From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 10 May 2012 16:14:26 +0000 (+0100)
Subject: JAL-972 JAL-1084 propagate reference to local authentication provider so it can be... 
X-Git-Tag: Jalview_2_9~532^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7526a82c54f0ef8434f826a1f2323ca5ec1eb3b1;p=jalview.git

JAL-972 JAL-1084 propagate reference to local authentication provider so it can be passed to JDAS clients when querying sources.
---

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 7a78d8d..4f053aa 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -25,8 +25,10 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SequenceClient;
 import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
+import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
 import org.biodas.jdas.client.threads.SequenceClientMultipleSources;
 import org.biodas.jdas.schema.sequence.SEQUENCE;
 import org.biodas.jdas.schema.sources.COORDINATES;
@@ -65,7 +67,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected String dbname = "DASCS";
 
   protected String dbrefname = "das:source";
-
+  protected MultipleConnectionPropertyProviderI connprops=null;
   /**
    * create a new DbSource proxy for a DAS 1 source
    * 
@@ -82,9 +84,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
    *           if source is not capable of the 'sequence' command
    */
   public DasSequenceSource(String dbname, String dbrefname, SOURCE source,
-          VERSION version, COORDINATES coordsys) throws Exception
+          VERSION version, COORDINATES coordsys, MultipleConnectionPropertyProviderI connprops) throws Exception
   {
-    if (!(jsrc = new JalviewSource(source, false)).isSequenceSource())
+    if (!(jsrc = new JalviewSource(source, connprops, false)).isSequenceSource())
     {
       throw new Exception("Source " + source.getTitle()
               + " does not support the sequence command.");
@@ -93,6 +95,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     this.dbname = dbname;
     this.dbrefname = dbrefname;
     this.coordsys = coordsys;
+    this.connprops=connprops;
   }
 
   public String getAccessionSeparator()
@@ -149,8 +152,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
           System.err
                   .println("Retrieving IDs individually from das source: "
                           + sr);
-          // todo : get conn property provider
-          org.biodas.jdas.client.SequenceClient sq = new SequenceClient();
+          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(connprops.getConnectionPropertyProviderFor(sr));
           for (String q : toks)
           {
             List<String> qset = Arrays.asList(new String[]
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 2bc33b6..3ed597e 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -83,7 +83,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
   private List<jalviewSourceI> getDASSources()
   {
 
-    return getDASSources(getDasRegistryURL());
+    return getDASSources(getDasRegistryURL(), this);
   }
 
   /**
@@ -92,7 +92,7 @@ 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
     {
@@ -108,7 +108,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
       Integer latest;
       for (SOURCE src : dassources)
       {
-        JalviewSource jsrc=new JalviewSource(src, false);
+        JalviewSource jsrc=new JalviewSource(src, registry, false);
         latest=latests.get(jsrc.getSourceURL());
         if (latest!=null)
         {
@@ -223,7 +223,7 @@ 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;
   }
diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index c9caf6e..11bdf02 100644
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -7,6 +7,7 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 
+import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
 import org.biodas.jdas.dassources.Capabilities;
 import org.biodas.jdas.dassources.utils.DasTimeFormat;
 import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
@@ -23,9 +24,10 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 public class JalviewSource implements jalviewSourceI
 {
   SOURCE source;
-
-  public JalviewSource(SOURCE local2, boolean local)
+  MultipleConnectionPropertyProviderI connprov;
+  public JalviewSource(SOURCE local2, MultipleConnectionPropertyProviderI connprov, boolean local)
   {
+    this.connprov=connprov;
     this.local = local;
     source = local2;
   }
@@ -257,7 +259,7 @@ public class JalviewSource implements jalviewSourceI
           seqsources.add(ds = new DasSequenceSource(getTitle() + " ("
                   + cs.getAuthority() + " " + cs.getSource()
                   + (cs.getVersion() != null ? " " + cs.getVersion() : "")
-                  + ")", cs.getAuthority(), source, v, cs));
+                  + ")", cs.getAuthority(), source, v, cs, connprov));
           if (seqsources.size() > 1)
           {
             System.err.println("Added another sequence DB source for "
@@ -277,7 +279,7 @@ public class JalviewSource implements jalviewSourceI
       try
       {
         seqsources.add(new DasSequenceSource(getTitle(), getTitle(),
-                source, getVersion(), null));
+                source, getVersion(), null, connprov));
       } catch (Exception e)
       {
         // TODO Auto-generated catch block