1 /* Copyright (c) 2009 Peter Troshin
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2 * Copyright (c) 2013 Alexander Sherstnev
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4 * Java Bioinformatics Analysis Web Services (JABAWS)
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7 * This library is free software; you can redistribute it and/or modify it under the terms of the
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8 * Apache License version 2 as published by the Apache Software Foundation
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10 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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11 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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12 * License for more details.
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14 * A copy of the license is in apache_license.txt. It is also available here:
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15 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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17 * Any republication or derived work distributed in source code form
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18 * must include this copyright and license notice.
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21 package compbio.runner.msa;
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23 import static org.testng.Assert.assertEquals;
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24 import static org.testng.Assert.assertNotNull;
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25 import static org.testng.Assert.assertTrue;
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26 import static org.testng.Assert.fail;
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28 import java.io.File;
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29 import java.io.FileInputStream;
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30 import java.io.FileNotFoundException;
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31 import java.io.IOException;
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32 import java.util.Arrays;
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34 import javax.xml.bind.ValidationException;
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36 import org.testng.annotations.BeforeMethod;
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37 import org.testng.annotations.Test;
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39 import compbio.data.sequence.Alignment;
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40 import compbio.engine.AsyncExecutor;
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41 import compbio.engine.Configurator;
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42 import compbio.engine.FilePuller;
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43 import compbio.engine.SyncExecutor;
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44 import compbio.engine.client.ConfExecutable;
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45 import compbio.engine.client.ConfiguredExecutable;
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46 import compbio.engine.client.Executable;
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47 import compbio.engine.client.RunConfiguration;
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48 import compbio.engine.cluster.drmaa.JobRunner;
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49 import compbio.engine.local.LocalRunner;
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50 import compbio.metadata.AllTestSuit;
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51 import compbio.metadata.ChunkHolder;
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52 import compbio.metadata.JobExecutionException;
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53 import compbio.metadata.JobStatus;
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54 import compbio.metadata.JobSubmissionException;
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55 import compbio.metadata.LimitsManager;
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56 import compbio.metadata.PresetManager;
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57 import compbio.metadata.ResultNotAvailableException;
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58 import compbio.metadata.RunnerConfig;
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59 import compbio.runner.msa.Tcoffee;
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60 import compbio.runner.predictors.Jpred;
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61 import compbio.util.FileWatcher;
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62 import compbio.util.SysPrefs;
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64 public class TcoffeeTester {
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66 private Tcoffee tcoffee;
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67 public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;
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68 public static String test_output = "tcoffee.out";
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69 public static String test_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "TO1381.fasta";
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71 @BeforeMethod(groups = {AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows})
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72 public void init() {
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73 tcoffee = new Tcoffee();
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74 tcoffee.setInput(test_input);
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75 tcoffee.setOutput(test_output);
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76 tcoffee.setError("tcoffee.progress");
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77 //System.out.println("Tcoffee has been configured!");
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80 @Test(groups = { AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })
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81 public void RunLocally() {
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83 ConfiguredExecutable<Tcoffee> ctcoffee = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Local);
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84 // matrix does not appear to work
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85 // ctcoffee.getParameters().setParam("-matrix","BLOSUM62");
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87 SyncExecutor sexecutor = Configurator.getSyncEngine(ctcoffee);
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88 sexecutor.executeJob();
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89 ConfiguredExecutable<?> al = sexecutor.waitForResult();
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90 Alignment align = al.getResults();
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91 assertNotNull(align);
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93 // LocalRunner sexecutor = new LocalRunner(ctcoffee);
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94 // sexecutor.executeJob();
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95 // ConfiguredExecutable<?> al = sexecutor.waitForResult();
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96 // Alignment align = al.getResults();
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97 // assertNotNull(align);
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99 } catch (JobSubmissionException e) {
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100 e.printStackTrace();
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101 fail(e.getMessage());
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102 } catch (JobExecutionException e) {
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103 e.printStackTrace();
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104 fail(e.getMessage());
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105 } catch (ResultNotAvailableException e) {
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106 e.printStackTrace();
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107 fail(e.getMessage());
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111 @Test(groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows})
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112 public void readStatistics() {
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114 Tcoffee tcoffee = new Tcoffee().setInput(AllTestSuit.test_input);
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115 ConfiguredExecutable<Tcoffee> confTcoffee = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Local);
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117 AsyncExecutor sexec = Configurator.getAsyncEngine(confTcoffee);
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118 String jobId = sexec.submitJob(confTcoffee);
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119 String file = confTcoffee.getWorkDirectory() + File.separator + tcoffee.getError();
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120 FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);
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124 while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED ||
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125 sexec.getJobStatus(jobId) == JobStatus.FAILED ||
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126 sexec.getJobStatus(jobId) == JobStatus.UNDEFINED) || fw.hasMoreData()) {
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127 if (fw.hasMoreData()) {
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128 ChunkHolder ch = fw.pull(position);
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129 String chunk = ch.getChunk();
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130 position = ch.getNextPosition();
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131 System.out.print(chunk);
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135 assertTrue(count > 1);
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136 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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137 assertNotNull(al.getResults());
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138 } catch (JobSubmissionException e) {
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139 e.printStackTrace();
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140 fail(e.getMessage());
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141 } catch (ResultNotAvailableException e) {
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142 e.printStackTrace();
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143 fail(e.getMessage());
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144 } catch (IOException e) {
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145 e.printStackTrace();
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146 fail(e.getMessage());
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150 @Test(groups = { AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })
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151 public void SetNcore() {
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152 Tcoffee tc = new Tcoffee();
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153 assertEquals(tc.getParameters(null).size(), 3);
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155 assertEquals(2, tc.getNCore());
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156 assertEquals(tc.getParameters(null).size(), 3);
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158 assertEquals(4, tc.getNCore());
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159 assertEquals(tc.getParameters(null).size(), 3);
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162 @Test(groups = { AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })
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163 public void Persistance() {
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165 Tcoffee tcoffee = new Tcoffee();
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166 tcoffee.setError("errrr.txt");
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167 tcoffee.setInput(AllTestSuit.test_input);
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168 tcoffee.setOutput("outtt.txt");
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169 assertEquals(tcoffee.getInput(), AllTestSuit.test_input);
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170 assertEquals(tcoffee.getError(), "errrr.txt");
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171 assertEquals(tcoffee.getOutput(), "outtt.txt");
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173 ConfiguredExecutable<Tcoffee> ctcofee = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Local);
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174 SyncExecutor sexec = Configurator.getSyncEngine(ctcofee);
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175 sexec.executeJob();
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176 ConfiguredExecutable<?> al = sexec.waitForResult();
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177 assertNotNull(al.getResults());
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178 // Save run configuration
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179 assertTrue(ctcofee.saveRunConfiguration());
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181 // See if loaded configuration is the same as saved
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182 RunConfiguration loadedRun = RunConfiguration.load(new FileInputStream(new File(ctcofee.getWorkDirectory(), RunConfiguration.rconfigFile)));
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183 assertEquals(((ConfExecutable<Tcoffee>) ctcofee).getRunConfiguration(), loadedRun);
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185 // Load run configuration as ConfExecutable
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186 ConfiguredExecutable<Tcoffee> resurrectedCTcoffee = (ConfiguredExecutable<Tcoffee>) ctcofee
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187 .loadRunConfiguration(new FileInputStream(new File(ctcofee.getWorkDirectory(), RunConfiguration.rconfigFile)));
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188 assertNotNull(resurrectedCTcoffee);
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190 // See in details whether executables are the same
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191 assertEquals(resurrectedCTcoffee.getExecutable(), tcoffee);
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193 // Finally rerun the job in the new task directory
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194 ConfiguredExecutable<Tcoffee> restcoffee = Configurator.configureExecutable(resurrectedCTcoffee.getExecutable(), Executable.ExecProvider.Local);
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196 sexec = Configurator.getSyncEngine(restcoffee,Executable.ExecProvider.Local);
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197 sexec.executeJob();
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198 al = sexec.waitForResult();
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201 } catch (JobSubmissionException e) {
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202 e.printStackTrace();
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203 fail(e.getMessage());
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204 } catch (JobExecutionException e) {
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205 e.printStackTrace();
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206 fail(e.getMessage());
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207 } catch (FileNotFoundException e) {
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208 e.printStackTrace();
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209 fail(e.getMessage());
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210 } catch (IOException e) {
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211 e.printStackTrace();
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212 fail(e.getMessage());
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213 } catch (ResultNotAvailableException e) {
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214 e.printStackTrace();
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215 fail(e.getMessage());
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219 @Test(groups = { AllTestSuit.test_group_runner })
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220 public void ConfigurationLoading() {
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222 RunnerConfig<Tcoffee> tcoffeeConfig = ConfExecutable.getRunnerOptions(Tcoffee.class);
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223 assertNotNull(tcoffeeConfig);
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224 assertTrue(tcoffeeConfig.getArguments().size() > 0);
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226 PresetManager<Tcoffee> tcoffeePresets = ConfExecutable.getRunnerPresets(Tcoffee.class);
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227 assertNotNull(tcoffeePresets);
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228 assertTrue(tcoffeePresets.getPresets().size() > 0);
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229 tcoffeePresets.validate(tcoffeeConfig);
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231 LimitsManager<Tcoffee> tcoffeeLimits = ConfExecutable.getRunnerLimits(Tcoffee.class);
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232 assertNotNull(tcoffeeLimits);
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233 assertTrue(tcoffeeLimits.getLimits().size() > 0);
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234 tcoffeeLimits.validate(tcoffeePresets);
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235 } catch (FileNotFoundException e) {
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236 e.printStackTrace();
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237 fail(e.getLocalizedMessage());
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238 } catch (IOException e) {
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239 e.printStackTrace();
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240 fail(e.getLocalizedMessage());
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241 } catch (ValidationException e) {
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242 e.printStackTrace();
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243 fail(e.getLocalizedMessage());
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248 @Test(enabled=false,groups = { AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner, AllTestSuit.test_group_non_windows })
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249 public void RunOnCluster() {
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251 ConfiguredExecutable<Tcoffee> cmafft = Configurator.configureExecutable(tcoffee, Executable.ExecProvider.Cluster);
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252 JobRunner sexecutor = (JobRunner) Configurator.getSyncEngine(cmafft, Executable.ExecProvider.Cluster);
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253 sexecutor.executeJob();
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254 ConfiguredExecutable<?> al = sexecutor.waitForResult();
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255 Alignment align = al.getResults();
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256 assertNotNull(align);
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257 } catch (JobSubmissionException e) {
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258 e.printStackTrace();
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259 fail(e.getMessage());
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260 } catch (JobExecutionException e) {
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261 e.printStackTrace();
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262 fail(e.getMessage());
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263 } catch (ResultNotAvailableException e) {
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264 e.printStackTrace();
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265 fail(e.getMessage());
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