1 /* Copyright (c) 2011 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
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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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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.Score;
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42 import compbio.data.sequence.ScoreManager;
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43 import compbio.data.sequence.ScoreManager.ScoreHolder;
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44 import compbio.data.sequence.SequenceUtil;
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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.SyncExecutor;
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48 import compbio.engine.client.ConfExecutable;
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49 import compbio.engine.client.ConfiguredExecutable;
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50 import compbio.engine.client.Executable;
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51 import compbio.engine.client.RunConfiguration;
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52 import compbio.engine.cluster.drmaa.ClusterUtil;
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53 import compbio.engine.cluster.drmaa.JobRunner;
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54 import compbio.engine.cluster.drmaa.StatisticManager;
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55 import compbio.engine.local.LocalRunner;
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56 import compbio.metadata.AllTestSuit;
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57 import compbio.metadata.JobExecutionException;
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58 import compbio.metadata.JobStatus;
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59 import compbio.metadata.JobSubmissionException;
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60 import compbio.metadata.LimitsManager;
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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.msa.Mafft;
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65 import compbio.util.SysPrefs;
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67 public class IUPredTester {
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69 private IUPred iupred;
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71 @BeforeMethod(alwaysRun = true)
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73 iupred = new IUPred();
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74 iupred.setInput(AllTestSuit.test_input);
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77 @Test(groups = {AllTestSuit.test_group_cluster,
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78 AllTestSuit.test_group_runner})
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79 public void testRunOnCluster() {
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80 assertFalse(SysPrefs.isWindows,
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81 "Cluster execution can only be in unix environment");
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83 ConfiguredExecutable<IUPred> confIUPred = Configurator
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84 .configureExecutable(iupred,
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85 Executable.ExecProvider.Cluster);
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86 JobRunner runner = JobRunner.getInstance(confIUPred);
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88 assertNotNull(runner, "Runner is NULL");
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89 runner.executeJob();
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90 // assertNotNull("JobId is null", jobId1);
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91 JobStatus status = runner.getJobStatus();
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92 assertTrue(status == JobStatus.PENDING
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93 || status == JobStatus.RUNNING,
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94 "Status of the process is wrong!");
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95 JobInfo info = runner.getJobInfo();
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96 assertNotNull(info, "JobInfo is null");
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97 StatisticManager sm = new StatisticManager(info);
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98 assertNotNull(sm, "Statictic manager is null");
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101 String exits = sm.getExitStatus();
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102 assertNotNull("Exit status is null", exits);
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103 // cut 4 trailing zeros from the number
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104 int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
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106 assertEquals(0, exitsInt);
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107 System.out.println(sm.getAllStats());
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109 } catch (ParseException e) {
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110 e.printStackTrace();
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111 fail("Parse Exception: " + e.getMessage());
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113 // assertFalse(runner.cleanup());
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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 * This tests fails from time to time depending on the cluster load or some
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133 * other factors. Any client code has to adjust for this issue
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135 @Test(groups = {AllTestSuit.test_group_cluster,
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136 AllTestSuit.test_group_runner})
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137 public void testRunOnClusterAsync() {
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138 assertFalse(SysPrefs.isWindows,
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139 "Cluster execution can only be in unix environment");
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141 ConfiguredExecutable<IUPred> confIUPred = Configurator
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142 .configureExecutable(iupred,
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143 Executable.ExecProvider.Cluster);
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144 AsyncExecutor aengine = Configurator.getAsyncEngine(confIUPred);
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145 String jobId = aengine.submitJob(confIUPred);
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146 assertNotNull(jobId, "Runner is NULL");
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147 // let drmaa to start
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149 JobStatus status = aengine.getJobStatus(jobId);
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150 while (status != JobStatus.FINISHED) {
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151 System.out.println("Job Status: " + status);
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152 Thread.sleep(1000);
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153 status = aengine.getJobStatus(jobId);
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154 ConfiguredExecutable<IUPred> result = (ConfiguredExecutable<IUPred>) aengine
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155 .getResults(jobId);
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156 assertNotNull(result);
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157 System.out.println("RES:" + result);
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158 // Some times the job could be removed from the cluster
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160 // before it has been reported to finish. Make sure
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161 // to stop waiting in such case
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162 if (status == JobStatus.UNDEFINED) {
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166 } catch (JobSubmissionException e) {
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167 e.printStackTrace();
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168 fail("DrmaaException caught:" + e.getMessage());
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169 } catch (InterruptedException e) {
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170 e.printStackTrace();
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171 fail(e.getMessage());
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172 } catch (ResultNotAvailableException e) {
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173 e.printStackTrace();
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174 fail(e.getMessage());
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179 @Test(groups = {AllTestSuit.test_group_runner})
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180 public void testSetParameter() {
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181 assertEquals(iupred.getInput(), AllTestSuit.test_input);
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182 assertTrue(iupred.getParameters(null).getCommandString().trim().endsWith(AllTestSuit.test_input));
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183 iupred.setParameter("long");
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184 assertEquals(iupred.getInput(), AllTestSuit.test_input);
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185 String cmd = iupred.getParameters(null).getCommandString().trim();
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186 assertTrue(cmd.endsWith("long"));
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187 assertTrue(cmd.contains(AllTestSuit.test_input));
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191 @Test(groups = {AllTestSuit.test_group_runner})
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192 public void testReadResults() {
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193 ScoreManager scoreMan;
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195 scoreMan = iupred.getResults(AllTestSuit.TEST_DATA_PATH_ABSOLUTE);
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196 System.out.println(scoreMan.asMap());
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197 } catch (ResultNotAvailableException e) {
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198 e.printStackTrace();
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199 fail(e.getMessage());
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203 @Test(groups = {AllTestSuit.test_group_runner})
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204 public void testRunLocally() {
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206 ConfiguredExecutable<IUPred> confIUPred = Configurator
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207 .configureExecutable(iupred, Executable.ExecProvider.Local);
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209 // For local execution use relative
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210 LocalRunner lr = new LocalRunner(confIUPred);
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212 ConfiguredExecutable<?> al1 = lr.waitForResult();
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213 assertNotNull(al1.getResults());
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214 ScoreManager al2 = confIUPred.getResults();
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215 assertNotNull(al2);
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216 assertEquals(al2.asMap().size(), 3);
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217 assertEquals(al2.getNumberOfSeq(),3);
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219 ScoreHolder sch = al2.getAnnotationForSequence("Foobar");
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220 assertEquals(sch.getNumberOfScores(), 3);
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222 Score sc = sch.getScoreByMethod("Long");
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223 assertEquals(sc.getMethod(), "Long");
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224 assertTrue(sc.getRanges().isEmpty());
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225 assertNotNull(sc.getScores());
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226 assertEquals(sc.getScores().size(), 481);
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227 assertEquals(al1.getResults(), al2);
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230 } catch (JobSubmissionException e) {
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231 e.printStackTrace();
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232 fail(e.getLocalizedMessage());
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233 } catch (ResultNotAvailableException e) {
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234 e.printStackTrace();
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235 fail(e.getLocalizedMessage());
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236 } catch (JobExecutionException e) {
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237 e.printStackTrace();
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238 fail(e.getLocalizedMessage());
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242 @Test(groups = {AllTestSuit.test_group_runner})
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243 public void testRunLocallyWithParams() {
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245 iupred.setParameter("short");
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246 ConfiguredExecutable<IUPred> confIUPred = Configurator
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247 .configureExecutable(iupred, Executable.ExecProvider.Local);
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249 // For local execution use relative
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250 LocalRunner lr = new LocalRunner(confIUPred);
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252 ConfiguredExecutable<?> al1 = lr.waitForResult();
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253 assertNotNull(al1.getResults());
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254 ScoreManager al2 = confIUPred.getResults();
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256 assertNotNull(al2.asMap());
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257 assertEquals(al2.asMap().size(), 3);
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258 ScoreHolder sch = al2.getAnnotationForSequence("Foobar");
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259 assertNotNull(sch);
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260 assertEquals(sch.getNumberOfScores(), 1);
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263 assertNotNull(al2);
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264 assertEquals(al2.asSet().size(), 1);
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265 assertEquals(al2.getNumberOfSeq(),1);
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266 Score sc = al2.asSet().iterator().next();
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267 assertEquals(sc.getMethod(), "Long");
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268 assertTrue(sc.getRanges().isEmpty());
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269 assertNotNull(sc.getScores());
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270 assertEquals(sc.getScores().size(), 568);
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271 assertEquals(al1.getResults(), al2);
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273 } catch (JobSubmissionException e) {
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274 e.printStackTrace();
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275 fail(e.getLocalizedMessage());
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276 } catch (ResultNotAvailableException e) {
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277 e.printStackTrace();
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278 fail(e.getLocalizedMessage());
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279 } catch (JobExecutionException e) {
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280 e.printStackTrace();
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281 fail(e.getLocalizedMessage());
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285 @Test(groups = {AllTestSuit.test_group_runner})
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286 public void testPersistance() {
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288 IUPred iupred = new IUPred();
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289 iupred.setError("errrr.txt").setInput(AllTestSuit.test_input);
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290 assertEquals(iupred.getInput(), AllTestSuit.test_input);
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291 assertEquals(iupred.getError(), "errrr.txt");
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293 ConfiguredExecutable<IUPred> cIUPred = Configurator
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294 .configureExecutable(iupred, Executable.ExecProvider.Local);
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296 SyncExecutor sexec = Configurator.getSyncEngine(cIUPred);
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297 sexec.executeJob();
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298 ConfiguredExecutable<?> al = sexec.waitForResult();
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299 assertNotNull(al.getResults());
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300 // Save run configuration
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301 assertTrue(cIUPred.saveRunConfiguration());
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303 // See if loaded configuration is the same as saved
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304 RunConfiguration loadedRun = RunConfiguration
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305 .load(new FileInputStream(new File(cIUPred
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306 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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308 ((ConfExecutable<IUPred>) cIUPred).getRunConfiguration(),
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310 // Load run configuration as ConfExecutable
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311 ConfiguredExecutable<IUPred> resurrectedCIUPred = (ConfiguredExecutable<IUPred>) cIUPred
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312 .loadRunConfiguration(new FileInputStream(new File(cIUPred
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313 .getWorkDirectory(), RunConfiguration.rconfigFile)));
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314 assertNotNull(resurrectedCIUPred);
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315 assertEquals(resurrectedCIUPred.getExecutable().getInput(),
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316 AllTestSuit.test_input);
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317 assertEquals(resurrectedCIUPred.getExecutable().getError(),
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320 // See in details whether executables are the same
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321 assertEquals(resurrectedCIUPred.getExecutable(), iupred);
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323 ConfiguredExecutable<IUPred> resIUPred = Configurator
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324 .configureExecutable(resurrectedCIUPred.getExecutable(),
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325 Executable.ExecProvider.Local);
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327 sexec = Configurator.getSyncEngine(resIUPred,
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328 Executable.ExecProvider.Local);
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329 sexec.executeJob();
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330 al = sexec.waitForResult();
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333 } catch (JobSubmissionException e) {
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334 e.printStackTrace();
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335 fail(e.getMessage());
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336 } catch (JobExecutionException e) {
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337 e.printStackTrace();
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338 fail(e.getMessage());
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339 } catch (FileNotFoundException e) {
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340 e.printStackTrace();
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341 fail(e.getMessage());
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342 } catch (IOException e) {
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343 e.printStackTrace();
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344 fail(e.getMessage());
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345 } catch (ResultNotAvailableException e) {
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346 e.printStackTrace();
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347 fail(e.getMessage());
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351 @Test(groups = {AllTestSuit.test_group_runner})
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352 public void testConfigurationLoading() {
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354 RunnerConfig<IUPred> iupredConfig = ConfExecutable
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355 .getRunnerOptions(IUPred.class);
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357 assertNotNull(iupredConfig);
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359 assertTrue(iupredConfig.getArguments().size() != 0);
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361 PresetManager<IUPred> iupredPresets = ConfExecutable
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362 .getRunnerPresets(IUPred.class);
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363 assertNull(iupredPresets); // there is no presets
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365 LimitsManager<IUPred> iupredLimits = ConfExecutable
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366 .getRunnerLimits(IUPred.class);
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367 assertNotNull(iupredLimits);
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368 assertTrue(iupredLimits.getLimits().size() > 0);
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369 iupredLimits.validate(iupredPresets);
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371 } catch (FileNotFoundException e) {
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372 e.printStackTrace();
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373 fail(e.getLocalizedMessage());
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374 } catch (IOException e) {
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375 e.printStackTrace();
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376 fail(e.getLocalizedMessage());
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377 } catch (ValidationException e) {
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378 e.printStackTrace();
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379 fail(e.getLocalizedMessage());
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