From d9eaabe4dc809405a9b207dc230e0738ea8f57f6 Mon Sep 17 00:00:00 2001
From: Jessica Severin <jessica@ebi.ac.uk>
Date: Mon, 18 Apr 2005 11:07:54 +0000
Subject: [PATCH] made more Registry friendly by setting -species to be the
$dbname thus allowing one to do hybrid URL/Registry code like... if($url) {
$dbc = Bio::EnsEMBL::Hive::URLFactory->fetch($url, 'compara')->dbc;
$dbname = $dbc->dbname(); } else { $dbc =
Bio::EnsEMBL::Registry->get_DBAdaptor($dbname,'compara')->dbc; } $fa =
Bio::EnsEMBL::Registry->get_adaptor($dbname,'compara','Family');
---
modules/Bio/EnsEMBL/Hive/URLFactory.pm | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/URLFactory.pm b/modules/Bio/EnsEMBL/Hive/URLFactory.pm
index fe8e7efca..134b77283 100755
--- a/modules/Bio/EnsEMBL/Hive/URLFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/URLFactory.pm
@@ -38,6 +38,7 @@ my $_URLFactory_global_instance;
package Bio::EnsEMBL::Hive::URLFactory;
use strict;
+use Switch;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
@@ -195,10 +196,15 @@ sub _get_db_connection
return ($dba,$path) if($dba);
#print("CONNECT via\n user=$user\n pass=$pass\n host=$host\n port=$port\n dbname=$dbname\n path=$path\n type=$type\n");
- $module = "Bio::EnsEMBL::DBSQL::DBAdaptor" if($type eq 'core');
- $module = "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor" if($type eq 'compara');
- $module = "Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor" if($type eq 'pipeline');
-
+ switch ($type) {
+ case 'core' { $module = "Bio::EnsEMBL::DBSQL::DBAdaptor"; }
+ case 'pipeline' { $module = "Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor"; }
+ case 'compara' {
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+ $module = "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
+ }
+ }
+
$dba = "$module"->new (
-disconnect_when_inactive => 0,
-driver => 'mysql',
@@ -206,7 +212,9 @@ sub _get_db_connection
-pass => $pass,
-host => $host,
-port => $port,
- -dbname => $dbname);
+ -dbname => $dbname,
+ -species => $dbname
+ );
$_URLFactory_global_instance->{$connectionKey} = $dba;
return ($dba,$path);
--
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