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Introduction to the AIM Template Service

The AIM Template Service (ATS) is a web service application that makes it possible for you to upload (publish) and download AIM templates created using a caBIG® Annotation and Image Markup (AIM) tool such as AIM Template Builder. You can import AIM template files to AIM Template Builder and modify them there. You can then use AIM Template Builder to export the template(s) to an AIM template file. If you want to share that file, you can upload it to ATS.

AIM templates contain a set of well-defined questions and answer choices to facilitate collecting information for a particular purpose, such as The Cancer Genome Atlas Glioblastoma (TCGA GBM) study. AIM templates ensure that users can annotate medical images using a controlled vocabulary and standard template. This results in simple and constrained annotations that are reproducible and consistent.

A valid AIM template is validated by AIM schemas (version 1, revision 18/19/23).

Refer to the AIM Template Service documentation for more information about ATS features.

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Installing the AIM Template Service

  1. Download the Berkley DB XML version suitable for your platform from
    http://www.oracle.com/technetwork/database/berkeleydb/downloads/index.html

    The version used for this installation guide is Berkley DB XML 2.5.16.

    1. Install the software.
    2. Select the Java integration option. On Unix, you may need to run this command from the installation folder: sh buildall.sh --enable-java.
    3. On Windows, modify the PATH environment variable to include the DB XML executables. The database executables must be included in the PATH for the software to work properly.
    4. [optional] Alternatively, you can download a pre-built Windows x64 version of Berkley DB XML from the ATS download location. Follow the instructions that are included with the downloaded file to configure your Windows 64-bit environment.
  2. Install Java 6 JDK with the latest updates from:
    http://www.oracle.com/technetwork/java/javase/downloads/index.html
  3. Download the ATS software package, ATS-1.1.rar, and store it in a folder.
  4. Uncompress the ATS package, ATS-1.1.rar. The archive file contains folder “ATS-1.1” with AIM Template Service executables.
    1. Windows – click the compressed file to open; drag its content out to a folder, e.g. C:\ATS-1.1
    2. Unix – unrar ATS-1.1.rar, a new folder named “ATS-1.1” will be created.
  5. Create certificate
    1. [optional] Create your certificate(s) for running ATS over HTTPS.
  6. Edit serverConfig.txt
    1. Go to “ATS-1.1” folder from above.
    2. Edit serverConfig.txt

                                               i.     port = 4433 (AIM template service server port)

                                             ii.     dbpath = C:\ATS-1.1\xmldb (Path to a location where you want to store ATS data)

                                            iii.     CaGridSecurityUrl = (URL for STS authentication service)

                                            iv.     keystorepath = (path to the keystore) (optional. required if running over https)

                                              v.     keystorename = (name of the keystore file) (optional. required if running over https)

  1. Create database
    1. Create writable database folder , e.g. C:\ATS-1.1\xmldb – must correspond to the value of dbpath specified in the serverConfig.txt
    2. [optional] Open command line and change to the database folder
    3. [optional] In the database folder, run ‘dbxml’ command. This will put you into XML DB shell.
    4. [optional] In the XML DB shell, run ‘createContainer ats_prod.dbxml’ command. This creates empty AIM Template Service database.
  2. Run ATS application
    1. Windows

                                               i.     Open Administrator command line prompt

                                             ii.     Go to “ATS-1.1” folder from above

                                            iii.     Type “%JAVA_HOME%\bin\java” -Djavax.net.ssl.trustStore=certificates/stsClient.jks -Djavax.net.ssl.trustStorePassword=yearkiwi -jar AimTemplateService.jar

(NOTE: JAVA_HOME environment variable must be set to point to your JDK location)

  1. Unix

                                               i.     Open a terminal window

                                             ii.     Go to “ATS-1.1” folder from above

                                            iii.     Type java -Djava.library.path=/home/john /dbxml-2.5.16/install/lib/ -Djavax.net.ssl.trustStore=certificate/stsClient.jks -Djavax.net.ssl.trustStorePassword=yearkiwi -jar AimTemplateService.jar

(NOTE: java.library.path value depends on where you have installed Oracle DB XML)

  1. Watch console output for errors and warnings
  2. Validate installation
    1. Open web browser on another computer
    2. Navigate to http[s]://<your server name>:<your port>/
    3. Login using caGRID login credentials or as a guest

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