X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=198f01d9872690467508996181dcf75d37251414;hb=a9514dd266ef856c485fd8f9108a3797b87add3f;hp=eccbdaf5946f9382880f95fed5db2f6a5809def8;hpb=044565fb3cd7d2d3c91b7592b3e007e584e264f2;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index eccbdaf..198f01d 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.ws.jws2;
 
 import java.awt.Color;
@@ -8,8 +25,10 @@ import java.beans.PropertyChangeListener;
 import java.io.Closeable;
 import java.net.ConnectException;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -23,6 +42,8 @@ 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;
@@ -69,7 +90,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     changeSupport.removePropertyChangeListener(listener);
   }
 
-  boolean running = false;
+  boolean running = false, aborted = false;
+
+  /**
+   * @return the aborted
+   */
+  public boolean isAborted()
+  {
+    return aborted;
+  }
+
+  /**
+   * @param aborted
+   *          the aborted to set
+   */
+  public void setAborted(boolean aborted)
+  {
+    this.aborted = aborted;
+  }
 
   Thread oldthread = null;
 
@@ -77,7 +115,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (running && oldthread != null && oldthread.isAlive())
     {
-      return;
+      if (!aborted)
+      {
+        return;
+      }
+      while (running)
+      {
+        try
+        {
+          Cache.log
+                  .debug("Waiting around for old discovery thread to finish.");
+          // wait around until old discoverer dies
+          Thread.sleep(100);
+        } catch (Exception e)
+        {
+        }
+      }
+      Cache.log.debug("Old discovery thread has finished.");
     }
     running = true;
     oldthread = Thread.currentThread();
@@ -88,62 +142,62 @@ 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();
     }
-    for (String jwsservers : getServiceUrls())
+    if (urlsWithoutServices != null)
+    {
+      urlsWithoutServices.removeAllElements();
+    }
+    if (invalidServiceUrls != null)
+    {
+      invalidServiceUrls.removeAllElements();
+    }
+
+    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    for (final String jwsservers : getServiceUrls())
+    {
+      JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+      qrys.add(squery);
+      new Thread(squery).start();
+    }
+    boolean finished = false;
+    do
     {
       try
       {
-        if (Jws2Client.validURL(jwsservers))
-        {
-          // look for services
-          for (Services srv : Services.values())
-          {
-            MsaWS service = null;
-            try
-            {
-              service = Jws2Client.connect(jwsservers, srv);
-            } catch (Exception e)
-            {
-              System.err.println("Jws2 Discoverer: Problem on "
-                      + jwsservers + " with service " + srv + ":\n"
-                      + e.getMessage());
-              if (!(e instanceof javax.xml.ws.WebServiceException))
-              {
-                e.printStackTrace();
-              }
-            }
-            ;
-            if (service != null)
-            {
-              addService(jwsservers, srv, service);
-            }
-          }
-
-        }
-        else
-        {
-          Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
-        }
+        Thread.sleep(100);
       } catch (Exception e)
       {
-        e.printStackTrace();
-        Cache.log.warn("Exception when discovering Jws2 services.", e);
-      } catch (Error e)
+      }
+      ;
+      for (JabaWsServerQuery squery : qrys)
+      {
+        finished |= !squery.isRunning();
+      }
+      if (aborted)
       {
-        Cache.log.error("Exception when discovering Jws2 services.", e);
+        Cache.log.debug("Aborting " + qrys.size()
+                + " JABAWS discovery threads.");
+        for (JabaWsServerQuery squery : qrys)
+        {
+          squery.setQuit(true);
+        }
       }
-    }
+    } while (!aborted && !finished);
     oldthread = null;
     running = false;
-    changeSupport.firePropertyChange("services", new Vector(), services);
+    if (!aborted)
+    {
+      changeSupport.firePropertyChange("services", new Vector(), services);
+    }
   }
 
   /**
@@ -153,7 +207,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * @param srv
    * @param service2
    */
-  private void addService(String jwsservers, Services srv, MsaWS service2)
+  synchronized void addService(String jwsservers, Services srv,
+          MsaWS service2)
   {
     if (services == null)
     {
@@ -161,7 +216,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
     System.out.println("Discovered service: " + jwsservers + " "
             + srv.toString());
-    services.add(new Jws2Instance(jwsservers, srv.toString(), service2));
+    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();
   }
 
   public class Jws2Instance
@@ -182,7 +243,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
     PresetManager presets = null;
 
-    public JabaParamStore paramStore=null;
+    public JabaParamStore paramStore = null;
 
     /**
      * non thread safe - gets the presets for this service (blocks whilst it
@@ -260,14 +321,44 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       if (paramStore == null)
       {
-        try {
-        paramStore = new JabaParamStore(this);
+        try
+        {
+          paramStore = new JabaParamStore(this,
+                  (Desktop.instance != null ? Desktop
+                          .getUserParameterStore() : null));
         } catch (Exception ex)
-        {}
-        
+        {
+        }
+
       }
       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)
+      {
+        lookedForParams = true;
+        try
+        {
+          hasParams = (getRunnerConfig().getArguments().size() > 0);
+        } catch (Exception e)
+        {
+
+        }
+      }
+      return hasParams;
+    }
   };
 
   /**
@@ -306,9 +397,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
     // dynamically regenerate service list.
-    final JMenu jws2al = new JMenu("JABA Alignment");
-    jws2al.addMenuListener(new MenuListener() {
-      // TODO: future: add menu listener to parent menu - so submenus are populated *before* they are selected.
+    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)
       {
@@ -319,19 +412,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       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)
@@ -348,6 +443,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     MsaWSClient msacl = new MsaWSClient();
     Vector hostLabels = new Vector();
     jws2al.removeAll();
+    String lasthost = null;
     for (final Jws2Instance service : services)
     {
       atpoint = jws2al;
@@ -369,16 +465,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           atpoint.setToolTipText(service.getActionText());
         }
       }
-      if (!byhost && !hostLabels.contains(host + 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;
         atpoint.addSeparator();
-        atpoint.add(hitm = new JMenuItem(host));
-        hitm.setForeground(Color.blue);
-        hostLabels.addElement(host);
+        if (lasthost == null || !lasthost.equals(host))
+        {
+          atpoint.add(hitm = new JMenuItem(host));
+          hitm.setForeground(Color.blue);
+          lasthost = host;
+        }
+        hostLabels.addElement(host + service.serviceType
+                + service.getActionText());
+        // hostLabels.addElement(host + (bytype ?
+        // service.serviceType+service.getActionText() : ""));
       }
       msacl.attachWSMenuEntry(atpoint, service, alignFrame);
       /*
@@ -397,17 +504,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public static void main(String[] args)
   {
-    Thread runner = new Thread(getDiscoverer());
-    getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
-    {
+    Thread runner = getDiscoverer().startDiscoverer(
+            new PropertyChangeListener()
+            {
 
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        System.out.println("Changesupport: There are now "
-                + getDiscoverer().services.size() + " services");
-      }
-    });
-    runner.start();
+              public void propertyChange(PropertyChangeEvent evt)
+              {
+                if (getDiscoverer().services != null)
+                {
+                  System.out.println("Changesupport: There are now "
+                          + getDiscoverer().services.size() + " services");
+
+                }
+              }
+            });
     while (runner.isAlive())
     {
       try
@@ -524,26 +634,157 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   /**
    * test the given URL with the JabaWS test code
+   * 
    * @param foo
    * @return
    */
   public static boolean testServiceUrl(URL foo)
   {
-    try {
-      compbio.ws.client.WSTester.main(new String[] { "-h="+foo.toString()});
+    try
+    {
+      compbio.ws.client.WSTester.main(new String[]
+      { "-h=" + foo.toString() });
     } catch (Exception e)
     {
+      e.printStackTrace();
       return false;
-    }
-    catch (OutOfMemoryError e)
+    } catch (OutOfMemoryError e)
     {
+      e.printStackTrace();
       return false;
-    }
-    catch (Error e)
+    } 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.
+   * 
+   * @param changeSupport2
+   * @return new thread
+   */
+  public Thread startDiscoverer(PropertyChangeListener changeSupport2)
+  {
+    if (isRunning())
+    {
+      setAborted(true);
+    }
+    addPropertyChangeListener(changeSupport2);
+    Thread thr = new Thread(this);
+    thr.start();
+    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;
+  }
+
 }