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