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.assertFalse;
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23 import static org.testng.Assert.assertNotNull;
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24 import static org.testng.Assert.assertNull;
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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.text.ParseException;
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33 import java.util.List;
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35 import javax.xml.bind.ValidationException;
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37 import org.ggf.drmaa.DrmaaException;
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38 import org.ggf.drmaa.JobInfo;
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39 import org.testng.annotations.BeforeMethod;
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40 import org.testng.annotations.Test;
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42 import compbio.data.sequence.AnnotatedSequence;
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43 import compbio.engine.AsyncExecutor;
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44 import compbio.engine.Configurator;
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45 import compbio.engine.FilePuller;
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46 import compbio.engine.SyncExecutor;
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47 import compbio.engine.client.ConfExecutable;
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48 import compbio.engine.client.ConfiguredExecutable;
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49 import compbio.engine.client.Executable;
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50 import compbio.engine.client.RunConfiguration;
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51 import compbio.engine.cluster.drmaa.ClusterUtil;
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52 import compbio.engine.cluster.drmaa.JobRunner;
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53 import compbio.engine.cluster.drmaa.StatisticManager;
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54 import compbio.engine.local.LocalRunner;
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55 import compbio.metadata.AllTestSuit;
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56 import compbio.metadata.ChunkHolder;
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57 import compbio.metadata.JobExecutionException;
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58 import compbio.metadata.JobStatus;
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59 import compbio.metadata.JobSubmissionException;
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60 import compbio.metadata.LimitsManager;
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61 import compbio.metadata.PresetManager;
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62 import compbio.metadata.ResultNotAvailableException;
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63 import compbio.metadata.RunnerConfig;
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64 import compbio.util.FileWatcher;
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65 import compbio.util.SysPrefs;
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67 public class JronnTester {
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69 public static String test_outfile = "TO1381.jronn.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out
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71 private Jronn jronn;
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73 @BeforeMethod(alwaysRun = true)
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75 jronn = new Jronn();
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76 jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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79 @Test(groups = { AllTestSuit.test_group_cluster,
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80 AllTestSuit.test_group_runner })
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81 public void testRunOnCluster() {
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82 assertFalse(SysPrefs.isWindows,
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83 "Cluster execution can only be in unix environment");
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85 ConfiguredExecutable<Jronn> confJronn = Configurator
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86 .configureExecutable(jronn, Executable.ExecProvider.Cluster);
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87 JobRunner runner = JobRunner.getInstance(confJronn);
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89 assertNotNull(runner, "Runner is NULL");
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90 runner.executeJob();
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91 // assertNotNull("JobId is null", jobId1);
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92 JobStatus status = runner.getJobStatus();
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93 assertTrue(status == JobStatus.PENDING
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94 || status == JobStatus.RUNNING,
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95 "Status of the process is wrong!");
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96 JobInfo info = runner.getJobInfo();
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97 assertNotNull(info, "JobInfo is null");
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98 StatisticManager sm = new StatisticManager(info);
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99 assertNotNull(sm, "Statictic manager is null");
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102 String exits = sm.getExitStatus();
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103 assertNotNull("Exit status is null", exits);
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104 // cut 4 trailing zeros from the number
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105 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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107 assertEquals(0, exitsInt);
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108 System.out.println(sm.getAllStats());
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110 } catch (ParseException e) {
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111 e.printStackTrace();
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112 fail("Parse Exception: " + e.getMessage());
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114 //assertFalse(runner.cleanup());
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115 assertTrue(sm.hasExited());
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116 assertFalse(sm.wasAborted());
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117 assertFalse(sm.hasDump());
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118 assertFalse(sm.hasSignaled());
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120 } catch (JobSubmissionException e) {
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121 e.printStackTrace();
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122 fail("DrmaaException caught:" + e.getMessage());
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123 } catch (JobExecutionException e) {
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124 e.printStackTrace();
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125 fail("DrmaaException caught:" + e.getMessage());
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126 } catch (DrmaaException e) {
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127 e.printStackTrace();
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128 fail("DrmaaException caught:" + e.getMessage());
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133 * This tests fails from time to time depending on the cluster load or some
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134 * other factors. Any client code has to adjust for this issue
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136 @Test(groups = { AllTestSuit.test_group_cluster,
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137 AllTestSuit.test_group_runner })
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138 public void testRunOnClusterAsync() {
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139 assertFalse(SysPrefs.isWindows,
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140 "Cluster execution can only be in unix environment");
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142 ConfiguredExecutable<Jronn> confJronn = Configurator
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143 .configureExecutable(jronn, Executable.ExecProvider.Cluster);
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144 AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);
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145 String jobId = aengine.submitJob(confJronn);
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146 assertNotNull(jobId, "Runner is NULL");
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147 // let drmaa to start
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149 JobStatus status = aengine.getJobStatus(jobId);
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150 while (status != JobStatus.FINISHED) {
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151 System.out.println("Job Status: " + status);
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152 Thread.sleep(1000);
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153 status = aengine.getJobStatus(jobId);
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154 ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine
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155 .getResults(jobId);
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156 assertNotNull(result);
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157 System.out.println("RES:" + result);
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158 // Some times the job could be removed from the cluster accounting
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159 // before it has been reported to finish. Make sure
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160 // to stop waiting in such case
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161 if (status == JobStatus.UNDEFINED) {
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165 } catch (JobSubmissionException e) {
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166 e.printStackTrace();
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167 fail("DrmaaException caught:" + e.getMessage());
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168 } catch (InterruptedException e) {
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169 e.printStackTrace();
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170 fail(e.getMessage());
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171 } catch (ResultNotAvailableException e) {
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172 e.printStackTrace();
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173 fail(e.getMessage());
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177 @Test(groups = { AllTestSuit.test_group_runner })
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178 public void testRunLocally() {
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180 ConfiguredExecutable<Jronn> confJronn = Configurator
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181 .configureExecutable(jronn, Executable.ExecProvider.Local);
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183 // For local execution use relative
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184 LocalRunner lr = new LocalRunner(confJronn);
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186 ConfiguredExecutable<?> al1 = lr.waitForResult();
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187 assertNotNull(al1.getResults());
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188 List<AnnotatedSequence> al2 = confJronn.getResults();
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189 assertNotNull(al2);
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190 assertEquals(al2.size(), 3);
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191 assertEquals(al1.getResults(), al2);
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192 } catch (JobSubmissionException e) {
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193 e.printStackTrace();
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194 fail(e.getLocalizedMessage());
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195 } catch (ResultNotAvailableException e) {
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196 e.printStackTrace();
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197 fail(e.getLocalizedMessage());
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198 } catch (JobExecutionException e) {
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199 e.printStackTrace();
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200 fail(e.getLocalizedMessage());
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204 @Test(groups = { AllTestSuit.test_group_runner })
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205 public void readStatistics() {
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207 ConfiguredExecutable<Jronn> confJronn = Configurator
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208 .configureExecutable(jronn, Executable.ExecProvider.Local);
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209 // For local execution use relavive
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211 AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);
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212 String jobId = sexec.submitJob(confJronn);
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213 FilePuller fw = FilePuller.newFilePuller(confJronn
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214 .getWorkDirectory()
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215 + File.separator + Jronn.getStatFile(),
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216 FileWatcher.MIN_CHUNK_SIZE_BYTES);
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220 JobStatus status = sexec.getJobStatus(jobId);
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221 while (status != JobStatus.FINISHED) {
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222 System.out.println((status != JobStatus.FINISHED) + " d: "
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223 + fw.hasMoreData());
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224 if (fw.hasMoreData()) {
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225 ChunkHolder ch = fw.pull(position);
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226 System.out.println("p:" + position);
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227 String chunk = ch.getChunk();
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228 position = ch.getNextPosition();
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229 System.out.println("np " + position + " c: " + chunk);
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232 // Make sure the loop is terminated if the job fails
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233 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
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237 status = sexec.getJobStatus(jobId);
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239 System.out.println("\nOut of the LOOP!! ");
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240 assertTrue(count > 1);
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241 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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242 assertNotNull(al.getResults());
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243 } catch (JobSubmissionException e) {
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244 e.printStackTrace();
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245 fail(e.getMessage());
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246 } catch (ResultNotAvailableException e) {
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247 e.printStackTrace();
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248 fail(e.getMessage());
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249 } catch (IOException e) {
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250 e.printStackTrace();
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251 fail(e.getMessage());
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252 } catch (InterruptedException e) {
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253 e.printStackTrace();
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254 fail(e.getMessage());
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258 @Test(groups = { AllTestSuit.test_group_runner })
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259 public void testPersistance() {
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261 Jronn jronn = new Jronn();
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262 jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)
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263 .setOutput("outtt.txt");
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264 assertEquals(jronn.getInput(), AllTestSuit.test_input);
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265 assertEquals(jronn.getError(), "errrr.txt");
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266 assertEquals(jronn.getOutput(), "outtt.txt");
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267 ConfiguredExecutable<Jronn> cJronn = Configurator
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268 .configureExecutable(jronn, Executable.ExecProvider.Local);
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270 SyncExecutor sexec = Configurator.getSyncEngine(cJronn);
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271 sexec.executeJob();
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272 ConfiguredExecutable<?> al = sexec.waitForResult();
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273 assertNotNull(al.getResults());
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274 // Save run configuration
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275 assertTrue(cJronn.saveRunConfiguration());
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277 // See if loaded configuration is the same as saved
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278 RunConfiguration loadedRun = RunConfiguration
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279 .load(new FileInputStream(new File(cJronn
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280 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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282 ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),
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284 // Load run configuration as ConfExecutable
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285 ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn
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286 .loadRunConfiguration(new FileInputStream(new File(cJronn
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287 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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288 assertNotNull(resurrectedCMuscle);
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289 assertEquals(resurrectedCMuscle.getExecutable().getInput(),
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290 AllTestSuit.test_input);
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291 assertEquals(resurrectedCMuscle.getExecutable().getError(),
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293 assertEquals(resurrectedCMuscle.getExecutable().getOutput(),
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295 // See in details whether executables are the same
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296 assertEquals(resurrectedCMuscle.getExecutable(), jronn);
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298 ConfiguredExecutable<Jronn> resJronn = Configurator
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299 .configureExecutable(resurrectedCMuscle.getExecutable(),
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300 Executable.ExecProvider.Local);
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302 sexec = Configurator.getSyncEngine(resJronn,
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303 Executable.ExecProvider.Local);
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304 sexec.executeJob();
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305 al = sexec.waitForResult();
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308 } catch (JobSubmissionException e) {
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309 e.printStackTrace();
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310 fail(e.getMessage());
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311 } catch (JobExecutionException e) {
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312 e.printStackTrace();
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313 fail(e.getMessage());
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314 } catch (FileNotFoundException e) {
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315 e.printStackTrace();
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316 fail(e.getMessage());
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317 } catch (IOException e) {
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318 e.printStackTrace();
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319 fail(e.getMessage());
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320 } catch (ResultNotAvailableException e) {
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321 e.printStackTrace();
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322 fail(e.getMessage());
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326 @Test(groups = { AllTestSuit.test_group_runner })
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327 public void testConfigurationLoading() {
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329 RunnerConfig<Jronn> jronnConfig = ConfExecutable
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330 .getRunnerOptions(Jronn.class);
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331 assertNotNull(jronnConfig);
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332 assertTrue(jronnConfig.getArguments().size() > 0);
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334 PresetManager<Jronn> jronnPresets = ConfExecutable
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335 .getRunnerPresets(Jronn.class);
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336 assertNull(jronnPresets); // there is no presets
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338 LimitsManager<Jronn> jronnLimits = ConfExecutable
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339 .getRunnerLimits(Jronn.class);
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340 assertNotNull(jronnLimits);
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341 assertTrue(jronnLimits.getLimits().size() > 0);
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342 jronnLimits.validate(jronnPresets);
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344 } catch (FileNotFoundException e) {
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345 e.printStackTrace();
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346 fail(e.getLocalizedMessage());
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347 } catch (IOException e) {
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348 e.printStackTrace();
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349 fail(e.getLocalizedMessage());
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350 } catch (ValidationException e) {
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351 e.printStackTrace();
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352 fail(e.getLocalizedMessage());
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