How to properly stop the Thread in Java?

In the IndexProcessor class you need a way of setting a flag which informs the thread that it will need to terminate, similar to the variable run that you have used just in the class scope.

When you wish to stop the thread, you set this flag and call join() on the thread and wait for it to finish.

Make sure that the flag is thread safe by using a volatile variable or by using getter and setter methods which are synchronised with the variable being used as the flag.

public class IndexProcessor implements Runnable {

    private static final Logger LOGGER = LoggerFactory.getLogger(IndexProcessor.class);
    private volatile boolean running = true;

    public void terminate() {
        running = false;
    }

    @Override
    public void run() {
        while (running) {
            try {
                LOGGER.debug("Sleeping...");
                Thread.sleep((long) 15000);

                LOGGER.debug("Processing");
            } catch (InterruptedException e) {
                LOGGER.error("Exception", e);
                running = false;
            }
        }

    }
}

Then in SearchEngineContextListener:

public class SearchEngineContextListener implements ServletContextListener {

    private static final Logger LOGGER = LoggerFactory.getLogger(SearchEngineContextListener.class);

    private Thread thread = null;
    private IndexProcessor runnable = null;

    @Override
    public void contextInitialized(ServletContextEvent event) {
        runnable = new IndexProcessor();
        thread = new Thread(runnable);
        LOGGER.debug("Starting thread: " + thread);
        thread.start();
        LOGGER.debug("Background process successfully started.");
    }

    @Override
    public void contextDestroyed(ServletContextEvent event) {
        LOGGER.debug("Stopping thread: " + thread);
        if (thread != null) {
            runnable.terminate();
            thread.join();
            LOGGER.debug("Thread successfully stopped.");
        }
    }
}

Using Thread.interrupt() is a perfectly acceptable way of doing this. In fact, it's probably preferrable to a flag as suggested above. The reason being that if you're in an interruptable blocking call (like Thread.sleep or using java.nio Channel operations), you'll actually be able to break out of those right away.

If you use a flag, you have to wait for the blocking operation to finish and then you can check your flag. In some cases you have to do this anyway, such as using standard InputStream/OutputStream which are not interruptable.

In that case, when a thread is interrupted, it will not interrupt the IO, however, you can easily do this routinely in your code (and you should do this at strategic points where you can safely stop and cleanup)

if (Thread.currentThread().isInterrupted()) {
  // cleanup and stop execution
  // for example a break in a loop
}

Like I said, the main advantage to Thread.interrupt() is that you can immediately break out of interruptable calls, which you can't do with the flag approach.