X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=5f1833168071d763100697fb4b50f3dd9456390b;hb=9829b31986b83957217a6b9086665ef7be9b1c8c;hp=22950f4010cfffca22b55190a44e131e76d18abe;hpb=98af16ccc5890b980f0c4f3acfb72d7128e3a6f0;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 22950f4..5f18331 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -18,13 +18,17 @@
 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.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;
@@ -63,7 +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
    * 
@@ -80,9 +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.");
@@ -91,6 +95,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     this.dbname = dbname;
     this.dbrefname = dbrefname;
     this.coordsys = coordsys;
+    this.connprops=connprops;
   }
 
   public String getAccessionSeparator()
@@ -120,31 +125,85 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     return coordsys.getVersion();
   }
 
-
   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);
+          org.biodas.jdas.client.SequenceClient sq = new SequenceClient(connprops.getConnectionPropertyProviderFor(sr));
+          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 '"
@@ -153,7 +212,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     }
     else
     {
-      Vector<SequenceI> seqs=null;
+      Vector<SequenceI> seqs = null;
       for (Map.Entry<String, Map<List<String>, DasSequenceAdapter>> resset : resultset
               .entrySet())
       {
@@ -183,14 +242,15 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
                                   + lbl
                                   + ") from "
                                   + resset.getKey()
-                                  + " (source is "
-                                  + getDbName());
+                                  + " (source is " + getDbName());
                   continue;
                 }
               }
               seqs = new java.util.Vector<SequenceI>();
-              // JDAS returns a sequence complete with any newlines and spaces in the XML
-              Sequence sq = new Sequence(lbl, e.getContent().replaceAll("\\s+", ""));
+              // JDAS returns a sequence complete with any newlines and spaces
+              // in the XML
+              Sequence sq = new Sequence(lbl, e.getContent().replaceAll(
+                      "\\s+", ""));
               sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion()
                       + ":" + e.getVersion(), lbl));
               seqs.addElement(sq);
@@ -211,12 +271,25 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
       {
         java.util.Vector<jalviewSourceI> srcs = new java.util.Vector<jalviewSourceI>();
         srcs.addElement(jsrc);
-        try {
-          new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
-                false);
+        try
+        {
+          jalview.ws.DasSequenceFeatureFetcher dssf=new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
+                  false, multiple);
+          while (dssf.isRunning())
+          {
+            try {
+              Thread.sleep(200);
+            } catch (InterruptedException x)
+            {
+              
+            }
+          }
+          
         } catch (Exception x)
         {
-          Cache.log.error("Couldn't retrieve features for sequence from its source.",x);
+          Cache.log
+                  .error("Couldn't retrieve features for sequence from its source.",
+                          x);
         }
       }