testsrc/compbio/ws/client/TestRNAalifoldWS.java

   1         package compbio.ws.client;
   2
   3 import static org.testng.Assert.assertNotNull;
   4 import static org.testng.Assert.fail;
   5
   6 import java.io.FileInputStream;
   7 import java.io.FileNotFoundException;
   8 import java.io.IOException;
   9 import java.io.OutputStreamWriter;
  10 import java.io.Writer;
  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.sequence.ClustalAlignmentUtil;
  24 import compbio.data.sequence.FastaSequence;
  25 import compbio.data.sequence.RNAStructScoreManager;
  26 import compbio.data.sequence.UnknownFileFormatException;
  27 import compbio.metadata.AllTestSuit;
  28 import compbio.metadata.JobSubmissionException;
  29 import compbio.metadata.LimitExceededException;
  30 import compbio.metadata.Option;
  31 import compbio.metadata.ResultNotAvailableException;
  32 import compbio.metadata.UnsupportedRuntimeException;
  33 import compbio.metadata.WrongParameterException;
  34 import compbio.ws.server.RNAalifoldWS;
  35
  36
  37 public class TestRNAalifoldWS {
  38
  39         SequenceAnnotation<RNAalifoldWS> foldws;
  40 //      RNAalifoldWS foldws;
  41
  42         @BeforeTest(groups = {AllTestSuit.test_group_webservices})
  43         void initConnection() {
  44
  45                 try {
  46                         JABAService client = Jws2Client.connect(
  47                                         "http://localhost:8080/jabaws", Services.RNAalifoldWS);
  48 //                      foldws = (RNAalifoldWS) client;
  49                         foldws = (SequenceAnnotation<RNAalifoldWS>) client;
  50                 } catch (ConnectException e) {
  51                         e.printStackTrace();
  52                         fail(e.getMessage());
  53                 } catch (WebServiceException e) {
  54                         e.printStackTrace();
  55                         fail(e.getMessage());
  56                 }
  57         }
  58
  59
  60         @Test(groups = {AllTestSuit.test_group_webservices})
  61         public void testFold() throws FileNotFoundException, IOException,
  62                         UnknownFileFormatException {
  63
  64                 Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
  65                                 AllTestSuit.test_input_aln));
  66
  67                 List<FastaSequence> fsl = aln.getSequences();
  68
  69                 try {
  70                         List<Option<RNAalifoldWS>> options  = new ArrayList<Option<RNAalifoldWS>>();
  71                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
  72                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
  73                         options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
  74
  75                         System.out.println("TestRNAalifoldWS: print options: " + options.toString());
  76
  77                         String jobId = foldws.customAnalize(fsl, options);
  78                         System.out.println("J: " + jobId);
  79                         RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
  80
  81                         Writer writer = new OutputStreamWriter(System.out);
  82                         result.writeOut(writer);
  83
  84                         assertNotNull(result);
  85
  86                 } catch (UnsupportedRuntimeException e) {
  87                         e.printStackTrace();
  88                         fail(e.getMessage());
  89                 } catch (LimitExceededException e) {
  90                         e.printStackTrace();
  91                         fail(e.getMessage());
  92                 } catch (JobSubmissionException e) {
  93                         e.printStackTrace();
  94                         fail(e.getMessage());
  95                 } catch (ResultNotAvailableException e) {
  96                         e.printStackTrace();
  97                         fail(e.getMessage());
  98                 } catch (WrongParameterException e) {
  99                         e.printStackTrace();
 100                         fail(e.getMessage());
 101                 }
 102         }
 103 }
 104
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