testsrc/compbio/runner/disorder/IUPredTester.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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 \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.ScoreManager;\r
  42 import compbio.engine.AsyncExecutor;\r
  43 import compbio.engine.Configurator;\r
  44 import compbio.engine.SyncExecutor;\r
  45 import compbio.engine.client.ConfExecutable;\r
  46 import compbio.engine.client.ConfiguredExecutable;\r
  47 import compbio.engine.client.Executable;\r
  48 import compbio.engine.client.RunConfiguration;\r
  49 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  50 import compbio.engine.cluster.drmaa.JobRunner;\r
  51 import compbio.engine.cluster.drmaa.StatisticManager;\r
  52 import compbio.engine.local.LocalRunner;\r
  53 import compbio.metadata.AllTestSuit;\r
  54 import compbio.metadata.JobExecutionException;\r
  55 import compbio.metadata.JobStatus;\r
  56 import compbio.metadata.JobSubmissionException;\r
  57 import compbio.metadata.LimitsManager;\r
  58 import compbio.metadata.PresetManager;\r
  59 import compbio.metadata.ResultNotAvailableException;\r
  60 import compbio.metadata.RunnerConfig;\r
  61 import compbio.util.SysPrefs;\r
  62 \r
  63 public class IUPredTester {\r
  64 \r
  65         public static String test_outfile = "output";\r
  66 \r
  67         private IUPred iupred;\r
  68 \r
  69         @BeforeMethod(alwaysRun = true)\r
  70         void init() {\r
  71                 iupred = new IUPred();\r
  72                 iupred.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
  73         }\r
  74 \r
  75         @Test(groups = {AllTestSuit.test_group_cluster,\r
  76                         AllTestSuit.test_group_runner})\r
  77         public void testRunOnCluster() {\r
  78                 assertFalse(SysPrefs.isWindows,\r
  79                                 "Cluster execution can only be in unix environment");\r
  80                 try {\r
  81                         ConfiguredExecutable<IUPred> confIUPred = Configurator\r
  82                                         .configureExecutable(iupred,\r
  83                                                         Executable.ExecProvider.Cluster);\r
  84                         JobRunner runner = JobRunner.getInstance(confIUPred);\r
  85 \r
  86                         assertNotNull(runner, "Runner is NULL");\r
  87                         runner.executeJob();\r
  88                         // assertNotNull("JobId is null", jobId1);\r
  89                         JobStatus status = runner.getJobStatus();\r
  90                         assertTrue(status == JobStatus.PENDING\r
  91                                         || status == JobStatus.RUNNING,\r
  92                                         "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 \r
  99                                 String exits = sm.getExitStatus();\r
 100                                 assertNotNull("Exit status is null", exits);\r
 101                                 // cut 4 trailing zeros from the number\r
 102                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 103                                                 .intValue();\r
 104                                 assertEquals(0, exitsInt);\r
 105                                 System.out.println(sm.getAllStats());\r
 106 \r
 107                         } catch (ParseException e) {\r
 108                                 e.printStackTrace();\r
 109                                 fail("Parse Exception: " + e.getMessage());\r
 110                         }\r
 111                         // assertFalse(runner.cleanup());\r
 112                         assertTrue(sm.hasExited());\r
 113                         assertFalse(sm.wasAborted());\r
 114                         assertFalse(sm.hasDump());\r
 115                         assertFalse(sm.hasSignaled());\r
 116 \r
 117                 } catch (JobSubmissionException e) {\r
 118                         e.printStackTrace();\r
 119                         fail("DrmaaException caught:" + e.getMessage());\r
 120                 } catch (JobExecutionException e) {\r
 121                         e.printStackTrace();\r
 122                         fail("DrmaaException caught:" + e.getMessage());\r
 123                 } catch (DrmaaException e) {\r
 124                         e.printStackTrace();\r
 125                         fail("DrmaaException caught:" + e.getMessage());\r
 126                 }\r
 127         }\r
 128 \r
 129         /**\r
 130          * This tests fails from time to time depending on the cluster load or some\r
 131          * other factors. Any client code has to adjust for this issue\r
 132          */\r
 133         @Test(groups = {AllTestSuit.test_group_cluster,\r
 134                         AllTestSuit.test_group_runner})\r
 135         public void testRunOnClusterAsync() {\r
 136                 assertFalse(SysPrefs.isWindows,\r
 137                                 "Cluster execution can only be in unix environment");\r
 138                 try {\r
 139                         ConfiguredExecutable<IUPred> confIUPred = Configurator\r
 140                                         .configureExecutable(iupred,\r
 141                                                         Executable.ExecProvider.Cluster);\r
 142                         AsyncExecutor aengine = Configurator.getAsyncEngine(confIUPred);\r
 143                         String jobId = aengine.submitJob(confIUPred);\r
 144                         assertNotNull(jobId, "Runner is NULL");\r
 145                         // let drmaa to start\r
 146                         Thread.sleep(500);\r
 147                         JobStatus status = aengine.getJobStatus(jobId);\r
 148                         while (status != JobStatus.FINISHED) {\r
 149                                 System.out.println("Job Status: " + status);\r
 150                                 Thread.sleep(1000);\r
 151                                 status = aengine.getJobStatus(jobId);\r
 152                                 ConfiguredExecutable<IUPred> result = (ConfiguredExecutable<IUPred>) aengine\r
 153                                                 .getResults(jobId);\r
 154                                 assertNotNull(result);\r
 155                                 System.out.println("RES:" + result);\r
 156                                 // Some times the job could be removed from the cluster\r
 157                                 // accounting\r
 158                                 // before it has been reported to finish. Make sure\r
 159                                 // to stop waiting in such case\r
 160                                 if (status == JobStatus.UNDEFINED) {\r
 161                                         break;\r
 162                                 }\r
 163                         }\r
 164                 } catch (JobSubmissionException e) {\r
 165                         e.printStackTrace();\r
 166                         fail("DrmaaException caught:" + e.getMessage());\r
 167                 } catch (InterruptedException e) {\r
 168                         e.printStackTrace();\r
 169                         fail(e.getMessage());\r
 170                 } catch (ResultNotAvailableException e) {\r
 171                         e.printStackTrace();\r
 172                         fail(e.getMessage());\r
 173                 }\r
 174         }\r
 175 \r
 176         @Test(groups = {AllTestSuit.test_group_runner})\r
 177         public void testRunLocally() {\r
 178                 try {\r
 179                         ConfiguredExecutable<IUPred> confIUPred = Configurator\r
 180                                         .configureExecutable(iupred, Executable.ExecProvider.Local);\r
 181 \r
 182                         // For local execution use relative\r
 183                         LocalRunner lr = new LocalRunner(confIUPred);\r
 184                         lr.executeJob();\r
 185                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 186                         assertNotNull(al1.getResults());\r
 187                         ScoreManager al2 = confIUPred.getResults();\r
 188                         assertNotNull(al2);\r
 189                         assertEquals(al2.asMap().size(), 3);\r
 190                         assertEquals(al1.getResults(), al2);\r
 191                 } catch (JobSubmissionException e) {\r
 192                         e.printStackTrace();\r
 193                         fail(e.getLocalizedMessage());\r
 194                 } catch (ResultNotAvailableException e) {\r
 195                         e.printStackTrace();\r
 196                         fail(e.getLocalizedMessage());\r
 197                 } catch (JobExecutionException e) {\r
 198                         e.printStackTrace();\r
 199                         fail(e.getLocalizedMessage());\r
 200                 }\r
 201         }\r
 202 \r
 203         @Test(groups = {AllTestSuit.test_group_runner})\r
 204         public void readStatistics() {\r
 205                 // No execution statistics is available!\r
 206         }\r
 207 \r
 208         @Test(groups = {AllTestSuit.test_group_runner})\r
 209         public void testPersistance() {\r
 210                 try {\r
 211                         IUPred disembl = new IUPred();\r
 212                         disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 213                                         .setOutput("outtt.txt");\r
 214                         assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
 215                         assertEquals(disembl.getError(), "errrr.txt");\r
 216                         assertEquals(disembl.getOutput(), "outtt.txt");\r
 217                         ConfiguredExecutable<IUPred> cIUPred = Configurator\r
 218                                         .configureExecutable(disembl, Executable.ExecProvider.Local);\r
 219 \r
 220                         SyncExecutor sexec = Configurator.getSyncEngine(cIUPred);\r
 221                         sexec.executeJob();\r
 222                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 223                         assertNotNull(al.getResults());\r
 224                         // Save run configuration\r
 225                         assertTrue(cIUPred.saveRunConfiguration());\r
 226 \r
 227                         // See if loaded configuration is the same as saved\r
 228                         RunConfiguration loadedRun = RunConfiguration\r
 229                                         .load(new FileInputStream(new File(cIUPred\r
 230                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 231                         assertEquals(\r
 232                                         ((ConfExecutable<IUPred>) cIUPred).getRunConfiguration(),\r
 233                                         loadedRun);\r
 234                         // Load run configuration as ConfExecutable\r
 235                         ConfiguredExecutable<IUPred> resurrectedCIUPred = (ConfiguredExecutable<IUPred>) cIUPred\r
 236                                         .loadRunConfiguration(new FileInputStream(new File(cIUPred\r
 237                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 238                         assertNotNull(resurrectedCIUPred);\r
 239                         assertEquals(resurrectedCIUPred.getExecutable().getInput(),\r
 240                                         AllTestSuit.test_input);\r
 241                         assertEquals(resurrectedCIUPred.getExecutable().getError(),\r
 242                                         "errrr.txt");\r
 243                         assertEquals(resurrectedCIUPred.getExecutable().getOutput(),\r
 244                                         "outtt.txt");\r
 245                         // See in details whether executables are the same\r
 246                         assertEquals(resurrectedCIUPred.getExecutable(), disembl);\r
 247 \r
 248                         ConfiguredExecutable<IUPred> resIUPred = Configurator\r
 249                                         .configureExecutable(resurrectedCIUPred.getExecutable(),\r
 250                                                         Executable.ExecProvider.Local);\r
 251 \r
 252                         sexec = Configurator.getSyncEngine(resIUPred,\r
 253                                         Executable.ExecProvider.Local);\r
 254                         sexec.executeJob();\r
 255                         al = sexec.waitForResult();\r
 256                         assertNotNull(al);\r
 257 \r
 258                 } catch (JobSubmissionException e) {\r
 259                         e.printStackTrace();\r
 260                         fail(e.getMessage());\r
 261                 } catch (JobExecutionException e) {\r
 262                         e.printStackTrace();\r
 263                         fail(e.getMessage());\r
 264                 } catch (FileNotFoundException e) {\r
 265                         e.printStackTrace();\r
 266                         fail(e.getMessage());\r
 267                 } catch (IOException e) {\r
 268                         e.printStackTrace();\r
 269                         fail(e.getMessage());\r
 270                 } catch (ResultNotAvailableException e) {\r
 271                         e.printStackTrace();\r
 272                         fail(e.getMessage());\r
 273                 }\r
 274         }\r
 275 \r
 276         @Test(groups = {AllTestSuit.test_group_runner})\r
 277         public void testConfigurationLoading() {\r
 278                 try {\r
 279                         RunnerConfig<IUPred> disemblConfig = ConfExecutable\r
 280                                         .getRunnerOptions(IUPred.class);\r
 281                         // There is no disembl parameters\r
 282                         assertNull(disemblConfig);\r
 283 \r
 284                         // If there were a IUPredParameter.xml file and reference to it,\r
 285                         // it would be like that\r
 286                         // assertTrue(disemblConfig.getArguments().size() == 0);\r
 287 \r
 288                         PresetManager<IUPred> disemblPresets = ConfExecutable\r
 289                                         .getRunnerPresets(IUPred.class);\r
 290                         assertNull(disemblPresets); // there is no presets\r
 291 \r
 292                         LimitsManager<IUPred> disemblLimits = ConfExecutable\r
 293                                         .getRunnerLimits(IUPred.class);\r
 294                         assertNotNull(disemblLimits);\r
 295                         assertTrue(disemblLimits.getLimits().size() > 0);\r
 296                         disemblLimits.validate(disemblPresets);\r
 297 \r
 298                 } catch (FileNotFoundException e) {\r
 299                         e.printStackTrace();\r
 300                         fail(e.getLocalizedMessage());\r
 301                 } catch (IOException e) {\r
 302                         e.printStackTrace();\r
 303                         fail(e.getLocalizedMessage());\r
 304                 } catch (ValidationException e) {\r
 305                         e.printStackTrace();\r
 306                         fail(e.getLocalizedMessage());\r
 307                 }\r
 308         }\r
 309 \r
 310 }\r