testsrc/compbio/engine/cluster/drmaa/DrmaaClusterEngineTester.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 \r
  19 package compbio.engine.cluster.drmaa;\r
  20 \r
  21 import static org.testng.AssertJUnit.assertEquals;\r
  22 import static org.testng.AssertJUnit.assertFalse;\r
  23 import static org.testng.AssertJUnit.assertNotNull;\r
  24 import static org.testng.AssertJUnit.assertTrue;\r
  25 import static org.testng.AssertJUnit.fail;\r
  26 \r
  27 import java.text.ParseException;\r
  28 \r
  29 import org.ggf.drmaa.DrmaaException;\r
  30 import org.ggf.drmaa.JobInfo;\r
  31 import org.testng.annotations.Test;\r
  32 \r
  33 import compbio.data.sequence.Alignment;\r
  34 import compbio.engine.Configurator;\r
  35 import compbio.engine.client.ConfiguredExecutable;\r
  36 import compbio.engine.client.Executable;\r
  37 import compbio.engine.client.EngineUtil;\r
  38 import compbio.metadata.AllTestSuit;\r
  39 import compbio.metadata.JobExecutionException;\r
  40 import compbio.metadata.JobStatus;\r
  41 import compbio.metadata.JobSubmissionException;\r
  42 import compbio.metadata.ResultNotAvailableException;\r
  43 import compbio.runner.msa.ClustalW;\r
  44 import compbio.util.SysPrefs;\r
  45 \r
  46 public class DrmaaClusterEngineTester {\r
  47 \r
  48         public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  49                         + "TO1381.fasta";\r
  50         public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
  51 \r
  52         /**\r
  53          * This test uses ClustalW executable as runnable to testing, thus depends\r
  54          * on its correct functioning\r
  55          */\r
  56         @Test(groups = { AllTestSuit.test_group_cluster,\r
  57                         AllTestSuit.test_group_engine })\r
  58         public void testSubmit() {\r
  59                 ClustalW clustal = new ClustalW();\r
  60                 assertFalse("Cluster execution can only be in unix environment",\r
  61                                 SysPrefs.isWindows);\r
  62                 clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
  63 \r
  64                 try {\r
  65                         ConfiguredExecutable<ClustalW> confClust = Configurator\r
  66                                         .configureExecutable(clustal,\r
  67                                                         Executable.ExecProvider.Cluster);\r
  68                         assertNotNull(confClust.getWorkDirectory());\r
  69 \r
  70                         JobRunner runner = JobRunner.getInstance(confClust);\r
  71                         assertEquals("Input was not set!", test_input, clustal.getInput());\r
  72                         assertNotNull("Runner is NULL", runner);\r
  73                         runner.executeJob();\r
  74                         // assertNotNull("JobId is null", jobId1);\r
  75                         JobStatus status = runner.getJobStatus();\r
  76                         assertTrue("Status of the process is wrong!",\r
  77                                         status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
  78                         JobInfo info = runner.getJobInfo();\r
  79 \r
  80                         assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
  81                                         JobStatus.CANCELLED));\r
  82                         assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
  83                                         JobStatus.STARTED));\r
  84                         assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
  85                                         JobStatus.COLLECTED));\r
  86                         assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
  87                                         JobStatus.FINISHED));\r
  88                         assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
  89                                         JobStatus.SUBMITTED));\r
  90 \r
  91                         ConfiguredExecutable<?> confExec = runner.waitForResult();\r
  92                         // At this point results are marked as collected\r
  93                         assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
  94                                         JobStatus.COLLECTED));\r
  95 \r
  96                         assertNotNull("JobInfo is null", info);\r
  97                         StatisticManager sm = new StatisticManager(info);\r
  98                         assertNotNull("Statistics manager is null", sm);\r
  99 \r
 100                         try {\r
 101 \r
 102                                 String exits = sm.getExitStatus();\r
 103                                 assertNotNull("Exit status is null", exits);\r
 104                                 // cut 4 trailing zeros from the number\r
 105                                 int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 106                                                 .intValue();\r
 107                                 assertEquals("Exit status is not 0", 0, exitsInt);\r
 108                                 System.out.println(sm.getAllStats());\r
 109 \r
 110                         } catch (ParseException e) {\r
 111                                 e.printStackTrace();\r
 112                                 fail("Parse Exception: " + e.getMessage());\r
 113                         }\r
 114                         assertTrue("Process exited:", sm.hasExited());\r
 115                         assertFalse("Process aborted:", sm.wasAborted());\r
 116                         assertFalse("Process hasdump:", sm.hasDump());\r
 117                         assertFalse("Process signaled:", sm.hasSignaled());\r
 118 \r
 119                         Alignment al = confExec.getResults();\r
 120                         assertNotNull(al);\r
 121                         assertFalse("Could not remove some files whilst cleaning up ",\r
 122                                         runner.cleanup());\r
 123 \r
 124                 } catch (JobSubmissionException e) {\r
 125                         e.printStackTrace();\r
 126                         fail("DrmaaException caught:" + e.getMessage());\r
 127                 } catch (JobExecutionException e) {\r
 128                         e.printStackTrace();\r
 129                         fail("DrmaaException caught:" + e.getMessage());\r
 130                 } catch (DrmaaException e) {\r
 131                         e.printStackTrace();\r
 132                         fail("DrmaaException caught:" + e.getMessage());\r
 133                 } catch (ResultNotAvailableException e) {\r
 134                         fail("DrmaaException caught:" + e.getMessage());\r
 135                 }\r
 136         }\r
 137 \r
 138         @Test(groups = { AllTestSuit.test_group_cluster,\r
 139                         AllTestSuit.test_group_engine })\r
 140         public void testCancel() {\r
 141                 ClustalW clustal = new ClustalW();\r
 142                 assertFalse("Cluster execution can only be in unix environment",\r
 143                                 SysPrefs.isWindows);\r
 144                 clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
 145 \r
 146                 try {\r
 147 \r
 148                         ConfiguredExecutable<ClustalW> confClust = Configurator\r
 149                                         .configureExecutable(clustal,\r
 150                                                         Executable.ExecProvider.Cluster);\r
 151                         assertNotNull(confClust.getWorkDirectory());\r
 152 \r
 153                         JobRunner runner = JobRunner.getInstance(confClust);\r
 154                         assertNotNull("Runner is NULL", runner);\r
 155 \r
 156                         runner.executeJob();\r
 157                         // assertNotNull("JobId is null", jobId1);\r
 158                         Thread.sleep(500);\r
 159                         JobStatus status = runner.getJobStatus();\r
 160                         assertTrue("Status of the process is wrong!",\r
 161                                         status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
 162                         runner.cancelJob();\r
 163                         Thread.sleep(200); // give fs time to write a file\r
 164                         JobInfo info = runner.getJobInfo();\r
 165                         assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
 166                                         JobStatus.CANCELLED));\r
 167                         assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
 168                                         JobStatus.STARTED));\r
 169                         assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
 170                                         JobStatus.COLLECTED));\r
 171                         assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
 172                                         JobStatus.FINISHED));\r
 173                         assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
 174                                         JobStatus.SUBMITTED));\r
 175 \r
 176                 } catch (JobSubmissionException e) {\r
 177                         e.printStackTrace();\r
 178                         fail("DrmaaException caught:" + e.getMessage());\r
 179                 } catch (JobExecutionException e) {\r
 180                         e.printStackTrace();\r
 181                         fail("DrmaaException caught:" + e.getMessage());\r
 182                 } catch (InterruptedException e) {\r
 183                         e.printStackTrace();\r
 184                         fail("Interupted exception caught:" + e.getMessage());\r
 185                 }\r
 186         }\r
 187 \r
 188 }\r