testsrc/compbio/runner/conservation/AAConTester.java

   1 /*\r
   2  * Copyright (c) 2010 Peter Troshin JAva Bioinformatics Analysis Web Services\r
   3  * (JABAWS) @version: 2.0 \r
   4  * \r
   5  * This library is free software; you can redistribute it and/or modify it under \r
   6  * the terms of the Apache License version 2 as published\r
   7  * by the Apache Software Foundation This library is distributed in the hope\r
   8  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
   9  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
  10  * Apache License for more details. A copy of the license is in\r
  11  * apache_license.txt. It is also available here:\r
  12  * \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 must include \r
  16  * this copyright and license notice.\r
  17  */\r
  18 package compbio.runner.conservation;\r
  19 \r
  20 import static org.testng.Assert.assertEquals;\r
  21 import static org.testng.Assert.assertFalse;\r
  22 import static org.testng.Assert.assertNotNull;\r
  23 import static org.testng.Assert.assertNull;\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 \r
  33 import javax.xml.bind.ValidationException;\r
  34 \r
  35 import org.ggf.drmaa.DrmaaException;\r
  36 import org.ggf.drmaa.JobInfo;\r
  37 import org.testng.annotations.BeforeMethod;\r
  38 import org.testng.annotations.Test;\r
  39 \r
  40 import compbio.conservation.Method;\r
  41 import compbio.data.sequence.MultiAnnotatedSequence;\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.ChunkHolder;\r
  55 import compbio.metadata.JobExecutionException;\r
  56 import compbio.metadata.JobStatus;\r
  57 import compbio.metadata.JobSubmissionException;\r
  58 import compbio.metadata.LimitsManager;\r
  59 import compbio.metadata.PresetManager;\r
  60 import compbio.metadata.ResultNotAvailableException;\r
  61 import compbio.metadata.RunnerConfig;\r
  62 import compbio.util.FileWatcher;\r
  63 import compbio.util.SysPrefs;\r
  64 \r
  65 public class AAConTester {\r
  66 \r
  67         public static final String CURRENT_DIRECTORY = SysPrefs\r
  68                         .getCurrentDirectory() + File.separator;\r
  69 \r
  70         public static String test_outfile = "TO1381.aacon.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
  71         public static String test_alignment_input = CURRENT_DIRECTORY + "testsrc"\r
  72                         + File.separator + "testdata" + File.separator + "TO1381.fasta.aln";\r
  73         private AACon aacon;\r
  74 \r
  75         @BeforeMethod(alwaysRun = true)\r
  76         void init() {\r
  77                 aacon = new AACon();\r
  78                 aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
  79         }\r
  80 \r
  81         @Test()\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<AACon> confAAcon = Configurator\r
  87                                         .configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
  88                         JobRunner runner = JobRunner.getInstance(confAAcon);\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()\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<AACon> confAAcon = Configurator\r
 143                                         .configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
 144                         AsyncExecutor aengine = Configurator.getAsyncEngine(confAAcon);\r
 145                         String jobId = aengine.submitJob(confAAcon);\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<AACon> result = (ConfiguredExecutable<AACon>) 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\r
 159                                 // accounting\r
 160                                 // before it has been reported to finish. Make sure\r
 161                                 // to stop waiting in such case\r
 162                                 if (status == JobStatus.UNDEFINED) {\r
 163                                         break;\r
 164                                 }\r
 165                         }\r
 166                 } catch (JobSubmissionException e) {\r
 167                         e.printStackTrace();\r
 168                         fail("DrmaaException caught:" + e.getMessage());\r
 169                 } catch (InterruptedException e) {\r
 170                         e.printStackTrace();\r
 171                         fail(e.getMessage());\r
 172                 } catch (ResultNotAvailableException e) {\r
 173                         e.printStackTrace();\r
 174                         fail(e.getMessage());\r
 175                 }\r
 176         }\r
 177 \r
 178         @Test()\r
 179         public void testRunLocally() {\r
 180                 try {\r
 181                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 182                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 183 \r
 184                         // For local execution use relative\r
 185                         LocalRunner lr = new LocalRunner(confAAcon);\r
 186                         lr.executeJob();\r
 187                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 188                         assertNotNull(al1.getResults());\r
 189                         MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
 190                         assertNotNull(annotations);\r
 191                         assertEquals(annotations.getAnnotations().size(), 18);\r
 192                         assertEquals(al1.getResults(), annotations);\r
 193                 } catch (JobSubmissionException e) {\r
 194                         e.printStackTrace();\r
 195                         fail(e.getLocalizedMessage());\r
 196                 } catch (ResultNotAvailableException e) {\r
 197                         e.printStackTrace();\r
 198                         fail(e.getLocalizedMessage());\r
 199                 } catch (JobExecutionException e) {\r
 200                         e.printStackTrace();\r
 201                         fail(e.getLocalizedMessage());\r
 202                 }\r
 203         }\r
 204 \r
 205         @Test()\r
 206         public void testRunLocallyOnTwoCpu() {\r
 207                 try {\r
 208                         aacon.setNCore(2);\r
 209                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 210                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 211 \r
 212                         // For local execution use relative\r
 213                         LocalRunner lr = new LocalRunner(confAAcon);\r
 214                         lr.executeJob();\r
 215                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 216                         assertNotNull(al1.getResults());\r
 217                         MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
 218                         assertNotNull(annotations);\r
 219                         assertEquals(annotations.getAnnotations().size(), 18);\r
 220                         assertEquals(al1.getResults(), annotations);\r
 221                 } catch (JobSubmissionException e) {\r
 222                         e.printStackTrace();\r
 223                         fail(e.getLocalizedMessage());\r
 224                 } catch (ResultNotAvailableException e) {\r
 225                         e.printStackTrace();\r
 226                         fail(e.getLocalizedMessage());\r
 227                 } catch (JobExecutionException e) {\r
 228                         e.printStackTrace();\r
 229                         fail(e.getLocalizedMessage());\r
 230                 }\r
 231         }\r
 232 \r
 233         @Test()\r
 234         public void readStatistics() {\r
 235                 try {\r
 236                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 237                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 238                         // For local execution use relative\r
 239 \r
 240                         AsyncExecutor sexec = Configurator.getAsyncEngine(confAAcon);\r
 241                         String jobId = sexec.submitJob(confAAcon);\r
 242                         FilePuller fw = FilePuller.newFilePuller(\r
 243                                         confAAcon.getWorkDirectory() + File.separator\r
 244                                                         + AACon.getStatFile(),\r
 245                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 246                         int count = 0;\r
 247                         long position = 0;\r
 248                         fw.waitForFile(2);\r
 249                         JobStatus status = sexec.getJobStatus(jobId);\r
 250                         do {\r
 251                                 ChunkHolder ch = fw.pull(position);\r
 252                                 String chunk = ch.getChunk();\r
 253                                 position = ch.getNextPosition();\r
 254                                 // System.out.println(chunk);\r
 255                                 count++;\r
 256                                 // Make sure the loop is terminated if the job fails\r
 257                                 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 258                                         fail("job failed!");\r
 259                                         break;\r
 260                                 }\r
 261                                 Thread.sleep(300);\r
 262                                 status = sexec.getJobStatus(jobId);\r
 263                         } while (status != JobStatus.FINISHED || fw.hasMoreData());\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()\r
 284         public void testPersistance() {\r
 285                 try {\r
 286                         AACon aacon = new AACon();\r
 287                         aacon.setError("errrr.txt").setInput(test_alignment_input)\r
 288                                         .setOutput("outtt.txt");\r
 289                         assertEquals(aacon.getInput(), test_alignment_input);\r
 290                         assertEquals(aacon.getError(), "errrr.txt");\r
 291                         assertEquals(aacon.getOutput(), "outtt.txt");\r
 292                         ConfiguredExecutable<AACon> cAAcon = Configurator\r
 293                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 294 \r
 295                         SyncExecutor sexec = Configurator.getSyncEngine(cAAcon);\r
 296                         sexec.executeJob();\r
 297                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 298                         assertNotNull(al.getResults());\r
 299                         // Save run configuration\r
 300                         assertTrue(cAAcon.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(cAAcon\r
 305                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 306                         assertEquals(\r
 307                                         ((ConfExecutable<AACon>) cAAcon).getRunConfiguration(),\r
 308                                         loadedRun);\r
 309                         // Load run configuration as ConfExecutable\r
 310                         ConfiguredExecutable<AACon> resurrectedCAAcon = (ConfiguredExecutable<AACon>) cAAcon\r
 311                                         .loadRunConfiguration(new FileInputStream(new File(cAAcon\r
 312                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 313                         assertNotNull(resurrectedCAAcon);\r
 314                         assertEquals(resurrectedCAAcon.getExecutable().getInput(),\r
 315                                         test_alignment_input);\r
 316                         assertEquals(resurrectedCAAcon.getExecutable().getError(),\r
 317                                         "errrr.txt");\r
 318                         assertEquals(resurrectedCAAcon.getExecutable().getOutput(),\r
 319                                         "outtt.txt");\r
 320                         // See in details whether executables are the same\r
 321                         assertEquals(resurrectedCAAcon.getExecutable(), aacon);\r
 322 \r
 323                         ConfiguredExecutable<AACon> resAAcon = Configurator\r
 324                                         .configureExecutable(resurrectedCAAcon.getExecutable(),\r
 325                                                         Executable.ExecProvider.Local);\r
 326 \r
 327                         sexec = Configurator.getSyncEngine(resAAcon,\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()\r
 352         public void testConfigurationLoading() {\r
 353                 try {\r
 354                         RunnerConfig<AACon> aaconConfig = ConfExecutable\r
 355                                         .getRunnerOptions(AACon.class);\r
 356                         assertNotNull(aaconConfig);\r
 357                         assertTrue(aaconConfig.getArguments().size() > 0);\r
 358 \r
 359                         PresetManager<AACon> aaconPresets = ConfExecutable\r
 360                                         .getRunnerPresets(AACon.class);\r
 361                         assertNull(aaconPresets); // there is no presets\r
 362 \r
 363                         LimitsManager<AACon> jronnLimits = ConfExecutable\r
 364                                         .getRunnerLimits(AACon.class);\r
 365                         assertNotNull(jronnLimits);\r
 366                         assertTrue(jronnLimits.getLimits().size() > 0);\r
 367                         jronnLimits.validate(aaconPresets);\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