X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=0782d57dba94f575044570955770a7de87bcf303;hb=2f4f1d8fb6878271b64f327bc58c895f458137af;hp=c0addfe15af47c67839584f56e5d4558c7574cbe;hpb=ead7c435d61624a226f459a0fca90fc24e94caa9;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index c0addfe..0782d57 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,19 +1,20 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws2;
 
@@ -23,6 +24,7 @@ import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.ws.WSMenuEntryProviderI;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ParamDatastoreI;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -37,6 +39,7 @@ import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -104,6 +107,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public void run()
   {
+
     if (running && oldthread != null && oldthread.isAlive())
     {
       if (!aborted)
@@ -125,6 +129,15 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       Cache.log.debug("Old discovery thread has finished.");
     }
     running = true;
+    
+    // first set up exclusion list if needed
+    final Set<String> ignoredServices = new HashSet<String>();
+    for (String ignored:jalview.bin.Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", Services.JpredWS.toString()).split("\\|"))
+    {
+      ignoredServices.add(ignored);
+    }
+
+    
     changeSupport.firePropertyChange("services", services, new Vector());
     oldthread = Thread.currentThread();
     try
@@ -156,18 +169,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       validServiceUrls.removeAllElements();
     }
-    ArrayList<String> svctypes=new ArrayList<String>();
+    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)
+      if (svctypes.size() == 0)
       {
-        // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services 
-        for (Services sv:squery.JABAWS2SERVERS)
+        // TODO: remove this ugly hack to get Canonical JABA service ordering
+        // for all possible services
+        for (Services sv : squery.JABAWS2SERVERS)
         {
-          svctypes.add(sv.toString());
+          if (!ignoredServices.contains(sv.toString()))
+          {
+            svctypes.add(sv.toString());
+          }
         }
 
       }
@@ -177,7 +194,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     boolean finished = true;
     do
     {
-      finished=true;
+      finished = true;
       try
       {
         Thread.sleep(100);
@@ -187,7 +204,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       ;
       for (JabaWsServerQuery squery : qrys)
       {
-        finished = finished && !squery.isRunning();
+        if (squery.isRunning()){
+          finished=false;
+        }
       }
       if (aborted)
       {
@@ -203,22 +222,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       // 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)
+
+      if (services != null && services.size() > 0)
       {
-        Jws2Instance[] svcs=new Jws2Instance[services.size()];
-        int[] spos=new int[services.size()];
-        int ipos=0;
+        Jws2Instance[] svcs = new Jws2Instance[services.size()];
+        int[] spos = new int[services.size()];
+        int ipos = 0;
         Vector svcUrls = getServiceUrls();
-        for (Jws2Instance svc:services)
+        for (Jws2Instance svc : services)
         {
-          svcs[ipos]=svc;
-          spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType);
+          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);
+        services = new Vector<Jws2Instance>();
+        for (Jws2Instance svc : svcs)
+        {
+          if (!ignoredServices.contains(svc.serviceType))
+          {
+            services.add(svc);
+          }
         }
       }
     }
@@ -242,16 +266,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
     System.out.println("Discovered service: " + jwsservers + " "
             + service.toString());
-//    Jws2Instance service = 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();
+    ParamDatastoreI pds = service.getParamStore();
+    if (pds != null)
+    {
+      pds.getPresets();
+    }
     service.hasParameters();
-    if (validServiceUrls==null)
+    if (validServiceUrls == null)
     {
-      validServiceUrls=new Vector();
+      validServiceUrls = new Vector();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -260,18 +288,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * holds list of services.
    */
   protected Vector<Jws2Instance> services;
+
   /**
-   * attach all available web services to the appropriate submenu in the given JMenu
+   * attach all available web services to the appropriate submenu in the given
+   * JMenu
    */
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
     // dynamically regenerate service list.
     populateWSMenuEntry(wsmenu, alignFrame, null);
   }
-  private boolean isRecalculable(String action) {
-    return (action!=null && action.equalsIgnoreCase("conservation"));
+
+  private boolean isRecalculable(String action)
+  {
+    return (action != null && action.equalsIgnoreCase("conservation"));
   }
-  private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+
+  private void populateWSMenuEntry(JMenu jws2al,
+          final AlignFrame alignFrame, String typeFilter)
   {
     if (running || services == null || services.size() == 0)
     {
@@ -284,20 +318,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    List<Jws2Instance> enumerableServices=new ArrayList<Jws2Instance>();
-    //jws2al.removeAll();
-    Map<String, Jws2Instance> preferredHosts=new HashMap<String,Jws2Instance>();
+    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
+      if (!isRecalculable(service.action))
+      {
+        // add 'one shot' services to be displayed using the classic menu
+        // structure
         enumerableServices.add(service);
-      } else {
+      }
+      else
+      {
         if (!preferredHosts.containsKey(service.serviceType))
         {
-          Jws2Instance preferredInstance = getPreferredServiceFor(alignFrame,
-                  service.serviceType);
+          Jws2Instance preferredInstance = getPreferredServiceFor(
+                  alignFrame, service.serviceType);
           if (preferredInstance != null)
           {
             preferredHosts.put(service.serviceType, preferredInstance);
@@ -307,12 +345,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             preferredHosts.put(service.serviceType, service);
           }
         }
-        List<Jws2Instance> ph=alternates.get(service.serviceType);
-        if (preferredHosts.get(service.serviceType)!=service)
+        List<Jws2Instance> ph = alternates.get(service.serviceType);
+        if (preferredHosts.get(service.serviceType) != service)
         {
-          if (ph==null)
+          if (ph == null)
           {
-            ph=new ArrayList<Jws2Instance>();
+            ph = new ArrayList<Jws2Instance>();
           }
           ph.add(service);
           alternates.put(service.serviceType, ph);
@@ -326,9 +364,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     // and the instantaneous services
     for (final Jws2Instance service : preferredHosts.values())
     {
-      atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+      atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
       JMenuItem hitm;
-      if (atpoint.getItemCount()>1) {
+      if (atpoint.getItemCount() > 1)
+      {
         // previous service of this type already present
         atpoint.addSeparator();
       }
@@ -349,12 +388,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       service.attachWSMenuEntry(atpoint, alignFrame);
       if (alternates.containsKey(service.serviceType))
       {
-        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))
+        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()));
+          hitm.add(itm = new JMenuItem(sv.getHost()));
           itm.setForeground(Color.blue);
           itm.addActionListener(new ActionListener()
           {
@@ -362,38 +402,39 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             @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);
+              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();
-                }
-              });*/
+        /*
+         * 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(); } });
+         */
       }
     }
   }
+
   /**
-   * add services using the Java 2.5/2.6/2.7 system which optionally creates submenus to index by host and service program type
+   * 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 void addEnumeratedServices(final JMenu jws2al, final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+  private void addEnumeratedServices(final JMenu jws2al,
+          final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
   {
     boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
             .getDefault("WSMENU_BYTYPE", false);
@@ -406,7 +447,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     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>();
+    ArrayList<String> hostlist = new ArrayList<String>();
     for (Jws2Instance service : enumerableServices)
     {
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
@@ -431,7 +472,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
       for (final Jws2Instance service : orderedsvcs)
       {
-        atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+        atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
         String type = service.serviceType;
         if (byhost)
         {
@@ -460,12 +501,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           // contiguous
           // group
           JMenuItem hitm;
-          if (hostLabels.contains(host)) {
+          if (hostLabels.contains(host))
+          {
             atpoint.addSeparator();
-          } else {
+          }
+          else
+          {
             hostLabels.add(host);
           }
-          if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host))
+          if (lasthostFor.get(service.action) == null
+                  || !lasthostFor.get(service.action).equals(host))
           {
             atpoint.add(hitm = new JMenuItem(host));
             hitm.setForeground(Color.blue);
@@ -480,25 +525,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             });
             hitm.setToolTipText(JvSwingUtils
                     .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
-            lasthostFor.put(service.action,host);
+            lasthostFor.put(service.action, host);
           }
           hostLabels.add(host + service.serviceType
                   + service.getActionText());
         }
-        
+
         service.attachWSMenuEntry(atpoint, alignFrame);
       }
     }
   }
+
   public static void main(String[] args)
   {
-    if (args.length>0)
+    if (args.length > 0)
     {
       testUrls = new Vector<String>();
-      for (String url:args)
+      for (String url : args)
       {
         testUrls.add(url);
-      };
+      }
+      ;
     }
     Thread runner = getDiscoverer().startDiscoverer(
             new PropertyChangeListener()
@@ -510,10 +557,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                 {
                   System.out.println("Changesupport: There are now "
                           + getDiscoverer().services.size() + " services");
-                  int i=1;
-                  for (Jws2Instance instance:getDiscoverer().services)
+                  int i = 1;
+                  for (Jws2Instance instance : getDiscoverer().services)
                   {
-                    System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText());
+                    System.out.println("Service " + i++ + " "
+                            + instance.getClass() + "@"
+                            + instance.getHost() + ": "
+                            + instance.getActionText());
                   }
 
                 }
@@ -529,9 +579,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       ;
     }
-    try {
+    try
+    {
       Thread.sleep(50);
-    } catch (InterruptedException x) {}
+    } catch (InterruptedException x)
+    {
+    }
   }
 
   private static Jws2Discoverer discoverer;
@@ -581,10 +634,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
-  private static Vector<String> testUrls=null;
+  private static Vector<String> testUrls = null;
+
   public static Vector<String> getServiceUrls()
   {
-    if (testUrls!=null)
+    if (testUrls != null)
     {
       // return test urls, if there are any, instead of touching cache
       return testUrls;
@@ -691,7 +745,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return thr;
   }
 
-  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
+  Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
+          validServiceUrls = null;
 
   /**
    * @return the invalidServiceUrls
@@ -800,13 +855,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public int getServerStatusFor(String url)
   {
-    if (validServiceUrls!=null && validServiceUrls.contains(url))
+    if (validServiceUrls != null && validServiceUrls.contains(url))
     {
       return 1;
     }
-    if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
-    return 0;
-    if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+    if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+      return 0;
+    if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
     {
       return -1;
     }
@@ -814,42 +869,53 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   }
 
   /**
-   * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class)
+   * 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>();
+    HashSet<String> urls = new HashSet<String>();
     urls.addAll(Arrays.asList(serviceURLs));
-    Jws2Instance match=null;
-    for (Jws2Instance svc:services)
+    Jws2Instance match = null;
+    if (services != null)
     {
-      if (urls.contains(svc.getServiceTypeURI()))
+      for (Jws2Instance svc : services)
       {
-        if (match==null) {
-          // for moment we always pick service from server ordered first in user's preferences
-          match=svc;
-        }
-        if (urls.contains(svc.getUri()))
+        if (urls.contains(svc.getServiceTypeURI()))
         {
-          // stop and return - we've matched type URI and URI for service endpoint
-          return svc;
+          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>>();
-;
+
+  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. 
+   * 
+   * @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)
@@ -864,11 +930,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         // recover global setting, if any
         prefmap = preferredServiceMap.get("");
       }
-        if (prefmap != null)
-        {
-          serviceurl = prefmap.get(serviceType);
-        }
-      
+      if (prefmap != null)
+      {
+        serviceurl = prefmap.get(serviceType);
+      }
+
     }
     Jws2Instance response = null;
     for (Jws2Instance svc : services)