testsrc/compbio/runner/disorder/JronnTester.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.runner.disorder;\r
  20 \r
  21 import static org.testng.Assert.assertEquals;\r
  22 import static org.testng.Assert.assertFalse;\r
  23 import static org.testng.Assert.assertNotNull;\r
  24 import static org.testng.Assert.assertTrue;\r
  25 import static org.testng.Assert.fail;\r
  26 \r
  27 import java.io.File;\r
  28 import java.io.FileInputStream;\r
  29 import java.io.FileNotFoundException;\r
  30 import java.io.IOException;\r
  31 import java.text.ParseException;\r
  32 import java.util.List;\r
  33 \r
  34 import javax.xml.bind.ValidationException;\r
  35 \r
  36 import org.ggf.drmaa.DrmaaException;\r
  37 import org.ggf.drmaa.JobInfo;\r
  38 import org.testng.annotations.BeforeMethod;\r
  39 import org.testng.annotations.Test;\r
  40 \r
  41 import compbio.data.sequence.AnnotatedSequence;\r
  42 import compbio.engine.AsyncExecutor;\r
  43 import compbio.engine.Configurator;\r
  44 import compbio.engine.FilePuller;\r
  45 import compbio.engine.SyncExecutor;\r
  46 import compbio.engine.client.ConfExecutable;\r
  47 import compbio.engine.client.ConfiguredExecutable;\r
  48 import compbio.engine.client.Executable;\r
  49 import compbio.engine.client.RunConfiguration;\r
  50 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  51 import compbio.engine.cluster.drmaa.JobRunner;\r
  52 import compbio.engine.cluster.drmaa.StatisticManager;\r
  53 import compbio.engine.local.LocalRunner;\r
  54 import compbio.metadata.AllTestSuit;\r
  55 import compbio.metadata.ChunkHolder;\r
  56 import compbio.metadata.JobExecutionException;\r
  57 import compbio.metadata.JobStatus;\r
  58 import compbio.metadata.JobSubmissionException;\r
  59 import compbio.metadata.LimitsManager;\r
  60 import compbio.metadata.PresetManager;\r
  61 import compbio.metadata.ResultNotAvailableException;\r
  62 import compbio.metadata.RunnerConfig;\r
  63 import compbio.util.FileWatcher;\r
  64 import compbio.util.SysPrefs;\r
  65 \r
  66 public class JronnTester {\r
  67 \r
  68     public static String test_outfile = "TO1381.jronn.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
  69 \r
  70     private Jronn jronn;\r
  71 \r
  72     @BeforeMethod(alwaysRun = true)\r
  73     void init() {\r
  74         jronn = new Jronn();\r
  75         jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
  76     }\r
  77 \r
  78     @Test(groups = { AllTestSuit.test_group_cluster,\r
  79             AllTestSuit.test_group_runner })\r
  80     public void testRunOnCluster() {\r
  81         assertFalse(SysPrefs.isWindows,\r
  82                 "Cluster execution can only be in unix environment");\r
  83         try {\r
  84             ConfiguredExecutable<Jronn> confJronn = Configurator\r
  85                     .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
  86             JobRunner runner = JobRunner.getInstance(confJronn);\r
  87 \r
  88             assertNotNull(runner, "Runner is NULL");\r
  89             runner.executeJob();\r
  90             // assertNotNull("JobId is null", jobId1);\r
  91             JobStatus status = runner.getJobStatus();\r
  92             assertTrue(status == JobStatus.PENDING\r
  93                     || status == JobStatus.RUNNING,\r
  94                     "Status of the process is wrong!");\r
  95             JobInfo info = runner.getJobInfo();\r
  96             assertNotNull(info, "JobInfo is null");\r
  97             StatisticManager sm = new StatisticManager(info);\r
  98             assertNotNull(sm, "Statictic manager is null");\r
  99             try {\r
 100 \r
 101                 String exits = sm.getExitStatus();\r
 102                 assertNotNull("Exit status is null", exits);\r
 103                 // cut 4 trailing zeros from the number\r
 104                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 105                         .intValue();\r
 106                 assertEquals(0, exitsInt);\r
 107                 System.out.println(sm.getAllStats());\r
 108 \r
 109             } catch (ParseException e) {\r
 110                 e.printStackTrace();\r
 111                 fail("Parse Exception: " + e.getMessage());\r
 112             }\r
 113             assertFalse(runner.cleanup());\r
 114             assertTrue(sm.hasExited());\r
 115             assertFalse(sm.wasAborted());\r
 116             assertFalse(sm.hasDump());\r
 117             assertFalse(sm.hasSignaled());\r
 118 \r
 119         } catch (JobSubmissionException e) {\r
 120             e.printStackTrace();\r
 121             fail("DrmaaException caught:" + e.getMessage());\r
 122         } catch (JobExecutionException e) {\r
 123             e.printStackTrace();\r
 124             fail("DrmaaException caught:" + e.getMessage());\r
 125         } catch (DrmaaException e) {\r
 126             e.printStackTrace();\r
 127             fail("DrmaaException caught:" + e.getMessage());\r
 128         }\r
 129     }\r
 130 \r
 131     /**\r
 132      * This tests fails from time to time depending on the cluster load or some\r
 133      * other factors. Any client code has to adjust for this issue\r
 134      */\r
 135     @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,\r
 136             AllTestSuit.test_group_runner })\r
 137     public void testRunOnClusterAsync() {\r
 138         assertFalse(SysPrefs.isWindows,\r
 139                 "Cluster execution can only be in unix environment");\r
 140         try {\r
 141             ConfiguredExecutable<Jronn> confJronn = Configurator\r
 142                     .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
 143             AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);\r
 144             String jobId = aengine.submitJob(confJronn);\r
 145             assertNotNull(jobId, "Runner is NULL");\r
 146             // let drmaa to start\r
 147             Thread.sleep(500);\r
 148             JobStatus status = aengine.getJobStatus(jobId);\r
 149             while (status != JobStatus.FINISHED\r
 150                     || status != JobStatus.UNDEFINED) {\r
 151                 System.out.println("Job Status: " + status);\r
 152                 Thread.sleep(1000);\r
 153                 status = aengine.getJobStatus(jobId);\r
 154             }\r
 155         } catch (JobSubmissionException e) {\r
 156             e.printStackTrace();\r
 157             fail("DrmaaException caught:" + e.getMessage());\r
 158         } catch (InterruptedException e) {\r
 159             e.printStackTrace();\r
 160             fail(e.getMessage());\r
 161         }\r
 162     }\r
 163 \r
 164     @Test(groups = { AllTestSuit.test_group_runner })\r
 165     public void testRunLocally() {\r
 166         try {\r
 167             ConfiguredExecutable<Jronn> confJronn = Configurator\r
 168                     .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 169 \r
 170             // For local execution use relative\r
 171             LocalRunner lr = new LocalRunner(confJronn);\r
 172             lr.executeJob();\r
 173             ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 174             assertNotNull(al1.getResults());\r
 175             List<AnnotatedSequence> al2 = confJronn.getResults();\r
 176             assertNotNull(al2);\r
 177             assertEquals(al2.size(), 3);\r
 178             assertEquals(al1.getResults(), al2);\r
 179         } catch (JobSubmissionException e) {\r
 180             e.printStackTrace();\r
 181             fail(e.getLocalizedMessage());\r
 182         } catch (ResultNotAvailableException e) {\r
 183             e.printStackTrace();\r
 184             fail(e.getLocalizedMessage());\r
 185         } catch (JobExecutionException e) {\r
 186             e.printStackTrace();\r
 187             fail(e.getLocalizedMessage());\r
 188         }\r
 189     }\r
 190 \r
 191     @Test(groups = { AllTestSuit.test_group_runner })\r
 192     public void readStatistics() {\r
 193         try {\r
 194             ConfiguredExecutable<Jronn> confJronn = Configurator\r
 195                     .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 196             // For local execution use relavive\r
 197 \r
 198             AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);\r
 199             String jobId = sexec.submitJob(confJronn);\r
 200             FilePuller fw = FilePuller.newFilePuller(confJronn\r
 201                     .getWorkDirectory()\r
 202                     + File.separator + Jronn.getStatFile(),\r
 203                     FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 204             int count = 0;\r
 205             long position = 0;\r
 206             fw.waitForFile(4);\r
 207             while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED\r
 208                     || sexec.getJobStatus(jobId) == JobStatus.FAILED || sexec\r
 209                     .getJobStatus(jobId) == JobStatus.UNDEFINED)\r
 210                     || fw.hasMoreData()) {\r
 211                 ChunkHolder ch = fw.pull(position);\r
 212                 String chunk = ch.getChunk();\r
 213                 position = ch.getNextPosition();\r
 214                 System.out.print(chunk);\r
 215                 count++;\r
 216             }\r
 217             assertTrue(count > 1);\r
 218             ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 219             assertNotNull(al.getResults());\r
 220         } catch (JobSubmissionException e) {\r
 221             e.printStackTrace();\r
 222             fail(e.getMessage());\r
 223         } catch (ResultNotAvailableException e) {\r
 224             e.printStackTrace();\r
 225             fail(e.getMessage());\r
 226         } catch (IOException e) {\r
 227             e.printStackTrace();\r
 228             fail(e.getMessage());\r
 229         }\r
 230     }\r
 231 \r
 232     @Test(groups = { AllTestSuit.test_group_runner })\r
 233     public void testPersistance() {\r
 234         try {\r
 235             Jronn jronn = new Jronn();\r
 236             jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 237                     .setOutput("outtt.txt");\r
 238             assertEquals(jronn.getInput(), AllTestSuit.test_input);\r
 239             assertEquals(jronn.getError(), "errrr.txt");\r
 240             assertEquals(jronn.getOutput(), "outtt.txt");\r
 241             ConfiguredExecutable<Jronn> cJronn = Configurator\r
 242                     .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 243 \r
 244             SyncExecutor sexec = Configurator.getSyncEngine(cJronn);\r
 245             sexec.executeJob();\r
 246             ConfiguredExecutable<?> al = sexec.waitForResult();\r
 247             assertNotNull(al.getResults());\r
 248             // Save run configuration\r
 249             assertTrue(cJronn.saveRunConfiguration());\r
 250 \r
 251             // See if loaded configuration is the same as saved\r
 252             RunConfiguration loadedRun = RunConfiguration\r
 253                     .load(new FileInputStream(new File(cJronn\r
 254                             .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 255             assertEquals(\r
 256                     ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),\r
 257                     loadedRun);\r
 258             // Load run configuration as ConfExecutable\r
 259             ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn\r
 260                     .loadRunConfiguration(new FileInputStream(new File(cJronn\r
 261                             .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 262             assertNotNull(resurrectedCMuscle);\r
 263             assertEquals(resurrectedCMuscle.getExecutable().getInput(),\r
 264                     AllTestSuit.test_input);\r
 265             assertEquals(resurrectedCMuscle.getExecutable().getError(),\r
 266                     "errrr.txt");\r
 267             assertEquals(resurrectedCMuscle.getExecutable().getOutput(),\r
 268                     "outtt.txt");\r
 269             // See in details whether executables are the same\r
 270             assertEquals(resurrectedCMuscle.getExecutable(), jronn);\r
 271 \r
 272             ConfiguredExecutable<Jronn> resJronn = Configurator\r
 273                     .configureExecutable(resurrectedCMuscle.getExecutable(),\r
 274                             Executable.ExecProvider.Local);\r
 275 \r
 276             sexec = Configurator.getSyncEngine(resJronn,\r
 277                     Executable.ExecProvider.Local);\r
 278             sexec.executeJob();\r
 279             al = sexec.waitForResult();\r
 280             assertNotNull(al);\r
 281 \r
 282         } catch (JobSubmissionException e) {\r
 283             e.printStackTrace();\r
 284             fail(e.getMessage());\r
 285         } catch (JobExecutionException e) {\r
 286             e.printStackTrace();\r
 287             fail(e.getMessage());\r
 288         } catch (FileNotFoundException e) {\r
 289             e.printStackTrace();\r
 290             fail(e.getMessage());\r
 291         } catch (IOException e) {\r
 292             e.printStackTrace();\r
 293             fail(e.getMessage());\r
 294         } catch (ResultNotAvailableException e) {\r
 295             e.printStackTrace();\r
 296             fail(e.getMessage());\r
 297         }\r
 298     }\r
 299 \r
 300     @Test(groups = { AllTestSuit.test_group_runner })\r
 301     public void testConfigurationLoading() {\r
 302         try {\r
 303             RunnerConfig<Jronn> jronnConfig = ConfExecutable\r
 304                     .getRunnerOptions(Jronn.class);\r
 305             assertNotNull(jronnConfig);\r
 306             assertTrue(jronnConfig.getArguments().size() > 0);\r
 307 \r
 308             PresetManager<Jronn> jronnPresets = ConfExecutable\r
 309                     .getRunnerPresets(Jronn.class);\r
 310             assertNotNull(jronnPresets);\r
 311             assertTrue(jronnPresets.getPresets().size() > 0);\r
 312             jronnPresets.validate(jronnConfig);\r
 313 \r
 314             LimitsManager<Jronn> jronnLimits = ConfExecutable\r
 315                     .getRunnerLimits(Jronn.class);\r
 316             assertNotNull(jronnLimits);\r
 317             assertTrue(jronnLimits.getLimits().size() > 0);\r
 318             jronnLimits.validate(jronnPresets);\r
 319 \r
 320         } catch (FileNotFoundException e) {\r
 321             e.printStackTrace();\r
 322             fail(e.getLocalizedMessage());\r
 323         } catch (IOException e) {\r
 324             e.printStackTrace();\r
 325             fail(e.getLocalizedMessage());\r
 326         } catch (ValidationException e) {\r
 327             e.printStackTrace();\r
 328             fail(e.getLocalizedMessage());\r
 329         }\r
 330     }\r
 331 \r
 332 }\r