Execute Query using Java API

Without context, about what an exception and what is around and passed, no one will be able to help.
Maybe see https://rsjazz.wordpress.com/2013/03/20/understanding-and-using-the-rtc-java-client-api/ and set your system up for debugging? E.g. find out some classes are null or something like that?

Usually, you don't need to get the ITeamRepository from the work item, because you should already be logged in.
The second method is more like it, however, for it to be able to run, it needs the Plain Java Client libraries to be in the classpath, either by creating a user library as described in Understanding and Using the RTC Java Client API section Setting Up Your Workspace for Plain Java Development, or by providing it in the classpath as described in Understanding and Using the RTC Java Client API in the section Run From Command Line.

A valid base program that should do the login looks like below.

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 *
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package com.ibm.js.team.workitem.automation.examples;

import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.NullProgressMonitor;

import com.ibm.team.repository.client.ITeamRepository;
import com.ibm.team.repository.client.ITeamRepository.ILoginHandler;
import com.ibm.team.repository.client.ITeamRepository.ILoginHandler.ILoginInfo;
import com.ibm.team.repository.client.TeamPlatform;
import com.ibm.team.repository.common.TeamRepositoryException;

/**
 * Skeleton for a plain-Java client, see
 * https://jazz.net/wiki/bin/view/Main/ProgrammaticWorkItemCreation.
 */
public class PlainJavaClient {

	private static class LoginHandler implements ILoginHandler, ILoginInfo {

		private String fUserId;
		private String fPassword;

		private LoginHandler(String userId, String password) {
			fUserId = userId;
			fPassword = password;
		}

		public String getUserId() {
			return fUserId;
		}

		public String getPassword() {
			return fPassword;
		}

		public ILoginInfo challenge(ITeamRepository repository) {
			return this;
		}
	}

	public static void main(String[] args) {

		boolean result;
		TeamPlatform.startup();
		try {
			result = run(args);
		} catch (TeamRepositoryException x) {
			x.printStackTrace();
			result = false;
		} finally {
			TeamPlatform.shutdown();
		}

		if (!result)
			System.exit(1);

	}

	private static boolean run(String[] args) throws TeamRepositoryException {

		if (args.length != 3) {
			System.out
					.println("Usage: PlainJavaClient [repositoryURI] [userId] [password]");
			return false;
		}

		IProgressMonitor monitor = new NullProgressMonitor();
		String repositoryURI = args[0];
		String userId = args[1];
		String password = args[2];

		ITeamRepository teamRepository = TeamPlatform
				.getTeamRepositoryService().getTeamRepository(repositoryURI);
		teamRepository.registerLoginHandler(new LoginHandler(userId, password));
		teamRepository.login(monitor);

		System.out.println("Logged in as: "
				+ teamRepository.loggedInContributor().getName());
		
		// your code goes here


		teamRepository.logout();

		return true;
	}
}