From b1ca6d5243d8e7a5232eafb821da18f5b0ba9b9d Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 10 Mar 2011 16:47:04 +0000
Subject: [PATCH] report warning if regitry call to get_alias is called with an
invalid species name. Also had to add option to get_DBAdaptor to not look up
aliases so that warning are not given the first time we use it
---
modules/Bio/EnsEMBL/Registry.pm | 16 ++++++++++++----
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm | 3 ++-
2 files changed, 14 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 0a1d13ec71..5359ea9e41 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -554,6 +554,7 @@ sub add_DBAdaptor {
Arg [1] : name of the species to get the adaptor for in the registry.
Arg [2] : name of the group to get the adaptor for in the registry.
+ Arg [3] : if set will not look for alias.
Example : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
Returntype : DBAdaptor
Exceptions : none
@@ -562,10 +563,11 @@ sub add_DBAdaptor {
=cut
sub get_DBAdaptor {
- my ( $class, $species, $group ) = @_;
+ my ( $class, $species, $group , $no_alias_check) = @_;
throw 'arrggh for '.$species if ! defined $species;
- $species = $class->get_alias($species);
-
+ if(!defined($no_alias_check) or !$no_alias_check){
+ $species = $class->get_alias($species);
+ }
return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
}
@@ -1104,7 +1106,13 @@ sub get_alias{
my ($class, $key) = @_;
if(!defined($registry_register{'_ALIAS'}{lc($key)})){
- return $key;
+ if(!defined( $registry_register{_SPECIES}{ lc($key) }) and !defined ($registry_register{_ALIAS}{ lc($key) })){
+ warn "$key is not a valid species name for this instance\n";
+ return undef;
+ }
+ else{
+ return $key;
+ }
}
return $registry_register{'_ALIAS'}{lc($key)};
}
diff --git a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
index 4eee78fff6..ed6b06c143 100644
--- a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
@@ -154,7 +154,7 @@ sub gen_load {
# return if the connection and species, group are the same
if ( defined( $dba->species ) ) {
- my $db_reg = $reg->get_DBAdaptor( $dba->species, $dba->group );
+ my $db_reg = $reg->get_DBAdaptor( $dba->species, $dba->group, 1 );
if ( defined($db_reg) ) {
if ( $dba->dbc->equals( $db_reg->dbc ) ) { return $db_reg }
else {
@@ -169,6 +169,7 @@ sub gen_load {
}
}
} else { # no species
+
my @db_reg =
@{ $reg->get_all_DBAdaptors_by_connection( $dba->dbc ) };
--
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