src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.ws.api.JobId;
   6 import jalview.ws.api.SequenceAnnotationServiceI;
   7 import jalview.ws.gui.AnnotationWsJob;
   8 import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
   9 import jalview.ws.params.ArgumentI;
  10 import jalview.ws.params.WsParamSetI;
  11
  12 import java.io.ByteArrayInputStream;
  13 import java.io.InputStream;
  14 import java.util.HashMap;
  15 import java.util.List;
  16
  17 import uk.ac.dundee.compbio.slivkaclient.FormField;
  18 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  19 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  20 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  21 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  22
  23 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  24 {
  25   public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
  26   {
  27     super(client, service, "Annotations");
  28   }
  29
  30   @Override
  31   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  32   {
  33     StringBuilder builder = new StringBuilder();
  34     for (SequenceI seq : seqs)
  35     {
  36       builder.append(">").append(seq.getName()).append("\n");
  37       builder.append(seq.getSequence()).append("\n");
  38     }
  39     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  40     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  41     SlivkaForm form = service.getForm();
  42     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  43     if (paramset != null)
  44     {
  45       for (ArgumentI arg : paramset)
  46       {
  47         values.put(arg.getName(), arg.getValue());
  48       }
  49     }
  50     for (FormField field : form.getFields())
  51     {
  52       switch (field.getType())
  53       {
  54       case FILE:
  55         form.insert(field.getName(), file);
  56         break;
  57       case BOOLEAN:
  58         String value = values.get(field.getName());
  59         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  60         break;
  61       default:
  62         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  63       }
  64     }
  65     return new JobId(service.getName(), service.getName(), form.submit());
  66   }
  67
  68   @Override
  69   public List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
  70       SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable
  71   {
  72     // TODO Auto-generated method stub
  73     return null;
  74   }
  75 }