testsrc/compbio/runner/msa/TcoffeeTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  * Copyright (c) 2013 Alexander Sherstnev\r
   3  *  \r
   4  *  Java Bioinformatics Analysis Web Services (JABAWS)\r
   5  *  @version: 2.5     \r
   6  * \r
   7  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   8  *  Apache License version 2 as published by the Apache Software Foundation\r
   9  * \r
  10  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
  11  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  12  *  License for more details.\r
  13  * \r
  14  *  A copy of the license is in apache_license.txt. It is also available here:\r
  15  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  16  * \r
  17  * Any republication or derived work distributed in source code form\r
  18  * must include this copyright and license notice.\r
  19  */\r
  20 \r
  21 package compbio.runner.msa;\r
  22 \r
  23 import static org.testng.Assert.assertEquals;\r
  24 import static org.testng.Assert.assertNotNull;\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.util.Arrays;\r
  33 \r
  34 import javax.xml.bind.ValidationException;\r
  35 \r
  36 import org.testng.annotations.BeforeMethod;\r
  37 import org.testng.annotations.Test;\r
  38 \r
  39 import compbio.data.sequence.Alignment;\r
  40 import compbio.engine.AsyncExecutor;\r
  41 import compbio.engine.Configurator;\r
  42 import compbio.engine.FilePuller;\r
  43 import compbio.engine.SyncExecutor;\r
  44 import compbio.engine.client.ConfExecutable;\r
  45 import compbio.engine.client.ConfiguredExecutable;\r
  46 import compbio.engine.client.Executable;\r
  47 import compbio.engine.client.RunConfiguration;\r
  48 import compbio.engine.cluster.drmaa.ClusterRunner;\r
  49 import compbio.engine.local.LocalRunner;\r
  50 import compbio.metadata.AllTestSuit;\r
  51 import compbio.metadata.ChunkHolder;\r
  52 import compbio.metadata.JobExecutionException;\r
  53 import compbio.metadata.JobStatus;\r
  54 import compbio.metadata.JobSubmissionException;\r
  55 import compbio.metadata.LimitsManager;\r
  56 import compbio.metadata.PresetManager;\r
  57 import compbio.metadata.ResultNotAvailableException;\r
  58 import compbio.metadata.RunnerConfig;\r
  59 import compbio.runner.msa.Tcoffee;\r
  60 import compbio.runner.predictors.Jpred;\r
  61 import compbio.util.FileWatcher;\r
  62 import compbio.util.SysPrefs;\r
  63 \r
  64 public class TcoffeeTester {\r
  65 \r
  66         private Tcoffee tcoffee;\r
  67         public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;\r
  68         public static String test_output = "tcoffee.out";\r
  69         public static String test_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "TO1381.fasta";\r
  70 \r
  71         @BeforeMethod(groups = {AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows})\r
  72         public void init() {\r
  73                 tcoffee = new Tcoffee();\r
  74                 tcoffee.setInput(test_input);\r
  75                 tcoffee.setOutput(test_output);\r
  76                 tcoffee.setError("tcoffee.progress");\r
  77                 //System.out.println("Tcoffee has been configured!");\r
  78         }\r
  79 \r
  80         @Test(groups = { AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
  81         public void RunLocally() {\r
  82                 try {\r
  83                         ConfiguredExecutable<Tcoffee> ctcoffee = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Local);\r
  84                         // matrix does not appear to work\r
  85                         // ctcoffee.getParameters().setParam("-matrix","BLOSUM62");\r
  86 \r
  87                         SyncExecutor sexecutor = Configurator.getSyncEngine(ctcoffee);\r
  88                         sexecutor.executeJob();\r
  89                         ConfiguredExecutable<?> al = sexecutor.waitForResult();\r
  90                         Alignment align = al.getResults();\r
  91                         assertNotNull(align);\r
  92 \r
  93 //                      LocalRunner sexecutor = new LocalRunner(ctcoffee);\r
  94 //                      sexecutor.executeJob();\r
  95 //                      ConfiguredExecutable<?> al = sexecutor.waitForResult();\r
  96 //                      Alignment align = al.getResults();\r
  97 //                      assertNotNull(align);\r
  98 \r
  99                 } catch (JobSubmissionException e) {\r
 100                         e.printStackTrace();\r
 101                         fail(e.getMessage());\r
 102                 } catch (JobExecutionException e) {\r
 103                         e.printStackTrace();\r
 104                         fail(e.getMessage());\r
 105                 } catch (ResultNotAvailableException e) {\r
 106                         e.printStackTrace();\r
 107                         fail(e.getMessage());\r
 108                 }\r
 109         }\r
 110 \r
 111         @Test(groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows})\r
 112         public void readStatistics() {\r
 113                 try {\r
 114                         Tcoffee tcoffee = new Tcoffee().setInput(AllTestSuit.test_input);\r
 115                         ConfiguredExecutable<Tcoffee> confTcoffee = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Local);\r
 116 \r
 117                         AsyncExecutor sexec = Configurator.getAsyncEngine(confTcoffee);\r
 118                         String jobId = sexec.submitJob(confTcoffee);\r
 119                         String file = confTcoffee.getWorkDirectory() + File.separator + tcoffee.getError();\r
 120                         FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
 121                         int count = 0;\r
 122                         long position = 0;\r
 123                         fw.waitForFile(4);\r
 124                         while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || \r
 125                                          sexec.getJobStatus(jobId) == JobStatus.FAILED || \r
 126                                          sexec.getJobStatus(jobId) == JobStatus.UNDEFINED) || fw.hasMoreData()) {\r
 127                                 if (fw.hasMoreData()) {\r
 128                                         ChunkHolder ch = fw.pull(position);\r
 129                                         String chunk = ch.getChunk();\r
 130                                         position = ch.getNextPosition();\r
 131                                         System.out.print(chunk);\r
 132                                 }\r
 133                                 count++;\r
 134                         }\r
 135                         assertTrue(count > 1);\r
 136                         ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
 137                         assertNotNull(al.getResults());\r
 138                 } catch (JobSubmissionException e) {\r
 139                         e.printStackTrace();\r
 140                         fail(e.getMessage());\r
 141                 } catch (ResultNotAvailableException e) {\r
 142                         e.printStackTrace();\r
 143                         fail(e.getMessage());\r
 144                 } catch (IOException e) {\r
 145                         e.printStackTrace();\r
 146                         fail(e.getMessage());\r
 147                 }\r
 148         }\r
 149 \r
 150         @Test(groups = { AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
 151         public void SetNcore() {\r
 152                 Tcoffee tc = new Tcoffee();\r
 153                 assertEquals(tc.getParameters(null).size(), 3);\r
 154                 tc.setNCore(2);\r
 155                 assertEquals(2, tc.getNCore());\r
 156                 assertEquals(tc.getParameters(null).size(), 3);\r
 157                 tc.setNCore(4);\r
 158                 assertEquals(4, tc.getNCore());\r
 159                 assertEquals(tc.getParameters(null).size(), 3);\r
 160         }\r
 161 \r
 162         @Test(groups = { AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
 163         public void Persistance() {\r
 164                 try {\r
 165                         Tcoffee tcoffee = new Tcoffee();\r
 166                         tcoffee.setError("errrr.txt");\r
 167                         tcoffee.setInput(AllTestSuit.test_input);\r
 168                         tcoffee.setOutput("outtt.txt");\r
 169                         assertEquals(tcoffee.getInput(), AllTestSuit.test_input);\r
 170                         assertEquals(tcoffee.getError(), "errrr.txt");\r
 171                         assertEquals(tcoffee.getOutput(), "outtt.txt");\r
 172 \r
 173                         ConfiguredExecutable<Tcoffee> ctcofee = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Local);\r
 174                         SyncExecutor sexec = Configurator.getSyncEngine(ctcofee);\r
 175                         sexec.executeJob();\r
 176                         ConfiguredExecutable<?> al = sexec.waitForResult();\r
 177                         assertNotNull(al.getResults());\r
 178                         // Save run configuration\r
 179                         assertTrue(ctcofee.saveRunConfiguration());\r
 180 \r
 181                         // See if loaded configuration is the same as saved\r
 182                         RunConfiguration loadedRun = RunConfiguration.load(new FileInputStream(new File(ctcofee.getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 183                         assertEquals(((ConfExecutable<Tcoffee>) ctcofee).getRunConfiguration(), loadedRun);\r
 184 \r
 185                         // Load run configuration as ConfExecutable\r
 186                         ConfiguredExecutable<Tcoffee> resurrectedCTcoffee = (ConfiguredExecutable<Tcoffee>) ctcofee\r
 187                                         .loadRunConfiguration(new FileInputStream(new File(ctcofee.getWorkDirectory(), RunConfiguration.rconfigFile)));\r
 188                         assertNotNull(resurrectedCTcoffee);\r
 189 \r
 190                         // See in details whether executables are the same\r
 191                         assertEquals(resurrectedCTcoffee.getExecutable(), tcoffee);\r
 192 \r
 193                         // Finally rerun the job in the new task directory\r
 194                         ConfiguredExecutable<Tcoffee> restcoffee = Configurator.configureExecutable(resurrectedCTcoffee.getExecutable(), Executable.ExecProvider.Local);\r
 195 \r
 196                         sexec = Configurator.getSyncEngine(restcoffee,Executable.ExecProvider.Local);\r
 197                         sexec.executeJob();\r
 198                         al = sexec.waitForResult();\r
 199                         assertNotNull(al);\r
 200 \r
 201                 } catch (JobSubmissionException e) {\r
 202                         e.printStackTrace();\r
 203                         fail(e.getMessage());\r
 204                 } catch (JobExecutionException e) {\r
 205                         e.printStackTrace();\r
 206                         fail(e.getMessage());\r
 207                 } catch (FileNotFoundException e) {\r
 208                         e.printStackTrace();\r
 209                         fail(e.getMessage());\r
 210                 } catch (IOException e) {\r
 211                         e.printStackTrace();\r
 212                         fail(e.getMessage());\r
 213                 } catch (ResultNotAvailableException e) {\r
 214                         e.printStackTrace();\r
 215                         fail(e.getMessage());\r
 216                 }\r
 217         }\r
 218 \r
 219         @Test(groups = { AllTestSuit.test_group_runner })\r
 220         public void ConfigurationLoading() {\r
 221                 try {\r
 222                         RunnerConfig<Tcoffee> tcoffeeConfig = ConfExecutable.getRunnerOptions(Tcoffee.class);\r
 223                         assertNotNull(tcoffeeConfig);\r
 224                         assertTrue(tcoffeeConfig.getArguments().size() > 0);\r
 225 \r
 226                         PresetManager<Tcoffee> tcoffeePresets = ConfExecutable.getRunnerPresets(Tcoffee.class);\r
 227                         assertNotNull(tcoffeePresets);\r
 228                         assertTrue(tcoffeePresets.getPresets().size() > 0);\r
 229                         tcoffeePresets.validate(tcoffeeConfig);\r
 230 \r
 231                         LimitsManager<Tcoffee> tcoffeeLimits = ConfExecutable.getRunnerLimits(Tcoffee.class);\r
 232                         assertNotNull(tcoffeeLimits);\r
 233                         assertTrue(tcoffeeLimits.getLimits().size() > 0);\r
 234                         tcoffeeLimits.validate(tcoffeePresets);\r
 235                 } catch (FileNotFoundException e) {\r
 236                         e.printStackTrace();\r
 237                         fail(e.getLocalizedMessage());\r
 238                 } catch (IOException e) {\r
 239                         e.printStackTrace();\r
 240                         fail(e.getLocalizedMessage());\r
 241                 } catch (ValidationException e) {\r
 242                         e.printStackTrace();\r
 243                         fail(e.getLocalizedMessage());\r
 244                 }\r
 245         }\r
 246 \r
 247         // disabled\r
 248         @Test(enabled=false,groups = { AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })\r
 249         public void RunOnCluster() {\r
 250                 try {\r
 251                         ConfiguredExecutable<Tcoffee> cmafft = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Cluster);\r
 252                         ClusterRunner sexecutor = (ClusterRunner) Configurator.getSyncEngine(cmafft, Executable.ExecProvider.Cluster);\r
 253                         sexecutor.executeJob();\r
 254                         ConfiguredExecutable<?> al = sexecutor.waitForResult();\r
 255                         Alignment align = al.getResults();\r
 256                         assertNotNull(align);\r
 257                 } catch (JobSubmissionException e) {\r
 258                         e.printStackTrace();\r
 259                         fail(e.getMessage());\r
 260                 } catch (JobExecutionException e) {\r
 261                         e.printStackTrace();\r
 262                         fail(e.getMessage());\r
 263                 } catch (ResultNotAvailableException e) {\r
 264                         e.printStackTrace();\r
 265                         fail(e.getMessage());\r
 266                 }\r
 267         }\r
 268 }\r