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.*;\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(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                                 System.out.println("Job Status: " + status);\r
 151                                 Thread.sleep(1000);\r
 152                                 status = aengine.getJobStatus(jobId);\r
 153                                 ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine.getResults(jobId);\r
 154                                 assertNotNull(result);\r
 155                                 System.out.println("RES:" + result);\r
 156                                 // Some times the job could be removed from the cluster accounting \r
 157                                 // before it has been reported to finish. Make sure \r
 158                                 // to stop waiting in such case\r
 159                                 if(status == JobStatus.UNDEFINED) {\r
 160                                         break;\r
 161                                 }\r
 162                         }\r
 163                 } catch (JobSubmissionException e) {\r
 164                         e.printStackTrace();\r
 165                         fail("DrmaaException caught:" + e.getMessage());\r
 166                 } catch (InterruptedException e) {\r
 167                         e.printStackTrace();\r
 168                         fail(e.getMessage());\r
 169                 } catch (ResultNotAvailableException e) {\r
 170                         e.printStackTrace();\r
 171                         fail(e.getMessage());\r
 172                 }\r
 173         }\r
 174 \r
 175         @Test(groups = { AllTestSuit.test_group_runner })\r
 176         public void testRunLocally() {\r
 177                 try {\r
 178                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
 179                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 180 \r
 181                         // For local execution use relative\r
 182                         LocalRunner lr = new LocalRunner(confJronn);\r
 183                         lr.executeJob();\r
 184                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 185                         assertNotNull(al1.getResults());\r
 186                         List<AnnotatedSequence> al2 = confJronn.getResults();\r
 187                         assertNotNull(al2);\r
 188                         assertEquals(al2.size(), 3);\r
 189                         assertEquals(al1.getResults(), al2);\r
 190                 } catch (JobSubmissionException e) {\r
 191                         e.printStackTrace();\r
 192                         fail(e.getLocalizedMessage());\r
 193                 } catch (ResultNotAvailableException e) {\r
 194                         e.printStackTrace();\r
 195                         fail(e.getLocalizedMessage());\r
 196                 } catch (JobExecutionException e) {\r
 197                         e.printStackTrace();\r
 198                         fail(e.getLocalizedMessage());\r
 199                 }\r
 200         }\r
 201 \r
 202         @Test( groups = { AllTestSuit.test_group_runner })\r
 203         public void readStatistics() {\r
 204                 try {\r
 205                         ConfiguredExecutable<Jronn> confJronn = Configurator\r
 206                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 207                         // For local execution use relavive\r
 208 \r
 209                         AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);\r
 210                         String jobId = sexec.submitJob(confJronn);\r
 211                         FilePuller fw = FilePuller.newFilePuller(confJronn\r
 212                                         .getWorkDirectory()\r
 213                                         + File.separator + Jronn.getStatFile(),\r
 214                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 215                         int count = 0;\r
 216                         long position = 0;\r
 217                         fw.waitForFile(4);\r
 218                         JobStatus status = sexec.getJobStatus(jobId);\r
 219                         while (status != JobStatus.FINISHED\r
 220                                         || fw.hasMoreData()) {\r
 221                                 ChunkHolder ch = fw.pull(position);\r
 222                                 String chunk = ch.getChunk();\r
 223                                 position = ch.getNextPosition();\r
 224                                 System.out.print("C: "+chunk);\r
 225                                 count++;\r
 226                                 // Make sure the loop is terminated if the job fails\r
 227                                 if((status == JobStatus.UNDEFINED || status== JobStatus.FAILED)) {\r
 228                                         break;\r
 229                                 }\r
 230                                 status = sexec.getJobStatus(jobId);\r
 231                         }\r
 232                         System.out.println("\nOut of the LOOP!! ");\r
 233                         assertTrue(count > 1);\r
 234                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 235                         assertNotNull(al.getResults());\r
 236                 } catch (JobSubmissionException e) {\r
 237                         e.printStackTrace();\r
 238                         fail(e.getMessage());\r
 239                 } catch (ResultNotAvailableException e) {\r
 240                         e.printStackTrace();\r
 241                         fail(e.getMessage());\r
 242                 } catch (IOException e) {\r
 243                         e.printStackTrace();\r
 244                         fail(e.getMessage());\r
 245                 }\r
 246         }\r
 247 \r
 248         @Test(groups = { AllTestSuit.test_group_runner })\r
 249         public void testPersistance() {\r
 250                 try {\r
 251                         Jronn jronn = new Jronn();\r
 252                         jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 253                         .setOutput("outtt.txt");\r
 254                         assertEquals(jronn.getInput(), AllTestSuit.test_input);\r
 255                         assertEquals(jronn.getError(), "errrr.txt");\r
 256                         assertEquals(jronn.getOutput(), "outtt.txt");\r
 257                         ConfiguredExecutable<Jronn> cJronn = Configurator\r
 258                         .configureExecutable(jronn, Executable.ExecProvider.Local);\r
 259 \r
 260                         SyncExecutor sexec = Configurator.getSyncEngine(cJronn);\r
 261                         sexec.executeJob();\r
 262                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 263                         assertNotNull(al.getResults());\r
 264                         // Save run configuration\r
 265                         assertTrue(cJronn.saveRunConfiguration());\r
 266 \r
 267                         // See if loaded configuration is the same as saved\r
 268                         RunConfiguration loadedRun = RunConfiguration\r
 269                         .load(new FileInputStream(new File(cJronn\r
 270                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 271                         assertEquals(\r
 272                                         ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),\r
 273                                         loadedRun);\r
 274                         // Load run configuration as ConfExecutable\r
 275                         ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn\r
 276                         .loadRunConfiguration(new FileInputStream(new File(cJronn\r
 277                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 278                         assertNotNull(resurrectedCMuscle);\r
 279                         assertEquals(resurrectedCMuscle.getExecutable().getInput(),\r
 280                                         AllTestSuit.test_input);\r
 281                         assertEquals(resurrectedCMuscle.getExecutable().getError(),\r
 282                                         "errrr.txt");\r
 283                         assertEquals(resurrectedCMuscle.getExecutable().getOutput(),\r
 284                         "outtt.txt");\r
 285                         // See in details whether executables are the same\r
 286                         assertEquals(resurrectedCMuscle.getExecutable(), jronn);\r
 287 \r
 288                         ConfiguredExecutable<Jronn> resJronn = Configurator\r
 289                         .configureExecutable(resurrectedCMuscle.getExecutable(),\r
 290                                         Executable.ExecProvider.Local);\r
 291 \r
 292                         sexec = Configurator.getSyncEngine(resJronn,\r
 293                                         Executable.ExecProvider.Local);\r
 294                         sexec.executeJob();\r
 295                         al = sexec.waitForResult();\r
 296                         assertNotNull(al);\r
 297 \r
 298                 } catch (JobSubmissionException e) {\r
 299                         e.printStackTrace();\r
 300                         fail(e.getMessage());\r
 301                 } catch (JobExecutionException e) {\r
 302                         e.printStackTrace();\r
 303                         fail(e.getMessage());\r
 304                 } catch (FileNotFoundException e) {\r
 305                         e.printStackTrace();\r
 306                         fail(e.getMessage());\r
 307                 } catch (IOException e) {\r
 308                         e.printStackTrace();\r
 309                         fail(e.getMessage());\r
 310                 } catch (ResultNotAvailableException e) {\r
 311                         e.printStackTrace();\r
 312                         fail(e.getMessage());\r
 313                 }\r
 314         }\r
 315 \r
 316         @Test(groups = { AllTestSuit.test_group_runner })\r
 317         public void testConfigurationLoading() {\r
 318                 try {\r
 319                         RunnerConfig<Jronn> jronnConfig = ConfExecutable\r
 320                         .getRunnerOptions(Jronn.class);\r
 321                         assertNotNull(jronnConfig);\r
 322                         assertTrue(jronnConfig.getArguments().size() > 0);\r
 323 \r
 324                         PresetManager<Jronn> jronnPresets = ConfExecutable\r
 325                         .getRunnerPresets(Jronn.class);\r
 326                         assertNull(jronnPresets); // there is no presets\r
 327 \r
 328                         LimitsManager<Jronn> jronnLimits = ConfExecutable\r
 329                         .getRunnerLimits(Jronn.class);\r
 330                         assertNotNull(jronnLimits);\r
 331                         assertTrue(jronnLimits.getLimits().size() > 0);\r
 332                         jronnLimits.validate(jronnPresets);\r
 333 \r
 334                 } catch (FileNotFoundException e) {\r
 335                         e.printStackTrace();\r
 336                         fail(e.getLocalizedMessage());\r
 337                 } catch (IOException e) {\r
 338                         e.printStackTrace();\r
 339                         fail(e.getLocalizedMessage());\r
 340                 } catch (ValidationException e) {\r
 341                         e.printStackTrace();\r
 342                         fail(e.getLocalizedMessage());\r
 343                 }\r
 344         }\r
 345 \r
 346 }\r