package jalview.ws.slivkaws;

import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.bin.Console;
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.IOError;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.Map;

import compbio.data.msa.Category;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;

public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
{
  public SlivkaAnnotationServiceInstance(SlivkaClient client,
          SlivkaService service, String category)
  {
    super(client, service, category);
    if (category == Category.CATEGORY_CONSERVATION)
    {
      /* FIXME: the category name is hardcoded for AACon, names other than
       * "AAConWS" doesn't work. */
      setAlignAnalysisUI(new AlignAnalysisUIText(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
  {
    return super.submit(seqs, preset, paramset);
  }

  @Override
  public List<AlignmentAnnotation> getAnnotationResult(JobId jobId,
          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  {
    RemoteFile annotFile = null;
    RemoteFile featFile = null;
    try
    {
      var slivkaJob = client.getJob(jobId.getJobId());
      Collection<RemoteFile> files = slivkaJob.getResults();
      for (RemoteFile f : files)
      {
        if (f.getMediaType().equals("application/jalview-annotations"))
        {
          annotFile = f;
        }
        else if (f.getMediaType().equals("application/jalview-features"))
        {
          featFile = f;
        }
      }
    } catch (IOException e)
    {
      throw new IOError(e);
    }
    Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
    if (annotFile == null
        || !new AnnotationFile().readAnnotationFileWithCalcId(aln, service.getId(), annotFile.getContentUrl().toString(), DataSourceType.URL))
    {
      Console.debug("No annotation from slivka job\n" + annotFile);
    }
    else {
      Console.debug("Annotation file loaded " + annotFile);
    }
    if (featFile == null
        || !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true))
    {
      Console.debug("No features from slivka job\n" + featFile);
    }
    else {
      Console.debug("Features feil loaded " + featFile);
    }
    return Arrays.asList(aln.getAlignmentAnnotation());
  }
}