X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;h=de7f380132869ccbc607fc1c5fcd004b2aed8676;hb=788e840cc150aa4777a370cebfdf5d17589bbbaf;hp=7257d0c47492c6ea2472d9d1b0ab4831749a31fa;hpb=831ad693b1320d74143011e1fe510496876e148a;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 7257d0c..de7f380 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -1,25 +1,39 @@
-/**
+/*
+ * 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.dbsources.das.datamodel;
 
+import jalview.bin.Cache;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
-import org.apache.http.auth.InvalidCredentialsException;
 import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SourcesClient;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
@@ -29,15 +43,11 @@ import org.biodas.jdas.schema.sources.SOURCE;
 import org.biodas.jdas.schema.sources.SOURCES;
 import org.biodas.jdas.schema.sources.VERSION;
 
-import jalview.bin.Cache;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
 /**
  *
  */
-public class DasSourceRegistry implements DasSourceRegistryI,
-        MultipleConnectionPropertyProviderI
+public class DasSourceRegistry
+        implements DasSourceRegistryI, MultipleConnectionPropertyProviderI
 {
   // private org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
   private List<jalviewSourceI> dasSources = null;
@@ -46,7 +56,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
 
   private Hashtable<String, jalviewSourceI> localSources = null;
 
-  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
+  // public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/";
+  public static String DEFAULT_REGISTRY = "http://www.ebi.ac.uk/das-srv/registry/das/";
 
   /**
    * true if thread is running and we are talking to DAS registry service
@@ -58,6 +69,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     return loadingDasSources;
   }
 
+  @Override
   public String getDasRegistryURL()
   {
     String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
@@ -69,6 +81,13 @@ public class DasSourceRegistry implements DasSourceRegistryI,
               DEFAULT_REGISTRY);
       registry = DEFAULT_REGISTRY;
     }
+    if (registry.lastIndexOf("sources.xml") == registry.length() - 11)
+    {
+      // no trailing sources.xml document for registry in JDAS
+      jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
+              registry = registry.substring(0,
+                      registry.lastIndexOf("sources.xml")));
+    }
     return registry;
   }
 
@@ -82,7 +101,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
   private List<jalviewSourceI> getDASSources()
   {
 
-    return getDASSources(getDasRegistryURL());
+    return getDASSources(getDasRegistryURL(), this);
   }
 
   /**
@@ -91,7 +110,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
    * @param registryURL
    *          return sources from registryURL
    */
-  private static List<jalviewSourceI> getDASSources(String registryURL)
+  private static List<jalviewSourceI> getDASSources(String registryURL,
+          MultipleConnectionPropertyProviderI registry)
   {
     try
     {
@@ -103,16 +123,35 @@ public class DasSourceRegistry implements DasSourceRegistryI,
 
       List<SOURCE> dassources = sources.getSOURCE();
       ArrayList<jalviewSourceI> dsrc = new ArrayList<jalviewSourceI>();
+      HashMap<String, Integer> latests = new HashMap<String, Integer>();
+      Integer latest;
       for (SOURCE src : dassources)
       {
-        dsrc.add(new JalviewSource(src, false));
+        JalviewSource jsrc = new JalviewSource(src, registry, false);
+        latest = latests.get(jsrc.getSourceURL());
+        if (latest != null)
+        {
+          if (jsrc.isNewerThan(dsrc.get(latest.intValue())))
+          {
+            dsrc.set(latest.intValue(), jsrc);
+          }
+          else
+          {
+            System.out.println(
+                    "Debug: Ignored older source " + jsrc.getTitle());
+          }
+        }
+        else
+        {
+          latests.put(jsrc.getSourceURL(), Integer.valueOf(dsrc.size()));
+          dsrc.add(jsrc);
+        }
       }
       return dsrc;
     } catch (Exception ex)
     {
-      System.err.println("Failed to contact DAS1 registry at "
-              + registryURL);
-      ex.printStackTrace();
+      System.out.println(
+              "DAS1 registry at " + registryURL + " no longer exists");
       return new ArrayList<jalviewSourceI>();
     }
   }
@@ -142,13 +181,21 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     {
       // get local sources from properties and initialise the local source list
       String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
+
       if (local != null)
       {
+        int n = 1;
         StringTokenizer st = new StringTokenizer(local, "\t");
         while (st.hasMoreTokens())
         {
           String token = st.nextToken();
           int bar = token.indexOf("|");
+          if (bar == -1)
+          {
+            System.err.println(
+                    "Warning: DAS user local source appears to have no nickname (expected a '|' followed by nickname)\nOffending definition: '"
+                            + token + "'");
+          }
           String url = token.substring(bar + 1);
           boolean features = true, sequence = false;
           if (url.startsWith("sequence:"))
@@ -157,8 +204,25 @@ public class DasSourceRegistry implements DasSourceRegistryI,
             // this source also serves sequences as well as features
             sequence = true;
           }
-          createLocalSource(url, token.substring(0, bar), sequence,
-                  features);
+          try
+          {
+            if (bar > -1)
+            {
+              createLocalSource(url, token.substring(0, bar), sequence,
+                      features);
+            }
+            else
+            {
+              createLocalSource(url, "User Source" + n, sequence, features);
+            }
+          } catch (Exception q)
+          {
+            System.err.println(
+                    "Unexpected exception when creating local source from '"
+                            + token + "'");
+            q.printStackTrace();
+          }
+          n++;
         }
       }
     }
@@ -194,8 +258,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
   }
 
   /*
- * 
- */
+  * 
+  */
 
   @Override
   public jalviewSourceI createLocalSource(String url, String name,
@@ -207,7 +271,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     {
       localSources = new Hashtable<String, jalviewSourceI>();
     }
-    jalviewSourceI src = new JalviewSource(local, true);
+    jalviewSourceI src = new JalviewSource(local, this, true);
     localSources.put(local.getTitle(), src);
     return src;
   }
@@ -308,8 +372,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
       {
         String token = en.nextElement().toString();
         jalviewSourceI srco = localSources.get(token);
-        sb.append(token + "|"
-                + (srco.isSequenceSource() ? "sequence:" : "")
+        sb.append(token + "|" + (srco.isSequenceSource() ? "sequence:" : "")
                 + srco.getUri() + "\t");
       }
       return sb.toString();
@@ -325,8 +388,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     try
     {
       // TODO: allow same credentials for https and http
-      authStash.put(new URL(
-              "http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
+      authStash.put(
+              new URL("http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
               "Basic SmltOm1pSg==");
     } catch (MalformedURLException e)
     {