X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=ca36a51d7e1622d6da59abceebd8a3ac58277d9b;hb=0d9e7c05b15bfd0ac59436066e2fe805673bbef0;hp=adca0fa7f9ab490fef4eb97d92c74fb30bfed2fb;hpb=5f631be878dd25f9b73d4ba09083e0fd3df8d153;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index adca0fa..ca36a51 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -21,6 +21,7 @@
 package jalview.ws.jws2;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
@@ -164,22 +165,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       {
         try
         {
-          Cache.log
-                  .debug("Waiting around for old discovery thread to finish.");
+          Console.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.");
+      aborted = false;
+      Console.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 : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES",
-            "").split("\\|"))
+    final Set<String> ignoredServices = new HashSet<>();
+    for (String ignored : Cache
+            .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
     {
       ignoredServices.add(ignored);
     }
@@ -189,12 +191,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     oldthread = Thread.currentThread();
     try
     {
-      Class foo = getClass().getClassLoader().loadClass(
-              "compbio.ws.client.Jws2Client");
+      Class foo = getClass().getClassLoader()
+              .loadClass("compbio.ws.client.Jws2Client");
     } catch (ClassNotFoundException e)
     {
-      System.err
-              .println("Not enabling JABA Webservices : client jar is not available."
+      jalview.bin.Console.errPrintln(
+              "Not enabling JABA Webservices : client jar is not available."
                       + "\nPlease check that your webstart JNLP file is up to date!");
       running = false;
       return;
@@ -216,9 +218,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       validServiceUrls.removeAllElements();
     }
-    ArrayList<String> svctypes = new ArrayList<String>();
+    ArrayList<String> svctypes = new ArrayList<>();
 
-    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    List<JabaWsServerQuery> qrys = new ArrayList<>();
     for (final String jwsserver : getServiceUrls())
     {
       JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
@@ -248,7 +250,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (Exception e)
       {
       }
-      ;
       for (JabaWsServerQuery squery : qrys)
       {
         if (squery.isRunning())
@@ -258,8 +259,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       if (aborted)
       {
-        Cache.log.debug("Aborting " + qrys.size()
-                + " JABAWS discovery threads.");
+        Console.debug(
+                "Aborting " + qrys.size() + " JABAWS discovery threads.");
         for (JabaWsServerQuery squery : qrys)
         {
           squery.setQuit(true);
@@ -284,7 +285,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   + svctypes.indexOf(svc.serviceType);
         }
         jalview.util.QuickSort.sort(spos, svcs);
-        services = new Vector<Jws2Instance>();
+        services = new Vector<>();
         for (Jws2Instance svc : svcs)
         {
           if (!ignoredServices.contains(svc.serviceType))
@@ -296,8 +297,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
     oldthread = null;
     running = false;
-    changeSupport.firePropertyChange("services",
-            new Vector<Jws2Instance>(), services);
+    changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
+            services);
   }
 
   /**
@@ -311,10 +312,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (services == null)
     {
-      services = new Vector<Jws2Instance>();
+      services = new Vector<>();
     }
-    System.out.println("Discovered service: " + jwsservers + " "
-            + service.toString());
+    jalview.bin.Console.outPrintln(
+            "Discovered service: " + jwsservers + " " + service.toString());
     // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
     // service2);
 
@@ -328,7 +329,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     service.hasParameters();
     if (validServiceUrls == null)
     {
-      validServiceUrls = new Vector<String>();
+      validServiceUrls = new Vector<>();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -362,10 +363,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+    List<Jws2Instance> enumerableServices = new ArrayList<>();
     // jws2al.removeAll();
-    Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
-    Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+    Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+    Map<String, List<Jws2Instance>> alternates = new HashMap<>();
     for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
     {
       if (!isRecalculable(service.action))
@@ -394,7 +395,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         {
           if (ph == null)
           {
-            ph = new ArrayList<Jws2Instance>();
+            ph = new ArrayList<>();
           }
           ph.add(service);
           alternates.put(service.serviceType, ph);
@@ -432,8 +433,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       service.attachWSMenuEntry(atpoint, alignFrame);
       if (alternates.containsKey(service.serviceType))
       {
-        atpoint.add(hitm = new JMenu(MessageManager
-                .getString("label.switch_server")));
+        atpoint.add(hitm = new JMenu(
+                MessageManager.getString("label.switch_server")));
         hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
                 MessageManager.getString("label.choose_jabaws_server")));
         for (final Jws2Instance sv : alternates.get(service.serviceType))
@@ -456,7 +457,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                           sv.action, sv);
                   changeSupport.firePropertyChange("services",
                           new Vector<Jws2Instance>(), services);
-                };
+                }
               }).start();
 
             }
@@ -471,27 +472,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    * submenus to index by host and service program type
    */
   private void addEnumeratedServices(final JMenu jws2al,
-          final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+          final AlignFrame alignFrame,
+          List<Jws2Instance> enumerableServices)
   {
-    boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
-            .getDefault("WSMENU_BYTYPE", false);
+    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;
 
-    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>();
+    List<String> hostLabels = new ArrayList<>();
+    Hashtable<String, String> lasthostFor = new Hashtable<>();
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+    ArrayList<String> hostlist = new ArrayList<>();
     for (Jws2Instance service : enumerableServices)
     {
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
       if (hostservices == null)
       {
-        hosts.put(service.getHost(),
-                hostservices = new ArrayList<Jws2Instance>());
+        hosts.put(service.getHost(), hostservices = new ArrayList<>());
         hostlist.add(service.getHost());
       }
       hostservices.add(service);
@@ -499,8 +500,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     // now add hosts in order of the given array
     for (String host : hostlist)
     {
-      Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
-              new Jws2Instance[1]);
+      Jws2Instance orderedsvcs[] = hosts.get(host)
+              .toArray(new Jws2Instance[1]);
       String sortbytype[] = new String[orderedsvcs.length];
       for (int i = 0; i < sortbytype.length; i++)
       {
@@ -516,8 +517,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
           if (atpoint.getToolTipText() == null)
           {
-            atpoint.setToolTipText(MessageManager.formatMessage(
-                    "label.services_at", new String[] { host }));
+            atpoint.setToolTipText(MessageManager
+                    .formatMessage("label.services_at", new String[]
+                    { host }));
           }
         }
         if (bytype)
@@ -528,9 +530,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
             atpoint.setToolTipText(service.getActionText());
           }
         }
-        if (!byhost
-                && !hostLabels.contains(host + service.serviceType
-                        + service.getActionText()))
+        if (!byhost && !hostLabels.contains(
+                host + service.serviceType + service.getActionText()))
         // !hostLabels.contains(host + (bytype ?
         // service.serviceType+service.getActionText() : "")))
         {
@@ -561,12 +562,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                 Desktop.showUrl(service.getHost());
               }
             });
-            hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
-                    MessageManager.getString("label.open_jabaws_web_page")));
+            hitm.setToolTipText(
+                    JvSwingUtils.wrapTooltip(true, MessageManager
+                            .getString("label.open_jabaws_web_page")));
             lasthostFor.put(service.action, host);
           }
-          hostLabels.add(host + service.serviceType
-                  + service.getActionText());
+          hostLabels.add(
+                  host + service.serviceType + service.getActionText());
         }
 
         service.attachWSMenuEntry(atpoint, alignFrame);
@@ -574,19 +576,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     if (args.length > 0)
     {
-      testUrls = new ArrayList<String>();
+      testUrls = new ArrayList<>();
       for (String url : args)
       {
         testUrls.add(url);
       }
-      ;
     }
-    Thread runner = getDiscoverer().startDiscoverer(
-            new PropertyChangeListener()
+    Thread runner = getDiscoverer()
+            .startDiscoverer(new PropertyChangeListener()
             {
 
               @Override
@@ -594,15 +600,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
               {
                 if (getDiscoverer().services != null)
                 {
-                  System.out.println("Changesupport: There are now "
+                  jalview.bin.Console.outPrintln("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());
+                    jalview.bin.Console.outPrintln("Service " + i++ + " "
+                            + instance.getClass() + "@" + instance.getHost()
+                            + ": " + instance.getActionText());
                   }
 
                 }
@@ -616,7 +621,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (InterruptedException e)
       {
       }
-      ;
     }
     try
     {
@@ -683,7 +687,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       // return test urls, if there are any, instead of touching cache
       return testUrls;
     }
-    List<String> urls = new ArrayList<String>();
+    List<String> urls = new ArrayList<>();
 
     if (this.preferredUrl != null)
     {
@@ -707,24 +711,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           }
           else
           {
-            Cache.log.warn("Ignoring duplicate url " + url + " in "
+            Console.warn("Ignoring duplicate url " + url + " in "
                     + JWS2HOSTURLS + " list");
           }
         } catch (MalformedURLException ex)
         {
-          Cache.log.warn("Problem whilst trying to make a URL from '"
+          Console.warn("Problem whilst trying to make a URL from '"
                   + ((url != null) ? url : "<null>") + "'");
-          Cache.log
-                  .warn("This was probably due to a malformed comma separated list"
-                          + " in the "
-                          + JWS2HOSTURLS
+          Console.warn(
+                  "This was probably due to a malformed comma separated list"
+                          + " in the " + JWS2HOSTURLS
                           + " entry of $(HOME)/.jalview_properties)");
-          Cache.log.debug("Exception was ", ex);
+          Console.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      Cache.log.warn("Error parsing comma separated list of urls in "
+      Console.warn("Error parsing comma separated list of urls in "
               + JWS2HOSTURLS + " preference.", ex);
     }
     return urls;
@@ -732,8 +735,7 @@ 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<>() : new Vector<>(services);
   }
 
   /**
@@ -747,7 +749,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     try
     {
       compbio.ws.client.WSTester
-              .main(new String[] { "-h=" + foo.toString() });
+              .main(new String[]
+              { "-h=" + foo.toString() });
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -765,6 +768,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return true;
   }
 
+  public boolean restart()
+  {
+    synchronized (this)
+    {
+      if (running)
+      {
+        aborted = true;
+      }
+      else
+      {
+        running = true;
+      }
+      return aborted;
+    }
+  }
+
   /**
    * 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
@@ -775,6 +794,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Thread startDiscoverer(PropertyChangeListener changeSupport2)
   {
+    /*    if (restart())
+        {
+          return;
+        }
+        else
+        {
+          Thread thr = new Thread(this);
+          thr.start();
+        }
+       */
     if (isRunning())
     {
       setAborted(true);
@@ -811,11 +840,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (urlsWithoutServices == null)
     {
-      urlsWithoutServices = new Vector<String>();
+      urlsWithoutServices = new Vector<>();
     }
 
-    if ((invalidServiceUrls == null || !invalidServiceUrls
-            .contains(jwsservers))
+    if ((invalidServiceUrls == null
+            || !invalidServiceUrls.contains(jwsservers))
             && !urlsWithoutServices.contains(jwsservers))
     {
       urlsWithoutServices.add(jwsservers);
@@ -831,7 +860,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (invalidServiceUrls == null)
     {
-      invalidServiceUrls = new Vector<String>();
+      invalidServiceUrls = new Vector<>();
     }
     if (!invalidServiceUrls.contains(jwsservers))
     {
@@ -870,7 +899,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       if (getUrlsWithoutServices() != null
               && getUrlsWithoutServices().size() > 0)
       {
-        ermsg.append(MessageManager.getString("warn.urls_no_jaba") + ": \n");
+        ermsg.append(
+                MessageManager.getString("warn.urls_no_jaba") + ": \n");
         for (String svcurl : getUrlsWithoutServices())
         {
           if (list)
@@ -918,7 +948,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
   {
-    HashSet<String> urls = new HashSet<String>();
+    HashSet<String> urls = new HashSet<>();
     urls.addAll(Arrays.asList(serviceURLs));
     Jws2Instance match = null;
     if (services != null)
@@ -945,7 +975,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return match;
   }
 
-  Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+  Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();
 
   /**
    * get current preferred service of the given type, or global default
@@ -997,12 +1027,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
     if (preferredServiceMap == null)
     {
-      preferredServiceMap = new HashMap<String, Map<String, String>>();
+      preferredServiceMap = new HashMap<>();
     }
     Map<String, String> prefmap = preferredServiceMap.get(afid);
     if (prefmap == null)
     {
-      prefmap = new HashMap<String, String>();
+      prefmap = new HashMap<>();
       preferredServiceMap.put(afid, prefmap);
     }
     prefmap.put(serviceType, selectedServer.getHost());
@@ -1012,7 +1042,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   public void setPreferredServiceFor(String serviceType,
           String serviceAction, Jws2Instance selectedServer)
   {
-    setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+    setPreferredServiceFor(null, serviceType, serviceAction,
+            selectedServer);
   }
 
   /**