From bf76233462b161c67e183072705581f2b5ce5979 Mon Sep 17 00:00:00 2001
From: Simon Brent <sb23@sanger.ac.uk>
Date: Fri, 12 Aug 2011 08:26:45 +0000
Subject: [PATCH] merging changes from branch-ensembl-63
---
modules/Bio/EnsEMBL/Utils/ConversionSupport.pm | 18 ++++++++++++------
1 file changed, 12 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index 1f00fdf4f6..eb409479c8 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -65,6 +65,8 @@ use Cwd qw(abs_path);
use DBI;
use Data::Dumper;
+my $species_c = 1; #counter to be used for each database connection made
+
=head2 new
Arg[1] : String $serverroot - root directory of your ensembl sandbox
@@ -722,13 +724,15 @@ sub get_database {
throw("Unknown database: $database") unless $adaptors{$database};
$self->dynamic_use($adaptors{$database});
+ my $species = 'species' . $species_c;
my $dba = $adaptors{$database}->new(
- -host => $self->param("${prefix}host"),
- -port => $self->param("${prefix}port"),
- -user => $self->param("${prefix}user"),
- -pass => $self->param("${prefix}pass") || '',
- -dbname => $self->param("${prefix}dbname"),
- -group => $database,
+ -host => $self->param("${prefix}host"),
+ -port => $self->param("${prefix}port"),
+ -user => $self->param("${prefix}user"),
+ -pass => $self->param("${prefix}pass") || '',
+ -dbname => $self->param("${prefix}dbname"),
+ -group => $database,
+ -species => $species,
);
#can use this approach to get dna from another db
# my $dna_db = $adaptors{$database}->new(
@@ -744,6 +748,8 @@ sub get_database {
# a group 'core' for this now
$dba->dnadb($dba);
+ $species_c++;
+
$self->{'_dba'}->{$database} = $dba;
$self->{'_dba'}->{'default'} = $dba unless $self->{'_dba'}->{'default'};
return $self->{'_dba'}->{$database};
--
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