1 /* Copyright (c) 2009 Peter Troshin
\r
3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
\r
5 * This library is free software; you can redistribute it and/or modify it under the terms of the
\r
6 * Apache License version 2 as published by the Apache Software Foundation
\r
8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
\r
9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
\r
10 * License for more details.
\r
12 * A copy of the license is in apache_license.txt. It is also available here:
\r
13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
\r
15 * Any republication or derived work distributed in source code form
\r
16 * must include this copyright and license notice.
\r
18 package compbio.runner._impl;
\r
20 import static org.testng.AssertJUnit.assertEquals;
\r
21 import static org.testng.AssertJUnit.assertFalse;
\r
22 import static org.testng.AssertJUnit.assertNotNull;
\r
23 import static org.testng.AssertJUnit.assertTrue;
\r
24 import static org.testng.AssertJUnit.fail;
\r
26 import java.text.ParseException;
\r
28 import org.ggf.drmaa.DrmaaException;
\r
29 import org.ggf.drmaa.JobInfo;
\r
30 import org.testng.annotations.Test;
\r
32 import compbio.engine.cluster.drmaa.ClusterUtil;
\r
33 import compbio.engine.cluster.drmaa.JobRunner;
\r
34 import compbio.engine.cluster.drmaa.StatisticManager;
\r
35 import compbio.metadata.AllTestSuit;
\r
36 import compbio.metadata.JobExecutionException;
\r
37 import compbio.metadata.JobStatus;
\r
38 import compbio.metadata.JobSubmissionException;
\r
40 public class DisEMBLTester {
\r
42 public static String test_input = "/homes/pvtroshin/TO1381.fasta";
\r
43 public static String test_outfile = "/homes/pvtroshin/TO1381.disEMBL.out";
\r
45 @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,
\r
46 AllTestSuit.test_group_runner })
\r
47 public void testBuildCommand() {
\r
48 Disembl disembl = new Disembl(AllTestSuit.OUTPUT_DIR_ABSOLUTE);
\r
50 // disembl.setInput(test_input).setOutput(test_outfile);
\r
54 JobRunner runner = JobRunner.getInstance(null);
\r
56 assertNotNull("Runner is NULL", runner);
\r
57 runner.executeJob();
\r
58 // assertNotNull("JobId is null", jobId1);
\r
59 JobStatus status = runner.getJobStatus();
\r
60 assertTrue("Status of the process is wrong!",
\r
61 status == JobStatus.PENDING || status == JobStatus.RUNNING);
\r
62 JobInfo info = runner.getJobInfo();
\r
63 assertNotNull("JobInfo is null", info);
\r
64 StatisticManager sm = new StatisticManager(info);
\r
65 assertNotNull("Statictic manager is null", sm);
\r
68 String exits = sm.getExitStatus();
\r
69 assertNotNull("Exit status is null", exits);
\r
70 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
\r
72 assertEquals("Exit status is not 0", 0, exitsInt);
\r
73 System.out.println(sm.getAllStats());
\r
75 } catch (ParseException e) {
\r
76 e.printStackTrace();
\r
77 fail("Parse Exception: " + e.getMessage());
\r
80 assertTrue("Process exited:", sm.hasExited());
\r
81 assertFalse("Process aborted:", sm.wasAborted());
\r
82 assertFalse("Process hasdump:", sm.hasDump());
\r
83 assertFalse("Process signaled:", sm.hasSignaled());
\r
85 } catch (JobSubmissionException e) {
\r
86 e.printStackTrace();
\r
87 fail("DrmaaException caught:" + e.getMessage());
\r
88 } catch (DrmaaException e) {
\r
89 e.printStackTrace();
\r
90 fail("DrmaaException caught:" + e.getMessage());
\r
91 } catch (JobExecutionException e) {
\r
92 e.printStackTrace();
\r
93 fail("DrmaaException caught:" + e.getMessage());
\r