package jalview.ws.slivkaws;

import jalview.api.FeatureColourI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;

import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.IOError;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Arrays;
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, boolean conservation)
  {
    super(client, service, !conservation ? "Annotations disorder"
            : "Alignment Conservation");
    if (conservation)
    {
      setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
              SlivkaAnnotationServiceInstance.class,
              "Slivka.AACons", false, true, true, true, true, 2,
              MessageManager.getString("label.aacon_calculations"),
              MessageManager.getString("tooltip.aacon_calculations"),
              MessageManager.getString("label.aacon_settings"),
              MessageManager.getString("tooltip.aacon_settings")));
    }
    style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  }

  @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
  {
    RemoteFile annotFile = null;
    RemoteFile featFile = null;
    try
    {
      List<RemoteFile> files = client.getJobResults(job.getJobId());
      for (RemoteFile f : files)
      {
        if (f.getMimeType().equals("application/jalview-annotations"))
        {
          annotFile = f;
        }
        else if (f.getMimeType().equals("application/jalview-features"))
        {
          featFile = f;
        }
      }
    } catch (IOException e)
    {
      throw new IOError(e);
    }
    Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
    BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
    new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
    if (featFile != null)
    {
      new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
    }
    return Arrays.asList(aln.getAlignmentAnnotation());
  }
}