From c9906fb2043babcf94a6146203d24580cbd15f52 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Mon, 21 Jan 2013 16:00:00 +0000
Subject: [PATCH] Adding patch from Dan Staines, see issue: ENSCORESW-340
---
modules/Bio/EnsEMBL/Registry.pm | 49 +++++++++++++++++++--------------
1 file changed, 29 insertions(+), 20 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 6c3204610f..20773368d5 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -2259,32 +2259,41 @@ sub find_and_add_aliases {
} else {
@dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) };
}
+
+ my $aliases_for_dbc = {};
foreach my $dba (@dbas) {
my @aliases;
my $species = $dba->species();
if ( defined($dbh) ) {
- my $dbname = $dba->dbc()->dbname();
- my $sth = $dbh->prepare( sprintf(
- "SELECT meta_value FROM %s.meta "
- . "WHERE meta_key = 'species.alias' "
- . "AND species_id = ?",
- $dbh->quote_identifier($dbname) ) );
-
- # Execute, and don't care about errors (there will be errors for
- # databases without a 'meta' table.
- $sth->{'PrintError'} = 0;
- $sth->{'RaiseError'} = 0;
- if ( !$sth->execute( $dba->species_id() ) ) { next }
- $sth->{'PrintError'} = $dbh->{'PrintError'};
- $sth->{'RaiseError'} = $dbh->{'RaiseError'};
-
- my $alias;
- $sth->bind_columns( \$alias );
- while ( $sth->fetch() ) {
- push( @aliases, $alias );
- }
+
+ my $dbname = $dba->dbc()->dbname();
+
+ if (!defined $aliases_for_dbc->{$dbname}) {
+
+ my $sth = $dbh->prepare(sprintf("SELECT species_id,meta_value FROM %s.meta "
+ . "WHERE meta_key = 'species.alias' ", $dbh->quote_identifier($dbname))
+ );
+
+ # Execute, and don't care about errors (there will be errors for
+ # databases without a 'meta' table.
+ $sth->{'PrintError'} = 0;
+ $sth->{'RaiseError'} = 0;
+ if (!$sth->execute()) { next }
+ $sth->{'PrintError'} = $dbh->{'PrintError'};
+ $sth->{'RaiseError'} = $dbh->{'RaiseError'};
+
+ my $alias;
+ my $species_id;
+ $sth->bind_columns(\$species_id, \$alias);
+ while ($sth->fetch()) {
+ push(@{$aliases_for_dbc->{$dbname}{$species_id}}, $alias);
+ }
+ }
+
+ @aliases = @{$aliases_for_dbc->{$dbname}{$dba->species_id()}||[]}
+
} else {
my $meta_container = eval { $dba->get_MetaContainer() };
--
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