package jalview.ws.slivkaws;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.WebserviceInfo;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.ws.api.JalviewServiceEndpointProviderI;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.gui.WsJob;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.ParamManager;
import jalview.ws.params.WsParamSetI;

import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.EnumMap;
import java.util.List;

import uk.ac.dundee.compbio.slivkaclient.Form;
import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
import uk.ac.dundee.compbio.slivkaclient.JobState;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.Service;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;

public class ClustaloWS extends ServiceWithParameters
    implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
{
  private SlivkaClient client;
  private Service service;

  private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  {
    stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
    stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
    stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
    stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
    stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
    stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
    stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  }


  ClustaloWS(SlivkaClient client)
  {
    super("ClustalO", "Alignment", "ClustalO", "foo", "http://foo.foo");

    this.client = client;
    try
    {
      service = client.getService("clustalo");
    } catch (IOException e)
    {
      throw new RuntimeException(e);
    }
  }

  @Override
  public void updateStatus(WsJob job)
  {
    try
    {
      job.setState(stateMap.get(client.getJobState(job.getJobId())));
    } catch (IOException e)
    {
      throw new RuntimeException(e);
    }
  }

  @Override
  public boolean updateJobProgress(WsJob job)
  {
    return false;
  }

  @Override
  public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
  {
    return false;
  }

  @Override
  public boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
  {
    return false;
  }

  @Override
  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws FormValidationException, IOException
  {
    StringBuilder builder = new StringBuilder();
    for (SequenceI seq : toalign)
    {
      builder.append(">").append(seq.getName()).append("\n");
      builder.append(seq.getSequence()).append("\n\n");
    }
    InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
    RemoteFile file = client.uploadFile(stream, "input.fasta",
            "application/fasta");
    Form form = service.getForm();
    form.insert("input", file);
    String jobUUID = form.submit();
    return new JobId("clustalo", "clustalo", jobUUID);
  }

  @Override
  public AlignmentI getAlignmentFor(JobId jobId)
  {
    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);
        }
      }
    } catch (IOException e1)
    {
      // TODO Auto-generated catch block
      e1.printStackTrace();
    }
    return null;
  }

  @Override
  public void initParamStore(ParamManager userParameterStore)
  {

  }

  @Override
  public Object getEndpoint()
  {
    return this;
  }
}