testsrc/compbio/runner/_impl/NetNglycTester.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.assertFalse;\r
  21 import static org.testng.AssertJUnit.assertNotNull;\r
  22 import static org.testng.AssertJUnit.assertTrue;\r
  23 import static org.testng.AssertJUnit.fail;\r
  24 \r
  25 import java.text.ParseException;\r
  26 \r
  27 import org.ggf.drmaa.DrmaaException;\r
  28 import org.ggf.drmaa.JobInfo;\r
  29 import org.testng.annotations.Test;\r
  30 \r
  31 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  32 import compbio.engine.cluster.drmaa.JobRunner;\r
  33 import compbio.engine.cluster.drmaa.StatisticManager;\r
  34 import compbio.metadata.AllTestSuit;\r
  35 import compbio.metadata.JobExecutionException;\r
  36 import compbio.metadata.JobStatus;\r
  37 import compbio.metadata.JobSubmissionException;\r
  38 \r
  39 public class NetNglycTester {\r
  40 \r
  41         public static String test_input = "/homes/pvtroshin/TO1381.fasta";\r
  42         public static String test_outfile = "/homes/pvtroshin/TO1381.netNGlycout";\r
  43 \r
  44         @Test()\r
  45         public void testGetTestCommand() {\r
  46                 assertNotNull(Tmhmm2.getTestCommand());\r
  47         }\r
  48 \r
  49         @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,\r
  50                         AllTestSuit.test_group_runner })\r
  51         public void testBuildCommand() {\r
  52                 NetNglyc netnGlyc = new NetNglyc();\r
  53                 // TODO netnGlyc.setInput(test_input).setOutput(test_outfile);\r
  54 \r
  55                 try {\r
  56                         JobRunner runner = JobRunner.getInstance(null);\r
  57                         assertNotNull("Runner is NULL", runner);\r
  58                         runner.executeJob();\r
  59                         assertNotNull("JobId is NULL");\r
  60                         JobStatus status = runner.getJobStatus();\r
  61                         assertTrue("Status of the job is wrong!",\r
  62                                         status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
  63                         JobInfo info = runner.getJobInfo();\r
  64                         assertNotNull("Cannot Obtain Job Info", info);\r
  65                         StatisticManager sm = new StatisticManager(info);\r
  66                         assertNotNull("StatisticManager is NULL", sm);\r
  67 \r
  68                         String exits = sm.getExitStatus();\r
  69                         assertNotNull("Status is NULL", exits);\r
  70                         int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
  71                                         .intValue();\r
  72                         assertTrue("Time elapsed is greater than 0", exitsInt >= 0);\r
  73                         System.out.println(sm.getAllStats());\r
  74 \r
  75                         assertTrue("Process exited:", sm.hasExited());\r
  76                         assertFalse("Process aborted:", sm.wasAborted());\r
  77                         assertFalse("Process hasdump:", sm.hasDump());\r
  78                         assertFalse("Process signaled:", sm.hasSignaled());\r
  79 \r
  80                 } catch (DrmaaException e) {\r
  81                         e.printStackTrace();\r
  82                         fail(e.getLocalizedMessage());\r
  83                 } catch (ParseException e) {\r
  84                         e.printStackTrace();\r
  85                         fail(e.getLocalizedMessage());\r
  86                 } catch (JobSubmissionException e) {\r
  87                         e.printStackTrace();\r
  88                         fail(e.getLocalizedMessage());\r
  89                 } catch (JobExecutionException e) {\r
  90                         e.printStackTrace();\r
  91                         fail(e.getLocalizedMessage());\r
  92                 }\r
  93         }\r
  94 }\r