testsrc/compbio/runner/msa/MafftParametersTester.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.assertFalse;\r
  22 import static org.testng.Assert.assertNotNull;\r
  23 import static org.testng.Assert.assertTrue;\r
  24 import static org.testng.Assert.fail;\r
  25 \r
  26 import java.io.File;\r
  27 import java.io.FileInputStream;\r
  28 import java.io.FileNotFoundException;\r
  29 import java.util.ArrayList;\r
  30 import java.util.Collections;\r
  31 import java.util.List;\r
  32 import java.util.Map;\r
  33 \r
  34 import javax.xml.bind.JAXBException;\r
  35 import javax.xml.bind.ValidationException;\r
  36 \r
  37 import org.apache.log4j.Level;\r
  38 import org.apache.log4j.Logger;\r
  39 import org.testng.annotations.BeforeMethod;\r
  40 import org.testng.annotations.Test;\r
  41 \r
  42 import compbio.engine.Configurator;\r
  43 import compbio.engine.SyncExecutor;\r
  44 import compbio.engine.client.ConfiguredExecutable;\r
  45 import compbio.engine.client.Executable.ExecProvider;\r
  46 import compbio.engine.conf.RunnerConfigMarshaller;\r
  47 import compbio.metadata.AllTestSuit;\r
  48 import compbio.metadata.JobExecutionException;\r
  49 import compbio.metadata.JobSubmissionException;\r
  50 import compbio.metadata.Option;\r
  51 import compbio.metadata.Parameter;\r
  52 import compbio.metadata.Preset;\r
  53 import compbio.metadata.PresetManager;\r
  54 import compbio.metadata.ResultNotAvailableException;\r
  55 import compbio.metadata.RunnerConfig;\r
  56 import compbio.runner.OptionCombinator;\r
  57 import compbio.runner.msa.Mafft;\r
  58 import compbio.util.Util;\r
  59 \r
  60 public class MafftParametersTester {\r
  61 \r
  62         static final String mafftConfigFile = AllTestSuit.TEST_DATA_PATH\r
  63                         + "MafftParameters.xml";\r
  64         public static String test_outfile = "TO1381.mafft.out";\r
  65         public static final String input = AllTestSuit.TEST_DATA_PATH\r
  66                         + "MafftPresets.xml";\r
  67 \r
  68         private static Logger log = Logger\r
  69                         .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
  70         static {\r
  71                 log.setLevel(Level.INFO);\r
  72         }\r
  73 \r
  74         PresetManager<Mafft> presets = null;\r
  75         RunnerConfig<Mafft> mafftConfig = null;\r
  76         OptionCombinator mafftOpc = null;\r
  77 \r
  78         @BeforeMethod(groups = { AllTestSuit.test_group_runner,\r
  79                         AllTestSuit.test_group_non_windows })\r
  80         public void setup() {\r
  81                 try {\r
  82                         // Load parameters\r
  83                         RunnerConfigMarshaller<Mafft> mafftmarsh = new RunnerConfigMarshaller<Mafft>(\r
  84                                         RunnerConfig.class);\r
  85                         mafftConfig = mafftmarsh.read(new FileInputStream(new File(\r
  86                                         mafftConfigFile)), RunnerConfig.class);\r
  87                         mafftOpc = new OptionCombinator(mafftConfig);\r
  88                         // Load presets\r
  89                         RunnerConfigMarshaller<Mafft> rconfigPresets = new RunnerConfigMarshaller<Mafft>(\r
  90                                         PresetManager.class);\r
  91                         File infile = new File(input);\r
  92                         assertTrue(infile.exists());\r
  93                         presets = rconfigPresets.read(new FileInputStream(infile),\r
  94                                         PresetManager.class);\r
  95                         assertNotNull(presets);\r
  96                         assertFalse(presets.getPresets().isEmpty());\r
  97 \r
  98                 } catch (JAXBException e) {\r
  99                         e.printStackTrace();\r
 100                         fail(e.getLocalizedMessage());\r
 101                 } catch (FileNotFoundException e) {\r
 102                         e.printStackTrace();\r
 103                         fail(e.getLocalizedMessage());\r
 104                 }\r
 105 \r
 106         }\r
 107 \r
 108         @Test\r
 109         public void testConfiguration() {\r
 110                 try {\r
 111                         this.mafftConfig.validate();\r
 112                 } catch (ValidationException e) {\r
 113                         e.printStackTrace();\r
 114                         fail(e.getLocalizedMessage());\r
 115                 } catch (IllegalStateException e) {\r
 116                         e.printStackTrace();\r
 117                         fail(e.getLocalizedMessage());\r
 118                 }\r
 119         }\r
 120 \r
 121         @Test(groups = { AllTestSuit.test_group_runner,\r
 122                         AllTestSuit.test_group_non_windows })\r
 123         public void testDefaultParameters() {\r
 124                 Mafft mafft = new Mafft();\r
 125                 mafft.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
 126 \r
 127                 try {\r
 128                         // For local execution use relavive\r
 129                         ConfiguredExecutable<Mafft> confMafft = Configurator\r
 130                                         .configureExecutable(mafft, ExecProvider.Cluster);\r
 131                         SyncExecutor sexecutor = Configurator.getSyncEngine(confMafft);\r
 132                         sexecutor.executeJob();\r
 133                         confMafft = (ConfiguredExecutable<Mafft>) sexecutor.waitForResult();\r
 134                         assertNotNull(confMafft.getResults());\r
 135                 } catch (JobSubmissionException e) {\r
 136                         e.printStackTrace();\r
 137                         fail(e.getLocalizedMessage());\r
 138                 } catch (JobExecutionException e) {\r
 139                         e.printStackTrace();\r
 140                         fail(e.getLocalizedMessage());\r
 141                 } catch (ResultNotAvailableException e) {\r
 142                         e.printStackTrace();\r
 143                         fail(e.getLocalizedMessage());\r
 144                 }\r
 145         }\r
 146 \r
 147         @Test(groups = { AllTestSuit.test_group_runner,\r
 148                         AllTestSuit.test_group_non_windows })\r
 149         public void testOptions() {\r
 150                 test(mafftOpc.getAllOptions());\r
 151         }\r
 152 \r
 153         @Test(groups = { AllTestSuit.test_group_runner,\r
 154                         AllTestSuit.test_group_non_windows })\r
 155         public void testParameters() {\r
 156                 List<Parameter<?>> params = mafftOpc.getAllParameters();\r
 157                 Collections.shuffle(params);\r
 158                 test(params);\r
 159         }\r
 160 \r
 161         @Test(groups = { AllTestSuit.test_group_runner,\r
 162                         AllTestSuit.test_group_non_windows })\r
 163         public void testArguments() {\r
 164                 List<Option<?>> options = new ArrayList<Option<?>>(mafftConfig\r
 165                                 .getOptions());\r
 166                 options.addAll(mafftOpc.getAllParameters());\r
 167                 Collections.shuffle(options);\r
 168                 test(options);\r
 169         }\r
 170 \r
 171         @Test(groups = { AllTestSuit.test_group_runner,\r
 172                         AllTestSuit.test_group_non_windows })\r
 173         public void testConstrainedParametersMinValues() {\r
 174                 Map<Parameter<?>, String> params = mafftOpc\r
 175                                 .getAllConstrainedParametersWithBorderValues(true);\r
 176                 test(params);\r
 177         }\r
 178 \r
 179         @Test(groups = { AllTestSuit.test_group_runner,\r
 180                         AllTestSuit.test_group_non_windows })\r
 181         public void testConstrainedParametersMaxValues() {\r
 182                 Map<Parameter<?>, String> params = mafftOpc\r
 183                                 .getAllConstrainedParametersWithBorderValues(false);\r
 184                 test(params);\r
 185         }\r
 186 \r
 187         @Test(groups = { AllTestSuit.test_group_runner,\r
 188                         AllTestSuit.test_group_non_windows })\r
 189         public void testConstrainedParametersRandomValues() {\r
 190                 for (int i = 0; i < 20; i++) {\r
 191                         Map<Parameter<?>, String> params = mafftOpc\r
 192                                         .getAllConstrainedParametersWithRandomValues();\r
 193                         List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(params\r
 194                                         .keySet());\r
 195                         Collections.shuffle(paramList);\r
 196                         List<Parameter<?>> subList = paramList.subList(0, Util\r
 197                                         .getRandomNumber(1, paramList.size()));\r
 198                         List<String> args = mafftOpc.parametersToCommandString(subList,\r
 199                                         params);\r
 200                         singleTest(args);\r
 201                 }\r
 202         }\r
 203 \r
 204         @Test(groups = { AllTestSuit.test_group_runner,\r
 205                         AllTestSuit.test_group_non_windows })\r
 206         public void testPresets() {\r
 207                 for (Preset<Mafft> p : presets.getPresets()) {\r
 208                         singleTest(p.getOptions());\r
 209                 }\r
 210         }\r
 211 \r
 212         void test(Map<Parameter<?>, String> paramValue) {\r
 213                 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue\r
 214                                 .keySet());\r
 215                 for (int i = 0; i < paramValue.size(); i++) {\r
 216                         List<String> args = mafftOpc.parametersToCommandString(paramList,\r
 217                                         paramValue);\r
 218                         singleTest(args);\r
 219                         Collections.shuffle(paramList);\r
 220                 }\r
 221                 log.info("NUMBER OF COBINATION TESTED: " + paramValue.size());\r
 222         }\r
 223 \r
 224         void test(List<? extends Option<?>> params) {\r
 225                 for (int i = 0; i < params.size(); i++) {\r
 226                         List<String> args = mafftOpc.argumentsToCommandString(params);\r
 227                         singleTest(args);\r
 228                         Collections.shuffle(params);\r
 229                 }\r
 230                 log.info("NUMBER OF COBINATION TESTED: " + params.size());\r
 231         }\r
 232 \r
 233         void singleTest(List<String> params) {\r
 234                 try {\r
 235                         log.info("Using arguments: " + params);\r
 236                         Mafft mafft = new Mafft();\r
 237                         mafft.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
 238 \r
 239                         // For local execution use relative\r
 240                         ConfiguredExecutable<Mafft> confMafft = Configurator\r
 241                                         .configureExecutable(mafft, ExecProvider.Local);\r
 242                         // Add options to the executable\r
 243                         confMafft.addParameters(params);\r
 244 \r
 245                         SyncExecutor sexecutor = Configurator.getSyncEngine(confMafft);\r
 246                         sexecutor.executeJob();\r
 247                         ConfiguredExecutable<?> al = sexecutor.waitForResult();\r
 248                         assertNotNull(al.getResults());\r
 249                         /*\r
 250                          * TODO File errors = new File(confMafft.getWorkDirectory(),\r
 251                          * ExecutableWrapper.PROC_ERR_FILE); if (errors.length() != 0) {\r
 252                          * log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors)); }\r
 253                          * assertTrue("Run with arguments : " + params + " FAILED!", errors\r
 254                          * .length() == 0);\r
 255                          */\r
 256                 } catch (JobSubmissionException e) {\r
 257                         e.printStackTrace();\r
 258                         fail(e.getLocalizedMessage());\r
 259                 } catch (JobExecutionException e) {\r
 260                         e.printStackTrace();\r
 261                         fail(e.getLocalizedMessage());\r
 262                 } catch (ResultNotAvailableException e) {\r
 263                         e.printStackTrace();\r
 264                         fail(e.getLocalizedMessage());\r
 265                 }\r
 266         }\r
 267 \r
 268 }\r