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.assertTrue;\r
  24 import static org.testng.Assert.fail;\r
  25 \r
  26 import java.io.File;\r
  27 import java.io.FileInputStream;\r
  28 import java.io.FileNotFoundException;\r
  29 import java.io.IOException;\r
  30 import java.text.ParseException;\r
  31 import java.util.Arrays;\r
  32 import java.util.HashSet;\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.Score;\r
  42 import compbio.data.sequence.ScoreManager;\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.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.Preset;\r
  61 import compbio.metadata.PresetManager;\r
  62 import compbio.metadata.ResultNotAvailableException;\r
  63 import compbio.metadata.RunnerConfig;\r
  64 import compbio.runner.Util;\r
  65 import compbio.util.FileWatcher;\r
  66 import compbio.util.SysPrefs;\r
  67 \r
  68 public class AAConTester {\r
  69 \r
  70         public static final String CURRENT_DIRECTORY = SysPrefs\r
  71                         .getCurrentDirectory() + File.separator;\r
  72 \r
  73         public static String test_outfile = "TO1381.aacon.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
  74         public static String test_alignment_input = CURRENT_DIRECTORY + "testsrc"\r
  75                         + File.separator + "testdata" + File.separator + "TO1381.fasta.aln";\r
  76         private AACon aacon;\r
  77 \r
  78         @BeforeMethod(alwaysRun = true)\r
  79         void init() {\r
  80                 aacon = new AACon();\r
  81                 aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
  82         }\r
  83 \r
  84         @Test()\r
  85         public void testRunOnCluster() {\r
  86                 assertFalse(SysPrefs.isWindows,\r
  87                                 "Cluster execution can only be in unix environment");\r
  88                 try {\r
  89                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
  90                                         .configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
  91                         JobRunner runner = JobRunner.getInstance(confAAcon);\r
  92 \r
  93                         assertNotNull(runner, "Runner is NULL");\r
  94                         runner.executeJob();\r
  95                         // assertNotNull("JobId is null", jobId1);\r
  96                         JobStatus status = runner.getJobStatus();\r
  97                         assertTrue(status == JobStatus.PENDING\r
  98                                         || status == JobStatus.RUNNING,\r
  99                                         "Status of the process is wrong!");\r
 100                         JobInfo info = runner.getJobInfo();\r
 101                         assertNotNull(info, "JobInfo is null");\r
 102                         StatisticManager sm = new StatisticManager(info);\r
 103                         assertNotNull(sm, "Statictic manager is null");\r
 104                         try {\r
 105 \r
 106                                 String exits = sm.getExitStatus();\r
 107                                 assertNotNull("Exit status is null", exits);\r
 108                                 // cut 4 trailing zeros from the number\r
 109                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 110                                                 .intValue();\r
 111                                 assertEquals(0, exitsInt);\r
 112                                 System.out.println(sm.getAllStats());\r
 113 \r
 114                         } catch (ParseException e) {\r
 115                                 e.printStackTrace();\r
 116                                 fail("Parse Exception: " + e.getMessage());\r
 117                         }\r
 118                         // assertFalse(runner.cleanup());\r
 119                         assertTrue(sm.hasExited());\r
 120                         assertFalse(sm.wasAborted());\r
 121                         assertFalse(sm.hasDump());\r
 122                         assertFalse(sm.hasSignaled());\r
 123 \r
 124                 } catch (JobSubmissionException e) {\r
 125                         e.printStackTrace();\r
 126                         fail("DrmaaException caught:" + e.getMessage());\r
 127                 } catch (JobExecutionException e) {\r
 128                         e.printStackTrace();\r
 129                         fail("DrmaaException caught:" + e.getMessage());\r
 130                 } catch (DrmaaException e) {\r
 131                         e.printStackTrace();\r
 132                         fail("DrmaaException caught:" + e.getMessage());\r
 133                 }\r
 134         }\r
 135 \r
 136         /**\r
 137          * This tests fails from time to time depending on the cluster load or some\r
 138          * other factors. Any client code has to adjust for this issue\r
 139          */\r
 140         @Test()\r
 141         public void testRunOnClusterAsync() {\r
 142                 assertFalse(SysPrefs.isWindows,\r
 143                                 "Cluster execution can only be in unix environment");\r
 144                 try {\r
 145                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 146                                         .configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
 147                         AsyncExecutor aengine = Configurator.getAsyncEngine(confAAcon);\r
 148                         String jobId = aengine.submitJob(confAAcon);\r
 149                         assertNotNull(jobId, "Runner is NULL");\r
 150                         // let drmaa to start\r
 151                         Thread.sleep(500);\r
 152                         JobStatus status = aengine.getJobStatus(jobId);\r
 153                         while (status != JobStatus.FINISHED) {\r
 154                                 System.out.println("Job Status: " + status);\r
 155                                 Thread.sleep(1000);\r
 156                                 status = aengine.getJobStatus(jobId);\r
 157                                 ConfiguredExecutable<AACon> result = (ConfiguredExecutable<AACon>) aengine\r
 158                                                 .getResults(jobId);\r
 159                                 assertNotNull(result);\r
 160                                 System.out.println("RES:" + result);\r
 161                                 // Some times the job could be removed from the cluster\r
 162                                 // accounting\r
 163                                 // before it has been reported to finish. Make sure\r
 164                                 // to stop waiting in such case\r
 165                                 if (status == JobStatus.UNDEFINED) {\r
 166                                         break;\r
 167                                 }\r
 168                         }\r
 169                 } catch (JobSubmissionException e) {\r
 170                         e.printStackTrace();\r
 171                         fail("DrmaaException caught:" + e.getMessage());\r
 172                 } catch (InterruptedException e) {\r
 173                         e.printStackTrace();\r
 174                         fail(e.getMessage());\r
 175                 } catch (ResultNotAvailableException e) {\r
 176                         e.printStackTrace();\r
 177                         fail(e.getMessage());\r
 178                 }\r
 179         }\r
 180 \r
 181         @Test()\r
 182         public void testRunLocally() {\r
 183                 try {\r
 184                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 185                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 186 \r
 187                         // For local execution use relative\r
 188                         LocalRunner lr = new LocalRunner(confAAcon);\r
 189                         lr.executeJob();\r
 190                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 191                         assertNotNull(al1.getResults());\r
 192                         ScoreManager annotations = confAAcon.getResults();\r
 193                         assertNotNull(annotations);\r
 194                         assertEquals(annotations.asSet().size(), 18);\r
 195                         assertEquals(al1.getResults(), annotations);\r
 196                 } catch (JobSubmissionException e) {\r
 197                         e.printStackTrace();\r
 198                         fail(e.getLocalizedMessage());\r
 199                 } catch (ResultNotAvailableException e) {\r
 200                         e.printStackTrace();\r
 201                         fail(e.getLocalizedMessage());\r
 202                 } catch (JobExecutionException e) {\r
 203                         e.printStackTrace();\r
 204                         fail(e.getLocalizedMessage());\r
 205                 }\r
 206         }\r
 207 \r
 208         @Test()\r
 209         public void testRunLocallyWithPreset() {\r
 210                 try {\r
 211                         PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);\r
 212                         assert aaconPresets != null;\r
 213                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 214                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 215                         Preset<AACon> quick = aaconPresets\r
 216                                         .getPresetByName("Quick conservation");\r
 217                         confAAcon.addParameters(quick.getOptions());\r
 218                         // For local execution use relative\r
 219                         LocalRunner lr = new LocalRunner(confAAcon);\r
 220                         lr.executeJob();\r
 221                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 222                         assertNotNull(al1.getResults());\r
 223                         ScoreManager annotations = confAAcon.getResults();\r
 224                         assertNotNull(annotations);\r
 225                         assertEquals(annotations.asSet().size(), 13);\r
 226                         assertEquals(al1.getResults(), annotations);\r
 227                 } catch (JobSubmissionException e) {\r
 228                         e.printStackTrace();\r
 229                         fail(e.getLocalizedMessage());\r
 230                 } catch (ResultNotAvailableException e) {\r
 231                         e.printStackTrace();\r
 232                         fail(e.getLocalizedMessage());\r
 233                 } catch (JobExecutionException e) {\r
 234                         e.printStackTrace();\r
 235                         fail(e.getLocalizedMessage());\r
 236                 }\r
 237         }\r
 238 \r
 239         @Test()\r
 240         public void testRunLocallyOnTwoCpu() {\r
 241                 try {\r
 242                         aacon = new AACon();\r
 243                         aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
 244 \r
 245                         aacon.setNCore(2);\r
 246                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 247                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 248                         confAAcon.addParameters(Arrays.asList("-m=KABAT,JORES"));\r
 249                         confAAcon.addParameters(Arrays.asList("-m=TAYLOR_GAPS"));\r
 250                         // For local execution use relative\r
 251                         LocalRunner lr = new LocalRunner(confAAcon);\r
 252 \r
 253                         lr.executeJob();\r
 254                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 255                         assertNotNull(al1.getResults());\r
 256                         ScoreManager annotations = confAAcon.getResults();\r
 257                         assertNotNull(annotations);\r
 258                         assertEquals(annotations.asSet().size(), 3);\r
 259                         assertEquals(al1.getResults(), annotations);\r
 260 \r
 261                 } catch (JobSubmissionException e) {\r
 262                         e.printStackTrace();\r
 263                         fail(e.getLocalizedMessage());\r
 264                 } catch (ResultNotAvailableException e) {\r
 265                         e.printStackTrace();\r
 266                         fail(e.getLocalizedMessage());\r
 267                 } catch (JobExecutionException e) {\r
 268                         e.printStackTrace();\r
 269                         fail(e.getLocalizedMessage());\r
 270                 }\r
 271         }\r
 272         @Test()\r
 273         public void readStatistics() {\r
 274                 try {\r
 275                         ConfiguredExecutable<AACon> confAAcon = Configurator\r
 276                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 277                         // For local execution use relative\r
 278 \r
 279                         AsyncExecutor sexec = Configurator.getAsyncEngine(confAAcon);\r
 280                         String jobId = sexec.submitJob(confAAcon);\r
 281                         FilePuller fw = FilePuller.newFilePuller(\r
 282                                         confAAcon.getWorkDirectory() + File.separator\r
 283                                                         + AACon.getStatFile(),\r
 284                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 285                         int count = 0;\r
 286                         long position = 0;\r
 287                         fw.waitForFile(2);\r
 288                         JobStatus status = sexec.getJobStatus(jobId);\r
 289                         do {\r
 290                                 ChunkHolder ch = fw.pull(position);\r
 291                                 String chunk = ch.getChunk();\r
 292                                 position = ch.getNextPosition();\r
 293                                 // System.out.println(chunk);\r
 294                                 count++;\r
 295                                 // Make sure the loop is terminated if the job fails\r
 296                                 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 297                                         fail("job failed!");\r
 298                                         break;\r
 299                                 }\r
 300                                 Thread.sleep(300);\r
 301                                 status = sexec.getJobStatus(jobId);\r
 302                         } while (status != JobStatus.FINISHED || fw.hasMoreData());\r
 303 \r
 304                         assertTrue(count >= 1);\r
 305                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 306                         assertNotNull(al.getResults());\r
 307                 } catch (JobSubmissionException 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                 } catch (IOException e) {\r
 314                         e.printStackTrace();\r
 315                         fail(e.getMessage());\r
 316                 } catch (InterruptedException e) {\r
 317                         e.printStackTrace();\r
 318                         fail(e.getMessage());\r
 319                 }\r
 320         }\r
 321 \r
 322         @Test()\r
 323         public void testPersistance() {\r
 324                 try {\r
 325                         AACon aacon = new AACon();\r
 326                         aacon.setError("errrr.txt").setInput(test_alignment_input)\r
 327                                         .setOutput("outtt.txt");\r
 328                         assertEquals(aacon.getInput(), test_alignment_input);\r
 329                         assertEquals(aacon.getError(), "errrr.txt");\r
 330                         assertEquals(aacon.getOutput(), "outtt.txt");\r
 331                         ConfiguredExecutable<AACon> cAAcon = Configurator\r
 332                                         .configureExecutable(aacon, Executable.ExecProvider.Local);\r
 333 \r
 334                         SyncExecutor sexec = Configurator.getSyncEngine(cAAcon);\r
 335                         sexec.executeJob();\r
 336                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 337                         assertNotNull(al.getResults());\r
 338                         // Save run configuration\r
 339                         assertTrue(cAAcon.saveRunConfiguration());\r
 340 \r
 341                         // See if loaded configuration is the same as saved\r
 342                         RunConfiguration loadedRun = RunConfiguration\r
 343                                         .load(new FileInputStream(new File(cAAcon\r
 344                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 345                         assertEquals(\r
 346                                         ((ConfExecutable<AACon>) cAAcon).getRunConfiguration(),\r
 347                                         loadedRun);\r
 348                         // Load run configuration as ConfExecutable\r
 349                         ConfiguredExecutable<AACon> resurrectedCAAcon = (ConfiguredExecutable<AACon>) cAAcon\r
 350                                         .loadRunConfiguration(new FileInputStream(new File(cAAcon\r
 351                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 352                         assertNotNull(resurrectedCAAcon);\r
 353                         assertEquals(resurrectedCAAcon.getExecutable().getInput(),\r
 354                                         test_alignment_input);\r
 355                         assertEquals(resurrectedCAAcon.getExecutable().getError(),\r
 356                                         "errrr.txt");\r
 357                         assertEquals(resurrectedCAAcon.getExecutable().getOutput(),\r
 358                                         "outtt.txt");\r
 359                         // See in details whether executables are the same\r
 360                         assertEquals(resurrectedCAAcon.getExecutable(), aacon);\r
 361 \r
 362                         ConfiguredExecutable<AACon> resAAcon = Configurator\r
 363                                         .configureExecutable(resurrectedCAAcon.getExecutable(),\r
 364                                                         Executable.ExecProvider.Local);\r
 365 \r
 366                         sexec = Configurator.getSyncEngine(resAAcon,\r
 367                                         Executable.ExecProvider.Local);\r
 368                         sexec.executeJob();\r
 369                         al = sexec.waitForResult();\r
 370                         assertNotNull(al);\r
 371 \r
 372                 } catch (JobSubmissionException e) {\r
 373                         e.printStackTrace();\r
 374                         fail(e.getMessage());\r
 375                 } catch (JobExecutionException e) {\r
 376                         e.printStackTrace();\r
 377                         fail(e.getMessage());\r
 378                 } catch (FileNotFoundException e) {\r
 379                         e.printStackTrace();\r
 380                         fail(e.getMessage());\r
 381                 } catch (IOException e) {\r
 382                         e.printStackTrace();\r
 383                         fail(e.getMessage());\r
 384                 } catch (ResultNotAvailableException e) {\r
 385                         e.printStackTrace();\r
 386                         fail(e.getMessage());\r
 387                 }\r
 388         }\r
 389 \r
 390         @Test()\r
 391         public void testConfigurationLoading() {\r
 392                 try {\r
 393                         RunnerConfig<AACon> aaconConfig = ConfExecutable\r
 394                                         .getRunnerOptions(AACon.class);\r
 395                         assertNotNull(aaconConfig);\r
 396                         assertTrue(aaconConfig.getArguments().size() > 0);\r
 397 \r
 398                         PresetManager<AACon> aaconPresets = ConfExecutable\r
 399                                         .getRunnerPresets(AACon.class);\r
 400                         assertNotNull(aaconPresets);\r
 401 \r
 402                         LimitsManager<AACon> jronnLimits = ConfExecutable\r
 403                                         .getRunnerLimits(AACon.class);\r
 404                         assertNotNull(jronnLimits);\r
 405                         assertTrue(jronnLimits.getLimits().size() > 0);\r
 406                         jronnLimits.validate(aaconPresets);\r
 407 \r
 408                 } catch (FileNotFoundException e) {\r
 409                         e.printStackTrace();\r
 410                         fail(e.getLocalizedMessage());\r
 411                 } catch (IOException e) {\r
 412                         e.printStackTrace();\r
 413                         fail(e.getLocalizedMessage());\r
 414                 } catch (ValidationException e) {\r
 415                         e.printStackTrace();\r
 416                         fail(e.getLocalizedMessage());\r
 417                 }\r
 418         }\r
 419 \r
 420 }\r