X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabaWsServerQuery.java;h=5b83e11915664a932ee10692f6bcbc0d9f38b98d;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=5a2db832528112841b9ea69707a9287bead8cecf;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java
index 5a2db83..5b83e11 100644
--- a/src/jalview/ws/jws2/JabaWsServerQuery.java
+++ b/src/jalview/ws/jws2/JabaWsServerQuery.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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.
  */
 /**
@@ -23,7 +25,11 @@ package jalview.ws.jws2;
 
 import jalview.bin.Cache;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
 
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -41,7 +47,7 @@ public class JabaWsServerQuery implements Runnable
 
   Jws2Discoverer jws2Discoverer = null;
 
-  String jwsservers = null;
+  String jwsserver = null;
 
   boolean quit = false, running = false;
 
@@ -62,10 +68,10 @@ public class JabaWsServerQuery implements Runnable
     this.quit = quit;
   }
 
-  public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
+  public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
   {
     this.jws2Discoverer = jws2Discoverer;
-    this.jwsservers = jwsservers;
+    this.jwsserver = server;
   }
 
   Services[] JABAWS1SERVERS = new Services[]
@@ -76,7 +82,7 @@ public class JabaWsServerQuery implements Runnable
   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
       Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
       Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
-      Services.JronnWS };
+      Services.JronnWS, Services.RNAalifoldWS };
 
   /*
    * (non-Javadoc)
@@ -89,7 +95,9 @@ public class JabaWsServerQuery implements Runnable
     running = true;
     try
     {
-      if (Jws2Client.validURL(jwsservers))
+      // TODO this test doesn't seem to attempt a connection - should it?
+      // would save a lot of failed tries with UnknownHostException
+      if (isValidUrl(jwsserver))
       {
         compbio.data.msa.RegistryWS registry = null;
         Set svccategories = null;
@@ -106,7 +114,7 @@ public class JabaWsServerQuery implements Runnable
         try
         {
           // JBPNote: why is RegistryWS in compbio.data.msa ?
-          registry = Jws2Client.connectToRegistry(jwsservers);
+          registry = Jws2Client.connectToRegistry(jwsserver);
           if (registry != null)
           {
             // System.err.println("Test Services Output\n"
@@ -116,8 +124,17 @@ public class JabaWsServerQuery implements Runnable
 
             jabasws2 = true;
             srv_set = registry.getSupportedServices();
+
+            // dan test
+            System.out.println("registry.getSupportedServices: "
+                    + srv_set.toString());
+
             svccategories = registry.getServiceCategories();
 
+            // dan test
+            // System.out.println("registry.getServiceCategories: " +
+            // svccategories.toString());
+
           }
         } catch (Exception ex)
         {
@@ -125,13 +142,14 @@ public class JabaWsServerQuery implements Runnable
           ex.printStackTrace();
           // if that failed, then we are probably working with a JABAWS1 server.
           // in that case, look for each service endpoint
-          System.err.println("JWS2 Discoverer: " + jwsservers
+          System.err.println("JWS2 Discoverer: " + jwsserver
                   + " is a JABAWS1 server. Using hardwired list.");
           for (Services srv : JABAWS1SERVERS)
           {
             srv_set.add(srv);
           }
         }
+
         for (Category cat : categories)
         {
           for (Services srv : cat.getServices())
@@ -148,21 +166,22 @@ public class JabaWsServerQuery implements Runnable
             JABAService service = null;
             try
             {
-              service = Jws2Client.connect(jwsservers, srv);
+              service = Jws2Client.connect(jwsserver, srv);
             } catch (Exception e)
             {
               System.err.println("Jws2 Discoverer: Problem on "
-                      + jwsservers + " with service " + srv + ":\n"
+                      + jwsserver + " with service " + srv + ":\n"
                       + e.getMessage());
               if (!(e instanceof javax.xml.ws.WebServiceException))
               {
                 e.printStackTrace();
               }
               // For moment, report service as a problem.
-              jws2Discoverer.addInvalidServiceUrl(jwsservers);
+              jws2Discoverer.addInvalidServiceUrl(jwsserver);
             }
             ;
-            if (service != null)
+            if (service != null
+                    && !Jws2InstanceFactory.ignoreService(srv.toString()))
             {
               noservices = false;
               Jws2Instance svc = null;
@@ -171,15 +190,16 @@ public class JabaWsServerQuery implements Runnable
 
                 String description = registry.getServiceDescription(srv);
 
-                svc = new Jws2Instance(jwsservers, srv.toString(),
-                        cat.name, description, service);
+                svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+                        srv.toString(), cat.name, description, service);
               }
               if (svc == null)
               {
-                svc = new Jws2Instance(jwsservers, srv.toString(),
-                        cat.name, "JABAWS 1 Alignment Service", service);
+                svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+                        srv.toString(), cat.name,
+                        "JABAWS 1 Alignment Service", service);
               }
-              jws2Discoverer.addService(jwsservers, svc);
+              jws2Discoverer.addService(jwsserver, svc);
             }
 
           }
@@ -187,25 +207,53 @@ public class JabaWsServerQuery implements Runnable
 
         if (noservices)
         {
-          jws2Discoverer.addUrlwithnoservices(jwsservers);
+          jws2Discoverer.addUrlwithnoservices(jwsserver);
         }
       }
       else
       {
-        jws2Discoverer.addInvalidServiceUrl(jwsservers);
-        Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+        jws2Discoverer.addInvalidServiceUrl(jwsserver);
+        Cache.log.warn("Ignoring invalid Jws2 service url " + jwsserver);
       }
     } catch (Exception e)
     {
       e.printStackTrace();
       Cache.log.warn("Exception when discovering Jws2 services.", e);
-      jws2Discoverer.addInvalidServiceUrl(jwsservers);
+      jws2Discoverer.addInvalidServiceUrl(jwsserver);
     } catch (Error e)
     {
       Cache.log.error("Exception when discovering Jws2 services.", e);
-      jws2Discoverer.addInvalidServiceUrl(jwsservers);
+      jws2Discoverer.addInvalidServiceUrl(jwsserver);
     }
     running = false;
   }
 
+  /**
+   * Check if the URL is valid and responding.
+   * 
+   * @return
+   */
+  private boolean isValidUrl(String server)
+  {
+    // return Jws2Client.validURL(jwsserver); // checks syntax only
+    boolean result = false;
+    if (server != null) {
+      try {
+        URL url = new URL(server);
+        url.openStream().close();
+        result = true;
+      } catch (MalformedURLException e)
+      {
+        System.err.println("Invalid server URL: " + server);
+        result = false;
+      } catch (IOException e)
+      {
+        System.err.println("Error connecting to server: " + server + ": "
+                + e.toString());
+        result = false;
+      }
+    }
+    return result;
+  }
+
 }