package jalview.ext.ensembl;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;

import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Iterator;
import java.util.List;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;

public class EnsemblMap extends EnsemblRestClient
{
  private static final String MAPPED = "mapped";

  private static final String MAPPINGS = "mappings";

  /**
   * Default constructor (to use rest.ensembl.org)
   */
  public EnsemblMap()
  {
    super();
  }

  /**
   * Constructor given the target domain to fetch data from
   * 
   * @param
   */
  public EnsemblMap(String domain)
  {
    super(domain);
  }

  @Override
  public String getDbName()
  {
    return DBRefSource.ENSEMBL;
  }

  @Override
  public AlignmentI getSequenceRecords(String queries) throws Exception
  {
    return null; // not used
  }

  /**
   * Constructs a URL of the format <code>
   * http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37?content-type=application/json
   * </code>
   * 
   * @param species
   * @param chromosome
   * @param fromRef
   * @param toRef
   * @param startPos
   * @param endPos
   * @return
   * @throws MalformedURLException
   */
  protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,
          String toRef, int startPos, int endPos)
          throws MalformedURLException
  {
    /*
     * start-end might be reverse strand - present forwards to the service
     */
    boolean forward = startPos <= endPos;
    int start = forward ? startPos : endPos;
    int end = forward ? endPos : startPos;
    String strand = forward ? "1" : "-1";
    String url = String.format(
            "%s/map/%s/%s/%s:%d..%d:%s/%s?content-type=application/json",
            getDomain(), species, fromRef, chromosome, start, end, strand,
            toRef);
    return new URL(url);
  }

  @Override
  protected boolean useGetRequest()
  {
    return true;
  }

  @Override
  protected URL getUrl(List<String> ids) throws MalformedURLException
  {
    return null; // not used
  }

  /**
   * Calls the REST /map service to get the chromosomal coordinates (start/end)
   * in 'toRef' that corresponding to the (start/end) queryRange in 'fromRef'
   * 
   * @param species
   * @param chromosome
   * @param fromRef
   * @param toRef
   * @param queryRange
   * @return
   * @see http://rest.ensemblgenomes.org/documentation/info/assembly_map
   */
  public int[] getAssemblyMapping(String species, String chromosome,
          String fromRef, String toRef, int[] queryRange)
  {
    URL url = null;
    BufferedReader br = null;

    try
    {
      url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
              queryRange[1]);
      br = getHttpResponse(url, null);
      return (parseAssemblyMappingResponse(br));
    } catch (Throwable t)
    {
      System.out.println("Error calling " + url + ": " + t.getMessage());
      return null;
    } finally
    {
      if (br != null)
      {
        try
        {
          br.close();
        } catch (IOException e)
        {
          // ignore
        }
      }
    }
  }

  /**
   * Parses the JSON response from the /map/&lt;species&gt;/ REST service. The
   * format is (with some fields omitted)
   * 
   * <pre>
   *  {"mappings": 
   *    [{
   *       "original": {"end":45109016,"start":45051610},
   *       "mapped"  : {"end":43186384,"start":43128978} 
   *  }] }
   * </pre>
   * 
   * @param br
   * @return
   */
  protected int[] parseAssemblyMappingResponse(BufferedReader br)
  {
    int[] result = null;
    JSONParser jp = new JSONParser();

    try
    {
      JSONObject parsed = (JSONObject) jp.parse(br);
      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);

      Iterator rvals = mappings.iterator();
      while (rvals.hasNext())
      {
        // todo check for "mapped"
        JSONObject val = (JSONObject) rvals.next();
        JSONObject mapped = (JSONObject) val.get(MAPPED);
        int start = Integer.parseInt(mapped.get("start").toString());
        int end = Integer.parseInt(mapped.get("end").toString());
        String strand = mapped.get("strand").toString();
        if ("1".equals(strand))
        {
          result = new int[] { start, end };
        }
        else
        {
          result = new int[] { end, start };
        }
      }
    } catch (IOException | ParseException | NumberFormatException e)
    {
      // ignore
    }
    return result;
  }

  /**
   * Constructs a URL to the /map/cds/<id> or /map/cdna/<id> REST service. The
   * REST call is to either ensembl or ensemblgenomes, as determined from the
   * division, e.g. Ensembl or EnsemblProtists.
   * 
   * @param domain
   * @param accession
   * @param start
   * @param end
   * @param cdsOrCdna
   * @return
   * @throws MalformedURLException
   */
  URL getIdMapUrl(String domain, String accession, int start, int end,
          String cdsOrCdna) throws MalformedURLException
  {
    String url = String
            .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
                    domain, cdsOrCdna, accession, start, end);
    return new URL(url);
  }

}