How to set a Timer in Java?

Use this

long startTime = System.currentTimeMillis();
long elapsedTime = 0L.

while (elapsedTime < 2*60*1000) {
    //perform db poll/check
    elapsedTime = (new Date()).getTime() - startTime;
}

//Throw your exception

Ok, I think I understand your problem now. You can use a Future to try to do something and then timeout after a bit if nothing has happened.

E.g.:

FutureTask<Void> task = new FutureTask<Void>(new Callable<Void>() {
  @Override
  public Void call() throws Exception {
    // Do DB stuff
    return null;
  }
});

Executor executor = Executors.newSingleThreadScheduledExecutor();
executor.execute(task);

try {
  task.get(5, TimeUnit.SECONDS);
}
catch(Exception ex) {
  // Handle your exception
}

So the first part of the answer is how to do what the subject asks as this was how I initially interpreted it and a few people seemed to find helpful. The question was since clarified and I've extended the answer to address that.

Setting a timer

First you need to create a Timer (I'm using the java.util version here):

import java.util.Timer;

..

Timer timer = new Timer();

To run the task once you would do:

timer.schedule(new TimerTask() {
  @Override
  public void run() {
    // Your database code here
  }
}, 2*60*1000);
// Since Java-8
timer.schedule(() -> /* your database code here */, 2*60*1000);

To have the task repeat after the duration you would do:

timer.scheduleAtFixedRate(new TimerTask() {
  @Override
  public void run() {
    // Your database code here
  }
}, 2*60*1000, 2*60*1000);

// Since Java-8
timer.scheduleAtFixedRate(() -> /* your database code here */, 2*60*1000, 2*60*1000);

Making a task timeout

To specifically do what the clarified question asks, that is attempting to perform a task for a given period of time, you could do the following:

ExecutorService service = Executors.newSingleThreadExecutor();

try {
    Runnable r = new Runnable() {
        @Override
        public void run() {
            // Database task
        }
    };

    Future<?> f = service.submit(r);

    f.get(2, TimeUnit.MINUTES);     // attempt the task for two minutes
}
catch (final InterruptedException e) {
    // The thread was interrupted during sleep, wait or join
}
catch (final TimeoutException e) {
    // Took too long!
}
catch (final ExecutionException e) {
    // An exception from within the Runnable task
}
finally {
    service.shutdown();
}

This will execute normally with exceptions if the task completes within 2 minutes. If it runs longer than that, the TimeoutException will be throw.

One issue is that although you'll get a TimeoutException after the two minutes, the task will actually continue to run, although presumably a database or network connection will eventually time out and throw an exception in the thread. But be aware it could consume resources until that happens.

    new java.util.Timer().schedule(new TimerTask(){
        @Override
        public void run() {
            System.out.println("Executed...");
           //your code here 
           //1000*5=5000 mlsec. i.e. 5 seconds. u can change accordngly 
        }
    },1000*5,1000*5);