X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=9a3796d3fdc3344553b813a02b9f88c2f96334e1;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;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..9a3796d 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.
  * 
@@ -44,7 +44,9 @@ import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JalviewChangeSupport;
+import jalview.gui.JvSwingUtils;
 import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
 import jalview.ws.params.ParamDatastoreI;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Option;
@@ -93,6 +95,14 @@ 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
    */
@@ -134,15 +144,25 @@ 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();
+    }
+
     List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
     for (final String jwsservers : getServiceUrls())
     {
@@ -320,8 +340,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       // this is only valid for Jaba 1.0 - this formula might have to change!
       return hosturl
-              + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/"
-                      : "") + serviceType;
+              + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
+                      : "/") + serviceType;
     }
 
     private boolean hasParams = false, lookedForParams = false;
@@ -348,38 +368,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   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
-   */
-  private JMenu findOrCreateMenu(JMenu menu, String submenu)
-  {
-    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");
+    final JMenu jws2al = wsmenu; // new JMenu("JABAWS Alignment");
     jws2al.addMenuListener(new MenuListener()
     {
       // TODO: future: add menu listener to parent menu - so submenus are
@@ -415,8 +407,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       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.
@@ -426,78 +418,119 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     Vector hostLabels = new Vector();
     jws2al.removeAll();
     String lasthost = null;
-    for (final Jws2Instance service : services)
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
+    String[] sorton;
+    for (Jws2Instance service : services)
     {
-      atpoint = jws2al;
-      String host = service.getHost();
-      String type = service.serviceType;
-      if (byhost)
+      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>());
       }
-      if (bytype)
+      hostservices.add(service);
+    }
+    sorton = hosts.keySet().toArray(new String[1]);
+    String hostlist[] = sorton.clone();
+    jalview.util.QuickSort.sort(sorton, hostlist);
+    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 = jws2al;
+        String type = service.serviceType;
+        if (byhost)
+        {
+          atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
+          if (atpoint.getToolTipText() == null)
+          {
+            atpoint.setToolTipText("Services at " + host);
+          }
+        }
+        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() : "")))
         {
-          atpoint.add(hitm = new JMenuItem(host));
-          hitm.setForeground(Color.blue);
-          lasthost = host;
+          // 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.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"));
+            lasthost = host;
+          }
+          hostLabels.addElement(host + service.serviceType
+                  + service.getActionText());
+          // hostLabels.addElement(host + (bytype ?
+          // service.serviceType+service.getActionText() : ""));
         }
-        hostLabels.addElement(host + service.serviceType
-                + service.getActionText());
-        // hostLabels.addElement(host + (bytype ?
-        // service.serviceType+service.getActionText() : ""));
+        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); }
+         * });
+         */
       }
-      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()
-    {
-
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        if (getDiscoverer().services!=null)
-          {System.out.println("Changesupport: There are now "
-                + getDiscoverer().services.size() + " services");
-          
-          }
-      }
-    });
+    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");
+
+                }
+              }
+            });
     while (runner.isAlive())
     {
       try
@@ -626,19 +659,26 @@ 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 +694,111 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return thr;
   }
 
+  Vector<String> invalidServiceUrls = null, urlsWithoutServices = 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;
+  }
+
 }