testsrc/compbio/casscode/msa/ProbconsTester.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.assertNotNull;\r
  23 import static org.testng.Assert.assertNull;\r
  24 import static org.testng.Assert.assertTrue;\r
  25 import static org.testng.Assert.fail;\r
  26 \r
  27 import java.io.File;\r
  28 import java.io.FileInputStream;\r
  29 import java.io.FileNotFoundException;\r
  30 import java.io.IOException;\r
  31 \r
  32 import javax.xml.bind.ValidationException;\r
  33 \r
  34 import org.testng.annotations.BeforeMethod;\r
  35 import org.testng.annotations.Test;\r
  36 \r
  37 import compbio.engine.AsyncExecutor;\r
  38 import compbio.engine.Configurator;\r
  39 import compbio.engine.FilePuller;\r
  40 import compbio.engine.SyncExecutor;\r
  41 import compbio.engine.client.ConfExecutable;\r
  42 import compbio.engine.client.ConfiguredExecutable;\r
  43 import compbio.engine.client.Executable;\r
  44 import compbio.engine.client.RunConfiguration;\r
  45 import compbio.engine.cluster.drmaa.ClusterRunner;\r
  46 import compbio.metadata.AllTestSuit;\r
  47 import compbio.metadata.ChunkHolder;\r
  48 import compbio.metadata.JobExecutionException;\r
  49 import compbio.metadata.JobSubmissionException;\r
  50 import compbio.metadata.LimitsManager;\r
  51 import compbio.metadata.PresetManager;\r
  52 import compbio.metadata.ResultNotAvailableException;\r
  53 import compbio.metadata.RunnerConfig;\r
  54 \r
  55 public class ProbconsTester {\r
  56 \r
  57         private Probcons probc;\r
  58 \r
  59         @BeforeMethod(groups = { AllTestSuit.test_group_cluster,\r
  60                         AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
  61         public void init() {\r
  62                 probc = new Probcons();\r
  63                 probc.setInput(AllTestSuit.test_input); // .setOutput("Mafft.out").setError("mafft.progress");\r
  64         }\r
  65 \r
  66         @Test(groups = { AllTestSuit.test_group_runner,\r
  67                         AllTestSuit.test_group_non_windows })\r
  68         public void testSetInputTester() {\r
  69                 Probcons mf = new Probcons();\r
  70                 // System.out.println(mf.getParameters(null));\r
  71                 mf.setInput("INNN");\r
  72                 // System.out.println(mf.getParameters(null));\r
  73                 mf.setError("ERRR");\r
  74                 mf.setInput("INN222");\r
  75                 mf.setOutput("OUT");\r
  76                 // System.out.println(mf.getParameters(null));\r
  77         }\r
  78 \r
  79         @Test(groups = { AllTestSuit.test_group_runner,\r
  80                         AllTestSuit.test_group_non_windows })\r
  81         public void testExecute() {\r
  82                 try {\r
  83                         ConfiguredExecutable<Probcons> cmafft = Configurator\r
  84                                         .configureExecutable(probc, Executable.ExecProvider.Local);\r
  85                         // option for sub matrix is not supported\r
  86                         // cmafft.getParameters().setParam("--matrixfile", "PAM200");\r
  87                         SyncExecutor sexecutor = Configurator.getSyncEngine(cmafft);\r
  88                         sexecutor.executeJob();\r
  89                         cmafft = (ConfiguredExecutable<Probcons>) sexecutor.waitForResult();\r
  90                         assertNotNull(cmafft.getResults());\r
  91                 } catch (JobSubmissionException e) {\r
  92                         e.printStackTrace();\r
  93                         fail(e.getMessage());\r
  94                 } catch (JobExecutionException e) {\r
  95                         e.printStackTrace();\r
  96                         fail(e.getMessage());\r
  97                 } catch (ResultNotAvailableException e) {\r
  98                         e.printStackTrace();\r
  99                         fail(e.getMessage());\r
 100                 }\r
 101         }\r
 102 \r
 103         @Test(groups = { AllTestSuit.test_group_runner,\r
 104                         AllTestSuit.test_group_non_windows })\r
 105         public void testPersistance() {\r
 106                 try {\r
 107                         Probcons mafft = new Probcons();\r
 108                         mafft.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
 109                                         .setOutput("outtt.txt");\r
 110                         assertEquals(mafft.getInput(), AllTestSuit.test_input);\r
 111                         assertEquals(mafft.getError(), "errrr.txt");\r
 112                         assertEquals(mafft.getOutput(), "outtt.txt");\r
 113                         ConfiguredExecutable<Probcons> cmafft = Configurator\r
 114                                         .configureExecutable(mafft, Executable.ExecProvider.Local);\r
 115 \r
 116                         SyncExecutor sexec = Configurator.getSyncEngine(cmafft);\r
 117                         sexec.executeJob();\r
 118                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 119                         assertNotNull(al.getResults());\r
 120                         // Save run configuration\r
 121                         assertTrue(cmafft.saveRunConfiguration());\r
 122 \r
 123                         // See if loaded configuration is the same as saved\r
 124                         RunConfiguration loadedRun = RunConfiguration\r
 125                                         .load(new FileInputStream(new File(cmafft\r
 126                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 127                         assertEquals(((ConfExecutable<Probcons>) cmafft)\r
 128                                         .getRunConfiguration(), loadedRun);\r
 129                         // Load run configuration as ConfExecutable\r
 130                         ConfiguredExecutable<Probcons> resurrectedCMafft = (ConfiguredExecutable<Probcons>) cmafft\r
 131                                         .loadRunConfiguration(new FileInputStream(new File(cmafft\r
 132                                                         .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 133                         assertNotNull(resurrectedCMafft);\r
 134                         // See in details whether executables are the same\r
 135                         assertEquals(resurrectedCMafft.getExecutable(), mafft);\r
 136 \r
 137                         // Finally rerun the job in the new task directory\r
 138                         ConfiguredExecutable<Probcons> resmafft = Configurator\r
 139                                         .configureExecutable(resurrectedCMafft.getExecutable(),\r
 140                                                         Executable.ExecProvider.Local);\r
 141 \r
 142                         sexec = Configurator.getSyncEngine(resmafft,\r
 143                                         Executable.ExecProvider.Local);\r
 144                         sexec.executeJob();\r
 145                         al = sexec.waitForResult();\r
 146                         assertNotNull(al);\r
 147 \r
 148                 } catch (JobSubmissionException e) {\r
 149                         e.printStackTrace();\r
 150                         fail(e.getMessage());\r
 151                 } catch (JobExecutionException e) {\r
 152                         e.printStackTrace();\r
 153                         fail(e.getMessage());\r
 154                 } catch (FileNotFoundException e) {\r
 155                         e.printStackTrace();\r
 156                         fail(e.getMessage());\r
 157                 } catch (IOException e) {\r
 158                         e.printStackTrace();\r
 159                         fail(e.getMessage());\r
 160                 } catch (ResultNotAvailableException e) {\r
 161                         e.printStackTrace();\r
 162                         fail(e.getMessage());\r
 163                 }\r
 164         }\r
 165 \r
 166         @Test(groups = { AllTestSuit.test_group_cluster,\r
 167                         AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
 168         public void testClusterExecute() {\r
 169                 try {\r
 170                         ConfiguredExecutable<Probcons> cmafft = Configurator\r
 171                                         .configureExecutable(probc, Executable.ExecProvider.Cluster);\r
 172                         ClusterRunner sexecutor = (ClusterRunner) Configurator.getSyncEngine(\r
 173                                         cmafft, Executable.ExecProvider.Cluster);\r
 174                         sexecutor.executeJob();\r
 175                         ConfiguredExecutable<?> al = sexecutor.waitForResult();\r
 176                         assertNotNull(al.getResults());\r
 177                 } catch (JobSubmissionException e) {\r
 178                         e.printStackTrace();\r
 179                         fail(e.getMessage());\r
 180                 } catch (JobExecutionException e) {\r
 181                         e.printStackTrace();\r
 182                         fail(e.getMessage());\r
 183                 } catch (ResultNotAvailableException e) {\r
 184                         e.printStackTrace();\r
 185                         fail(e.getMessage());\r
 186                 }\r
 187         }\r
 188 \r
 189         @Test(groups = { AllTestSuit.test_group_runner,\r
 190                         AllTestSuit.test_group_non_windows })\r
 191         public void readStatistics() {\r
 192                 Probcons probs = new Probcons();\r
 193                 probs.setError("errrr.txt").setInput(AllTestSuit.test_input).setOutput(\r
 194                                 "outtt.txt");\r
 195                 ConfiguredExecutable<Probcons> cprobs;\r
 196 \r
 197                 try {\r
 198                         cprobs = Configurator.configureExecutable(probs,\r
 199                                         Executable.ExecProvider.Local);\r
 200                         AsyncExecutor sexec = Configurator.getAsyncEngine(cprobs);\r
 201                         String jobId = sexec.submitJob(cprobs);\r
 202                         FilePuller fw = FilePuller.newFilePuller(compbio.engine.client.EngineUtil\r
 203                                         .getFullPath(cprobs.getWorkDirectory(), cprobs.getError()),\r
 204                                         256);\r
 205                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 206                         assertNotNull(al.getResults());\r
 207                         // Code below is performance dependent \r
 208                         // thus cannot be moved up before the results is obtained\r
 209                         int count = 0;\r
 210                         long position = 0;\r
 211                         fw.waitForFile(6);\r
 212                         while (fw.hasMoreData()) {\r
 213                                 ChunkHolder ch = fw.pull(position);\r
 214                                 String chunk = ch.getChunk();\r
 215                                 position = ch.getNextPosition();\r
 216                                 System.out.print("CHUNK:" + chunk);\r
 217                                 count++;\r
 218                         }\r
 219                         assertTrue(count > 1, "TaskId:" + jobId);\r
 220 \r
 221                 } catch (JobSubmissionException e) {\r
 222                         e.printStackTrace();\r
 223                         fail(e.getMessage());\r
 224                 } catch (ResultNotAvailableException e) {\r
 225                         e.printStackTrace();\r
 226                         fail(e.getMessage());\r
 227                 } catch (IOException e) {\r
 228                         e.printStackTrace();\r
 229                         fail(e.getMessage());\r
 230                 }\r
 231         }\r
 232 \r
 233         @Test(groups = { AllTestSuit.test_group_runner })\r
 234         public void testConfigurationLoading() {\r
 235                 try {\r
 236                         RunnerConfig<Probcons> probsConfig = ConfExecutable\r
 237                                         .getRunnerOptions(Probcons.class);\r
 238                         assertNotNull(probsConfig);\r
 239                         assertTrue(probsConfig.getArguments().size() > 0);\r
 240 \r
 241                         PresetManager<Probcons> probsPresets = ConfExecutable\r
 242                                         .getRunnerPresets(Probcons.class);\r
 243                         assertNull(probsPresets);\r
 244 \r
 245                         LimitsManager<Probcons> probsLimits = ConfExecutable\r
 246                                         .getRunnerLimits(Probcons.class);\r
 247                         assertNotNull(probsLimits);\r
 248                         assertTrue(probsLimits.getLimits().size() > 0);\r
 249                         probsLimits.validate(probsPresets);\r
 250 \r
 251                 } catch (FileNotFoundException e) {\r
 252                         e.printStackTrace();\r
 253                         fail(e.getLocalizedMessage());\r
 254                 } catch (IOException e) {\r
 255                         e.printStackTrace();\r
 256                         fail(e.getLocalizedMessage());\r
 257                 } catch (ValidationException e) {\r
 258                         e.printStackTrace();\r
 259                         fail(e.getLocalizedMessage());\r
 260                 }\r
 261         }\r
 262 }\r