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.Arrays;
import java.util.List;

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

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

  private static boolean ensemblRestavailable = false;

  private static long lastCheck = -1;

  public boolean isEnsemblAvailable()
  {
    if (isTesting || !ensemblRestavailable
            || System.currentTimeMillis() - lastCheck > 10000)
    {
      checkEnsembl();
      lastCheck = System.currentTimeMillis();
    }
    return ensemblRestavailable;
  }

  private boolean isTesting, testEnsemblStatus;

  /**
   * @return the isTesting
   */
  public boolean isTesting()
  {
    return isTesting;
  }

  /**
   * @param isTesting
   *          the isTesting to set
   */
  public void setTesting(boolean isTesting)
  {
    this.isTesting = isTesting;
  }

  /**
   * @return the testEnsemblStatus
   */
  public boolean isTestEnsemblStatus()
  {
    return testEnsemblStatus;
  }

  /**
   * @param testEnsemblStatus
   *          the testEnsemblStatus to set
   */
  public void setTestEnsemblStatus(boolean testEnsemblStatus)
  {
    this.testEnsemblStatus = testEnsemblStatus;
  }

  private void checkEnsembl()
  {
    if (isTesting)
    {
      ensemblRestavailable = testEnsemblStatus;
      return;
    }
    try
    {
      URL ping = new URL("http://" + ensemblRest + "/info/ping");
      HttpURLConnection conn = (HttpURLConnection) (ping.openConnection());
      if (conn.getResponseCode() >= 200 && conn.getResponseCode() < 300)
      {
        ensemblRestavailable = true;
        return;
      }
    } catch (Error err)
    {
      err.printStackTrace();
    } catch (Exception exx)
    {
      exx.printStackTrace();
    }
    ensemblRestavailable = false;
  }

  public SeqFetcher()
  {

    // TODO Auto-generated constructor stub
  }

  public enum EnsemblSeqType
  {
    GENOMIC, CDS, TRANSCRIPT, PROTEIN, CDNA;
  }

  /**
   * reolve request type as an argument for sequence and features queries
   * 
   * @param type
   */
  public List<NameValuePair> getObjectTypeArg(EnsemblSeqType type)
  {
    String arg;
    switch (type)
    {
    case CDS:
      arg = "cds";
      break;
    case TRANSCRIPT:
      arg = "cds";
      break;
    case CDNA:
      arg = "cdna";
      break;
    case PROTEIN:
      arg = "protein";
      break;
    case GENOMIC:
    default:
      arg = "genomic";
    }
    return Arrays.asList(new NameValuePair[]
    { new BasicNameValuePair("type", arg) });
  }

  /**
   * 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
  {

    // adapted From the rest.ensembl.org documentation for sequence_id

    String urls = "http://" + ensemblRest + "/sequence/id";
    List<NameValuePair> vals = getObjectTypeArg(returnType);
    boolean f = true;
    for (NameValuePair nvp : vals)
    {
      if (f)
      {
        f = false;
        urls += "?";
      }
      else
      {
        urls += "&";
      }
      urls += nvp.getName() + "=" + nvp.getValue();
    }

    URL url = new URL(urls);

    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\":[");
      boolean first = true;
      for (String id : ids)
      {
        if (first)
        {
          first = false;
        }
        else
        {
          postBody.append(",");
        }
        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;
  }

}