Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / ws / jws1 / Discoverer.java

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 9a6c445..a5b73da 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.jws1;
 
+
 import java.net.URL;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
@@ -31,6 +32,7 @@ import ext.vamsas.RegistryServiceSoapBindingStub;
 import ext.vamsas.ServiceHandle;
 import ext.vamsas.ServiceHandles;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.ApplicationSingletonProvider;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.gui.JvOptionPane;
@@ -38,7 +40,6 @@ import jalview.util.MessageManager;
 
 public class Discoverer implements Runnable, ApplicationSingletonI
 {
-
   public static Discoverer getInstance()
   {
     return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
@@ -48,7 +49,6 @@ public class Discoverer implements Runnable, ApplicationSingletonI
   {
     // use getInstance()
   }
-
   ext.vamsas.IRegistry registry; // the root registry service.
 
   private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
@@ -111,7 +111,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
       // timeout
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
+      Console.error(
               "Serious!  Service location failed\nfor URL :" + WsURL + "\n",
               ex);
 
@@ -143,7 +143,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
   private Vector<URL> getDiscoveryURLS()
   {
     Vector<URL> urls = new Vector<>();
-    String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+    String RootServiceURLs = Cache.getDefault("DISCOVERY_URLS",
             "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
 
     try
@@ -161,23 +161,21 @@ public class Discoverer implements Runnable, ApplicationSingletonI
           }
           else
           {
-            jalview.bin.Cache.log
-                    .info("Ignoring duplicate url in DISCOVERY_URLS list");
+            Console.info("Ignoring duplicate url in DISCOVERY_URLS list");
           }
         } catch (Exception ex)
         {
-          jalview.bin.Cache.log
-                  .warn("Problem whilst trying to make a URL from '"
-                          + ((url != null) ? url : "<null>") + "'");
-          jalview.bin.Cache.log.warn(
+          Console.warn("Problem whilst trying to make a URL from '"
+                  + ((url != null) ? url : "<null>") + "'");
+          Console.warn(
                   "This was probably due to a malformed comma separated list"
                           + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
-          jalview.bin.Cache.log.debug("Exception was ", ex);
+          Console.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.warn(
+      Console.warn(
               "Error parsing comma separated list of urls in DISCOVERY_URLS.",
               ex);
     }
@@ -198,12 +196,12 @@ public class Discoverer implements Runnable, ApplicationSingletonI
 
   private void discovery()
   {
-    jalview.bin.Cache.log
+    Console
             .debug("(Re)-Initialising the discovery URL list.");
     try
     {
       Discoverer d = getInstance();
-      reallyDiscoverServices = jalview.bin.Cache
+      reallyDiscoverServices = Cache
               .getDefault("DISCOVERY_START", false);
       if (reallyDiscoverServices)
       {
@@ -211,7 +209,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
       }
       else
       {
-        jalview.bin.Cache.log.debug("Setting default services");
+        Console.debug("Setting default services");
         services = new Hashtable<>();
         // Muscle, Clustal and JPred.
         ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
@@ -262,7 +260,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
     ServiceHandles shs = null;
     try
     {
-      jalview.bin.Cache.log.debug("Discovering services using " + location);
+      Console.debug("Discovering services using " + location);
       shs = locateWebService(location).getServices();
     } catch (org.apache.axis.AxisFault f)
     {
@@ -280,13 +278,13 @@ public class Discoverer implements Runnable, ApplicationSingletonI
       }
       else
       {
-        jalview.bin.Cache.log.warn("No Discovery service at " + location);
-        jalview.bin.Cache.log.debug("Axis Fault", f);
+        Console.warn("No Discovery service at " + location);
+        Console.debug("Axis Fault", f);
       }
     } catch (Exception e)
     {
-      jalview.bin.Cache.log.warn("No Discovery service at " + location);
-      jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
+      Console.warn("No Discovery service at " + location);
+      Console.debug("Discovery Service General Exception", e);
     }
     if ((shs != null) && shs.getServices().length > 0)
     {
@@ -316,9 +314,9 @@ public class Discoverer implements Runnable, ApplicationSingletonI
     {
       if (!cat.contains(sh[i]))
       {
-        jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
-                + " service called " + sh[i].getName() + " exists at "
-                + sh[i].getEndpointURL() + "\n");
+        Console.debug("A " + sh[i].getAbstractName() + " service called "
+                + sh[i].getName() + " exists at " + sh[i].getEndpointURL()
+                + "\n");
         if (!sscat.containsKey(sh[i].getAbstractName()))
         {
           sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
@@ -338,16 +336,15 @@ public class Discoverer implements Runnable, ApplicationSingletonI
               disc_serv = new java.net.URL(sh[i].getEndpointURL());
               if (!ServiceURLList.contains(disc_serv))
               {
-                jalview.bin.Cache.log.debug(
+                Console.debug(
                         "Adding new discovery service at " + disc_serv);
                 ServiceURLList.add(disc_serv);
                 seenNewDiscovery = true;
               }
             } catch (Exception e)
             {
-              jalview.bin.Cache.log
-                      .debug("Ignoring bad discovery service URL "
-                              + sh[i].getEndpointURL(), e);
+              Console.debug("Ignoring bad discovery service URL "
+                      + sh[i].getEndpointURL(), e);
             }
           }
         }
@@ -364,8 +361,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
     int s_url = 0;
     if (ServiceURLList == null)
     {
-      jalview.bin.Cache.log
-              .debug("No service endpoints to use for service discovery.");
+      Console.debug("No service endpoints to use for service discovery.");
       return;
     }
     while (s_url < ServiceURLList.size())
@@ -378,8 +374,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
       }
       else
       {
-        jalview.bin.Cache.log.warn("No services at "
-                + (ServiceURLList.get(s_url))
+        Console.warn("No services at " + (ServiceURLList.get(s_url))
                 + " - check DISCOVERY_URLS property in .jalview_properties");
       }
       s_url++;
@@ -402,7 +397,7 @@ public class Discoverer implements Runnable, ApplicationSingletonI
   @Override
   public void run()
   {
-    Cache.log.info("Discovering jws1 services");
+    Console.info("Discovering jws1 services");
     Discoverer.doDiscovery();
     discoverServices();
   }
@@ -458,7 +453,6 @@ public class Discoverer implements Runnable, ApplicationSingletonI
     }
     return instance;
   }
-
   public static Hashtable<String, Vector<ServiceHandle>> getServices()
   {
     return getInstance().services;