testsrc/compbio/casscode/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 import java.util.Map;\r
  35 import java.util.Set;\r
  36 \r
  37 import javax.xml.bind.ValidationException;\r
  38 \r
  39 import org.ggf.drmaa.DrmaaException;\r
  40 import org.ggf.drmaa.JobInfo;\r
  41 import org.testng.annotations.BeforeMethod;\r
  42 import org.testng.annotations.Test;\r
  43 \r
  44 import compbio.data.sequence.Score;\r
  45 import compbio.data.sequence.ScoreManager;\r
  46 import compbio.engine.AsyncExecutor;\r
  47 import compbio.engine.Configurator;\r
  48 import compbio.engine.FilePuller;\r
  49 import compbio.engine.SyncExecutor;\r
  50 import compbio.engine.client.ConfExecutable;\r
  51 import compbio.engine.client.ConfiguredExecutable;\r
  52 import compbio.engine.client.Executable;\r
  53 import compbio.engine.client.RunConfiguration;\r
  54 import compbio.engine.cluster.drmaa.ClusterEngineUtil;\r
  55 import compbio.engine.cluster.drmaa.ClusterRunner;\r
  56 import compbio.engine.cluster.drmaa.StatisticManager;\r
  57 import compbio.engine.local.LocalRunner;\r
  58 import compbio.metadata.AllTestSuit;\r
  59 import compbio.metadata.ChunkHolder;\r
  60 import compbio.metadata.JobExecutionException;\r
  61 import compbio.metadata.JobStatus;\r
  62 import compbio.metadata.JobSubmissionException;\r
  63 import compbio.metadata.LimitsManager;\r
  64 import compbio.metadata.PresetManager;\r
  65 import compbio.metadata.ResultNotAvailableException;\r
  66 import compbio.metadata.RunnerConfig;\r
  67 import compbio.util.FileWatcher;\r
  68 import compbio.util.SysPrefs;\r
  69 \r
  70 public class DisemblTester {\r
  71 \r
  72         public static String test_outfile = "TO1381.disembl.out";\r
  73 \r
  74         private Disembl disembl;\r
  75 \r
  76         @BeforeMethod(alwaysRun = true)\r
  77         void init() {\r
  78                 disembl = new Disembl();\r
  79                 disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
  80         }\r
  81 \r
  82         @Test(groups = {AllTestSuit.test_group_cluster,\r
  83                         AllTestSuit.test_group_runner})\r
  84         public void testRunOnCluster() {\r
  85                 assertFalse(SysPrefs.isWindows,\r
  86                                 "Cluster execution can only be in unix environment");\r
  87                 try {\r
  88                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
  89                                         .configureExecutable(disembl,\r
  90                                                         Executable.ExecProvider.Cluster);\r
  91                         ClusterRunner runner = ClusterRunner.getInstance(confDisembl);\r
  92 \r
  93                         assertNotNull(runner, "Runner is NULL");\r
  94                         runner.executeJob();\r
  95                         // assertNotNull("JobId is null", jobId1);\r
  96                         JobStatus status = runner.getJobStatus();\r
  97                         assertTrue(status == JobStatus.PENDING\r
  98                                         || status == JobStatus.RUNNING,\r
  99                                         "Status of the process is wrong!");\r
 100                         JobInfo info = runner.getJobInfo();\r
 101                         assertNotNull(info, "JobInfo is null");\r
 102                         StatisticManager sm = new StatisticManager(info);\r
 103                         assertNotNull(sm, "Statictic manager is null");\r
 104                         try {\r
 105 \r
 106                                 String exits = sm.getExitStatus();\r
 107                                 assertNotNull("Exit status is null", exits);\r
 108                                 // cut 4 trailing zeros from the number\r
 109                                 int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 110                                                 .intValue();\r
 111                                 assertEquals(0, exitsInt);\r
 112                                 System.out.println(sm.getAllStats());\r
 113 \r
 114                         } catch (ParseException e) {\r
 115                                 e.printStackTrace();\r
 116                                 fail("Parse Exception: " + e.getMessage());\r
 117                         }\r
 118                         // assertFalse(runner.cleanup());\r
 119                         assertTrue(sm.hasExited());\r
 120                         assertFalse(sm.wasAborted());\r
 121                         assertFalse(sm.hasDump());\r
 122                         assertFalse(sm.hasSignaled());\r
 123 \r
 124                 } catch (JobSubmissionException e) {\r
 125                         e.printStackTrace();\r
 126                         fail("DrmaaException caught:" + e.getMessage());\r
 127                 } catch (JobExecutionException e) {\r
 128                         e.printStackTrace();\r
 129                         fail("DrmaaException caught:" + e.getMessage());\r
 130                 } catch (DrmaaException e) {\r
 131                         e.printStackTrace();\r
 132                         fail("DrmaaException caught:" + e.getMessage());\r
 133                 }\r
 134         }\r
 135 \r
 136         /**\r
 137          * This tests fails from time to time depending on the cluster load or some\r
 138          * other factors. Any client code has to adjust for this issue\r
 139          */\r
 140         @Test(groups = {AllTestSuit.test_group_cluster,\r
 141                         AllTestSuit.test_group_runner})\r
 142         public void testRunOnClusterAsync() {\r
 143                 assertFalse(SysPrefs.isWindows,\r
 144                                 "Cluster execution can only be in unix environment");\r
 145                 try {\r
 146                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 147                                         .configureExecutable(disembl,\r
 148                                                         Executable.ExecProvider.Cluster);\r
 149                         AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);\r
 150                         String jobId = aengine.submitJob(confDisembl);\r
 151                         assertNotNull(jobId, "Runner is NULL");\r
 152                         // let drmaa to start\r
 153                         Thread.sleep(500);\r
 154                         JobStatus status = aengine.getJobStatus(jobId);\r
 155                         while (status != JobStatus.FINISHED) {\r
 156                                 System.out.println("Job Status: " + status);\r
 157                                 Thread.sleep(1000);\r
 158                                 status = aengine.getJobStatus(jobId);\r
 159                                 ConfiguredExecutable<Disembl> result = (ConfiguredExecutable<Disembl>) aengine\r
 160                                                 .getResults(jobId);\r
 161                                 assertNotNull(result);\r
 162                                 System.out.println("RES:" + result);\r
 163                                 // Some times the job could be removed from the cluster\r
 164                                 // accounting\r
 165                                 // before it has been reported to finish. Make sure\r
 166                                 // to stop waiting in such case\r
 167                                 if (status == JobStatus.UNDEFINED) {\r
 168                                         break;\r
 169                                 }\r
 170                         }\r
 171                 } catch (JobSubmissionException e) {\r
 172                         e.printStackTrace();\r
 173                         fail("DrmaaException caught:" + e.getMessage());\r
 174                 } catch (InterruptedException e) {\r
 175                         e.printStackTrace();\r
 176                         fail(e.getMessage());\r
 177                 } catch (ResultNotAvailableException e) {\r
 178                         e.printStackTrace();\r
 179                         fail(e.getMessage());\r
 180                 }\r
 181         }\r
 182 \r
 183         @Test(groups = {AllTestSuit.test_group_runner})\r
 184         public void testRunLocally() {\r
 185                 try {\r
 186                         ConfiguredExecutable<Disembl> confDisembl = Configurator\r
 187                                         .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 188 \r
 189                         // For local execution use relative\r
 190                         LocalRunner lr = new LocalRunner(confDisembl);\r
 191                         lr.executeJob();\r
 192                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 193                         assertNotNull(al1.getResults());\r
 194                         ScoreManager al2 = confDisembl.getResults();\r
 195                         assertNotNull(al2);\r
 196                         assertEquals(al2.asMap().size(), 3);\r
 197                         assertEquals(al1.getResults(), al2);\r
 198                 } catch (JobSubmissionException e) {\r
 199                         e.printStackTrace();\r
 200                         fail(e.getLocalizedMessage());\r
 201                 } catch (ResultNotAvailableException e) {\r
 202                         e.printStackTrace();\r
 203                         fail(e.getLocalizedMessage());\r
 204                 } catch (JobExecutionException e) {\r
 205                         e.printStackTrace();\r
 206                         fail(e.getLocalizedMessage());\r
 207                 }\r
 208         }\r
 209 \r
 210         @Test(groups = {AllTestSuit.test_group_runner})\r
 211         public void readStatistics() {\r
 212                 // No execution statistics is available!\r
 213         }\r
 214 \r
 215         @Test(groups = {AllTestSuit.test_group_runner})\r
 216         public void testPersistance() {\r
 217                 try {\r
 218                         Disembl disembl = new Disembl();\r
 219                         disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 220                                         .setOutput("outtt.txt");\r
 221                         assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
 222                         assertEquals(disembl.getError(), "errrr.txt");\r
 223                         assertEquals(disembl.getOutput(), "outtt.txt");\r
 224                         ConfiguredExecutable<Disembl> cDisembl = Configurator\r
 225                                         .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 226 \r
 227                         SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);\r
 228                         sexec.executeJob();\r
 229                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 230                         assertNotNull(al.getResults());\r
 231                         // Save run configuration\r
 232                         assertTrue(cDisembl.saveRunConfiguration());\r
 233 \r
 234                         // See if loaded configuration is the same as saved\r
 235                         RunConfiguration loadedRun = RunConfiguration\r
 236                                         .load(new FileInputStream(new File(cDisembl\r
 237                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 238                         assertEquals(\r
 239                                         ((ConfExecutable<Disembl>) cDisembl).getRunConfiguration(),\r
 240                                         loadedRun);\r
 241                         // Load run configuration as ConfExecutable\r
 242                         ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl\r
 243                                         .loadRunConfiguration(new FileInputStream(new File(cDisembl\r
 244                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 245                         assertNotNull(resurrectedCDisembl);\r
 246                         assertEquals(resurrectedCDisembl.getExecutable().getInput(),\r
 247                                         AllTestSuit.test_input);\r
 248                         assertEquals(resurrectedCDisembl.getExecutable().getError(),\r
 249                                         "errrr.txt");\r
 250                         assertEquals(resurrectedCDisembl.getExecutable().getOutput(),\r
 251                                         "outtt.txt");\r
 252                         // See in details whether executables are the same\r
 253                         assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
 254 \r
 255                         ConfiguredExecutable<Disembl> resDisembl = Configurator\r
 256                                         .configureExecutable(resurrectedCDisembl.getExecutable(),\r
 257                                                         Executable.ExecProvider.Local);\r
 258 \r
 259                         sexec = Configurator.getSyncEngine(resDisembl,\r
 260                                         Executable.ExecProvider.Local);\r
 261                         sexec.executeJob();\r
 262                         al = sexec.waitForResult();\r
 263                         assertNotNull(al);\r
 264 \r
 265                 } catch (JobSubmissionException e) {\r
 266                         e.printStackTrace();\r
 267                         fail(e.getMessage());\r
 268                 } catch (JobExecutionException e) {\r
 269                         e.printStackTrace();\r
 270                         fail(e.getMessage());\r
 271                 } catch (FileNotFoundException e) {\r
 272                         e.printStackTrace();\r
 273                         fail(e.getMessage());\r
 274                 } catch (IOException e) {\r
 275                         e.printStackTrace();\r
 276                         fail(e.getMessage());\r
 277                 } catch (ResultNotAvailableException e) {\r
 278                         e.printStackTrace();\r
 279                         fail(e.getMessage());\r
 280                 }\r
 281         }\r
 282 \r
 283         @Test(groups = {AllTestSuit.test_group_runner})\r
 284         public void testConfigurationLoading() {\r
 285                 try {\r
 286                         RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
 287                                         .getRunnerOptions(Disembl.class);\r
 288                         // There is no disembl parameters\r
 289                         assertNull(disemblConfig);\r
 290 \r
 291                         //If there were a DisemblParameter.xml file and reference to it, \r
 292                         // it would be like that \r
 293                         // assertTrue(disemblConfig.getArguments().size() == 0);\r
 294 \r
 295                         PresetManager<Disembl> disemblPresets = ConfExecutable\r
 296                                         .getRunnerPresets(Disembl.class);\r
 297                         assertNull(disemblPresets); // there is no presets\r
 298 \r
 299                         LimitsManager<Disembl> disemblLimits = ConfExecutable\r
 300                                         .getRunnerLimits(Disembl.class);\r
 301                         assertNotNull(disemblLimits);\r
 302                         assertTrue(disemblLimits.getLimits().size() > 0);\r
 303                         disemblLimits.validate(disemblPresets);\r
 304 \r
 305                 } catch (FileNotFoundException e) {\r
 306                         e.printStackTrace();\r
 307                         fail(e.getLocalizedMessage());\r
 308                 } catch (IOException e) {\r
 309                         e.printStackTrace();\r
 310                         fail(e.getLocalizedMessage());\r
 311                 } catch (ValidationException e) {\r
 312                         e.printStackTrace();\r
 313                         fail(e.getLocalizedMessage());\r
 314                 }\r
 315         }\r
 316 \r
 317 }\r