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