testsrc/compbio/ws/client/TestRNAalifoldWS.java

   1 package compbio.ws.client;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertNotNull;
   5 import static org.testng.Assert.fail;
   6
   7 import java.io.File;
   8 import java.io.FileInputStream;
   9 import java.io.FileNotFoundException;
  10 import java.io.IOException;
  11 import java.net.ConnectException;
  12 import java.util.ArrayList;
  13 import java.util.List;
  14
  15 import javax.xml.ws.WebServiceException;
  16
  17 import org.testng.annotations.BeforeTest;
  18 import org.testng.annotations.Test;
  19
  20 import compbio.data.msa.JABAService;
  21 import compbio.data.msa.SequenceAnnotation;
  22 import compbio.data.sequence.Alignment;
  23 import compbio.data.structure.FoldWS;
  24 import compbio.data.sequence.RNAstruct;
  25 import compbio.data.sequence.ClustalAlignmentUtil;
  26 import compbio.data.sequence.ConservationMethod;
  27 import compbio.data.sequence.FastaSequence;
  28 import compbio.data.sequence.ScoreManager;
  29 import compbio.data.sequence.SequenceUtil;
  30 import compbio.data.sequence.UnknownFileFormatException;
  31 import compbio.metadata.AllTestSuit;
  32 import compbio.metadata.JobSubmissionException;
  33 import compbio.metadata.LimitExceededException;
  34 import compbio.metadata.Option;
  35 import compbio.metadata.PresetManager;
  36 import compbio.metadata.ResultNotAvailableException;
  37 import compbio.metadata.RunnerConfig;
  38 import compbio.metadata.UnsupportedRuntimeException;
  39 import compbio.metadata.WrongParameterException;
  40
  41 import compbio.runner.conservation.AACon;
  42 import compbio.util.SysPrefs;
  43 import compbio.ws.server.RNAalifoldWS;
  44
  45 public class TestRNAalifoldWS {
  46
  47         FoldWS<RNAalifoldWS> foldws;
  48
  49 //      @BeforeTest(groups = {AllTestSuit.test_group_webservices})
  50 //      void initConnection() {
  51 //
  52 //              try {
  53 //                      JABAService client = Jws2Client.connect(
  54 //                                      "http://localhost:8080/jabaws", Services.RNAalifoldWS);
  55 //                      foldws = (FoldWS<RNAalifoldWS>) client;
  56 //              } catch (ConnectException e) {
  57 //                      e.printStackTrace();
  58 //                      fail(e.getMessage());
  59 //              } catch (WebServiceException e) {
  60 //                      e.printStackTrace();
  61 //                      fail(e.getMessage());
  62 //              }
  63 //      }
  64
  65
  66         @Test(groups = {AllTestSuit.test_group_webservices})
  67         public void testFold() throws FileNotFoundException, IOException,
  68                         UnknownFileFormatException {
  69
  70                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
  71                                 + File.separator;
  72
  73                 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
  74                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
  75                                         + File.separator + "unfolded_RF00031.aln"));
  76
  77                 try {
  78                         String jobId = foldws.fold(aln);
  79                         System.out.println("J: " + jobId);
  80                         RNAstruct result = foldws.getResult(jobId);
  81                         assertNotNull(result);
  82
  83                 } catch (UnsupportedRuntimeException e) {
  84                         e.printStackTrace();
  85                         fail(e.getMessage());
  86                 } catch (LimitExceededException e) {
  87                         e.printStackTrace();
  88                         fail(e.getMessage());
  89                 } catch (JobSubmissionException e) {
  90                         e.printStackTrace();
  91                         fail(e.getMessage());
  92                 } catch (ResultNotAvailableException e) {
  93                         e.printStackTrace();
  94                         fail(e.getMessage());
  95                 }
  96         }
  97 }
  98
  99
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