testsrc/compbio/runner/predictors/JpredTester.java

   1 /* Copyright (c) 2013 Alexander Sherstnev\r
   2  * \r
   3  *  Java Bioinformatics Analysis Web Services (JABAWS)\r
   4  *  @version: 2.5\r
   5  * \r
   6  * This library is free software; you can redistribute it and/or modify it under \r
   7  * the terms of the Apache License version 2 as published\r
   8  * by the Apache Software Foundation This library is distributed in the hope\r
   9  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
  10  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
  11  * Apache License for more details. A copy of the license is in\r
  12  * apache_license.txt. It is also available here:\r
  13  * \r
  14  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt \r
  15  * \r
  16  * Any republication or derived work distributed in source code form must include \r
  17  * this copyright and license notice.\r
  18  */\r
  19 //package compbio.runner.predictors;\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.Arrays;\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.JpredAlignment;\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.ClusterEngineUtil;\r
  51 //import compbio.engine.cluster.drmaa.ClusterRunner;\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.Preset;\r
  61 //import compbio.metadata.PresetManager;\r
  62 //import compbio.metadata.ResultNotAvailableException;\r
  63 //import compbio.metadata.RunnerConfig;\r
  64 //import compbio.runner.RunnerUtil;\r
  65 //import compbio.util.FileWatcher;\r
  66 //import compbio.util.SysPrefs;\r
  67 //\r
  68 //public class JpredTester {\r
  69 //\r
  70 //      public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;\r
  71 //\r
  72 //      public static String test_output = "Jpred.test1.out";\r
  73 //      public static String test_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "Jpred.test1.fasta";\r
  74 //      private Jpred pred;\r
  75 //\r
  76 //      @BeforeMethod(alwaysRun = true)\r
  77 //      void init() {\r
  78 //              pred = new Jpred();\r
  79 //              pred.setInput(test_input);\r
  80 //              pred.setOutput(test_output);\r
  81 //      }\r
  82 //\r
  83 //      // disabled\r
  84 //      @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
  85 //      public void RunOnCluster() {\r
  86 //              assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
  87 //              try {\r
  88 //                      PresetManager<Jpred> jpredPreset = RunnerUtil.getPresets(Jpred.class);\r
  89 //                      assert jpredPreset != null;\r
  90 //                      ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);\r
  91 //                      Preset<Jpred> conf = jpredPreset.getPresetByName("cluster configuration");\r
  92 //                      confpred.addParameters(conf.getOptions());\r
  93 //                      ClusterRunner runner = ClusterRunner.getInstance(confpred);\r
  94 //                      assertNotNull(runner, "Runner is NULL");\r
  95 //\r
  96 //                      runner.executeJob();\r
  97 //                      JobStatus status = runner.getJobStatus();\r
  98 //                      assertTrue(status == JobStatus.PENDING || status == JobStatus.RUNNING, "Status of the process is wrong!");\r
  99 //                      JobInfo info = runner.getJobInfo();\r
 100 //                      assertNotNull(info, "JobInfo is null");\r
 101 //                      StatisticManager sm = new StatisticManager(info);\r
 102 //                      assertNotNull(sm, "Statistic manager is null");\r
 103 //                      try {\r
 104 //                              String exits = sm.getExitStatus();\r
 105 //                              assertNotNull("Exit status is null", exits);\r
 106 //                              // cut 4 trailing zeros from the number\r
 107 //                              int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();\r
 108 //                              assertEquals(0, exitsInt);\r
 109 //                              System.out.println(sm.getAllStats());\r
 110 //                      } catch (ParseException e) {\r
 111 //                              e.printStackTrace();\r
 112 //                              fail("Parse Exception: " + e.getMessage());\r
 113 //                      }\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 //      // disabled\r
 132 //      @Test(enabled=false,groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_cluster})\r
 133 //      public void RunOnClusterAsync() {\r
 134 //              assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
 135 //              try {\r
 136 //                      pred.addParameters(Arrays.asList("-dbname uniref90", "-dbpath /homes/www-jpred/databases/"));\r
 137 //                      ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);\r
 138 //                      AsyncExecutor aengine = Configurator.getAsyncEngine(confpred);\r
 139 //                      String jobId = aengine.submitJob(confpred);\r
 140 //                      assertNotNull(jobId, "Runner is NULL");\r
 141 //                      // let drmaa to start\r
 142 //                      Thread.sleep(500);\r
 143 //                      JobStatus status = aengine.getJobStatus(jobId);\r
 144 //                      while (status != JobStatus.FINISHED) {\r
 145 //                              Thread.sleep(1000);\r
 146 //                              status = aengine.getJobStatus(jobId);\r
 147 //                              ConfiguredExecutable<Jpred> result = (ConfiguredExecutable<Jpred>) aengine.getResults(jobId);\r
 148 //                              assertNotNull(result);\r
 149 //                              if (status == JobStatus.UNDEFINED || status == JobStatus.FAILED) {\r
 150 //                                      fail("job " + jobId +" failed!");\r
 151 //                                      break;\r
 152 //                              }\r
 153 //                      }\r
 154 //              } catch (JobSubmissionException e) {\r
 155 //                      e.printStackTrace();\r
 156 //                      fail("DrmaaException caught:" + e.getMessage());\r
 157 //              } catch (InterruptedException e) {\r
 158 //                      e.printStackTrace();\r
 159 //                      fail(e.getMessage());\r
 160 //              } catch (ResultNotAvailableException e) {\r
 161 //                      e.printStackTrace();\r
 162 //                      fail(e.getMessage());\r
 163 //              }\r
 164 //      }\r
 165 //\r
 166 //      @Test(groups = {AllTestSuit.test_group_runner})\r
 167 //      public void RunLocally() {\r
 168 //              try {\r
 169 //                      ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);\r
 170 //                      confpred.addParameters(Arrays.asList("-dbname ported_db", "-dbpath /data/UNIREFdb/"));\r
 171 //\r
 172 //                      // For local execution use relative\r
 173 //                      LocalRunner lr = new LocalRunner(confpred);\r
 174 //                      lr.executeJob();\r
 175 //                      ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 176 //                      assertNotNull(al1.getResults());\r
 177 //                      JpredAlignment totalign = (JpredAlignment) confpred.getResults();\r
 178 //                      assertNotNull(totalign);\r
 179 //                      assertEquals(totalign.getSize(), 14);\r
 180 //                      assertEquals(al1.getResults(), totalign);\r
 181 //              } catch (JobSubmissionException e) {\r
 182 //                      e.printStackTrace();\r
 183 //                      fail(e.getLocalizedMessage());\r
 184 //              } catch (ResultNotAvailableException e) {\r
 185 //                      e.printStackTrace();\r
 186 //                      fail(e.getLocalizedMessage());\r
 187 //              } catch (JobExecutionException e) {\r
 188 //                      e.printStackTrace();\r
 189 //                      fail(e.getLocalizedMessage());\r
 190 //              }\r
 191 //      }\r
 192 //\r
 193 //      @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
 194 //      public void RunLocallyWithPreset() {\r
 195 //              try {\r
 196 //                      ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);\r
 197 //                      PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);\r
 198 //                      assert preset != null;\r
 199 //                      Preset<Jpred> conf = preset.getPresetByName("laptop configuration");\r
 200 //                      confpred.addParameters(conf.getOptions());\r
 201 //\r
 202 //                      // For local execution use relative\r
 203 //                      LocalRunner lr = new LocalRunner(confpred);\r
 204 //                      lr.executeJob();\r
 205 //                      ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 206 //                      assertNotNull(al1.getResults());\r
 207 //                      JpredAlignment totalign = (JpredAlignment) confpred.getResults();\r
 208 //                      assertNotNull(totalign);\r
 209 //                      assertEquals(totalign.getSize(), 19);\r
 210 //                      assertEquals(al1.getResults(), totalign);\r
 211 //              } catch (JobSubmissionException e) {\r
 212 //                      e.printStackTrace();\r
 213 //                      fail(e.getLocalizedMessage());\r
 214 //              } catch (ResultNotAvailableException e) {\r
 215 //                      e.printStackTrace();\r
 216 //                      fail(e.getLocalizedMessage());\r
 217 //              } catch (JobExecutionException e) {\r
 218 //                      e.printStackTrace();\r
 219 //                      fail(e.getLocalizedMessage());\r
 220 //              }\r
 221 //      }\r
 222 //\r
 223 //      @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
 224 //      public void readStatistics() {\r
 225 //              try {\r
 226 //                      Jpred jpred = new Jpred();\r
 227 //                      jpred.setInput(test_input);\r
 228 //                      jpred.setOutput(test_output);\r
 229 //                      ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);\r
 230 //                      PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);\r
 231 //                      assert preset != null;\r
 232 //                      Preset<Jpred> conf = preset.getPresetByName("laptop configuration");\r
 233 //                      confpred.addParameters(conf.getOptions());\r
 234 //\r
 235 //                      // For local execution use relative\r
 236 //                      AsyncExecutor sexec = Configurator.getAsyncEngine(confpred);\r
 237 //                      String jobId = sexec.submitJob(confpred);\r
 238 //                      String file = confpred.getWorkDirectory() + File.separator + Jpred.getStatFile();\r
 239 //                      FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 240 //                      int count = 0;\r
 241 //                      long position = 0;\r
 242 //                      fw.waitForFile(2);\r
 243 //                      JobStatus status = sexec.getJobStatus(jobId);\r
 244 //                      do {\r
 245 //                              if (fw.hasMoreData()) {\r
 246 //                                      ChunkHolder ch = fw.pull(position);\r
 247 //                                      String chunk = ch.getChunk();\r
 248 //                                      position = ch.getNextPosition();\r
 249 //                              }\r
 250 //                              count++;\r
 251 //                              // Make sure the loop is terminated if the job fails\r
 252 //                              if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 253 //                                      fail("job " + jobId +" failed!");\r
 254 //                                      break;\r
 255 //                              }\r
 256 //                              Thread.sleep(200);\r
 257 //                              status = sexec.getJobStatus(jobId);\r
 258 //                      }  while (status != JobStatus.FINISHED || fw.hasMoreData());\r
 259 //\r
 260 //                      assertTrue(count >= 1);\r
 261 //                      ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 262 //                      assertNotNull(al.getResults());\r
 263 //              } catch (JobSubmissionException e) {\r
 264 //                      e.printStackTrace();\r
 265 //                      fail(e.getMessage());\r
 266 //              } catch (ResultNotAvailableException e) {\r
 267 //                      e.printStackTrace();\r
 268 //                      fail(e.getMessage());\r
 269 //              } catch (IOException e) {\r
 270 //                      e.printStackTrace();\r
 271 //                      fail(e.getMessage());\r
 272 //              } catch (InterruptedException e) {\r
 273 //                      e.printStackTrace();\r
 274 //                      fail(e.getMessage());\r
 275 //              }\r
 276 //      }\r
 277 //\r
 278 //      @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
 279 //      public void Persistance() {\r
 280 //              try {\r
 281 //                      Jpred jpred = new Jpred();\r
 282 //                      jpred.setError("errrr.txt");\r
 283 //                      jpred.setInput(test_input);\r
 284 //                      jpred.setOutput("outtt.txt");\r
 285 //                      assertEquals(jpred.getInput(), test_input);\r
 286 //                      assertEquals(jpred.getError(), "errrr.txt");\r
 287 //                      assertEquals(jpred.getOutput(), "outtt.txt");\r
 288 //                      ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);\r
 289 //                      confpred.addParameters(Arrays.asList("-dbname ported_db", "-dbpath /data/UNIREFdb/"));\r
 290 //\r
 291 //                      SyncExecutor sexec = Configurator.getSyncEngine(confpred);\r
 292 //                      sexec.executeJob();\r
 293 //                      ConfiguredExecutable<?> al = sexec.waitForResult();\r
 294 //                      assertNotNull(al.getResults());\r
 295 //\r
 296 //                      // Save run configuration\r
 297 //                      assertTrue(confpred.saveRunConfiguration());\r
 298 //\r
 299 //                      // See if loaded configuration is the same as saved\r
 300 //                      RunConfiguration loadedRun = RunConfiguration.load(new FileInputStream(new File(confpred.getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 301 //                      assertEquals(((ConfExecutable<Jpred>) confpred).getRunConfiguration(),loadedRun);\r
 302 //\r
 303 //                      // Load run configuration as ConfExecutable\r
 304 //                      ConfiguredExecutable<Jpred> jpred2 = (ConfiguredExecutable<Jpred>) confpred.loadRunConfiguration(new FileInputStream(new File(confpred.getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 305 //                      assertNotNull(jpred2);\r
 306 //                      assertEquals(jpred2.getExecutable().getInput(), test_input);\r
 307 //                      assertEquals(jpred2.getExecutable().getError(), "errrr.txt");\r
 308 //                      assertEquals(jpred2.getExecutable().getOutput(), "outtt.txt");\r
 309 //\r
 310 //                      // See in details whether executables are the same\r
 311 //                      assertEquals(jpred2.getExecutable(), jpred);\r
 312 //                      ConfiguredExecutable<Jpred> resjpred2 = Configurator.configureExecutable(jpred2.getExecutable(), Executable.ExecProvider.Local);\r
 313 //\r
 314 //                      sexec = Configurator.getSyncEngine(resjpred2, Executable.ExecProvider.Local);\r
 315 //                      sexec.executeJob();\r
 316 //                      al = sexec.waitForResult();\r
 317 //                      assertNotNull(al);\r
 318 //              } catch (JobSubmissionException e) {\r
 319 //                      e.printStackTrace();\r
 320 //                      fail(e.getMessage());\r
 321 //              } catch (JobExecutionException e) {\r
 322 //                      e.printStackTrace();\r
 323 //                      fail(e.getMessage());\r
 324 //              } catch (FileNotFoundException e) {\r
 325 //                      e.printStackTrace();\r
 326 //                      fail(e.getMessage());\r
 327 //              } catch (IOException e) {\r
 328 //                      e.printStackTrace();\r
 329 //                      fail(e.getMessage());\r
 330 //              } catch (ResultNotAvailableException e) {\r
 331 //                      e.printStackTrace();\r
 332 //                      fail(e.getMessage());\r
 333 //              }\r
 334 //      }\r
 335 //\r
 336 //      @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
 337 //      public void ConfigurationLoading() {\r
 338 //              try {\r
 339 //                      RunnerConfig<Jpred> jpredConfig = ConfExecutable.getRunnerOptions(Jpred.class);\r
 340 //                      assertNotNull(jpredConfig);\r
 341 //                      assertTrue(jpredConfig.getArguments().size() > 0);\r
 342 //\r
 343 //                      PresetManager<Jpred> jpredPreset = ConfExecutable.getRunnerPresets(Jpred.class);\r
 344 //                      assertNotNull(jpredPreset);\r
 345 //\r
 346 //                      LimitsManager<Jpred> jpredLimits = ConfExecutable.getRunnerLimits(Jpred.class);\r
 347 //                      assertNotNull(jpredLimits);\r
 348 //                      assertTrue(jpredLimits.getLimits().size() > 0);\r
 349 //                      jpredLimits.validate(jpredPreset);\r
 350 //              } catch (FileNotFoundException e) {\r
 351 //                      e.printStackTrace();\r
 352 //                      fail(e.getLocalizedMessage());\r
 353 //              } catch (IOException e) {\r
 354 //                      e.printStackTrace();\r
 355 //                      fail(e.getLocalizedMessage());\r
 356 //              } catch (ValidationException e) {\r
 357 //                      e.printStackTrace();\r
 358 //                      fail(e.getLocalizedMessage());\r
 359 //              }\r
 360 //      }\r
 361 //\r
 362 //}\r