X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDiscoverer.java;h=a7f139f7262329a1d5bff31d8aa139ab29b5fc3e;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=40d29e7ffc9739704dc4b71d5920295bffa7991d;hpb=ae0f884be559f2f706945b379d110e9c60642364;p=jalview.git

diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index 40d29e7..a7f139f 100755
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -1,3 +1,21 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program 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 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 package jalview.ws;
 
 /**
@@ -16,6 +34,7 @@ import ext.vamsas.*;
 import java.util.Vector;
 import java.util.Hashtable;
 import java.util.ArrayList;
+import java.util.StringTokenizer;
 
 public class Discoverer
     extends Thread implements Runnable
@@ -92,7 +111,40 @@ public class Discoverer
 
   public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string
   public static java.util.Vector serviceList = null; // flat list of services
+  static private Vector getDiscoveryURLS() {
+    Vector urls = new Vector();
+    String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+        "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
 
+    try{
+      StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
+      while (st.hasMoreElements())
+      {
+        String url = null;
+        try
+        {
+          java.net.URL u = new java.net.URL(url = st.nextToken());
+          if (!urls.contains(u))
+            urls.add(u);
+          else
+            jalview.bin.Jalview.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
+        }
+        catch (Exception ex)
+        {
+          jalview.bin.Jalview.log.warn(
+              "Problem whilst trying to make a URL from '" +
+              ( (url != null) ? url : "<null>")+"'");
+          jalview.bin.Jalview.log.warn("This was probably due to a malformed comma separated list"
+                                       +" in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
+          jalview.bin.Jalview.log.debug("Exception was ",ex);
+        }
+      }
+    }catch(Exception ex)
+    {jalview.bin.Jalview.log.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",ex);}
+    if (urls.size()>0)
+      return urls;
+    return null;
+  }
   static
   {
 
@@ -101,16 +153,7 @@ public class Discoverer
       reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
       if (reallyDiscoverServices)
       {
-        RootServiceURL = new java.net.URL(
-            "http://webservices.compbio.dundee.ac.uk:8080/jalTestWS/services/ServiceRegistry");
-        if (ServiceURLList == null)
-        {
-          ServiceURLList = new Vector();
-        }
-        if (!ServiceURLList.contains(RootServiceURL))
-        {
-          ServiceURLList.add(RootServiceURL);
-        }
+        ServiceURLList = getDiscoveryURLS();
       }
       else
       {
@@ -137,7 +180,7 @@ public class Discoverer
                 "Cuff J. A and Barton G.J (1999) Application of enhanced " +
                 "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
                 "Proteins 40:502-511",
-                "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JPred Secondary Structure Prediction"
+                "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction"
                 )};
         services = new Hashtable();
         serviceList = new Vector();
@@ -166,9 +209,9 @@ public class Discoverer
     }
     catch (Exception e)
     {
-      System.err.println("failed to locate Services through URL : " +
-                         location + "\n");
-      e.printStackTrace();
+      jalview.bin.Jalview.log.debug("No Discovery service at " +
+                         location);
+      jalview.bin.Jalview.log.debug(e);
 
     }
     if ( (shs != null) && shs.getServices().length > 0)
@@ -253,6 +296,11 @@ public class Discoverer
       {
 
         buildServiceLists(sh, cat, sscat);
+      } else {
+        jalview.bin.Jalview.log.warn(
+            "No services at "
+            +((java.net.URL) ServiceURLList.get(s_url))
+            +" - check DISCOVERY_URLS property in .jalview_properties");
       }
       s_url++;
     }