From d3ae6172994393435dde1d0448b472ade6929628 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@bioperl.org>
Date: Thu, 7 Apr 2011 15:46:50 -0500
Subject: [PATCH] enable fast loading with namespaces; empty tables were being
 generated that had concatenated table names via _qualify() (e.g.
 volvox_volvox_feature); this fix checks for the presence of the namespace
 just in case and returns it w/o modification if it is found

---
 Bio/DB/SeqFeature/Store/DBI/mysql.pm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
index f9a217093..d6191fa7a 100644
--- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -566,12 +566,14 @@ sub _finish_bulk_update {
     my $fh = $self->dump_filehandle($table);
     my $path = $self->dump_path($table);
     $fh->close;
+    print STDERR "$path\n";
+    
     $dbh->do("LOAD DATA LOCAL INFILE '$path' REPLACE INTO TABLE $table FIELDS OPTIONALLY ENCLOSED BY '\\''") 
       or $self->throw($dbh->errstr);
     unlink $path;
   }
   delete $self->{bulk_update_in_progress};
-  delete $self->{filehandles};
+  delete $self->{   filehandles};
   $self->commit;
 }
 
@@ -736,7 +738,9 @@ sub _qualify {
   my $self = shift;
   my $table_name = shift;
   my $namespace = $self->namespace;
-  return $table_name unless defined $namespace;
+  return $table_name if (!defined $namespace ||
+                         # is namespace already present in table name?
+                         index($table_name, $namespace) == 0); 
   return "${namespace}_${table_name}";
 }
 
-- 
2.11.4.GIT