Vanderbilt University Medical Center

Supporting Tool Suite for Production Proteomics

File Name Generator (FNG)

Overview

The purpose of the instrument file naming utility FNG is to generate a sequence of filenames which correspond to an equal number of aliquots being loaded into a sample tray on an instrument. The FNG application provides a way to quickly generate filenames in a standard consistent fashion as opposed to manually entering each filename into the instrument control software. The goals this software achieves are keeping filenames organized, controlling the length of the filenames, and saving time by removing data entry.

 

Requirements

 jboss-5.1.0.GA-jdk6

 jboss-seam-2.2.0.GA

 hibernate-distribution-3.5.0-CR-2-dist

 JSF-mojarra-1.2_12

 richfaces-ui-3.3.2.SR1

 eclipse-jee-helios-SR2 (JVM - jdk1.6.0_22)

 Plugins (update sites)

 jbossTools3.2

 Subclipse

 

This application is a seam application which uses EJBs 3.0 and must run in an application server with an EJB container. JBoss is such a container and is what we use to deploy FNG.

 

Installation Instructions:

Summary

JBoss Configuration

In JBOSS_HOME\server\default\lib add ojdbc5.jar (or another driver specific for database being used)

Add ldap certificate to keystore in JBOSS_HOME\server\default\conf (if LDAP is used for authentication)

Security

Authentication is handled by the Authenticator service class located in package edu.vanderbilt.ayers.fng.service. We use our LDAP server to authenticate users, so in our case, Authenticator calls the LDAPManager EJB class which authenticates the users credentials against our LDAP Server.  To configure the application to use an LDAP server, modification of the LDAPManagerEJB class is required.  The PROVIDER_URL will need to be modified to specify the appropriate LDAP url and port. If authentication is handled by some other means, then the logic in Authenticator will need to be changed accordingly.

Database Connection

The application uses a datasource file to make the database connection. This file is named FileNameGenerator-ds.xml and should be modified to configure a connection specific to your environment. The datasource resource file should be deployed separate from the EAR to JBOSS_HOME\server\default\deploy.

Deployment

To deploy locally the JBoss Tools plugin is used within Eclipse. First bring up a server, JBoss AS 5.1 under JBoss Community folder. Next add the datasource xml file and the FileNameGenerator-ear file as deployable resources to the application server. Now start the server and wait for JBoss to start and deploy the application. If this is the first deploy and tables do not exist in the database, the tables, constraints, and sequences will be created if the username specified in the datasource has the appropriate permissions to do so. Once the application is deployed, it can be accessed from the localhost: http://localhost:8080/FileNameGenerator/

To deploy to a remote application server such as test or prod environments. Export the EAR project as a EAR from eclipse and copy the datasource and the exported EAR file to JBOSS_HOME\server\default\deploy and it will deploy the same as the above local application server: http://hostname:8080/FileNameGenerator

 

Details

Full installation details can be obtained in the FNG directory in the distribution package or here, including screen shots for step-by-step installation instructions.