testsrc/compbio/runner/msa/MuscleTester.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.msa;\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.assertNotSame;\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.Alignment;\r
  42 import compbio.engine.AsyncExecutor;\r
  43 import compbio.engine.Configurator;\r
  44 import compbio.engine.FilePuller;\r
  45 import compbio.engine.SyncExecutor;\r
  46 import compbio.engine.client.ConfExecutable;\r
  47 import compbio.engine.client.ConfiguredExecutable;\r
  48 import compbio.engine.client.Executable;\r
  49 import compbio.engine.client.RunConfiguration;\r
  50 import compbio.engine.cluster.drmaa.ClusterUtil;\r
  51 import compbio.engine.cluster.drmaa.JobRunner;\r
  52 import compbio.engine.cluster.drmaa.StatisticManager;\r
  53 import compbio.engine.local.LocalRunner;\r
  54 import compbio.metadata.AllTestSuit;\r
  55 import compbio.metadata.ChunkHolder;\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.runner.msa.Muscle;\r
  64 import compbio.util.FileWatcher;\r
  65 import compbio.util.SysPrefs;\r
  66 \r
  67 public class MuscleTester {\r
  68 \r
  69         public static String test_outfile = "TO1381.muscle.out"; // homes/pvtroshin/TO1381.clustal.out\r
  70         public static String cluster_test_outfile = "TO1381.muscle.cluster.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
  71 \r
  72         private Muscle muscle;\r
  73 \r
  74         @BeforeMethod(alwaysRun = true)\r
  75         void init() {\r
  76                 muscle = new Muscle();\r
  77                 muscle.setInput(AllTestSuit.test_input).setOutput(cluster_test_outfile);\r
  78         }\r
  79 \r
  80         @Test(groups = { AllTestSuit.test_group_cluster,\r
  81                         AllTestSuit.test_group_runner })\r
  82         public void testRunOnCluster() {\r
  83                 assertFalse(SysPrefs.isWindows,\r
  84                                 "Cluster execution can only be in unix environment");\r
  85                 try {\r
  86                         ConfiguredExecutable<Muscle> confMuscle = Configurator\r
  87                                         .configureExecutable(muscle,\r
  88                                                         Executable.ExecProvider.Cluster);\r
  89                         JobRunner runner = JobRunner.getInstance(confMuscle);\r
  90 \r
  91                         assertNotNull(runner, "Runner is NULL");\r
  92                         runner.executeJob();\r
  93                         // assertNotNull("JobId is null", jobId1);\r
  94                         JobStatus status = runner.getJobStatus();\r
  95                         assertTrue(status == JobStatus.PENDING\r
  96                                         || status == JobStatus.RUNNING,\r
  97                                         "Status of the process is wrong!");\r
  98                         JobInfo info = runner.getJobInfo();\r
  99                         assertNotNull(info, "JobInfo is null");\r
 100                         StatisticManager sm = new StatisticManager(info);\r
 101                         assertNotNull(sm, "Statictic manager is null");\r
 102                         try {\r
 103 \r
 104                                 String exits = sm.getExitStatus();\r
 105                                 assertNotNull("Exit status is null", exits);\r
 106                                 // cut 4 trailing zeros from the number\r
 107                                 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
 108                                                 .intValue();\r
 109                                 assertEquals(0, exitsInt);\r
 110                                 System.out.println(sm.getAllStats());\r
 111 \r
 112                         } catch (ParseException e) {\r
 113                                 e.printStackTrace();\r
 114                                 fail("Parse Exception: " + e.getMessage());\r
 115                         }\r
 116                         assertFalse(runner.cleanup());\r
 117                         assertTrue(sm.hasExited());\r
 118                         assertFalse(sm.wasAborted());\r
 119                         assertFalse(sm.hasDump());\r
 120                         assertFalse(sm.hasSignaled());\r
 121 \r
 122                 } catch (JobSubmissionException e) {\r
 123                         e.printStackTrace();\r
 124                         fail("DrmaaException caught:" + e.getMessage());\r
 125                 } catch (JobExecutionException e) {\r
 126                         e.printStackTrace();\r
 127                         fail("DrmaaException caught:" + e.getMessage());\r
 128                 } catch (DrmaaException e) {\r
 129                         e.printStackTrace();\r
 130                         fail("DrmaaException caught:" + e.getMessage());\r
 131                 }\r
 132         }\r
 133 \r
 134         /**\r
 135          * This tests fails from time to time depending on the cluster load or some\r
 136          * other factors. Any client code has to adjust for this issue\r
 137          */\r
 138         @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,\r
 139                         AllTestSuit.test_group_runner })\r
 140         public void testRunOnClusterAsync() {\r
 141                 assertFalse(SysPrefs.isWindows,\r
 142                                 "Cluster execution can only be in unix environment");\r
 143                 try {\r
 144                         ConfiguredExecutable<Muscle> confMuscle = Configurator\r
 145                                         .configureExecutable(muscle,\r
 146                                                         Executable.ExecProvider.Cluster);\r
 147                         AsyncExecutor aengine = Configurator.getAsyncEngine(confMuscle);\r
 148                         String jobId = aengine.submitJob(confMuscle);\r
 149                         assertNotNull(jobId, "Runner is NULL");\r
 150                         // let drmaa to start\r
 151                         Thread.sleep(500);\r
 152                         JobStatus status = aengine.getJobStatus(jobId);\r
 153                         while (status != JobStatus.FINISHED || status !=JobStatus.UNDEFINED) {\r
 154                                 System.out.println("Job Status: " + status);\r
 155                                 Thread.sleep(1000);\r
 156                                 status = aengine.getJobStatus(jobId);\r
 157                         }\r
 158                 } catch (JobSubmissionException e) {\r
 159                         e.printStackTrace();\r
 160                         fail("DrmaaException caught:" + e.getMessage());\r
 161                 } catch (InterruptedException e) {\r
 162                         e.printStackTrace();\r
 163                         fail(e.getMessage());\r
 164                 }\r
 165         }\r
 166 \r
 167         @Test(groups = { AllTestSuit.test_group_runner })\r
 168         public void testRunLocally() {\r
 169                 try {\r
 170                         ConfiguredExecutable<Muscle> confMuscle = Configurator\r
 171                                         .configureExecutable(muscle, Executable.ExecProvider.Local);\r
 172                         confMuscle.getParameters().setParam("-matrix", "BLOSUM62");\r
 173 \r
 174                         // For local execution use relative\r
 175                         LocalRunner lr = new LocalRunner(confMuscle);\r
 176                         lr.executeJob();\r
 177                         ConfiguredExecutable<?> al1 = lr.waitForResult();\r
 178                         assertNotNull(al1.getResults());\r
 179                         Alignment al2 = confMuscle.getResults();\r
 180                         assertNotNull(al2);\r
 181                         assertEquals(al1.getResults(), al2);\r
 182                 } catch (JobSubmissionException e) {\r
 183                         e.printStackTrace();\r
 184                         fail(e.getLocalizedMessage());\r
 185                 } catch (ResultNotAvailableException e) {\r
 186                         e.printStackTrace();\r
 187                         fail(e.getLocalizedMessage());\r
 188                 } catch (JobExecutionException e) {\r
 189                         e.printStackTrace();\r
 190                         fail(e.getLocalizedMessage());\r
 191                 }\r
 192         }\r
 193 \r
 194         @Test(groups = { AllTestSuit.test_group_runner })\r
 195         public void readStatistics() {\r
 196                 try {\r
 197                         ConfiguredExecutable<Muscle> confMuscle = Configurator\r
 198                                         .configureExecutable(muscle, Executable.ExecProvider.Local);\r
 199                         // For local execution use relavive\r
 200 \r
 201                         AsyncExecutor sexec = Configurator.getAsyncEngine(confMuscle);\r
 202                         String jobId = sexec.submitJob(confMuscle);\r
 203                         FilePuller fw = FilePuller.newFilePuller(confMuscle\r
 204                                         .getWorkDirectory()\r
 205                                         + File.separator + Muscle.getStatFile(),\r
 206                                         FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 207                         int count = 0;\r
 208                         long position = 0;\r
 209                         fw.waitForFile(4);\r
 210                         while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec\r
 211                                         .getJobStatus(jobId) == JobStatus.FAILED || sexec\r
 212                                         .getJobStatus(jobId) == JobStatus.UNDEFINED)\r
 213                                         || fw.hasMoreData()) {\r
 214                                 ChunkHolder ch = fw.pull(position);\r
 215                                 String chunk = ch.getChunk();\r
 216                                 position = ch.getNextPosition();\r
 217                                 System.out.print(chunk);\r
 218                                 count++;\r
 219                         }\r
 220                         assertTrue(count > 1);\r
 221                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 222                         assertNotNull(al.getResults());\r
 223                 } catch (JobSubmissionException e) {\r
 224                         e.printStackTrace();\r
 225                         fail(e.getMessage());\r
 226                 } catch (ResultNotAvailableException e) {\r
 227                         e.printStackTrace();\r
 228                         fail(e.getMessage());\r
 229                 } catch (IOException e) {\r
 230                         e.printStackTrace();\r
 231                         fail(e.getMessage());\r
 232                 }\r
 233         }\r
 234 \r
 235         @Test(groups = { AllTestSuit.test_group_runner })\r
 236         public void testPersistance() {\r
 237                 try {\r
 238                         Muscle muscle = new Muscle();\r
 239                         muscle.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 240                                         .setOutput("outtt.txt");\r
 241                         assertEquals(muscle.getInput(), AllTestSuit.test_input);\r
 242                         assertEquals(muscle.getError(), "errrr.txt");\r
 243                         assertEquals(muscle.getOutput(), "outtt.txt");\r
 244                         ConfiguredExecutable<Muscle> cmuscle = Configurator\r
 245                                         .configureExecutable(muscle, Executable.ExecProvider.Local);\r
 246 \r
 247                         SyncExecutor sexec = Configurator.getSyncEngine(cmuscle);\r
 248                         sexec.executeJob();\r
 249                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 250                         assertNotNull(al.getResults());\r
 251                         // Save run configuration\r
 252                         assertTrue(cmuscle.saveRunConfiguration());\r
 253 \r
 254                         // See if loaded configuration is the same as saved\r
 255                         RunConfiguration loadedRun = RunConfiguration\r
 256                                         .load(new FileInputStream(new File(cmuscle\r
 257                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 258                         assertEquals(((ConfExecutable<Muscle>) cmuscle)\r
 259                                         .getRunConfiguration(), loadedRun);\r
 260                         // Load run configuration as ConfExecutable\r
 261                         ConfiguredExecutable<Muscle> resurrectedCMuscle = (ConfiguredExecutable<Muscle>) cmuscle\r
 262                                         .loadRunConfiguration(new FileInputStream(new File(cmuscle\r
 263                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 264                         assertNotNull(resurrectedCMuscle);\r
 265                         assertEquals(resurrectedCMuscle.getExecutable().getInput(),\r
 266                                         AllTestSuit.test_input);\r
 267                         assertEquals(resurrectedCMuscle.getExecutable().getError(),\r
 268                                         "errrr.txt");\r
 269                         assertEquals(resurrectedCMuscle.getExecutable().getOutput(),\r
 270                                         "outtt.txt");\r
 271                         // See in details whether executables are the same\r
 272                         assertEquals(resurrectedCMuscle.getExecutable(), muscle);\r
 273 \r
 274                         ConfiguredExecutable<Muscle> resmuscle = Configurator\r
 275                                         .configureExecutable(resurrectedCMuscle.getExecutable(),\r
 276                                                         Executable.ExecProvider.Local);\r
 277 \r
 278                         sexec = Configurator.getSyncEngine(resmuscle,\r
 279                                         Executable.ExecProvider.Local);\r
 280                         sexec.executeJob();\r
 281                         al = sexec.waitForResult();\r
 282                         assertNotNull(al);\r
 283 \r
 284                 } catch (JobSubmissionException e) {\r
 285                         e.printStackTrace();\r
 286                         fail(e.getMessage());\r
 287                 } catch (JobExecutionException e) {\r
 288                         e.printStackTrace();\r
 289                         fail(e.getMessage());\r
 290                 } catch (FileNotFoundException e) {\r
 291                         e.printStackTrace();\r
 292                         fail(e.getMessage());\r
 293                 } catch (IOException e) {\r
 294                         e.printStackTrace();\r
 295                         fail(e.getMessage());\r
 296                 } catch (ResultNotAvailableException e) {\r
 297                         e.printStackTrace();\r
 298                         fail(e.getMessage());\r
 299                 }\r
 300         }\r
 301 \r
 302         @Test(groups = { AllTestSuit.test_group_runner })\r
 303         public void testConfigurationLoading() {\r
 304                 try {\r
 305                         RunnerConfig<Muscle> muscleConfig = ConfExecutable\r
 306                                         .getRunnerOptions(Muscle.class);\r
 307                         assertNotNull(muscleConfig);\r
 308                         assertTrue(muscleConfig.getArguments().size() > 0);\r
 309 \r
 310                         PresetManager<Muscle> musclePresets = ConfExecutable\r
 311                                         .getRunnerPresets(Muscle.class);\r
 312                         assertNotNull(musclePresets);\r
 313                         assertTrue(musclePresets.getPresets().size() > 0);\r
 314                         musclePresets.validate(muscleConfig);\r
 315 \r
 316                         LimitsManager<Muscle> muscleLimits = ConfExecutable\r
 317                                         .getRunnerLimits(Muscle.class);\r
 318                         assertNotNull(muscleLimits);\r
 319                         assertTrue(muscleLimits.getLimits().size() > 0);\r
 320                         muscleLimits.validate(musclePresets);\r
 321 \r
 322                 } catch (FileNotFoundException e) {\r
 323                         e.printStackTrace();\r
 324                         fail(e.getLocalizedMessage());\r
 325                 } catch (IOException e) {\r
 326                         e.printStackTrace();\r
 327                         fail(e.getLocalizedMessage());\r
 328                 } catch (ValidationException e) {\r
 329                         e.printStackTrace();\r
 330                         fail(e.getLocalizedMessage());\r
 331                 }\r
 332         }\r
 333 \r
 334 }\r