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.List;
import java.util.Optional;

import uk.ac.dundee.compbio.slivkaclient.FieldType;
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");
    style = ServiceClient.MSAWSCLIENT;
  }

  @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();
    Optional<FormField> inputField = form.getFields().stream()
        .filter(f -> f.getType() == FieldType.FILE).findFirst();
    if (inputField.isPresent())
    {
      form.insert(inputField.get().getName(), file);
    }
    if (list != null)
    {
      for (ArgumentI arg : list)
      {
        FormField field = form.getField(arg.getName());
        if (field.getType() == FieldType.BOOLEAN)
        {
          form.insert(arg.getName(), (arg.getValue() != null && !arg.getValue().isBlank()) ? true : false);
        }
        else
        {
          form.insert(arg.getName(), field.valueOf(arg.getValue()));
        }
      }
    }
    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;
  }
}