X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=blobdiff_plain;f=testsrc%2Fcompbio%2Frunner%2F_impl%2FTmhmm2Tester.java;fp=testsrc%2Fcompbio%2Frunner%2F_impl%2FTmhmm2Tester.java;h=0000000000000000000000000000000000000000;hp=fe920482bfbe9026cca637ce90b7e1767d4a3637;hb=a6f4c70ca7af2302c60217480a534a9ac2320acb;hpb=bea86782341eb4d30559dea2857dace7f9f3a313

diff --git a/testsrc/compbio/runner/_impl/Tmhmm2Tester.java b/testsrc/compbio/runner/_impl/Tmhmm2Tester.java
deleted file mode 100644
index fe92048..0000000
--- a/testsrc/compbio/runner/_impl/Tmhmm2Tester.java
+++ /dev/null
@@ -1,100 +0,0 @@
-/* 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());
-		}
-	}
-
-}