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