From 3801c0618827d556f7182c6a4880b65b6a6e01e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 26 Mar 2009 15:56:04 +0000
Subject: [PATCH] Simplify much of the SQL.
Add beginnings of fetch_ancestor_chart(), which will return a simple
hash with some form of ancestor chart information for a term.
---
.../Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm | 102 ++++++++++--------
1 file changed, 58 insertions(+), 44 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
index 47091afdd0..cef6114c4c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
@@ -34,6 +34,8 @@ Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
my @parent_terms = @{ $goa->fetch_by_child_term($term) };
my @ancestor_terms = @{ $goa->fetch_all_by_child_term($term) };
+ my %ancestor_chart = %{ $goa->fetch_ancestor_chart($term) };
+
=head1 DESCRIPTION
An adaptor for fetching ontology terms, creates
@@ -195,22 +197,15 @@ SELECT child_term.term_id,
child_term.name,
child_term.definition,
rt.name
-FROM ontology,
- term child_term,
- term parent_term,
+FROM term child_term,
relation,
relation_type rt
-WHERE ontology.name = ?
- AND ontology.ontology_id = child_term.ontology_id
- AND ontology.ontology_id = parent_term.ontology_id
- AND relation.child_term_id = child_term.term_id
- AND relation.parent_term_id = parent_term.term_id
- AND relation.relation_type_id = rt.relation_type_id
- AND parent_term.accession = ?);
+WHERE relation.child_term_id = child_term.term_id
+ AND relation.parent_term_id = ?
+ AND relation.relation_type_id = rt.relation_type_id);
my $sth = $this->prepare($statement);
- $sth->bind_param( 1, $this->{'ontology'}, SQL_VARCHAR );
- $sth->bind_param( 2, $term->{'accession'}, SQL_VARCHAR );
+ $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
$sth->execute();
@@ -273,22 +268,15 @@ SELECT DISTINCT
child_term.accession,
child_term.name,
child_term.definition
-FROM ontology,
- term child_term,
- term parent_term,
+FROM term child_term,
closure
-WHERE ontology.name = ?
- AND ontology.ontology_id = child_term.ontology_id
- AND ontology.ontology_id = parent_term.ontology_id
- AND closure.child_term_id = child_term.term_id
- AND closure.parent_term_id = parent_term.term_id
+WHERE closure.child_term_id = child_term.term_id
+ AND closure.parent_term_id = ?
AND closure.distance > 0
- AND parent_term.accession = ?
ORDER BY closure.distance, child_term.accession);
my $sth = $this->prepare($statement);
- $sth->bind_param( 1, $this->{'ontology'}, SQL_VARCHAR );
- $sth->bind_param( 2, $term->{'accession'}, SQL_VARCHAR );
+ $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
$sth->execute();
@@ -343,22 +331,15 @@ SELECT parent_term.term_id,
parent_term.name,
parent_term.definition,
rt.name
-FROM ontology,
- term child_term,
- term parent_term,
+FROM term parent_term,
relation,
relation_type rt
-WHERE ontology.name = ?
- AND ontology.ontology_id = child_term.ontology_id
- AND ontology.ontology_id = parent_term.ontology_id
- AND relation.child_term_id = child_term.term_id
+WHERE relation.child_term_id = ?
AND relation.parent_term_id = parent_term.term_id
- AND relation.relation_type_id = rt.relation_type_id
- AND child_term.accession = ?);
+ AND relation.relation_type_id = rt.relation_type_id);
my $sth = $this->prepare($statement);
- $sth->bind_param( 1, $this->{'ontology'}, SQL_VARCHAR );
- $sth->bind_param( 2, $term->{'accession'}, SQL_VARCHAR );
+ $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
$sth->execute();
@@ -420,22 +401,15 @@ SELECT DISTINCT
parent_term.accession,
parent_term.name,
parent_term.definition
-FROM ontology,
- term child_term,
- term parent_term,
+FROM term parent_term,
closure
-WHERE ontology.name = ?
- AND ontology.ontology_id = child_term.ontology_id
- AND ontology.ontology_id = parent_term.ontology_id
- AND closure.child_term_id = child_term.term_id
+WHERE closure.child_term_id = ?
AND closure.parent_term_id = parent_term.term_id
AND closure.distance > 0
- AND child_term.accession = ?
ORDER BY closure.distance, parent_term.accession);
my $sth = $this->prepare($statement);
- $sth->bind_param( 1, $this->{'ontology'}, SQL_VARCHAR );
- $sth->bind_param( 2, $term->{'accession'}, SQL_VARCHAR );
+ $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
$sth->execute();
@@ -459,6 +433,46 @@ ORDER BY closure.distance, parent_term.accession);
return \@terms;
} ## end sub fetch_all_by_child_term
+
+sub fetch_ancestor_chart {
+ my ( $this, $term ) = @_;
+
+ my $statement = q(
+SELECT subparent_term.accession,
+ parent_term.accession,
+ relation_type.name
+FROM closure,
+ relation,
+ relation_type,
+ term subparent_term,
+ term parent_term
+WHERE closure.child_term_id = ?
+ AND relation.parent_term_id = closure.parent_term_id
+ AND relation.child_term_id = closure.subparent_term_id
+ AND relation.relation_type_id = relation_type.relation_type_id
+ AND subparent_term.term_id = closure.subparent_term_id
+ AND parent_term.term_id = closure.parent_term_id
+ORDER BY closure.distance);
+
+ my $sth = $this->prepare($statement);
+ $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
+
+ $sth->execute();
+
+ my ( $subparent_id, $parent_id, $relation );
+ $sth->bind_columns( \( $subparent_id, $parent_id, $relation ) );
+
+ my %chart;
+ while ( $sth->fetch() ) {
+ if ( !exists( $chart{$parent_id} ) ) {
+ $chart{$parent_id} = {};
+ }
+ push( @{ $chart{$subparent_id}{$relation} }, $parent_id );
+ }
+
+ return \%chart;
+} ## end sub fetch_ancestor_chart
+
#-----------------------------------------------------------------------
# Useful public methods that implement functionality not properly
# provided by the parent class Bio::EnsEMBL::DBSQL::BaseAdaptor.
--
GitLab