testsrc/compbio/casscode/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