testsrc/compbio/runner/_impl/DisEMBLTester.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 public class DisEMBLTester {\r
  41 \r
  42         public static String test_input = "/homes/pvtroshin/TO1381.fasta";\r
  43         public static String test_outfile = "/homes/pvtroshin/TO1381.disEMBL.out";\r
  44 \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
  49                 // TODO\r
  50                 // disembl.setInput(test_input).setOutput(test_outfile);\r
  51 \r
  52                 try {\r
  53 \r
  54                         JobRunner runner = JobRunner.getInstance(null);\r
  55 \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
  66                         try {\r
  67 \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
  71                                                 .intValue();\r
  72                                 assertEquals("Exit status is not 0", 0, exitsInt);\r
  73                                 System.out.println(sm.getAllStats());\r
  74 \r
  75                         } catch (ParseException e) {\r
  76                                 e.printStackTrace();\r
  77                                 fail("Parse Exception: " + e.getMessage());\r
  78                         }\r
  79 \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
  84 \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
  94                 }\r
  95         }\r
  96 }\r