testsrc/compbio/runner/_impl/OBTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \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
   7  * \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
  11  * \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
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.runner._impl;\r
  19 \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
  25 \r
  26 import java.text.ParseException;\r
  27 \r
  28 import org.ggf.drmaa.DrmaaException;\r
  29 import org.ggf.drmaa.JobInfo;\r
  30 import org.testng.annotations.Test;\r
  31 \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
  39 \r
  40 /**\r
  41  * TODO this needs fixing! Executable does not work\r
  42  * \r
  43  * @author pvtroshin\r
  44  * \r
  45  */\r
  46 public class OBTester {\r
  47 \r
  48         public static String test_input = "/homes/pvtroshin/TO1381.fasta";\r
  49         public static String test_outfile = "/homes/pvtroshin/TO1381.OB.out";\r
  50 \r
  51         @Test\r
  52         public void testGetTestCommand() {\r
  53                 System.out.println(OB.getTestCommand());\r
  54         }\r
  55 \r
  56         @Test\r
  57         public void testGetTestArgsCommand() {\r
  58                 System.out.println(new OB().getTestArgs());\r
  59         }\r
  60 \r
  61         @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,\r
  62                         AllTestSuit.test_group_runner })\r
  63         public void testBuildCommand() {\r
  64                 OB ob = new OB(AllTestSuit.OUTPUT_DIR_ABSOLUTE);\r
  65                 // TODO ob.setInput(test_input).setOutput(test_outfile);\r
  66                 // ob.setParameters(ob.getTestArgs());\r
  67 \r
  68                 try {\r
  69                         JobRunner runner = JobRunner.getInstance(null);\r
  70                         assertNotNull("Runner is NULL", runner);\r
  71                         runner.executeJob();\r
  72                         // assertNotNull("Job id is null", jobId1);\r
  73                         JobStatus status = runner.getJobStatus();\r
  74                         assertTrue("Status is not queing but " + status,\r
  75                                         status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
  76                         JobInfo info = runner.getJobInfo();\r
  77                         assertNotNull("JobInfo is null", info);\r
  78                         StatisticManager sm = new StatisticManager(info);\r
  79                         assertNotNull("Stat manager is null", sm);\r
  80                         try {\r
  81                                 String time_s = sm.getCalculationTime();\r
  82                                 assertNotNull("Time is null", time_s);\r
  83                                 float time = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(time_s)\r
  84                                                 .floatValue();\r
  85                                 String exits = sm.getExitStatus();\r
  86                                 assertNotNull("Exit status is null", exits);\r
  87                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
  88                                                 .intValue();\r
  89                                 assertEquals("Exit status is not 0", 0, exitsInt);\r
  90                                 System.out.println(sm.getAllStats());\r
  91 \r
  92                         } catch (ParseException e) {\r
  93                                 e.printStackTrace();\r
  94                                 fail("Parse Exception: " + e.getLocalizedMessage());\r
  95                         }\r
  96 \r
  97                         assertTrue("Process exited:", sm.hasExited());\r
  98                         assertFalse("Process aborted:", sm.wasAborted());\r
  99                         assertFalse("Process hasdump:", sm.hasDump());\r
 100                         assertFalse("Process signaled:", sm.hasSignaled());\r
 101 \r
 102                 } catch (DrmaaException e) {\r
 103                         e.printStackTrace();\r
 104                         fail("Drmaa exception: " + e.getLocalizedMessage());\r
 105                 } catch (JobSubmissionException e) {\r
 106                         e.printStackTrace();\r
 107                         fail("JobSubmission failure: " + e.getLocalizedMessage());\r
 108                 } catch (JobExecutionException e) {\r
 109                         e.printStackTrace();\r
 110                         fail("JobSubmission failure: " + e.getLocalizedMessage());\r
 111                 }\r
 112         }\r
 113 }\r