testsrc/compbio/casscode/conservation/AAConTester.java

   1 /* Copyright (c) 2010 Peter Troshin\r
   2  * Copyright (c) 2013 Alexander Sherstnev\r
   3  * \r
   4  * Java Bioinformatics Analysis Web Services (JABAWS)\r
   5  * (JABAWS) @version: 2.5 \r
   6  * \r
   7  * This library is free software; you can redistribute it and/or modify it under \r
   8  * the terms of the Apache License version 2 as published\r
   9  * by the Apache Software Foundation This library is distributed in the hope\r
  10  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
  11  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
  12  * Apache License for more details. A copy of the license is in\r
  13  * apache_license.txt. It is also available here:\r
  14  * \r
  15  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt \r
  16  * \r
  17  * Any republication or derived work distributed in source code form must include \r
  18  * this copyright and license notice.\r
  19  */\r
  20 package compbio.runner.conservation;\r
  21 \r
  22 import static org.testng.Assert.assertEquals;\r
  23 import static org.testng.Assert.assertFalse;\r
  24 import static org.testng.Assert.assertNotNull;\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.Arrays;\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.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.ClusterEngineUtil;\r
  52 import compbio.engine.cluster.drmaa.ClusterRunner;\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.Preset;\r
  62 import compbio.metadata.PresetManager;\r
  63 import compbio.metadata.ResultNotAvailableException;\r
  64 import compbio.metadata.RunnerConfig;\r
  65 import compbio.runner.RunnerUtil;\r
  66 import compbio.util.FileWatcher;\r
  67 import compbio.util.SysPrefs;\r
  68 \r
  69 public class AAConTester {\r
  70 \r
  71         public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;\r
  72         public static String test_outfile = "TO1381.aacon.out";\r
  73         public static String test_alignment_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "TO1381.fasta.aln";\r
  74         private AACon aacon;\r
  75 \r
  76         @BeforeMethod(alwaysRun = true)\r
  77         void init() {\r
  78                 aacon = new AACon();\r
  79                 aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
  80         }\r
  81 \r
  82         @Test(groups = {AllTestSuit.test_group_runner})\r
  83         public void RunOnCluster() {\r
  84                 assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
  85                 try {\r
  86                         ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
  87                         ClusterRunner runner = ClusterRunner.getInstance(confAAcon);\r
  88 \r
  89                         assertNotNull(runner, "Runner is NULL");\r
  90                         runner.executeJob();\r
  91                         JobStatus status = runner.getJobStatus();\r
  92                         assertTrue(status == JobStatus.PENDING || status == JobStatus.RUNNING, "Status of the process is wrong!");\r
  93                         JobInfo info = runner.getJobInfo();\r
  94                         assertNotNull(info, "JobInfo is null");\r
  95                         StatisticManager sm = new StatisticManager(info);\r
  96                         assertNotNull(sm, "Statictic manager is null");\r
  97                         try {\r
  98                                 String exits = sm.getExitStatus();\r
  99                                 assertNotNull("Exit status is null", exits);\r
 100                                 // cut 4 trailing zeros from the number\r
 101                                 int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();\r
 102                                 assertEquals(0, exitsInt);\r
 103                                 System.out.println(sm.getAllStats());\r
 104 \r
 105                         } catch (ParseException e) {\r
 106                                 e.printStackTrace();\r
 107                                 fail("Parse Exception: " + e.getMessage());\r
 108                         }\r
 109                         assertTrue(sm.hasExited());\r
 110                         assertFalse(sm.wasAborted());\r
 111                         assertFalse(sm.hasDump());\r
 112                         assertFalse(sm.hasSignaled());\r
 113                 } catch (JobSubmissionException e) {\r
 114                         e.printStackTrace();\r
 115                         fail("DrmaaException caught:" + e.getMessage());\r
 116                 } catch (JobExecutionException e) {\r
 117                         e.printStackTrace();\r
 118                         fail("DrmaaException caught:" + e.getMessage());\r
 119                 } catch (DrmaaException e) {\r
 120                         e.printStackTrace();\r
 121                         fail("DrmaaException caught:" + e.getMessage());\r
 122                 }\r
 123         }\r
 124 \r
 125         /**\r
 126          * This test fails from time to time depending on the cluster load or some\r
 127          * other factors. Any client code has to adjust for this issue\r
 128          */\r
 129         @Test(groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_cluster})\r
 130         public void RunOnClusterAsync() {\r
 131                 assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
 132                 try {\r
 133                         ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Cluster);\r
 134                         AsyncExecutor aengine = Configurator.getAsyncEngine(confAAcon);\r
 135                         String jobId = aengine.submitJob(confAAcon);\r
 136                         assertNotNull(jobId, "Runner is NULL");\r
 137                         // let drmaa to start\r
 138                         Thread.sleep(500);\r
 139                         JobStatus status = aengine.getJobStatus(jobId);\r
 140                         while (status != JobStatus.FINISHED) {\r
 141                                 System.out.println("Job Status: " + status);\r
 142                                 Thread.sleep(1000);\r
 143                                 status = aengine.getJobStatus(jobId);\r
 144                                 ConfiguredExecutable<AACon> result = (ConfiguredExecutable<AACon>) aengine.getResults(jobId);\r
 145                                 assertNotNull(result);\r
 146                                 System.out.println("RES:" + result);\r
 147                                 // Some times the job could be removed from the cluster accounting \r
 148                                 // before it has been reported to finish. Make sure to stop waiting in such case\r
 149                                 if (status == JobStatus.UNDEFINED) {\r
 150                                         break;\r
 151                                 }\r
 152                         }\r
 153                 } catch (JobSubmissionException e) {\r
 154                         e.printStackTrace();\r
 155                         fail("DrmaaException caught:" + e.getMessage());\r
 156                 } catch (InterruptedException e) {\r
 157                         e.printStackTrace();\r
 158                         fail(e.getMessage());\r
 159                 } catch (ResultNotAvailableException e) {\r
 160                         e.printStackTrace();\r
 161                         fail(e.getMessage());\r
 162                 }\r
 163         }\r
 164 \r
 165         @Test(groups = {AllTestSuit.test_group_runner})\r
 166         public void RunLocally() {\r
 167                 try {\r
 168                         ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
 169 \r
 170                         // For local execution use relative\r
 171                         LocalRunner lr = new LocalRunner(confAAcon);\r
 172                         lr.executeJob();\r
 173                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 174                         assertNotNull(al1.getResults());\r
 175                         ScoreManager annotations = confAAcon.getResults();\r
 176                         assertNotNull(annotations);\r
 177                         assertEquals(annotations.asSet().size(), 18);\r
 178                         assertEquals(al1.getResults(), annotations);\r
 179                 } catch (JobSubmissionException e) {\r
 180                         e.printStackTrace();\r
 181                         fail(e.getLocalizedMessage());\r
 182                 } catch (ResultNotAvailableException e) {\r
 183                         e.printStackTrace();\r
 184                         fail(e.getLocalizedMessage());\r
 185                 } catch (JobExecutionException e) {\r
 186                         e.printStackTrace();\r
 187                         fail(e.getLocalizedMessage());\r
 188                 }\r
 189         }\r
 190 \r
 191         @Test(groups = {AllTestSuit.test_group_runner})\r
 192         public void RunLocallyWithPreset() {\r
 193                 try {\r
 194                         PresetManager<AACon> aaconPresets = RunnerUtil.getPresets(AACon.class);\r
 195                         assert aaconPresets != null;\r
 196                         ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
 197                         Preset<AACon> quick = aaconPresets.getPresetByName("Quick conservation");\r
 198                         confAAcon.addParameters(quick.getOptions());\r
 199                         // For local execution use relative\r
 200                         LocalRunner lr = new LocalRunner(confAAcon);\r
 201                         lr.executeJob();\r
 202                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 203                         assertNotNull(al1.getResults());\r
 204                         ScoreManager annotations = confAAcon.getResults();\r
 205                         assertNotNull(annotations);\r
 206                         assertEquals(annotations.asSet().size(), 13);\r
 207                         assertEquals(al1.getResults(), annotations);\r
 208                 } catch (JobSubmissionException e) {\r
 209                         e.printStackTrace();\r
 210                         fail(e.getLocalizedMessage());\r
 211                 } catch (ResultNotAvailableException e) {\r
 212                         e.printStackTrace();\r
 213                         fail(e.getLocalizedMessage());\r
 214                 } catch (JobExecutionException e) {\r
 215                         e.printStackTrace();\r
 216                         fail(e.getLocalizedMessage());\r
 217                 }\r
 218         }\r
 219 \r
 220         @Test(groups = {AllTestSuit.test_group_runner})\r
 221         public void RunLocallyOnTwoCpu() {\r
 222                 try {\r
 223                         aacon = new AACon();\r
 224                         aacon.setInput(test_alignment_input).setOutput(test_outfile);\r
 225 \r
 226                         aacon.setNCore(2);\r
 227                         ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
 228                         confAAcon.addParameters(Arrays.asList("-m=KABAT,JORES"));\r
 229                         confAAcon.addParameters(Arrays.asList("-m=TAYLOR_GAPS"));\r
 230                         // For local execution use relative\r
 231                         LocalRunner lr = new LocalRunner(confAAcon);\r
 232 \r
 233                         lr.executeJob();\r
 234                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 235                         assertNotNull(al1.getResults());\r
 236                         ScoreManager annotations = confAAcon.getResults();\r
 237                         assertNotNull(annotations);\r
 238                         assertEquals(annotations.asSet().size(), 3);\r
 239                         assertEquals(al1.getResults(), annotations);\r
 240                 } catch (JobSubmissionException e) {\r
 241                         e.printStackTrace();\r
 242                         fail(e.getLocalizedMessage());\r
 243                 } catch (ResultNotAvailableException e) {\r
 244                         e.printStackTrace();\r
 245                         fail(e.getLocalizedMessage());\r
 246                 } catch (JobExecutionException e) {\r
 247                         e.printStackTrace();\r
 248                         fail(e.getLocalizedMessage());\r
 249                 }\r
 250         }\r
 251         \r
 252         @Test(groups = {AllTestSuit.test_group_runner})\r
 253         public void readStatistics() {\r
 254                 try {\r
 255                         ConfiguredExecutable<AACon> confAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
 256                         // For local execution use relative\r
 257 \r
 258                         AsyncExecutor sexec = Configurator.getAsyncEngine(confAAcon);\r
 259                         String jobId = sexec.submitJob(confAAcon);\r
 260                         String file = confAAcon.getWorkDirectory() + File.separator + AACon.getStatFile();\r
 261                         FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 262                         int count = 0;\r
 263                         long position = 0;\r
 264                         fw.waitForFile(2);\r
 265                         JobStatus status = sexec.getJobStatus(jobId);\r
 266                         do {\r
 267                                 if (fw.hasMoreData()) {\r
 268                                         ChunkHolder ch = fw.pull(position);\r
 269                                         String chunk = ch.getChunk();\r
 270                                         position = ch.getNextPosition();\r
 271                                 }\r
 272                                 count++;\r
 273                                 // Make sure the loop is terminated if the job fails\r
 274                                 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 275                                         fail("job failed!");\r
 276                                         break;\r
 277                                 }\r
 278                                 Thread.sleep(300);\r
 279                                 status = sexec.getJobStatus(jobId);\r
 280                         } while (status != JobStatus.FINISHED || fw.hasMoreData());\r
 281                         assertTrue(count >= 1);\r
 282                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 283                         assertNotNull(al.getResults());\r
 284                 } catch (JobSubmissionException e) {\r
 285                         e.printStackTrace();\r
 286                         fail(e.getMessage());\r
 287                 } catch (ResultNotAvailableException e) {\r
 288                         e.printStackTrace();\r
 289                         fail(e.getMessage());\r
 290                 } catch (IOException e) {\r
 291                         e.printStackTrace();\r
 292                         fail(e.getMessage());\r
 293                 } catch (InterruptedException e) {\r
 294                         e.printStackTrace();\r
 295                         fail(e.getMessage());\r
 296                 }\r
 297         }\r
 298 \r
 299         @Test(groups = {AllTestSuit.test_group_runner})\r
 300         public void Persistance() {\r
 301                 try {\r
 302                         AACon aacon = new AACon();\r
 303                         aacon.setError("errrr.txt");\r
 304                         aacon.setInput(test_alignment_input);\r
 305                         aacon.setOutput("outtt.txt");\r
 306                         assertEquals(aacon.getInput(), test_alignment_input);\r
 307                         assertEquals(aacon.getError(), "errrr.txt");\r
 308                         assertEquals(aacon.getOutput(), "outtt.txt");\r
 309                         ConfiguredExecutable<AACon> cAAcon = Configurator.configureExecutable(aacon, Executable.ExecProvider.Local);\r
 310 \r
 311                         SyncExecutor sexec = Configurator.getSyncEngine(cAAcon);\r
 312                         sexec.executeJob();\r
 313                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 314                         assertNotNull(al.getResults());\r
 315 \r
 316                         // Save run configuration\r
 317                         assertTrue(cAAcon.saveRunConfiguration());\r
 318 \r
 319                         // See if loaded configuration is the same as saved\r
 320                         RunConfiguration loadedRun = RunConfiguration\r
 321                                         .load(new FileInputStream(new File(cAAcon\r
 322                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 323                         assertEquals(((ConfExecutable<AACon>) cAAcon).getRunConfiguration(),loadedRun);\r
 324 \r
 325                         // Load run configuration as ConfExecutable\r
 326                         ConfiguredExecutable<AACon> resurrectedCAAcon = (ConfiguredExecutable<AACon>) cAAcon\r
 327                                         .loadRunConfiguration(new FileInputStream(new File(cAAcon\r
 328                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 329                         assertNotNull(resurrectedCAAcon);\r
 330                         assertEquals(resurrectedCAAcon.getExecutable().getInput(), test_alignment_input);\r
 331                         assertEquals(resurrectedCAAcon.getExecutable().getError(), "errrr.txt");\r
 332                         assertEquals(resurrectedCAAcon.getExecutable().getOutput(), "outtt.txt");\r
 333 \r
 334                         // See in details whether executables are the same\r
 335                         assertEquals(resurrectedCAAcon.getExecutable(), aacon);\r
 336 \r
 337                         ConfiguredExecutable<AACon> resAAcon = Configurator.configureExecutable(resurrectedCAAcon.getExecutable(),\r
 338                                                         Executable.ExecProvider.Local);\r
 339 \r
 340                         sexec = Configurator.getSyncEngine(resAAcon, Executable.ExecProvider.Local);\r
 341                         sexec.executeJob();\r
 342                         al = sexec.waitForResult();\r
 343                         assertNotNull(al);\r
 344                 } catch (JobSubmissionException e) {\r
 345                         e.printStackTrace();\r
 346                         fail(e.getMessage());\r
 347                 } catch (JobExecutionException e) {\r
 348                         e.printStackTrace();\r
 349                         fail(e.getMessage());\r
 350                 } catch (FileNotFoundException e) {\r
 351                         e.printStackTrace();\r
 352                         fail(e.getMessage());\r
 353                 } catch (IOException e) {\r
 354                         e.printStackTrace();\r
 355                         fail(e.getMessage());\r
 356                 } catch (ResultNotAvailableException e) {\r
 357                         e.printStackTrace();\r
 358                         fail(e.getMessage());\r
 359                 }\r
 360         }\r
 361 \r
 362         @Test(groups = {AllTestSuit.test_group_runner})\r
 363         public void ConfigurationLoading() {\r
 364                 try {\r
 365                         RunnerConfig<AACon> aaconConfig = ConfExecutable.getRunnerOptions(AACon.class);\r
 366                         assertNotNull(aaconConfig);\r
 367                         assertTrue(aaconConfig.getArguments().size() > 0);\r
 368 \r
 369                         PresetManager<AACon> aaconPresets = ConfExecutable.getRunnerPresets(AACon.class);\r
 370                         assertNotNull(aaconPresets);\r
 371 \r
 372                         LimitsManager<AACon> aaconLimits = ConfExecutable.getRunnerLimits(AACon.class);\r
 373                         assertNotNull(aaconLimits);\r
 374                         assertTrue(aaconLimits.getLimits().size() > 0);\r
 375                         aaconLimits.validate(aaconPresets);\r
 376                 } catch (FileNotFoundException e) {\r
 377                         e.printStackTrace();\r
 378                         fail(e.getLocalizedMessage());\r
 379                 } catch (IOException e) {\r
 380                         e.printStackTrace();\r
 381                         fail(e.getLocalizedMessage());\r
 382                 } catch (ValidationException e) {\r
 383                         e.printStackTrace();\r
 384                         fail(e.getLocalizedMessage());\r
 385                 }\r
 386         }\r
 387 }\r