/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.ws;

import ext.vamsas.*;

import jalview.analysis.AlignSeq;

import jalview.datamodel.*;

import jalview.gui.*;

import java.util.*;

import javax.swing.*;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class MsaWSClient
    extends WSClient
{
  /**
   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
   */
  ext.vamsas.MuscleWS server;


  /**
   * Creates a new MsaWSClient object that uses a service
   * given by an externally retrieved ServiceHandle
   *
   * @param sh service handle of type AbstractName(MsaWS)
   * @param altitle DOCUMENT ME!
   * @param msa DOCUMENT ME!
   * @param submitGaps DOCUMENT ME!
   * @param preserveOrder DOCUMENT ME!
   */

  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,
                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
  {

    if (!sh.getAbstractName().equals("MsaWS"))
    {
      JOptionPane.showMessageDialog(Desktop.desktop,
                                    "The Service called \n" + sh.getName() +
          "\nis not a \nMultiple Sequence Alignment Service !",
                                    "Internal Jalview Error",
                                    JOptionPane.WARNING_MESSAGE);

      return;
    }

    if ((wsInfo = this.setWebService(sh))==null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
                                     "The Multiple Sequence Alignment Service named " +
                                     sh.getName() +
                                     " is unknown", "Internal Jalview Error",
                                     JOptionPane.WARNING_MESSAGE);

       return;
     }
    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);

  }


  private void startMsaWSClient(String altitle, SequenceI[] msa,
                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
  {
    if (!locateWebService())
    {
      return;
    }

    wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
                           " of " + altitle + "\nJob details\n");

    MsaWSThread musclethread = new MsaWSThread(WebServiceName +
                                               " alignment of " + altitle, msa,
                                               submitGaps, preserveOrder, seqdataset);
    wsInfo.setthisService(musclethread);
    musclethread.start();
  }

  /**
   * Initializes the server field with a valid service implementation.
   *
   * @return true if service was located.
   */
  private boolean locateWebService()
  {
    // TODO: MuscleWS transmuted to generic MsaWS client
    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default

    try
    {
      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
      ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
    }
    catch (Exception ex)
    {
      wsInfo.setProgressText("Serious! " + WebServiceName +
                             " Service location failed\nfor URL :" + WsURL +
                             "\n" +
                             ex.getMessage());
      wsInfo.setStatus(WebserviceInfo.ERROR);
      ex.printStackTrace();

      return false;
    }

    loc.getEngine().setOption("axis", "1");

    return true;
  }

  protected class MsaWSThread
      extends Thread implements WSClientI
  {
    String ServiceName = WebServiceName;
    String OutputHeader;
    vamsas.objects.simple.MsaResult result = null;
    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
        SequenceSet();
    Hashtable SeqNames = null;
    boolean submitGaps = false; // pass sequences including gaps to alignment service
    boolean preserveOrder = true; // and always store and recover sequence order
    String jobId;
    String alTitle; // name which will be used to form new alignment window.
    int allowedServerExceptions = 3; // thread dies if too many exceptions.
    boolean jobComplete = false;

    Alignment dataset; // dataset to which the new alignment will be associated.

    MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
                boolean presorder, Alignment seqset)
    {
      alTitle = title;
      submitGaps = subgaps;
      preserveOrder = presorder;
      dataset = seqset;
      OutputHeader = wsInfo.getProgressText();
      SeqNames = new Hashtable();

      vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
          Sequence[msa.length];

      for (int i = 0; i < msa.length; i++)
      {
        String newname = jalview.analysis.SeqsetUtils.unique_name(i);

        // uniquify as we go
        // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
        SeqNames.put(newname,
                     jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
        seqarray[i] = new vamsas.objects.simple.Sequence();
        seqarray[i].setId(newname);
        seqarray[i].setSeq( (submitGaps) ? msa[i].getSequence()
                           : AlignSeq.extractGaps(
                               jalview.util.Comparison.GapChars,
                               msa[i].getSequence()));
      }

      this.seqs = new vamsas.objects.simple.SequenceSet();
      this.seqs.setSeqs(seqarray);
    }

    public boolean isCancellable()
    {
      return true;
    }

    public void cancelJob()
    {
      if ( (jobId != null) && !jobId.equals("") && !jobComplete)
      {
        String cancelledMessage = "";

        try
        {
          vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);

          if (cancelledJob.getStatus() == 2)
          {
            // CANCELLED_JOB
            cancelledMessage = "Job cancelled.";
            wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
            jobComplete = true;
            jobsRunning--;
            result = null;
          }
          else if (cancelledJob.getStatus() == 3)
          {
            // VALID UNSTOPPABLE JOB
            cancelledMessage +=
                "Server cannot cancel this job. just close the window.\n";
          }

          if (cancelledJob.getJobId() != null)
          {
            cancelledMessage += ("[" + cancelledJob.getJobId() +
                                 "]");
          }

          cancelledMessage += "\n";
        }
        catch (Exception exc)
        {
          cancelledMessage +=
              ("\nProblems cancelling the job : Exception received...\n" +
               exc + "\n");
          exc.printStackTrace();
        }

        wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
      }
      else
      {
        if (!jobComplete)
        {
          wsInfo.setProgressText(OutputHeader +
                                 "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
        }
      }
    }

    public void run()
    {
      StartJob();

      while (!jobComplete && (allowedServerExceptions > 0))
      {
        try
        {
          if ( (result = server.getResult(jobId)) == null)
          {
            throw (new Exception(
                "Timed out when communicating with server\nTry again later.\n"));
          }
          jalview.bin.Cache.log.debug("Result state " + result.getState() +
                                        "(ServerError=" + result.isServerError() +
                                        ")");
          if (result.isRunning())
          {
            wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
          }
          else if (result.isQueued())
          {
            wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
          }

          if (result.isFinished())
          {
            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
            parseResult();
            jobComplete = true;
            jobsRunning--;
          }
          else
          {
            if (result.getStatus() != null)
            {
              wsInfo.setProgressText(OutputHeader + "\n"+   result.getStatus());
            }
            if (result.isServerError())
            {
              jobComplete = true;
              jobsRunning--;

              break;
            }
            if (! (result.isJobFailed() || result.isServerError() ||
                   result.isBroken() || result.isFailed()))
            {
              Thread.sleep(5000);

              //  System.out.println("I'm alive "+seqid+" "+jobid);
            }
            else
            {
              jobComplete = true;
              jobsRunning--;
              break;
            }
          }
        }
        catch (Exception ex)
        {
          allowedServerExceptions--;
          wsInfo.appendProgressText("\n" + ServiceName +
                                    " Server exception!\n" + ex.getMessage());
          System.err.println(ServiceName + " Server exception: " +
                             ex.getMessage());

          //          ex.printStackTrace(); JBPNote Debug
          try
          {
            if (allowedServerExceptions > 0)
            {
              Thread.sleep(5000);
            }
          }
          catch (InterruptedException ex1)
          {
          }
        }
        catch(OutOfMemoryError er)
        {
          jobComplete = true;
          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
          JOptionPane.showInternalMessageDialog(Desktop.desktop,
              "Out of memory handling result!!"
             +"\nSee help files for increasing Java Virtual Machine memory."
             ,"Out of memory", JOptionPane.WARNING_MESSAGE );
          System.out.println("MsaWSClient: "+er);
          System.gc();
        }
      }

      if (allowedServerExceptions == 0)
      {
        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
      }
      else
      {
        if (result != null)
        {
          if ( !(result.isJobFailed() || result.isServerError()))
          {
            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
          }

          if (result.isBroken() || result.isFailed())
          {
            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
          }

          if (result.isServerError())
          {
            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
          }
        }
      }
    }

    void StartJob()
    {
      try
      {
        vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);

        if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
        {
          jobId = jobsubmit.getJobId();
          System.out.println(WsURL + " Job Id '" + jobId + "'");
        }
        else
        {
          if (jobsubmit == null)
          {
            throw new Exception("Server at " + WsURL +
                                " returned null object, it probably cannot be contacted. Try again later ?");
          }

          throw new Exception(jobsubmit.getJobId());
        }
      }
      catch (Exception e)
      {
        // TODO: JBPNote catch timeout or other fault types explicitly
        // For unexpected errors
        System.err.println(WebServiceName +
                           "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +
                           "When contacting Server:" + WsURL + "\n" +
                           e.toString() +
                           "\n");
        this.allowedServerExceptions = 0;
        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
        wsInfo.appendProgressText(
            "Failed to submit sequences for alignment.\n" +
            "It is most likely that there is a problem with the server.\n" +
            "Just close the window\n");

        // e.printStackTrace(); // TODO: JBPNote DEBUG
      }
    }

    private jalview.datamodel.Sequence[] getVamsasAlignment(
        vamsas.objects.simple.Alignment valign)
    {
      vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
      jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
          length];

      for (int i = 0, j = seqs.length; i < j; i++)
      {
        msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
                                                seqs[i].getSeq());
      }

      return msa;
    }

    void parseResult()
    {
      SequenceI[] seqs = null;

      try
      {
        // OutputHeader = output.getText();
        if (result.isFailed())
        {
          OutputHeader += "Job failed.\n";
        }

        if (result.getStatus() != null)
        {
          OutputHeader += ("\n" + result.getStatus());
        }

        if (result.getMsa() != null)
        {
          OutputHeader += "\nAlignment Object Method Notes\n";

          String[] lines = result.getMsa().getMethod();

          for (int line = 0; line < lines.length; line++)
          {
            OutputHeader += (lines[line] + "\n");
          }

          // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
          seqs = getVamsasAlignment(result.getMsa());
        }

        wsInfo.setProgressText(OutputHeader);

        if (seqs != null)
        {
          AlignmentOrder msaorder = new AlignmentOrder(seqs);

          if (preserveOrder)
          {
            jalview.analysis.AlignmentSorter.recoverOrder(seqs);
          }

          jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);

          Alignment al = new Alignment(seqs);
          if (dataset!=null) {
            al.setDataset(dataset);
          }
          // TODO: JBPNote Should also rename the query sequence sometime...
          AlignFrame af = new AlignFrame(al);
          af.addSortByOrderMenuItem(ServiceName + " Ordering",
                                    msaorder);

          Desktop.addInternalFrame(af, alTitle,
                                   AlignFrame.NEW_WINDOW_WIDTH,
                                   AlignFrame.NEW_WINDOW_HEIGHT);
        }
      }
      catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }
  }
}