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.MalformedURLException;
import java.net.URL;
import java.util.List;

import javax.ws.rs.HttpMethod;

import com.stevesoft.pat.Regex;

/**
 * Base class for Ensembl REST service clients
 * 
 * @author gmcarstairs
 */
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
  private final static String ENSEMBL_REST = "http://rest.ensembl.org";

  protected final static String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";

  // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
  private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";

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

  private static final Regex TRANSCRIPT_REGEX = new Regex(
            "(ENS)([A-Z]{3}|)T[0-9]{11}$");

  private static final Regex GENE_REGEX = new Regex(
            "(ENS)([A-Z]{3}|)G[0-9]{11}$");

  private String domain = ENSEMBL_REST;

  private static boolean ensemblRestAvailable = false;

  private static long lastCheck = -1;

  /*
   * absolute time to wait till if we overloaded the REST service
   */
  private static long retryAfter;

  protected volatile boolean inProgress = false;

  /**
   * Default constructor to use rest.ensembl.org
   */
  public EnsemblRestClient()
  {
    this(ENSEMBL_REST);
  }

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

  String getDomain()
  {
    return domain;
  }

  void setDomain(String d)
  {
    domain = d;
  }

  public boolean isTranscriptIdentifier(String query)
  {
    return query == null ? false : TRANSCRIPT_REGEX.search(query);
  }

  public boolean isGeneIdentifier(String query)
  {
    return query == null ? false : GENE_REGEX.search(query);
  }

  @Override
  public boolean queryInProgress()
  {
    return inProgress;
  }

  @Override
  public StringBuffer getRawRecords()
  {
    return null;
  }

  /**
   * Returns the URL for the client http request
   * 
   * @param ids
   * @return
   * @throws MalformedURLException
   */
  protected abstract URL getUrl(List<String> ids)
          throws MalformedURLException;

  /**
   * Returns true if client uses GET method, false if it uses POST
   * 
   * @return
   */
  protected abstract boolean useGetRequest();

  /**
   * Return the desired value for the Content-Type request header
   * 
   * @param multipleIds
   * 
   * @return
   * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
   */
  protected abstract String getRequestMimeType(boolean multipleIds);

  /**
   * Return the desired value for the Accept request header
   * 
   * @return
   * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
   */
  protected abstract String getResponseMimeType();

  /**
   * Tries to connect to Ensembl's REST 'ping' endpoint, and returns true if
   * successful, else false
   * 
   * @return
   */
  private boolean checkEnsembl()
  {
    try
    {
      // note this format works for both ensembl and ensemblgenomes
      // info/ping.json works for ensembl only (March 2016)
      URL ping = new URL(getDomain()
              + "/info/ping?content-type=application/json");
      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;
  }

  /**
   * returns a reader to a Fasta response from the Ensembl sequence endpoint
   * 
   * @param ids
   * @return
   * @throws IOException
   */
  protected FileParse getSequenceReader(List<String> ids)
          throws IOException
  {
    URL url = getUrl(ids);
  
    BufferedReader reader = getHttpResponse(url, ids);
    FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
    return fp;
  }

  /**
   * Writes the HTTP request and gets the response as a reader.
   * 
   * @param url
   * @param ids
   *          written as Json POST body if more than one
   * @return
   * @throws IOException
   *           if response code was not 200, or other I/O error
   */
  protected BufferedReader getHttpResponse(URL url, List<String> ids)
          throws IOException
  {
    // long now = System.currentTimeMillis();
    HttpURLConnection connection = (HttpURLConnection) url.openConnection();
  
    /*
     * POST method allows multiple queries in one request; it is supported for
     * sequence queries, but not for overlap
     */
    boolean multipleIds = ids.size() > 1;// useGetRequest();
    connection.setRequestMethod(multipleIds ? HttpMethod.POST
            : HttpMethod.GET);
    connection.setRequestProperty("Content-Type",
            getRequestMimeType(multipleIds));
    connection.setRequestProperty("Accept", getResponseMimeType());

    connection.setUseCaches(false);
    connection.setDoInput(true);
    connection.setDoOutput(multipleIds);

    if (multipleIds)
    {
      writePostBody(connection, ids);
    }
  
    InputStream response = connection.getInputStream();
    int responseCode = connection.getResponseCode();
  
    if (responseCode != 200)
    {
      /*
       * note: a GET request for an invalid id returns an error code e.g. 415
       * but POST request returns 200 and an empty Fasta response 
       */
      throw new IOException(
              "Response code was not 200. Detected response was "
                      + responseCode);
    }
    // System.out.println(getClass().getName() + " took "
    // + (System.currentTimeMillis() - now) + "ms to fetch");

    checkRateLimits(connection);
  
    BufferedReader reader = null;
    reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
    return reader;
  }

  /**
   * Inspect response headers for any sign of server overload and respect any
   * 'retry-after' directive
   * 
   * @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
   * @param connection
   */
  void checkRateLimits(HttpURLConnection connection)
  {
    // number of requests allowed per time interval:
    String limit = connection.getHeaderField("X-RateLimit-Limit");
    // length of quota time interval in seconds:
    // String period = connection.getHeaderField("X-RateLimit-Period");
    // seconds remaining until usage quota is reset:
    String reset = connection.getHeaderField("X-RateLimit-Reset");
    // number of requests remaining from quota for current period:
    String remaining = connection.getHeaderField("X-RateLimit-Remaining");
    // number of seconds to wait before retrying (if remaining == 0)
    String retryDelay = connection.getHeaderField("Retry-After");

    // to test:
    // retryDelay = "5";

    if (retryDelay != null)
    {
      System.err.println("Ensembl REST service rate limit exceeded, wait "
              + retryDelay + " seconds before retrying");
      try
      {
        retryAfter = System.currentTimeMillis()
                + (1000 * Integer.valueOf(retryDelay));
      } catch (NumberFormatException e)
      {
        System.err.println("Unexpected value for Retry-After: "
                + retryDelay);
      }
    }
    else
    {
      retryAfter = 0;
      // debug:
      // System.out.println(String.format(
      // "%s Ensembl requests remaining of %s (reset in %ss)",
      // remaining, limit, reset));
    }
  }
  /**
   * 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
   */
  protected boolean isEnsemblAvailable()
  {
    long now = System.currentTimeMillis();

    /*
     * check if we are waiting for 'Retry-After' to expire
     */
    if (retryAfter > now)
    {
      System.err.println("Still " + (1 + (retryAfter - now) / 1000)
              + " secs to wait before retrying Ensembl");
      return false;
    }
    else
    {
      retryAfter = 0;
    }

    boolean retest = now - lastCheck > RETEST_INTERVAL;
    if (ensemblRestAvailable && !retest)
    {
      return true;
    }
    ensemblRestAvailable = checkEnsembl();
    lastCheck = now;
    return ensemblRestAvailable;
  }

  /**
   * Constructs, writes and flushes the POST body of the request, containing the
   * query ids in JSON format
   * 
   * @param connection
   * @param ids
   * @throws IOException
   */
  protected void writePostBody(HttpURLConnection connection,
          List<String> ids) throws IOException
  {
    boolean first;
    StringBuilder postBody = new StringBuilder(64);
    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("]}");
    byte[] thepostbody = postBody.toString().getBytes();
    connection.setRequestProperty("Content-Length",
            Integer.toString(thepostbody.length));
    DataOutputStream wr = new DataOutputStream(connection.getOutputStream());
    wr.write(thepostbody);
    wr.flush();
    wr.close();
  }

}