X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=c0addfe15af47c67839584f56e5d4558c7574cbe;hb=23a5ed32b702d4d3682b8cdc8fd8e3f238202f7d;hp=8cc39d741e8979ef8fedc19da761cc0da4c7b12a;hpb=43e280af80c060ad0bca76e5025ebabc38a52a21;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 8cc39d7..c0addfe 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,41 +17,32 @@
  */
 package jalview.ws.jws2;
 
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.io.Closeable;
-import java.net.ConnectException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
 
-import org.apache.log4j.Level;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JalviewChangeSupport;
-import jalview.ws.WSMenuEntryProviderI;
-import jalview.ws.params.ParamDatastoreI;
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.RunnerConfig;
-import compbio.ws.client.Jws2Client;
 import compbio.ws.client.Services;
 
 /**
@@ -93,6 +84,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   boolean running = false, aborted = false;
 
   /**
+   * @return the aborted
+   */
+  public boolean isAborted()
+  {
+    return aborted;
+  }
+
+  /**
    * @param aborted
    *          the aborted to set
    */
@@ -126,6 +125,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       Cache.log.debug("Old discovery thread has finished.");
     }
     running = true;
+    changeSupport.firePropertyChange("services", services, new Vector());
     oldthread = Thread.currentThread();
     try
     {
@@ -134,25 +134,50 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     } catch (ClassNotFoundException e)
     {
       System.err
-              .println("Not enabling Jalview Webservices version 2: client jar is not available."
+              .println("Not enabling JABA Webservices : client jar is not available."
                       + "\nPlease check that your webstart JNLP file is up to date!");
       running = false;
       return;
     }
+    // reinitialise records of good and bad service URLs
     if (services != null)
     {
       services.removeAllElements();
     }
+    if (urlsWithoutServices != null)
+    {
+      urlsWithoutServices.removeAllElements();
+    }
+    if (invalidServiceUrls != null)
+    {
+      invalidServiceUrls.removeAllElements();
+    }
+    if (validServiceUrls != null)
+    {
+      validServiceUrls.removeAllElements();
+    }
+    ArrayList<String> svctypes=new ArrayList<String>();
+
     List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
     for (final String jwsservers : getServiceUrls())
     {
       JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+      if (svctypes.size()==0)
+      {
+        // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services 
+        for (Services sv:squery.JABAWS2SERVERS)
+        {
+          svctypes.add(sv.toString());
+        }
+
+      }
       qrys.add(squery);
       new Thread(squery).start();
     }
-    boolean finished = false;
+    boolean finished = true;
     do
     {
+      finished=true;
       try
       {
         Thread.sleep(100);
@@ -162,7 +187,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       ;
       for (JabaWsServerQuery squery : qrys)
       {
-        finished |= !squery.isRunning();
+        finished = finished && !squery.isRunning();
       }
       if (aborted)
       {
@@ -174,12 +199,32 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         }
       }
     } while (!aborted && !finished);
-    oldthread = null;
-    running = false;
     if (!aborted)
     {
-      changeSupport.firePropertyChange("services", new Vector(), services);
+      // resort services according to order found in jabaws service list
+      // also ensure servics for each host are ordered in same way.
+      
+      if (services!=null && services.size()>0)
+      {
+        Jws2Instance[] svcs=new Jws2Instance[services.size()];
+        int[] spos=new int[services.size()];
+        int ipos=0;
+        Vector svcUrls = getServiceUrls();
+        for (Jws2Instance svc:services)
+        {
+          svcs[ipos]=svc;
+          spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType);
+        }
+        jalview.util.QuickSort.sort(spos, svcs);
+        services=new Vector<Jws2Instance>();
+        for (Jws2Instance svc:svcs) {
+          services.add(svc);
+        }
+      }
     }
+    oldthread = null;
+    running = false;
+    changeSupport.firePropertyChange("services", new Vector(), services);
   }
 
   /**
@@ -189,315 +234,291 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * @param srv
    * @param service2
    */
-  synchronized void addService(String jwsservers, Services srv,
-          MsaWS service2)
+  synchronized void addService(String jwsservers, Jws2Instance service)
   {
     if (services == null)
     {
       services = new Vector<Jws2Instance>();
     }
     System.out.println("Discovered service: " + jwsservers + " "
-            + srv.toString());
-    Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
-            service2);
+            + service.toString());
+//    Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+//            service2);
 
     services.add(service);
     // retrieve the presets and parameter set and cache now
     service.getParamStore().getPresets();
     service.hasParameters();
+    if (validServiceUrls==null)
+    {
+      validServiceUrls=new Vector();
+    }
+    validServiceUrls.add(jwsservers);
   }
 
-  public class Jws2Instance
+  /**
+   * holds list of services.
+   */
+  protected Vector<Jws2Instance> services;
+  /**
+   * attach all available web services to the appropriate submenu in the given JMenu
+   */
+  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
-    public String hosturl;
-
-    public String serviceType;
-
-    public MsaWS service;
-
-    public Jws2Instance(String hosturl, String serviceType, MsaWS service)
+    // dynamically regenerate service list.
+    populateWSMenuEntry(wsmenu, alignFrame, null);
+  }
+  private boolean isRecalculable(String action) {
+    return (action!=null && action.equalsIgnoreCase("conservation"));
+  }
+  private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+  {
+    if (running || services == null || services.size() == 0)
     {
-      super();
-      this.hosturl = hosturl;
-      this.serviceType = serviceType;
-      this.service = service;
+      return;
     }
-
-    PresetManager presets = null;
-
-    public JabaParamStore paramStore = null;
-
+    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+            .getDefault("WSMENU_BYTYPE", false);
     /**
-     * non thread safe - gets the presets for this service (blocks whilst it
-     * calls the service to get the preset set)
-     * 
-     * @return service presets or null if exceptions were raised.
+     * eventually, JWS2 services will appear under the same align/etc submenus.
+     * for moment we keep them separate.
      */
-    public PresetManager getPresets()
-    {
-      if (presets == null)
-      {
-        try
+    JMenu atpoint;
+    List<Jws2Instance> enumerableServices=new ArrayList<Jws2Instance>();
+    //jws2al.removeAll();
+    Map<String, Jws2Instance> preferredHosts=new HashMap<String,Jws2Instance>();
+    Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+    for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
+    {
+      if (!isRecalculable(service.action)) {
+        // add 'one shot' services to be displayed using the classic menu structure
+        enumerableServices.add(service);
+      } else {
+        if (!preferredHosts.containsKey(service.serviceType))
         {
-          presets = service.getPresets();
-        } catch (Exception ex)
+          Jws2Instance preferredInstance = getPreferredServiceFor(alignFrame,
+                  service.serviceType);
+          if (preferredInstance != null)
+          {
+            preferredHosts.put(service.serviceType, preferredInstance);
+          }
+          else
+          {
+            preferredHosts.put(service.serviceType, service);
+          }
+        }
+        List<Jws2Instance> ph=alternates.get(service.serviceType);
+        if (preferredHosts.get(service.serviceType)!=service)
         {
-          System.err
-                  .println("Exception when retrieving presets for service "
-                          + serviceType + " at " + hosturl);
+          if (ph==null)
+          {
+            ph=new ArrayList<Jws2Instance>();
+          }
+          ph.add(service);
+          alternates.put(service.serviceType, ph);
         }
       }
-      return presets;
-    }
-
-    public String getHost()
-    {
-      return hosturl;
-      /*
-       * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
-       * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
-       * serviceurl.getHost(); } catch (Exception e) {
-       * System.err.println("Failed to parse service URL '" + hosturl +
-       * "' as a valid URL!"); } return null;
-       */
-    }
-
-    /**
-     * @return short description of what the service will do
-     */
-    public String getActionText()
-    {
-      return "Align with " + serviceType;
-    }
 
-    /**
-     * non-thread safe - blocks whilst accessing service to get complete set of
-     * available options and parameters
-     * 
-     * @return
-     */
-    public RunnerConfig getRunnerConfig()
-    {
-      return service.getRunnerOptions();
     }
 
-    @Override
-    protected void finalize() throws Throwable
+    // create GUI element for classic services
+    addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+    // and the instantaneous services
+    for (final Jws2Instance service : preferredHosts.values())
     {
-      if (service != null)
-      {
-        try
-        {
-          Closeable svc = (Closeable) service;
-          service = null;
-          svc.close();
-        } catch (Exception e)
-        {
-        }
-        ;
+      atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+      JMenuItem hitm;
+      if (atpoint.getItemCount()>1) {
+        // previous service of this type already present
+        atpoint.addSeparator();
       }
-      super.finalize();
-    }
-
-    public ParamDatastoreI getParamStore()
-    {
-      if (paramStore == null)
+      atpoint.add(hitm = new JMenuItem(service.getHost()));
+      hitm.setForeground(Color.blue);
+      hitm.addActionListener(new ActionListener()
       {
-        try
-        {
-          paramStore = new JabaParamStore(this,
-                  (Desktop.instance != null ? Desktop
-                          .getUserParameterStore() : null));
-        } catch (Exception ex)
+
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
+          Desktop.showUrl(service.getHost());
         }
+      });
+      hitm.setToolTipText(JvSwingUtils
+              .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
 
-      }
-      return paramStore;
-    }
-
-    public String getUri()
-    {
-      // this is only valid for Jaba 1.0 - this formula might have to change!
-      return hosturl
-              + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/"
-                      : "") + serviceType;
-    }
-
-    private boolean hasParams = false, lookedForParams = false;
-
-    public boolean hasParameters()
-    {
-      if (!lookedForParams)
+      service.attachWSMenuEntry(atpoint, alignFrame);
+      if (alternates.containsKey(service.serviceType))
       {
-        lookedForParams = true;
-        try
-        {
-          hasParams = (getRunnerConfig().getArguments().size() > 0);
-        } catch (Exception e)
+        atpoint.add(hitm=new JMenu("Switch server"));
+        hitm.setToolTipText(JvSwingUtils.wrapTooltip("Choose a server for running this service"));
+        for (final Jws2Instance sv:alternates.get(service.serviceType))
         {
+          JMenuItem itm;
+          hitm.add(itm=new JMenuItem(sv.getHost()));
+          itm.setForeground(Color.blue);
+          itm.addActionListener(new ActionListener()
+          {
 
+            @Override
+            public void actionPerformed(ActionEvent arg0)
+            {
+              new Thread(new Runnable() { 
+                public void run() {
+                  setPreferredServiceFor(alignFrame, sv.serviceType, sv.action, sv);
+                  changeSupport.firePropertyChange("services", new Vector(), services);
+                };
+              }).start();
+
+            }
+          });
         }
+        /*hitm.addActionListener(new ActionListener()
+              {
+
+                @Override
+                public void actionPerformed(ActionEvent arg0)
+                {
+                  new Thread(new Runnable() {
+                    @Override
+                    public void run()
+                    {
+                      new SetPreferredServer(alignFrame, service.serviceType, service.action);
+                    }
+                  }).start();
+                }
+              });*/
       }
-      return hasParams;
     }
-  };
-
-  /**
-   * holds list of services.
-   */
-  protected Vector<Jws2Instance> services;
-
+  }
   /**
-   * find or add a submenu with the given title in the given menu
-   * 
-   * @param menu
-   * @param submenu
-   * @return the new or existing submenu
+   * add services using the Java 2.5/2.6/2.7 system which optionally creates submenus to index by host and service program type
    */
-  private JMenu findOrCreateMenu(JMenu menu, String submenu)
+  private void addEnumeratedServices(final JMenu jws2al, final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
   {
-    JMenu submenuinstance = null;
-    for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
-    {
-      if (menu.getMenuComponent(i) instanceof JMenu
-              && ((JMenu) menu.getMenuComponent(i)).getText().equals(
-                      submenu))
-      {
-        submenuinstance = (JMenu) menu.getMenuComponent(i);
-      }
-    }
-    if (submenuinstance == null)
-    {
-      submenuinstance = new JMenu(submenu);
-      menu.add(submenuinstance);
-    }
-    return submenuinstance;
-
-  }
-
-  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
-  {
-    // dynamically regenerate service list.
-    final JMenu jws2al = new JMenu("JABAWS Alignment");
-    jws2al.addMenuListener(new MenuListener()
-    {
-      // TODO: future: add menu listener to parent menu - so submenus are
-      // populated *before* they are selected.
-      @Override
-      public void menuSelected(MenuEvent e)
-      {
-        populateWSMenuEntry(jws2al, alignFrame);
-      }
-
-      @Override
-      public void menuDeselected(MenuEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void menuCanceled(MenuEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-    });
-    wsmenu.add(jws2al);
-
-  }
-
-  private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
-  {
-    if (running || services == null || services.size() == 0)
-    {
-      return;
-    }
-    boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache
-            .getDefault("WSMENU_BYTYPE", true);
+    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+            .getDefault("WSMENU_BYTYPE", false);
     /**
      * eventually, JWS2 services will appear under the same align/etc submenus.
      * for moment we keep them separate.
      */
     JMenu atpoint;
     MsaWSClient msacl = new MsaWSClient();
-    Vector hostLabels = new Vector();
-    jws2al.removeAll();
-    String lasthost = null;
-    for (final Jws2Instance service : services)
-    {
-      atpoint = jws2al;
-      String host = service.getHost();
-      String type = service.serviceType;
-      if (byhost)
+    List<String> hostLabels = new ArrayList<String>();
+    Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
+    ArrayList<String> hostlist=new ArrayList<String>();
+    for (Jws2Instance service : enumerableServices)
+    {
+      ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+      if (hostservices == null)
       {
-        atpoint = findOrCreateMenu(atpoint, host);
-        if (atpoint.getToolTipText() == null)
-        {
-          atpoint.setToolTipText("Services at " + host);
-        }
+        hosts.put(service.getHost(),
+                hostservices = new ArrayList<Jws2Instance>());
+        hostlist.add(service.getHost());
       }
-      if (bytype)
+      hostservices.add(service);
+    }
+    // now add hosts in order of the given array
+    for (String host : hostlist)
+    {
+      Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
+              new Jws2Instance[1]);
+      String sortbytype[] = new String[orderedsvcs.length];
+      for (int i = 0; i < sortbytype.length; i++)
       {
-        atpoint = findOrCreateMenu(atpoint, type);
-        if (atpoint.getToolTipText() == null)
-        {
-          atpoint.setToolTipText(service.getActionText());
-        }
+        sortbytype[i] = orderedsvcs[i].serviceType;
       }
-      if (!byhost
-              && !hostLabels.contains(host + service.serviceType
-                      + service.getActionText()))
-      // !hostLabels.contains(host + (bytype ?
-      // service.serviceType+service.getActionText() : "")))
+      jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
+      for (final Jws2Instance service : orderedsvcs)
       {
-        // add a marker indicating where this service is hosted
-        // relies on services from the same host being listed in a contiguous
-        // group
-        JMenuItem hitm;
-        atpoint.addSeparator();
-        if (lasthost == null || !lasthost.equals(host))
+        atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+        String type = service.serviceType;
+        if (byhost)
         {
-          atpoint.add(hitm = new JMenuItem(host));
-          hitm.setForeground(Color.blue);
-          lasthost = host;
+          atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
+          if (atpoint.getToolTipText() == null)
+          {
+            atpoint.setToolTipText("Services at " + host);
+          }
         }
-        hostLabels.addElement(host + service.serviceType
-                + service.getActionText());
-        // hostLabels.addElement(host + (bytype ?
-        // service.serviceType+service.getActionText() : ""));
+        if (bytype)
+        {
+          atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
+          if (atpoint.getToolTipText() == null)
+          {
+            atpoint.setToolTipText(service.getActionText());
+          }
+        }
+        if (!byhost
+                && !hostLabels.contains(host + service.serviceType
+                        + service.getActionText()))
+        // !hostLabels.contains(host + (bytype ?
+        // service.serviceType+service.getActionText() : "")))
+        {
+          // add a marker indicating where this service is hosted
+          // relies on services from the same host being listed in a
+          // contiguous
+          // group
+          JMenuItem hitm;
+          if (hostLabels.contains(host)) {
+            atpoint.addSeparator();
+          } else {
+            hostLabels.add(host);
+          }
+          if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host))
+          {
+            atpoint.add(hitm = new JMenuItem(host));
+            hitm.setForeground(Color.blue);
+            hitm.addActionListener(new ActionListener()
+            {
+
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                Desktop.showUrl(service.getHost());
+              }
+            });
+            hitm.setToolTipText(JvSwingUtils
+                    .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+            lasthostFor.put(service.action,host);
+          }
+          hostLabels.add(host + service.serviceType
+                  + service.getActionText());
+        }
+        
+        service.attachWSMenuEntry(atpoint, alignFrame);
       }
-      msacl.attachWSMenuEntry(atpoint, service, alignFrame);
-      /*
-       * JMenuItem sitem = new JMenuItem(service.serviceType);
-       * sitem.setToolTipText("Hosted at " + service.hosturl);
-       * sitem.addActionListener(new ActionListener() {
-       * 
-       * @Override public void actionPerformed(ActionEvent e) { AlignmentView
-       * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client =
-       * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(),
-       * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
-       * alignFrame); } });
-       */
     }
   }
-
   public static void main(String[] args)
   {
-    Thread runner = getDiscoverer().startDiscoverer(new PropertyChangeListener()
+    if (args.length>0)
     {
-
-      public void propertyChange(PropertyChangeEvent evt)
+      testUrls = new Vector<String>();
+      for (String url:args)
       {
-        if (getDiscoverer().services!=null)
-          {System.out.println("Changesupport: There are now "
-                + getDiscoverer().services.size() + " services");
-          
-          }
-      }
-    });
+        testUrls.add(url);
+      };
+    }
+    Thread runner = getDiscoverer().startDiscoverer(
+            new PropertyChangeListener()
+            {
+
+              public void propertyChange(PropertyChangeEvent evt)
+              {
+                if (getDiscoverer().services != null)
+                {
+                  System.out.println("Changesupport: There are now "
+                          + getDiscoverer().services.size() + " services");
+                  int i=1;
+                  for (Jws2Instance instance:getDiscoverer().services)
+                  {
+                    System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText());
+                  }
+
+                }
+              }
+            });
     while (runner.isAlive())
     {
       try
@@ -508,6 +529,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       ;
     }
+    try {
+      Thread.sleep(50);
+    } catch (InterruptedException x) {}
   }
 
   private static Jws2Discoverer discoverer;
@@ -557,8 +581,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
+  private static Vector<String> testUrls=null;
   public static Vector<String> getServiceUrls()
   {
+    if (testUrls!=null)
+    {
+      // return test urls, if there are any, instead of touching cache
+      return testUrls;
+    }
     String surls = Cache.getDefault(JWS2HOSTURLS,
             "http://www.compbio.dundee.ac.uk/jabaws");
     Vector<String> urls = new Vector<String>();
@@ -626,19 +656,26 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       { "-h=" + foo.toString() });
     } catch (Exception e)
     {
+      e.printStackTrace();
       return false;
     } catch (OutOfMemoryError e)
     {
+      e.printStackTrace();
       return false;
     } catch (Error e)
     {
+      e.printStackTrace();
       return false;
     }
+
     return true;
   }
 
   /**
-   * Start a fresh discovery thread and notify the given object when we're finished. Any known existing threads will be killed before this one is started. 
+   * Start a fresh discovery thread and notify the given object when we're
+   * finished. Any known existing threads will be killed before this one is
+   * started.
+   * 
    * @param changeSupport2
    * @return new thread
    */
@@ -654,4 +691,221 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return thr;
   }
 
+  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
+
+  /**
+   * @return the invalidServiceUrls
+   */
+  public Vector<String> getInvalidServiceUrls()
+  {
+    return invalidServiceUrls;
+  }
+
+  /**
+   * @return the urlsWithoutServices
+   */
+  public Vector<String> getUrlsWithoutServices()
+  {
+    return urlsWithoutServices;
+  }
+
+  /**
+   * add an 'empty' JABA server to the list. Only servers not already in the
+   * 'bad URL' list will be added to this list.
+   * 
+   * @param jwsservers
+   */
+  public synchronized void addUrlwithnoservices(String jwsservers)
+  {
+    if (urlsWithoutServices == null)
+    {
+      urlsWithoutServices = new Vector<String>();
+    }
+
+    if ((invalidServiceUrls == null || !invalidServiceUrls
+            .contains(jwsservers))
+            && !urlsWithoutServices.contains(jwsservers))
+    {
+      urlsWithoutServices.add(jwsservers);
+    }
+  }
+
+  /**
+   * add a bad URL to the list
+   * 
+   * @param jwsservers
+   */
+  public synchronized void addInvalidServiceUrl(String jwsservers)
+  {
+    if (invalidServiceUrls == null)
+    {
+      invalidServiceUrls = new Vector<String>();
+    }
+    if (!invalidServiceUrls.contains(jwsservers))
+    {
+      invalidServiceUrls.add(jwsservers);
+    }
+  }
+
+  /**
+   * 
+   * @return a human readable report of any problems with the service URLs used
+   *         for discovery
+   */
+  public String getErrorMessages()
+  {
+    if (!isRunning() && !isAborted())
+    {
+      StringBuffer ermsg = new StringBuffer();
+      boolean list = false;
+      if (getInvalidServiceUrls() != null
+              && getInvalidServiceUrls().size() > 0)
+      {
+        ermsg.append("URLs that could not be contacted: \n");
+        for (String svcurl : getInvalidServiceUrls())
+        {
+          if (list)
+          {
+            ermsg.append(", ");
+          }
+          list = true;
+          ermsg.append(svcurl);
+        }
+        ermsg.append("\n\n");
+      }
+      list = false;
+      if (getUrlsWithoutServices() != null
+              && getUrlsWithoutServices().size() > 0)
+      {
+        ermsg.append("URLs without any JABA Services : \n");
+        for (String svcurl : getUrlsWithoutServices())
+        {
+          if (list)
+          {
+            ermsg.append(", ");
+          }
+          list = true;
+          ermsg.append(svcurl);
+        }
+        ermsg.append("\n");
+      }
+      if (ermsg.length() > 1)
+      {
+        return ermsg.toString();
+      }
+
+    }
+    return null;
+  }
+
+  public int getServerStatusFor(String url)
+  {
+    if (validServiceUrls!=null && validServiceUrls.contains(url))
+    {
+      return 1;
+    }
+    if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
+    return 0;
+    if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+    {
+      return -1;
+    }
+    return -2;
+  }
+
+  /**
+   * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class)
+   * 
+   * @param serviceURL
+   * @return null or best match for given uri/ls.
+   */
+  public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
+  {
+    HashSet<String> urls=new HashSet<String>();
+    urls.addAll(Arrays.asList(serviceURLs));
+    Jws2Instance match=null;
+    for (Jws2Instance svc:services)
+    {
+      if (urls.contains(svc.getServiceTypeURI()))
+      {
+        if (match==null) {
+          // for moment we always pick service from server ordered first in user's preferences
+          match=svc;
+        }
+        if (urls.contains(svc.getUri()))
+        {
+          // stop and return - we've matched type URI and URI for service endpoint
+          return svc;
+        }
+      }
+    }
+    return match;
+  }
+  
+  Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();
+;
+
+  /**
+   * get current preferred service of the given type, or global default
+   * @param af null or a specific alignFrame 
+   * @param serviceType Jws2Instance.serviceType for service
+   * @return null if no service of this type is available, the preferred service for the serviceType and af if specified and if defined. 
+   */
+  public Jws2Instance getPreferredServiceFor(AlignFrame af,
+          String serviceType)
+  {
+    String serviceurl = null;
+    synchronized (preferredServiceMap)
+    {
+      String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+      Map<String, String> prefmap = preferredServiceMap.get(afid);
+      if (afid.length() > 0 && prefmap == null)
+      {
+        // recover global setting, if any
+        prefmap = preferredServiceMap.get("");
+      }
+        if (prefmap != null)
+        {
+          serviceurl = prefmap.get(serviceType);
+        }
+      
+    }
+    Jws2Instance response = null;
+    for (Jws2Instance svc : services)
+    {
+      if (svc.serviceType.equals(serviceType))
+      {
+        if (serviceurl == null || serviceurl.equals(svc.getHost()))
+        {
+          response = svc;
+          break;
+        }
+      }
+    }
+    return response;
+  }
+
+  public void setPreferredServiceFor(AlignFrame af, String serviceType,
+          String serviceAction, Jws2Instance selectedServer)
+  {
+    String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+    if (preferredServiceMap == null)
+    {
+      preferredServiceMap = new HashMap<String, Map<String, String>>();
+    }
+    Map<String, String> prefmap = preferredServiceMap.get(afid);
+    if (prefmap == null)
+    {
+      prefmap = new HashMap<String, String>();
+      preferredServiceMap.put(afid, prefmap);
+    }
+    prefmap.put(serviceType, selectedServer.getHost());
+    prefmap.put(serviceAction, selectedServer.getHost());
+  }
+
+  public void setPreferredServiceFor(String serviceType,
+          String serviceAction, Jws2Instance selectedServer)
+  {
+    setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+  }
 }