From c49afa836a2a182bfcdef8a26c10584f369c7de1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 25 Jul 2008 10:21:32 +0000
Subject: [PATCH] Being slightly more restrictive with the parsing of
multispecies database names and making sure none of them are picked out when
looking for core (single species) databases.
---
modules/Bio/EnsEMBL/Registry.pm | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 0fb2f51930..166aa1f35b 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -1199,7 +1199,7 @@ sub load_registry_from_db {
}
for my $db (@dbnames) {
- if ( $db =~ /^(\w+)_collection_core_(\w+)/ ) { # NEEDS TO BE FIRST
+ if ( $db =~ /^([a-z]+)_collection_core_(\w+)/ ) { # NEEDS TO BE FIRST
if ( $2 eq $software_version ) {
$temp{$1} = 'collection_core_' . $2;
}
@@ -1235,6 +1235,8 @@ sub load_registry_from_db {
my @core_dbs = grep { /^[a-z]+_[a-z]+_core_\d+_/ } @dbnames;
foreach my $coredb (@core_dbs) {
+ next if ($coredb =~ /collection/); # Skip multi-species databases
+
my ( $species, $num ) =
( $coredb =~ /(^[a-z]+_[a-z]+)_core_(\d+)/ );
@@ -1259,14 +1261,15 @@ sub load_registry_from_db {
}
# Register multi-species databases
- my @multi_dbs = grep { /_collection_core_\w+$/ } @dbnames;
+ my @multi_dbs = grep { /^[a-z]+_collection_core_\w+$/ } @dbnames;
foreach my $multidb (@multi_dbs) {
my $sth =
$dbh->prepare(
- sprintf( 'SELECT species_id, meta_value FROM %s.meta ',
- $dbh->quote_identifier($multidb) )
- . "WHERE meta_key = 'species.db_name'" );
+ sprintf( 'SELECT species_id, meta_value FROM %s.meta ',
+ $dbh->quote_identifier($multidb) )
+ . "WHERE meta_key = 'species.db_name'" );
+
$sth->execute();
my ( $species_id, $species );
--
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