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