testsrc/compbio/runner/structure/RNAalifoldTester.java

   1 package compbio.runner.structure;
   2
   3
   4 import static org.testng.Assert.assertEquals;
   5 import static org.testng.Assert.assertFalse;
   6 import static org.testng.Assert.assertNotNull;
   7 import static org.testng.Assert.assertNull;
   8 import static org.testng.Assert.assertTrue;
   9 import static org.testng.Assert.fail;
  10
  11 import java.io.File;
  12 import java.io.FileInputStream;
  13 import java.io.FileNotFoundException;
  14 import java.io.IOException;
  15 import java.text.ParseException;
  16
  17 import javax.xml.bind.ValidationException;
  18
  19 import org.apache.log4j.*;
  20 import org.ggf.drmaa.DrmaaException;
  21 import org.ggf.drmaa.JobInfo;
  22 import org.testng.annotations.BeforeMethod;
  23 import org.testng.annotations.Test;
  24
  25 import compbio.data.sequence.Score;
  26 import compbio.data.sequence.ScoreManager;
  27 import compbio.data.sequence.ScoreManager.ScoreHolder;
  28 import compbio.data.sequence.SequenceUtil;
  29 import compbio.engine.AsyncExecutor;
  30 import compbio.engine.Configurator;
  31 import compbio.engine.SyncExecutor;
  32 import compbio.engine.client.ConfExecutable;
  33 import compbio.engine.client.ConfiguredExecutable;
  34 import compbio.engine.client.Executable;
  35 import compbio.engine.client.RunConfiguration;
  36 import compbio.engine.cluster.drmaa.ClusterUtil;
  37 import compbio.engine.cluster.drmaa.JobRunner;
  38 import compbio.engine.cluster.drmaa.StatisticManager;
  39 import compbio.engine.local.AsyncLocalRunner;
  40 import compbio.engine.local.LocalExecutorService;
  41 import compbio.engine.local.LocalRunner;
  42 import compbio.metadata.AllTestSuit;
  43 import compbio.metadata.JobExecutionException;
  44 import compbio.metadata.JobStatus;
  45 import compbio.metadata.JobSubmissionException;
  46 import compbio.metadata.LimitsManager;
  47 import compbio.metadata.PresetManager;
  48 import compbio.metadata.ResultNotAvailableException;
  49 import compbio.metadata.RunnerConfig;
  50 import compbio.runner.msa.ClustalW;
  51 import compbio.runner.structure.RNAalifold;
  52
  53 public class RNAalifoldTester {
  54
  55         private static Logger log = Logger
  56                         .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
  57
  58
  59         private RNAalifold rnaalifold;
  60
  61         static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH
  62                         + "RNAalifoldParameters.xml";
  63         public static String test_outfile = "rnaalifold.out";
  64
  65         @Test(groups = { AllTestSuit.test_group_runner })
  66         public void testRunLocally() {
  67                 RNAalifold rnaalifold = new RNAalifold();
  68                 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
  69                 try{
  70
  71                         ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
  72                                         .configureExecutable(rnaalifold, Executable.ExecProvider.Local);
  73                         LocalRunner lr = new LocalRunner(confRNAalifold);
  74                         lr.executeJob();
  75                         confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
  76                         assertNotNull(confRNAalifold.getResults());
  77                 } catch (JobSubmissionException e) {
  78                         e.printStackTrace();
  79                         fail(e.getLocalizedMessage());
  80                 } catch (JobExecutionException e) {
  81                         e.printStackTrace();
  82                         fail(e.getLocalizedMessage());
  83                 } catch (ResultNotAvailableException e) {
  84                         e.printStackTrace();
  85                         fail(e.getLocalizedMessage());
  86                 }
  87         }
  88
  89
  90         public static void main(String[] args) throws JobSubmissionException,
  91                         JobExecutionException, InterruptedException {
  92
  93
  94                 log.warn("Logger test :- Run RNAalifold.main()");
  95
  96                 RNAalifold rnaalifold = new RNAalifold();
  97                 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");
  98
  99                 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
 100                                         .configureExecutable(rnaalifold);
 101                 AsyncExecutor lr = new AsyncLocalRunner();
 102                 lr.submitJob(confRNAalifold);
 103
 104                 Thread.sleep(3000);
 105                 LocalExecutorService.shutDown();
 106
 107         }
 108
 109 }