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.List;\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.AnnotatedSequence;\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 accounting \r
 161                 // before it has been reported to finish. Make sure \r
 162                 // to stop waiting in such case\r
 163                 if (status == JobStatus.UNDEFINED) {\r
 164                     break;\r
 165                 }\r
 166             }\r
 167         } catch (JobSubmissionException e) {\r
 168             e.printStackTrace();\r
 169             fail("DrmaaException caught:" + e.getMessage());\r
 170         } catch (InterruptedException e) {\r
 171             e.printStackTrace();\r
 172             fail(e.getMessage());\r
 173         } catch (ResultNotAvailableException e) {\r
 174             e.printStackTrace();\r
 175             fail(e.getMessage());\r
 176         }\r
 177     }\r
 178 \r
 179     @Test(groups = { AllTestSuit.test_group_runner })\r
 180     public void testRunLocally() {\r
 181         try {\r
 182             ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 183                     .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 184 \r
 185             // For local execution use relative\r
 186             LocalRunner lr = new LocalRunner(confDisembl);\r
 187             lr.executeJob();\r
 188             ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 189             assertNotNull(al1.getResults());\r
 190             List<AnnotatedSequence> al2 = confDisembl.getResults();\r
 191             assertNotNull(al2);\r
 192             assertEquals(al2.size(), 3);\r
 193             assertEquals(al1.getResults(), al2);\r
 194         } catch (JobSubmissionException e) {\r
 195             e.printStackTrace();\r
 196             fail(e.getLocalizedMessage());\r
 197         } catch (ResultNotAvailableException e) {\r
 198             e.printStackTrace();\r
 199             fail(e.getLocalizedMessage());\r
 200         } catch (JobExecutionException e) {\r
 201             e.printStackTrace();\r
 202             fail(e.getLocalizedMessage());\r
 203         }\r
 204     }\r
 205 \r
 206     @Test(groups = { AllTestSuit.test_group_runner })\r
 207     public void readStatistics() {\r
 208         try {\r
 209             ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 210                     .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 211             // For local execution use relavive\r
 212 \r
 213             AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);\r
 214             String jobId = sexec.submitJob(confDisembl);\r
 215             FilePuller fw = FilePuller.newFilePuller(confDisembl\r
 216                     .getWorkDirectory()\r
 217                     + File.separator + Jronn.getStatFile(),\r
 218                     FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 219             int count = 0;\r
 220             long position = 0;\r
 221             fw.waitForFile(4);\r
 222             JobStatus status = sexec.getJobStatus(jobId);\r
 223             while (status != JobStatus.FINISHED) {\r
 224                 if (fw.hasMoreData()) {\r
 225                     ChunkHolder ch = fw.pull(position);\r
 226                     String chunk = ch.getChunk();\r
 227                     position = ch.getNextPosition();\r
 228                 }\r
 229                 count++;\r
 230                 // Make sure the loop is terminated if the job fails\r
 231                 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
 232                     break;\r
 233                 }\r
 234                 Thread.sleep(300);\r
 235                 status = sexec.getJobStatus(jobId);\r
 236             }\r
 237             assertTrue(count > 1);\r
 238             ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 239             assertNotNull(al.getResults());\r
 240         } catch (JobSubmissionException e) {\r
 241             e.printStackTrace();\r
 242             fail(e.getMessage());\r
 243         } catch (ResultNotAvailableException e) {\r
 244             e.printStackTrace();\r
 245             fail(e.getMessage());\r
 246         } catch (IOException e) {\r
 247             e.printStackTrace();\r
 248             fail(e.getMessage());\r
 249         } catch (InterruptedException e) {\r
 250             e.printStackTrace();\r
 251             fail(e.getMessage());\r
 252         }\r
 253     }\r
 254 \r
 255     @Test(groups = { AllTestSuit.test_group_runner })\r
 256     public void testPersistance() {\r
 257         try {\r
 258             Disembl disembl = new Disembl();\r
 259             disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 260                     .setOutput("outtt.txt");\r
 261             assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
 262             assertEquals(disembl.getError(), "errrr.txt");\r
 263             assertEquals(disembl.getOutput(), "outtt.txt");\r
 264             ConfiguredExecutable<Disembl> cDisembl = Configurator\r
 265                     .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 266 \r
 267             SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);\r
 268             sexec.executeJob();\r
 269             ConfiguredExecutable<?> al = sexec.waitForResult();\r
 270             assertNotNull(al.getResults());\r
 271             // Save run configuration\r
 272             assertTrue(cDisembl.saveRunConfiguration());\r
 273 \r
 274             // See if loaded configuration is the same as saved\r
 275             RunConfiguration loadedRun = RunConfiguration\r
 276                     .load(new FileInputStream(new File(cDisembl\r
 277                             .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 278             assertEquals(((ConfExecutable<Disembl>) cDisembl)\r
 279                     .getRunConfiguration(), loadedRun);\r
 280             // Load run configuration as ConfExecutable\r
 281             ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl\r
 282                     .loadRunConfiguration(new FileInputStream(new File(cDisembl\r
 283                             .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 284             assertNotNull(resurrectedCDisembl);\r
 285             assertEquals(resurrectedCDisembl.getExecutable().getInput(),\r
 286                     AllTestSuit.test_input);\r
 287             assertEquals(resurrectedCDisembl.getExecutable().getError(),\r
 288                     "errrr.txt");\r
 289             assertEquals(resurrectedCDisembl.getExecutable().getOutput(),\r
 290                     "outtt.txt");\r
 291             // See in details whether executables are the same\r
 292             assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
 293 \r
 294             ConfiguredExecutable<Disembl> resJronn = Configurator\r
 295                     .configureExecutable(resurrectedCDisembl.getExecutable(),\r
 296                             Executable.ExecProvider.Local);\r
 297 \r
 298             sexec = Configurator.getSyncEngine(resJronn,\r
 299                     Executable.ExecProvider.Local);\r
 300             sexec.executeJob();\r
 301             al = sexec.waitForResult();\r
 302             assertNotNull(al);\r
 303 \r
 304         } catch (JobSubmissionException e) {\r
 305             e.printStackTrace();\r
 306             fail(e.getMessage());\r
 307         } catch (JobExecutionException e) {\r
 308             e.printStackTrace();\r
 309             fail(e.getMessage());\r
 310         } catch (FileNotFoundException e) {\r
 311             e.printStackTrace();\r
 312             fail(e.getMessage());\r
 313         } catch (IOException e) {\r
 314             e.printStackTrace();\r
 315             fail(e.getMessage());\r
 316         } catch (ResultNotAvailableException e) {\r
 317             e.printStackTrace();\r
 318             fail(e.getMessage());\r
 319         }\r
 320     }\r
 321 \r
 322     @Test(groups = { AllTestSuit.test_group_runner })\r
 323     public void testConfigurationLoading() {\r
 324         try {\r
 325             RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
 326                     .getRunnerOptions(Disembl.class);\r
 327             assertNotNull(disemblConfig);\r
 328             assertTrue(disemblConfig.getArguments().size() > 0);\r
 329 \r
 330             PresetManager<Disembl> disemblPresets = ConfExecutable\r
 331                     .getRunnerPresets(Disembl.class);\r
 332             assertNull(disemblPresets); // there is no presets\r
 333 \r
 334             LimitsManager<Disembl> disemblLimits = ConfExecutable\r
 335                     .getRunnerLimits(Disembl.class);\r
 336             assertNotNull(disemblLimits);\r
 337             assertTrue(disemblLimits.getLimits().size() > 0);\r
 338             disemblLimits.validate(disemblPresets);\r
 339 \r
 340         } catch (FileNotFoundException e) {\r
 341             e.printStackTrace();\r
 342             fail(e.getLocalizedMessage());\r
 343         } catch (IOException e) {\r
 344             e.printStackTrace();\r
 345             fail(e.getLocalizedMessage());\r
 346         } catch (ValidationException e) {\r
 347             e.printStackTrace();\r
 348             fail(e.getLocalizedMessage());\r
 349         }\r
 350     }\r
 351 \r
 352 }\r