Differences between revisions 47 and 48

Ranker

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.

The focus of Tyler's thesis was how to rank automatically, but for stability reasons this functionality is not in the current version of Ranker. However, we hope to include this functionality in a future version of Ranker.

Prerequisites to Running Ranker

If your computer is not connected to Duke's network--where Papio is hosted--you must first connect to Duke via Duke's VPN.
- Important: Until 2018, a different VPN (see BabaseVPN) was required by most users to use Ranker. That VPN will no longer work. Non-Duke users must use the Duke VPN.
You must have a Babase login.
Your computer must have Java Standard Edition 5 or later.

Running the Ranker

Verify that you are connected to Duke's network, either by being at Duke or by connecting via VPN.
Now, you need to make a connection directly with the server. Open a terminal and enter the following (all on one line):
```
ssh -L 5432:localhost:5432 MYPAPIOLOGIN@papio.biology.duke.edu
```
(Note that MYPAPIOLOGIN is your SSH login to the server, not your Babase login.) You will be prompted for your password. After entering this, your connection to the server is complete and you likely won't need the terminal anymore. Feel free to hide or minimize it (but don't close it!).
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.
When the "Welcome" window appears, choose "Create/load ranking from Babase". A login screen will appear.
- The "Host" has been preset to papio-vpn.biology.duke.edu. This default text is out of date, and should be updated in a future version of Ranker. Remove the text and replace it with localhost.
- The "Port" is preset to 5432. Leave this alone.
- The "Use SSL?" field is preset to be unchecked. Leave it unchecked.
- The "User Name" and "Password" are your Babase credentials.
- The "Database" defaults to "babase". You should probably leave this as-is unless you know that you want to connect to a different database.
Hit "Connect" to log in.
You take it from here!
When you're done using Ranker, return to your terminal and enter, simply:
```
exit
```
You're now free to close your terminal window and disconnect from the VPN.

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.

Development Environment

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:
- PostgeSQL JDBC Driver, at http://jdbc.postgresql.org/
- TableLayout manager, at https://tablelayout.dev.java.net/
- jcalendar, at http://www.toedter.com/en/jcalendar/

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

Change Log

Ranker version 1.2 (2012-11-19)

Ranker version 1.2 contains a major bug fix.

Detail:

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.