From e04c42710f41ec0e1d12161a6379de280407c081 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 10 May 2012 17:06:39 +0100
Subject: [PATCH] JAL-1083 - graceful failover to single ID query mode for
 fetching features

---
 src/jalview/ws/DasSequenceFeatureFetcher.java      |   46 +++++++++++++++++++-
 .../dbsources/das/datamodel/DasSequenceSource.java |    4 +-
 2 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index c530b62..2a5476b 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -29,6 +29,7 @@ import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -41,6 +42,7 @@ import java.util.Vector;
 
 import javax.swing.JOptionPane;
 
+import org.biodas.jdas.client.FeaturesClient;
 import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
 import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
 import org.biodas.jdas.client.threads.FeaturesClientMultipleSources;
@@ -97,7 +99,7 @@ public class DasSequenceFeatureFetcher
   long startTime;
 
   private DasSourceRegistryI sourceRegistry;
-
+  private boolean useJDASMultiThread=true;
   /**
    * Creates a new SequenceFeatureFetcher object. Uses default
    * 
@@ -109,13 +111,20 @@ public class DasSequenceFeatureFetcher
   public DasSequenceFeatureFetcher(SequenceI[] sequences,
           FeatureSettings fsettings, Vector selectedSources)
   {
-    this(sequences, fsettings, selectedSources, true, true);
+    this(sequences, fsettings, selectedSources, true, true, true);
   }
 
   public DasSequenceFeatureFetcher(SequenceI[] oursequences,
           FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,
           boolean checkDbrefs, boolean promptFetchDbrefs)
   {
+    this(oursequences,fsettings,selectedSources2,checkDbrefs,promptFetchDbrefs,true);
+  }
+  public DasSequenceFeatureFetcher(SequenceI[] oursequences,
+          FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,
+          boolean checkDbrefs, boolean promptFetchDbrefs, boolean useJDasMultiThread)
+  {
+    this.useJDASMultiThread=useJDasMultiThread;
     this.selectedSources = new ArrayList<jalviewSourceI>();
     // filter both sequences and sources to eliminate duplicates
     for (jalviewSourceI src : selectedSources2)
@@ -343,6 +352,38 @@ public class DasSequenceFeatureFetcher
     }
     Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
     Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<String, Map<List<String>, DasGFFAdapter>>();
+    if (!useJDASMultiThread)
+    {
+      Iterator<String> sources=src.iterator();
+      // iterate over each query for each source and do each one individually
+      for (List<String> idl:ids)
+      {
+        String source=sources.next();
+        FeaturesClient featuresc=new FeaturesClient(sourceRegistry.getSessionHandler().getConnectionPropertyProviderFor(source));
+        for (String id:idl)
+        {
+          List<String> qid=Arrays.asList(new String[] { id});
+          try {
+            DasGFFAdapter dga=featuresc.fetchData(source, qid);
+            Map<List<String>,DasGFFAdapter> ers=results.get(source);
+            if (ers==null)
+            {
+              results.put(source, ers=new HashMap<List<String>,DasGFFAdapter>());
+            }
+            ers.put(qid, dga);
+          } catch (Exception ex)
+          {
+            Map<List<String>,Exception> ers=errors.get(source);
+            if (ers==null)
+            {
+              errors.put(source, ers=new HashMap<List<String>,Exception>());
+            }
+            ers.put(qid, ex);
+          }
+        }
+      }
+    } else {
+      // pass them all at once
     fc.fetchData(src, ids, false, results, errors);
     fc.shutDown();
     while (!fc.isTerminated())
@@ -355,6 +396,7 @@ public class DasSequenceFeatureFetcher
 
       }
     }
+    }
     Iterator<List<String>> idset = ids.iterator();
     Iterator<List<DBRefEntry>> idobjset = idobj.iterator();
     Iterator<Map<String, SequenceI>> seqset = sqset.iterator();
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 4a7b4bd..7a78d8d 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -271,8 +271,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
         srcs.addElement(jsrc);
         try
         {
-          new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
-                  false);
+          jalview.ws.DasSequenceFeatureFetcher dssf=new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
+                  false, multiple);
         } catch (Exception x)
         {
           Cache.log
-- 
1.7.10.2