From fdfac3779e6ba36612c0c5794c6b841646107865 Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Thu, 23 Feb 2006 15:25:14 +0000
Subject: [PATCH] modified LIMIT to use a function from DBConnection
---
.../EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm | 14 +++++-------
.../Bio/EnsEMBL/Utils/ConversionSupport.pm | 22 ++++++++++---------
2 files changed, 17 insertions(+), 19 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index 511afd1f84..1b820bcb37 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
@@ -556,15 +556,11 @@ sub _lookup_version {
if( ! defined $arch_id->{'db_name'} ) {
# latest version of this stable id
-
- $sql = qq(
- SELECT new_db_name, new_version
- FROM stable_id_event sie, mapping_session m
- WHERE sie.mapping_session_id = m.mapping_session_id
- AND new_stable_id = "@{[$arch_id->stable_id]}"
- $EXTRA_SQL
- ORDER BY m.created DESC
- LIMIT 1);
+ my $sql_tmp = "SELECT new_db_name, new_version ";
+ $sql_tmp .= "FROM stable_id_event sie, mapping_session m ";
+ $sql_tmp .= "WHERE sie.mapping_session_id = m.mapping_session_id AND new_stable_id = \"@{[$arch_id->stable_id]}\" $EXTRA_SQL ";
+ $sql_tmp .= "ORDER BY m.created DESC";
+ $sql = $self->dbc->add_limit_clause($sql_tmp,1);
} else {
$sql = qq(
SELECT old_db_name, old_version
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index 7d3faa5823..aa2f69a730 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -874,7 +874,7 @@ sub get_taxonomy_id {
Description : Retrieves the species scientific name (Genus species) from the
meta table
Return type : String - species scientific name
- Exceptions : thrown if species name can't be determined from db
+ Exceptions : thrown if species name can not be determined from db
Caller : general
=cut
@@ -882,15 +882,17 @@ sub get_taxonomy_id {
sub get_species_scientific_name {
my ($self, $dba) = @_;
$dba ||= $self->dba;
- my $sql = qq(
- SELECT
- meta_value
- FROM
- meta
- WHERE meta_key = "species.classification"
- ORDER BY meta_id
- LIMIT 2
- );
+ my $sql_tmp = "SELECT meta_value FROM meta WHERE meta_key = \'species.classification\' ORDER BY meta_id";
+ my $sql = $dba->dbc->add_limit_clause($sql_tmp,2);
+# my $sql = qq(
+# SELECT
+# meta_value
+# FROM
+# meta
+# WHERE meta_key = "species.classification"
+# ORDER BY meta_id
+# LIMIT 2
+# );
my $sth = $dba->dbc->db_handle->prepare($sql);
$sth->execute;
my @sp;
--
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