1 package compbio.runner.structure;
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4 import static org.testng.Assert.assertEquals;
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5 import static org.testng.Assert.assertFalse;
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6 import static org.testng.Assert.assertNotNull;
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7 import static org.testng.Assert.assertNull;
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8 import static org.testng.Assert.assertTrue;
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9 import static org.testng.Assert.fail;
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11 import java.io.File;
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12 import java.io.FileInputStream;
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13 import java.io.FileNotFoundException;
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14 import java.io.IOException;
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15 import java.text.ParseException;
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17 import javax.xml.bind.ValidationException;
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19 import org.apache.log4j.*;
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20 import org.ggf.drmaa.DrmaaException;
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21 import org.ggf.drmaa.JobInfo;
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22 import org.testng.annotations.BeforeMethod;
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23 import org.testng.annotations.Test;
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25 import compbio.data.sequence.RNAStructScoreManager;
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26 import compbio.data.sequence.Score;
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27 import compbio.data.sequence.ScoreManager;
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28 import compbio.data.sequence.ScoreManager.ScoreHolder;
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29 import compbio.data.sequence.SequenceUtil;
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30 import compbio.engine.AsyncExecutor;
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31 import compbio.engine.Configurator;
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32 import compbio.engine.SyncExecutor;
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33 import compbio.engine.client.ConfExecutable;
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34 import compbio.engine.client.ConfiguredExecutable;
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35 import compbio.engine.client.Executable;
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36 import compbio.engine.client.RunConfiguration;
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37 import compbio.engine.cluster.drmaa.ClusterEngineUtil;
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38 import compbio.engine.cluster.drmaa.ClusterRunner;
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39 import compbio.engine.cluster.drmaa.StatisticManager;
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40 import compbio.engine.local.AsyncLocalRunner;
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41 import compbio.engine.local.LocalExecutorService;
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42 import compbio.engine.local.LocalRunner;
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43 import compbio.metadata.AllTestSuit;
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44 import compbio.metadata.JobExecutionException;
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45 import compbio.metadata.JobStatus;
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46 import compbio.metadata.JobSubmissionException;
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47 import compbio.metadata.LimitsManager;
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48 import compbio.metadata.PresetManager;
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49 import compbio.metadata.ResultNotAvailableException;
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50 import compbio.metadata.RunnerConfig;
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51 import compbio.runner.msa.ClustalW;
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52 import compbio.runner.structure.RNAalifold;
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54 public class RNAalifoldTester {
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56 private static Logger log = Logger
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57 .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
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60 private RNAalifold rnaalifold;
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62 static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH
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63 + "RNAalifoldParameters.xml";
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64 public static String test_outfile = "rnaalifold.out";
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67 @Test(groups = { AllTestSuit.test_group_runner })
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68 public void testRunLocally() {
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69 RNAalifold rnaalifold = new RNAalifold();
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70 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
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73 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
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74 .configureExecutable(rnaalifold, Executable.ExecProvider.Local);
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75 LocalRunner lr = new LocalRunner(confRNAalifold);
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77 confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
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79 System.out.println("TEST");
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80 System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());
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82 assertNotNull(confRNAalifold.getResults());
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83 } catch (JobSubmissionException e) {
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84 e.printStackTrace();
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85 fail(e.getLocalizedMessage());
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86 } catch (JobExecutionException e) {
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87 e.printStackTrace();
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88 fail(e.getLocalizedMessage());
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89 } catch (ResultNotAvailableException e) {
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90 e.printStackTrace();
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91 fail(e.getLocalizedMessage());
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96 public static void main(String[] args) throws JobSubmissionException,
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97 JobExecutionException, InterruptedException, ResultNotAvailableException {
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100 log.warn("Logger test :- Run RNAalifold.main()");
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102 RNAalifold rnaalifold = new RNAalifold();
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103 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");
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105 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
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106 .configureExecutable(rnaalifold);
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107 AsyncExecutor lr = new AsyncLocalRunner();
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108 lr.submitJob(confRNAalifold);
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111 System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());
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114 Thread.sleep(3000);
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115 LocalExecutorService.shutDown();
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