test/jalview/ws/jabaws/MinJabawsClientTests.java

   1 package jalview.ws.jabaws;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4
   5 import java.util.ArrayList;
   6 import java.util.List;
   7
   8 import org.testng.Assert;
   9 import org.testng.annotations.Test;
  10
  11 import compbio.data.msa.MsaWS;
  12 import compbio.data.msa.RegistryWS;
  13 import compbio.data.sequence.FastaSequence;
  14 import compbio.metadata.JobStatus;
  15 import compbio.ws.client.Jws2Client;
  16 import compbio.ws.client.Services;
  17
  18 public class MinJabawsClientTests
  19 {
  20
  21         /**
  22          * simple test for the benefit of JAL-1338
  23          * @throws Exception
  24          */
  25         @SuppressWarnings("rawtypes")
  26         @Test
  27         public void msaTest() throws Exception {
  28                 String url;
  29                 RegistryWS registry = Jws2Client
  30                                 .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
  31                 if (registry != null) {
  32
  33                         MsaWS msaservice = null;
  34                         for (Services service : registry.getSupportedServices()) {
  35                                 if (service.equals(Services.ClustalOWS)) {
  36                                         msaservice = (MsaWS) Jws2Client.connect(url, service);
  37                                         if (msaservice != null) {
  38                                                 break;
  39                                         }
  40                                 }
  41                         }
  42                         if (msaservice == null) {
  43                                 Assert.fail("couldn't find a clustalO service on the public registry");
  44                         }
  45                         FastaSequence fsq = new FastaSequence("seqA",
  46                                         "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
  47                         List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
  48                         for (int i = 0; i < 9; i++) {
  49                                 iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
  50                                                 + fsq.getSequence().substring(i + 3, i + 3 + i)));
  51                         }
  52
  53                         String jobid = msaservice.align(iseqs);
  54       if (jobid != null)
  55       {
  56         JobStatus js = null;
  57         do
  58         {
  59           try
  60           {
  61             Thread.sleep(500);
  62           } catch (InterruptedException q)
  63           {
  64           }
  65           ;
  66           js = msaservice.getJobStatus(jobid);
  67         } while (!js.equals(JobStatus.FAILED)
  68                 && !js.equals(JobStatus.CANCELLED)
  69                 && !js.equals(JobStatus.FINISHED));
  70         assertEquals("Trial alignment failed. State was " + js.name(), js,
  71                 JobStatus.FINISHED);
  72         assertEquals(
  73                 "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
  74                 msaservice.getResult(jobid).getSequences().size(),
  75                 iseqs.size());
  76         for (FastaSequence t : msaservice.getResult(jobid).getSequences())
  77         {
  78           System.out.println(">" + t.getId());
  79           System.out.println(t.getFormattedFasta());
  80         }
  81         // .forEach(new Consumer<FastaSequence>() {
  82         // @Override
  83         // public void accept(FastaSequence t) {
  84         // System.out.println(">"+t.getId());
  85         // System.out.println(t.getFormattedFasta());
  86         // }
  87         // });
  88                         }
  89
  90                 }
  91         }
  92 }