X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=testsrc%2Fcompbio%2Frunner%2Fdisorder%2FDisemblTester.java;h=d77648e6070049e6ab38b21884e64a74e19c97f6;hb=8033a51860de2200a54e64add0809d6780f5b092;hp=85d5e91f48011212aab61d0dea8c90f66ff40c79;hpb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;p=jabaws.git

diff --git a/testsrc/compbio/runner/disorder/DisemblTester.java b/testsrc/compbio/runner/disorder/DisemblTester.java
index 85d5e91..d77648e 100644
--- a/testsrc/compbio/runner/disorder/DisemblTester.java
+++ b/testsrc/compbio/runner/disorder/DisemblTester.java
@@ -30,7 +30,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.text.ParseException;
-import java.util.List;
+import java.util.HashSet;
 
 import javax.xml.bind.ValidationException;
 
@@ -39,7 +39,7 @@ import org.ggf.drmaa.JobInfo;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import compbio.data.sequence.AnnotatedSequence;
+import compbio.data.sequence.Score;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.FilePuller;
@@ -66,287 +66,289 @@ import compbio.util.SysPrefs;
 
 public class DisemblTester {
 
-    public static String test_outfile = "TO1381.disembl.out";
+	public static String test_outfile = "TO1381.disembl.out";
 
-    private Disembl disembl;
+	private Disembl disembl;
 
-    @BeforeMethod(alwaysRun = true)
-    void init() {
-	disembl = new Disembl();
-	disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);
-    }
+	@BeforeMethod(alwaysRun = true)
+	void init() {
+		disembl = new Disembl();
+		disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);
+	}
 
-    @Test(groups = { AllTestSuit.test_group_cluster,
-	    AllTestSuit.test_group_runner })
-    public void testRunOnCluster() {
-	assertFalse(SysPrefs.isWindows,
-		"Cluster execution can only be in unix environment");
-	try {
-	    ConfiguredExecutable<Disembl> confDisembl = Configurator
-		    .configureExecutable(disembl,
-			    Executable.ExecProvider.Cluster);
-	    JobRunner runner = JobRunner.getInstance(confDisembl);
+	@Test(groups = {AllTestSuit.test_group_cluster,
+			AllTestSuit.test_group_runner})
+	public void testRunOnCluster() {
+		assertFalse(SysPrefs.isWindows,
+				"Cluster execution can only be in unix environment");
+		try {
+			ConfiguredExecutable<Disembl> confDisembl = Configurator
+					.configureExecutable(disembl,
+							Executable.ExecProvider.Cluster);
+			JobRunner runner = JobRunner.getInstance(confDisembl);
 
-	    assertNotNull(runner, "Runner is NULL");
-	    runner.executeJob();
-	    // assertNotNull("JobId is null", jobId1);
-	    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, "Statictic manager is null");
-	    try {
+			assertNotNull(runner, "Runner is NULL");
+			runner.executeJob();
+			// assertNotNull("JobId is null", jobId1);
+			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, "Statictic manager is null");
+			try {
 
-		String exits = sm.getExitStatus();
-		assertNotNull("Exit status is null", exits);
-		// cut 4 trailing zeros from the number
-		int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
-			.intValue();
-		assertEquals(0, exitsInt);
-		System.out.println(sm.getAllStats());
+				String exits = sm.getExitStatus();
+				assertNotNull("Exit status is null", exits);
+				// cut 4 trailing zeros from the number
+				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.getMessage());
-	    }
-	    //assertFalse(runner.cleanup());
-	    assertTrue(sm.hasExited());
-	    assertFalse(sm.wasAborted());
-	    assertFalse(sm.hasDump());
-	    assertFalse(sm.hasSignaled());
+			} catch (ParseException e) {
+				e.printStackTrace();
+				fail("Parse Exception: " + e.getMessage());
+			}
+			// assertFalse(runner.cleanup());
+			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());
+		} 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());
+		}
 	}
-    }
 
-    /**
-     * This tests fails from time to time depending on the cluster load or some
-     * other factors. Any client code has to adjust for this issue
-     */
-    @Test(groups = { AllTestSuit.test_group_cluster,
-	    AllTestSuit.test_group_runner })
-    public void testRunOnClusterAsync() {
-	assertFalse(SysPrefs.isWindows,
-		"Cluster execution can only be in unix environment");
-	try {
-	    ConfiguredExecutable<Disembl> confDisembl = Configurator
-		    .configureExecutable(disembl,
-			    Executable.ExecProvider.Cluster);
-	    AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);
-	    String jobId = aengine.submitJob(confDisembl);
-	    assertNotNull(jobId, "Runner is NULL");
-	    // let drmaa to start
-	    Thread.sleep(500);
-	    JobStatus status = aengine.getJobStatus(jobId);
-	    while (status != JobStatus.FINISHED) {
-		System.out.println("Job Status: " + status);
-		Thread.sleep(1000);
-		status = aengine.getJobStatus(jobId);
-		ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine
-			.getResults(jobId);
-		assertNotNull(result);
-		System.out.println("RES:" + result);
-		// Some times the job could be removed from the cluster accounting 
-		// before it has been reported to finish. Make sure 
-		// to stop waiting in such case
-		if (status == JobStatus.UNDEFINED) {
-		    break;
+	/**
+	 * This tests fails from time to time depending on the cluster load or some
+	 * other factors. Any client code has to adjust for this issue
+	 */
+	@Test(groups = {AllTestSuit.test_group_cluster,
+			AllTestSuit.test_group_runner})
+	public void testRunOnClusterAsync() {
+		assertFalse(SysPrefs.isWindows,
+				"Cluster execution can only be in unix environment");
+		try {
+			ConfiguredExecutable<Disembl> confDisembl = Configurator
+					.configureExecutable(disembl,
+							Executable.ExecProvider.Cluster);
+			AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);
+			String jobId = aengine.submitJob(confDisembl);
+			assertNotNull(jobId, "Runner is NULL");
+			// let drmaa to start
+			Thread.sleep(500);
+			JobStatus status = aengine.getJobStatus(jobId);
+			while (status != JobStatus.FINISHED) {
+				System.out.println("Job Status: " + status);
+				Thread.sleep(1000);
+				status = aengine.getJobStatus(jobId);
+				ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine
+						.getResults(jobId);
+				assertNotNull(result);
+				System.out.println("RES:" + result);
+				// Some times the job could be removed from the cluster
+				// accounting
+				// before it has been reported to finish. Make sure
+				// to stop waiting in such case
+				if (status == JobStatus.UNDEFINED) {
+					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());
 		}
-	    }
-	} 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 testRunLocally() {
-	try {
-	    ConfiguredExecutable<Disembl> confDisembl = Configurator
-		    .configureExecutable(disembl, Executable.ExecProvider.Local);
+	@Test(groups = {AllTestSuit.test_group_runner})
+	public void testRunLocally() {
+		try {
+			ConfiguredExecutable<Disembl> confDisembl = Configurator
+					.configureExecutable(disembl, Executable.ExecProvider.Local);
 
-	    // For local execution use relative
-	    LocalRunner lr = new LocalRunner(confDisembl);
-	    lr.executeJob();
-	    ConfiguredExecutable<?> al1 = lr.waitForResult();
-	    assertNotNull(al1.getResults());
-	    List<AnnotatedSequence> al2 = confDisembl.getResults();
-	    assertNotNull(al2);
-	    assertEquals(al2.size(), 3);
-	    assertEquals(al1.getResults(), al2);
-	} catch (JobSubmissionException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (ResultNotAvailableException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (JobExecutionException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
+			// For local execution use relative
+			LocalRunner lr = new LocalRunner(confDisembl);
+			lr.executeJob();
+			ConfiguredExecutable<?> al1 = lr.waitForResult();
+			assertNotNull(al1.getResults());
+			HashSet<Score> al2 = confDisembl.getResults();
+			assertNotNull(al2);
+			assertEquals(al2.size(), 3);
+			assertEquals(al1.getResults(), al2);
+		} 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(groups = { AllTestSuit.test_group_runner })
-    public void readStatistics() {
-	try {
-	    ConfiguredExecutable<Disembl> confDisembl = Configurator
-		    .configureExecutable(disembl, Executable.ExecProvider.Local);
-	    // For local execution use relavive
+	@Test(groups = {AllTestSuit.test_group_runner})
+	public void readStatistics() {
+		try {
+			ConfiguredExecutable<Disembl> confDisembl = Configurator
+					.configureExecutable(disembl, Executable.ExecProvider.Local);
+			// For local execution use relavive
 
-	    AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);
-	    String jobId = sexec.submitJob(confDisembl);
-	    FilePuller fw = FilePuller.newFilePuller(confDisembl
-		    .getWorkDirectory()
-		    + File.separator + Jronn.getStatFile(),
-		    FileWatcher.MIN_CHUNK_SIZE_BYTES);
-	    int count = 0;
-	    long position = 0;
-	    fw.waitForFile(4);
-	    JobStatus status = sexec.getJobStatus(jobId);
-	    while (status != JobStatus.FINISHED) {
-		if (fw.hasMoreData()) {
-		    ChunkHolder ch = fw.pull(position);
-		    String chunk = ch.getChunk();
-		    position = ch.getNextPosition();
+			AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);
+			String jobId = sexec.submitJob(confDisembl);
+			FilePuller fw = FilePuller.newFilePuller(
+					confDisembl.getWorkDirectory() + File.separator
+							+ Jronn.getStatFile(),
+					FileWatcher.MIN_CHUNK_SIZE_BYTES);
+			int count = 0;
+			long position = 0;
+			fw.waitForFile(4);
+			JobStatus status = sexec.getJobStatus(jobId);
+			while (status != JobStatus.FINISHED) {
+				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)) {
+					break;
+				}
+				Thread.sleep(300);
+				status = sexec.getJobStatus(jobId);
+			}
+			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());
 		}
-		count++;
-		// Make sure the loop is terminated if the job fails
-		if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
-		    break;
-		}
-		Thread.sleep(300);
-		status = sexec.getJobStatus(jobId);
-	    }
-	    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(groups = { AllTestSuit.test_group_runner })
-    public void testPersistance() {
-	try {
-	    Disembl disembl = new Disembl();
-	    disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)
-		    .setOutput("outtt.txt");
-	    assertEquals(disembl.getInput(), AllTestSuit.test_input);
-	    assertEquals(disembl.getError(), "errrr.txt");
-	    assertEquals(disembl.getOutput(), "outtt.txt");
-	    ConfiguredExecutable<Disembl> cDisembl = Configurator
-		    .configureExecutable(disembl, Executable.ExecProvider.Local);
+	@Test(groups = {AllTestSuit.test_group_runner})
+	public void testPersistance() {
+		try {
+			Disembl disembl = new Disembl();
+			disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)
+					.setOutput("outtt.txt");
+			assertEquals(disembl.getInput(), AllTestSuit.test_input);
+			assertEquals(disembl.getError(), "errrr.txt");
+			assertEquals(disembl.getOutput(), "outtt.txt");
+			ConfiguredExecutable<Disembl> cDisembl = Configurator
+					.configureExecutable(disembl, Executable.ExecProvider.Local);
 
-	    SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);
-	    sexec.executeJob();
-	    ConfiguredExecutable<?> al = sexec.waitForResult();
-	    assertNotNull(al.getResults());
-	    // Save run configuration
-	    assertTrue(cDisembl.saveRunConfiguration());
+			SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);
+			sexec.executeJob();
+			ConfiguredExecutable<?> al = sexec.waitForResult();
+			assertNotNull(al.getResults());
+			// Save run configuration
+			assertTrue(cDisembl.saveRunConfiguration());
 
-	    // See if loaded configuration is the same as saved
-	    RunConfiguration loadedRun = RunConfiguration
-		    .load(new FileInputStream(new File(cDisembl
-			    .getWorkDirectory(), RunConfiguration.rconfigFile)));
-	    assertEquals(((ConfExecutable<Disembl>) cDisembl)
-		    .getRunConfiguration(), loadedRun);
-	    // Load run configuration as ConfExecutable
-	    ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl
-		    .loadRunConfiguration(new FileInputStream(new File(cDisembl
-			    .getWorkDirectory(), RunConfiguration.rconfigFile)));
-	    assertNotNull(resurrectedCDisembl);
-	    assertEquals(resurrectedCDisembl.getExecutable().getInput(),
-		    AllTestSuit.test_input);
-	    assertEquals(resurrectedCDisembl.getExecutable().getError(),
-		    "errrr.txt");
-	    assertEquals(resurrectedCDisembl.getExecutable().getOutput(),
-		    "outtt.txt");
-	    // See in details whether executables are the same
-	    assertEquals(resurrectedCDisembl.getExecutable(), disembl);
+			// See if loaded configuration is the same as saved
+			RunConfiguration loadedRun = RunConfiguration
+					.load(new FileInputStream(new File(cDisembl
+							.getWorkDirectory(), RunConfiguration.rconfigFile)));
+			assertEquals(
+					((ConfExecutable<Disembl>) cDisembl).getRunConfiguration(),
+					loadedRun);
+			// Load run configuration as ConfExecutable
+			ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl
+					.loadRunConfiguration(new FileInputStream(new File(cDisembl
+							.getWorkDirectory(), RunConfiguration.rconfigFile)));
+			assertNotNull(resurrectedCDisembl);
+			assertEquals(resurrectedCDisembl.getExecutable().getInput(),
+					AllTestSuit.test_input);
+			assertEquals(resurrectedCDisembl.getExecutable().getError(),
+					"errrr.txt");
+			assertEquals(resurrectedCDisembl.getExecutable().getOutput(),
+					"outtt.txt");
+			// See in details whether executables are the same
+			assertEquals(resurrectedCDisembl.getExecutable(), disembl);
 
-	    ConfiguredExecutable<Disembl> resJronn = Configurator
-		    .configureExecutable(resurrectedCDisembl.getExecutable(),
-			    Executable.ExecProvider.Local);
+			ConfiguredExecutable<Disembl> resJronn = Configurator
+					.configureExecutable(resurrectedCDisembl.getExecutable(),
+							Executable.ExecProvider.Local);
 
-	    sexec = Configurator.getSyncEngine(resJronn,
-		    Executable.ExecProvider.Local);
-	    sexec.executeJob();
-	    al = sexec.waitForResult();
-	    assertNotNull(al);
+			sexec = Configurator.getSyncEngine(resJronn,
+					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());
+		} 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(groups = { AllTestSuit.test_group_runner })
-    public void testConfigurationLoading() {
-	try {
-	    RunnerConfig<Disembl> disemblConfig = ConfExecutable
-		    .getRunnerOptions(Disembl.class);
-	    assertNotNull(disemblConfig);
-	    assertTrue(disemblConfig.getArguments().size() > 0);
+	@Test(groups = {AllTestSuit.test_group_runner})
+	public void testConfigurationLoading() {
+		try {
+			RunnerConfig<Disembl> disemblConfig = ConfExecutable
+					.getRunnerOptions(Disembl.class);
+			assertNotNull(disemblConfig);
+			assertTrue(disemblConfig.getArguments().size() > 0);
 
-	    PresetManager<Disembl> disemblPresets = ConfExecutable
-		    .getRunnerPresets(Disembl.class);
-	    assertNull(disemblPresets); // there is no presets
+			PresetManager<Disembl> disemblPresets = ConfExecutable
+					.getRunnerPresets(Disembl.class);
+			assertNull(disemblPresets); // there is no presets
 
-	    LimitsManager<Disembl> disemblLimits = ConfExecutable
-		    .getRunnerLimits(Disembl.class);
-	    assertNotNull(disemblLimits);
-	    assertTrue(disemblLimits.getLimits().size() > 0);
-	    disemblLimits.validate(disemblPresets);
+			LimitsManager<Disembl> disemblLimits = ConfExecutable
+					.getRunnerLimits(Disembl.class);
+			assertNotNull(disemblLimits);
+			assertTrue(disemblLimits.getLimits().size() > 0);
+			disemblLimits.validate(disemblPresets);
 
-	} catch (FileNotFoundException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (IOException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (ValidationException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ValidationException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
 	}
-    }
 
 }