From d971da0bf6fe106e2717896b01c91440fce35c65 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 21 Jul 2009 12:43:48 +0000
Subject: [PATCH] Use FIND_IN_SET() when a specific subset name is specified,
otherwise use LIKE.
---
modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
index 9f6ea47def..0917bfeaae 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
@@ -403,8 +403,10 @@ WHERE relation.child_term_id = ?
Arg [2] : (optional) String
The subset within the ontolgy to which the query
- should be restricted. The subset may be specified
- as a SQL pattern, e.g., "goslim%".
+ should be restricted. The subset may be specified as
+ a SQL pattern, e.g., "%goslim%" (but "goslim%" might
+ not do what you expect), or as a specific subset name,
+ e.g., "goslim_goa".
Arg [3] : (optional) Boolean
If true (non-zero), only return the closest
@@ -453,8 +455,13 @@ WHERE closure.child_term_id = ?
AND closure.distance > 0);
if ( defined($subset) ) {
- $statement .= q(
+ if ( index( $subset, '%' ) != -1 ) {
+ $statement .= q(
AND parent_term.subsets LIKE ?);
+ } else {
+ $statement .= q(
+ AND FIND_IN_SET(?, parent_term.subsets) > 0);
+ }
}
$statement .= q(
@@ -480,6 +487,7 @@ ORDER BY closure.distance, parent_term.accession);
$subsets ||= '';
$min_distance ||= $distance;
+ print "min_distance = $min_distance\n";
if ( !$closest_only || $distance == $min_distance ) {
push(
@terms,
--
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