From a303f43b70ec333d0d5d6ede80a0183fab272010 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 4 Nov 2010 12:10:04 +0000
Subject: [PATCH] get_species_and_object_type() now only uses one database
handle per host do its thing.
---
modules/Bio/EnsEMBL/Registry.pm | 84 +++++++++++++++++----------------
1 file changed, 43 insertions(+), 41 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 373b73fbdd..4814aa2038 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -2423,39 +2423,39 @@ sub version_check {
=cut
my %stable_id_stmts = (
- 'gene' => "SELECT meta.meta_value "
- . "FROM gene_stable_id si "
- . "JOIN gene USING (gene_id) "
- . "JOIN seq_region USING (seq_region_id) "
- . "JOIN coord_system USING (coord_system_id) "
- . "JOIN meta USING (species_id) "
- . "WHERE si.stable_id = ? "
- . "AND meta.meta_key = 'species.production_name'",
- 'transcript' => "SELECT meta.meta_value "
- . "FROM transcript_stable_id si "
- . "JOIN transcript USING (transcript_id) "
- . "JOIN seq_region USING (seq_region_id) "
- . "JOIN coord_system USING (coord_system_id) "
- . "JOIN meta USING (species_id) "
- . "WHERE si.stable_id = ? "
- . "AND meta.meta_key = 'species.production_name'",
- 'exon' => "SELECT meta.meta_value "
- . "FROM exon_stable_id si "
- . "JOIN exon USING (exon_id) "
- . "JOIN seq_region USING (seq_region_id) "
- . "JOIN coord_system USING (coord_system_id) "
- . "JOIN meta USING (species_id) "
- . "WHERE si.stable_id = ? "
- . "AND meta.meta_key = 'species.production_name'",
- 'translation' => "SELECT meta.meta_value "
- . "FROM translation_stable_id si "
- . "JOIN translation USING (translation_id) "
- . "JOIN transcript USING (transcript_id) "
- . "JOIN seq_region USING (seq_region_id) "
- . "JOIN coord_system USING (coord_system_id) "
- . "JOIN meta USING (species_id) "
- . "WHERE si.stable_id = ? "
- . "AND meta.meta_key = 'species.production_name'",
+ "gene" => 'SELECT m.meta_value '
+ . 'FROM %1$s.gene_stable_id si '
+ . 'JOIN %1$s.gene USING (gene_id) '
+ . 'JOIN %1$s.seq_region USING (seq_region_id) '
+ . 'JOIN %1$s.coord_system USING (coord_system_id) '
+ . 'JOIN %1$s.meta m USING (species_id) '
+ . 'WHERE si.stable_id = ? '
+ . 'AND m.meta_key = "species.production_name"',
+ "transcript" => 'SELECT m.meta_value '
+ . 'FROM %1$s.transcript_stable_id si '
+ . 'JOIN %1$s.transcript USING (transcript_id) '
+ . 'JOIN %1$s.seq_region USING (seq_region_id) '
+ . 'JOIN %1$s.coord_system USING (coord_system_id) '
+ . 'JOIN %1$s.meta m USING (species_id) '
+ . 'WHERE si.stable_id = ? '
+ . 'AND m.meta_key = "species.production_name"',
+ "exon" => 'SELECT m.meta_value '
+ . 'FROM %1$s.exon_stable_id si '
+ . 'JOIN %1$s.exon USING (exon_id) '
+ . 'JOIN %1$s.seq_region USING (seq_region_id) '
+ . 'JOIN %1$s.coord_system USING (coord_system_id) '
+ . 'JOIN %1$s.meta m USING (species_id) '
+ . 'WHERE si.stable_id = ? '
+ . 'AND m.meta_key = "species.production_name"',
+ "translation" => 'SELECT m.meta_value '
+ . 'FROM %1$s.translation_stable_id si '
+ . 'JOIN %1$s.translation USING (translation_id) '
+ . 'JOIN %1$s.transcript USING (transcript_id) '
+ . 'JOIN %1$s.seq_region USING (seq_region_id) '
+ . 'JOIN %1$s.coord_system USING (coord_system_id) '
+ . 'JOIN %1$s.meta m USING (species_id) '
+ . 'WHERE si.stable_id = ? '
+ . 'AND m.meta_key = "species.production_name"',
);
sub get_species_and_object_type {
@@ -2474,22 +2474,24 @@ sub get_species_and_object_type {
my @match;
my $dbc;
+ my $dbh;
OUTER:
- foreach
- my $dba ( @{ $self->get_all_DBAdaptors( '-group' => 'Core' ) } )
+ foreach my $dba ( sort { $a->dbc()->host() cmp $b->dbc()->host() }
+ @{ $self->get_all_DBAdaptors( '-group' => 'Core' ) } )
{
if ( !defined($dbc)
- || !( $dbc->host() eq $dba->dbc()->host()
- && $dbc->dbname() eq $dba->dbc()->dbname() ) )
+ || $dbc->host() ne $dba->dbc()->host() )
{
$dbc = $dba->dbc();
+ $dbh = $dbc->db_handle();
}
- my $dbh = $dbc->db_handle();
-
foreach my $type (@types) {
- my $sth = $dbh->prepare( $stable_id_stmts{ lc($type) } );
+ my $statement =
+ sprintf( $stable_id_stmts{ lc($type) }, $dba->dbc()->dbname() );
+
+ my $sth = $dbh->prepare($statement);
$sth->bind_param( 1, $stable_id, SQL_VARCHAR );
$sth->execute();
@@ -2504,7 +2506,7 @@ OUTER:
}
}
- } ## end foreach my $dba ( @{ $self->get_all_DBAdaptors...})
+ } ## end foreach my $dba ( sort { $a...})
return @match;
} ## end sub get_species_and_object_type
--
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