testsrc/compbio/runner/_impl/RPSBlastTester.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 RPSBlastTester {\r
  40 \r
  41         public static String test_input = "/homes/pvtroshin/TO1381.fasta";\r
  42         public static String test_outfile = "/homes/pvtroshin/TO1381.rpsblastpout";\r
  43 \r
  44         @Test()\r
  45         public void testGetTestCommand() {\r
  46                 System.out.println(RPSBlast.getTestCommand());\r
  47         }\r
  48 \r
  49         @Test()\r
  50         public void testGetTestArgsCommand() {\r
  51                 System.out.println(RPSBlast.getTestArgs());\r
  52         }\r
  53 \r
  54         @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,\r
  55                         AllTestSuit.test_group_runner })\r
  56         public void testBuildCommand() {\r
  57                 RPSBlast rpsblast = new RPSBlast(AllTestSuit.OUTPUT_DIR_ABSOLUTE);\r
  58                 // TODO rpsblast.setInput(test_input).setOutput(test_outfile);\r
  59                 // rpsblast.setParameters(RPSBlast.getTestArgs());\r
  60 \r
  61                 try {\r
  62                         JobRunner runner = JobRunner.getInstance(null);\r
  63                         assertNotNull("Runner is NULL", runner);\r
  64                         runner.executeJob();\r
  65                         // assertNotNull(jobId1);\r
  66 \r
  67                         JobStatus status = runner.getJobStatus();\r
  68                         assertTrue(status == JobStatus.PENDING\r
  69                                         || status == JobStatus.RUNNING);\r
  70                         JobInfo info = runner.getJobInfo();\r
  71                         assertNotNull(info);\r
  72                         StatisticManager sm = new StatisticManager(info);\r
  73                         assertNotNull(sm);\r
  74                         try {\r
  75                                 String time_s = sm.getCalculationTime();\r
  76                                 assertNotNull(time_s);\r
  77                                 float time = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(time_s)\r
  78                                                 .floatValue();\r
  79                                 assertTrue(time > 0);\r
  80                                 String exits = sm.getExitStatus();\r
  81                                 assertNotNull(exits);\r
  82                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
  83                                                 .intValue();\r
  84                                 // assertEquals(0, exitsInt);\r
  85                                 System.out.println(sm.getAllStats());\r
  86 \r
  87                         } catch (ParseException e) {\r
  88                                 e.printStackTrace();\r
  89                                 fail("Parse Exception: " + e.getLocalizedMessage());\r
  90                         }\r
  91 \r
  92                         assertTrue(sm.hasExited());\r
  93                         assertFalse(sm.wasAborted());\r
  94                         assertFalse(sm.hasDump());\r
  95                         assertFalse(sm.hasSignaled());\r
  96 \r
  97                 } catch (DrmaaException e) {\r
  98                         e.printStackTrace();\r
  99                         fail(e.getLocalizedMessage());\r
 100                 } catch (JobSubmissionException e) {\r
 101                         e.printStackTrace();\r
 102                         fail(e.getLocalizedMessage());\r
 103                 } catch (JobExecutionException e) {\r
 104                         e.printStackTrace();\r
 105                         fail(e.getLocalizedMessage());\r
 106                 }\r
 107         }\r
 108 \r
 109 }\r