From 422e390ae130d475ad7bc716ec0bbe360d28a07e Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Tue, 22 Jul 2003 16:11:42 +0000
Subject: [PATCH] Use cahching for all values. Added get_max_assembly_contig
for optimized queries on assembly table.
---
modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm | 78 +++++++++-------------
1 file changed, 32 insertions(+), 46 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
index 68ab76f5b3..7406b2bbe4 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
@@ -65,6 +65,11 @@ sub list_value_by_key {
my ($self,$key) = @_;
my @result;
+ $self->{'cache'} ||= {};
+ if( exists $self->{'cache'}->{$key} ) {
+ return $self->{'cache'}->{$key};
+ }
+
my $sth = $self->prepare( "SELECT meta_value
FROM meta
WHERE meta_key = ? ORDER BY meta_id" );
@@ -72,7 +77,8 @@ sub list_value_by_key {
while( my $arrRef = $sth->fetchrow_arrayref() ) {
push( @result, $arrRef->[0] );
}
-
+ $self->{'cache'}->{$key} = \@result;
+
return \@result;
}
@@ -98,29 +104,11 @@ sub store_key_value {
VALUES( ?, ? )" );
my $res = $sth->execute( $key, $value );
- return;
-}
-
-=head2 update_key_value
-
- Arg [1] : string $key
- a key under which $value should be updated
- Arg [2] : string $value
- the value to update in the meta table
- Example : $meta_container->update_key_value($key, $value);
- Description: update a value in the meta container, accessable by a key
- Returntype : none
- Exceptions : none
- Caller : ?
-
-=cut
-sub update_key_value {
- my ( $self, $key, $value ) = @_;
+ $self->{'cache'} ||= {};
- my $sth = $self->prepare( "UPDATE meta SET meta_value = ? WHERE meta_key = ?" );
+ delete $self->{'cache'}->{$key};
- my $res = $sth->execute( $value, $key );
return;
}
@@ -142,12 +130,9 @@ sub update_key_value {
sub get_Species {
my $self = shift;
- my $sth = $self->prepare( "SELECT meta_value
- FROM meta
- WHERE meta_key = 'species.common_name'" );
- $sth->execute;
+ my $arrRef = $self->list_value_by_key( 'species.common_name' );
my $common_name;
- if( my $arrRef = $sth->fetchrow_arrayref() ) {
+ if( @$arrRef ) {
$common_name = $arrRef->[0];
} else {
return undef;
@@ -179,22 +164,15 @@ sub get_Species {
sub get_taxonomy_id {
my $self = shift;
+
+ my $arrRef = $self->list_value_by_key( 'species.taxonomy_id' );
- if( ! defined $self->{'_taxonomy_id'} ) {
- my $sth = $self->prepare( "SELECT meta_value
- FROM meta
- WHERE meta_key = 'species.taxonomy_id'" );
- $sth->execute();
-
- my ( $tax ) = $sth->fetchrow_array();
- if( ! defined $tax ) {
- $self->warn("Please insert meta_key 'species.taxonomy_id' " .
- "in meta table at core db.\n");
- }
- $self->{'_taxonomy_id'} = $tax;
+ if( @$arrRef ) {
+ return $arrRef->[0];
+ } else {
+ $self->warn("Please insert meta_key 'species.taxonomy_id' " .
+ "in meta table at core db.\n");
}
-
- return $self->{'_taxonomy_id'};
}
@@ -213,18 +191,26 @@ sub get_taxonomy_id {
sub get_default_assembly {
my $self = shift;
- my $sth = $self->prepare( "SELECT meta_value
- FROM meta
- WHERE meta_key = 'assembly.default'" );
- $sth->execute;
-
- if( my $arrRef = $sth->fetchrow_arrayref() ) {
+ my $arrRef = $self->list_value_by_key('assembly.default' );
+
+ if( @$arrRef ) {
return $arrRef->[0];
} else {
return undef;
}
}
+sub get_max_assembly_contig {
+ my $self = shift;
+
+ my $value_list = $self->list_value_by_key( "assembly.maxcontig" );
+ if( @$value_list ) {
+ return $value_list->[0];
+ } else {
+ return undef;
+ }
+}
+
1;
--
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