1 package compbio.ws.client;
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3 import static org.testng.Assert.assertEquals;
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4 import static org.testng.Assert.assertNotNull;
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5 import static org.testng.Assert.fail;
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8 import java.io.FileInputStream;
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9 import java.io.FileNotFoundException;
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10 import java.io.IOException;
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11 import java.net.URL;
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12 import java.util.HashSet;
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13 import java.util.List;
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15 import javax.xml.namespace.QName;
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16 import javax.xml.ws.Service;
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18 import org.testng.annotations.Test;
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20 import compbio.conservation.Method;
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21 import compbio.data.msa.Annotation;
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22 import compbio.data.sequence.FastaSequence;
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23 import compbio.data.sequence.Score;
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24 import compbio.data.sequence.SequenceUtil;
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25 import compbio.metadata.JobSubmissionException;
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26 import compbio.metadata.LimitExceededException;
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27 import compbio.metadata.ResultNotAvailableException;
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28 import compbio.metadata.UnsupportedRuntimeException;
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29 import compbio.util.SysPrefs;
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30 import compbio.ws.server.AAConWS;
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32 public class TestWSClient {
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35 public void test() throws FileNotFoundException, IOException {
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37 URL url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");
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38 String namespace = "http://msa.data.compbio/01/12/2010/";
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39 QName qname = new QName(namespace, "AAConWS");
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40 Service serv = Service.create(url, qname);
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42 * MsaWS msaws = serv.getPort(new QName(
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43 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
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46 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,
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47 // "ClustalWSPort"), Annotation.class);
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49 Annotation<AAConWS> msaws = serv.getPort(new QName(namespace,
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50 "AAConWSPort"), Annotation.class);
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52 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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53 // AAConTester.test_alignment_input));
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55 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
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58 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
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59 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
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60 + File.separator + "TO1381.fasta.aln"));
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63 System.out.println("Pres: "
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64 + msaws.getPresets().getPresets().get(0));
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65 String jobId = msaws.analize(fsl);
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66 System.out.println("J: " + jobId);
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67 HashSet<Score> result = msaws.getConservation(jobId);
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68 assertNotNull(result);
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69 assertEquals(result.size(), 1);
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70 assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);
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71 List<Float> scores = result.iterator().next().getScores();
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72 assertNotNull(scores);
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73 assertEquals(scores.size(), 568);
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75 } catch (UnsupportedRuntimeException e) {
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76 e.printStackTrace();
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77 fail(e.getMessage());
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78 } catch (LimitExceededException e) {
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79 e.printStackTrace();
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80 fail(e.getMessage());
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81 } catch (JobSubmissionException e) {
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82 e.printStackTrace();
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83 fail(e.getMessage());
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84 } catch (ResultNotAvailableException e) {
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85 e.printStackTrace();
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86 fail(e.getMessage());
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