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