/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ext.ensembl;

import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
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;

/**
 * A client for the Ensembl xrefs/symbol REST service;
 * 
 * @see http://rest.ensembl.org/documentation/info/xref_external
 * @author gmcarstairs
 *
 */
public class EnsemblSymbol extends EnsemblXref
{
  private static final String COLON = ":";
  private static final String GENE = "gene";
  private static final String TYPE = "type";
  private static final String ID = "id";

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

  /**
   * Returns the first "id" value in gene identifier format from the JSON
   * response, or null if none found
   * 
   * @param br
   * @return
   * @throws IOException
   */
  protected String parseSymbolResponse(BufferedReader br) throws IOException
  {
    JSONParser jp = new JSONParser();
    String result = null;
    try
    {
      JSONArray responses = (JSONArray) jp.parse(br);
      Iterator rvals = responses.iterator();
      while (rvals.hasNext())
      {
        JSONObject val = (JSONObject) rvals.next();
        String id = val.get(ID).toString();
        String type = val.get(TYPE).toString();
        if (id != null && GENE.equals(type))
        {
          result = id;
          break;
        }
      }
    } catch (ParseException e)
    {
      // ignore
    }
    return result;
  }

  /**
   * Constructs the URL for the REST symbol endpoint
   * 
   * @param id
   *          the accession id (Ensembl or external)
   * @param species
   *          a species name recognisable by Ensembl
   * @param type
   *          an optional type to filter the response (gene, transcript,
   *          translation)
   * @return
   */
  protected URL getUrl(String id, String species, String... type)
  {
    StringBuilder sb = new StringBuilder();
    sb.append(getDomain()).append("/xrefs/symbol/").append(species)
            .append("/").append(id).append(CONTENT_TYPE_JSON);
    for (String t : type)
    {
      sb.append("&object_type=").append(t);
    }
    try
    {
      String url = sb.toString();
      return new URL(url);
    } catch (MalformedURLException e)
    {
      return null;
    }
  }

  /**
   * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves gene id(s) for
   * the given identifier. If the identifier has the format species:symbol then
   * the gene id for the specified species is returned, else any matched gene ids
   * for model organisms. If lookup fails, the returned list is empty.
   * 
   * @param identifier
   * @return
   */
  public List<String> getGeneIds(String identifier)
  {
    List<String> result = new ArrayList<>();
    List<String> ids = Collections.<String> emptyList();
    List<String> species = getSpecies(identifier);

    String symbol = identifier.substring(identifier.indexOf(COLON) + 1);
    BufferedReader br = null;
    try
    {
      for (String taxon : species)
        {
        URL url = getUrl(symbol, taxon, GENE);
          if (url != null)
          {
            br = getHttpResponse(url, ids);
            if (br != null)
            {
              String geneId = parseSymbolResponse(br);
              if (geneId != null && !result.contains(geneId))
              {
                result.add(geneId);
              }
            }
          }
        }
    } catch (IOException e)
    {
      // ignore
    } finally
    {
      if (br != null)
      {
        try
        {
          br.close();
        } catch (IOException e)
        {
          // ignore
        }
      }
    }
    return result;
  }

  /**
   * Answers a list of species names which is
   * <ul>
   * <li>the species in the identifier if it is of the form species:symbol</li>
   * <li>else a fixed list of 'model organism' species</li>
   * </ul>
   * 
   * @param identifier
   * @return
   */
  private List<String> getSpecies(String identifier)
  {
    int pos = identifier.indexOf(COLON);
    if (pos > 0)
    {
      return Collections.singletonList(identifier.substring(0, pos));
    }
    else
    {
      return Species.getModelOrganisms();
    }
  }

}