1 /* Copyright (c) 2013 Alexander Sherstnev
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3 * Java Bioinformatics Analysis Web Services (JABAWS)
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6 * This library is free software; you can redistribute it and/or modify it under
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7 * the terms of the Apache License version 2 as published
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8 * by the Apache Software Foundation This library is distributed in the hope
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9 * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
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10 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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11 * Apache License for more details. A copy of the license is in
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12 * apache_license.txt. It is also available here:
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14 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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16 * Any republication or derived work distributed in source code form must include
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17 * this copyright and license notice.
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19 package compbio.runner.predictors;
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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.assertTrue;
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25 import static org.testng.Assert.fail;
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27 import java.io.File;
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28 import java.io.FileInputStream;
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29 import java.io.FileNotFoundException;
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30 import java.io.IOException;
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31 import java.text.ParseException;
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32 import java.util.Arrays;
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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.JpredAlignment;
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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.ClusterEngineUtil;
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51 import compbio.engine.cluster.drmaa.ClusterRunner;
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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.Preset;
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61 import compbio.metadata.PresetManager;
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62 import compbio.metadata.ResultNotAvailableException;
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63 import compbio.metadata.RunnerConfig;
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64 import compbio.runner.RunnerUtil;
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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 JpredTester {
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70 public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;
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72 public static String test_output = "Jpred.test1.out";
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73 public static String test_input = CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata" + File.separator + "Jpred.test1.fasta";
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76 @BeforeMethod(alwaysRun = true)
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79 pred.setInput(test_input);
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80 pred.setOutput(test_output);
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84 @Test(enabled=false,groups = {AllTestSuit.test_group_runner})
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85 public void RunOnCluster() {
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86 assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");
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88 PresetManager<Jpred> jpredPreset = RunnerUtil.getPresets(Jpred.class);
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89 assert jpredPreset != null;
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90 ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);
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91 Preset<Jpred> conf = jpredPreset.getPresetByName("cluster configuration");
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92 confpred.addParameters(conf.getOptions());
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93 ClusterRunner runner = ClusterRunner.getInstance(confpred);
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94 assertNotNull(runner, "Runner is NULL");
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96 runner.executeJob();
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97 JobStatus status = runner.getJobStatus();
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98 assertTrue(status == JobStatus.PENDING || status == JobStatus.RUNNING, "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, "Statistic 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 = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();
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108 assertEquals(0, exitsInt);
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109 System.out.println(sm.getAllStats());
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110 } catch (ParseException e) {
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111 e.printStackTrace();
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112 fail("Parse Exception: " + e.getMessage());
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114 assertTrue(sm.hasExited());
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115 assertFalse(sm.wasAborted());
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116 assertFalse(sm.hasDump());
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117 assertFalse(sm.hasSignaled());
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119 } catch (JobSubmissionException e) {
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120 e.printStackTrace();
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121 fail("DrmaaException caught:" + e.getMessage());
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122 } catch (JobExecutionException e) {
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123 e.printStackTrace();
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124 fail("DrmaaException caught:" + e.getMessage());
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125 } catch (DrmaaException e) {
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126 e.printStackTrace();
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127 fail("DrmaaException caught:" + e.getMessage());
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132 @Test(enabled=false,groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_cluster})
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133 public void RunOnClusterAsync() {
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134 assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");
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136 pred.addParameters(Arrays.asList("-dbname uniref90", "-dbpath /homes/www-jpred/databases/"));
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137 ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);
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138 AsyncExecutor aengine = Configurator.getAsyncEngine(confpred);
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139 String jobId = aengine.submitJob(confpred);
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140 assertNotNull(jobId, "Runner is NULL");
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141 // let drmaa to start
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143 JobStatus status = aengine.getJobStatus(jobId);
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144 while (status != JobStatus.FINISHED) {
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145 Thread.sleep(1000);
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146 status = aengine.getJobStatus(jobId);
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147 ConfiguredExecutable<Jpred> result = (ConfiguredExecutable<Jpred>) aengine.getResults(jobId);
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148 assertNotNull(result);
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149 if (status == JobStatus.UNDEFINED || status == JobStatus.FAILED) {
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150 fail("job " + jobId +" failed!");
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154 } catch (JobSubmissionException e) {
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155 e.printStackTrace();
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156 fail("DrmaaException caught:" + e.getMessage());
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157 } catch (InterruptedException e) {
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158 e.printStackTrace();
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159 fail(e.getMessage());
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160 } catch (ResultNotAvailableException e) {
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161 e.printStackTrace();
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162 fail(e.getMessage());
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166 @Test(groups = {AllTestSuit.test_group_runner})
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167 public void RunLocally() {
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169 ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);
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170 confpred.addParameters(Arrays.asList("-dbname ported_db", "-dbpath /data/UNIREFdb/"));
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172 // For local execution use relative
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173 LocalRunner lr = new LocalRunner(confpred);
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175 ConfiguredExecutable<?> al1 = lr.waitForResult();
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176 assertNotNull(al1.getResults());
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177 JpredAlignment totalign = (JpredAlignment) confpred.getResults();
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178 assertNotNull(totalign);
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179 assertEquals(totalign.getSize(), 14);
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180 assertEquals(al1.getResults(), totalign);
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181 } catch (JobSubmissionException e) {
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182 e.printStackTrace();
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183 fail(e.getLocalizedMessage());
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184 } catch (ResultNotAvailableException e) {
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185 e.printStackTrace();
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186 fail(e.getLocalizedMessage());
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187 } catch (JobExecutionException e) {
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188 e.printStackTrace();
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189 fail(e.getLocalizedMessage());
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193 @Test(enabled=false,groups = {AllTestSuit.test_group_runner})
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194 public void RunLocallyWithPreset() {
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196 ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);
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197 PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);
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198 assert preset != null;
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199 Preset<Jpred> conf = preset.getPresetByName("laptop configuration");
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200 confpred.addParameters(conf.getOptions());
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202 // For local execution use relative
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203 LocalRunner lr = new LocalRunner(confpred);
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205 ConfiguredExecutable<?> al1 = lr.waitForResult();
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206 assertNotNull(al1.getResults());
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207 JpredAlignment totalign = (JpredAlignment) confpred.getResults();
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208 assertNotNull(totalign);
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209 assertEquals(totalign.getSize(), 19);
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210 assertEquals(al1.getResults(), totalign);
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211 } catch (JobSubmissionException e) {
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212 e.printStackTrace();
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213 fail(e.getLocalizedMessage());
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214 } catch (ResultNotAvailableException e) {
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215 e.printStackTrace();
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216 fail(e.getLocalizedMessage());
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217 } catch (JobExecutionException e) {
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218 e.printStackTrace();
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219 fail(e.getLocalizedMessage());
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223 @Test(enabled=false,groups = {AllTestSuit.test_group_runner})
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224 public void readStatistics() {
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226 Jpred jpred = new Jpred();
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227 jpred.setInput(test_input);
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228 jpred.setOutput(test_output);
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229 ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);
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230 PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);
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231 assert preset != null;
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232 Preset<Jpred> conf = preset.getPresetByName("laptop configuration");
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233 confpred.addParameters(conf.getOptions());
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235 // For local execution use relative
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236 AsyncExecutor sexec = Configurator.getAsyncEngine(confpred);
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237 String jobId = sexec.submitJob(confpred);
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238 String file = confpred.getWorkDirectory() + File.separator + Jpred.getStatFile();
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239 FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);
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243 JobStatus status = sexec.getJobStatus(jobId);
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245 if (fw.hasMoreData()) {
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246 ChunkHolder ch = fw.pull(position);
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247 String chunk = ch.getChunk();
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248 position = ch.getNextPosition();
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251 // Make sure the loop is terminated if the job fails
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252 if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
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253 fail("job " + jobId +" failed!");
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257 status = sexec.getJobStatus(jobId);
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258 } while (status != JobStatus.FINISHED || fw.hasMoreData());
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260 assertTrue(count >= 1);
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261 ConfiguredExecutable<?> al = sexec.getResults(jobId);
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262 assertNotNull(al.getResults());
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263 } catch (JobSubmissionException e) {
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264 e.printStackTrace();
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265 fail(e.getMessage());
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266 } catch (ResultNotAvailableException e) {
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267 e.printStackTrace();
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268 fail(e.getMessage());
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269 } catch (IOException e) {
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270 e.printStackTrace();
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271 fail(e.getMessage());
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272 } catch (InterruptedException e) {
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273 e.printStackTrace();
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274 fail(e.getMessage());
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278 @Test(enabled=false,groups = {AllTestSuit.test_group_runner})
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279 public void Persistance() {
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281 Jpred jpred = new Jpred();
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282 jpred.setError("errrr.txt");
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283 jpred.setInput(test_input);
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284 jpred.setOutput("outtt.txt");
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285 assertEquals(jpred.getInput(), test_input);
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286 assertEquals(jpred.getError(), "errrr.txt");
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287 assertEquals(jpred.getOutput(), "outtt.txt");
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288 ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);
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289 confpred.addParameters(Arrays.asList("-dbname ported_db", "-dbpath /data/UNIREFdb/"));
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291 SyncExecutor sexec = Configurator.getSyncEngine(confpred);
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292 sexec.executeJob();
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293 ConfiguredExecutable<?> al = sexec.waitForResult();
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294 assertNotNull(al.getResults());
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296 // Save run configuration
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297 assertTrue(confpred.saveRunConfiguration());
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299 // See if loaded configuration is the same as saved
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300 RunConfiguration loadedRun = RunConfiguration.load(new FileInputStream(new File(confpred.getWorkDirectory(), RunConfiguration.rconfigFile)));
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301 assertEquals(((ConfExecutable<Jpred>) confpred).getRunConfiguration(),loadedRun);
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303 // Load run configuration as ConfExecutable
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304 ConfiguredExecutable<Jpred> jpred2 = (ConfiguredExecutable<Jpred>) confpred.loadRunConfiguration(new FileInputStream(new File(confpred.getWorkDirectory(), RunConfiguration.rconfigFile)));
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305 assertNotNull(jpred2);
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306 assertEquals(jpred2.getExecutable().getInput(), test_input);
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307 assertEquals(jpred2.getExecutable().getError(), "errrr.txt");
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308 assertEquals(jpred2.getExecutable().getOutput(), "outtt.txt");
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310 // See in details whether executables are the same
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311 assertEquals(jpred2.getExecutable(), jpred);
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312 ConfiguredExecutable<Jpred> resjpred2 = Configurator.configureExecutable(jpred2.getExecutable(), Executable.ExecProvider.Local);
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314 sexec = Configurator.getSyncEngine(resjpred2, Executable.ExecProvider.Local);
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315 sexec.executeJob();
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316 al = sexec.waitForResult();
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318 } catch (JobSubmissionException e) {
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319 e.printStackTrace();
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320 fail(e.getMessage());
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321 } catch (JobExecutionException e) {
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322 e.printStackTrace();
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323 fail(e.getMessage());
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324 } catch (FileNotFoundException e) {
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325 e.printStackTrace();
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326 fail(e.getMessage());
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327 } catch (IOException e) {
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328 e.printStackTrace();
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329 fail(e.getMessage());
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330 } catch (ResultNotAvailableException e) {
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331 e.printStackTrace();
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332 fail(e.getMessage());
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336 @Test(enabled=false,groups = {AllTestSuit.test_group_runner})
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337 public void ConfigurationLoading() {
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339 RunnerConfig<Jpred> jpredConfig = ConfExecutable.getRunnerOptions(Jpred.class);
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340 assertNotNull(jpredConfig);
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341 assertTrue(jpredConfig.getArguments().size() > 0);
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343 PresetManager<Jpred> jpredPreset = ConfExecutable.getRunnerPresets(Jpred.class);
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344 assertNotNull(jpredPreset);
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346 LimitsManager<Jpred> jpredLimits = ConfExecutable.getRunnerLimits(Jpred.class);
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347 assertNotNull(jpredLimits);
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348 assertTrue(jpredLimits.getLimits().size() > 0);
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349 jpredLimits.validate(jpredPreset);
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350 } catch (FileNotFoundException e) {
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351 e.printStackTrace();
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352 fail(e.getLocalizedMessage());
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353 } catch (IOException e) {
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354 e.printStackTrace();
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355 fail(e.getLocalizedMessage());
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356 } catch (ValidationException e) {
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357 e.printStackTrace();
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358 fail(e.getLocalizedMessage());
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