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.Map;\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.Score;\r
  43 import compbio.data.sequence.ScoreManager;\r
  44 import compbio.engine.AsyncExecutor;\r
  45 import compbio.engine.Configurator;\r
  46 import compbio.engine.FilePuller;\r
  47 import compbio.engine.SyncExecutor;\r
  48 import compbio.engine.client.ConfExecutable;\r
  49 import compbio.engine.client.ConfiguredExecutable;\r
  50 import compbio.engine.client.Executable;\r
  51 import compbio.engine.client.RunConfiguration;\r
  52 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  53 import compbio.engine.cluster.drmaa.JobRunner;\r
  54 import compbio.engine.cluster.drmaa.StatisticManager;\r
  55 import compbio.engine.local.LocalRunner;\r
  56 import compbio.metadata.AllTestSuit;\r
  57 import compbio.metadata.ChunkHolder;\r
  58 import compbio.metadata.JobExecutionException;\r
  59 import compbio.metadata.JobStatus;\r
  60 import compbio.metadata.JobSubmissionException;\r
  61 import compbio.metadata.LimitsManager;\r
  62 import compbio.metadata.PresetManager;\r
  63 import compbio.metadata.ResultNotAvailableException;\r
  64 import compbio.metadata.RunnerConfig;\r
  65 import compbio.util.FileWatcher;\r
  66 import compbio.util.SysPrefs;\r
  67 \r
  68 public class JronnTester {\r
  69 \r
  70         public static String test_outfile = "TO1381.jronn.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
  71 \r
  72         private Jronn jronn;\r
  73 \r
  74         @BeforeMethod(alwaysRun = true)\r
  75         void init() {\r
  76                 jronn = new Jronn();\r
  77                 jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
  78         }\r
  79 \r
  80         @Test(groups = {AllTestSuit.test_group_cluster,\r
  81                         AllTestSuit.test_group_runner})\r
  82         public void testRunOnCluster() {\r
  83                 assertFalse(SysPrefs.isWindows,\r
  84                                 "Cluster execution can only be in unix environment");\r
  85                 try {\r
  86                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
  87                                         .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
  88                         JobRunner runner = JobRunner.getInstance(confJronn);\r
  89 \r
  90                         assertNotNull(runner, "Runner is NULL");\r
  91                         runner.executeJob();\r
  92                         // assertNotNull("JobId is null", jobId1);\r
  93                         JobStatus status = runner.getJobStatus();\r
  94                         assertTrue(status == JobStatus.PENDING\r
  95                                         || status == JobStatus.RUNNING,\r
  96                                         "Status of the process is wrong!");\r
  97                         JobInfo info = runner.getJobInfo();\r
  98                         assertNotNull(info, "JobInfo is null");\r
  99                         StatisticManager sm = new StatisticManager(info);\r
 100                         assertNotNull(sm, "Statictic manager is null");\r
 101                         try {\r
 102 \r
 103                                 String exits = sm.getExitStatus();\r
 104                                 assertNotNull("Exit status is null", exits);\r
 105                                 // cut 4 trailing zeros from the number\r
 106                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 107                                                 .intValue();\r
 108                                 assertEquals(0, exitsInt);\r
 109                                 System.out.println(sm.getAllStats());\r
 110 \r
 111                         } catch (ParseException e) {\r
 112                                 e.printStackTrace();\r
 113                                 fail("Parse Exception: " + e.getMessage());\r
 114                         }\r
 115                         // assertFalse(runner.cleanup());\r
 116                         assertTrue(sm.hasExited());\r
 117                         assertFalse(sm.wasAborted());\r
 118                         assertFalse(sm.hasDump());\r
 119                         assertFalse(sm.hasSignaled());\r
 120 \r
 121                 } catch (JobSubmissionException e) {\r
 122                         e.printStackTrace();\r
 123                         fail("DrmaaException caught:" + e.getMessage());\r
 124                 } catch (JobExecutionException e) {\r
 125                         e.printStackTrace();\r
 126                         fail("DrmaaException caught:" + e.getMessage());\r
 127                 } catch (DrmaaException e) {\r
 128                         e.printStackTrace();\r
 129                         fail("DrmaaException caught:" + e.getMessage());\r
 130                 }\r
 131         }\r
 132 \r
 133         /**\r
 134          * This tests fails from time to time depending on the cluster load or some\r
 135          * other factors. Any client code has to adjust for this issue\r
 136          */\r
 137         @Test(groups = {AllTestSuit.test_group_cluster,\r
 138                         AllTestSuit.test_group_runner})\r
 139         public void testRunOnClusterAsync() {\r
 140                 assertFalse(SysPrefs.isWindows,\r
 141                                 "Cluster execution can only be in unix environment");\r
 142                 try {\r
 143                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
 144                                         .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
 145                         AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);\r
 146                         String jobId = aengine.submitJob(confJronn);\r
 147                         assertNotNull(jobId, "Runner is NULL");\r
 148                         // let drmaa to start\r
 149                         Thread.sleep(500);\r
 150                         JobStatus status = aengine.getJobStatus(jobId);\r
 151                         while (status != JobStatus.FINISHED) {\r
 152                                 System.out.println("Job Status: " + status);\r
 153                                 Thread.sleep(1000);\r
 154                                 status = aengine.getJobStatus(jobId);\r
 155                                 ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
 156                                                 .getResults(jobId);\r
 157                                 assertNotNull(result);\r
 158                                 System.out.println("RES:" + result);\r
 159                                 // Some times the job could be removed from the cluster\r
 160                                 // accounting\r
 161                                 // before it has been reported to finish. Make sure\r
 162                                 // to stop waiting in such case\r
 163                                 if (status == JobStatus.UNDEFINED) {\r
 164                                         break;\r
 165                                 }\r
 166                         }\r
 167                 } catch (JobSubmissionException e) {\r
 168                         e.printStackTrace();\r
 169                         fail("DrmaaException caught:" + e.getMessage());\r
 170                 } catch (InterruptedException e) {\r
 171                         e.printStackTrace();\r
 172                         fail(e.getMessage());\r
 173                 } catch (ResultNotAvailableException e) {\r
 174                         e.printStackTrace();\r
 175                         fail(e.getMessage());\r
 176                 }\r
 177         }\r
 178 \r
 179         @Test(groups = {AllTestSuit.test_group_runner})\r
 180         public void testRunLocally() {\r
 181                 try {\r
 182                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
 183                                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 184 \r
 185                         // For local execution use relative\r
 186                         LocalRunner lr = new LocalRunner(confJronn);\r
 187                         lr.executeJob();\r
 188                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 189                         assertNotNull(al1.getResults());\r
 190                         ScoreManager al2 = confJronn.getResults();\r
 191                         assertNotNull(al2);\r
 192                         assertEquals(al2.asMap().size(), 3);\r
 193                         assertEquals(al1.getResults(), al2);\r
 194                 } catch (JobSubmissionException e) {\r
 195                         e.printStackTrace();\r
 196                         fail(e.getLocalizedMessage());\r
 197                 } catch (ResultNotAvailableException e) {\r
 198                         e.printStackTrace();\r
 199                         fail(e.getLocalizedMessage());\r
 200                 } catch (JobExecutionException e) {\r
 201                         e.printStackTrace();\r
 202                         fail(e.getLocalizedMessage());\r
 203                 }\r
 204         }\r
 205 \r
 206         @Test(groups = {AllTestSuit.test_group_runner})\r
 207         public void testRunLocallyOnTwoCpu() {\r
 208                 try {\r
 209                         jronn.setNCore(2);\r
 210                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
 211                                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 212 \r
 213                         // For local execution use relative\r
 214                         LocalRunner lr = new LocalRunner(confJronn);\r
 215                         lr.executeJob();\r
 216                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 217                         assertNotNull(al1.getResults());\r
 218                         ScoreManager al2 = confJronn.getResults();\r
 219                         assertNotNull(al2);\r
 220                         assertEquals(al2.asMap().size(), 3);\r
 221                         assertEquals(al1.getResults(), al2);\r
 222                 } catch (JobSubmissionException e) {\r
 223                         e.printStackTrace();\r
 224                         fail(e.getLocalizedMessage());\r
 225                 } catch (ResultNotAvailableException e) {\r
 226                         e.printStackTrace();\r
 227                         fail(e.getLocalizedMessage());\r
 228                 } catch (JobExecutionException e) {\r
 229                         e.printStackTrace();\r
 230                         fail(e.getLocalizedMessage());\r
 231                 }\r
 232         }\r
 233 \r
 234         @Test(groups = {AllTestSuit.test_group_runner})\r
 235         public void readStatistics() {\r
 236                 try {\r
 237                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
 238                                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 239                         // For local execution use relavive\r
 240 \r
 241                         AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);\r
 242                         String jobId = sexec.submitJob(confJronn);\r
 243                         FilePuller fw = FilePuller.newFilePuller(\r
 244                                         confJronn.getWorkDirectory() + File.separator\r
 245                                                         + Jronn.getStatFile(),\r
 246                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 247                         int count = 0;\r
 248                         long position = 0;\r
 249                         fw.waitForFile(4);\r
 250                         JobStatus status = sexec.getJobStatus(jobId);\r
 251                         while (status != JobStatus.FINISHED) {\r
 252                                 if (fw.hasMoreData()) {\r
 253                                         ChunkHolder ch = fw.pull(position);\r
 254                                         String chunk = ch.getChunk();\r
 255                                         position = ch.getNextPosition();\r
 256                                 }\r
 257                                 count++;\r
 258                                 // Make sure the loop is terminated if the job fails\r
 259                                 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 260                                         break;\r
 261                                 }\r
 262                                 Thread.sleep(300);\r
 263                                 status = sexec.getJobStatus(jobId);\r
 264                         }\r
 265                         assertTrue(count > 1);\r
 266                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 267                         assertNotNull(al.getResults());\r
 268                 } catch (JobSubmissionException e) {\r
 269                         e.printStackTrace();\r
 270                         fail(e.getMessage());\r
 271                 } catch (ResultNotAvailableException e) {\r
 272                         e.printStackTrace();\r
 273                         fail(e.getMessage());\r
 274                 } catch (IOException e) {\r
 275                         e.printStackTrace();\r
 276                         fail(e.getMessage());\r
 277                 } catch (InterruptedException e) {\r
 278                         e.printStackTrace();\r
 279                         fail(e.getMessage());\r
 280                 }\r
 281         }\r
 282 \r
 283         @Test(groups = {AllTestSuit.test_group_runner})\r
 284         public void testPersistance() {\r
 285                 try {\r
 286                         Jronn jronn = new Jronn();\r
 287                         jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 288                                         .setOutput("outtt.txt");\r
 289                         assertEquals(jronn.getInput(), AllTestSuit.test_input);\r
 290                         assertEquals(jronn.getError(), "errrr.txt");\r
 291                         assertEquals(jronn.getOutput(), "outtt.txt");\r
 292                         ConfiguredExecutable<Jronn> cJronn = Configurator\r
 293                                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 294 \r
 295                         SyncExecutor sexec = Configurator.getSyncEngine(cJronn);\r
 296                         sexec.executeJob();\r
 297                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 298                         assertNotNull(al.getResults());\r
 299                         // Save run configuration\r
 300                         assertTrue(cJronn.saveRunConfiguration());\r
 301 \r
 302                         // See if loaded configuration is the same as saved\r
 303                         RunConfiguration loadedRun = RunConfiguration\r
 304                                         .load(new FileInputStream(new File(cJronn\r
 305                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 306                         assertEquals(\r
 307                                         ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),\r
 308                                         loadedRun);\r
 309                         // Load run configuration as ConfExecutable\r
 310                         ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn\r
 311                                         .loadRunConfiguration(new FileInputStream(new File(cJronn\r
 312                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 313                         assertNotNull(resurrectedCMuscle);\r
 314                         assertEquals(resurrectedCMuscle.getExecutable().getInput(),\r
 315                                         AllTestSuit.test_input);\r
 316                         assertEquals(resurrectedCMuscle.getExecutable().getError(),\r
 317                                         "errrr.txt");\r
 318                         assertEquals(resurrectedCMuscle.getExecutable().getOutput(),\r
 319                                         "outtt.txt");\r
 320                         // See in details whether executables are the same\r
 321                         assertEquals(resurrectedCMuscle.getExecutable(), jronn);\r
 322 \r
 323                         ConfiguredExecutable<Jronn> resJronn = Configurator\r
 324                                         .configureExecutable(resurrectedCMuscle.getExecutable(),\r
 325                                                         Executable.ExecProvider.Local);\r
 326 \r
 327                         sexec = Configurator.getSyncEngine(resJronn,\r
 328                                         Executable.ExecProvider.Local);\r
 329                         sexec.executeJob();\r
 330                         al = sexec.waitForResult();\r
 331                         assertNotNull(al);\r
 332 \r
 333                 } catch (JobSubmissionException e) {\r
 334                         e.printStackTrace();\r
 335                         fail(e.getMessage());\r
 336                 } catch (JobExecutionException e) {\r
 337                         e.printStackTrace();\r
 338                         fail(e.getMessage());\r
 339                 } catch (FileNotFoundException e) {\r
 340                         e.printStackTrace();\r
 341                         fail(e.getMessage());\r
 342                 } catch (IOException e) {\r
 343                         e.printStackTrace();\r
 344                         fail(e.getMessage());\r
 345                 } catch (ResultNotAvailableException e) {\r
 346                         e.printStackTrace();\r
 347                         fail(e.getMessage());\r
 348                 }\r
 349         }\r
 350 \r
 351         @Test(groups = {AllTestSuit.test_group_runner})\r
 352         public void testConfigurationLoading() {\r
 353                 try {\r
 354                         RunnerConfig<Jronn> jronnConfig = ConfExecutable\r
 355                                         .getRunnerOptions(Jronn.class);\r
 356                         // There is not supported parameters for Jronn\r
 357                         assertNull(jronnConfig);\r
 358 \r
 359                         PresetManager<Jronn> jronnPresets = ConfExecutable\r
 360                                         .getRunnerPresets(Jronn.class);\r
 361                         assertNull(jronnPresets); // there is no presets\r
 362 \r
 363                         LimitsManager<Jronn> jronnLimits = ConfExecutable\r
 364                                         .getRunnerLimits(Jronn.class);\r
 365                         assertNotNull(jronnLimits);\r
 366                         assertTrue(jronnLimits.getLimits().size() > 0);\r
 367                         jronnLimits.validate(jronnPresets);\r
 368 \r
 369                 } catch (FileNotFoundException e) {\r
 370                         e.printStackTrace();\r
 371                         fail(e.getLocalizedMessage());\r
 372                 } catch (IOException e) {\r
 373                         e.printStackTrace();\r
 374                         fail(e.getLocalizedMessage());\r
 375                 } catch (ValidationException e) {\r
 376                         e.printStackTrace();\r
 377                         fail(e.getLocalizedMessage());\r
 378                 }\r
 379         }\r
 380 \r
 381 }\r