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.disorder;
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21 import static org.testng.Assert.assertEquals;
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22 import static org.testng.Assert.*;
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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.List;
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34 import javax.xml.bind.ValidationException;
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36 import org.ggf.drmaa.DrmaaException;
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37 import org.ggf.drmaa.JobInfo;
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38 import org.testng.annotations.BeforeMethod;
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39 import org.testng.annotations.Test;
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41 import compbio.data.sequence.AnnotatedSequence;
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42 import compbio.engine.AsyncExecutor;
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43 import compbio.engine.Configurator;
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44 import compbio.engine.FilePuller;
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45 import compbio.engine.SyncExecutor;
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46 import compbio.engine.client.ConfExecutable;
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47 import compbio.engine.client.ConfiguredExecutable;
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48 import compbio.engine.client.Executable;
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49 import compbio.engine.client.RunConfiguration;
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50 import compbio.engine.cluster.drmaa.ClusterUtil;
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51 import compbio.engine.cluster.drmaa.JobRunner;
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52 import compbio.engine.cluster.drmaa.StatisticManager;
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53 import compbio.engine.local.LocalRunner;
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54 import compbio.metadata.AllTestSuit;
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55 import compbio.metadata.ChunkHolder;
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56 import compbio.metadata.JobExecutionException;
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57 import compbio.metadata.JobStatus;
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58 import compbio.metadata.JobSubmissionException;
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59 import compbio.metadata.LimitsManager;
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60 import compbio.metadata.PresetManager;
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61 import compbio.metadata.ResultNotAvailableException;
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62 import compbio.metadata.RunnerConfig;
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63 import compbio.util.FileWatcher;
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64 import compbio.util.SysPrefs;
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66 public class JronnTester {
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68 public static String test_outfile = "TO1381.jronn.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out
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70 private Jronn jronn;
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72 @BeforeMethod(alwaysRun = true)
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74 jronn = new Jronn();
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75 jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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78 @Test(groups = { AllTestSuit.test_group_cluster,
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79 AllTestSuit.test_group_runner })
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80 public void testRunOnCluster() {
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81 assertFalse(SysPrefs.isWindows,
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82 "Cluster execution can only be in unix environment");
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84 ConfiguredExecutable<Jronn> confJronn = Configurator
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85 .configureExecutable(jronn, Executable.ExecProvider.Cluster);
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86 JobRunner runner = JobRunner.getInstance(confJronn);
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88 assertNotNull(runner, "Runner is NULL");
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89 runner.executeJob();
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90 // assertNotNull("JobId is null", jobId1);
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91 JobStatus status = runner.getJobStatus();
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92 assertTrue(status == JobStatus.PENDING
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93 || status == JobStatus.RUNNING,
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94 "Status of the process is wrong!");
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95 JobInfo info = runner.getJobInfo();
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96 assertNotNull(info, "JobInfo is null");
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97 StatisticManager sm = new StatisticManager(info);
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98 assertNotNull(sm, "Statictic manager is null");
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101 String exits = sm.getExitStatus();
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102 assertNotNull("Exit status is null", exits);
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103 // cut 4 trailing zeros from the number
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104 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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106 assertEquals(0, exitsInt);
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107 System.out.println(sm.getAllStats());
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109 } catch (ParseException e) {
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110 e.printStackTrace();
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111 fail("Parse Exception: " + e.getMessage());
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113 //assertFalse(runner.cleanup());
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114 assertTrue(sm.hasExited());
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115 assertFalse(sm.wasAborted());
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116 assertFalse(sm.hasDump());
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117 assertFalse(sm.hasSignaled());
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119 } catch (JobSubmissionException e) {
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120 e.printStackTrace();
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121 fail("DrmaaException caught:" + e.getMessage());
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122 } catch (JobExecutionException e) {
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123 e.printStackTrace();
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124 fail("DrmaaException caught:" + e.getMessage());
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125 } catch (DrmaaException e) {
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126 e.printStackTrace();
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127 fail("DrmaaException caught:" + e.getMessage());
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132 * This tests fails from time to time depending on the cluster load or some
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133 * other factors. Any client code has to adjust for this issue
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135 @Test(groups = { AllTestSuit.test_group_cluster,
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136 AllTestSuit.test_group_runner })
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137 public void testRunOnClusterAsync() {
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138 assertFalse(SysPrefs.isWindows,
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139 "Cluster execution can only be in unix environment");
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141 ConfiguredExecutable<Jronn> confJronn = Configurator
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142 .configureExecutable(jronn, Executable.ExecProvider.Cluster);
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143 AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);
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144 String jobId = aengine.submitJob(confJronn);
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145 assertNotNull(jobId, "Runner is NULL");
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146 // let drmaa to start
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148 JobStatus status = aengine.getJobStatus(jobId);
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149 while (status != JobStatus.FINISHED) {
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150 System.out.println("Job Status: " + status);
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151 Thread.sleep(1000);
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152 status = aengine.getJobStatus(jobId);
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153 ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine.getResults(jobId);
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154 assertNotNull(result);
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155 System.out.println("RES:" + result);
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156 // Some times the job could be removed from the cluster accounting
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157 // before it has been reported to finish. Make sure
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158 // to stop waiting in such case
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159 if(status == JobStatus.UNDEFINED) {
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163 } catch (JobSubmissionException e) {
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164 e.printStackTrace();
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165 fail("DrmaaException caught:" + e.getMessage());
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166 } catch (InterruptedException e) {
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167 e.printStackTrace();
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168 fail(e.getMessage());
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169 } catch (ResultNotAvailableException e) {
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170 e.printStackTrace();
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171 fail(e.getMessage());
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175 @Test(groups = { AllTestSuit.test_group_runner })
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176 public void testRunLocally() {
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178 ConfiguredExecutable<Jronn> confJronn = Configurator
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179 .configureExecutable(jronn, Executable.ExecProvider.Local);
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181 // For local execution use relative
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182 LocalRunner lr = new LocalRunner(confJronn);
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184 ConfiguredExecutable<?> al1 = lr.waitForResult();
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185 assertNotNull(al1.getResults());
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186 List<AnnotatedSequence> al2 = confJronn.getResults();
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187 assertNotNull(al2);
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188 assertEquals(al2.size(), 3);
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189 assertEquals(al1.getResults(), al2);
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190 } catch (JobSubmissionException e) {
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191 e.printStackTrace();
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192 fail(e.getLocalizedMessage());
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193 } catch (ResultNotAvailableException e) {
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194 e.printStackTrace();
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195 fail(e.getLocalizedMessage());
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196 } catch (JobExecutionException e) {
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197 e.printStackTrace();
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198 fail(e.getLocalizedMessage());
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202 @Test( groups = { AllTestSuit.test_group_runner })
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203 public void readStatistics() {
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205 ConfiguredExecutable<Jronn> confJronn = Configurator
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206 .configureExecutable(jronn, Executable.ExecProvider.Local);
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207 // For local execution use relavive
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209 AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);
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210 String jobId = sexec.submitJob(confJronn);
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211 FilePuller fw = FilePuller.newFilePuller(confJronn
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212 .getWorkDirectory()
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213 + File.separator + Jronn.getStatFile(),
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214 FileWatcher.MIN_CHUNK_SIZE_BYTES);
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218 JobStatus status = sexec.getJobStatus(jobId);
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219 while (status != JobStatus.FINISHED
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220 || fw.hasMoreData()) {
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221 ChunkHolder ch = fw.pull(position);
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222 String chunk = ch.getChunk();
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223 position = ch.getNextPosition();
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224 System.out.print("C: "+chunk);
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226 // Make sure the loop is terminated if the job fails
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227 if((status == JobStatus.UNDEFINED || status== JobStatus.FAILED)) {
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230 status = sexec.getJobStatus(jobId);
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232 System.out.println("\nOut of the LOOP!! ");
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233 assertTrue(count > 1);
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234 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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235 assertNotNull(al.getResults());
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236 } catch (JobSubmissionException e) {
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237 e.printStackTrace();
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238 fail(e.getMessage());
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239 } catch (ResultNotAvailableException e) {
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240 e.printStackTrace();
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241 fail(e.getMessage());
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242 } catch (IOException e) {
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243 e.printStackTrace();
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244 fail(e.getMessage());
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248 @Test(groups = { AllTestSuit.test_group_runner })
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249 public void testPersistance() {
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251 Jronn jronn = new Jronn();
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252 jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)
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253 .setOutput("outtt.txt");
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254 assertEquals(jronn.getInput(), AllTestSuit.test_input);
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255 assertEquals(jronn.getError(), "errrr.txt");
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256 assertEquals(jronn.getOutput(), "outtt.txt");
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257 ConfiguredExecutable<Jronn> cJronn = Configurator
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258 .configureExecutable(jronn, Executable.ExecProvider.Local);
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260 SyncExecutor sexec = Configurator.getSyncEngine(cJronn);
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261 sexec.executeJob();
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262 ConfiguredExecutable<?> al = sexec.waitForResult();
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263 assertNotNull(al.getResults());
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264 // Save run configuration
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265 assertTrue(cJronn.saveRunConfiguration());
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267 // See if loaded configuration is the same as saved
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268 RunConfiguration loadedRun = RunConfiguration
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269 .load(new FileInputStream(new File(cJronn
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270 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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272 ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),
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274 // Load run configuration as ConfExecutable
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275 ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn
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276 .loadRunConfiguration(new FileInputStream(new File(cJronn
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277 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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278 assertNotNull(resurrectedCMuscle);
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279 assertEquals(resurrectedCMuscle.getExecutable().getInput(),
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280 AllTestSuit.test_input);
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281 assertEquals(resurrectedCMuscle.getExecutable().getError(),
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283 assertEquals(resurrectedCMuscle.getExecutable().getOutput(),
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285 // See in details whether executables are the same
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286 assertEquals(resurrectedCMuscle.getExecutable(), jronn);
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288 ConfiguredExecutable<Jronn> resJronn = Configurator
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289 .configureExecutable(resurrectedCMuscle.getExecutable(),
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290 Executable.ExecProvider.Local);
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292 sexec = Configurator.getSyncEngine(resJronn,
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293 Executable.ExecProvider.Local);
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294 sexec.executeJob();
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295 al = sexec.waitForResult();
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298 } catch (JobSubmissionException e) {
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299 e.printStackTrace();
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300 fail(e.getMessage());
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301 } catch (JobExecutionException e) {
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302 e.printStackTrace();
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303 fail(e.getMessage());
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304 } catch (FileNotFoundException e) {
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305 e.printStackTrace();
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306 fail(e.getMessage());
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307 } catch (IOException e) {
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308 e.printStackTrace();
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309 fail(e.getMessage());
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310 } catch (ResultNotAvailableException e) {
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311 e.printStackTrace();
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312 fail(e.getMessage());
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316 @Test(groups = { AllTestSuit.test_group_runner })
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317 public void testConfigurationLoading() {
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319 RunnerConfig<Jronn> jronnConfig = ConfExecutable
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320 .getRunnerOptions(Jronn.class);
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321 assertNotNull(jronnConfig);
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322 assertTrue(jronnConfig.getArguments().size() > 0);
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324 PresetManager<Jronn> jronnPresets = ConfExecutable
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325 .getRunnerPresets(Jronn.class);
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326 assertNull(jronnPresets); // there is no presets
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328 LimitsManager<Jronn> jronnLimits = ConfExecutable
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329 .getRunnerLimits(Jronn.class);
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330 assertNotNull(jronnLimits);
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331 assertTrue(jronnLimits.getLimits().size() > 0);
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332 jronnLimits.validate(jronnPresets);
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334 } catch (FileNotFoundException e) {
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335 e.printStackTrace();
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336 fail(e.getLocalizedMessage());
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337 } catch (IOException e) {
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338 e.printStackTrace();
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339 fail(e.getLocalizedMessage());
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340 } catch (ValidationException e) {
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341 e.printStackTrace();
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342 fail(e.getLocalizedMessage());
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