Ranker

The New Ranker Program for Babase was designed by Dr Jun Yang of Duke's Computer Science Department and Tyler Brock, Senior at Duke University as his graduation project.

Running the Ranker

This section describes how to run the ranker normally without the need to make changes to or see the code.

Go to https://papio.biology.duke.edu and click on the ranker.jnlp, the program should launch

• Make sure you say that you trust the certificate if asked.

Making Changes and Running the Program

Install Software

You will need the following environment in order to be able to make changes to the ranker code:

• Sun Java JDK with version greater than 5.0 available at http://java.sun.com

• Eclipse Software Development Version 3.2 available at http://www.eclipse.org

• A copy of the code available [http://papio.biology.duke.edu/babasewiki/RankerProgram?action=AttachFile&do=get&target=currentbabase.zip here]

Import Project

Once the JDK and Eclipse are installed you can unzip the code for the project and open eclipse. Then, if you import->general->existing project into workspace and select the project file within the extracted folder, the project should appear within your eclipse workspace.

Make Changes

After the project is open one can make changes to the code within the eclipse environment, most of which is within the babase.ranker package.

Compile and Run Program With Changes

To run the program, make sure you are connected to the VPN bring the ranker.java file to the focus of the editor and click on the run menu. From there, select to run as a Java application. Before the program runs, the changes are compiled.

Updating the Ranker Program

Exporting the JAR files

Export the project choosing Java->Jar File as the type of exported file.

Get the libraries

You can find the libraries in the lib folder within the archive of the code.

Put it in the right spot

• Make sure the ranker.jar and the library JARs in the same folder.

Create the Keys

From the command line in Mac OS X this can be accomplished by doing the following:

Typing the following into the terminal

• keytool -genkey -alias babase -keyStore babasestore.ks

It will ask you for a password

• Type babase as the password

Then it will ask for information regarding the certificate

• Fill out the information.

When asked "Enter key password for <babase> (RETURN if same as keystore password):"

• Simply hit enter and the keystore will be generated.

Sign the JARs

From the command line in Mac OS X this can be accomplished by doing the following:

Change directories to the folder containing both the JARs and the keystore file babasestore.ks and type the following for each JAR file to sign that particular JAR. (All of them must be signed)

• jarsigner -keystore babasestore.ks -storepass babase jarname.jar babase

The JAR file is now signed and can be uploaded to the webserver.