package jalview.ext.ensembl;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.util.DBRefUtils;

import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
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 class to fetch cross-references from Ensembl by calling the /xrefs REST
 * service
 * 
 * @author gmcarstairs
 * @see http://rest.ensembl.org/documentation/info/xref_id
 */
class EnsemblXref extends EnsemblRestClient
{

  private static final String GO_GENE_ONTOLOGY = "GO";

  private String dbName = "ENSEMBL (xref)";

  /**
   * Constructor given the target domain to fetch data from
   * 
   * @param d
   */
  public EnsemblXref(String d, String dbSource, String version)
  {
    super(d);
    dbName = dbSource;
    xrefVersion = dbSource + ":" + version;

  }

  @Override
  public String getDbName()
  {
    return dbName;
  }

  @Override
  public AlignmentI getSequenceRecords(String queries) throws Exception
  {
    return null;
  }

  @Override
  protected URL getUrl(List<String> ids) throws MalformedURLException
  {
    return getUrl(ids.get(0));
  }

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

  @Override
  protected String getRequestMimeType(boolean multipleIds)
  {
    return "application/json";
  }

  @Override
  protected String getResponseMimeType()
  {
    return "application/json";
  }

  /**
   * Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
   * ("primary_id") for the given identifier (Ensembl accession id) and database
   * names. The "dbname" returned by Ensembl is canonicalised to Jalview's
   * standard version, and a DBRefEntry constructed. Currently takes all
   * identifiers apart from GO terms and synonyms.
   * 
   * @param identifier
   *          an Ensembl stable identifier
   * @return
   */
  public List<DBRefEntry> getCrossReferences(String identifier)
  {
    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
    List<String> ids = new ArrayList<String>();
    ids.add(identifier);

    BufferedReader br = null;
    try
    {
      URL url = getUrl(identifier);
      if (url != null)
      {
        br = getHttpResponse(url, ids);
      }
      return (parseResponse(br));
    } catch (IOException e)
    {
      // ignore
    } finally
    {
      if (br != null)
      {
        try
        {
          br.close();
        } catch (IOException e)
        {
          // ignore
        }
      }
    }

    return result;
  }

  /**
   * Parses "primary_id" and "dbname" values from the JSON response and
   * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
   * don't parse "synonyms" as they appear to be either redirected or obsolete
   * in Uniprot.
   * 
   * @param br
   * @return
   * @throws IOException
   */
  protected List<DBRefEntry> parseResponse(BufferedReader br)
          throws IOException
  {
    JSONParser jp = new JSONParser();
    List<DBRefEntry> result = new ArrayList<DBRefEntry>();
    try
    {
      JSONArray responses = (JSONArray) jp.parse(br);
      Iterator rvals = responses.iterator();
      while (rvals.hasNext())
      {
        JSONObject val = (JSONObject) rvals.next();
        String dbName = val.get("dbname").toString();
        if (dbName.equals(GO_GENE_ONTOLOGY))
        {
          continue;
        }
        String id = val.get("primary_id").toString();
        if (dbName != null && id != null)
        {
          dbName = DBRefUtils.getCanonicalName(dbName);
          DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
          result.add(dbref);
        }
      }
    } catch (ParseException e)
    {
      // ignore
    }
    return result;
  }

  private String xrefVersion = "ENSEMBL:0";

  /**
   * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
   * 
   * @return
   */
  public String getXRefVersion()
  {
    return xrefVersion;
  }

  /**
   * Returns the URL for the REST endpoint to fetch all cross-references for an
   * identifier. Note this may return protein cross-references for nucleotide.
   * Filter the returned list as required.
   * 
   * @param identifier
   * @return
   */
  protected URL getUrl(String identifier)
  {
    String url = getDomain() + "/xrefs/id/" + identifier
            + "?content-type=application/json&all_levels=1";
    try
    {
      return new URL(url);
    } catch (MalformedURLException e)
    {
      return null;
    }
  }

}