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(groups =
  27   { "Network" })
  28         public void msaTest() throws Exception {
  29                 String url;
  30                 RegistryWS registry = Jws2Client
  31                                 .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
  32                 if (registry != null) {
  33
  34                         MsaWS msaservice = null;
  35                         for (Services service : registry.getSupportedServices()) {
  36                                 if (service.equals(Services.ClustalOWS)) {
  37                                         msaservice = (MsaWS) Jws2Client.connect(url, service);
  38                                         if (msaservice != null) {
  39                                                 break;
  40                                         }
  41                                 }
  42                         }
  43                         if (msaservice == null) {
  44                                 Assert.fail("couldn't find a clustalO service on the public registry");
  45                         }
  46                         FastaSequence fsq = new FastaSequence("seqA",
  47                                         "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
  48                         List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
  49                         for (int i = 0; i < 9; i++) {
  50                                 iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
  51                                                 + fsq.getSequence().substring(i + 3, i + 3 + i)));
  52                         }
  53
  54                         String jobid = msaservice.align(iseqs);
  55       if (jobid != null)
  56       {
  57         JobStatus js = null;
  58         do
  59         {
  60           try
  61           {
  62             Thread.sleep(500);
  63           } catch (InterruptedException q)
  64           {
  65           }
  66           ;
  67           js = msaservice.getJobStatus(jobid);
  68         } while (!js.equals(JobStatus.FAILED)
  69                 && !js.equals(JobStatus.CANCELLED)
  70                 && !js.equals(JobStatus.FINISHED));
  71         assertEquals("Trial alignment failed. State was " + js.name(), js,
  72                 JobStatus.FINISHED);
  73         assertEquals(
  74                 "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
  75                 msaservice.getResult(jobid).getSequences().size(),
  76                 iseqs.size());
  77         for (FastaSequence t : msaservice.getResult(jobid).getSequences())
  78         {
  79           System.out.println(">" + t.getId());
  80           System.out.println(t.getFormattedFasta());
  81         }
  82         // .forEach(new Consumer<FastaSequence>() {
  83         // @Override
  84         // public void accept(FastaSequence t) {
  85         // System.out.println(">"+t.getId());
  86         // System.out.println(t.getFormattedFasta());
  87         // }
  88         // });
  89                         }
  90
  91                 }
  92         }
  93 }