/* Copyright (c) 2009 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */
package compbio.runner._impl;

import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;

import java.text.ParseException;

import org.ggf.drmaa.DrmaaException;
import org.ggf.drmaa.JobInfo;
import org.testng.annotations.Test;

import compbio.engine.cluster.drmaa.ClusterUtil;
import compbio.engine.cluster.drmaa.JobRunner;
import compbio.engine.cluster.drmaa.StatisticManager;
import compbio.metadata.AllTestSuit;
import compbio.metadata.JobExecutionException;
import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;

public class Tmhmm2Tester {

	public static String test_input = "/homes/pvtroshin/TO1381.fasta";
	public static String test_outfile = "/homes/pvtroshin/TO1381.tmhmm2.out";
	public static String test_outDir = "/homes/pvtroshin/HMM2";

	@Test
	public void testGetTestCommand() {
		System.out.println(Tmhmm2.getTestCommand());
	}

	@Test(enabled = false, groups = { AllTestSuit.test_group_cluster,
			AllTestSuit.test_group_runner })
	public void testBuildCommand() {
		Tmhmm2 hmm = new Tmhmm2(AllTestSuit.OUTPUT_DIR_ABSOLUTE);
		// TODO hmm.setInput(test_input).setOutput(test_outfile);
		// hmm.setParameters(new Tmhmm2().getParameters());

		try {
			JobRunner runner = JobRunner.getInstance(null);
			assertNotNull("Runner is NULL", runner);
			// runner.setWorkDirectory(test_outDir);
			runner.executeJob();
			// assertNotNull(jobId1);
			JobStatus status = runner.getJobStatus();
			assertTrue(status == JobStatus.PENDING
					|| status == JobStatus.RUNNING);
			JobInfo info = runner.getJobInfo();
			assertNotNull(info);
			StatisticManager sm = new StatisticManager(info);
			assertNotNull(sm);
			try {
				String exits = sm.getExitStatus();
				assertNotNull(exits);
				int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
						.intValue();
				// assertEquals(0, exitsInt);
				System.out.println(sm.getAllStats());

			} catch (ParseException e) {
				e.printStackTrace();
				fail("Parse Exception: " + e.getLocalizedMessage());
			}

			assertTrue(sm.hasExited());
			assertFalse(sm.wasAborted());
			assertFalse(sm.hasDump());
			assertFalse(sm.hasSignaled());

		} catch (DrmaaException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (JobSubmissionException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (JobExecutionException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		}
	}

}