package jalview.ws.slivkaws;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;

import java.io.ByteArrayInputStream;
import java.io.IOError;
import java.io.IOException;
import java.io.InputStream;
import java.rmi.ServerError;
import java.util.HashMap;
import java.util.List;

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 SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
{
  SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
    super(client, service, "Alignment");
  }

  @Override
  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  {
    StringBuilder builder = new StringBuilder();
    for (SequenceI seq : toalign)
    {
      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<>(list != null ? list.size() : 0);
    if (list != null)
    {
      for (ArgumentI arg : list)
      {
        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 AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  {
    List<RemoteFile> files;
    try
    {
      files = client.getJobResults(jobId.getJobId());
      for (RemoteFile f : files)
      {
        if (f.getMimeType().equals("application/clustal"))
        {
          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
        }
        else if (f.getMimeType().equals("application/fasta"))
        {
          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
        }
      }
    } catch (IOException e)
    {
      throw new IOError(e);
    }
    return null;
  }
}