use iBatis transactions

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4635 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/util/DatabaseDocument.java

@@ -116,7 +116,7 @@ public class DatabaseDocument extends Document
    * 
    * @param location
    *          This should be a URL string giving:
-   *          jdbc:postgresql://host:port/datbase_name?user=username
+   *          jdbc:postgresql://host:port/database_name?user=username
    * @param feature_id
    *          ID of a feature to be extracted.
    * 
@@ -291,20 +291,25 @@ public class DatabaseDocument extends Document
     try
     {
       ChadoDAO dao = getDAO();
+      ByteBuffer entry = new ByteBuffer();
       
+      try
+      {
+        if(dao instanceof IBatisDAO)
+          ((IBatisDAO) dao).startTransaction();
 
         // if creating a gene builder
         if(gene_builder)
         {
           List schemaList = new Vector();
           schemaList.add(schema);
-        return new ByteArrayInputStream(
-            getGeneFeature(feature_id, schemaList, dao).getBytes());
+          return new ByteArrayInputStream(getGeneFeature(feature_id,
+              schemaList, dao).getBytes());
         }
 
         gff_buffer = getGff(dao, feature_id);
 
-      ByteBuffer entry = new ByteBuffer();
+        
         if(splitGFFEntry)
         {
           if(gff_buffer[0].size() > 0)
@@ -323,6 +328,15 @@ public class DatabaseDocument extends Document
           getChadoSequence(dao, entry);
         }
 
+        if(dao instanceof IBatisDAO)
+          ((IBatisDAO) dao).commitTransaction();
+      }
+      finally
+      {
+        if(dao instanceof IBatisDAO)
+          ((IBatisDAO) dao).endTransaction();
+      }
+
       instream = new ByteArrayInputStream(entry.getBytes());
       return instream;
     }
@@ -707,9 +721,14 @@ public class DatabaseDocument extends Document
       for(int j=0; j<v_synonyms.size(); j++)
       {
         alias = (ChadoFeatureSynonym)v_synonyms.get(j);
-        this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
+        
+        this_buff.append( getCvtermName(alias.getSynonym().getCvterm().getCvtermId(), dao) + "=" );
+        //this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
         this_buff.append(alias.getSynonym().getName());
         
+        //System.out.println(getCvtermName(alias.getSynonym().getCvterm().getCvtermId(), dao)+" "+
+        //    alias.getSynonym().getCvterm().getName());
+        
         if(j<v_synonyms.size()-1)
           this_buff.append(";");
       }
@@ -845,6 +864,9 @@ public class DatabaseDocument extends Document
       
     try
     {
+      if(dao instanceof IBatisDAO)
+        ((IBatisDAO) dao).startTransaction();
+      
       schema_list = dao.getSchema();
       Iterator it      = schema_list.iterator();
 
@@ -869,6 +891,9 @@ public class DatabaseDocument extends Document
         }
       }
       
+      if(dao instanceof IBatisDAO)
+        ((IBatisDAO) dao).commitTransaction();
+      
     }
     catch(java.sql.SQLException sqlExp)
     {
@@ -878,6 +903,12 @@ public class DatabaseDocument extends Document
                                     JOptionPane.ERROR_MESSAGE);
       sqlExp.printStackTrace();
     }
+    finally
+    {
+      if(dao instanceof IBatisDAO)
+        ((IBatisDAO) dao).endTransaction();
+    }
+    
     return db;
   }