Changing the code and now we issue a begin_work() call and eval the call.

modules/Bio/EnsEMBL/Utils/SqlHelper.pm

@@ -468,11 +468,13 @@ previous setting. If your DBI/DBD driver does not support manual commits
 then this code will break. The code will turn off the 
 C<disconnect_when_idle()> method to allow transactions to work as expected.
 
-If the connection given already had AutoCommit off we will issue a rollback
-before handing the connection into the closure. This ensures the connection
-contains as fresh information from the database as possible. An effect of
-using REPEATABLE READ transaction isolation (InnoDB's default) is that
-your data is as fresh as when you started your current transaction. To
+All connections are issued a C<begin_work()> call on the DBI handle which
+informs the target engine we are starting a transaction. Giving this method
+a connection already in a transaction will cause an error to be raised and
+the abortion of the running transaction.
+
+An effect of using REPEATABLE READ transaction isolation (InnoDB's default) 
+is that your data is as fresh as when you started your current transaction. To
 ensure the freshest data use C<SELECT ... from ... LOCK IN SHARE MODE>
 or C<SELECT ... from ... LOCK FOR UPDATE> if you are going to issue
 updates.
@@ -496,6 +498,9 @@ sub transaction {
   my $original_dwi;
   my $ac;
   
+  my $error;
+  my $result;
+  
   #If we were already in a transaction then we do not do any management of the
   #session & wait for the parent transaction(s) to finish
   my $perform_transaction = $self->_perform_transaction_code();
@@ -503,19 +508,18 @@ sub transaction {
     $original_dwi = $dbc->disconnect_when_inactive();
     $ac = $dbc->db_handle()->{'AutoCommit'};
     $dbc->db_handle()->{'AutoCommit'} = 0;
-    #Issue a rollback as a signal for a fresh transaction if AutoCommit was off
-    $dbc->db_handle()->rollback() if(! $ac);
-    $self->_enable_transaction();
+    eval { $dbc->db_handle()->begin_work() };
+    $error = $@ if $@;
+    $self->_enable_transaction() unless $error;
   }
   
-  my $error;
-  my $result;
-  
-  eval {
-    $result = $callback->($dbc);
-    $dbc->db_handle()->commit() if $perform_transaction;
-  };
-  $error = $@;
+  if(!$error) {
+    eval {
+      $result = $callback->($dbc);
+      $dbc->db_handle()->commit() if $perform_transaction;
+    };
+    $error = $@;
+  }
   
   if($perform_transaction) {
     if($error) {