Ranker

The new Ranker program for Babase was developed by [:JunYang: Jun Yang] and [:TylerBrock: Tyler J. Brock] from Fall 2006 to Spring 2007. It was Tyler's Graduation with Distinction project when he graduated from Duke University in 2007.

Prerequisites to Running the Ranker

• If your computer is not on the same trusted network as papio (e.g., your computer is outside the biology.duke.edu domain), you must have VPN access to papio. See [:BabaseVPN: Babase VPN] for details on how to set up VPN on your computer.
• You must have a Babase PostgreSQL account on papio.
• Your computer must have Sun's Java Platform, Standard Edition 5 or later.

Running the Ranker

• If your computer is not on the same trusted network as papio, first establish a VPN connection to papio. See [:BabaseVPN: Babase VPN] for detailed instructions.

• Point your browser to [https://papio.biology.duke.edu/ranker/ranker.jnlp]; this will launch the Ranker.

  • If, for some reason, the Ranker does not launch automatically and you are shown the text contents of the ranker.jnlp file or are prompted to download it, save the file on your desktop and double-click it to launch the Ranker manually.
• You may get a security warning about papio's certificate; click "Yes" to continue.
• You may get a security warning about the application's digital signature; click "Run" to proceed.

Software Development for Ranker

This section is currently under development.

Development Environment

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]

• Obtain the following third-party libraries:

  • PostgeSQL JDBC Driver, at http://jdbc.postgresql.org/

  • TableLayout manager, at http://java.sun.com/products/jfc/tsc/articles/tablelayout/apps/TableLayout.jar

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.

Exporting the JAR files

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

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