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                         MsaWS msaservice = null;
  33                         for (Services service : registry.getSupportedServices()) {
  34                                 if (service.equals(Services.ClustalOWS)) {
  35                                         msaservice = (MsaWS) Jws2Client.connect(url, service);
  36                                         if (msaservice != null) {
  37                                                 break;
  38                                         }
  39                                 }
  40                         }
  41                         if (msaservice == null) {
  42                                 fail("couldn't find a clustalO service on the public registry");
  43                         }
  44                         FastaSequence fsq = new FastaSequence("seqA",
  45                                         "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
  46                         List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
  47                         for (int i = 0; i < 9; i++) {
  48                                 iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
  49                                                 + fsq.getSequence().substring(i + 3, i + 3 + i)));
  50                         }
  51
  52                         String jobid = msaservice.align(iseqs);
  53                         if (jobid != null) {
  54                                 JobStatus js = null;
  55                                 do {
  56                                         try {
  57                                                 Thread.sleep(500);
  58                                         } catch (InterruptedException q) {
  59                                         }
  60                                         ;
  61                                         js = msaservice.getJobStatus(jobid);
  62                                 } while (!js.equals(JobStatus.FAILED)
  63                                                 && !js.equals(JobStatus.CANCELLED)
  64                                                 && !js.equals(JobStatus.FINISHED));
  65                                 assertEquals("Trial alignment failed. State was " + js.name(),
  66                                                 js, JobStatus.FINISHED);
  67                                 assertEquals(
  68                                                 "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
  69                                                 msaservice.getResult(jobid).getSequences().size(),
  70                                                 iseqs.size());
  71                                 List<FastaSequence> seqList = msaservice.getResult(jobid).getSequences();
  72                                 for(FastaSequence fSeq : seqList){
  73                                         System.out.println(">"+fSeq.getId());
  74                                         System.out.println(fSeq.getFormattedFasta());
  75                                 }
  76                         }
  77
  78                 }
  79         }
  80 }