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