From 3363312360247deff4b98aa64e8eecd190c459a3 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 23 Oct 2013 09:24:53 +0000
Subject: [PATCH] [ENSCORESW-686]. Adding a method to automatically add aliases
for a DBAdaptor.
Currently this is functionality wanted for compara when people just build
a connection and then they lack any kind of link back to the compara
schema.
---
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm | 29 ++++++++++++++++++++++++--
1 file changed, 27 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 67d1fc5286..8377eeea61 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -82,6 +82,10 @@ my $registry = "Bio::EnsEMBL::Registry";
the database if not used properly. If in doubt, do
not use it or ask in the developer mailing list.
+ Arg [-ADD_ALIASES]: (optional) boolean
+ Used to automatically load aliases for this
+ species into the Registry upon loading.
+
Arg [..] : Other args are passed to superclass
Bio::EnsEMBL::DBSQL::DBConnection
@@ -125,10 +129,11 @@ sub new {
my $self = bless {}, $class;
my ( $is_multispecies, $species, $species_id, $group, $con, $dnadb,
- $no_cache, $dbname )
+ $no_cache, $dbname, $add_aliases )
= rearrange( [
'MULTISPECIES_DB', 'SPECIES', 'SPECIES_ID', 'GROUP',
- 'DBCONN', 'DNADB', 'NO_CACHE', 'DBNAME'
+ 'DBCONN', 'DNADB', 'NO_CACHE', 'DBNAME',
+ 'ADD_ALIASES'
],
@args
);
@@ -154,6 +159,7 @@ sub new {
if ( defined($dnadb) ) { $self->dnadb($dnadb) }
if ( defined($no_cache) ) { $self->no_cache($no_cache) }
+ if ( defined($add_aliases) ) { $self->find_and_add_aliases($add_aliases) }
return $self;
} ## end sub new
@@ -182,6 +188,25 @@ sub clear_caches {
return;
}
+=head2 find_and_add_aliases
+
+ Example : $dba->find_and_add_aliases();
+ Description : When executed we delegate to the find_and_add_aliases
+ method in Bio::EnsEMBL::Registry which scans the
+ database's MetaContainer for species.alias entries
+ indicating alternative names for this species. This
+ is best executed on a core DBAdaptor instance.
+ Returntype : None
+ Exceptions : None
+
+=cut
+
+sub find_and_add_aliases {
+ my ($self) = @_;
+ $registry->find_and_add_aliases(-ADAPTOR => $self);
+ return;
+}
+
=head2 dbc
Arg[1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection
--
GitLab