testsrc/compbio/engine/cluster/drmaa/DrmaaAsyncClusterEngineTester.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.assertNull;\r
  25 import static org.testng.AssertJUnit.assertTrue;\r
  26 import static org.testng.AssertJUnit.fail;\r
  27 \r
  28 import org.testng.annotations.Test;\r
  29 \r
  30 import compbio.engine.AsyncExecutor;\r
  31 import compbio.engine.Configurator;\r
  32 import compbio.engine.client.ConfiguredExecutable;\r
  33 import compbio.engine.client.Executable;\r
  34 import compbio.metadata.AllTestSuit;\r
  35 import compbio.metadata.JobStatus;\r
  36 import compbio.metadata.JobSubmissionException;\r
  37 import compbio.metadata.ResultNotAvailableException;\r
  38 import compbio.runner.msa.ClustalW;\r
  39 import compbio.util.SysPrefs;\r
  40 \r
  41 public class DrmaaAsyncClusterEngineTester {\r
  42 \r
  43         public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  44                         + "TO1381.fasta";\r
  45         public static String large_test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  46                         + "1000x3000Dna.fasta";\r
  47         public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
  48 \r
  49         /**\r
  50          * This test uses ClustalW executable as runnable to testing, thus depends\r
  51          * on its correct functioning\r
  52          */\r
  53         @Test(groups = { AllTestSuit.test_group_cluster,\r
  54                         AllTestSuit.test_group_engine })\r
  55         public void testSubmit() {\r
  56                 ClustalW clustal = new ClustalW();\r
  57                 assertFalse("Cluster execution can only be in unix environment",\r
  58                                 SysPrefs.isWindows);\r
  59                 clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
  60                 try {\r
  61                         ConfiguredExecutable<ClustalW> confClustal = Configurator\r
  62                                         .configureExecutable(clustal);\r
  63                         AsyncExecutor runner = new AsyncClusterRunner();\r
  64                         assertNotNull("Runner is NULL", runner);\r
  65                         String jobId = runner.submitJob(confClustal);\r
  66                         assertEquals("Input was not set!", test_input, clustal.getInput());\r
  67                         assertNotNull("JobId is null", jobId);\r
  68                         JobStatus status = runner.getJobStatus(jobId);\r
  69                         assertTrue("Status of the process is wrong!",\r
  70                                         status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
  71                         JobStatus info = runner.getJobStatus(jobId);\r
  72                         assertNotNull("JobInfo is null", info);\r
  73                         Executable<?> result = runner.getResults(jobId);\r
  74 \r
  75                 } catch (JobSubmissionException e) {\r
  76                         e.printStackTrace();\r
  77                         fail(e.getMessage());\r
  78                 } catch (ResultNotAvailableException e) {\r
  79                         e.printStackTrace();\r
  80                         fail(e.getMessage());\r
  81                 }\r
  82         }\r
  83 \r
  84         @Test(expectedExceptions = ResultNotAvailableException.class, groups = {\r
  85                         AllTestSuit.test_group_cluster, AllTestSuit.test_group_engine })\r
  86         // expectedExceptions = ResultNotAvailableException.class,\r
  87         public void testCancel() throws ResultNotAvailableException {\r
  88                 ClustalW clustal = new ClustalW();\r
  89                 assertFalse("Cluster execution can only be in unix environment",\r
  90                                 SysPrefs.isWindows);\r
  91                 clustal.setInput(large_test_input).setOutput(cluster_test_outfile);\r
  92 \r
  93                 try {\r
  94                         ConfiguredExecutable<ClustalW> confClustal = Configurator\r
  95                                         .configureExecutable(clustal);\r
  96                         AsyncClusterRunner runner = new AsyncClusterRunner();\r
  97                         String jobId = runner.submitJob(confClustal);\r
  98                         assertNotNull("Runner is NULL", runner);\r
  99                         // assertNotNull("JobId is null", jobId1);\r
 100                         Thread.sleep(200);\r
 101                         JobStatus status = runner.getJobStatus(jobId);\r
 102                         assertTrue("Status of the process is wrong!",\r
 103                                         status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
 104                         assertFalse("Status of the process is wrong!",\r
 105                                         status == JobStatus.FINISHED);\r
 106                         runner.cancelJob(jobId);\r
 107                         // This is never NULL as long as the job has started!\r
 108                         ConfiguredExecutable<?> exec = runner.getResults(jobId);\r
 109                         assertNull(exec.getResults());\r
 110                 } catch (JobSubmissionException e) {\r
 111                         e.printStackTrace();\r
 112                         fail("DrmaaException caught:" + e.getMessage());\r
 113                 } catch (InterruptedException e) {\r
 114                         e.printStackTrace();\r
 115                         fail("Interupted exception caught:" + e.getMessage());\r
 116                 }\r
 117         }\r
 118 \r
 119         @Test(groups = { AllTestSuit.test_group_cluster,\r
 120                         AllTestSuit.test_group_engine })\r
 121         public void testGetJobStatus() {\r
 122                 ClustalW clustal = new ClustalW();\r
 123                 assertFalse("Cluster execution can only be in unix environment",\r
 124                                 SysPrefs.isWindows);\r
 125                 clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
 126 \r
 127                 try {\r
 128                         AsyncClusterRunner runner = new AsyncClusterRunner();\r
 129                         ConfiguredExecutable<ClustalW> confClustal = Configurator\r
 130                                         .configureExecutable(clustal);\r
 131                         String jobId = runner.submitJob(confClustal);\r
 132                         assertNotNull("Runner is NULL", runner);\r
 133                         AsyncClusterRunner runner2 = new AsyncClusterRunner();\r
 134 \r
 135                         boolean hasRun = false;\r
 136                         boolean hasPended = false;\r
 137                         Thread.sleep(500); \r
 138                         JobStatus status = runner2.getJobStatus(jobId);\r
 139                         while (status != JobStatus.FINISHED) {\r
 140                                 if (status == JobStatus.CANCELLED) {\r
 141                                         fail("Job is not cancelled!");\r
 142                                 }\r
 143                                 if (status == JobStatus.FAILED) {\r
 144                                         fail("Job should not fail!");\r
 145                                 }\r
 146                                 if (status == JobStatus.RUNNING) {\r
 147                                         hasRun = true;\r
 148                                 }\r
 149                                 if (status == JobStatus.PENDING) {\r
 150                                         hasPended = true;\r
 151                                 }\r
 152                                 if (status == JobStatus.UNDEFINED) {\r
 153                                         System.out.println("Wrong status (UNDEFINED) reported by cluster engine!");\r
 154                                         break;\r
 155                                 }\r
 156                                 status = runner2.getJobStatus(jobId);\r
 157                         }\r
 158                         assertTrue(hasRun);\r
 159                         assertTrue(hasPended);\r
 160                         assertTrue(hasRun);\r
 161                         // Bear in mind that if the task were not put in the queue\r
 162                         // immediately\r
 163                         // the status could be UNDEFINED!\r
 164                         // assertFalse(hasUndefined);\r
 165                         AsyncClusterRunner runner3 = new AsyncClusterRunner();\r
 166                         Executable<?> exec = runner3.getResults(jobId);\r
 167                         assertNotNull(exec);\r
 168                         // Now try collecting result for the second time\r
 169                         exec=null;\r
 170                         Thread.sleep(1000);\r
 171                         exec = runner3.getResults(jobId);\r
 172                         assertNotNull(exec);\r
 173                 } catch (JobSubmissionException e) {\r
 174                         e.printStackTrace();\r
 175                         fail("DrmaaException caught:" + e.getMessage());\r
 176                 } catch (ResultNotAvailableException e) {\r
 177                         e.printStackTrace();\r
 178                         fail(e.getMessage());\r
 179                 } catch (InterruptedException e) {\r
 180                         e.printStackTrace();\r
 181                         fail(e.getMessage());\r
 182                 }\r
 183         }\r
 184 }\r