package jalview.ws.ebi;

import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileParse;

import java.io.File;
import java.io.IOException;
import java.util.regex.Matcher;

import org.apache.axis.transport.http.HTTPConstants;
import org.apache.http.Header;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.util.EntityUtils;
import org.json.JSONArray;
import org.json.JSONObject;

import compbio.util.FileUtil;

public class hmmerClient
{
  /**
   * URLs for ebi api
   */
  static String baseUrl = "http://www.ebi.ac.uk/Tools/hmmer",
          jackH = "/search/jackhmmer", phmmer = "/search/phmmer",
          hmmscan = "/search/hmmscan", hmmsearch = "/search/hmmsearch";

  static String edseq = ">2abl_A mol:protein length:163  ABL TYROSINE KINASE\nMGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHS\nWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAE\nLVHHHSTVADGLITTLHYPAP";

  public static void main(String[] args)
  {
    String instr = edseq;
    if (args.length > 0)
    {
      try
      {
        instr = FileUtil.readFileToString(new File(args[0]));
      } catch (Exception f)
      {
        f.printStackTrace();
        return;
      }
    }
    String res = new hmmerClient().submitJackhmmerSearch(instr,
            "jackhmmer", "pdb", 5);
    if (res == null)
    {
      throw new Error("Failed.");
    }
    System.out.println("Result\n" + res);
    return;
  }

  /**
   * 
   * @param input
   *          - fasta or other formatted sequence or alignment
   * @param algo
   *          - jackhmmer
   * @param db
   *          - pdb, uniprot, etc.
   * @param niter
   *          number of iterations
   * @return job id
   */
  String submitJackhmmerSearch(String input, String algo, String db,
          int niter)
  {
    JSONObject inparam = new JSONObject();
    HttpPost jackhp = new HttpPost(baseUrl + jackH);
    String lastiter = null;
    try
    {
      inparam.put("algo", algo);
      inparam.put("seq", input);
      inparam.put("seqdb", db);
      inparam.put("iterations", niter);
      // #Now POST the request and generate the search job.
      // dumb json post service
      jackhp.setHeader("content-type", "application/json");
      jackhp.setEntity(new StringEntity(inparam.toString()));
    } catch (Exception f)
    {
      f.printStackTrace();
      return null;
    }
    HttpResponse r = null;
    try
    {
      DefaultHttpClient httpCl = new DefaultHttpClient();

      r = httpCl.execute(jackhp);

    } catch (Exception x)
    {
      System.err.println("Submit failed.");
      x.printStackTrace();
    }
    if (r.getStatusLine().getStatusCode() != 201)
    {
      throw new Error(r.toString());
    }
    // get uid for job
    String jobid = null, redir = null;
    try
    {
      JSONObject res = new JSONObject(EntityUtils.toString(r.getEntity()));
      jobid = res.getString("job_id");

      Header[] loc;
      if ((loc = r.getHeaders(HTTPConstants.HEADER_LOCATION)) != null
              && loc.length > 0)
      {
        if (loc.length > 1)
        {
          System.err
                  .println("Ignoring additional "
                          + (loc.length - 1)
                          + " location(s) provided in response header ( next one is '"
                          + loc[1].getValue() + "' )");
        }
        redir = loc[0].getValue();
      }
    } catch (Exception x)
    {
      System.err.println("job id extraction failed.");
      x.printStackTrace();
    }
    int tries = 0;
    boolean finished = false;
    JSONObject jobstate = null;
    do
    {
      try
      {
        DefaultHttpClient httpCl = new DefaultHttpClient();

        HttpGet jackcheck = new HttpGet(redir);
        jackcheck.setHeader("content-type", "application/json");
        r = httpCl.execute(jackcheck);
        switch (r.getStatusLine().getStatusCode())
        {
        case 200:
          jobstate = new JSONObject(EntityUtils.toString(r.getEntity()));
          String st = jobstate.getString("status");
          if ("DONE".equals(st))
          {
            finished = true;
          }
          if ("ERROR".equals(st))
          {
            System.err.println("Error");
            finished = true;
          }
          if ("PEND".equals(st) || "RUN".equals("st"))
          {
            JSONArray iters = jobstate.getJSONArray("result");
            lastiter = iters.getJSONObject(iters.length() - 1).getString(
                    "uuid");
            if (lastiter.length() > 0)
            {
              java.util.regex.Pattern p = java.util.regex.Pattern
                      .compile(".+(\\d+)");
              Matcher m = p.matcher(lastiter);
              if (m.matches())
              {
                System.out.println("On iteration " + m.group(1));
              }
            }
          }
          break;

        default:
          tries++;
          Thread.sleep(2000);
        }
      } catch (Exception q)
      {
        q.printStackTrace();
        return null;
      }
    } while (!finished && tries < 50);

    if (!finished)
    {
      System.err.println("Giving up with job " + jobid + " at " + redir);
      return null;
    }
    // get results
    // http://www.ebi.ac.uk/Tools/hmmer/download/60048B38-7CEC-11E5-A230-CED6D26C98AD.5/score?format=csv
    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
    // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
    // 2 1cj1_J 1gri_B
    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
    // PROTEIN 2 1cj1_J 1gri_B
    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
    // phosphatase non-receptor typ 4h1o_A
    //
    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 2 2 7.6e-31 3.7e-28
    // 102.219146728516 0.03 66 161 127 236 124 238 0.94 Tyrosine-protein
    // phosphatase non-receptor typ 4h1o_A
    //
    // $ua->get( $rootUrl."/results/".$lastIteration->{uuid} . "/score"
    return lastiter;
    /*
     * * #Job should have finished, but we may have converged, so get the last
     * job. my $results = $json->decode( $response->content ); my $lastIteration
     * = pop( @{ $results->{result} } ); #Now fetch the results of the last
     * iteration my $searchResult = $ua->get( $rootUrl."/results/" .
     * $lastIteration->{uuid} . "/score", 'Accept' => 'application/json' );
     * unless( $searchResult->status_line eq "200 OK"){ die
     * "Failed to get search results\n"; }
     * 
     * #Decode the content of the full set of results $results = $json->decode(
     * $searchResult->content ); print
     * "Matched ".$results->{'results'}->{'stats'}->{'nincluded'}." sequences
     * ($lastIteration->{uuid})!\n"; #Now do something more interesting with the
     * results......
     */
  }

  /**
   * retrieve an alignment annotated with scores from JackHmmer
   * 
   * @param jobid
   * @param dataset
   * @return
   */
  AlignmentI retrieveJackhmmerResult(String jobid, AlignmentI dataset)
          throws OutOfMemoryError, IOException
  {
    AlignmentI searchResult = null;

    // get results

    searchResult = new AppletFormatAdapter().readFile(baseUrl
            + "/download/" + jobid + "/score?format=afa&t=.gz",
            DataSourceType.URL, FileFormat.Fasta);

    // TODO extract gapped columns as '.' - inserts to query profile

    // TODO match up jackhammer results to dataset.

    // do scores
    FileParse jsonsource = new FileParse(baseUrl + "/download/" + jobid
            + "/score?format=json", DataSourceType.URL);
    if (!jsonsource.isValid())
    {
      throw new IOException("Couldn't access scores for Jackhammer results");
    }
    readJackhmmerScores(searchResult, jsonsource);
    return searchResult;
  }

  /**
   * // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
   * 
   * // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND
   * PROTEIN // 2 1cj1_J 1gri_B // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62
   * 212.4 0.1 2 2 1.6e-17 7.9e-15 // 58.8796501159668 0.01 7 66 157 215 153 216
   * 0.95 GROWTH FACTOR BOUND // PROTEIN 2 1cj1_J 1gri_B // 4h1o_A 4h1o_A 560
   * jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25 // 92.4921493530273
   * 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein // phosphatase non-receptor
   * typ 4h1o_A
   */
  private static String[] _hmmsearchcols = new String[] { "acc", "name", "" };

  private void readJackhmmerScores(AlignmentI searchResult,
          FileParse jsonsource) throws IOException, OutOfMemoryError
  {
    HmmerJSONProcessor hjp = new HmmerJSONProcessor(searchResult);
    hjp.parseFrom(jsonsource);

    // http://www.ebi.ac.uk/Tools/hmmer/download/60048B38-7CEC-11E5-A230-CED6D26C98AD.5/score?format=csv
    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
    // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
    // 2 1cj1_J 1gri_B
    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
    // PROTEIN 2 1cj1_J 1gri_B
    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
    // phosphatase non-receptor typ 4h1o_A
    // each line scores a fragment
    // so for a combined score ?

    /**
     * for a sequence q sort any t against q according to overallScore(q,t)
     * maxFragment(q,t) in sequence features parlance: for alignment
     * s.getFeature("overallScore",q) -> range on q and range on s
     * 
     * 
     */

    // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
    // 2 1cj1_J 1gri_B
    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
    // PROTEIN 2 1cj1_J 1gri_B
    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
    // phosphatase non-receptor typ 4h1o_A
    //
    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 2 2 7.6e-31 3.7e-28
    // 102.219146728516 0.03 66 161 127 236 124 238 0.94 Tyrosine-protein
    // phosphatase non-receptor typ 4h1o_A

  }

}