From 8048b47b86997fb693da060c15f5709269ce83ef Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 5 Apr 2013 09:28:10 +0000
Subject: [PATCH] ENSCORESW-308: added support for is_obsolete
---
.../Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm | 233 ++++++++++--------
modules/Bio/EnsEMBL/OntologyTerm.pm | 23 +-
2 files changed, 153 insertions(+), 103 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
index b58bfc4285..94523b0698 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
@@ -81,7 +81,7 @@ use base qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
=cut
sub fetch_all_by_name {
- my ( $this, $pattern, $ontology ) = @_;
+ my ( $this, $pattern, $ontology, $include_obsolete ) = @_;
my $statement = q(
SELECT DISTINCT
@@ -91,6 +91,7 @@ SELECT DISTINCT
term.definition,
term.subsets,
term.is_root,
+ term.is_obsolete,
ontology.name,
ontology.namespace
FROM ontology
@@ -101,6 +102,7 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
if ( defined($ontology) ) {
$statement .= " AND ontology.name = ?";
}
+ $statement .= " AND term.is_obsolete = 0" unless $include_obsolete;
my $sth = $this->prepare($statement);
$sth->bind_param( 1, $pattern, SQL_VARCHAR );
@@ -112,9 +114,9 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $namespace );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $namespace );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology, $namespace ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology, $namespace ) );
my @terms;
@@ -127,6 +129,7 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
'-adaptor' => $this,
'-accession' => $accession,
'-is_root' => $is_root,
+ '-is_obsolete' => $is_obsolete,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
@@ -156,7 +159,7 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
=cut
sub fetch_by_accession {
- my ( $this, $accession ) = @_;
+ my ( $this, $accession, $include_obsolete ) = @_;
my $statement = q(
SELECT term.term_id,
@@ -165,20 +168,23 @@ SELECT term.term_id,
term.definition,
term.subsets,
term.is_root,
+ term.is_obsolete,
ontology.name,
ontology.namespace
FROM ontology
JOIN term USING (ontology_id)
WHERE term.accession = ?);
+ $statement .= " AND term.is_obsolete = 0" unless $include_obsolete;
+
my $sth = $this->prepare($statement);
$sth->bind_param( 1, $accession, SQL_VARCHAR );
$sth->execute();
- my ( $dbid, $name, $definition, $subsets, $is_root, $ontology, $namespace );
+ my ( $dbid, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology, $namespace );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology, $namespace ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology, $namespace ) );
$sth->fetch();
@@ -193,6 +199,7 @@ WHERE term.accession = ?);
'-adaptor' => $this,
'-accession' => $accession,
'-is_root' => $is_root,
+ '-is_obsolete'=> $is_obsolete,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
@@ -223,7 +230,7 @@ WHERE term.accession = ?);
=cut
sub fetch_all_by_parent_term {
- my ( $this, $term, $ontology ) = @_;
+ my ( $this, $term, $ontology, $include_obsolete ) = @_;
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
@@ -237,6 +244,7 @@ SELECT child_term.term_id,
child_term.definition,
child_term.subsets,
child_term.is_root,
+ child_term.is_obsolete,
rt.name
FROM term child_term
JOIN relation ON (relation.child_term_id = child_term.term_id)
@@ -245,6 +253,8 @@ FROM term child_term
WHERE relation.parent_term_id = ?
AND ontology.name = ?);
+ $statement .= " AND child_term.is_obsolete = 0" unless $include_obsolete;
+
my $sth = $this->prepare($statement);
$sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
@@ -256,25 +266,26 @@ WHERE relation.parent_term_id = ?
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $relation );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $relation ) );
while ( $sth->fetch() ) {
$subsets ||= '';
my $child_term =
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
'-is_root' => $is_root,
- '-ontology' => $term->{'ontology'},
- '-namespace' => $term->{'namespace'},
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $term->{'ontology'},
+ '-namespace' => $term->{'namespace'},
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
push( @terms, $child_term );
@@ -322,7 +333,8 @@ SELECT DISTINCT
child_term.name,
child_term.definition,
child_term.subsets,
- child_term.is_root
+ child_term.is_root,
+ child_term.is_obsolete
FROM term child_term
JOIN closure ON (closure.child_term_id = child_term.term_id)
JOIN ontology ON (closure.ontology_id = ontology.ontology_id)
@@ -340,9 +352,9 @@ ORDER BY closure.distance, child_term.accession);
$sth->bind_param( 2, $ontology, SQL_VARCHAR );
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete ) );
my @terms;
@@ -351,16 +363,17 @@ ORDER BY closure.distance, child_term.accession);
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
'-is_root' => $is_root,
- '-ontology' => $term->{'ontology'},
- '-namespace' => $term->{'namespace'},
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $term->{'ontology'},
+ '-namespace' => $term->{'namespace'},
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
}
@@ -398,6 +411,7 @@ SELECT parent_term.term_id,
parent_term.definition,
parent_term.subsets,
parent_term.is_root,
+ parent_term.is_obsolete,
rt.name
FROM term parent_term
JOIN relation ON (relation.parent_term_id = parent_term.term_id)
@@ -416,25 +430,26 @@ WHERE relation.child_term_id = ?
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $relation );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $relation ) );
while ( $sth->fetch() ) {
$subsets ||= '';
my $parent_term =
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
'-is_root' => $is_root,
- '-ontology' => $term->{'ontology'},
- '-namespace' => $term->{'namespace'},
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $term->{'ontology'},
+ '-namespace' => $term->{'namespace'},
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
push( @terms, $parent_term );
@@ -506,6 +521,7 @@ SELECT DISTINCT
parent_term.definition,
parent_term.subsets,
parent_term.is_root,
+ parent_term.is_obsolete,
closure.distance
FROM term parent_term
JOIN closure ON (closure.parent_term_id = parent_term.term_id)
@@ -543,9 +559,9 @@ ORDER BY closure.distance, parent_term.accession);
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $distance );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $distance );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root, $distance ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $distance ) );
my @terms;
my $min_distance;
@@ -557,16 +573,17 @@ ORDER BY closure.distance, parent_term.accession);
if ( !$closest_only || $distance == $min_distance ) {
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
'-is_root' => $is_root,
- '-ontology' => $term->{'ontology'},
- '-namespace' => $term->{'namespace'},
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $term->{'ontology'},
+ '-namespace' => $term->{'namespace'},
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
} else {
$sth->finish();
@@ -707,7 +724,7 @@ ORDER BY closure.distance);
# provided by the parent class Bio::EnsEMBL::DBSQL::BaseAdaptor.
sub fetch_by_dbID {
- my ( $this, $dbid ) = @_;
+ my ( $this, $dbid, $include_obsolete ) = @_;
my $statement = q(
SELECT term.term_id,
@@ -716,21 +733,24 @@ SELECT term.term_id,
term.definition,
term.subsets,
term.is_root,
+ term.is_obsolete,
ontology.name,
ontology.namespace
FROM ontology
JOIN term USING (ontology_id)
WHERE term.term_id = ?);
+ $statement .= " AND term.is_obsolete = 0" unless $include_obsolete;
+
my $sth = $this->prepare($statement);
$sth->bind_param( 1, $dbid, SQL_INTEGER );
$sth->execute();
- my ( $accession, $name, $definition, $subsets, $is_root, $ontology,
+ my ( $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology,
$namespace );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology, $namespace
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology, $namespace
) );
$sth->fetch();
@@ -741,16 +761,17 @@ WHERE term.term_id = ?);
my $term =
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
'-is_root' => $is_root,
- '-ontology' => $ontology,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $ontology,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
$sth->finish();
@@ -758,7 +779,7 @@ WHERE term.term_id = ?);
} ## end sub fetch_by_dbID
sub fetch_all_by_dbID_list {
- my ( $this, $dbids ) = @_;
+ my ( $this, $dbids, $include_obsolete ) = @_;
if ( !@{$dbids} ) { return [] }
@@ -769,6 +790,7 @@ SELECT term.term_id,
term.definition,
term.subsets,
term.is_root,
+ term.is_obsolete,
ontology.name,
ontology.namespace
FROM ontology
@@ -783,14 +805,16 @@ WHERE term.term_id IN (%s));
$this->dbc()->db_handle()->quote( $_, SQL_INTEGER )
} @{$dbids} ) );
+ $statement .= " AND term.is_obsolete = 0" unless $include_obsolete;
+
my $sth = $this->prepare($statement);
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology,
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
- $subsets, $is_root, $ontology, $namespace ) );
+ $subsets, $is_root, $is_obsolete, $ontology, $namespace ) );
my @terms;
@@ -799,16 +823,17 @@ WHERE term.term_id IN (%s));
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
'-is_root' => $is_root,
- '-ontology' => $ontology,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $ontology,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
}
@@ -845,6 +870,7 @@ SELECT term.term_id,
term.definition,
term.subsets,
term.is_root,
+ term.is_obsolete,
ontology.name,
ontology.namespace
FROM ontology
@@ -861,10 +887,10 @@ FROM ontology
}
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology,
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
- $subsets, $is_root, $ontology, $namespace ) );
+ $subsets, $is_root, $is_obsolete, $ontology, $namespace ) );
my @terms;
@@ -873,16 +899,17 @@ FROM ontology
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
- '-is_root' => $is_root,
- '-ontology' => $ontology,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
+ '-is_root' => $is_root,
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $ontology,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
));
}
@@ -892,7 +919,7 @@ FROM ontology
sub fetch_all {
- my ($this) = @_;
+ my ($this, $include_obsolete) = @_;
my $statement = q(
SELECT term.term_id,
@@ -901,18 +928,21 @@ SELECT term.term_id,
term.definition,
term.subsets,
term.is_root,
+ term.is_obsolete,
ontology.name,
ontology.namespace
FROM ontology
JOIN term USING (ontology_id));
+ $statement .= " AND term.is_obsolete = 0" unless $include_obsolete;
+
my $sth = $this->prepare($statement);
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology,
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $is_obsolete, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
- $subsets, $is_root, $ontology, $namespace ) );
+ $subsets, $is_root, $is_obsolete, $ontology, $namespace ) );
my @terms;
@@ -921,16 +951,17 @@ FROM ontology
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
- '-is_root' => $is_root,
- '-ontology' => $ontology,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
+ '-is_root' => $is_root,
+ '-is_obsolete' => $is_obsolete,
+ '-ontology' => $ontology,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
}
diff --git a/modules/Bio/EnsEMBL/OntologyTerm.pm b/modules/Bio/EnsEMBL/OntologyTerm.pm
index 2057883785..93b238cee1 100644
--- a/modules/Bio/EnsEMBL/OntologyTerm.pm
+++ b/modules/Bio/EnsEMBL/OntologyTerm.pm
@@ -99,9 +99,9 @@ sub new {
my $this = $proto->SUPER::new(@_);
- my ( $accession, $ontology, $namespace, $name, $definition, $is_root, $subsets )
+ my ( $accession, $ontology, $namespace, $name, $definition, $is_root, $is_obsolete, $subsets )
= rearrange( [ 'ACCESSION', 'ONTOLOGY', 'NAMESPACE', 'NAME',
- 'DEFINITION', 'IS_ROOT', 'SUBSETS' ],
+ 'DEFINITION', 'IS_ROOT', 'IS_OBSOLETE', 'SUBSETS' ],
@_ );
$this->{'accession'} = $accession;
@@ -110,6 +110,7 @@ sub new {
$this->{'name'} = $name;
$this->{'definition'} = $definition;
$this->{'is_root'} = $is_root;
+ $this->{'is_obsolete'}= $is_obsolete;
$this->{'subsets'} = [ @{$subsets} ];
$this->{'child_terms_fetched'} = 0;
@@ -220,6 +221,24 @@ sub is_root {
return $this->{'is_root'};
}
+=head2 is_obsolete
+
+ Arg : None
+
+ Description : Returns true if the term is obsolete
+
+ Example : my $is_obsolete = $term->is_obsolete();
+
+ Return type : Boolean (TRUE if it is obsolete, else FALSE)
+
+=cut
+
+sub is_obsolete {
+ my ($this) = @_;
+ return $this->{'is_obsolete'};
+}
+
+
=head2 synonyms
--
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