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.HashSet;
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34 import java.util.Map;
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35 import java.util.Set;
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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.BeforeMethod;
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42 import org.testng.annotations.Test;
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44 import compbio.data.sequence.Score;
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45 import compbio.engine.AsyncExecutor;
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46 import compbio.engine.Configurator;
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47 import compbio.engine.FilePuller;
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48 import compbio.engine.SyncExecutor;
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49 import compbio.engine.client.ConfExecutable;
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50 import compbio.engine.client.ConfiguredExecutable;
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51 import compbio.engine.client.Executable;
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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.local.LocalRunner;
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57 import compbio.metadata.AllTestSuit;
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58 import compbio.metadata.ChunkHolder;
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59 import compbio.metadata.JobExecutionException;
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60 import compbio.metadata.JobStatus;
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61 import compbio.metadata.JobSubmissionException;
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62 import compbio.metadata.LimitsManager;
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63 import compbio.metadata.PresetManager;
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64 import compbio.metadata.ResultNotAvailableException;
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65 import compbio.metadata.RunnerConfig;
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66 import compbio.util.FileWatcher;
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67 import compbio.util.SysPrefs;
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69 public class DisemblTester {
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71 public static String test_outfile = "TO1381.disembl.out";
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73 private Disembl disembl;
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75 @BeforeMethod(alwaysRun = true)
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77 disembl = new Disembl();
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78 disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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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 assertFalse(SysPrefs.isWindows,
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85 "Cluster execution can only be in unix environment");
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87 ConfiguredExecutable<Disembl> confDisembl = Configurator
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88 .configureExecutable(disembl,
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89 Executable.ExecProvider.Cluster);
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90 JobRunner runner = JobRunner.getInstance(confDisembl);
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92 assertNotNull(runner, "Runner is NULL");
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93 runner.executeJob();
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94 // assertNotNull("JobId is null", jobId1);
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95 JobStatus status = runner.getJobStatus();
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96 assertTrue(status == JobStatus.PENDING
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97 || status == JobStatus.RUNNING,
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98 "Status of the process is wrong!");
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99 JobInfo info = runner.getJobInfo();
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100 assertNotNull(info, "JobInfo is null");
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101 StatisticManager sm = new StatisticManager(info);
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102 assertNotNull(sm, "Statictic manager is null");
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105 String exits = sm.getExitStatus();
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106 assertNotNull("Exit status is null", exits);
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107 // cut 4 trailing zeros from the number
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108 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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110 assertEquals(0, exitsInt);
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111 System.out.println(sm.getAllStats());
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113 } catch (ParseException e) {
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114 e.printStackTrace();
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115 fail("Parse Exception: " + e.getMessage());
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117 // assertFalse(runner.cleanup());
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118 assertTrue(sm.hasExited());
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119 assertFalse(sm.wasAborted());
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120 assertFalse(sm.hasDump());
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121 assertFalse(sm.hasSignaled());
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123 } catch (JobSubmissionException e) {
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124 e.printStackTrace();
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125 fail("DrmaaException caught:" + e.getMessage());
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126 } catch (JobExecutionException e) {
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127 e.printStackTrace();
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128 fail("DrmaaException caught:" + e.getMessage());
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129 } catch (DrmaaException e) {
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130 e.printStackTrace();
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131 fail("DrmaaException caught:" + e.getMessage());
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136 * This tests fails from time to time depending on the cluster load or some
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137 * other factors. Any client code has to adjust for this issue
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139 @Test(groups = {AllTestSuit.test_group_cluster,
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140 AllTestSuit.test_group_runner})
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141 public void testRunOnClusterAsync() {
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142 assertFalse(SysPrefs.isWindows,
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143 "Cluster execution can only be in unix environment");
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145 ConfiguredExecutable<Disembl> confDisembl = Configurator
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146 .configureExecutable(disembl,
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147 Executable.ExecProvider.Cluster);
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148 AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);
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149 String jobId = aengine.submitJob(confDisembl);
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150 assertNotNull(jobId, "Runner is NULL");
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151 // let drmaa to start
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153 JobStatus status = aengine.getJobStatus(jobId);
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154 while (status != JobStatus.FINISHED) {
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155 System.out.println("Job Status: " + status);
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156 Thread.sleep(1000);
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157 status = aengine.getJobStatus(jobId);
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158 ConfiguredExecutable<Disembl> result = (ConfiguredExecutable<Disembl>) aengine
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159 .getResults(jobId);
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160 assertNotNull(result);
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161 System.out.println("RES:" + result);
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162 // Some times the job could be removed from the cluster
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164 // before it has been reported to finish. Make sure
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165 // to stop waiting in such case
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166 if (status == JobStatus.UNDEFINED) {
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170 } catch (JobSubmissionException e) {
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171 e.printStackTrace();
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172 fail("DrmaaException caught:" + e.getMessage());
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173 } catch (InterruptedException e) {
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174 e.printStackTrace();
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175 fail(e.getMessage());
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176 } catch (ResultNotAvailableException e) {
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177 e.printStackTrace();
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178 fail(e.getMessage());
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182 @Test(groups = {AllTestSuit.test_group_runner})
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183 public void testRunLocally() {
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185 ConfiguredExecutable<Disembl> confDisembl = Configurator
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186 .configureExecutable(disembl, Executable.ExecProvider.Local);
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188 // For local execution use relative
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189 LocalRunner lr = new LocalRunner(confDisembl);
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191 ConfiguredExecutable<?> al1 = lr.waitForResult();
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192 assertNotNull(al1.getResults());
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193 Map<String,Set<Score>> al2 = confDisembl.getResults();
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194 assertNotNull(al2);
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195 assertEquals(al2.size(), 3);
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196 assertEquals(al1.getResults(), al2);
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197 } catch (JobSubmissionException e) {
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198 e.printStackTrace();
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199 fail(e.getLocalizedMessage());
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200 } catch (ResultNotAvailableException e) {
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201 e.printStackTrace();
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202 fail(e.getLocalizedMessage());
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203 } catch (JobExecutionException e) {
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204 e.printStackTrace();
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205 fail(e.getLocalizedMessage());
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209 @Test(groups = {AllTestSuit.test_group_runner})
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210 public void readStatistics() {
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211 // No execution statistics is available!
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214 @Test(groups = {AllTestSuit.test_group_runner})
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215 public void testPersistance() {
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217 Disembl disembl = new Disembl();
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218 disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)
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219 .setOutput("outtt.txt");
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220 assertEquals(disembl.getInput(), AllTestSuit.test_input);
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221 assertEquals(disembl.getError(), "errrr.txt");
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222 assertEquals(disembl.getOutput(), "outtt.txt");
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223 ConfiguredExecutable<Disembl> cDisembl = Configurator
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224 .configureExecutable(disembl, Executable.ExecProvider.Local);
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226 SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);
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227 sexec.executeJob();
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228 ConfiguredExecutable<?> al = sexec.waitForResult();
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229 assertNotNull(al.getResults());
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230 // Save run configuration
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231 assertTrue(cDisembl.saveRunConfiguration());
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233 // See if loaded configuration is the same as saved
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234 RunConfiguration loadedRun = RunConfiguration
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235 .load(new FileInputStream(new File(cDisembl
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236 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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238 ((ConfExecutable<Disembl>) cDisembl).getRunConfiguration(),
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240 // Load run configuration as ConfExecutable
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241 ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl
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242 .loadRunConfiguration(new FileInputStream(new File(cDisembl
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243 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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244 assertNotNull(resurrectedCDisembl);
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245 assertEquals(resurrectedCDisembl.getExecutable().getInput(),
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246 AllTestSuit.test_input);
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247 assertEquals(resurrectedCDisembl.getExecutable().getError(),
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249 assertEquals(resurrectedCDisembl.getExecutable().getOutput(),
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251 // See in details whether executables are the same
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252 assertEquals(resurrectedCDisembl.getExecutable(), disembl);
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254 ConfiguredExecutable<Disembl> resDisembl = Configurator
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255 .configureExecutable(resurrectedCDisembl.getExecutable(),
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256 Executable.ExecProvider.Local);
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258 sexec = Configurator.getSyncEngine(resDisembl,
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259 Executable.ExecProvider.Local);
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260 sexec.executeJob();
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261 al = sexec.waitForResult();
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264 } catch (JobSubmissionException e) {
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265 e.printStackTrace();
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266 fail(e.getMessage());
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267 } catch (JobExecutionException e) {
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268 e.printStackTrace();
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269 fail(e.getMessage());
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270 } catch (FileNotFoundException e) {
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271 e.printStackTrace();
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272 fail(e.getMessage());
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273 } catch (IOException e) {
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274 e.printStackTrace();
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275 fail(e.getMessage());
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276 } catch (ResultNotAvailableException e) {
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277 e.printStackTrace();
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278 fail(e.getMessage());
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282 @Test(groups = {AllTestSuit.test_group_runner})
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283 public void testConfigurationLoading() {
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285 RunnerConfig<Disembl> disemblConfig = ConfExecutable
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286 .getRunnerOptions(Disembl.class);
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287 assertNotNull(disemblConfig);
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288 // There is no disembl parameters
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289 assertTrue(disemblConfig.getArguments().size() == 0);
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291 PresetManager<Disembl> disemblPresets = ConfExecutable
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292 .getRunnerPresets(Disembl.class);
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293 assertNull(disemblPresets); // there is no presets
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295 LimitsManager<Disembl> disemblLimits = ConfExecutable
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296 .getRunnerLimits(Disembl.class);
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297 assertNotNull(disemblLimits);
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298 assertTrue(disemblLimits.getLimits().size() > 0);
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299 disemblLimits.validate(disemblPresets);
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301 } catch (FileNotFoundException e) {
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302 e.printStackTrace();
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303 fail(e.getLocalizedMessage());
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304 } catch (IOException e) {
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305 e.printStackTrace();
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306 fail(e.getLocalizedMessage());
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307 } catch (ValidationException e) {
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308 e.printStackTrace();
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309 fail(e.getLocalizedMessage());
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