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| The new Ranker program for Babase was developed by ["JunYang"] and ["TylerBrock"] from Fall 2006 to Spring 2007. It was Tyler's Graduation with Distinction project when he graduated from Duke University in 2007. | 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. |
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| * 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"] for details on how to set up VPN on your computer. | * 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. |
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| * Your computer must have Sun's Java Platform, Standard Edition 5 or later. | * Your computer must have Java Standard Edition 5 or later. |
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| * If your computer is not on the same trusted network as papio, first establish a VPN connection to papio. See ["BabaseVPN"] for detailed instructions. * Point your browser to [https://papio.biology.duke.edu/ranker/ranker.jnlp]; this will launch 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. |
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=== Running the Ranker from Duke === 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). If you are running VPN, you do not need to modify the default value. * To login to {{{papio-vpn.biology.duke.edu}}} use your database username and password. * To login to {{{papio.biology.duke.edu}}} use your Unix username and password. |
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| * 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] |
* 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, which you can request from [:JunYang:Jun Yang] |
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| * TableLayout manager, at http://java.sun.com/products/jfc/tsc/articles/tablelayout/apps/TableLayout.jar | * TableLayout manager, at https://tablelayout.dev.java.net/ |
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| ==== 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. |
==== 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. |
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 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 [: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.
Running the Ranker from Duke
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). If you are running VPN, you do not need to modify the default value.
To login to papio-vpn.biology.duke.edu use your database username and password.
To login to papio.biology.duke.edu use your Unix username and password.
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:
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, which you can request from [:JunYang:Jun Yang]
- Obtain the following third-party libraries:
PostgeSQL JDBC Driver, at http://jdbc.postgresql.org/
TableLayout manager, at https://tablelayout.dev.java.net/
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.