1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.runner.msa;
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21 import static org.testng.Assert.assertFalse;
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22 import static org.testng.Assert.assertNotNull;
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23 import static org.testng.Assert.assertTrue;
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24 import static org.testng.Assert.fail;
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26 import java.io.File;
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27 import java.io.FileInputStream;
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28 import java.io.FileNotFoundException;
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29 import java.util.ArrayList;
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30 import java.util.Collections;
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31 import java.util.List;
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32 import java.util.Map;
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34 import javax.xml.bind.JAXBException;
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35 import javax.xml.bind.ValidationException;
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37 import org.apache.log4j.Level;
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38 import org.apache.log4j.Logger;
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39 import org.testng.annotations.BeforeMethod;
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40 import org.testng.annotations.Test;
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42 import compbio.engine.Configurator;
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43 import compbio.engine.SyncExecutor;
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44 import compbio.engine.client.ConfiguredExecutable;
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45 import compbio.engine.client.Executable.ExecProvider;
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46 import compbio.engine.conf.RunnerConfigMarshaller;
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47 import compbio.metadata.AllTestSuit;
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48 import compbio.metadata.JobExecutionException;
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49 import compbio.metadata.JobSubmissionException;
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50 import compbio.metadata.Option;
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51 import compbio.metadata.Parameter;
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52 import compbio.metadata.Preset;
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53 import compbio.metadata.PresetManager;
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54 import compbio.metadata.ResultNotAvailableException;
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55 import compbio.metadata.RunnerConfig;
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56 import compbio.runner.OptionCombinator;
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57 import compbio.runner.msa.Mafft;
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58 import compbio.util.Util;
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60 public class MafftParametersTester {
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62 static final String mafftConfigFile = AllTestSuit.TEST_DATA_PATH
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63 + "MafftParameters.xml";
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64 public static String test_outfile = "TO1381.mafft.out";
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65 public static final String input = AllTestSuit.TEST_DATA_PATH
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66 + "MafftPresets.xml";
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68 private static Logger log = Logger
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69 .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
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71 log.setLevel(Level.INFO);
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74 PresetManager<Mafft> presets = null;
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75 RunnerConfig<Mafft> mafftConfig = null;
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76 OptionCombinator mafftOpc = null;
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78 @BeforeMethod(groups = { AllTestSuit.test_group_runner,
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79 AllTestSuit.test_group_non_windows })
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80 public void setup() {
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83 RunnerConfigMarshaller<Mafft> mafftmarsh = new RunnerConfigMarshaller<Mafft>(
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84 RunnerConfig.class);
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85 mafftConfig = mafftmarsh.read(new FileInputStream(new File(
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86 mafftConfigFile)), RunnerConfig.class);
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87 mafftOpc = new OptionCombinator(mafftConfig);
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89 RunnerConfigMarshaller<Mafft> rconfigPresets = new RunnerConfigMarshaller<Mafft>(
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90 PresetManager.class);
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91 File infile = new File(input);
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92 assertTrue(infile.exists());
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93 presets = rconfigPresets.read(new FileInputStream(infile),
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94 PresetManager.class);
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95 assertNotNull(presets);
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96 assertFalse(presets.getPresets().isEmpty());
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98 } catch (JAXBException e) {
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99 e.printStackTrace();
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100 fail(e.getLocalizedMessage());
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101 } catch (FileNotFoundException e) {
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102 e.printStackTrace();
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103 fail(e.getLocalizedMessage());
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109 public void testConfiguration() {
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111 this.mafftConfig.validate();
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112 } catch (ValidationException e) {
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113 e.printStackTrace();
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114 fail(e.getLocalizedMessage());
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115 } catch (IllegalStateException e) {
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116 e.printStackTrace();
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117 fail(e.getLocalizedMessage());
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121 @Test(groups = { AllTestSuit.test_group_runner,
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122 AllTestSuit.test_group_non_windows })
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123 public void testDefaultParameters() {
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124 Mafft mafft = new Mafft();
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125 mafft.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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128 // For local execution use relavive
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129 ConfiguredExecutable<Mafft> confMafft = Configurator
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130 .configureExecutable(mafft, ExecProvider.Cluster);
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131 SyncExecutor sexecutor = Configurator.getSyncEngine(confMafft);
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132 sexecutor.executeJob();
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133 confMafft = (ConfiguredExecutable<Mafft>) sexecutor.waitForResult();
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134 assertNotNull(confMafft.getResults());
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135 } catch (JobSubmissionException e) {
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136 e.printStackTrace();
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137 fail(e.getLocalizedMessage());
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138 } catch (JobExecutionException e) {
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139 e.printStackTrace();
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140 fail(e.getLocalizedMessage());
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141 } catch (ResultNotAvailableException e) {
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142 e.printStackTrace();
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143 fail(e.getLocalizedMessage());
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147 @Test(groups = { AllTestSuit.test_group_runner,
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148 AllTestSuit.test_group_non_windows })
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149 public void testOptions() {
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150 test(mafftOpc.getAllOptions());
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153 @Test(groups = { AllTestSuit.test_group_runner,
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154 AllTestSuit.test_group_non_windows })
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155 public void testParameters() {
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156 List<Parameter<?>> params = mafftOpc.getAllParameters();
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157 Collections.shuffle(params);
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161 @Test(groups = { AllTestSuit.test_group_runner,
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162 AllTestSuit.test_group_non_windows })
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163 public void testArguments() {
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164 List<Option<?>> options = new ArrayList<Option<?>>(mafftConfig
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166 options.addAll(mafftOpc.getAllParameters());
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167 Collections.shuffle(options);
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171 @Test(groups = { AllTestSuit.test_group_runner,
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172 AllTestSuit.test_group_non_windows })
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173 public void testConstrainedParametersMinValues() {
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174 Map<Parameter<?>, String> params = mafftOpc
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175 .getAllConstrainedParametersWithBorderValues(true);
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179 @Test(groups = { AllTestSuit.test_group_runner,
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180 AllTestSuit.test_group_non_windows })
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181 public void testConstrainedParametersMaxValues() {
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182 Map<Parameter<?>, String> params = mafftOpc
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183 .getAllConstrainedParametersWithBorderValues(false);
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187 @Test(groups = { AllTestSuit.test_group_runner,
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188 AllTestSuit.test_group_non_windows })
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189 public void testConstrainedParametersRandomValues() {
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190 for (int i = 0; i < 20; i++) {
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191 Map<Parameter<?>, String> params = mafftOpc
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192 .getAllConstrainedParametersWithRandomValues();
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193 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(params
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195 Collections.shuffle(paramList);
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196 List<Parameter<?>> subList = paramList.subList(0, Util
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197 .getRandomNumber(1, paramList.size()));
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198 List<String> args = mafftOpc.parametersToCommandString(subList,
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204 @Test(groups = { AllTestSuit.test_group_runner,
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205 AllTestSuit.test_group_non_windows })
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206 public void testPresets() {
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207 for (Preset<Mafft> p : presets.getPresets()) {
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208 singleTest(p.getOptions());
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212 void test(Map<Parameter<?>, String> paramValue) {
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213 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue
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215 for (int i = 0; i < paramValue.size(); i++) {
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216 List<String> args = mafftOpc.parametersToCommandString(paramList,
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219 Collections.shuffle(paramList);
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221 log.info("NUMBER OF COBINATION TESTED: " + paramValue.size());
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224 void test(List<? extends Option<?>> params) {
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225 for (int i = 0; i < params.size(); i++) {
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226 List<String> args = mafftOpc.argumentsToCommandString(params);
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228 Collections.shuffle(params);
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230 log.info("NUMBER OF COBINATION TESTED: " + params.size());
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233 void singleTest(List<String> params) {
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235 log.info("Using arguments: " + params);
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236 Mafft mafft = new Mafft();
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237 mafft.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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239 // For local execution use relative
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240 ConfiguredExecutable<Mafft> confMafft = Configurator
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241 .configureExecutable(mafft, ExecProvider.Local);
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242 // Add options to the executable
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243 confMafft.addParameters(params);
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245 SyncExecutor sexecutor = Configurator.getSyncEngine(confMafft);
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246 sexecutor.executeJob();
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247 ConfiguredExecutable<?> al = sexecutor.waitForResult();
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248 assertNotNull(al.getResults());
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250 * TODO File errors = new File(confMafft.getWorkDirectory(),
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251 * ExecutableWrapper.PROC_ERR_FILE); if (errors.length() != 0) {
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252 * log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors)); }
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253 * assertTrue("Run with arguments : " + params + " FAILED!", errors
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256 } catch (JobSubmissionException e) {
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257 e.printStackTrace();
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258 fail(e.getLocalizedMessage());
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259 } catch (JobExecutionException e) {
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260 e.printStackTrace();
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261 fail(e.getLocalizedMessage());
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262 } catch (ResultNotAvailableException e) {
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263 e.printStackTrace();
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264 fail(e.getLocalizedMessage());
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