/**
 * 
 */
package jalview.ws;

import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.util.GroupUrlLink;

import java.awt.Cursor;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.Hashtable;
import java.util.Vector;

import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;

import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;

/**
 * Lightweight runnable to discover dynamic 'one way' group URL services
 * @author JimP
 *
 */
public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSMenuEntryProviderI 
{
  private static EnfinEnvision2OneWay groupURLLinksGatherer=null;
  public static EnfinEnvision2OneWay getInstance() {
    if (groupURLLinksGatherer==null) {
      groupURLLinksGatherer = new EnfinEnvision2OneWay();
    }
    return groupURLLinksGatherer;
  }
  private void waitForCompletion() {
    if (groupURLLinksGatherer.isRunning())
    {
    // wait around and show a visual delay indicator  
    Cursor oldCursor = Desktop.instance.getCursor();
    Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
    while (groupURLLinksGatherer.isRunning())
    {
      try {
        Thread.sleep(100);
      } catch (InterruptedException e ){};
    }
    Desktop.instance.setCursor(oldCursor);
    } 
  }
  public Vector getEnvisionServiceGroupURLS() {
    waitForCompletion();
    return groupURLLinks;
  }
  /**
   * indicate if 
   */
  private static String BACKGROUND="BACKGROUNDPARAM";
  /**
   * contains null strings or one of the above constants - indicate if this URL is a special case.
   */
  private Vector additionalPar = new Vector();
  /**
   * the enfin service URL
   */
  private String enfinService=null;
  private String description=null;
  private String wfname;
  /* (non-Javadoc)
   * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String, java.lang.String)
   */
  public void endElement(String uri, String localName, String qName)
          throws SAXException
  {
    
//  System.err.println("End element: : '"+uri+" "+localName+" "+qName);
    if (qName.equalsIgnoreCase("workflow") && description!=null && description.length()>0)
    {
      //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
      //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
      System.err.println("Adding entry for "+wfname+" "+description);
      if (wfname.toLowerCase().indexOf("funcnet")==-1)
      {
        groupURLdescr.addElement(description);
        groupURLdescr.addElement(description);
        groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
        groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
      }
    }
  }

  /* (non-Javadoc)
   * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
   */
  public void characters(char[] ch, int start, int length)
          throws SAXException
  {
    if (description!=null) {
      for (int i=start; i<start+length; i++) {
      description+=ch[i];
      }
    }
  }

  /* (non-Javadoc)
   * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
   */
  public void startElement(String uri, String localName, String qName,
          Attributes attributes) throws SAXException
  {
    if (qName.equalsIgnoreCase("workflow"))
    {
      description = null;
      wfname = attributes.getValue("name");
    }
    if (qName.equalsIgnoreCase("description"))
    {
      description = "";
    } 
    
    
    //System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
    // super.startElement(uri,localName,qname,attributes);
  }

  private boolean started=false;
  private boolean running=false;
  private Vector groupURLLinks = null;
  private Vector groupURLdescr = null;
  
  public EnfinEnvision2OneWay() {
    groupURLLinks = new Vector();
    groupURLdescr = new Vector();
    
    enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE", "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
    new Thread(this).start();
  }

  public void run()
  {
    started = true;
    running = true;
    try {
      SAXParserFactory spf = SAXParserFactory.newInstance();
      SAXParser sp = spf.newSAXParser();
      sp.parse(new URL(enfinService).openStream(), this);      
    } catch (Exception e)
    {
      Cache.log.warn("Exception when discovering One Way services: ",e);      
    }
    catch (Error e)
    {
      Cache.log.warn("Error when discovering One Way services: ",e);
    }
    running = false;
    Cache.log.debug("Finished running.");
  }

  /**
   * have we finished running yet ?
   * @return false if we have been run.
   */
  public boolean isRunning()
  {
    
    // TODO Auto-generated method stub
    return !started || running;
  }
  public static void main(String[] args){
    Cache.initLogger();
    EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
    while (ow.isRunning())
    {
      try {
        Thread.sleep(50);
      } catch (Exception e){};
     
    }
    for (int i=0;i<ow.groupURLLinks.size();i++) {
      System.err.println("Description"+ow.groupURLdescr.elementAt(i)+"Service URL: "+ow.groupURLLinks.elementAt(i));
    }
  }
  /// Copied from jalview.gui.PopupMenu
  /**
   * add a late bound URL service item to the given menu
   * 
   * @param linkMenu
   * @param label -
   *                menu label string
   * @param urlgenerator GroupURLLink used to generate URL  
   * @param urlstub Object array returned from the makeUrlStubs function.
   */
  private void addshowLink(JMenu linkMenu, String label, String descr, final GroupUrlLink urlgenerator, final Object[] urlstub)
  {
    JMenuItem item = new JMenuItem(label);
    item.setToolTipText("Submit ("+urlgenerator.getNumberInvolved(urlstub)+" seqs) to workflow: "+descr);
    item.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        new Thread(new Runnable()
        {

          public void run()
          {
            showLink(urlgenerator.constructFrom(urlstub));
          }

        }).start();
      }
    });

    linkMenu.add(item);
  }

  /**
   * open the given link in a new browser window
   * @param url
   */
  public void showLink(String url)
  {
    try
    {
      jalview.util.BrowserLauncher.openURL(url);
    } catch (Exception ex)
    {
      JOptionPane
              .showInternalMessageDialog(
                      Desktop.desktop,
                      "Unixers: Couldn't find default web browser."
                              + "\nAdd the full path to your browser in Preferences.",
                      "Web browser not found", JOptionPane.WARNING_MESSAGE);

      ex.printStackTrace();
    }
  }
  /**
   * called by a web service menu instance when it is opened.
   * @param enfinServiceMenu
   * @param alignFrame
   */
  private void buildGroupLinkMenu(JMenu enfinServiceMenu,
          AlignFrame alignFrame)
  {
    SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
    SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
    if (sg==null) {
      // consider visible regions here/
    }
    enfinServiceMenu.removeAll();
    JMenu entries = buildGroupURLMenu(seqs,sg);
    if (entries!=null)
    {
      for (int i=0,iSize=entries.getMenuComponentCount();i<iSize;i++)
      {
        // transfer - menu component is removed from entries automatically
        enfinServiceMenu.add(entries.getMenuComponent(0));
      }
      // entries.removeAll();
      enfinServiceMenu.setEnabled(true);
    } else {
      enfinServiceMenu.setEnabled(false);
    }
  }

  /**
   * construct a dynamic enfin services menu given a sequence selection
   * @param seqs
   * @param sg
   * @param groupLinks
   * @return
   */
  private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
  {
    
    // TODO: usability: thread off the generation of group url content so root menu appears asap
    // sequence only URLs
    // ID/regex match URLs
    JMenu groupLinksMenu = new JMenu("Group Link");
    JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
    String[][] idandseqs = GroupUrlLink.formStrings(seqs);
    Hashtable commonDbrefs = new Hashtable();
    for (int sq = 0; sq<seqs.length;sq++) {

      int start,end;
      if (sg!=null) {
        start = seqs[sq].findPosition(sg.getStartRes());
        end=seqs[sq].findPosition(sg.getEndRes()); 
      } else {
        // get total width of alignment.
        start = seqs[sq].getStart();
        end = seqs[sq].findPosition(seqs[sq].getLength());
      }
      // we skip sequences which do not have any non-gaps in the region of interest
      if (start>end)
      {
        continue;
      }
      // just collect ids from dataset sequence
      // TODO: check if IDs collected from selecton group intersects with the current selection, too
      SequenceI sqi = seqs[sq];
      while (sqi.getDatasetSequence()!=null) {
        sqi = sqi.getDatasetSequence(); }
      DBRefEntry[] dbr = sqi.getDBRef();
      if (dbr!=null && dbr.length>0)
      {
        for (int d=0;d<dbr.length;d++)
        {
          String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
          Object[] sarray = (Object[]) commonDbrefs.get(src);
          if (sarray==null)
          {
            sarray = new Object[2];
            sarray[0] = new int[] { 0 };
            sarray[1] = new String[seqs.length];
            
            commonDbrefs.put(src,sarray);
          }
          
          if (((String[])sarray[1])[sq]==null) {
            if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
              ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
              ((int[])sarray[0])[0]++;
            }
          }
        }
      }
    }
    // now create group links for all distinct ID/sequence sets.
    boolean addMenu = false; // indicates if there are any group links to give to user  
    for (int i = 0; i < groupURLLinks.size(); i++) {
        String link = groupURLLinks.elementAt(i).toString();
        String descr = groupURLdescr.elementAt(i).toString();
//        boolean specialCase = additionalPar.elementAt(i).toString().equals(BACKGROUND);
        GroupUrlLink urlLink = null;
        try
        {
          urlLink = new GroupUrlLink(link);
        } catch (Exception foo)
        {
          jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
                  + "'", foo);
          continue;
        }
        ;
        if (!urlLink.isValid())
        {
          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
          continue;
        }
        final String label = urlLink.getLabel();
        boolean usingNames = false;
        // Now see which parts of the group apply for this URL
        String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
        Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
        String[] seqstr,ids; // input to makeUrl
        if (idset!=null)
        {
          int numinput = ((int[])idset[0])[0];
          String[] allids = ((String[])idset[1]);
          seqstr = new String[numinput];
          ids = new String[numinput];
          for (int sq=0,idcount=0;sq<seqs.length;sq++)
          {
            if (allids[sq]!=null) {
              ids[idcount] = allids[sq];
              seqstr[idcount++] = idandseqs[1][sq];
            }
          }
        } else {
          // just use the id/seq set
          seqstr = idandseqs[1];
          ids = idandseqs[0];
          usingNames=true;
        }
        // and try and make the groupURL!
        
        Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
        if (urlset!=null)
        {
          int type = urlLink.getGroupURLType() & 3;
          //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
          // first two bits ofurlLink type bitfield are sequenceids and sequences
          // TODO: FUTURE: ensure the groupURL menu structure can be generalised
          addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
          addMenu = true;
        }
      }
    if (addMenu)
    {
      groupLinksMenu = new JMenu("Group Links");
      for (int m=0;m<linkMenus.length; m++)
      {
        if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
        {
          groupLinksMenu.add(linkMenus[m]);
        }
      }
      
      return groupLinksMenu;
    }
    return null;
  }

  /// end of stuff copied from popupmenu
  public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame)
  {
    final JMenu enfinServiceMenu = new JMenu("Envision 2");
    wsmenu.add(enfinServiceMenu);
    enfinServiceMenu.setEnabled(false);
    wsmenu.addMenuListener(new MenuListener()
      {
        // this listener remembers when the menu was first selected, and
        // doesn't rebuild the session list until it has been cleared and
        // reselected again.
        boolean refresh = true;

        public void menuCanceled(MenuEvent e)
        {
          refresh = true;
        }

        public void menuDeselected(MenuEvent e)
        {
          refresh = true;
        }

        public void menuSelected(MenuEvent e)
        {
          if (refresh)
          {
            try {
              buildGroupLinkMenu(enfinServiceMenu,alignFrame);
            } catch (OutOfMemoryError ex)
            {
              Cache.log.error("Out of memory when calculating the Envision2 links.",ex);
              enfinServiceMenu.setEnabled(false);
            }
            refresh = false;
          }
        }
     });
    
    
  }

}