From 486e70a70e56b8ac23fd191c2ac9f8c7366f4fd7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 1 Apr 2010 14:19:25 +0000
Subject: [PATCH] refactored copy of groupURL mechanism into new Envision
 service discovery class.

---
 src/jalview/gui/AlignFrame.java          |   12 +-
 src/jalview/gui/IdPanel.java             |    2 +-
 src/jalview/gui/Preferences.java         |   10 +-
 src/jalview/ws/EnfinEnvision2OneWay.java |  462 ++++++++++++++++++++++++++++++
 4 files changed, 482 insertions(+), 4 deletions(-)
 create mode 100644 src/jalview/ws/EnfinEnvision2OneWay.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1bccb66..5529f2c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3778,9 +3778,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   .getServiceClient(sh);
           impl.attachWSMenuEntry(seqsrchmenu, this);
         }
-        // finally, add the whole shebang onto the webservices menu
         wsmenu.add(seqsrchmenu);
       }
+      // finally, add the whole shebang onto the webservices menu
       resetWebServiceMenu();
       for (int i = 0, j = wsmenu.size(); i < j; i++)
       {
@@ -3803,6 +3803,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     webService.removeAll();
     build_fetchdbmenu(webService);
+    build_urlServiceMenu(webService);
+  }
+
+  /**
+   * construct any groupURL type service menu entries.
+   * @param webService
+   */
+  private void build_urlServiceMenu(JMenu webService)
+  {
+    jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(webService, this);
   }
 
   /*
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 52ac6ad..6330926 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -330,7 +330,7 @@ public class IdPanel extends JPanel implements MouseListener,
       
       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
               sq,
-              nlinks, new Vector(Preferences.groupURLLinks));
+              nlinks, new Vector(Preferences.getGroupURLLinks()));
       pop.show(this, e.getX(), e.getY());
 
       return;
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6273fbc..88f438e 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -29,6 +29,7 @@ import jalview.bin.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
+import jalview.ws.EnfinEnvision2OneWay;
 
 /**
  * DOCUMENT ME!
@@ -84,8 +85,8 @@ public class Preferences extends GPreferences
      */
     
     groupURLLinks = new Vector();
-    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|,");
+    //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|,");
     
   }
 
@@ -593,4 +594,9 @@ public class Preferences extends GPreferences
   private void jbInit() throws Exception
   {
   }
+
+  public static Collection getGroupURLLinks()
+  {
+    return groupURLLinks;
+  }
 }
diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
new file mode 100644
index 0000000..8e596b7
--- /dev/null
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -0,0 +1,462 @@
+/**
+ * 
+ */
+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;
+          }
+        }
+     });
+    
+    
+  }
+
+}
-- 
1.7.10.2