testsrc/compbio/runner/disorder/IUPredTester.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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.assertFalse;\r
  23 import static org.testng.Assert.assertNotNull;\r
  24 import static org.testng.Assert.assertNull;\r
  25 import static org.testng.Assert.assertTrue;\r
  26 import static org.testng.Assert.fail;\r
  27 \r
  28 import java.io.File;\r
  29 import java.io.FileInputStream;\r
  30 import java.io.FileNotFoundException;\r
  31 import java.io.IOException;\r
  32 import java.text.ParseException;\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.data.sequence.ScoreManager.ScoreHolder;\r
  44 import compbio.data.sequence.SequenceUtil;\r
  45 import compbio.engine.AsyncExecutor;\r
  46 import compbio.engine.Configurator;\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.RunConfiguration;\r
  52 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  53 import compbio.engine.cluster.drmaa.JobRunner;\r
  54 import compbio.engine.cluster.drmaa.StatisticManager;\r
  55 import compbio.engine.local.LocalRunner;\r
  56 import compbio.metadata.AllTestSuit;\r
  57 import compbio.metadata.JobExecutionException;\r
  58 import compbio.metadata.JobStatus;\r
  59 import compbio.metadata.JobSubmissionException;\r
  60 import compbio.metadata.LimitsManager;\r
  61 import compbio.metadata.PresetManager;\r
  62 import compbio.metadata.ResultNotAvailableException;\r
  63 import compbio.metadata.RunnerConfig;\r
  64 import compbio.runner.msa.Mafft;\r
  65 import compbio.util.SysPrefs;\r
  66 \r
  67 public class IUPredTester {\r
  68 \r
  69         private IUPred iupred;\r
  70 \r
  71         @BeforeMethod(alwaysRun = true)\r
  72         void init() {\r
  73                 iupred = new IUPred();\r
  74                 iupred.setInput(AllTestSuit.test_input);\r
  75         }\r
  76 \r
  77         @Test(groups = {AllTestSuit.test_group_cluster,\r
  78                         AllTestSuit.test_group_runner})\r
  79         public void testRunOnCluster() {\r
  80                 assertFalse(SysPrefs.isWindows,\r
  81                                 "Cluster execution can only be in unix environment");\r
  82                 try {\r
  83                         ConfiguredExecutable<IUPred> confIUPred = Configurator\r
  84                                         .configureExecutable(iupred,\r
  85                                                         Executable.ExecProvider.Cluster);\r
  86                         JobRunner runner = JobRunner.getInstance(confIUPred);\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<IUPred> confIUPred = Configurator\r
 142                                         .configureExecutable(iupred,\r
 143                                                         Executable.ExecProvider.Cluster);\r
 144                         AsyncExecutor aengine = Configurator.getAsyncEngine(confIUPred);\r
 145                         String jobId = aengine.submitJob(confIUPred);\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<IUPred> result = (ConfiguredExecutable<IUPred>) 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         \r
 179         @Test(enabled = false, groups = {AllTestSuit.test_group_runner})\r
 180         public void testSetParameter() {\r
 181                 assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
 182                 assertTrue(iupred.getParameters(null).getCommandString().trim().endsWith(AllTestSuit.test_input));\r
 183                 iupred.setParameter("all");\r
 184                 assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
 185                 String cmd = iupred.getParameters(null).getCommandString().trim();  \r
 186                 assertTrue(cmd.endsWith("all"));\r
 187                 assertTrue(cmd.contains(AllTestSuit.test_input)); \r
 188         }\r
 189         \r
 190         \r
 191         @Test(groups = {AllTestSuit.test_group_runner})\r
 192         public void testReadResults() {\r
 193                 ScoreManager scoreMan;\r
 194                 try {\r
 195                         scoreMan = iupred.getResults(AllTestSuit.TEST_DATA_PATH_ABSOLUTE);\r
 196                         System.out.println(scoreMan.asMap());\r
 197                 } catch (ResultNotAvailableException e) {\r
 198                         e.printStackTrace();\r
 199                         fail(e.getMessage());\r
 200                 }\r
 201         }\r
 202         \r
 203         @Test(groups = {AllTestSuit.test_group_runner})\r
 204         public void testRunLocally() {\r
 205                 try {\r
 206                         ConfiguredExecutable<IUPred> confIUPred = Configurator\r
 207                                         .configureExecutable(iupred, Executable.ExecProvider.Local);\r
 208 \r
 209                         // For local execution use relative\r
 210                         LocalRunner lr = new LocalRunner(confIUPred);\r
 211                         lr.executeJob();\r
 212                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 213                         assertNotNull(al1.getResults());\r
 214                         ScoreManager al2 = confIUPred.getResults();\r
 215                         assertNotNull(al2);\r
 216                         assertEquals(al2.asMap().size(), 3);\r
 217                         assertEquals(al2.getNumberOfSeq(),3);\r
 218                         ScoreHolder sch = al2.getAnnotationForSequence("Foobar");\r
 219                         Score sc = sch.getScoreByMethod("Long");\r
 220                         \r
 221                         assertEquals(sc.getMethod(), "Long");\r
 222                         assertTrue(sc.getRanges().isEmpty());\r
 223                         assertNotNull(sc.getScores());\r
 224                         assertEquals(sc.getScores().size(), 481);\r
 225                         assertEquals(al1.getResults(), al2);\r
 226 \r
 227                 \r
 228                 } catch (JobSubmissionException e) {\r
 229                         e.printStackTrace();\r
 230                         fail(e.getLocalizedMessage());\r
 231                 } catch (ResultNotAvailableException e) {\r
 232                         e.printStackTrace();\r
 233                         fail(e.getLocalizedMessage());\r
 234                 } catch (JobExecutionException e) {\r
 235                         e.printStackTrace();\r
 236                         fail(e.getLocalizedMessage());\r
 237                 }\r
 238         }\r
 239 \r
 240         @Test(enabled=false, groups = {AllTestSuit.test_group_runner})\r
 241         public void testRunLocallyWithParams() {\r
 242                 try {\r
 243                         iupred.setParameter("all");\r
 244                         ConfiguredExecutable<IUPred> confIUPred = Configurator\r
 245                                         .configureExecutable(iupred, Executable.ExecProvider.Local);\r
 246 \r
 247                         // For local execution use relative\r
 248                         LocalRunner lr = new LocalRunner(confIUPred);\r
 249                         lr.executeJob();\r
 250                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 251                         assertNotNull(al1.getResults());\r
 252                         ScoreManager al2 = confIUPred.getResults();\r
 253         \r
 254                         System.out.println("!!!"+al2.asMap());\r
 255                         \r
 256                         /*\r
 257                         assertNotNull(al2);\r
 258                         assertEquals(al2.asSet().size(), 1);\r
 259                         assertEquals(al2.getNumberOfSeq(),1);\r
 260                         Score sc = al2.asSet().iterator().next(); \r
 261                         assertEquals(sc.getMethod(), "Long");\r
 262                         assertTrue(sc.getRanges().isEmpty());\r
 263                         assertNotNull(sc.getScores());\r
 264                         assertEquals(sc.getScores().size(), 568);\r
 265                         assertEquals(al1.getResults(), al2);\r
 266 */\r
 267                         } catch (JobSubmissionException e) {\r
 268                         e.printStackTrace();\r
 269                         fail(e.getLocalizedMessage());\r
 270                 } catch (ResultNotAvailableException e) {\r
 271                         e.printStackTrace();\r
 272                         fail(e.getLocalizedMessage());\r
 273                 } catch (JobExecutionException e) {\r
 274                         e.printStackTrace();\r
 275                         fail(e.getLocalizedMessage());\r
 276                 }\r
 277         }\r
 278 \r
 279         @Test(groups = {AllTestSuit.test_group_runner})\r
 280         public void testPersistance() {\r
 281                 try {\r
 282                         IUPred iupred = new IUPred();\r
 283                         iupred.setError("errrr.txt").setInput(AllTestSuit.test_input);\r
 284                         assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
 285                         assertEquals(iupred.getError(), "errrr.txt");\r
 286 \r
 287                         ConfiguredExecutable<IUPred> cIUPred = Configurator\r
 288                                         .configureExecutable(iupred, Executable.ExecProvider.Local);\r
 289 \r
 290                         SyncExecutor sexec = Configurator.getSyncEngine(cIUPred);\r
 291                         sexec.executeJob();\r
 292                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 293                         assertNotNull(al.getResults());\r
 294                         // Save run configuration\r
 295                         assertTrue(cIUPred.saveRunConfiguration());\r
 296 \r
 297                         // See if loaded configuration is the same as saved\r
 298                         RunConfiguration loadedRun = RunConfiguration\r
 299                                         .load(new FileInputStream(new File(cIUPred\r
 300                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 301                         assertEquals(\r
 302                                         ((ConfExecutable<IUPred>) cIUPred).getRunConfiguration(),\r
 303                                         loadedRun);\r
 304                         // Load run configuration as ConfExecutable\r
 305                         ConfiguredExecutable<IUPred> resurrectedCIUPred = (ConfiguredExecutable<IUPred>) cIUPred\r
 306                                         .loadRunConfiguration(new FileInputStream(new File(cIUPred\r
 307                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 308                         assertNotNull(resurrectedCIUPred);\r
 309                         assertEquals(resurrectedCIUPred.getExecutable().getInput(),\r
 310                                         AllTestSuit.test_input);\r
 311                         assertEquals(resurrectedCIUPred.getExecutable().getError(),\r
 312                                         "errrr.txt");\r
 313 \r
 314                         // See in details whether executables are the same\r
 315                         assertEquals(resurrectedCIUPred.getExecutable(), iupred);\r
 316 \r
 317                         ConfiguredExecutable<IUPred> resIUPred = Configurator\r
 318                                         .configureExecutable(resurrectedCIUPred.getExecutable(),\r
 319                                                         Executable.ExecProvider.Local);\r
 320 \r
 321                         sexec = Configurator.getSyncEngine(resIUPred,\r
 322                                         Executable.ExecProvider.Local);\r
 323                         sexec.executeJob();\r
 324                         al = sexec.waitForResult();\r
 325                         assertNotNull(al);\r
 326 \r
 327                 } catch (JobSubmissionException e) {\r
 328                         e.printStackTrace();\r
 329                         fail(e.getMessage());\r
 330                 } catch (JobExecutionException e) {\r
 331                         e.printStackTrace();\r
 332                         fail(e.getMessage());\r
 333                 } catch (FileNotFoundException e) {\r
 334                         e.printStackTrace();\r
 335                         fail(e.getMessage());\r
 336                 } catch (IOException e) {\r
 337                         e.printStackTrace();\r
 338                         fail(e.getMessage());\r
 339                 } catch (ResultNotAvailableException e) {\r
 340                         e.printStackTrace();\r
 341                         fail(e.getMessage());\r
 342                 }\r
 343         }\r
 344 \r
 345         @Test(groups = {AllTestSuit.test_group_runner})\r
 346         public void testConfigurationLoading() {\r
 347                 try {\r
 348                         RunnerConfig<IUPred> iupredConfig = ConfExecutable\r
 349                                         .getRunnerOptions(IUPred.class);\r
 350 \r
 351                         assertNotNull(iupredConfig);\r
 352 \r
 353                         assertTrue(iupredConfig.getArguments().size() != 0);\r
 354 \r
 355                         PresetManager<IUPred> iupredPresets = ConfExecutable\r
 356                                         .getRunnerPresets(IUPred.class);\r
 357                         assertNull(iupredPresets); // there is no presets\r
 358 \r
 359                         LimitsManager<IUPred> iupredLimits = ConfExecutable\r
 360                                         .getRunnerLimits(IUPred.class);\r
 361                         assertNotNull(iupredLimits);\r
 362                         assertTrue(iupredLimits.getLimits().size() > 0);\r
 363                         iupredLimits.validate(iupredPresets);\r
 364 \r
 365                 } catch (FileNotFoundException e) {\r
 366                         e.printStackTrace();\r
 367                         fail(e.getLocalizedMessage());\r
 368                 } catch (IOException e) {\r
 369                         e.printStackTrace();\r
 370                         fail(e.getLocalizedMessage());\r
 371                 } catch (ValidationException e) {\r
 372                         e.printStackTrace();\r
 373                         fail(e.getLocalizedMessage());\r
 374                 }\r
 375         }\r
 376 \r
 377 }\r