test/jalview/ws/jabaws/MinJabawsClientTests.java

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