/*
* 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.
     *
     * @param MsaWSName DOCUMENT ME!
     * @param altitle DOCUMENT ME!
     * @param msa DOCUMENT ME!
     * @param submitGaps DOCUMENT ME!
     * @param preserveOrder DOCUMENT ME!
     */
    public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,
        boolean submitGaps, boolean preserveOrder)
    {
        if (setWebService(MsaWSName) == false)
        {
            JOptionPane.showMessageDialog(Desktop.desktop,
                "The Multiple Sequence Alignment Service named " + MsaWSName +
                " is unknown", "Internal Jalview Error",
                JOptionPane.WARNING_MESSAGE);

            return;
        }

        wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,
                WebServiceReference);

        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);
        wsInfo.setthisService(musclethread);
        musclethread.start();
    }

    // JBPNote Nasty object-global state setting methods shouldn't be allowed
    private boolean setWebService(String MsaWSName)
    {
        if (MsaWServices.info.containsKey(MsaWSName))
        {
            WebServiceName = MsaWSName;

            String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
            WsURL = wsinfo[0];
            WebServiceJobTitle = wsinfo[1];
            WebServiceReference = wsinfo[2];

            return true;
        }
        else
        {
            return false;
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    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(wsInfo.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; // and always store and recover sequence order
        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;

        MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
            boolean presorder)
        {
            alTitle = title;
            submitGaps = subgaps;
            preserveOrder = presorder;

            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"));
                    }

                    if (result.isRunning())
                    {
                        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
                    }
                    else if (result.isQueued())
                    {
                        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
                    }

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

                        if (!(result.isJobFailed() || result.isServerError()))
                        {
                            Thread.sleep(5000);

                            //  System.out.println("I'm alive "+seqid+" "+jobid);
                        }
                        else
                        {
                            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)
                    {
                    }
                }
            }

            if (allowedServerExceptions == 0)
            {
                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
            }
            else
            {
                if (!((result != null) &&
                        (result.isJobFailed() || result.isServerError())))
                {
                    wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
                }
                else
                {
                    if (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(wsInfo.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 void addFloatAnnotations(Alignment al, int[] gapmap,
            Vector values, String Symname, String Visname, float min,
            float max, int winLength)
        {
            Annotation[] annotations = new Annotation[al.getWidth()];

            for (int j = 0; j < values.size(); j++)
            {
                float value = Float.parseFloat(values.get(j).toString());
                annotations[gapmap[j]] = new Annotation("", value + "", ' ',
                        value);
            }

            al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
                    annotations, min, max, winLength));
        }

        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);

                    // 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();
            }
        }
    }
}