testsrc/compbio/runner/disorder/DisemblTester.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.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 import java.util.HashSet;\r
  34 \r
  35 import javax.xml.bind.ValidationException;\r
  36 \r
  37 import org.ggf.drmaa.DrmaaException;\r
  38 import org.ggf.drmaa.JobInfo;\r
  39 import org.testng.annotations.BeforeMethod;\r
  40 import org.testng.annotations.Test;\r
  41 \r
  42 import compbio.data.sequence.Score;\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.AllTestSuit;\r
  56 import compbio.metadata.ChunkHolder;\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.util.FileWatcher;\r
  65 import compbio.util.SysPrefs;\r
  66 \r
  67 public class DisemblTester {\r
  68 \r
  69         public static String test_outfile = "TO1381.disembl.out";\r
  70 \r
  71         private Disembl disembl;\r
  72 \r
  73         @BeforeMethod(alwaysRun = true)\r
  74         void init() {\r
  75                 disembl = new Disembl();\r
  76                 disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
  77         }\r
  78 \r
  79         @Test(groups = {AllTestSuit.test_group_cluster,\r
  80                         AllTestSuit.test_group_runner})\r
  81         public void testRunOnCluster() {\r
  82                 assertFalse(SysPrefs.isWindows,\r
  83                                 "Cluster execution can only be in unix environment");\r
  84                 try {\r
  85                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
  86                                         .configureExecutable(disembl,\r
  87                                                         Executable.ExecProvider.Cluster);\r
  88                         JobRunner runner = JobRunner.getInstance(confDisembl);\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(groups = {AllTestSuit.test_group_cluster,\r
 138                         AllTestSuit.test_group_runner})\r
 139         public void testRunOnClusterAsync() {\r
 140                 assertFalse(SysPrefs.isWindows,\r
 141                                 "Cluster execution can only be in unix environment");\r
 142                 try {\r
 143                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 144                                         .configureExecutable(disembl,\r
 145                                                         Executable.ExecProvider.Cluster);\r
 146                         AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);\r
 147                         String jobId = aengine.submitJob(confDisembl);\r
 148                         assertNotNull(jobId, "Runner is NULL");\r
 149                         // let drmaa to start\r
 150                         Thread.sleep(500);\r
 151                         JobStatus status = aengine.getJobStatus(jobId);\r
 152                         while (status != JobStatus.FINISHED) {\r
 153                                 System.out.println("Job Status: " + status);\r
 154                                 Thread.sleep(1000);\r
 155                                 status = aengine.getJobStatus(jobId);\r
 156                                 ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
 157                                                 .getResults(jobId);\r
 158                                 assertNotNull(result);\r
 159                                 System.out.println("RES:" + result);\r
 160                                 // Some times the job could be removed from the cluster\r
 161                                 // accounting\r
 162                                 // before it has been reported to finish. Make sure\r
 163                                 // to stop waiting in such case\r
 164                                 if (status == JobStatus.UNDEFINED) {\r
 165                                         break;\r
 166                                 }\r
 167                         }\r
 168                 } catch (JobSubmissionException e) {\r
 169                         e.printStackTrace();\r
 170                         fail("DrmaaException caught:" + e.getMessage());\r
 171                 } catch (InterruptedException e) {\r
 172                         e.printStackTrace();\r
 173                         fail(e.getMessage());\r
 174                 } catch (ResultNotAvailableException e) {\r
 175                         e.printStackTrace();\r
 176                         fail(e.getMessage());\r
 177                 }\r
 178         }\r
 179 \r
 180         @Test(groups = {AllTestSuit.test_group_runner})\r
 181         public void testRunLocally() {\r
 182                 try {\r
 183                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 184                                         .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 185 \r
 186                         // For local execution use relative\r
 187                         LocalRunner lr = new LocalRunner(confDisembl);\r
 188                         lr.executeJob();\r
 189                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 190                         assertNotNull(al1.getResults());\r
 191                         HashSet<Score> al2 = confDisembl.getResults();\r
 192                         assertNotNull(al2);\r
 193                         assertEquals(al2.size(), 3);\r
 194                         assertEquals(al1.getResults(), al2);\r
 195                 } catch (JobSubmissionException e) {\r
 196                         e.printStackTrace();\r
 197                         fail(e.getLocalizedMessage());\r
 198                 } catch (ResultNotAvailableException e) {\r
 199                         e.printStackTrace();\r
 200                         fail(e.getLocalizedMessage());\r
 201                 } catch (JobExecutionException e) {\r
 202                         e.printStackTrace();\r
 203                         fail(e.getLocalizedMessage());\r
 204                 }\r
 205         }\r
 206 \r
 207         @Test(groups = {AllTestSuit.test_group_runner})\r
 208         public void readStatistics() {\r
 209                 try {\r
 210                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 211                                         .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 212                         // For local execution use relavive\r
 213 \r
 214                         AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);\r
 215                         String jobId = sexec.submitJob(confDisembl);\r
 216                         FilePuller fw = FilePuller.newFilePuller(\r
 217                                         confDisembl.getWorkDirectory() + File.separator\r
 218                                                         + Jronn.getStatFile(),\r
 219                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 220                         int count = 0;\r
 221                         long position = 0;\r
 222                         fw.waitForFile(4);\r
 223                         JobStatus status = sexec.getJobStatus(jobId);\r
 224                         while (status != JobStatus.FINISHED) {\r
 225                                 if (fw.hasMoreData()) {\r
 226                                         ChunkHolder ch = fw.pull(position);\r
 227                                         String chunk = ch.getChunk();\r
 228                                         position = ch.getNextPosition();\r
 229                                 }\r
 230                                 count++;\r
 231                                 // Make sure the loop is terminated if the job fails\r
 232                                 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 233                                         break;\r
 234                                 }\r
 235                                 Thread.sleep(300);\r
 236                                 status = sexec.getJobStatus(jobId);\r
 237                         }\r
 238                         assertTrue(count > 1);\r
 239                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 240                         assertNotNull(al.getResults());\r
 241                 } catch (JobSubmissionException e) {\r
 242                         e.printStackTrace();\r
 243                         fail(e.getMessage());\r
 244                 } catch (ResultNotAvailableException e) {\r
 245                         e.printStackTrace();\r
 246                         fail(e.getMessage());\r
 247                 } catch (IOException e) {\r
 248                         e.printStackTrace();\r
 249                         fail(e.getMessage());\r
 250                 } catch (InterruptedException e) {\r
 251                         e.printStackTrace();\r
 252                         fail(e.getMessage());\r
 253                 }\r
 254         }\r
 255 \r
 256         @Test(groups = {AllTestSuit.test_group_runner})\r
 257         public void testPersistance() {\r
 258                 try {\r
 259                         Disembl disembl = new Disembl();\r
 260                         disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 261                                         .setOutput("outtt.txt");\r
 262                         assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
 263                         assertEquals(disembl.getError(), "errrr.txt");\r
 264                         assertEquals(disembl.getOutput(), "outtt.txt");\r
 265                         ConfiguredExecutable<Disembl> cDisembl = Configurator\r
 266                                         .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 267 \r
 268                         SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);\r
 269                         sexec.executeJob();\r
 270                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 271                         assertNotNull(al.getResults());\r
 272                         // Save run configuration\r
 273                         assertTrue(cDisembl.saveRunConfiguration());\r
 274 \r
 275                         // See if loaded configuration is the same as saved\r
 276                         RunConfiguration loadedRun = RunConfiguration\r
 277                                         .load(new FileInputStream(new File(cDisembl\r
 278                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 279                         assertEquals(\r
 280                                         ((ConfExecutable<Disembl>) cDisembl).getRunConfiguration(),\r
 281                                         loadedRun);\r
 282                         // Load run configuration as ConfExecutable\r
 283                         ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl\r
 284                                         .loadRunConfiguration(new FileInputStream(new File(cDisembl\r
 285                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 286                         assertNotNull(resurrectedCDisembl);\r
 287                         assertEquals(resurrectedCDisembl.getExecutable().getInput(),\r
 288                                         AllTestSuit.test_input);\r
 289                         assertEquals(resurrectedCDisembl.getExecutable().getError(),\r
 290                                         "errrr.txt");\r
 291                         assertEquals(resurrectedCDisembl.getExecutable().getOutput(),\r
 292                                         "outtt.txt");\r
 293                         // See in details whether executables are the same\r
 294                         assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
 295 \r
 296                         ConfiguredExecutable<Disembl> resJronn = Configurator\r
 297                                         .configureExecutable(resurrectedCDisembl.getExecutable(),\r
 298                                                         Executable.ExecProvider.Local);\r
 299 \r
 300                         sexec = Configurator.getSyncEngine(resJronn,\r
 301                                         Executable.ExecProvider.Local);\r
 302                         sexec.executeJob();\r
 303                         al = sexec.waitForResult();\r
 304                         assertNotNull(al);\r
 305 \r
 306                 } catch (JobSubmissionException e) {\r
 307                         e.printStackTrace();\r
 308                         fail(e.getMessage());\r
 309                 } catch (JobExecutionException e) {\r
 310                         e.printStackTrace();\r
 311                         fail(e.getMessage());\r
 312                 } catch (FileNotFoundException e) {\r
 313                         e.printStackTrace();\r
 314                         fail(e.getMessage());\r
 315                 } catch (IOException e) {\r
 316                         e.printStackTrace();\r
 317                         fail(e.getMessage());\r
 318                 } catch (ResultNotAvailableException e) {\r
 319                         e.printStackTrace();\r
 320                         fail(e.getMessage());\r
 321                 }\r
 322         }\r
 323 \r
 324         @Test(groups = {AllTestSuit.test_group_runner})\r
 325         public void testConfigurationLoading() {\r
 326                 try {\r
 327                         RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
 328                                         .getRunnerOptions(Disembl.class);\r
 329                         assertNotNull(disemblConfig);\r
 330                         assertTrue(disemblConfig.getArguments().size() > 0);\r
 331 \r
 332                         PresetManager<Disembl> disemblPresets = ConfExecutable\r
 333                                         .getRunnerPresets(Disembl.class);\r
 334                         assertNull(disemblPresets); // there is no presets\r
 335 \r
 336                         LimitsManager<Disembl> disemblLimits = ConfExecutable\r
 337                                         .getRunnerLimits(Disembl.class);\r
 338                         assertNotNull(disemblLimits);\r
 339                         assertTrue(disemblLimits.getLimits().size() > 0);\r
 340                         disemblLimits.validate(disemblPresets);\r
 341 \r
 342                 } catch (FileNotFoundException e) {\r
 343                         e.printStackTrace();\r
 344                         fail(e.getLocalizedMessage());\r
 345                 } catch (IOException e) {\r
 346                         e.printStackTrace();\r
 347                         fail(e.getLocalizedMessage());\r
 348                 } catch (ValidationException e) {\r
 349                         e.printStackTrace();\r
 350                         fail(e.getLocalizedMessage());\r
 351                 }\r
 352         }\r
 353 \r
 354 }\r