package jalview.ws2.client.slivka;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.Collections;
import java.util.EnumMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;

import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.ws.params.ArgumentI;
import jalview.ws2.api.Credentials;
import jalview.ws2.api.JobStatus;
import jalview.ws2.api.WebServiceJobHandle;
import jalview.ws2.client.api.AlignmentWebServiceClientI;
import jalview.ws2.client.api.AnnotationWebServiceClientI;
import jalview.ws2.client.api.WebServiceClientI;
import uk.ac.dundee.compbio.slivkaclient.Job;
import uk.ac.dundee.compbio.slivkaclient.Parameter;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;

import static java.lang.String.format;

public class SlivkaWSClient implements WebServiceClientI
{
  final SlivkaService service;

  final SlivkaClient client;

  SlivkaWSClient(SlivkaService service)
  {
    this.service = service;
    this.client = service.getClient();
  }

  @Override
  public String getUrl()
  {
    return client.getUrl().toString();
  }

  @Override
  public String getClientName()
  {
    return "slivka";
  }

  // pattern for matching media types
  static final Pattern mediaTypePattern = Pattern.compile(
      "(?:text|application)\\/(?:x-)?([\\w-]+)");

  @Override
  public WebServiceJobHandle submit(List<SequenceI> sequences,
      List<ArgumentI> args, Credentials credentials) throws IOException
  {
    var request = new uk.ac.dundee.compbio.slivkaclient.JobRequest();
    for (Parameter param : service.getParameters())
    {
      // TODO: restrict input sequences parameter name to "sequences"
      if (param instanceof Parameter.FileParameter)
      {
        Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
        FileFormat format = null;
        var match = mediaTypePattern.matcher(fileParam.getMediaType());
        if (match.find())
        {
          String fmt = match.group(1);
          if (fmt.equalsIgnoreCase("pfam"))
            format = FileFormat.Pfam;
          else if (fmt.equalsIgnoreCase("stockholm"))
            format = FileFormat.Stockholm;
          else if (fmt.equalsIgnoreCase("clustal"))
            format = FileFormat.Clustal;
          else if (fmt.equalsIgnoreCase("fasta"))
            format = FileFormat.Fasta;
        }
        if (format == null)
        {
          Cache.log.warn(String.format(
              "Unknown input format %s, assuming fasta.",
              fileParam.getMediaType()));
          format = FileFormat.Fasta;
        }
        InputStream stream = new ByteArrayInputStream(format.getWriter(null)
            .print(sequences.toArray(new SequenceI[0]), false)
            .getBytes());
        request.addFile(param.getId(), stream);
      }
    }
    if (args != null)
    {
      for (ArgumentI arg : args)
      {
        // multiple choice field names are name$number to avoid duplications
        // the number is stripped here
        String paramId = arg.getName().split("\\$", 2)[0];
        Parameter param = service.getParameter(paramId);
        if (param instanceof Parameter.FlagParameter)
        {
          if (arg.getValue() != null && !arg.getValue().isBlank())
            request.addData(paramId, true);
          else
            request.addData(paramId, false);
        }
        else if (param instanceof Parameter.FileParameter)
        {
          request.addFile(paramId, new File(arg.getValue()));
        }
        else
        {
          request.addData(paramId, arg.getValue());
        }
      }
    }
    var job = service.submitJob(request);
    return createJobHandle(job.getId());
  }

  protected WebServiceJobHandle createJobHandle(String jobId)
  {
    return new WebServiceJobHandle(
        getClientName(), service.getName(), client.getUrl().toString(),
        jobId);
  }

  @Override
  public JobStatus getStatus(WebServiceJobHandle job) throws IOException
  {
    var slivkaJob = client.getJob(job.getJobId());
    return statusMap.getOrDefault(slivkaJob.getStatus(), JobStatus.UNKNOWN);
  }

  protected static final EnumMap<Job.Status, JobStatus> statusMap = new EnumMap<>(Job.Status.class);
  static
  {
    statusMap.put(Job.Status.PENDING, JobStatus.SUBMITTED);
    statusMap.put(Job.Status.REJECTED, JobStatus.INVALID);
    statusMap.put(Job.Status.ACCEPTED, JobStatus.SUBMITTED);
    statusMap.put(Job.Status.QUEUED, JobStatus.QUEUED);
    statusMap.put(Job.Status.RUNNING, JobStatus.RUNNING);
    statusMap.put(Job.Status.COMPLETED, JobStatus.COMPLETED);
    statusMap.put(Job.Status.INTERRUPTED, JobStatus.CANCELLED);
    statusMap.put(Job.Status.DELETED, JobStatus.CANCELLED);
    statusMap.put(Job.Status.FAILED, JobStatus.FAILED);
    statusMap.put(Job.Status.ERROR, JobStatus.SERVER_ERROR);
    statusMap.put(Job.Status.UNKNOWN, JobStatus.UNKNOWN);
  }

  @Override
  public String getLog(WebServiceJobHandle job) throws IOException
  {
    var slivkaJob = client.getJob(job.getJobId());
    for (var f : slivkaJob.getResults())
    {
      if (f.getLabel().equals("log"))
      {
        ByteArrayOutputStream stream = new ByteArrayOutputStream();
        f.writeTo(stream);
        return stream.toString(StandardCharsets.UTF_8);
      }
    }
    return "";
  }

  @Override
  public String getErrorLog(WebServiceJobHandle job) throws IOException
  {
    var slivkaJob = client.getJob(job.getJobId());
    for (var f : slivkaJob.getResults())
    {
      if (f.getLabel().equals("error-log"))
      {
        ByteArrayOutputStream stream = new ByteArrayOutputStream();
        f.writeTo(stream);
        return stream.toString(StandardCharsets.UTF_8);
      }
    }
    return "";
  }

  @Override
  public void cancel(WebServiceJobHandle job)
      throws IOException, UnsupportedOperationException
  {
    Cache.log.warn(
        "slivka client does not support job cancellation");
  }
}

class SlivkaAlignmentWSClient extends SlivkaWSClient
    implements AlignmentWebServiceClientI
{

  SlivkaAlignmentWSClient(SlivkaService service)
  {
    super(service);
  }

  @Override
  public AlignmentI getAlignment(WebServiceJobHandle job) throws IOException
  {
    var slivkaJob = client.getJob(job.getJobId());
    for (var f : slivkaJob.getResults())
    {
      // TODO: restrict result file label to "alignment"
      FileFormat format;
      var match = mediaTypePattern.matcher(f.getMediaType());
      if (!match.find())
        continue;
      String fmt = match.group(1);
      if (fmt.equalsIgnoreCase("clustal"))
        format = FileFormat.Clustal;
      else if (fmt.equalsIgnoreCase("fasta"))
        format = FileFormat.Fasta;
      else
        continue;
      return new FormatAdapter().readFile(f.getContentUrl().toString(),
          DataSourceType.URL, format);
    }
    Cache.log.warn("No alignment found on the server");
    throw new IOException("no alignment found");
  }

}

class SlivkaAnnotationWSClient extends SlivkaWSClient
    implements AnnotationWebServiceClientI
{
  SlivkaAnnotationWSClient(SlivkaService service)
  {
    super(service);
  }

  @Override
  public List<AlignmentAnnotation> attachAnnotations(WebServiceJobHandle job,
      List<SequenceI> sequences, Map<String, FeatureColourI> colours,
      Map<String, FeatureMatcherSetI> filters) throws IOException
  {
    var slivkaJob = client.getJob(job.getJobId());
    var aln = new Alignment(sequences.toArray(new SequenceI[sequences.size()]));
    boolean featPresent = false, annotPresent = false;
    for (var f : slivkaJob.getResults())
    {
      // TODO: restrict file label to "annotations" or "features"
      var match = mediaTypePattern.matcher(f.getMediaType());
      if (!match.find())
        continue;
      String fmt = match.group(1);
      if (fmt.equalsIgnoreCase("jalview-annotations"))
      {
        annotPresent = new AnnotationFile().readAnnotationFileWithCalcId(
            aln, service.getId(), f.getContentUrl().toString(),
            DataSourceType.URL);
        if (annotPresent)
          Cache.log.debug(format("loaded annotations for %s", service.getId()));
      }
      else if (fmt.equalsIgnoreCase("jalview-features"))
      {
        FeaturesFile ff = new FeaturesFile(f.getContentUrl().toString(),
            DataSourceType.URL);
        featPresent = ff.parse(aln, colours, true);
        if (featPresent)
          Cache.log.debug(format("loaded features for %s", service.getId()));
      }
    }
    if (!annotPresent)
      Cache.log.debug(format("no annotations found for %s", service.getId()));
    if (!featPresent)
      Cache.log.debug(format("no features found for %s", service.getId()));
    return aln.getAlignmentAnnotation() != null ? Arrays.asList(aln.getAlignmentAnnotation())
        : Collections.emptyList();
  }
}