testsrc/compbio/runner/msa/ClustalWParametersTester.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.ClustalW;\r
  60 import compbio.util.FileUtil;\r
  61 \r
  62 @Test(sequential = true)\r
  63 public class ClustalWParametersTester {\r
  64 \r
  65         static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
  66                         + "ClustalParameters.xml";\r
  67 \r
  68         public static String test_outfile = "TO1381.clustal.out";\r
  69         public static String test_error = "TO1381.clustal.error";\r
  70         public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
  71         public static final String input = AllTestSuit.TEST_DATA_PATH\r
  72                         + "ClustalPresets.xml";\r
  73 \r
  74         private static Logger log = Logger\r
  75                         .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
  76         static {\r
  77                 log.setLevel(Level.INFO);\r
  78         }\r
  79 \r
  80         RunnerConfig<ClustalW> clustalConfig = null;\r
  81         OptionCombinator clustalOpc = null;\r
  82         PresetManager<ClustalW> presets = null;\r
  83 \r
  84         @BeforeMethod(groups = { AllTestSuit.test_group_runner })\r
  85         public void setup() {\r
  86                 try {\r
  87                         RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
  88                                         RunnerConfig.class);\r
  89                         clustalConfig = clustalmarsh.read(new FileInputStream(new File(\r
  90                                         clustalConfigFile)), RunnerConfig.class);\r
  91                         clustalOpc = new OptionCombinator(clustalConfig);\r
  92 \r
  93                         // Load presets\r
  94                         RunnerConfigMarshaller<ClustalW> rconfigPresets = new RunnerConfigMarshaller<ClustalW>(\r
  95                                         PresetManager.class);\r
  96                         File infile = new File(input);\r
  97                         assertTrue(infile.exists());\r
  98                         presets = rconfigPresets.read(new FileInputStream(infile),\r
  99                                         PresetManager.class);\r
 100                         assertNotNull(presets);\r
 101                         assertFalse(presets.getPresets().isEmpty());\r
 102 \r
 103                 } catch (JAXBException e) {\r
 104                         e.printStackTrace();\r
 105                         fail(e.getLocalizedMessage());\r
 106                 } catch (FileNotFoundException e) {\r
 107                         e.printStackTrace();\r
 108                         fail(e.getLocalizedMessage());\r
 109                 }\r
 110 \r
 111         }\r
 112 \r
 113         @Test\r
 114         public void testConfiguration() {\r
 115                 try {\r
 116                         this.clustalConfig.validate();\r
 117                 } catch (ValidationException e) {\r
 118                         e.printStackTrace();\r
 119                         fail(e.getLocalizedMessage());\r
 120                 } catch (IllegalStateException e) {\r
 121                         e.printStackTrace();\r
 122                         fail(e.getLocalizedMessage());\r
 123                 }\r
 124         }\r
 125 \r
 126         @Test(groups = { AllTestSuit.test_group_runner })\r
 127         public void testDefaultParameters() {\r
 128                 ClustalW clustal = new ClustalW();\r
 129                 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
 130 \r
 131                 try {\r
 132                         // For local execution use relavive\r
 133                         ConfiguredExecutable<ClustalW> confClustal = Configurator\r
 134                                         .configureExecutable(clustal);\r
 135                         LocalRunner lr = new LocalRunner(confClustal);\r
 136                         lr.executeJob();\r
 137                         confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
 138                         assertNotNull(confClustal.getResults());\r
 139                 } catch (JobSubmissionException e) {\r
 140                         e.printStackTrace();\r
 141                         fail(e.getLocalizedMessage());\r
 142                 } catch (JobExecutionException e) {\r
 143                         e.printStackTrace();\r
 144                         fail(e.getLocalizedMessage());\r
 145                 } catch (ResultNotAvailableException e) {\r
 146                         e.printStackTrace();\r
 147                         fail(e.getLocalizedMessage());\r
 148                 }\r
 149         }\r
 150 \r
 151         @Test(groups = { AllTestSuit.test_group_runner })\r
 152         public void testOptions() {\r
 153                 test(clustalOpc.getAllOptions());\r
 154         }\r
 155 \r
 156         @Test(groups = { AllTestSuit.test_group_runner })\r
 157         public void testParameters() {\r
 158                 List<Parameter<?>> params = clustalOpc.getAllParameters();\r
 159                 Collections.shuffle(params);\r
 160                 test(params);\r
 161         }\r
 162 \r
 163         @Test(groups = { AllTestSuit.test_group_runner })\r
 164         public void testArguments() {\r
 165                 List<Option<?>> options = clustalOpc.getAllOptions();\r
 166                 options.addAll(clustalOpc.getAllParameters());\r
 167                 Collections.shuffle(options);\r
 168                 test(options);\r
 169         }\r
 170 \r
 171         @Test(groups = { AllTestSuit.test_group_runner })\r
 172         public void testConstrainedParametersMinValues() {\r
 173                 Map<Parameter<?>, String> params = clustalOpc\r
 174                                 .getAllConstrainedParametersWithBorderValues(true);\r
 175                 test(params);\r
 176         }\r
 177 \r
 178         @Test(groups = { AllTestSuit.test_group_runner })\r
 179         public void testConstrainedParametersMaxValues() {\r
 180                 Map<Parameter<?>, String> params = clustalOpc\r
 181                                 .getAllConstrainedParametersWithBorderValues(false);\r
 182                 test(params);\r
 183         }\r
 184 \r
 185         @Test(groups = { AllTestSuit.test_group_runner })\r
 186         public void testConstrainedParametersRandomValues() {\r
 187                 for (int i = 0; i < 5; i++) {\r
 188                         Map<Parameter<?>, String> params = clustalOpc\r
 189                                         .getAllConstrainedParametersWithRandomValues();\r
 190                         List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(params\r
 191                                         .keySet());\r
 192                         Collections.shuffle(paramList);\r
 193                         List<String> args = clustalOpc.parametersToCommandString(paramList,\r
 194                                         params);\r
 195                         singleTest(args);\r
 196                 }\r
 197         }\r
 198 \r
 199         void test(Map<Parameter<?>, String> paramValue) {\r
 200                 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue\r
 201                                 .keySet());\r
 202                 for (int i = 0; i < paramValue.size(); i++) {\r
 203                         List<String> args = clustalOpc.parametersToCommandString(paramList,\r
 204                                         paramValue);\r
 205                         singleTest(args);\r
 206                         Collections.shuffle(paramList);\r
 207                 }\r
 208                 log.info("NUMBER OF COBINATION TESTED: " + paramValue.size());\r
 209         }\r
 210 \r
 211         void test(List<? extends Option<?>> params) {\r
 212                 for (int i = 0; i < params.size(); i++) {\r
 213                         List<String> args = clustalOpc.argumentsToCommandString(params);\r
 214                         singleTest(args);\r
 215                         Collections.shuffle(params);\r
 216                 }\r
 217                 log.info("NUMBER OF COBINATION TESTED: " + params.size());\r
 218         }\r
 219 \r
 220         void singleTest(List<String> params) {\r
 221                 try {\r
 222                         log.info("Using arguments: " + params);\r
 223                         ClustalW clustal = new ClustalW();\r
 224                         clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
 225 \r
 226                         // For local execution use relative\r
 227                         ConfiguredExecutable<ClustalW> confClustal = Configurator\r
 228                                         .configureExecutable(clustal, ExecProvider.Local);\r
 229                         // Add options to the executable\r
 230                         confClustal.addParameters(params);\r
 231                         LocalRunner lr = new LocalRunner(confClustal);\r
 232                         lr.executeJob();\r
 233                         confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
 234                         assertNotNull(confClustal.getResults());\r
 235                         File errors = new File(confClustal.getWorkDirectory(),\r
 236                                         ExecutableWrapper.PROC_ERR_FILE);\r
 237                         if (errors.length() != 0) {\r
 238                                 log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));\r
 239                         }\r
 240                         assertTrue(errors.length() == 0, "Run with arguments : " + params\r
 241                                         + " FAILED!");\r
 242                         Collections.shuffle(params);\r
 243                 } catch (JobSubmissionException e) {\r
 244                         e.printStackTrace();\r
 245                         fail(e.getLocalizedMessage());\r
 246                 } catch (JobExecutionException e) {\r
 247                         e.printStackTrace();\r
 248                         fail(e.getLocalizedMessage());\r
 249                 } catch (IOException e) {\r
 250                         e.printStackTrace();\r
 251                         fail(e.getLocalizedMessage());\r
 252                 } catch (ResultNotAvailableException e) {\r
 253                         e.printStackTrace();\r
 254                         fail(e.getLocalizedMessage());\r
 255                 }\r
 256         }\r
 257 \r
 258         @Test(groups = { AllTestSuit.test_group_runner })\r
 259         public void testPresets() {\r
 260                 for (Preset<ClustalW> p : presets.getPresets()) {\r
 261                         singleTest(p.getOptions());\r
 262                 }\r
 263         }\r
 264 \r
 265 }\r