From 996d3319402197c787ced05f24b201cc66f6ed50 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 10 May 2012 16:04:06 +0100
Subject: [PATCH] JAL-1083 graceful failover to one ID per sequences query for
 sources that fail for multiple ID queries

---
 .../dbsources/das/datamodel/DasSequenceSource.java |   82 +++++++++++++++++---
 1 file changed, 70 insertions(+), 12 deletions(-)

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 22950f4..3883245 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -18,12 +18,14 @@
 package jalview.ws.dbsources.das.datamodel;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import org.biodas.jdas.client.SequenceClient;
 import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
 import org.biodas.jdas.client.threads.SequenceClientMultipleSources;
 import org.biodas.jdas.schema.sequence.SEQUENCE;
@@ -124,27 +126,83 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     StringTokenizer st = new StringTokenizer(queries, "\t");
-    List<String> toks = new ArrayList<String>(), src = new ArrayList<String>(),acIds=new ArrayList<String>();
+    List<String> toks = new ArrayList<String>(), src = new ArrayList<String>(), acIds = new ArrayList<String>();
     while (st.hasMoreTokens())
     {
       String t;
-      toks.add(t=st.nextToken());
+      toks.add(t = st.nextToken());
       acIds.add(t.replaceAll(":[0-9,]+", ""));
     }
     src.add(jsrc.getSourceURL());
     Map<String, Map<List<String>, DasSequenceAdapter>> resultset = new HashMap<String, Map<List<String>, DasSequenceAdapter>>();
     Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
-    SequenceClientMultipleSources sclient;
-    sclient = new SequenceClientMultipleSources();
-    sclient.fetchData(src, toks, resultset, errors);
-    sclient.shutDown();
-    while (!sclient.isTerminated())
+    
+    // First try multiple sources
+    boolean multiple = true, retry = false;
+    do
     {
-      try {Thread.sleep(200);
-      
-      } catch (InterruptedException x) {}
-    }
-            
+      if (!multiple)
+      {
+        retry = false;
+        // slow, fetch one at a time.
+        for (String sr : src)
+        {
+          System.err
+                  .println("Retrieving IDs individually from das source: "
+                          + sr);
+          // todo : get conn property provider
+          org.biodas.jdas.client.SequenceClient sq = new SequenceClient();
+          for (String q : toks)
+          {
+            List<String> qset = Arrays.asList(new String[]
+            { q });
+            try
+            {
+              DasSequenceAdapter s = sq.fetchData(sr, qset);
+              Map<List<String>, DasSequenceAdapter> dss = resultset.get(sr);
+              if (dss == null)
+              {
+                resultset
+                        .put(sr,
+                                dss = new HashMap<List<String>, DasSequenceAdapter>());
+              }
+              dss.put(qset, s);
+            } catch (Exception x)
+            {
+              Map<List<String>, Exception> ers = errors.get(sr);
+              if (ers == null)
+              {
+                errors.put(sr, ers = new HashMap<List<String>, Exception>());
+              }
+              ers.put(qset, x);
+            }
+          }
+        }
+      }
+      else
+      {
+        SequenceClientMultipleSources sclient;
+        sclient = new SequenceClientMultipleSources();
+        sclient.fetchData(src, toks, resultset, errors);
+        sclient.shutDown();
+        while (!sclient.isTerminated())
+        {
+          try
+          {
+            Thread.sleep(200);
+
+          } catch (InterruptedException x)
+          {
+          }
+        }
+        if (resultset.isEmpty() && !errors.isEmpty())
+        {
+          retry = true;
+          multiple = false;
+        }
+      }
+    } while (retry);
+
     if (resultset.isEmpty())
     {
       System.err.println("Sequence Query to " + jsrc.getTitle() + " with '"
-- 
1.7.10.2