/* Copyright (c) 2013 Alexander Sherstnev
 * 
 *  Java Bioinformatics Analysis Web Services (JABAWS)
 *  @version: 2.5
 * 
 * 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.predictors;
//
//import static org.testng.Assert.assertEquals;
//import static org.testng.Assert.assertFalse;
//import static org.testng.Assert.assertNotNull;
//import static org.testng.Assert.assertTrue;
//import static org.testng.Assert.fail;
//
//import java.io.File;
//import java.io.FileInputStream;
//import java.io.FileNotFoundException;
//import java.io.IOException;
//import java.text.ParseException;
//import java.util.Arrays;
//
//import javax.xml.bind.ValidationException;
//
//import org.ggf.drmaa.DrmaaException;
//import org.ggf.drmaa.JobInfo;
//import org.testng.annotations.BeforeMethod;
//import org.testng.annotations.Test;
//
//import compbio.data.sequence.JpredAlignment;
//import compbio.engine.AsyncExecutor;
//import compbio.engine.Configurator;
//import compbio.engine.FilePuller;
//import compbio.engine.SyncExecutor;
//import compbio.engine.client.ConfExecutable;
//import compbio.engine.client.ConfiguredExecutable;
//import compbio.engine.client.Executable;
//import compbio.engine.client.RunConfiguration;
//import compbio.engine.cluster.drmaa.ClusterEngineUtil;
//import compbio.engine.cluster.drmaa.ClusterRunner;
//import compbio.engine.cluster.drmaa.StatisticManager;
//import compbio.engine.local.LocalRunner;
//import compbio.metadata.AllTestSuit;
//import compbio.metadata.ChunkHolder;
//import compbio.metadata.JobExecutionException;
//import compbio.metadata.JobStatus;
//import compbio.metadata.JobSubmissionException;
//import compbio.metadata.LimitsManager;
//import compbio.metadata.Preset;
//import compbio.metadata.PresetManager;
//import compbio.metadata.ResultNotAvailableException;
//import compbio.metadata.RunnerConfig;
//import compbio.runner.RunnerUtil;
//import compbio.util.FileWatcher;
//import compbio.util.SysPrefs;
//
//public class JpredTester {
//
//	public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;
//
//	public static String test_output = "Jpred.test1.out";
//	public static String test_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "Jpred.test1.fasta";
//	private Jpred pred;
//
//	@BeforeMethod(alwaysRun = true)
//	void init() {
//		pred = new Jpred();
//		pred.setInput(test_input);
//		pred.setOutput(test_output);
//	}
//
//	// disabled
//	@Test(enabled=false,groups = {AllTestSuit.test_group_runner})
//	public void RunOnCluster() {
//		assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");
//		try {
//			PresetManager<Jpred> jpredPreset = RunnerUtil.getPresets(Jpred.class);
//			assert jpredPreset != null;
//			ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);
//			Preset<Jpred> conf = jpredPreset.getPresetByName("cluster configuration");
//			confpred.addParameters(conf.getOptions());
//			ClusterRunner runner = ClusterRunner.getInstance(confpred);
//			assertNotNull(runner, "Runner is NULL");
//
//			runner.executeJob();
//			JobStatus status = runner.getJobStatus();
//			assertTrue(status == JobStatus.PENDING || status == JobStatus.RUNNING, "Status of the process is wrong!");
//			JobInfo info = runner.getJobInfo();
//			assertNotNull(info, "JobInfo is null");
//			StatisticManager sm = new StatisticManager(info);
//			assertNotNull(sm, "Statistic manager is null");
//			try {
//				String exits = sm.getExitStatus();
//				assertNotNull("Exit status is null", exits);
//				// cut 4 trailing zeros from the number
//				int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();
//				assertEquals(0, exitsInt);
//				System.out.println(sm.getAllStats());
//			} catch (ParseException e) {
//				e.printStackTrace();
//				fail("Parse Exception: " + e.getMessage());
//			}
//			assertTrue(sm.hasExited());
//			assertFalse(sm.wasAborted());
//			assertFalse(sm.hasDump());
//			assertFalse(sm.hasSignaled());
//
//		} catch (JobSubmissionException e) {
//			e.printStackTrace();
//			fail("DrmaaException caught:" + e.getMessage());
//		} catch (JobExecutionException e) {
//			e.printStackTrace();
//			fail("DrmaaException caught:" + e.getMessage());
//		} catch (DrmaaException e) {
//			e.printStackTrace();
//			fail("DrmaaException caught:" + e.getMessage());
//		}
//	}
//
//	// disabled
//	@Test(enabled=false,groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_cluster})
//	public void RunOnClusterAsync() {
//		assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");
//		try {
//			pred.addParameters(Arrays.asList("-dbname uniref90", "-dbpath /homes/www-jpred/databases/"));
//			ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);
//			AsyncExecutor aengine = Configurator.getAsyncEngine(confpred);
//			String jobId = aengine.submitJob(confpred);
//			assertNotNull(jobId, "Runner is NULL");
//			// let drmaa to start
//			Thread.sleep(500);
//			JobStatus status = aengine.getJobStatus(jobId);
//			while (status != JobStatus.FINISHED) {
//				Thread.sleep(1000);
//				status = aengine.getJobStatus(jobId);
//				ConfiguredExecutable<Jpred> result = (ConfiguredExecutable<Jpred>) aengine.getResults(jobId);
//				assertNotNull(result);
//				if (status == JobStatus.UNDEFINED || status == JobStatus.FAILED) {
//					fail("job " + jobId +" failed!");
//					break;
//				}
//			}
//		} catch (JobSubmissionException e) {
//			e.printStackTrace();
//			fail("DrmaaException caught:" + e.getMessage());
//		} catch (InterruptedException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (ResultNotAvailableException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		}
//	}
//
//	@Test(groups = {AllTestSuit.test_group_runner})
//	public void RunLocally() {
//		try {
//			ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);
//			confpred.addParameters(Arrays.asList("-dbname ported_db", "-dbpath /data/UNIREFdb/"));
//
//			// For local execution use relative
//			LocalRunner lr = new LocalRunner(confpred);
//			lr.executeJob();
//			ConfiguredExecutable<?> al1 = lr.waitForResult();
//			assertNotNull(al1.getResults());
//			JpredAlignment totalign = (JpredAlignment) confpred.getResults();
//			assertNotNull(totalign);
//			assertEquals(totalign.getSize(), 14);
//			assertEquals(al1.getResults(), totalign);
//		} catch (JobSubmissionException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		} catch (ResultNotAvailableException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		} catch (JobExecutionException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		}
//	}
//
//	@Test(enabled=false,groups = {AllTestSuit.test_group_runner})
//	public void RunLocallyWithPreset() {
//		try {
//			ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);
//			PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);
//			assert preset != null;
//			Preset<Jpred> conf = preset.getPresetByName("laptop configuration");
//			confpred.addParameters(conf.getOptions());
//
//			// For local execution use relative
//			LocalRunner lr = new LocalRunner(confpred);
//			lr.executeJob();
//			ConfiguredExecutable<?> al1 = lr.waitForResult();
//			assertNotNull(al1.getResults());
//			JpredAlignment totalign = (JpredAlignment) confpred.getResults();
//			assertNotNull(totalign);
//			assertEquals(totalign.getSize(), 19);
//			assertEquals(al1.getResults(), totalign);
//		} catch (JobSubmissionException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		} catch (ResultNotAvailableException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		} catch (JobExecutionException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		}
//	}
//
//	@Test(enabled=false,groups = {AllTestSuit.test_group_runner})
//	public void readStatistics() {
//		try {
//			Jpred jpred = new Jpred();
//			jpred.setInput(test_input);
//			jpred.setOutput(test_output);
//			ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);
//			PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);
//			assert preset != null;
//			Preset<Jpred> conf = preset.getPresetByName("laptop configuration");
//			confpred.addParameters(conf.getOptions());
//
//			// For local execution use relative
//			AsyncExecutor sexec = Configurator.getAsyncEngine(confpred);
//			String jobId = sexec.submitJob(confpred);
//			String file = confpred.getWorkDirectory() + File.separator + Jpred.getStatFile();
//			FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);
//			int count = 0;
//			long position = 0;
//			fw.waitForFile(2);
//			JobStatus status = sexec.getJobStatus(jobId);
//			do {
//				if (fw.hasMoreData()) {
//					ChunkHolder ch = fw.pull(position);
//					String chunk = ch.getChunk();
//					position = ch.getNextPosition();
//				}
//				count++;
//				// Make sure the loop is terminated if the job fails
//				if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
//					fail("job " + jobId +" failed!");
//					break;
//				}
//				Thread.sleep(200);
//				status = sexec.getJobStatus(jobId);
//			}  while (status != JobStatus.FINISHED || fw.hasMoreData());
//
//			assertTrue(count >= 1);
//			ConfiguredExecutable<?> al = sexec.getResults(jobId);
//			assertNotNull(al.getResults());
//		} catch (JobSubmissionException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (ResultNotAvailableException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (IOException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (InterruptedException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		}
//	}
//
//	@Test(enabled=false,groups = {AllTestSuit.test_group_runner})
//	public void Persistance() {
//		try {
//			Jpred jpred = new Jpred();
//			jpred.setError("errrr.txt");
//			jpred.setInput(test_input);
//			jpred.setOutput("outtt.txt");
//			assertEquals(jpred.getInput(), test_input);
//			assertEquals(jpred.getError(), "errrr.txt");
//			assertEquals(jpred.getOutput(), "outtt.txt");
//			ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);
//			confpred.addParameters(Arrays.asList("-dbname ported_db", "-dbpath /data/UNIREFdb/"));
//
//			SyncExecutor sexec = Configurator.getSyncEngine(confpred);
//			sexec.executeJob();
//			ConfiguredExecutable<?> al = sexec.waitForResult();
//			assertNotNull(al.getResults());
//
//			// Save run configuration
//			assertTrue(confpred.saveRunConfiguration());
//
//			// See if loaded configuration is the same as saved
//			RunConfiguration loadedRun = RunConfiguration.load(new FileInputStream(new File(confpred.getWorkDirectory(), RunConfiguration.rconfigFile)));
//			assertEquals(((ConfExecutable<Jpred>) confpred).getRunConfiguration(),loadedRun);
//
//			// Load run configuration as ConfExecutable
//			ConfiguredExecutable<Jpred> jpred2 = (ConfiguredExecutable<Jpred>) confpred.loadRunConfiguration(new FileInputStream(new File(confpred.getWorkDirectory(), RunConfiguration.rconfigFile)));
//			assertNotNull(jpred2);
//			assertEquals(jpred2.getExecutable().getInput(), test_input);
//			assertEquals(jpred2.getExecutable().getError(), "errrr.txt");
//			assertEquals(jpred2.getExecutable().getOutput(), "outtt.txt");
//
//			// See in details whether executables are the same
//			assertEquals(jpred2.getExecutable(), jpred);
//			ConfiguredExecutable<Jpred> resjpred2 = Configurator.configureExecutable(jpred2.getExecutable(), Executable.ExecProvider.Local);
//
//			sexec = Configurator.getSyncEngine(resjpred2, Executable.ExecProvider.Local);
//			sexec.executeJob();
//			al = sexec.waitForResult();
//			assertNotNull(al);
//		} catch (JobSubmissionException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (JobExecutionException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (FileNotFoundException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (IOException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		} catch (ResultNotAvailableException e) {
//			e.printStackTrace();
//			fail(e.getMessage());
//		}
//	}
//
//	@Test(enabled=false,groups = {AllTestSuit.test_group_runner})
//	public void ConfigurationLoading() {
//		try {
//			RunnerConfig<Jpred> jpredConfig = ConfExecutable.getRunnerOptions(Jpred.class);
//			assertNotNull(jpredConfig);
//			assertTrue(jpredConfig.getArguments().size() > 0);
//
//			PresetManager<Jpred> jpredPreset = ConfExecutable.getRunnerPresets(Jpred.class);
//			assertNotNull(jpredPreset);
//
//			LimitsManager<Jpred> jpredLimits = ConfExecutable.getRunnerLimits(Jpred.class);
//			assertNotNull(jpredLimits);
//			assertTrue(jpredLimits.getLimits().size() > 0);
//			jpredLimits.validate(jpredPreset);
//		} catch (FileNotFoundException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		} catch (IOException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		} catch (ValidationException e) {
//			e.printStackTrace();
//			fail(e.getLocalizedMessage());
//		}
//	}
//
//}