testsrc/compbio/runner/structure/RNAalifoldTester.java

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