X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=ed808f6e03a5022f501c5e9879beec63994a1bc8;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=95100e0adb0eed0c07354a08bdbe9315a403de5c;hpb=0b273bf4779ad04c866a7abc56af4fc11ded4264;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 95100e0..ed808f6 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 2.7)
+ * Copyright (C) 2011 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;
@@ -5,29 +22,39 @@ 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.HashSet;
 import java.util.Hashtable;
+import java.util.List;
 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.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;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
-import compbio.ws.client.Jws2Base;
-import compbio.ws.client.Jws2Base.Services;
+import compbio.ws.client.Jws2Client;
+import compbio.ws.client.Services;
 
 /**
  * discoverer for jws2 services. Follows the lightweight service discoverer
@@ -65,82 +92,114 @@ 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;
 
-  @Override
   public void run()
   {
     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();
     try
     {
       Class foo = getClass().getClassLoader().loadClass(
-              "compbio.ws.client.Jws2Base");
+              "compbio.ws.client.Jws2Client");
     } 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 (Jws2Base.validURL(jwsservers))
-        {
-          // look for services
-          for (Services srv : Jws2Base.Services.values())
-          {
-            MsaWS service = null;
-            try
-            {
-              service = Jws2Base.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)
       {
-        Cache.log.error("Exception when discovering Jws2 services.", e);
+        finished |= !squery.isRunning();
       }
-    }
+      if (aborted)
+      {
+        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);
+    }
   }
 
   /**
@@ -150,7 +209,8 @@ 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)
     {
@@ -158,7 +218,13 @@ 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
@@ -179,6 +245,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
     PresetManager presets = null;
 
+    public JabaParamStore paramStore = null;
+
     /**
      * non thread safe - gets the presets for this service (blocks whilst it
      * calls the service to get the preset set)
@@ -205,37 +273,94 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     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; */
+      /*
+       * 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;
+    public String getActionText()
+    {
+      return "Align with " + serviceType;
     }
 
     /**
-     * non-thread safe - blocks whilst accessing service to get complete set of available options and parameters
+     * 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
+    {
+      if (service != null)
+      {
+        try
+        {
+          Closeable svc = (Closeable) service;
+          service = null;
+          svc.close();
+        } catch (Exception e)
+        {
+        }
+        ;
+      }
+      super.finalize();
+    }
+
+    public ParamDatastoreI getParamStore()
+    {
+      if (paramStore == null)
+      {
+        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;
+    }
   };
 
   /**
@@ -243,110 +368,169 @@ 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)
+  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
-    JMenu submenuinstance = null;
-    for (int i=0,iSize=menu.getMenuComponentCount(); i<iSize; i++)
+    // dynamically regenerate service list.
+    final JMenu jws2al = wsmenu; // new JMenu("JABAWS Alignment");
+    jws2al.addMenuListener(new MenuListener()
     {
-      if (menu.getMenuComponent(i) instanceof JMenu && 
-               ((JMenu)menu.getMenuComponent(i)).getText().equals(submenu))
+      // TODO: future: add menu listener to parent menu - so submenus are
+      // populated *before* they are selected.
+      @Override
+      public void menuSelected(MenuEvent e)
       {
-        submenuinstance = (JMenu) menu.getMenuComponent(i);
+        populateWSMenuEntry(jws2al, alignFrame);
       }
-    }
-    if (submenuinstance==null)
-    {
-      submenuinstance = new JMenu(submenu);
-      menu.add(submenuinstance);
-    }
-    return submenuinstance;
-  
+
+      @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);
+
   }
-  @Override
-  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+
+  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, jws2al = new JMenu("JABA Alignment");
+    JMenu atpoint;
     MsaWSClient msacl = new MsaWSClient();
-    Vector hostLabels=new Vector();
-    for (final Jws2Instance service : services)
+    Vector hostLabels = new Vector();
+    jws2al.removeAll();
+    String lasthost = null;
+    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.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();
-        atpoint.add(hitm=new JMenuItem(host));
-        hitm.setForeground(Color.blue);
-        hostLabels.addElement(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() : "")))
+        {
+          // 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() : ""));
+        }
+        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); } });
-       */
-    }
-    if (services.size() > 0)
-    {
-      wsmenu.add(jws2al);
     }
 
   }
 
   public static void main(String[] args)
   {
-    Thread runner = new Thread(getDiscoverer());
-    getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
-    {
+    Thread runner = getDiscoverer().startDiscoverer(
+            new PropertyChangeListener()
+            {
 
-      @Override
-      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
@@ -409,7 +593,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   public static Vector<String> getServiceUrls()
   {
     String surls = Cache.getDefault(JWS2HOSTURLS,
-            "http://www.compbio.dundee.ac.uk/jaba");
+            "http://www.compbio.dundee.ac.uk/jabaws");
     Vector<String> urls = new Vector<String>();
     try
     {
@@ -457,7 +641,164 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public Vector<Jws2Instance> getServices()
   {
-    return (services==null) ? new Vector<Jws2Instance>(): new Vector<Jws2Instance>(services);
+    return (services == null) ? new Vector<Jws2Instance>()
+            : new Vector<Jws2Instance>(services);
+  }
+
+  /**
+   * 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() });
+    } 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.
+   * 
+   * @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;
   }
 
 }