test/jalview/ws/jabaws/MinJabawsClientTests.java

   1 package jalview.ws.jabaws;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.fail;
   5
   6 import java.util.ArrayList;
   7 import java.util.List;
   8
   9 import org.junit.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    * simple test for the benefit of JAL-1338
  22    * @throws Exception
  23    */
  24   @SuppressWarnings("rawtypes")
  25   @Test
  26   public void msaTest() throws Exception {
  27     String url;
  28     RegistryWS registry = Jws2Client
  29             .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
  30     if (registry != null)
  31     {
  32
  33       MsaWS msaservice = null;
  34       for (Services service : registry.getSupportedServices())
  35       {
  36         if (service.equals(Services.ClustalOWS))
  37         {
  38           msaservice = (MsaWS) Jws2Client.connect(url, service);
  39           if (msaservice != null)
  40           {
  41             break;
  42           }
  43         }
  44       }
  45       if (msaservice == null)
  46       {
  47         fail("couldn't find a clustalO service on the public registry");
  48       }
  49       FastaSequence fsq = new FastaSequence("seqA",
  50               "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
  51       List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
  52       for (int i = 0; i < 9; i++)
  53       {
  54         iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
  55                 + fsq.getSequence().substring(i + 3, i + 3 + i)));
  56       }
  57
  58       String jobid = msaservice.align(iseqs);
  59       if (jobid != null)
  60       {
  61         JobStatus js = null;
  62         do
  63         {
  64           try
  65           {
  66             Thread.sleep(500);
  67           } catch (InterruptedException q)
  68           {
  69           }
  70           ;
  71           js = msaservice.getJobStatus(jobid);
  72         } while (!js.equals(JobStatus.FAILED)
  73                 && !js.equals(JobStatus.CANCELLED)
  74                 && !js.equals(JobStatus.FINISHED));
  75         assertEquals("Trial alignment failed. State was " + js.name(), js,
  76                 JobStatus.FINISHED);
  77         assertEquals(
  78                 "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
  79                 msaservice.getResult(jobid).getSequences().size(),
  80                 iseqs.size());
  81
  82         List<FastaSequence> fastaSequences = msaservice.getResult(jobid).getSequences();
  83         for(FastaSequence fastaSequence : fastaSequences){
  84           System.out.println(">" + fastaSequence.getId());
  85           System.out.println(fastaSequence.getFormattedFasta());
  86         }
  87       }
  88
  89       //        msaservice.getResult(jobid).getSequences()
  90       //        .forEach(new Consumer<FastaSequence>()
  91       //                {
  92       //                  @Override
  93       //                  public void accept(FastaSequence t)
  94       //                  {
  95       //                    System.out.println(">" + t.getId());
  96       //                    System.out.println(t.getFormattedFasta());
  97       //                  }
  98       //                });
  99     }
 100
 101   }
 102 }
 103