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.io.IOException;
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30 import java.util.ArrayList;
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31 import java.util.Collections;
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32 import java.util.List;
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33 import java.util.Map;
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35 import javax.xml.bind.JAXBException;
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36 import javax.xml.bind.ValidationException;
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38 import org.apache.log4j.Level;
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39 import org.apache.log4j.Logger;
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40 import org.testng.annotations.BeforeMethod;
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41 import org.testng.annotations.Test;
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43 import compbio.engine.Configurator;
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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.engine.local.ExecutableWrapper;
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48 import compbio.engine.local.LocalRunner;
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49 import compbio.metadata.AllTestSuit;
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50 import compbio.metadata.JobExecutionException;
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51 import compbio.metadata.JobSubmissionException;
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52 import compbio.metadata.Option;
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53 import compbio.metadata.Parameter;
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54 import compbio.metadata.Preset;
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55 import compbio.metadata.PresetManager;
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56 import compbio.metadata.ResultNotAvailableException;
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57 import compbio.metadata.RunnerConfig;
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58 import compbio.runner.OptionCombinator;
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59 import compbio.runner.msa.Muscle;
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60 import compbio.util.FileUtil;
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61 import compbio.util.Util;
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63 public class MuscleParametersTester {
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65 static final String muscleConfigFile = AllTestSuit.TEST_DATA_PATH
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66 + "MuscleParameters.xml";
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67 public static String test_outfile = "TO1381.muscle.out";
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68 public static String cluster_test_outfile = "TO1381.muscle.cluster.out";
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69 public static final String input = AllTestSuit.TEST_DATA_PATH
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70 + "MusclePresets.xml";
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72 private static Logger log = Logger
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73 .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
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75 log.setLevel(Level.INFO);
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78 RunnerConfig<Muscle> muscleConfig = null;
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79 OptionCombinator muscleOpc = null;
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80 PresetManager<Muscle> presets = null;
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82 @BeforeMethod(groups = { AllTestSuit.test_group_runner })
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83 public void setup() {
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85 RunnerConfigMarshaller<Muscle> clustalmarsh = new RunnerConfigMarshaller<Muscle>(
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86 RunnerConfig.class);
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87 muscleConfig = clustalmarsh.read(new FileInputStream(new File(
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88 muscleConfigFile)), RunnerConfig.class);
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89 muscleOpc = new OptionCombinator(muscleConfig);
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92 RunnerConfigMarshaller<Muscle> rconfigPresets = new RunnerConfigMarshaller<Muscle>(
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93 PresetManager.class);
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94 File infile = new File(input);
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95 assertTrue(infile.exists());
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96 presets = rconfigPresets.read(new FileInputStream(infile),
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97 PresetManager.class);
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98 assertNotNull(presets);
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99 assertFalse(presets.getPresets().isEmpty());
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101 } catch (JAXBException e) {
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102 e.printStackTrace();
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103 fail(e.getLocalizedMessage());
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104 } catch (FileNotFoundException e) {
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105 e.printStackTrace();
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106 fail(e.getLocalizedMessage());
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111 @Test(groups = { AllTestSuit.test_group_runner })
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112 public void testDefaultParameters() {
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113 Muscle muscle = new Muscle();
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114 muscle.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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117 // For local execution use relavive
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118 ConfiguredExecutable<Muscle> confMuscle = Configurator
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119 .configureExecutable(muscle);
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120 LocalRunner lr = new LocalRunner(confMuscle);
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122 ConfiguredExecutable<?> al = lr.waitForResult();
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123 assertNotNull(al.getResults());
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124 } catch (JobSubmissionException e) {
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125 e.printStackTrace();
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126 fail(e.getLocalizedMessage());
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127 } catch (JobExecutionException e) {
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128 e.printStackTrace();
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129 fail(e.getLocalizedMessage());
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130 } catch (ResultNotAvailableException e) {
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131 e.printStackTrace();
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132 fail(e.getLocalizedMessage());
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137 public void testConfiguration() {
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139 muscleConfig.validate();
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140 } catch (ValidationException e) {
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141 e.printStackTrace();
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142 fail(e.getLocalizedMessage());
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143 } catch (IllegalStateException e) {
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144 e.printStackTrace();
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145 fail(e.getLocalizedMessage());
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149 @Test(groups = { AllTestSuit.test_group_runner })
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150 public void testOptions() {
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151 test(muscleOpc.getAllOptions());
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154 @Test(groups = { AllTestSuit.test_group_runner })
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155 public void testParameters() {
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156 List<Parameter<?>> params = muscleOpc.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 public void testArguments() {
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163 List<Option<?>> options = new ArrayList<Option<?>>(muscleConfig
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165 options.addAll(muscleOpc.getAllParameters());
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166 Collections.shuffle(options);
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170 @Test(groups = { AllTestSuit.test_group_runner })
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171 public void testConstrainedParametersMinValues() {
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172 Map<Parameter<?>, String> params = muscleOpc
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173 .getAllConstrainedParametersWithBorderValues(true);
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177 @Test(groups = { AllTestSuit.test_group_runner })
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178 public void testConstrainedParametersMaxValues() {
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179 Map<Parameter<?>, String> params = muscleOpc
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180 .getAllConstrainedParametersWithBorderValues(false);
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184 @Test(groups = { AllTestSuit.test_group_runner })
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185 public void testConstrainedParametersRandomValues() {
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186 for (int i = 0; i < 20; i++) {
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187 Map<Parameter<?>, String> params = muscleOpc
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188 .getAllConstrainedParametersWithRandomValues();
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189 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(params
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191 Collections.shuffle(paramList);
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192 List<Parameter<?>> subList = paramList.subList(0, Util
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193 .getRandomNumber(1, paramList.size()));
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194 List<String> args = muscleOpc.parametersToCommandString(subList,
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200 @Test(groups = { AllTestSuit.test_group_runner })
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201 public void testPresets() {
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202 for (Preset<Muscle> p : presets.getPresets()) {
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203 singleTest(p.getOptions());
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207 void test(Map<Parameter<?>, String> paramValue) {
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208 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue
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210 for (int i = 0; i < paramValue.size(); i++) {
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211 List<String> args = muscleOpc.parametersToCommandString(paramList,
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214 Collections.shuffle(paramList);
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216 log.info("NUMBER OF COBINATION TESTED: " + paramValue.size());
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219 void test(List<? extends Option<?>> params) {
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220 for (int i = 0; i < params.size(); i++) {
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221 List<String> args = muscleOpc.argumentsToCommandString(params);
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223 Collections.shuffle(params);
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225 log.info("NUMBER OF COBINATION TESTED: " + params.size());
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228 void singleTest(List<String> params) {
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230 log.info("Using arguments: " + params);
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231 Muscle muscle = new Muscle();
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232 muscle.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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234 // For local execution use relative
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235 ConfiguredExecutable<Muscle> confMuscle = Configurator
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236 .configureExecutable(muscle, ExecProvider.Local);
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237 System.out.println("Using params:" + params);
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238 // Add options to the executable
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239 confMuscle.addParameters(params);
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241 LocalRunner lr = new LocalRunner(confMuscle);
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243 ConfiguredExecutable<?> al = lr.waitForResult();
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244 assertNotNull(al.getResults());
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245 File errors = new File(confMuscle.getWorkDirectory(),
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246 ExecutableWrapper.PROC_ERR_FILE);
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247 if (errors.length() != 0) {
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248 log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));
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250 assertTrue(errors.length() == 0, "Run with arguments : " + params
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253 } catch (JobSubmissionException e) {
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254 e.printStackTrace();
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255 fail(e.getLocalizedMessage());
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256 } catch (JobExecutionException e) {
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257 e.printStackTrace();
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258 fail(e.getLocalizedMessage());
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259 } catch (IOException 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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