be common to all neuroimaging projects. It includes complex types for subjects, projects, experiments, image sessions, and session assessors. You can extend the data types defined in the XNAT schema to create your own data types that fit easily into the XNAT framework. Schemas not based on xnat.xsd can also be included in XNAT projects, but require additional setup.

EXAMPLE: The XNAT distribution includes a sample schema named ext.xsd. This extends the XNAT schema (see sidebar). You can use this sample to try out the instructions in this tutorial. ext.xsd includes data types that extend the subjectAssessor and mrAssessor abstract types in defined in the core XNAT schema.

XNAT Schema Extension

A sample schema, ext.xsd, which extends the XNAT schema is available in XNAT_HOME/deployments/PROJECT_NAME/src/schemas/ext folder. This schema has three root elements viz. ClinicalAssessment, AtlasScalingFactor and SegmentationFast. ClinicalAssessment extends xnat:subjectAssessorData and AtlasScalingFactor, SegmentationFast extend xnat:mrAssessorData

2) Add your schema to the project

Once you have created a new data type, you need to add your data type to your XNAT installation. Adding an additional schema to an XNAT project involves two steps: placing a copy of the schema inside the project and configuring the project's InstanceSettings.xml document.

Step 1. Copy your schema file to a subdirectory in the XNAT_HOME/projects/PROJECT/src/schemas directory. By convention, we create a subfolder (named after the schema) and place the schema in that subfolder. This seperates the content of different schemas. Mirror the structure of the other schemas in the other directories.

EXAMPLE: The ext.xsd schema has already been inserted in the appropriate place in your XNAT (XNAT_HOME/projects/xnat/src/schemas/ext/ext.xsd).

Step 2.Add an entry for the schema in the project settings document (XNAT_HOME/projects/PROJECT/InstanceSettings.xml). Schema entries are represented in <Data_Model> elements. Adding a new <Data_Model> entry should be as simple as copying and pasting an one of the <Data_Model> elements already in the document and editing the values of the file name and path attributes to point to your schema. The ordering of the data models is important. If your schema references one of the other schemas (like xnat.xsd), then it must come after the referenced schema. If you place your data model entry after the others, you should avoid any issues. The File_Location attribute should be similar to the other schemas File_Locations.

EXAMPLE: A <Data_Model> entry for the ext.xsd schema is already included in XNAT_HOME/projects/xnat/InstanceSettings.xml. To activate it, remove the comment tags (<!-- and -->).

3) Run the update script (bin/ or bin\update.bat)

  1. Run the update script in the XNAT_HOME directory. This script will generate files for your new schema and deploy the updated project to the deployment folder.

  2. After the update script completes, descend into the XNAT_HOME/projects/PROJECT directory and browse the files which where created. It will have added a 'display' directory in the same directory as your schema.xsd (ext.xsd). In that display directory, display.xml files will now exist for each of your root level data types. These dictate how your data types will be displayed in listings in the web application.

  3. Next, browse to the XNAT_HOME/projects/PROJECT/src/java/org/nrg/xdat/om directory. Here you will find Java classes which correspond to all of the complex types in your schema (and other schemas). These can be used in later development.

  4. Next, browse to the XNAT_HOME/projects/PROJECT/src/base-templates directory. Here you will see the generated velocity templates for your root level data types. These will be used later.

4) Update the database

The sql to update your database is in XNAT_HOME/deployments/PROJECT/sql. To update your database, run the PROJECT-update.sql file using psql or pgAdminIII.

EXAMPLE: The code to update your database is in XNAT_HOME/deployments/xnat/sql/xnat-update.sql. Execute this file on your database.

5) Re-Deploy the webapp

To finish the installation you will need to re-deploy the generated WAR to your webapp (this can be skipped if you used the -Ddeploy=true tag).

Re-start your Tomcat server and navigate to the xnat webapp on your local host (usually http:_localhost:8080/PROJECT (http:_localhost.8080-xnat)).

6) Setup XNAT security to allow access to your new data types

By default you cannot 'Browse' data types in the web application. You have to specifically, configure the access of any data types which you want to allow. You will need to configure the access settings for the pertinent data types in your schema in order to browse them through the web application.

  1. Login to the site using the username 'admin' and the password 'admin'. This logs you in as the Admin account (use a seperate admin account if you have created one).

  2. Proceed to the 'Data Types' section of the Administration page. Click the 'Setup Additional Data Type' link to access the Data Type Wizard.

Wizard page 1:

The drop down list contains all root-level elements from all loaded schemas which have not been previously defined for web access. Select your data type from the list. (If your data type does not appear, verify that your root-level elements are defined according to XNAT standards).

Wizard page 2:

Configure access to your data type. Whether or not the Data Type is Browsable will determine whether or not the data type is available in the Browse list in the navigation menu. For more information on security, see this.

Wizard page 3:

Configure actions for your data type. These are the options you will have on the report page for data of this type. The default actions are usually sufficient. For more information on actions, see this.

Your Data Type is now setup! You will need to logout/login to see the new data type in your browse options.

SAMPLE: Users of the ext.xsd sample will need to allow access to the three data types in the schema (ext:atlasScalingFactorData, ext:clinicalAssessmentData & ext:segmentationFastData) according to the above instructions. Next, you will need to set the permissions for these types on the USER edit page.