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.assertEquals;
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22 import static org.testng.Assert.assertFalse;
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23 import static org.testng.Assert.assertNotNull;
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24 import static org.testng.Assert.assertTrue;
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25 import static org.testng.Assert.fail;
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27 import java.io.File;
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28 import java.io.FileInputStream;
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29 import java.io.FileNotFoundException;
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30 import java.io.IOException;
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31 import java.text.ParseException;
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32 import java.util.ArrayList;
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33 import java.util.Collections;
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34 import java.util.List;
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36 import javax.xml.bind.JAXBException;
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37 import javax.xml.bind.ValidationException;
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39 import org.ggf.drmaa.DrmaaException;
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40 import org.ggf.drmaa.JobInfo;
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41 import org.testng.annotations.Test;
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43 import compbio.data.sequence.FastaSequence;
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44 import compbio.engine.AsyncExecutor;
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45 import compbio.engine.Configurator;
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46 import compbio.engine.FilePuller;
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47 import compbio.engine.SyncExecutor;
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48 import compbio.engine.client.ConfExecutable;
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49 import compbio.engine.client.ConfiguredExecutable;
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50 import compbio.engine.client.Executable;
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51 import compbio.engine.client.Executable.ExecProvider;
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52 import compbio.engine.client.RunConfiguration;
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53 import compbio.engine.cluster.drmaa.ClusterUtil;
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54 import compbio.engine.cluster.drmaa.JobRunner;
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55 import compbio.engine.cluster.drmaa.StatisticManager;
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56 import compbio.engine.conf.RunnerConfigMarshaller;
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57 import compbio.engine.local.AsyncLocalRunner;
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58 import compbio.engine.local.LocalExecutorService;
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59 import compbio.engine.local.LocalRunner;
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60 import compbio.metadata.AllTestSuit;
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61 import compbio.metadata.ChunkHolder;
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62 import compbio.metadata.JobExecutionException;
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63 import compbio.metadata.JobStatus;
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64 import compbio.metadata.JobSubmissionException;
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65 import compbio.metadata.LimitsManager;
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66 import compbio.metadata.PresetManager;
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67 import compbio.metadata.ResultNotAvailableException;
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68 import compbio.metadata.RunnerConfig;
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69 import compbio.runner.OptionCombinator;
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70 import compbio.runner.Util;
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71 import compbio.util.FileWatcher;
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72 import compbio.util.SysPrefs;
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74 public class ClustalOTester {
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76 static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH
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77 + "ClustalParameters.xml";
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78 public static String test_outfile = "TO1381.clustal.out";
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79 public static String cluster_test_outfile = "TO1381.clustal.cluster.out";
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81 @Test(groups = {AllTestSuit.test_group_cluster,
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82 AllTestSuit.test_group_runner})
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83 public void testRunOnCluster() {
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84 ClustalW clustal = new ClustalW();
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85 assertFalse(SysPrefs.isWindows,
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86 "Cluster execution can only be in unix environment");
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87 clustal.setInput(AllTestSuit.test_input)
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88 .setOutput(cluster_test_outfile);
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92 ConfiguredExecutable<ClustalW> confClustal = Configurator
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93 .configureExecutable(clustal);
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94 JobRunner runner = JobRunner.getInstance(confClustal);
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95 // ClusterSession csession = JobRunner.getSession();
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96 assertNotNull(runner);
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97 runner.executeJob();
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98 // assertNotNull("JobId is null", jobId1);
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99 JobStatus status = runner.getJobStatus();
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100 assertTrue(status == JobStatus.PENDING
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101 || status == JobStatus.RUNNING);
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102 JobInfo info = runner.getJobInfo();
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103 assertNotNull(info);
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104 StatisticManager sm = new StatisticManager(info);
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107 String exits = sm.getExitStatus();
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108 assertNotNull("Exit status is null", exits);
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109 // cut 4 trailing zeros from the number
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110 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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112 assertEquals(0, exitsInt);
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113 System.out.println(sm.getAllStats());
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115 } catch (ParseException e) {
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116 e.printStackTrace();
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117 fail("Parse Exception: " + e.getMessage());
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119 // At present the task directory could not be completely removed
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120 // @see JobRunner.cleanup()
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121 assertFalse(runner.cleanup(),
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122 "Could not remove some files whilst cleaning up ");
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123 assertTrue(sm.hasExited());
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124 assertFalse(sm.wasAborted());
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125 assertFalse(sm.hasDump());
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126 assertFalse(sm.hasSignaled());
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128 } catch (JobSubmissionException e) {
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129 e.printStackTrace();
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130 fail("DrmaaException caught:" + e.getMessage());
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131 } catch (JobExecutionException e) {
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132 e.printStackTrace();
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133 fail("DrmaaException caught:" + e.getMessage());
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134 } catch (DrmaaException e) {
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135 e.printStackTrace();
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136 fail("DrmaaException caught:" + e.getMessage());
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140 @Test(groups = {AllTestSuit.test_group_runner})
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141 public void testRunLocally() {
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142 ClustalO clustal = new ClustalO();
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143 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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146 // For local execution use relavive
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147 ConfiguredExecutable<ClustalO> confClustal = Configurator
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148 .configureExecutable(clustal, Executable.ExecProvider.Local);
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149 LocalRunner lr = new LocalRunner(confClustal);
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151 confClustal = (ConfiguredExecutable<ClustalO>) lr.waitForResult();
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152 assertNotNull(confClustal.getResults());
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153 } catch (JobSubmissionException e) {
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154 e.printStackTrace();
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155 fail(e.getLocalizedMessage());
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156 } catch (JobExecutionException e) {
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157 e.printStackTrace();
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158 fail(e.getLocalizedMessage());
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159 } catch (ResultNotAvailableException e) {
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160 e.printStackTrace();
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161 fail(e.getLocalizedMessage());
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165 @Test(groups = {AllTestSuit.test_group_runner})
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166 public void testConfigurationLoading() {
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168 RunnerConfig<ClustalW> clustalConfig = ConfExecutable
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169 .getRunnerOptions(ClustalW.class);
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170 assertNotNull(clustalConfig);
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171 assertTrue(clustalConfig.getArguments().size() > 0);
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173 PresetManager<ClustalW> clustalPresets = ConfExecutable
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174 .getRunnerPresets(ClustalW.class);
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175 assertNotNull(clustalPresets);
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176 assertTrue(clustalPresets.getPresets().size() > 0);
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177 clustalPresets.validate(clustalConfig);
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179 LimitsManager<ClustalW> clustalLimits = ConfExecutable
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180 .getRunnerLimits(ClustalW.class);
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181 assertNotNull(clustalLimits);
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182 assertTrue(clustalLimits.getLimits().size() > 0);
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183 clustalLimits.validate(clustalPresets);
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185 } catch (FileNotFoundException e) {
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186 e.printStackTrace();
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187 fail(e.getLocalizedMessage());
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188 } catch (IOException e) {
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189 e.printStackTrace();
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190 fail(e.getLocalizedMessage());
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191 } catch (ValidationException e) {
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192 e.printStackTrace();
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193 fail(e.getLocalizedMessage());
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197 @Test(groups = {AllTestSuit.test_group_runner})
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198 public void testOptionsLocally() {
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201 RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(
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202 RunnerConfig.class);
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204 RunnerConfig<ClustalW> clustalConfig = clustalmarsh.read(
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205 new FileInputStream(new File(clustalConfigFile)),
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206 RunnerConfig.class);
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208 OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);
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209 List<String> options = clustalOpc.getOptionsAtRandom();
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210 for (int i = 0; i < options.size(); i++) {
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211 System.out.println("Using options: " + options);
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212 ClustalW clustal = new ClustalW();
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213 clustal.setInput(AllTestSuit.test_input)
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214 .setOutput(test_outfile);
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216 // For local execution use relavive
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217 ConfiguredExecutable<ClustalW> confClustal = Configurator
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218 .configureExecutable(clustal, ExecProvider.Local);
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220 // Add options to the executable
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221 confClustal.addParameters(options);
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223 LocalRunner lr = new LocalRunner(confClustal);
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225 confClustal = (ConfiguredExecutable<ClustalW>) lr
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227 assertNotNull(confClustal.getResults());
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228 Collections.shuffle(options);
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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 (JAXBException e) {
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238 e.printStackTrace();
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239 fail(e.getLocalizedMessage());
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240 } catch (ResultNotAvailableException e) {
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241 e.printStackTrace();
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242 fail(e.getLocalizedMessage());
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243 } catch (FileNotFoundException e) {
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244 e.printStackTrace();
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245 fail(e.getLocalizedMessage());
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249 public static final void main(String[] args) throws JobSubmissionException,
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250 JobExecutionException, InterruptedException {
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251 ClustalW clustal = new ClustalW();
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252 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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253 // For local execution use relavive
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254 ConfiguredExecutable<ClustalW> confClustal = Configurator
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255 .configureExecutable(clustal);
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256 AsyncExecutor lr = new AsyncLocalRunner();
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257 lr.submitJob(confClustal);
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258 Thread.sleep(3000);
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259 LocalExecutorService.shutDown();
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262 @Test(enabled = false)
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263 public void testAddParameters() {
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264 ArrayList<FastaSequence> seqs = new ArrayList<FastaSequence>();
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265 FastaSequence fs = new FastaSequence("tests1",
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266 "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");
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267 FastaSequence fs2 = new FastaSequence("tests2",
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268 "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");
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269 FastaSequence fs3 = new FastaSequence("tests3",
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270 "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");
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274 ClustalW cl = new ClustalW();
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275 cl.setInput("input.txt").setOutput("output.txt");
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276 ConfiguredExecutable<ClustalW> confClustal;
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278 confClustal = Configurator.configureExecutable(cl);
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279 Util.writeInput(seqs, confClustal);
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281 LocalRunner lr = new LocalRunner(confClustal);
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283 confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();
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284 assertNotNull(confClustal.getResults());
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286 assertTrue(confClustal.saveRunConfiguration());
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287 ConfiguredExecutable<ClustalW> cexec = (ConfiguredExecutable<ClustalW>) confClustal
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288 .loadRunConfiguration(new FileInputStream(new File(
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289 confClustal.getWorkDirectory(),
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290 RunConfiguration.rconfigFile)));
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291 assertNotNull(cexec);
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293 lr = new LocalRunner(cexec);
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295 confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();
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296 assertNotNull(confClustal.getResults());
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298 System.out.println("CE:" + cexec);
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299 } catch (JobSubmissionException e) {
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300 e.printStackTrace();
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301 fail(e.getMessage());
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302 } catch (FileNotFoundException e) {
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303 e.printStackTrace();
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304 fail(e.getMessage());
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305 } catch (JobExecutionException e) {
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306 e.printStackTrace();
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307 fail(e.getMessage());
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308 } catch (ResultNotAvailableException e) {
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309 e.printStackTrace();
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310 fail(e.getMessage());
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311 } catch (IOException e) {
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312 e.printStackTrace();
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313 fail(e.getMessage());
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317 @Test(groups = {AllTestSuit.test_group_runner})
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318 public void testPersistance() {
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320 ClustalW clustal = new ClustalW();
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321 clustal.setError("errrr.txt").setInput(AllTestSuit.test_input)
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322 .setOutput("outtt.txt");
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323 assertEquals(clustal.getInput(), AllTestSuit.test_input);
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324 assertEquals(clustal.getError(), "errrr.txt");
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325 assertEquals(clustal.getOutput(), "outtt.txt");
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326 ConfiguredExecutable<ClustalW> cClustal = Configurator
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327 .configureExecutable(clustal, Executable.ExecProvider.Local);
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329 SyncExecutor sexec = Configurator.getSyncEngine(cClustal);
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330 sexec.executeJob();
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331 cClustal = (ConfiguredExecutable<ClustalW>) sexec.waitForResult();
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332 assertNotNull(cClustal.getResults());
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333 // Save run configuration
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334 assertTrue(cClustal.saveRunConfiguration());
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336 // See if loaded configuration is the same as saved
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337 RunConfiguration loadedRun = RunConfiguration
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338 .load(new FileInputStream(new File(cClustal
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339 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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340 assertTrue(((ConfExecutable<ClustalW>) cClustal)
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341 .getRunConfiguration().equals(loadedRun));
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342 // Load run configuration as ConfExecutable
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343 ConfiguredExecutable<ClustalW> resurrectedCclustal = (ConfiguredExecutable<ClustalW>) cClustal
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344 .loadRunConfiguration(new FileInputStream(new File(cClustal
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345 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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346 assertNotNull(resurrectedCclustal);
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347 // See in details whether executables are the same
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348 assertEquals(resurrectedCclustal.getExecutable(), clustal);
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350 // Finally rerun the job in the new task directory
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351 ConfiguredExecutable<ClustalW> resclustal = Configurator
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352 .configureExecutable(resurrectedCclustal.getExecutable(),
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353 Executable.ExecProvider.Local);
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355 sexec = Configurator.getSyncEngine(resclustal,
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356 Executable.ExecProvider.Local);
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357 sexec.executeJob();
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358 cClustal = (ConfiguredExecutable<ClustalW>) sexec.waitForResult();
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359 assertNotNull(cClustal.getResults());
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361 } catch (JobSubmissionException e) {
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362 e.printStackTrace();
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363 fail(e.getMessage());
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364 } catch (JobExecutionException e) {
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365 e.printStackTrace();
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366 fail(e.getMessage());
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367 } catch (FileNotFoundException e) {
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368 e.printStackTrace();
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369 fail(e.getMessage());
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370 } catch (IOException e) {
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371 e.printStackTrace();
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372 fail(e.getMessage());
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373 } catch (ResultNotAvailableException e) {
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374 e.printStackTrace();
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375 fail(e.getMessage());
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379 @Test(groups = {AllTestSuit.test_group_runner})
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380 public void readStatistics() {
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382 ClustalW clustal = new ClustalW().setInput(AllTestSuit.test_input)
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383 .setOutput(test_outfile);
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384 ConfiguredExecutable<ClustalW> confClustal = Configurator
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385 .configureExecutable(clustal, Executable.ExecProvider.Local);
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387 AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);
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388 String jobId = sexec.submitJob(confClustal);
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389 FilePuller fw = FilePuller.newFilePuller(
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390 confClustal.getWorkDirectory() + File.separator
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391 + ClustalW.getStatFile(),
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392 FileWatcher.MIN_CHUNK_SIZE_BYTES);
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396 while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED
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397 || sexec.getJobStatus(jobId) == JobStatus.FAILED || sexec
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398 .getJobStatus(jobId) == JobStatus.UNDEFINED)
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399 || fw.hasMoreData()) {
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400 ChunkHolder ch = fw.pull(position);
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401 String chunk = ch.getChunk();
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402 position = ch.getNextPosition();
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403 System.out.print(chunk);
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406 assertTrue(count > 1);
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407 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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408 assertNotNull(al.getResults());
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409 } catch (JobSubmissionException e) {
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410 e.printStackTrace();
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411 fail(e.getMessage());
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412 } catch (ResultNotAvailableException e) {
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413 e.printStackTrace();
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414 fail(e.getMessage());
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415 } catch (IOException e) {
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416 e.printStackTrace();
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417 fail(e.getMessage());
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421 @Test(groups = {AllTestSuit.test_group_cluster,
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422 AllTestSuit.test_group_runner})
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423 public void readStatisticsClusterExecution() {
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425 ClustalW clustal = new ClustalW().setInput(AllTestSuit.test_input)
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426 .setOutput(test_outfile);
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427 ConfiguredExecutable<ClustalW> confClustal = Configurator
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428 .configureExecutable(clustal,
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429 Executable.ExecProvider.Cluster);
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431 AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);
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432 String jobId = sexec.submitJob(confClustal);
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433 FilePuller fw = FilePuller.newFilePuller(
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434 confClustal.getWorkDirectory() + File.separator
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435 + ClustalW.getStatFile(),
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436 FileWatcher.MIN_CHUNK_SIZE_BYTES);
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439 fw.waitForFile(200);
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441 * Under certain circumstances DRMAA could report the status wrongly
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442 * thus this loop never ends TODO deal with this!
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444 while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec
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445 .getJobStatus(jobId) == JobStatus.FAILED)
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446 || fw.hasMoreData()) {
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447 ChunkHolder ch = fw.pull(position);
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448 String chunk = ch.getChunk();
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449 position = ch.getNextPosition();
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450 System.out.print(chunk);
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452 if (sexec.getJobStatus(jobId) == JobStatus.UNDEFINED) {
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453 System.out.println("DRMAA reported wrong status for job + "
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454 + jobId + " continue anyway!");
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458 assertTrue(count > 1);
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459 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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460 assertNotNull(al.getResults());
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461 } catch (JobSubmissionException e) {
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462 e.printStackTrace();
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463 fail(e.getMessage());
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464 } catch (ResultNotAvailableException e) {
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465 e.printStackTrace();
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466 fail(e.getMessage());
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467 } catch (IOException e) {
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468 e.printStackTrace();
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469 fail(e.getMessage());
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