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.disorder;
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23 import static org.testng.Assert.assertEquals;
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24 import static org.testng.Assert.assertFalse;
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25 import static org.testng.Assert.assertNotNull;
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26 import static org.testng.Assert.assertNull;
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27 import static org.testng.Assert.assertTrue;
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28 import static org.testng.Assert.fail;
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30 import java.io.File;
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31 import java.io.FileInputStream;
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32 import java.io.FileNotFoundException;
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33 import java.io.IOException;
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34 import java.text.ParseException;
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36 import javax.xml.bind.ValidationException;
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38 import org.ggf.drmaa.DrmaaException;
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39 import org.ggf.drmaa.JobInfo;
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40 import org.testng.annotations.BeforeMethod;
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41 import org.testng.annotations.Test;
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43 import compbio.data.sequence.ScoreManager;
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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.RunConfiguration;
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52 import compbio.engine.cluster.drmaa.ClusterUtil;
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53 import compbio.engine.cluster.drmaa.JobRunner;
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54 import compbio.engine.cluster.drmaa.StatisticManager;
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55 import compbio.engine.local.LocalRunner;
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56 import compbio.metadata.AllTestSuit;
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57 import compbio.metadata.ChunkHolder;
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58 import compbio.metadata.JobExecutionException;
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59 import compbio.metadata.JobStatus;
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60 import compbio.metadata.JobSubmissionException;
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61 import compbio.metadata.LimitsManager;
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62 import compbio.metadata.PresetManager;
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63 import compbio.metadata.ResultNotAvailableException;
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64 import compbio.metadata.RunnerConfig;
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65 import compbio.util.FileWatcher;
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66 import compbio.util.SysPrefs;
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68 public class JronnTester {
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70 public static String test_outfile = "TO1381.jronn.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, AllTestSuit.test_group_runner})
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80 public void RunOnCluster() {
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81 assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");
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83 ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Cluster);
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84 JobRunner runner = JobRunner.getInstance(confJronn);
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86 assertNotNull(runner, "Runner is NULL");
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87 runner.executeJob();
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88 JobStatus status = runner.getJobStatus();
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89 assertTrue(status == JobStatus.PENDING || status == JobStatus.RUNNING, "Status of the process is wrong!");
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90 JobInfo info = runner.getJobInfo();
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91 assertNotNull(info, "JobInfo is null");
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92 StatisticManager sm = new StatisticManager(info);
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93 assertNotNull(sm, "Statictic manager is null");
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95 String exits = sm.getExitStatus();
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96 assertNotNull("Exit status is null", exits);
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97 // cut 4 trailing zeros from the number
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98 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();
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99 assertEquals(0, exitsInt);
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100 //System.out.println(sm.getAllStats());
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101 } catch (ParseException e) {
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102 e.printStackTrace();
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103 fail("Parse Exception: " + e.getMessage());
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105 assertTrue(sm.hasExited());
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106 assertFalse(sm.wasAborted());
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107 assertFalse(sm.hasDump());
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108 assertFalse(sm.hasSignaled());
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109 } catch (JobSubmissionException e) {
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110 e.printStackTrace();
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111 fail("DrmaaException caught:" + e.getMessage());
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112 } catch (JobExecutionException e) {
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113 e.printStackTrace();
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114 fail("DrmaaException caught:" + e.getMessage());
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115 } catch (DrmaaException e) {
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116 e.printStackTrace();
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117 fail("DrmaaException caught:" + e.getMessage());
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122 * This tests fails from time to time depending on the cluster load or some
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123 * other factors. Any client code has to adjust for this issue
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125 @Test(groups = {AllTestSuit.test_group_cluster, AllTestSuit.test_group_runner})
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126 public void RunOnClusterAsync() {
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127 assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");
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129 ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Cluster);
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130 AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);
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131 String jobId = aengine.submitJob(confJronn);
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132 assertNotNull(jobId, "Runner is NULL");
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133 // let drmaa to start
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135 JobStatus status = aengine.getJobStatus(jobId);
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136 while (status != JobStatus.FINISHED) {
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137 System.out.println("Job Status: " + status);
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138 Thread.sleep(1000);
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139 status = aengine.getJobStatus(jobId);
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140 ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine.getResults(jobId);
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141 assertNotNull(result);
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142 System.out.println("RES:" + result);
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143 // Some times the job could be removed from the cluster accounting before
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144 // it has been reported to finish. Make sure to stop waiting in such case
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145 if (status == JobStatus.UNDEFINED) {
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149 } catch (JobSubmissionException e) {
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150 e.printStackTrace();
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151 fail("DrmaaException caught:" + e.getMessage());
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152 } catch (InterruptedException e) {
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153 e.printStackTrace();
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154 fail(e.getMessage());
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155 } catch (ResultNotAvailableException e) {
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156 e.printStackTrace();
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157 fail(e.getMessage());
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161 @Test(groups = {AllTestSuit.test_group_runner})
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162 public void RunLocally() {
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164 ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);
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166 // For local execution use relative
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167 LocalRunner lr = new LocalRunner(confJronn);
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169 ConfiguredExecutable<?> al1 = lr.waitForResult();
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170 assertNotNull(al1.getResults());
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171 ScoreManager al2 = confJronn.getResults();
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172 assertNotNull(al2);
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173 assertEquals(al2.asMap().size(), 3);
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174 assertEquals(al1.getResults(), al2);
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175 } catch (JobSubmissionException e) {
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176 e.printStackTrace();
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177 fail(e.getLocalizedMessage());
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178 } catch (ResultNotAvailableException e) {
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179 e.printStackTrace();
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180 fail(e.getLocalizedMessage());
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181 } catch (JobExecutionException e) {
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182 e.printStackTrace();
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183 fail(e.getLocalizedMessage());
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187 @Test(groups = {AllTestSuit.test_group_runner})
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188 public void RunLocallyOnTwoCpu() {
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191 ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);
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193 // For local execution use relative
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194 LocalRunner lr = new LocalRunner(confJronn);
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196 ConfiguredExecutable<?> al1 = lr.waitForResult();
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197 assertNotNull(al1.getResults());
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198 ScoreManager al2 = confJronn.getResults();
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199 assertNotNull(al2);
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200 assertEquals(al2.asMap().size(), 3);
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201 assertEquals(al1.getResults(), al2);
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202 } catch (JobSubmissionException e) {
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203 e.printStackTrace();
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204 fail(e.getLocalizedMessage());
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205 } catch (ResultNotAvailableException e) {
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206 e.printStackTrace();
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207 fail(e.getLocalizedMessage());
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208 } catch (JobExecutionException e) {
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209 e.printStackTrace();
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210 fail(e.getLocalizedMessage());
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214 @Test(groups = {AllTestSuit.test_group_runner})
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215 public void readStatistics() {
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217 ConfiguredExecutable<Jronn> confJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);
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218 // For local execution use relavive
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220 AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);
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221 String jobId = sexec.submitJob(confJronn);
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222 String file = confJronn.getWorkDirectory() + File.separator + Jronn.getStatFile();
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223 FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);
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227 JobStatus status = sexec.getJobStatus(jobId);
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228 while (status != JobStatus.FINISHED) {
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229 if (fw.hasMoreData()) {
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230 ChunkHolder ch = fw.pull(position);
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231 String chunk = ch.getChunk();
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232 position = ch.getNextPosition();
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235 // Make sure the loop is terminated if the job fails
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236 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
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240 status = sexec.getJobStatus(jobId);
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242 assertTrue(count > 1);
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243 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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244 assertNotNull(al.getResults());
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245 } catch (JobSubmissionException e) {
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246 e.printStackTrace();
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247 fail(e.getMessage());
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248 } catch (ResultNotAvailableException e) {
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249 e.printStackTrace();
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250 fail(e.getMessage());
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251 } catch (IOException e) {
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252 e.printStackTrace();
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253 fail(e.getMessage());
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254 } catch (InterruptedException e) {
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255 e.printStackTrace();
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256 fail(e.getMessage());
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260 @Test(groups = {AllTestSuit.test_group_runner})
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261 public void Persistance() {
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263 Jronn jronn = new Jronn();
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264 jronn.setError("errrr.txt");
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265 jronn.setInput(AllTestSuit.test_input);
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266 jronn.setOutput("outtt.txt");
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267 assertEquals(jronn.getInput(), AllTestSuit.test_input);
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268 assertEquals(jronn.getError(), "errrr.txt");
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269 assertEquals(jronn.getOutput(), "outtt.txt");
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270 ConfiguredExecutable<Jronn> cJronn = Configurator.configureExecutable(jronn, Executable.ExecProvider.Local);
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271 SyncExecutor sexec = Configurator.getSyncEngine(cJronn);
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272 sexec.executeJob();
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273 ConfiguredExecutable<?> al = sexec.waitForResult();
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274 assertNotNull(al.getResults());
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275 // Save run configuration
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276 assertTrue(cJronn.saveRunConfiguration());
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278 // See if loaded configuration is the same as saved
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279 RunConfiguration loadedRun = RunConfiguration
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280 .load(new FileInputStream(new File(cJronn
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281 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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283 ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),
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285 // Load run configuration as ConfExecutable
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286 ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn
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287 .loadRunConfiguration(new FileInputStream(new File(cJronn.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, Executable.ExecProvider.Local);
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303 sexec.executeJob();
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304 al = sexec.waitForResult();
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306 } catch (JobSubmissionException e) {
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307 e.printStackTrace();
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308 fail(e.getMessage());
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309 } catch (JobExecutionException e) {
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310 e.printStackTrace();
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311 fail(e.getMessage());
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312 } catch (FileNotFoundException e) {
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313 e.printStackTrace();
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314 fail(e.getMessage());
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315 } catch (IOException e) {
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316 e.printStackTrace();
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317 fail(e.getMessage());
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318 } catch (ResultNotAvailableException e) {
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319 e.printStackTrace();
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320 fail(e.getMessage());
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324 @Test(groups = {AllTestSuit.test_group_runner})
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325 public void ConfigurationLoading() {
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327 RunnerConfig<Jronn> jronnConfig = ConfExecutable.getRunnerOptions(Jronn.class);
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328 assertNull(jronnConfig); // There is no supported parameters for Jronn
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330 PresetManager<Jronn> jronnPresets = ConfExecutable.getRunnerPresets(Jronn.class);
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331 assertNull(jronnPresets); // there is no presets
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333 LimitsManager<Jronn> jronnLimits = ConfExecutable.getRunnerLimits(Jronn.class);
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334 assertNotNull(jronnLimits);
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335 assertTrue(jronnLimits.getLimits().size() > 0);
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336 jronnLimits.validate(jronnPresets);
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338 } catch (FileNotFoundException e) {
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339 e.printStackTrace();
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340 fail(e.getLocalizedMessage());
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341 } catch (IOException e) {
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342 e.printStackTrace();
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343 fail(e.getLocalizedMessage());
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344 } catch (ValidationException e) {
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345 e.printStackTrace();
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346 fail(e.getLocalizedMessage());
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