package jalview.ext.ensembl;

import jalview.io.FileParse;

import java.io.BufferedReader;
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.List;

import org.apache.http.NameValuePair;
import org.apache.http.message.BasicNameValuePair;

public class SeqFetcher
{
  private final static String ENSEMBL_REST = "rest.ensembl.org";

  private static final String SEQUENCE_ID_URL = "http://" + ENSEMBL_REST + "/sequence/id";

  private static final String PING_URL = "http://" + ENSEMBL_REST + "/info/ping";

  private final static long RETEST_INTERVAL = 10000L; // 10 seconds

  private static boolean ensemblRestAvailable = false;

  private static long lastCheck = -1;

  /**
   * Rechecks if Ensembl is responding, unless the last check was successful and
   * the retest interval has not yet elapsed. Returns true if Ensembl is up,
   * else false.
   * 
   * @return
   */
  public boolean isEnsemblAvailable()
  {
    long now = System.currentTimeMillis();
    boolean retest = now - lastCheck > RETEST_INTERVAL;
    if (ensemblRestAvailable && !retest)
    {
      return true;
    }
    ensemblRestAvailable = checkEnsembl();
    lastCheck = now;
    return ensemblRestAvailable;
  }

  /**
   * Tries to connect to Ensembl's REST 'ping' endpoint, and returns true if
   * successful, else false
   * 
   * @return
   */
  private boolean checkEnsembl()
  {
    try
    {
      URL ping = new URL(PING_URL);
      HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
      int rc = conn.getResponseCode();
      conn.disconnect();
      if (rc >= 200 && rc < 300)
      {
        return true;
      }
    } catch (Throwable t)
    {
      System.err.println("Error connecting to " + PING_URL + ": "
              + t.getMessage());
    }
    return false;
  }

  public SeqFetcher()
  {
  }

  public enum EnsemblSeqType
  {
    GENOMIC("genomic"), CDS("cds"), TRANSCRIPT("cds"), PROTEIN("protein"), CDNA(
            "cdna");

    private String type;

    EnsemblSeqType(String t)
    {
      type = t;
    }

    public String getType()
    {
      return type;
    }
  }

  /**
   * Returns a list of additional URL query parameters to specify the desired
   * sequence type (genomic/cds/protein etc), and data format Fasta
   * 
   * @param type
   */
  public List<NameValuePair> getAdditionalParameters(EnsemblSeqType type)
  {
    List<NameValuePair> params = new ArrayList<NameValuePair>();
    params.add(new BasicNameValuePair("type", type.getType()));
    params.add(new BasicNameValuePair("content-type", "text/x-fasta"));
    return params;
  }

  /**
   * return a reader to a Fasta response from the Ensembl sequence endpoint
   * 
   * @param returnType
   * @param ids
   * @return
   * @throws IOException
   */
  public FileParse getSequenceReader(EnsemblSeqType returnType,
          List<String> ids) throws IOException
  {
    // see http://rest.ensembl.org/documentation/info/sequence_id

    String urlstring = SEQUENCE_ID_URL;
    List<NameValuePair> vals = getAdditionalParameters(returnType);
    boolean first = true;
    for (NameValuePair nvp : vals)
    {
      urlstring += first ? "?" : "&";
      first = false;
      urlstring += nvp.getName() + "=" + nvp.getValue();
    }

    URL url = new URL(urlstring);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection) connection;

    httpConnection.setRequestMethod("POST");
    httpConnection.setRequestProperty("Content-Type", "application/json");
    httpConnection.setRequestProperty("Accept", "text/x-fasta");
    byte[] thepostbody;
    {
      StringBuilder postBody = new StringBuilder();
      postBody.append("{\"ids\":[");
      first = true;
      for (String id : ids)
      {
        if (!first)
        {
          postBody.append(",");
        }
        first = false;
        postBody.append("\"");
        postBody.append(id.trim());
        postBody.append("\"");
      }
      postBody.append("]}");
      thepostbody = postBody.toString().getBytes();
    }
    httpConnection.setRequestProperty("Content-Length",
            Integer.toString(thepostbody.length));
    httpConnection.setUseCaches(false);
    httpConnection.setDoInput(true);
    httpConnection.setDoOutput(true);

    DataOutputStream wr = new DataOutputStream(
            httpConnection.getOutputStream());
    wr.write(thepostbody);
    wr.flush();
    wr.close();

    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if (responseCode != 200)
    {
      throw new RuntimeException(
              "Response code was not 200. Detected response was "
                      + responseCode);
    }

    BufferedReader reader = null;
    reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
    FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
    return fp;
  }

}