X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabaWsServerQuery.java;h=5831df860f1ae584ecbfacbc1291e5c6a51ec8a0;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=2799e98f360f13df3b282a4403cec322d194ea20;hpb=4674dbf3f27eee61a7e21174649aa4c9ec7a04dd;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java
index 2799e98..5831df8 100644
--- a/src/jalview/ws/jws2/JabaWsServerQuery.java
+++ b/src/jalview/ws/jws2/JabaWsServerQuery.java
@@ -1,111 +1,260 @@
+/*
+ * 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.
+ *  
+ * 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;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
 
-import compbio.data.msa.MsaWS;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashSet;
+import java.util.Set;
+
+import compbio.data.msa.Category;
+import compbio.data.msa.JABAService;
 import compbio.ws.client.Jws2Client;
 import compbio.ws.client.Services;
 
 /**
  * @author JimP
- *
+ * 
  */
 public class JabaWsServerQuery implements Runnable
 {
 
-  Jws2Discoverer jws2Discoverer=null;
-  String jwsservers=null;
-  boolean quit=false,
-  running=false;
+  Jws2Discoverer jws2Discoverer = null;
+
+  String jwsserver = null;
+
+  boolean quit = false, running = false;
+
   /**
    * @return the running
    */
-  public  boolean isRunning()
+  public boolean isRunning()
   {
     return running;
   }
 
   /**
-   * @param quit the quit to set
+   * @param quit
+   *          the quit to set
    */
   public void setQuit(boolean quit)
   {
     this.quit = quit;
   }
 
-  public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
+  public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
   {
     this.jws2Discoverer = jws2Discoverer;
-    this.jwsservers=jwsservers;
+    this.jwsserver = server;
   }
 
-  /* (non-Javadoc)
+  Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS,
+      Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+      Services.TcoffeeWS };
+
+  Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS,
+      Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+      Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS,
+      Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS,
+      Services.RNAalifoldWS };
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see java.lang.Runnable#run()
    */
   @Override
   public void run()
   {
-    running=true;
-        try
+    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))
       {
-        boolean noservices=true;
+        compbio.data.msa.RegistryWS registry = null;
+        Set svccategories = null;
+        boolean noservices = true;
         // look for services
-        for (Services srv : Services.values())
+        boolean jabasws2 = false;
+        // If we are dealing with a JABAWS2 service, then just go and ask the
+        // JABAWS 2 service registry
+        Set<Services> srv_set = new HashSet<Services>();
+
+        Set<Category> categories = Category.getCategories();
+        String svc_cat;
+
+        try
         {
-          if (quit)
+          // JBPNote: why is RegistryWS in compbio.data.msa ?
+          registry = Jws2Client.connectToRegistry(jwsserver);
+          if (registry != null)
           {
-            running=false;
-            return;
+            // System.err.println("Test Services Output\n"
+            // + registry.testAllServices());
+            // TODO: enumerate services and test those that haven't been tested
+            // in the last n-days/hours/etc.
+
+            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());
+
           }
-          MsaWS service = null;
-          try
+        } catch (Exception ex)
+        {
+          System.err.println("Exception whilst trying to get at registry:");
+          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: " + jwsserver
+                  + " is a JABAWS1 server. Using hardwired list.");
+          for (Services srv : JABAWS1SERVERS)
           {
-            service = Jws2Client.connect(jwsservers, srv);
-          } catch (Exception e)
+            srv_set.add(srv);
+          }
+        }
+
+        for (Category cat : categories)
+        {
+          for (Services srv : cat.getServices())
           {
-            System.err.println("Jws2 Discoverer: Problem on "
-                    + jwsservers + " with service " + srv + ":\n"
-                    + e.getMessage());
-            if (!(e instanceof javax.xml.ws.WebServiceException))
+            if (quit)
             {
-              e.printStackTrace();
+              running = false;
+              return;
             }
-            // For moment, report service as a problem.
-            jws2Discoverer.addInvalidServiceUrl(jwsservers);
-          }
-          ;
-          if (service != null)
-          {
-            noservices=false;
-            jws2Discoverer.addService(jwsservers, srv, service);
+            if (!srv_set.contains(srv))
+            {
+              continue;
+            }
+            JABAService service = null;
+            try
+            {
+              service = Jws2Client.connect(jwsserver, srv);
+            } catch (Exception e)
+            {
+              System.err.println("Jws2 Discoverer: Problem on " + 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(jwsserver);
+            }
+            ;
+            if (service != null
+                    && !Jws2InstanceFactory.ignoreService(srv.toString()))
+            {
+              noservices = false;
+              Jws2Instance svc = null;
+              if (registry != null)
+              {
+
+                String description = registry.getServiceDescription(srv);
+
+                svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+                        srv.toString(), cat.name, description, service);
+              }
+              if (svc == null)
+              {
+                svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+                        srv.toString(), cat.name,
+                        "JABAWS 1 Alignment Service", service);
+              }
+              jws2Discoverer.addService(jwsserver, svc);
+            }
+
           }
         }
+
         if (noservices)
         {
-          jws2Discoverer.addUrlwithnoservices(jwsservers);
+          jws2Discoverer.addUrlwithnoservices(jwsserver);
         }
       }
       else
       {
-        jws2Discoverer.addInvalidServiceUrl(jwsservers);
-        Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+        jws2Discoverer.addInvalidServiceUrl(jwsserver);
+        Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
       }
     } catch (Exception e)
     {
       e.printStackTrace();
-      Cache.log.warn("Exception when discovering Jws2 services.", e);
-      jws2Discoverer.addInvalidServiceUrl(jwsservers);
+      Console.warn("Exception when discovering Jws2 services.", e);
+      jws2Discoverer.addInvalidServiceUrl(jwsserver);
     } catch (Error e)
     {
-      Cache.log.error("Exception when discovering Jws2 services.", e);
-      jws2Discoverer.addInvalidServiceUrl(jwsservers);
+      Console.error("Exception when discovering Jws2 services.", e);
+      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;
+      }
     }
-    running=false;
+    return result;
   }
 
 }