Skip to content

GitLab

Commit c4921f02 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Do not use a special ontology adaptor for each and every ontology. 

Asking for a a GOTerm adaptor, or a SOTerm adaptor, still works, but the
correct call to get_adaptor() should request an OntologyTerm adaptor.
parent 4c219bf2
Hide whitespace changes
Inline Side-by-side
Showing with 153 additions and 227 deletions
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
View file @ c4921f02
......@@ -63,6 +63,7 @@ package Bio::EnsEMBL::DBSQL::GeneAdaptor;
use strict;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
......@@ -811,10 +812,8 @@ sub fetch_all_by_external_name {
sub fetch_all_by_GOTerm {
my ( $self, $term ) = @_;
if ( !ref($term)
|| !$term->isa('Bio::EnsEMBL::OntologyTerm')
|| $term->ontology() ne 'GO' )
{
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
if ( $term->ontology() ne 'GO' ) {
throw('Argument is not a GO term');
}
......@@ -822,7 +821,7 @@ sub fetch_all_by_GOTerm {
my %unique_dbIDs;
foreach my $accession ( map { $_->accession() }
( $term, @{ $term->descendants() } ) )
( $term, @{ $term->descendants() } ) )
{
my @ids =
$entryAdaptor->list_gene_ids_by_extids( $accession, 'GO' );
......@@ -831,10 +830,11 @@ sub fetch_all_by_GOTerm {
my @result = @{
$self->fetch_all_by_dbID_list(
[ sort { $a <=> $b } keys(%unique_dbIDs) ] ) };
[ sort { $a <=> $b } keys(%unique_dbIDs) ]
) };
return \@result;
}
} ## end sub fetch_all_by_GOTerm
=head2 fetch_all_by_GOTerm_accession
......@@ -873,7 +873,7 @@ sub fetch_all_by_GOTerm_accession {
my $goAdaptor =
Bio::EnsEMBL::Registry->get_adaptor( 'Multi', 'Ontology',
'GOTerm' );
'OntologyTerm' );
my $term = $goAdaptor->fetch_by_accession($accession);
......
modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
View file @ c4921f02
......@@ -40,9 +40,9 @@ use base qw ( Bio::EnsEMBL::DBSQL::DBAdaptor );
sub get_available_adaptors {
return {
'GOTerm' => 'Bio::EnsEMBL::DBSQL::GOTermAdaptor',
'SOTerm' => 'Bio::EnsEMBL::DBSQL::SOTermAdaptor'
};
'GOTerm' => 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor', #deprecated
'SOTerm' => 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor', #deprecated
'OntologyTerm' => 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor' };
}
1;
modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
View file @ c4921f02
=head1 LICENSE
Copyright (c) 1999-2011 The European Bioinformatics Institute and
......@@ -25,7 +24,8 @@ Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
=head1 SYNOPSIS
my $goa = $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' );
my $goa =
$registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
my $term = $goa->fetch_by_accession('GO:0010885');
......@@ -41,8 +41,6 @@ Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
An abstract adaptor class for fetching ontology
terms, creates Bio::EnsEMBL::OntologyTerm objects.
Specialized by Bio::EnsEMBL::DBSQL::GOTermAdaptor and
Bio::EnsEMBL::DBSQL::SOTermAdaptor
=head1 METHODS
......@@ -56,70 +54,12 @@ use warnings;
use DBI qw( :sql_types );
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use Bio::EnsEMBL::OntologyTerm;
use base qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
=head2 new
Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
Argument required for parent class
Bio::EnsEMBL::DBSQL::BaseAdaptor.
Arg [2] : String
The particular ontology that this ontology adaptor
deals with.
Caller : Bio::EnsEMBL::DBSQL::GOTermAdaptor
Bio::EnsEMBL::DBSQL::SOTermAdaptor
Description : Creates an ontology term adaptor.
Example :
my $ot_adaptor =
Bio::EnsEMBL::DBSQL::OntologyTermAdaptor->new( $dba, 'GO' );
Return type : Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
=cut
sub new {
my ( $proto, $dba, $ontology ) = @_;
if ( !ref($dba) || !$dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
throw('First argument needs to be a '
. 'Bio::EnsEMBL::DBSQL::DBAdaptor object' );
}
my $this = $proto->SUPER::new($dba);
$this->{'ontology'} = $ontology;
return $this;
}
=head2 ontology
Arg : None
Description : Returns the name of the ontology which this
adaptor is used to retrieve terms for.
Example :
my $ontology = $ot_adaptor->ontology();
Return type : String
=cut
sub ontology {
my ($this) = @_;
return $this->{'ontology'};
}
=head2 fetch_by_accession
Arg [1] : String
......@@ -142,6 +82,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
ontology.name,
ontology.namespace
FROM ontology,
term
......@@ -149,25 +90,27 @@ WHERE ontology.ontology_id = term.ontology_id
AND term.accession = ?);
my $sth = $this->prepare($statement);
$sth->bind_param( 1, $accession, SQL_VARCHAR );
$sth->bind_param( 1, $accession, SQL_VARCHAR );
$sth->execute();
my ( $dbid, $name, $definition, $subsets, $namespace );
my ( $dbid, $name, $definition, $subsets, $ontology, $namespace );
$sth->bind_columns(
\( $dbid, $name, $definition, $subsets, $namespace ) );
\( $dbid, $name, $definition, $subsets, $ontology, $namespace ) );
$sth->fetch();
$subsets ||= '';
my $term = Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition
);
my $term =
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition );
$sth->finish();
return $term;
......@@ -193,9 +136,7 @@ WHERE ontology.ontology_id = term.ontology_id
sub fetch_all_by_parent_term {
my ( $this, $term ) = @_;
if ( !ref($term) || !$term->isa('Bio::EnsEMBL::OntologyTerm') ) {
throw('Argument needs to be a Bio::EnsEMBL::OntologyTerm object');
}
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
my @terms;
......@@ -226,22 +167,21 @@ WHERE relation.child_term_id = child_term.term_id
while ( $sth->fetch() ) {
$subsets ||= '';
my $child_term = Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition,
);
my $child_term =
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, );
push( @terms, $child_term );
push( @{ $term->{'children'}{$relation} }, $child_term );
}
$sth->finish();
$term->{'child_terms_fetched'} = 1;
} else {
foreach my $relation ( values( %{ $term->{'children'} } ) ) {
......@@ -274,9 +214,7 @@ WHERE relation.child_term_id = child_term.term_id
sub fetch_all_by_ancestor_term {
my ( $this, $term ) = @_;
if ( !ref($term) || !$term->isa('Bio::EnsEMBL::OntologyTerm') ) {
throw('Argument needs to be a Bio::EnsEMBL::OntologyTerm object');
}
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
my $statement = q(
SELECT DISTINCT
......@@ -299,28 +237,25 @@ ORDER BY closure.distance, child_term.accession);
my ( $dbid, $accession, $name, $definition, $subsets );
$sth->bind_columns(
\( $dbid, $accession, $name, $definition, $subsets ) );
\( $dbid, $accession, $name, $definition, $subsets ) );
my @terms;
while ( $sth->fetch() ) {
$subsets ||= '';
push(
@terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition,
) );
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, ) );
}
$sth->finish();
return \@terms;
} ## end sub fetch_all_by_ancestor_term
......@@ -343,9 +278,7 @@ ORDER BY closure.distance, child_term.accession);
sub fetch_all_by_child_term {
my ( $this, $term ) = @_;
if ( !ref($term) || !$term->isa('Bio::EnsEMBL::OntologyTerm') ) {
throw('Argument needs to be a Bio::EnsEMBL::OntologyTerm object');
}
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
my @terms;
......@@ -376,22 +309,21 @@ WHERE relation.child_term_id = ?
while ( $sth->fetch() ) {
$subsets ||= '';
my $parent_term = Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition,
);
my $parent_term =
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, );
push( @terms, $parent_term );
push( @{ $term->{'parents'}{$relation} }, $parent_term );
}
$sth->finish();
$term->{'parent_terms_fetched'} = 1;
} else {
foreach my $relation ( values( %{ $term->{'parents'} } ) ) {
......@@ -440,9 +372,7 @@ WHERE relation.child_term_id = ?
sub fetch_all_by_descendant_term {
my ( $this, $term, $subset, $closest_only ) = @_;
if ( !ref($term) || !$term->isa('Bio::EnsEMBL::OntologyTerm') ) {
throw('Argument needs to be a Bio::EnsEMBL::OntologyTerm object');
}
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
$closest_only ||= 0;
......@@ -484,7 +414,7 @@ ORDER BY closure.distance, parent_term.accession);
my ( $dbid, $accession, $name, $definition, $subsets, $distance );
$sth->bind_columns(
\( $dbid, $accession, $name, $definition, $subsets, $distance ) );
\( $dbid, $accession, $name, $definition, $subsets, $distance ) );
my @terms;
my $min_distance;
......@@ -494,24 +424,22 @@ ORDER BY closure.distance, parent_term.accession);
$min_distance ||= $distance;
if ( !$closest_only || $distance == $min_distance ) {
push(
@terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition,
) );
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, ) );
} else {
$sth->finish();
last;
}
}
$sth->finish();
return \@terms;
} ## end sub fetch_all_by_descendant_term
......@@ -548,9 +476,7 @@ ORDER BY closure.distance, parent_term.accession);
sub _fetch_ancestor_chart {
my ( $this, $term ) = @_;
if ( !ref($term) || !$term->isa('Bio::EnsEMBL::OntologyTerm') ) {
throw('Argument needs to be a Bio::EnsEMBL::OntologyTerm object');
}
assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );
my $statement = q(
SELECT subparent_term.term_id,
......@@ -587,8 +513,6 @@ ORDER BY closure.distance);
push( @{ $id_chart{$subparent_id}{$relation} }, $parent_id );
}
$sth->finish();
my @terms = @{ $this->fetch_all_by_dbID_list( [ keys(%id_chart) ] ) };
foreach my $term (@terms) {
......@@ -604,9 +528,8 @@ ORDER BY closure.distance);
if ( $relation eq 'term' ) { next }
foreach my $id ( @{ $id_chart{$dbID}{$relation} } ) {
push(
@{ $acc_chart{$accession}{$relation} },
$id_chart{$id}{'term'} );
push( @{ $acc_chart{$accession}{$relation} },
$id_chart{$id}{'term'} );
}
}
}
......@@ -626,6 +549,7 @@ SELECT term.accession,
term.name,
term.definition,
term.subsets,
ontology.name,
ontology.namespace
FROM ontology,
term
......@@ -637,21 +561,25 @@ WHERE ontology.ontology_id = term.ontology_id
$sth->execute();
my ( $accession, $name, $definition, $subsets, $namespace );
my ( $accession, $name, $definition, $subsets, $ontology,
$namespace );
$sth->bind_columns(
\( $accession, $name, $definition, $subsets, $namespace ) );
\( $accession, $name, $definition, $subsets, $ontology, $namespace
) );
$sth->fetch();
$subsets ||= '';
my $term = Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition
);
my $term =
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition );
$sth->finish();
return $term;
......@@ -668,6 +596,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
ontology.name,
ontology.namespace
FROM ontology,
term
......@@ -676,38 +605,38 @@ WHERE ontology.ontology_id = term.ontology_id
my $statement = sprintf(
$stmt,
join( ',',
map { $this->dbc()->db_handle()->quote( $_, SQL_INTEGER ) }
@{$dbids} ) );
join(
',',
map {
$this->dbc()->db_handle()->quote( $_, SQL_INTEGER )
} @{$dbids} ) );
my $sth = $this->prepare($statement);
$sth->execute();
my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
$sth->bind_columns(
\( $dbid, $accession, $name, $definition, $subsets, $namespace ) );
my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
$subsets, $ontology, $namespace ) );
my @terms;
while ( $sth->fetch() ) {
$subsets ||= '';
push(
@terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition
) );
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition ) );
}
$sth->finish();
return \@terms;
} ## end sub fetch_all_by_dbID_list
......@@ -720,42 +649,37 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
ontology.name,
ontology.namespace
FROM ontology,
term
WHERE ontology.ontology_id = term.ontology_id
AND ontology.name = ?);
WHERE ontology.ontology_id = term.ontology_id );
my $sth = $this->prepare($statement);
$sth->bind_param( 1, $this->{'ontology'}, SQL_VARCHAR );
$sth->execute();
my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
$sth->bind_columns(
\( $dbid, $accession, $name, $definition, $subsets, $namespace ) );
my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
$subsets, $ontology, $namespace ) );
my @terms;
while ( $sth->fetch() ) {
$subsets ||= '';
push(
@terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition
) );
push( @terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition ) );
}
$sth->finish();
return \@terms;
} ## end sub fetch_all
......
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
View file @ c4921f02
<
......@@ -535,10 +535,8 @@ sub fetch_all_by_external_name {
sub fetch_all_by_GOTerm {
my ( $self, $term ) = @_;
if ( !ref($term)
|| !$term->isa('Bio::EnsEMBL::OntologyTerm')
|| $term->ontology() ne 'GO' )
{