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