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