Differences between revisions 52 and 55 (spanning 3 versions)

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.

Downloading Ranker

A zipped version of Ranker is available to download at https://papio.biology.duke.edu/ranker.tgz. Download and unzip it; this should yield a folder called "ranker". Save this "ranker" folder in an easily-accessible place on your computer (e.g. your Desktop).

Running 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.
- Important: This step is not an alternative to the requirement to be at Duke or use its VPN. This is a discrete requirement for Ranker to work, entirely separate from the requirement to connect to Duke's network. (The connection to Duke is required for this step to work, however.)
Open a terminal and enter the following (all on one line):
```
ssh -L 5432:localhost:5432 MYNETID@papio.biology.duke.edu
```
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!).
To launch Ranker, the steps vary a little, depending on your operating system.
- Windows
  - Hold the "Shift" key and right click on the "ranker" folder that (above) you unzipped and stored in an accessible place. In the window that opens, select "Open Command Window Here".
  - In the Command Prompt Window that opens, enter this command:
```
java -cp ranker.jar;lib\jcalendar-1.3.2.jar;lib\postgresql-8.2-506.jdbc3.jar;lib\TableLayout.jar babase.ranker.Main
```
  - As above, feel free to hide or minimize this Command Prompt window (but don't close it!)
- macOS, Unix
  - Open a terminal (a different one from the one you've opened to connect to Papio) and navigate to the "ranker" directory, that (above) you unzipped and stored in an accessible place.
    - If you're on a Mac and saved it your Desktop, you might enter:
```
cd /Users/YOURUSERNAME/Desktop/ranker
```
  - Enter the following command:
```
java -cp ranker.jar:lib/jcalendar-1.3.2.jar:lib/postgresql-8.2-506.jdbc3.jar:lib/TableLayout.jar babase.ranker.Main
```
  - As above, feel free to hide or minimize this terminal window (but don't close it!)
- 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" is localhost.
- The "Port" is 5432.
- The "Use SSL?" field should stay 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, you can close the terminal/command prompt window you used to launch it (your OS may close it by itself). Next, return to the terminal you used to SSH into Papio and enter, simply:
```
exit
```
You're now free to close the 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.

Change Log

Ranker version 1.3 (2018-03-27)

Ranker version 1.3 contains a few updates to reflect changes that have occurred to the database and/or the VM that hosts it.

Details:

Changed the default "Host" in the Welcome UI to localhost.
In the tooltip that appears when hovering over an individual's sname:
- Removed "Dcauseconfidence" column
- Added the following columns:
  - Dcausenatureconfidence
  - Dcauseagentconfidence
  - Entrydate
  - Entrytype
- Changed Bstatus data type from integer to "Bigdecimal"

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.