src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.datamodel.features.FeatureMatcherSetI;
   7 import jalview.ws.api.JobId;
   8 import jalview.ws.api.SequenceAnnotationServiceI;
   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 import java.util.Map;
  17
  18 import uk.ac.dundee.compbio.slivkaclient.FormField;
  19 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  20 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  21 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  22 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  23
  24 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  25 {
  26   public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
  27   {
  28     super(client, service, "Annotations");
  29   }
  30
  31   @Override
  32   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  33   {
  34     StringBuilder builder = new StringBuilder();
  35     for (SequenceI seq : seqs)
  36     {
  37       builder.append(">").append(seq.getName()).append("\n");
  38       builder.append(seq.getSequence()).append("\n");
  39     }
  40     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  41     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  42     SlivkaForm form = service.getForm();
  43     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  44     if (paramset != null)
  45     {
  46       for (ArgumentI arg : paramset)
  47       {
  48         values.put(arg.getName(), arg.getValue());
  49       }
  50     }
  51     for (FormField field : form.getFields())
  52     {
  53       switch (field.getType())
  54       {
  55       case FILE:
  56         form.insert(field.getName(), file);
  57         break;
  58       case BOOLEAN:
  59         String value = values.get(field.getName());
  60         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  61         break;
  62       default:
  63         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  64       }
  65     }
  66     return new JobId(service.getName(), service.getName(), form.submit());
  67   }
  68
  69   @Override
  70   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  71           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  72           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  73   {
  74     // TODO Auto-generated method stub
  75     return null;
  76   }
  77 }