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