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