testsrc/compbio/ws/client/TestIUPredWS.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.ConservationMethod;
  23 import compbio.data.sequence.FastaSequence;
  24 import compbio.data.sequence.ScoreManager;
  25 import compbio.data.sequence.SequenceUtil;
  26 import compbio.metadata.AllTestSuit;
  27 import compbio.metadata.JobSubmissionException;
  28 import compbio.metadata.LimitExceededException;
  29 import compbio.metadata.Option;
  30 import compbio.metadata.PresetManager;
  31 import compbio.metadata.ResultNotAvailableException;
  32 import compbio.metadata.RunnerConfig;
  33 import compbio.metadata.UnsupportedRuntimeException;
  34 import compbio.metadata.WrongParameterException;
  35 import compbio.runner.conservation.AACon;
  36 import compbio.util.SysPrefs;
  37 import compbio.ws.server.IUPredWS;
  38
  39 public class TestIUPredWS {
  40
  41         SequenceAnnotation<IUPredWS> msaws;
  42
  43         @BeforeTest(groups = {AllTestSuit.test_group_webservices})
  44         void initConnection() {
  45                 /*
  46                  * URL url = null; try { url = new
  47                  * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
  48                  * (MalformedURLException e) { e.printStackTrace();
  49                  * fail(e.getLocalizedMessage()); } String namespace =
  50                  * "http://msa.data.compbio/01/12/2010/"; QName qname = new
  51                  * QName(namespace, "AAConWS"); Service serv = Service.create(url,
  52                  * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
  53                  * Annotation.class);
  54                  */try {
  55                         JABAService client = Jws2Client.connect(
  56                                         "http://localhost:8080/jabaws", Services.IUPredWS);
  57                         msaws = (SequenceAnnotation<IUPredWS>) client;
  58                 } catch (ConnectException e) {
  59                         e.printStackTrace();
  60                         fail(e.getMessage());
  61                 } catch (WebServiceException e) {
  62                         e.printStackTrace();
  63                         fail(e.getMessage());
  64                 }
  65         }
  66
  67         @Test(groups = {AllTestSuit.test_group_webservices})
  68         public void testCustomAnalize() throws FileNotFoundException, IOException {
  69
  70                 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
  71                                 + File.separator;
  72
  73                 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
  74                                 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
  75                                                 + File.separator + "TO1381.fasta"));
  76
  77                 try {
  78                         List<Option<IUPredWS>> opts=new ArrayList<Option<IUPredWS>>();
  79                         opts.add(msaws.getRunnerOptions().getArgumentByOptionName("Long"));
  80                         String jobId = msaws.customAnalize(fsl,opts);
  81                         System.out.println("J: " + jobId);
  82                         ScoreManager result = msaws.getAnnotation(jobId);
  83                         assertNotNull(result);
  84 //                      assertEquals(result.asSet().size(), 1);
  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 }