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Best Way to Update Database Periodically in Java Web Application

I have a java web application which is running on Glassfish server. Using war file i use to deploy the application in various servers. Now to keep my application's database updated, i want to run some class (inside from application)periodically without any user interaction (should not depends on application is running or not/current users/session). i have seen that using some Timer and TimerTask class i can run any job periodically. But how to initialize it for the first time?
Please put your thoughts on how to complete this process.

Use a Job scheduler. Consider Quartz http://quartz-scheduler.org/ and start it when the program starts. The good part about using a scheduler is your program is more maintainable and you can easily create other new jobs

Create a servlet and make it load on startup. There you can initialize your task, I think.

Quartz is a good solution like already suggested. But if you need something more lite weight, I would have a look at the scheduled executor:
http://docs.oracle.com/javase/7/docs/api/java/util/concurrent/ScheduledExecutorService.html
It is less flexible than Quartz, but you don't need to add any dependency and it might be that it is good enough for your needs.
About starting up; I normally use Spring to wire up my application and its dependencies. So starting schedulers and running scheduled tasks is then a no brainer.

The answer changes depending on the version of Java EE you are using. In Java EE 5 and previous versions you would use a ServletContextListener to run code (call an EJB) at deployment time that used the Timer API. In Java EE 6+ you can use the #Schedule annotation which uses annotations and a cron-type syntax to schedule your task at deployment time.
Of course if you don't need automatic deployment time scheduling then you'd just create some web form that calls a EJB when submitted which in turn calls the Timer API programmatically.
For more see the Java EE tutorial

Running Multiple Jobs using Scheduler in Real time application

Can anyone help me out to choose which scheduler between "Quartz" or "Quartz+Spring" to run multiple jobs simultaneously in real time application.

Quartz can run multiple jobs without Spring. Use Spring if you want the features that Spring brings to the table. I would use Spring, because Spring is a great integration framework and makes it easy to integrate technologies like Quartz into an application.

I prefer TimerTask class.
Refer this tutorial
http://www.mkyong.com/java/how-to-run-a-task-periodically-in-java/

Can I configure a kind of trigger isolation with Quartz?

My application is split into 2 web applications running in the same container sharing one db.
The first war does only background processing and the other is for the client GUI + some background stuffs.
The application with the client GUI allows the user to configure the scheduling of some tasks that will be executed by the "background application". Basically it configures the Quartz jobs and triggers.
I'd like that the scheduler of the background application handles only the jobs of a certain group (bg-jobs), and that the other scheduler handles the other group (fg-jobs).
Is it possible to configure this kind of isolation with quartz?
Note: I'd like to keep it simple and if I can avoid to use Quartz Where which seems to be liek a hammer to sledge this probably overkill for my need.
Thanks in advance

The simplest and quickest way is to create a separate load of tables for each application. So have one set of quartz tables prefixed with "bg-" and another prefixed with "fg-". Then just change your schedulers configs to point at the appropriate tables. I know it might be a little awkward but you did say you wanted to keep it simple :).

Scheduling tasks in Java/Spring

There is a requirement in the project that will have a scheduled task that will do some job.
The project is Spring based and the scheduled job will be part of the application war.I have
never implemented this kind of functionality before.
I have heard of Quartz. Also, I read somewhere that Spring provides some functionality to schedule tasks. So, I was thinking if I am already using Spring then why to go for some other API(Quartz).
I am not sure which one to use? what will be the pros/cons of one over another?
Please suggest what will be the best way to approach my requirement.

I have used Spring's Task execution and scheduling - http://static.springsource.org/spring/docs/3.0.x/reference/scheduling.html

Running scheduled methods on tomcat

I am trying to set up a method that will be automatically run by the server at a specific time. For instance, a method that sends out emails to contacts every Friday at 9.00 am. I have seen methods that are run when the server is first started and was wondering if what I want to do is possible. If it is possible, can someone point me to where I can start reading up how to do this. Any help will be highly appreciated.

There is an excellent library quartz which can help you create scheduled tasks within your application. See e.g., the Job Scheduling in Java guide by o'reilly.

If you really want to do it manually (and not use specific tools like Quartz), you could use a Timer, which would be created when the application is deployed and canceled when the application is destroyed, using a ServletContextListener declared in your web.xml.
Be prepared for additional complexity if your application is clustered on multiple servers, though.

I also recommend using Quartz as Johan already suggested, it is a well-established solution for job scheduling in Java applications and also allows for central job storage in a database and clustering of multiple Tomcat instances.
In case your web application uses the Spring Framework, you could instead use the built-in scheduling support instead.