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.msa;
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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.assertNotSame;
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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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34 import javax.xml.bind.ValidationException;
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36 import org.ggf.drmaa.DrmaaException;
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37 import org.ggf.drmaa.JobInfo;
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38 import org.testng.annotations.BeforeMethod;
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39 import org.testng.annotations.Test;
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41 import compbio.data.sequence.Alignment;
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42 import compbio.engine.AsyncExecutor;
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43 import compbio.engine.Configurator;
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44 import compbio.engine.FilePuller;
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45 import compbio.engine.SyncExecutor;
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46 import compbio.engine.client.ConfExecutable;
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47 import compbio.engine.client.ConfiguredExecutable;
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48 import compbio.engine.client.Executable;
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49 import compbio.engine.client.RunConfiguration;
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50 import compbio.engine.cluster.drmaa.ClusterUtil;
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51 import compbio.engine.cluster.drmaa.JobRunner;
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52 import compbio.engine.cluster.drmaa.StatisticManager;
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53 import compbio.engine.local.LocalRunner;
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54 import compbio.metadata.AllTestSuit;
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55 import compbio.metadata.ChunkHolder;
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56 import compbio.metadata.JobExecutionException;
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57 import compbio.metadata.JobStatus;
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58 import compbio.metadata.JobSubmissionException;
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59 import compbio.metadata.LimitsManager;
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60 import compbio.metadata.PresetManager;
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61 import compbio.metadata.ResultNotAvailableException;
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62 import compbio.metadata.RunnerConfig;
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63 import compbio.runner.msa.Muscle;
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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 MuscleTester {
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69 public static String test_outfile = "TO1381.muscle.out"; // homes/pvtroshin/TO1381.clustal.out
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70 public static String cluster_test_outfile = "TO1381.muscle.cluster.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out
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72 private Muscle muscle;
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74 @BeforeMethod(alwaysRun = true)
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76 muscle = new Muscle();
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77 muscle.setInput(AllTestSuit.test_input).setOutput(cluster_test_outfile);
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80 @Test(groups = { AllTestSuit.test_group_cluster,
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81 AllTestSuit.test_group_runner })
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82 public void testRunOnCluster() {
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83 assertFalse(SysPrefs.isWindows,
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84 "Cluster execution can only be in unix environment");
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86 ConfiguredExecutable<Muscle> confMuscle = Configurator
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87 .configureExecutable(muscle,
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88 Executable.ExecProvider.Cluster);
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89 JobRunner runner = JobRunner.getInstance(confMuscle);
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91 assertNotNull(runner, "Runner is NULL");
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92 runner.executeJob();
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93 // assertNotNull("JobId is null", jobId1);
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94 JobStatus status = runner.getJobStatus();
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95 assertTrue(status == JobStatus.PENDING
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96 || status == JobStatus.RUNNING,
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97 "Status of the process is wrong!");
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98 JobInfo info = runner.getJobInfo();
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99 assertNotNull(info, "JobInfo is null");
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100 StatisticManager sm = new StatisticManager(info);
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101 assertNotNull(sm, "Statictic manager is null");
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104 String exits = sm.getExitStatus();
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105 assertNotNull("Exit status is null", exits);
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106 // cut 4 trailing zeros from the number
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107 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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109 assertEquals(0, exitsInt);
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110 System.out.println(sm.getAllStats());
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112 } catch (ParseException e) {
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113 e.printStackTrace();
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114 fail("Parse Exception: " + e.getMessage());
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116 assertFalse(runner.cleanup());
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117 assertTrue(sm.hasExited());
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118 assertFalse(sm.wasAborted());
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119 assertFalse(sm.hasDump());
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120 assertFalse(sm.hasSignaled());
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122 } catch (JobSubmissionException e) {
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123 e.printStackTrace();
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124 fail("DrmaaException caught:" + e.getMessage());
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125 } catch (JobExecutionException e) {
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126 e.printStackTrace();
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127 fail("DrmaaException caught:" + e.getMessage());
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128 } catch (DrmaaException e) {
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129 e.printStackTrace();
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130 fail("DrmaaException caught:" + e.getMessage());
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135 * This tests fails from time to time depending on the cluster load or some
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136 * other factors. Any client code has to adjust for this issue
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138 @Test(enabled = false, groups = { AllTestSuit.test_group_cluster,
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139 AllTestSuit.test_group_runner })
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140 public void testRunOnClusterAsync() {
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141 assertFalse(SysPrefs.isWindows,
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142 "Cluster execution can only be in unix environment");
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144 ConfiguredExecutable<Muscle> confMuscle = Configurator
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145 .configureExecutable(muscle,
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146 Executable.ExecProvider.Cluster);
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147 AsyncExecutor aengine = Configurator.getAsyncEngine(confMuscle);
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148 String jobId = aengine.submitJob(confMuscle);
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149 assertNotNull(jobId, "Runner is NULL");
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150 // let drmaa to start
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152 JobStatus status = aengine.getJobStatus(jobId);
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153 while (status != JobStatus.FINISHED || status !=JobStatus.UNDEFINED) {
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154 System.out.println("Job Status: " + status);
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155 Thread.sleep(1000);
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156 status = aengine.getJobStatus(jobId);
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158 } catch (JobSubmissionException e) {
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159 e.printStackTrace();
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160 fail("DrmaaException caught:" + e.getMessage());
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161 } catch (InterruptedException e) {
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162 e.printStackTrace();
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163 fail(e.getMessage());
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167 @Test(groups = { AllTestSuit.test_group_runner })
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168 public void testRunLocally() {
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170 ConfiguredExecutable<Muscle> confMuscle = Configurator
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171 .configureExecutable(muscle, Executable.ExecProvider.Local);
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172 confMuscle.getParameters().setParam("-matrix", "BLOSUM62");
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174 // For local execution use relative
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175 LocalRunner lr = new LocalRunner(confMuscle);
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177 ConfiguredExecutable<?> al1 = lr.waitForResult();
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178 assertNotNull(al1.getResults());
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179 Alignment al2 = confMuscle.getResults();
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180 assertNotNull(al2);
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181 assertEquals(al1.getResults(), al2);
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182 } catch (JobSubmissionException e) {
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183 e.printStackTrace();
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184 fail(e.getLocalizedMessage());
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185 } catch (ResultNotAvailableException e) {
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186 e.printStackTrace();
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187 fail(e.getLocalizedMessage());
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188 } catch (JobExecutionException e) {
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189 e.printStackTrace();
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190 fail(e.getLocalizedMessage());
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194 @Test(groups = { AllTestSuit.test_group_runner })
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195 public void readStatistics() {
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197 ConfiguredExecutable<Muscle> confMuscle = Configurator
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198 .configureExecutable(muscle, Executable.ExecProvider.Local);
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199 // For local execution use relavive
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201 AsyncExecutor sexec = Configurator.getAsyncEngine(confMuscle);
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202 String jobId = sexec.submitJob(confMuscle);
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203 FilePuller fw = FilePuller.newFilePuller(confMuscle
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204 .getWorkDirectory()
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205 + File.separator + Muscle.getStatFile(),
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206 FileWatcher.MIN_CHUNK_SIZE_BYTES);
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210 while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec
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211 .getJobStatus(jobId) == JobStatus.FAILED || sexec
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212 .getJobStatus(jobId) == JobStatus.UNDEFINED)
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213 || fw.hasMoreData()) {
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214 ChunkHolder ch = fw.pull(position);
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215 String chunk = ch.getChunk();
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216 position = ch.getNextPosition();
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217 System.out.print(chunk);
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220 assertTrue(count > 1);
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221 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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222 assertNotNull(al.getResults());
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223 } catch (JobSubmissionException e) {
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224 e.printStackTrace();
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225 fail(e.getMessage());
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226 } catch (ResultNotAvailableException e) {
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227 e.printStackTrace();
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228 fail(e.getMessage());
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229 } catch (IOException e) {
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230 e.printStackTrace();
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231 fail(e.getMessage());
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235 @Test(groups = { AllTestSuit.test_group_runner })
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236 public void testPersistance() {
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238 Muscle muscle = new Muscle();
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239 muscle.setError("errrr.txt").setInput(AllTestSuit.test_input)
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240 .setOutput("outtt.txt");
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241 assertEquals(muscle.getInput(), AllTestSuit.test_input);
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242 assertEquals(muscle.getError(), "errrr.txt");
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243 assertEquals(muscle.getOutput(), "outtt.txt");
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244 ConfiguredExecutable<Muscle> cmuscle = Configurator
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245 .configureExecutable(muscle, Executable.ExecProvider.Local);
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247 SyncExecutor sexec = Configurator.getSyncEngine(cmuscle);
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248 sexec.executeJob();
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249 ConfiguredExecutable<?> al = sexec.waitForResult();
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250 assertNotNull(al.getResults());
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251 // Save run configuration
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252 assertTrue(cmuscle.saveRunConfiguration());
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254 // See if loaded configuration is the same as saved
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255 RunConfiguration loadedRun = RunConfiguration
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256 .load(new FileInputStream(new File(cmuscle
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257 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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258 assertEquals(((ConfExecutable<Muscle>) cmuscle)
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259 .getRunConfiguration(), loadedRun);
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260 // Load run configuration as ConfExecutable
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261 ConfiguredExecutable<Muscle> resurrectedCMuscle = (ConfiguredExecutable<Muscle>) cmuscle
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262 .loadRunConfiguration(new FileInputStream(new File(cmuscle
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263 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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264 assertNotNull(resurrectedCMuscle);
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265 assertEquals(resurrectedCMuscle.getExecutable().getInput(),
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266 AllTestSuit.test_input);
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267 assertEquals(resurrectedCMuscle.getExecutable().getError(),
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269 assertEquals(resurrectedCMuscle.getExecutable().getOutput(),
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271 // See in details whether executables are the same
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272 assertEquals(resurrectedCMuscle.getExecutable(), muscle);
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274 ConfiguredExecutable<Muscle> resmuscle = Configurator
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275 .configureExecutable(resurrectedCMuscle.getExecutable(),
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276 Executable.ExecProvider.Local);
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278 sexec = Configurator.getSyncEngine(resmuscle,
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279 Executable.ExecProvider.Local);
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280 sexec.executeJob();
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281 al = sexec.waitForResult();
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284 } catch (JobSubmissionException e) {
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285 e.printStackTrace();
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286 fail(e.getMessage());
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287 } catch (JobExecutionException e) {
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288 e.printStackTrace();
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289 fail(e.getMessage());
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290 } catch (FileNotFoundException e) {
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291 e.printStackTrace();
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292 fail(e.getMessage());
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293 } catch (IOException e) {
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294 e.printStackTrace();
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295 fail(e.getMessage());
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296 } catch (ResultNotAvailableException e) {
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297 e.printStackTrace();
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298 fail(e.getMessage());
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302 @Test(groups = { AllTestSuit.test_group_runner })
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303 public void testConfigurationLoading() {
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305 RunnerConfig<Muscle> muscleConfig = ConfExecutable
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306 .getRunnerOptions(Muscle.class);
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307 assertNotNull(muscleConfig);
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308 assertTrue(muscleConfig.getArguments().size() > 0);
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310 PresetManager<Muscle> musclePresets = ConfExecutable
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311 .getRunnerPresets(Muscle.class);
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312 assertNotNull(musclePresets);
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313 assertTrue(musclePresets.getPresets().size() > 0);
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314 musclePresets.validate(muscleConfig);
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316 LimitsManager<Muscle> muscleLimits = ConfExecutable
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317 .getRunnerLimits(Muscle.class);
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318 assertNotNull(muscleLimits);
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319 assertTrue(muscleLimits.getLimits().size() > 0);
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320 muscleLimits.validate(musclePresets);
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322 } catch (FileNotFoundException e) {
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323 e.printStackTrace();
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324 fail(e.getLocalizedMessage());
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325 } catch (IOException e) {
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326 e.printStackTrace();
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327 fail(e.getLocalizedMessage());
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328 } catch (ValidationException e) {
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329 e.printStackTrace();
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330 fail(e.getLocalizedMessage());
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