testsrc/compbio/runner/msa/ClustalOTester.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.msa;\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.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.ArrayList;\r
  33 import java.util.Collections;\r
  34 import java.util.List;\r
  35 \r
  36 import javax.xml.bind.JAXBException;\r
  37 import javax.xml.bind.ValidationException;\r
  38 \r
  39 import org.ggf.drmaa.DrmaaException;\r
  40 import org.ggf.drmaa.JobInfo;\r
  41 import org.testng.annotations.Test;\r
  42 \r
  43 import compbio.data.sequence.FastaSequence;\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.Executable.ExecProvider;\r
  52 import compbio.engine.client.RunConfiguration;\r
  53 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  54 import compbio.engine.cluster.drmaa.JobRunner;\r
  55 import compbio.engine.cluster.drmaa.StatisticManager;\r
  56 import compbio.engine.conf.RunnerConfigMarshaller;\r
  57 import compbio.engine.local.AsyncLocalRunner;\r
  58 import compbio.engine.local.LocalExecutorService;\r
  59 import compbio.engine.local.LocalRunner;\r
  60 import compbio.metadata.AllTestSuit;\r
  61 import compbio.metadata.ChunkHolder;\r
  62 import compbio.metadata.JobExecutionException;\r
  63 import compbio.metadata.JobStatus;\r
  64 import compbio.metadata.JobSubmissionException;\r
  65 import compbio.metadata.LimitsManager;\r
  66 import compbio.metadata.PresetManager;\r
  67 import compbio.metadata.ResultNotAvailableException;\r
  68 import compbio.metadata.RunnerConfig;\r
  69 import compbio.runner.OptionCombinator;\r
  70 import compbio.runner.Util;\r
  71 import compbio.util.FileWatcher;\r
  72 import compbio.util.SysPrefs;\r
  73 \r
  74 public class ClustalOTester {\r
  75 \r
  76         static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
  77                         + "ClustaloParameters.xml";\r
  78         public static String test_outfile = "TO1381.clustalo.out";\r
  79         public static String cluster_test_outfile = "TO1381.clustalo.cluster.out";\r
  80 \r
  81         @Test(groups = {AllTestSuit.test_group_cluster,\r
  82                         AllTestSuit.test_group_runner})\r
  83         public void testRunOnCluster() {\r
  84                 ClustalO clustal = new ClustalO();\r
  85                 assertFalse(SysPrefs.isWindows,\r
  86                                 "Cluster execution can only be in unix environment");\r
  87                 clustal.setInput(AllTestSuit.test_input)\r
  88                                 .setOutput(cluster_test_outfile);\r
  89 \r
  90                 try {\r
  91 \r
  92                         ConfiguredExecutable<ClustalO> confClustal = Configurator\r
  93                                         .configureExecutable(clustal);\r
  94                         JobRunner runner = JobRunner.getInstance(confClustal);\r
  95                         // ClusterSession csession = JobRunner.getSession();\r
  96                         assertNotNull(runner);\r
  97                         runner.executeJob();\r
  98                         // assertNotNull("JobId is null", jobId1);\r
  99                         JobStatus status = runner.getJobStatus();\r
 100                         assertTrue(status == JobStatus.PENDING\r
 101                                         || status == JobStatus.RUNNING);\r
 102                         JobInfo info = runner.getJobInfo();\r
 103                         assertNotNull(info);\r
 104                         StatisticManager sm = new StatisticManager(info);\r
 105                         assertNotNull(sm);\r
 106                         try {\r
 107                                 String exits = sm.getExitStatus();\r
 108                                 assertNotNull("Exit status is null", exits);\r
 109                                 // cut 4 trailing zeros from the number\r
 110                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 111                                                 .intValue();\r
 112                                 assertEquals(0, exitsInt);\r
 113                                 System.out.println(sm.getAllStats());\r
 114 \r
 115                         } catch (ParseException e) {\r
 116                                 e.printStackTrace();\r
 117                                 fail("Parse Exception: " + e.getMessage());\r
 118                         }\r
 119                         // At present the task directory could not be completely removed\r
 120                         // @see JobRunner.cleanup()\r
 121                         assertFalse(runner.cleanup(),\r
 122                                         "Could not remove some files whilst cleaning up ");\r
 123                         assertTrue(sm.hasExited());\r
 124                         assertFalse(sm.wasAborted());\r
 125                         assertFalse(sm.hasDump());\r
 126                         assertFalse(sm.hasSignaled());\r
 127 \r
 128                 } catch (JobSubmissionException e) {\r
 129                         e.printStackTrace();\r
 130                         fail("DrmaaException caught:" + e.getMessage());\r
 131                 } catch (JobExecutionException e) {\r
 132                         e.printStackTrace();\r
 133                         fail("DrmaaException caught:" + e.getMessage());\r
 134                 } catch (DrmaaException e) {\r
 135                         e.printStackTrace();\r
 136                         fail("DrmaaException caught:" + e.getMessage());\r
 137                 }\r
 138         }\r
 139 \r
 140         @Test(groups = {AllTestSuit.test_group_runner})\r
 141         public void testRunLocally() {\r
 142                 ClustalO clustal = new ClustalO();\r
 143                 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
 144                 try {\r
 145 \r
 146                         // For local execution use relavive\r
 147                         ConfiguredExecutable<ClustalO> confClustal = Configurator\r
 148                                         .configureExecutable(clustal, Executable.ExecProvider.Local);\r
 149                         LocalRunner lr = new LocalRunner(confClustal);\r
 150                         lr.executeJob();\r
 151                         confClustal = (ConfiguredExecutable<ClustalO>) lr.waitForResult();\r
 152                         assertNotNull(confClustal.getResults());\r
 153                 } catch (JobSubmissionException e) {\r
 154                         e.printStackTrace();\r
 155                         fail(e.getLocalizedMessage());\r
 156                 } catch (JobExecutionException e) {\r
 157                         e.printStackTrace();\r
 158                         fail(e.getLocalizedMessage());\r
 159                 } catch (ResultNotAvailableException e) {\r
 160                         e.printStackTrace();\r
 161                         fail(e.getLocalizedMessage());\r
 162                 }\r
 163         }\r
 164 \r
 165         @Test(groups = {AllTestSuit.test_group_runner})\r
 166         public void testConfigurationLoading() {\r
 167                 try {\r
 168                         RunnerConfig<ClustalO> clustalConfig = ConfExecutable\r
 169                                         .getRunnerOptions(ClustalO.class);\r
 170                         assertNotNull(clustalConfig);\r
 171                         assertTrue(clustalConfig.getArguments().size() > 0);\r
 172 \r
 173                         /* Unsupported\r
 174                         PresetManager<ClustalO> clustalPresets = ConfExecutable\r
 175                                         .getRunnerPresets(ClustalO.class);\r
 176                         assertNotNull(clustalPresets);\r
 177                         assertTrue(clustalPresets.getPresets().size() > 0);\r
 178                         clustalPresets.validate(clustalConfig);\r
 179                          */\r
 180                         LimitsManager<ClustalO> clustalLimits = ConfExecutable\r
 181                                         .getRunnerLimits(ClustalO.class);\r
 182                         assertNotNull(clustalLimits);\r
 183                         assertTrue(clustalLimits.getLimits().size() > 0);\r
 184                         //clustalLimits.validate(clustalPresets);\r
 185 \r
 186                 } catch (FileNotFoundException e) {\r
 187                         e.printStackTrace();\r
 188                         fail(e.getLocalizedMessage());\r
 189                 } catch (IOException e) {\r
 190                         e.printStackTrace();\r
 191                         fail(e.getLocalizedMessage());\r
 192                 }\r
 193         }\r
 194 \r
 195         @Test(groups = {AllTestSuit.test_group_runner})\r
 196         public void testOptionsLocally() {\r
 197                 try {\r
 198 \r
 199                         RunnerConfigMarshaller<ClustalO> clustalmarsh = new RunnerConfigMarshaller<ClustalO>(\r
 200                                         RunnerConfig.class);\r
 201 \r
 202                         RunnerConfig<ClustalO> clustalConfig = clustalmarsh.read(\r
 203                                         new FileInputStream(new File(clustalConfigFile)),\r
 204                                         RunnerConfig.class);\r
 205 \r
 206                         OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
 207                         List<String> options = clustalOpc.getOptionsAtRandom();\r
 208                         for (int i = 0; i < options.size(); i++) {\r
 209                                 System.out.println("Using options: " + options);\r
 210                                 ClustalO clustal = new ClustalO();\r
 211                                 clustal.setInput(AllTestSuit.test_input)\r
 212                                                 .setOutput(test_outfile);\r
 213 \r
 214                                 // For local execution use relavive\r
 215                                 ConfiguredExecutable<ClustalO> confClustal = Configurator\r
 216                                                 .configureExecutable(clustal, ExecProvider.Local);\r
 217 \r
 218                                 // Add options to the executable\r
 219                                 confClustal.addParameters(options);\r
 220 \r
 221                                 LocalRunner lr = new LocalRunner(confClustal);\r
 222                                 lr.executeJob();\r
 223                                 confClustal = (ConfiguredExecutable<ClustalO>) lr\r
 224                                                 .waitForResult();\r
 225                                 assertNotNull(confClustal.getResults());\r
 226                                 Collections.shuffle(options);\r
 227                         }\r
 228 \r
 229                 } catch (JobSubmissionException e) {\r
 230                         e.printStackTrace();\r
 231                         fail(e.getLocalizedMessage());\r
 232                 } catch (JobExecutionException e) {\r
 233                         e.printStackTrace();\r
 234                         fail(e.getLocalizedMessage());\r
 235                 } catch (JAXBException e) {\r
 236                         e.printStackTrace();\r
 237                         fail(e.getLocalizedMessage());\r
 238                 } catch (ResultNotAvailableException e) {\r
 239                         e.printStackTrace();\r
 240                         fail(e.getLocalizedMessage());\r
 241                 } catch (FileNotFoundException e) {\r
 242                         e.printStackTrace();\r
 243                         fail(e.getLocalizedMessage());\r
 244                 }\r
 245         }\r
 246 \r
 247         public static final void main(String[] args) throws JobSubmissionException,\r
 248                         JobExecutionException, InterruptedException {\r
 249                 ClustalO clustal = new ClustalO();\r
 250                 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
 251                 // For local execution use relavive\r
 252                 ConfiguredExecutable<ClustalO> confClustal = Configurator\r
 253                                 .configureExecutable(clustal);\r
 254                 AsyncExecutor lr = new AsyncLocalRunner();\r
 255                 lr.submitJob(confClustal);\r
 256                 Thread.sleep(3000);\r
 257                 LocalExecutorService.shutDown();\r
 258         }\r
 259 \r
 260         @Test(groups = {AllTestSuit.test_group_runner})\r
 261         public void testPersistance() {\r
 262                 try {\r
 263                         ClustalO clustal = new ClustalO();\r
 264                         clustal.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 265                                         .setOutput("outtt.txt");\r
 266                         assertEquals(clustal.getInput(), AllTestSuit.test_input);\r
 267                         assertEquals(clustal.getError(), "errrr.txt");\r
 268                         assertEquals(clustal.getOutput(), "outtt.txt");\r
 269                         ConfiguredExecutable<ClustalO> cClustal = Configurator\r
 270                                         .configureExecutable(clustal, Executable.ExecProvider.Local);\r
 271 \r
 272                         SyncExecutor sexec = Configurator.getSyncEngine(cClustal);\r
 273                         sexec.executeJob();\r
 274                         cClustal = (ConfiguredExecutable<ClustalO>) sexec.waitForResult();\r
 275                         assertNotNull(cClustal.getResults());\r
 276                         // Save run configuration\r
 277                         assertTrue(cClustal.saveRunConfiguration());\r
 278 \r
 279                         // See if loaded configuration is the same as saved\r
 280                         RunConfiguration loadedRun = RunConfiguration\r
 281                                         .load(new FileInputStream(new File(cClustal\r
 282                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 283                         assertTrue(((ConfExecutable<ClustalO>) cClustal)\r
 284                                         .getRunConfiguration().equals(loadedRun));\r
 285                         // Load run configuration as ConfExecutable\r
 286                         ConfiguredExecutable<ClustalO> resurrectedCclustal = (ConfiguredExecutable<ClustalO>) cClustal\r
 287                                         .loadRunConfiguration(new FileInputStream(new File(cClustal\r
 288                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 289                         assertNotNull(resurrectedCclustal);\r
 290                         // See in details whether executables are the same\r
 291                         assertEquals(resurrectedCclustal.getExecutable(), clustal);\r
 292 \r
 293                         // Finally rerun the job in the new task directory\r
 294                         ConfiguredExecutable<ClustalO> resclustal = Configurator\r
 295                                         .configureExecutable(resurrectedCclustal.getExecutable(),\r
 296                                                         Executable.ExecProvider.Local);\r
 297 \r
 298                         sexec = Configurator.getSyncEngine(resclustal,\r
 299                                         Executable.ExecProvider.Local);\r
 300                         sexec.executeJob();\r
 301                         cClustal = (ConfiguredExecutable<ClustalO>) sexec.waitForResult();\r
 302                         assertNotNull(cClustal.getResults());\r
 303 \r
 304                 } catch (JobSubmissionException e) {\r
 305                         e.printStackTrace();\r
 306                         fail(e.getMessage());\r
 307                 } catch (JobExecutionException e) {\r
 308                         e.printStackTrace();\r
 309                         fail(e.getMessage());\r
 310                 } catch (FileNotFoundException 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 (ResultNotAvailableException e) {\r
 317                         e.printStackTrace();\r
 318                         fail(e.getMessage());\r
 319                 }\r
 320         }\r
 321 \r
 322         @Test(groups = {AllTestSuit.test_group_runner})\r
 323         public void readStatistics() {\r
 324                 try {\r
 325                         ClustalO clustal = new ClustalO().setInput(AllTestSuit.test_input)\r
 326                                         .setOutput(test_outfile);\r
 327                         ConfiguredExecutable<ClustalO> confClustal = Configurator\r
 328                                         .configureExecutable(clustal, Executable.ExecProvider.Local);\r
 329 \r
 330                         AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);\r
 331                         String jobId = sexec.submitJob(confClustal);\r
 332                         FilePuller fw = FilePuller.newFilePuller(\r
 333                                         confClustal.getWorkDirectory() + File.separator\r
 334                                                         + ClustalW.getStatFile(),\r
 335                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 336                         int count = 0;\r
 337                         long position = 0;\r
 338                         fw.waitForFile(4);\r
 339                         while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED\r
 340                                         || sexec.getJobStatus(jobId) == JobStatus.FAILED || sexec\r
 341                                         .getJobStatus(jobId) == JobStatus.UNDEFINED)\r
 342                                         || fw.hasMoreData()) {\r
 343                                 ChunkHolder ch = fw.pull(position);\r
 344                                 String chunk = ch.getChunk();\r
 345                                 position = ch.getNextPosition();\r
 346                                 System.out.print(chunk);\r
 347                                 count++;\r
 348                         }\r
 349                         assertTrue(count > 1);\r
 350                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 351                         assertNotNull(al.getResults());\r
 352                 } catch (JobSubmissionException e) {\r
 353                         e.printStackTrace();\r
 354                         fail(e.getMessage());\r
 355                 } catch (ResultNotAvailableException e) {\r
 356                         e.printStackTrace();\r
 357                         fail(e.getMessage());\r
 358                 } catch (IOException e) {\r
 359                         e.printStackTrace();\r
 360                         fail(e.getMessage());\r
 361                 }\r
 362         }\r
 363 \r
 364         @Test(groups = {AllTestSuit.test_group_cluster,\r
 365                         AllTestSuit.test_group_runner})\r
 366         public void readStatisticsClusterExecution() {\r
 367                 try {\r
 368                         ClustalO clustal = new ClustalO().setInput(AllTestSuit.test_input)\r
 369                                         .setOutput(test_outfile);\r
 370                         ConfiguredExecutable<ClustalO> confClustal = Configurator\r
 371                                         .configureExecutable(clustal,\r
 372                                                         Executable.ExecProvider.Cluster);\r
 373 \r
 374                         AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);\r
 375                         String jobId = sexec.submitJob(confClustal);\r
 376                         FilePuller fw = FilePuller.newFilePuller(\r
 377                                         confClustal.getWorkDirectory() + File.separator\r
 378                                                         + ClustalW.getStatFile(),\r
 379                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 380                         int count = 0;\r
 381                         long position = 0;\r
 382                         fw.waitForFile(200);\r
 383                         /*\r
 384                          * Under certain circumstances DRMAA could report the status wrongly\r
 385                          * thus this loop never ends TODO deal with this!\r
 386                          */\r
 387                         while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec\r
 388                                         .getJobStatus(jobId) == JobStatus.FAILED)\r
 389                                         || fw.hasMoreData()) {\r
 390                                 ChunkHolder ch = fw.pull(position);\r
 391                                 String chunk = ch.getChunk();\r
 392                                 position = ch.getNextPosition();\r
 393                                 System.out.print(chunk);\r
 394                                 count++;\r
 395                                 Thread.sleep(200);\r
 396                                 if (sexec.getJobStatus(jobId) == JobStatus.UNDEFINED) {\r
 397                                         System.out.println("DRMAA reported wrong status for job + "\r
 398                                                         + jobId + " continue anyway!");\r
 399                                         break;\r
 400                                 }\r
 401                         }\r
 402                         assertTrue(count > 1);\r
 403                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 404                         assertNotNull(al.getResults());\r
 405                 } catch (JobSubmissionException e) {\r
 406                         e.printStackTrace();\r
 407                         fail(e.getMessage());\r
 408                 } catch (ResultNotAvailableException e) {\r
 409                         e.printStackTrace();\r
 410                         fail(e.getMessage());\r
 411                 } catch (IOException e) {\r
 412                         e.printStackTrace();\r
 413                         fail(e.getMessage());\r
 414                 } catch (InterruptedException e) {\r
 415                         e.printStackTrace();\r
 416                         fail(e.getMessage());\r
 417                 }\r
 418         }\r
 419 }\r