The current version of the Ranker program (v1.2) for Babase was developed by Karl O. Pinc. It consists of minor changes amd a major bug fix to the version developed by Jun Yang. This version was based on an earlier version developed by Jun Yang and 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. Tyler's thesis has been attached to this page and includes visuals of the program as well as conceptual visuals describing how the program works. It is a PDF file; use Acrobat Reader to view it.
The focus of Tyler's thesis was how to rank automatically; however, for stability reasons, this functionality is not in the current version of the Ranker. However, we plan to include this functionality in the next version of the Ranker.
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 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 Java 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 Babase VPN for detailed instructions.
Point your browser to https://papio.biology.duke.edu/ranker/ranker.jnlp to 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.
At the login menu, the host has been preset to papio-vpn.biology.duke.edu. If you are NOT running VPN (because your computer is on the same trusted network as papio), change the host to papio.biology.duke.edu (by removing "-vpn" from the string), and then check the "Use SSL?" box. If you are running VPN, you do not need to modify the default values.
To login to papio-vpn.biology.duke.edu use your database username and password.
To login to papio.biology.duke.edu use your database username and password.
Software Development for Ranker
This section is currently under development.
The Ranker code currently resides under ~junyang/ranker/ on papio.biology.duke.edu. It should be managed by a source control system eventually.
You will need the following environment in order to be able to make changes to the ranker code:
Java version 5.0 or later, available at http://java.sun.com/
Ant version 1.7 or later, available at http://ant.apache.org/
- A copy of the code; tarballs are attached to this page
- Obtain the following third-party libraries:
Sign the JAR file
See instructions in signature/README.txt in the ranker development directory on papio. The signed JAR file can now be copied under install/, a symbolic link to the installation directory on papio. Note that all third-party jars must be signed by the same certificate as well, as per Java security policy. The Makefile does all these automatically.
Command line execution
From /var/www/html/ranker/ run:
java -cp ranker.jar:lib/jcalendar-1.3.2.jar:lib/postgresql-8.2-506.jdbc3.jar:lib/TableLayout.jar babase.ranker.Main
Ranker version 1.2 (2012-11-19)
Ranker version 1.2 contains a major bug fix.
- Program was not sorting by anything when loading ranks by the db, resulting in a ranking that was often but not always the rank, depending on the order in which rows were saved and the order in which the db happened to return rows. Fixed by sorting by rank when loading arrays.
Ranker version 1.1
Ranker version 1.1 corresponds to the release of Babase 3.0 and contains the necessary fixes to account for backwards incompatible changes.
- Change the BIOGRAPH.Dcausestatus column name to Dcauseconfidence.