package jalview.ws.slivkaws;

import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;

import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import uk.ac.dundee.compbio.slivkaclient.FormField;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;

public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
{
  public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
  {
    super(client, service, "Annotations");
  }

  @Override
  public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  {
    StringBuilder builder = new StringBuilder();
    for (SequenceI seq : seqs)
    {
      builder.append(">").append(seq.getName()).append("\n");
      builder.append(seq.getSequence()).append("\n");
    }
    InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
    RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
    SlivkaForm form = service.getForm();
    HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
    if (paramset != null)
    {
      for (ArgumentI arg : paramset)
      {
        values.put(arg.getName(), arg.getValue());
      }
    }
    for (FormField field : form.getFields())
    {
      switch (field.getType())
      {
      case FILE:
        form.insert(field.getName(), file);
        break;
      case BOOLEAN:
        String value = values.get(field.getName());
        form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
        break;
      default:
        form.insert(field.getName(), field.valueOf(values.get(field.getName())));
      }
    }
    return new JobId(service.getName(), service.getName(), form.submit());
  }

  @Override
  public List<AlignmentAnnotation> getAnnotationResult(JobId job,
          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  {
    // TODO Auto-generated method stub
    return null;
  }
}