From 9825a9c1b372f78abc6e4a2349eb52063b2638b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 25 Oct 2011 12:54:07 +0000
Subject: [PATCH] Throw an exception if the real species name for an alias can
not be found in get_adaptor(). Suggested by jm18 on dev.
Also reformat get_alias() and get_DBAdaptor().
---
modules/Bio/EnsEMBL/Registry.pm | 38 ++++++++++++++++++++-------------
1 file changed, 23 insertions(+), 15 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 74eba4c9bd..0baf778bd2 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -572,12 +572,12 @@ sub add_DBAdaptor {
=cut
sub get_DBAdaptor {
- my ( $class, $species, $group , $no_alias_check) = @_;
-throw 'Species not defined.' if ! defined $species;
+ my ( $class, $species, $group, $no_alias_check ) = @_;
+ throw 'Species not defined.' if !defined $species;
-# if(!defined($no_alias_check) or !$no_alias_check){
- $species = $class->get_alias($species, $no_alias_check) || $species;
-# }
+ #if ( !defined($no_alias_check) or !$no_alias_check ) {
+ $species = $class->get_alias( $species, $no_alias_check ) || $species;
+ #}
return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
}
@@ -936,7 +936,12 @@ sub add_adaptor {
sub get_adaptor {
my ( $class, $species, $group, $type ) = @_;
- $species = $class->get_alias($species);
+ my $ispecies = $class->get_alias($species);
+
+ if ( !defined($species) ) {
+ throw("Can not find internal name for species '$species'");
+ }
+ else { $species = $ispecies }
my %dnadb_adaptors = (
'sequence' => 1,
@@ -1130,19 +1135,22 @@ sub remove_alias{
=cut
-sub get_alias{
- my ($class, $key, $no_warn) = @_;
+sub get_alias {
+ my ( $class, $key, $no_warn ) = @_;
- if(!defined($registry_register{'_ALIAS'}{lc($key)})){
- if((!defined( $registry_register{_SPECIES}{ lc($key) })) and (!defined ($registry_register{_ALIAS}{ lc($key) }))){
- warn "$key is not a valid species name for this instance\n" if((!defined($no_warn)) or (!$no_warn));
+ if ( !defined( $registry_register{'_ALIAS'}{ lc($key) } ) ) {
+ if ( ( !defined( $registry_register{_SPECIES}{ lc($key) } ) ) and
+ ( !defined( $registry_register{_ALIAS}{ lc($key) } ) ) )
+ {
+ if ( ( !defined($no_warn) ) or ( !$no_warn ) ) {
+ warn "$key is not a valid species name for this instance\n";
+ }
return;
}
- else{
- return $key;
- }
+ else { return $key }
}
- return $registry_register{'_ALIAS'}{lc($key)};
+
+ return $registry_register{'_ALIAS'}{ lc($key) };
}
=head2 get_all_aliases
--
GitLab