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.data.sequence.ScoreManager;
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46 import compbio.engine.AsyncExecutor;
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47 import compbio.engine.Configurator;
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48 import compbio.engine.FilePuller;
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49 import compbio.engine.SyncExecutor;
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50 import compbio.engine.client.ConfExecutable;
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51 import compbio.engine.client.ConfiguredExecutable;
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52 import compbio.engine.client.Executable;
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53 import compbio.engine.client.RunConfiguration;
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54 import compbio.engine.cluster.drmaa.ClusterUtil;
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55 import compbio.engine.cluster.drmaa.JobRunner;
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56 import compbio.engine.cluster.drmaa.StatisticManager;
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57 import compbio.engine.local.LocalRunner;
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58 import compbio.metadata.AllTestSuit;
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59 import compbio.metadata.ChunkHolder;
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60 import compbio.metadata.JobExecutionException;
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61 import compbio.metadata.JobStatus;
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62 import compbio.metadata.JobSubmissionException;
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63 import compbio.metadata.LimitsManager;
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64 import compbio.metadata.PresetManager;
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65 import compbio.metadata.ResultNotAvailableException;
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66 import compbio.metadata.RunnerConfig;
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67 import compbio.util.FileWatcher;
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68 import compbio.util.SysPrefs;
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70 public class DisemblTester {
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72 public static String test_outfile = "TO1381.disembl.out";
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74 private Disembl disembl;
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76 @BeforeMethod(alwaysRun = true)
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78 disembl = new Disembl();
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79 disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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82 @Test(groups = {AllTestSuit.test_group_cluster,
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83 AllTestSuit.test_group_runner})
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84 public void testRunOnCluster() {
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85 assertFalse(SysPrefs.isWindows,
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86 "Cluster execution can only be in unix environment");
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88 ConfiguredExecutable<Disembl> confDisembl = Configurator
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89 .configureExecutable(disembl,
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90 Executable.ExecProvider.Cluster);
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91 JobRunner runner = JobRunner.getInstance(confDisembl);
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93 assertNotNull(runner, "Runner is NULL");
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94 runner.executeJob();
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95 // assertNotNull("JobId is null", jobId1);
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96 JobStatus status = runner.getJobStatus();
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97 assertTrue(status == JobStatus.PENDING
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98 || status == JobStatus.RUNNING,
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99 "Status of the process is wrong!");
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100 JobInfo info = runner.getJobInfo();
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101 assertNotNull(info, "JobInfo is null");
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102 StatisticManager sm = new StatisticManager(info);
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103 assertNotNull(sm, "Statictic manager is null");
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106 String exits = sm.getExitStatus();
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107 assertNotNull("Exit status is null", exits);
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108 // cut 4 trailing zeros from the number
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109 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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111 assertEquals(0, exitsInt);
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112 System.out.println(sm.getAllStats());
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114 } catch (ParseException e) {
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115 e.printStackTrace();
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116 fail("Parse Exception: " + e.getMessage());
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118 // assertFalse(runner.cleanup());
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119 assertTrue(sm.hasExited());
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120 assertFalse(sm.wasAborted());
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121 assertFalse(sm.hasDump());
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122 assertFalse(sm.hasSignaled());
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124 } catch (JobSubmissionException e) {
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125 e.printStackTrace();
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126 fail("DrmaaException caught:" + e.getMessage());
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127 } catch (JobExecutionException e) {
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128 e.printStackTrace();
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129 fail("DrmaaException caught:" + e.getMessage());
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130 } catch (DrmaaException e) {
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131 e.printStackTrace();
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132 fail("DrmaaException caught:" + e.getMessage());
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137 * This tests fails from time to time depending on the cluster load or some
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138 * other factors. Any client code has to adjust for this issue
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140 @Test(groups = {AllTestSuit.test_group_cluster,
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141 AllTestSuit.test_group_runner})
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142 public void testRunOnClusterAsync() {
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143 assertFalse(SysPrefs.isWindows,
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144 "Cluster execution can only be in unix environment");
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146 ConfiguredExecutable<Disembl> confDisembl = Configurator
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147 .configureExecutable(disembl,
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148 Executable.ExecProvider.Cluster);
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149 AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);
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150 String jobId = aengine.submitJob(confDisembl);
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151 assertNotNull(jobId, "Runner is NULL");
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152 // let drmaa to start
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154 JobStatus status = aengine.getJobStatus(jobId);
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155 while (status != JobStatus.FINISHED) {
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156 System.out.println("Job Status: " + status);
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157 Thread.sleep(1000);
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158 status = aengine.getJobStatus(jobId);
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159 ConfiguredExecutable<Disembl> result = (ConfiguredExecutable<Disembl>) aengine
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160 .getResults(jobId);
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161 assertNotNull(result);
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162 System.out.println("RES:" + result);
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163 // Some times the job could be removed from the cluster
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165 // before it has been reported to finish. Make sure
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166 // to stop waiting in such case
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167 if (status == JobStatus.UNDEFINED) {
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171 } catch (JobSubmissionException e) {
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172 e.printStackTrace();
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173 fail("DrmaaException caught:" + e.getMessage());
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174 } catch (InterruptedException e) {
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175 e.printStackTrace();
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176 fail(e.getMessage());
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177 } catch (ResultNotAvailableException e) {
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178 e.printStackTrace();
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179 fail(e.getMessage());
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183 @Test(groups = {AllTestSuit.test_group_runner})
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184 public void testRunLocally() {
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186 ConfiguredExecutable<Disembl> confDisembl = Configurator
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187 .configureExecutable(disembl, Executable.ExecProvider.Local);
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189 // For local execution use relative
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190 LocalRunner lr = new LocalRunner(confDisembl);
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192 ConfiguredExecutable<?> al1 = lr.waitForResult();
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193 assertNotNull(al1.getResults());
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194 ScoreManager al2 = confDisembl.getResults();
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195 assertNotNull(al2);
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196 assertEquals(al2.asMap().size(), 3);
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197 assertEquals(al1.getResults(), al2);
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198 } catch (JobSubmissionException e) {
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199 e.printStackTrace();
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200 fail(e.getLocalizedMessage());
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201 } catch (ResultNotAvailableException e) {
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202 e.printStackTrace();
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203 fail(e.getLocalizedMessage());
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204 } catch (JobExecutionException e) {
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205 e.printStackTrace();
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206 fail(e.getLocalizedMessage());
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210 @Test(groups = {AllTestSuit.test_group_runner})
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211 public void readStatistics() {
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212 // No execution statistics is available!
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215 @Test(groups = {AllTestSuit.test_group_runner})
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216 public void testPersistance() {
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218 Disembl disembl = new Disembl();
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219 disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)
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220 .setOutput("outtt.txt");
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221 assertEquals(disembl.getInput(), AllTestSuit.test_input);
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222 assertEquals(disembl.getError(), "errrr.txt");
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223 assertEquals(disembl.getOutput(), "outtt.txt");
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224 ConfiguredExecutable<Disembl> cDisembl = Configurator
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225 .configureExecutable(disembl, Executable.ExecProvider.Local);
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227 SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);
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228 sexec.executeJob();
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229 ConfiguredExecutable<?> al = sexec.waitForResult();
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230 assertNotNull(al.getResults());
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231 // Save run configuration
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232 assertTrue(cDisembl.saveRunConfiguration());
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234 // See if loaded configuration is the same as saved
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235 RunConfiguration loadedRun = RunConfiguration
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236 .load(new FileInputStream(new File(cDisembl
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237 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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239 ((ConfExecutable<Disembl>) cDisembl).getRunConfiguration(),
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241 // Load run configuration as ConfExecutable
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242 ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl
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243 .loadRunConfiguration(new FileInputStream(new File(cDisembl
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244 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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245 assertNotNull(resurrectedCDisembl);
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246 assertEquals(resurrectedCDisembl.getExecutable().getInput(),
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247 AllTestSuit.test_input);
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248 assertEquals(resurrectedCDisembl.getExecutable().getError(),
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250 assertEquals(resurrectedCDisembl.getExecutable().getOutput(),
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252 // See in details whether executables are the same
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253 assertEquals(resurrectedCDisembl.getExecutable(), disembl);
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255 ConfiguredExecutable<Disembl> resDisembl = Configurator
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256 .configureExecutable(resurrectedCDisembl.getExecutable(),
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257 Executable.ExecProvider.Local);
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259 sexec = Configurator.getSyncEngine(resDisembl,
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260 Executable.ExecProvider.Local);
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261 sexec.executeJob();
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262 al = sexec.waitForResult();
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265 } catch (JobSubmissionException e) {
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266 e.printStackTrace();
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267 fail(e.getMessage());
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268 } catch (JobExecutionException e) {
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269 e.printStackTrace();
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270 fail(e.getMessage());
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271 } catch (FileNotFoundException e) {
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272 e.printStackTrace();
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273 fail(e.getMessage());
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274 } catch (IOException e) {
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275 e.printStackTrace();
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276 fail(e.getMessage());
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277 } catch (ResultNotAvailableException e) {
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278 e.printStackTrace();
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279 fail(e.getMessage());
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283 @Test(groups = {AllTestSuit.test_group_runner})
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284 public void testConfigurationLoading() {
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286 RunnerConfig<Disembl> disemblConfig = ConfExecutable
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287 .getRunnerOptions(Disembl.class);
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288 // There is no disembl parameters
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289 assertNull(disemblConfig);
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291 //If there were a DisemblParameter.xml file and reference to it,
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292 // it would be like that
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293 // assertTrue(disemblConfig.getArguments().size() == 0);
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295 PresetManager<Disembl> disemblPresets = ConfExecutable
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296 .getRunnerPresets(Disembl.class);
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297 assertNull(disemblPresets); // there is no presets
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299 LimitsManager<Disembl> disemblLimits = ConfExecutable
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300 .getRunnerLimits(Disembl.class);
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301 assertNotNull(disemblLimits);
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302 assertTrue(disemblLimits.getLimits().size() > 0);
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303 disemblLimits.validate(disemblPresets);
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305 } catch (FileNotFoundException e) {
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306 e.printStackTrace();
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307 fail(e.getLocalizedMessage());
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308 } catch (IOException e) {
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309 e.printStackTrace();
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310 fail(e.getLocalizedMessage());
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311 } catch (ValidationException e) {
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312 e.printStackTrace();
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313 fail(e.getLocalizedMessage());
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