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Commit 44514875 authored by Magali Ruffier's avatar Magali Ruffier
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input and return list of values made more consistent between methods

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modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+ 40
− 18
View file @ 44514875
......@@ -90,6 +90,7 @@ SELECT DISTINCT
term.name,
term.definition,
term.subsets,
ontology.name,
ontology.namespace
FROM ontology
JOIN term USING (ontology_id)
......@@ -112,7 +113,7 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
$sth->bind_columns(
\( $dbid, $accession, $name, $definition, $subsets, $namespace ) );
\( $dbid, $accession, $name, $definition, $subsets, $ontology, $namespace ) );
my @terms;
......@@ -121,13 +122,17 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
push @terms,
Bio::EnsEMBL::OntologyTerm->new(
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, );
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
}
return \@terms;
......@@ -153,6 +158,7 @@ sub fetch_by_accession {
my $statement = q(
SELECT term.term_id,
term.accession,
term.name,
term.definition,
term.subsets,
......@@ -169,7 +175,7 @@ WHERE term.accession = ?);
my ( $dbid, $name, $definition, $subsets, $ontology, $namespace );
$sth->bind_columns(
\( $dbid, $name, $definition, $subsets, $ontology, $namespace ) );
\( $dbid, $accession, $name, $definition, $subsets, $ontology, $namespace ) );
$sth->fetch();
......@@ -261,7 +267,9 @@ WHERE relation.parent_term_id = ?
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
push( @terms, $child_term );
push( @{ $term->{'children'}{$relation} }, $child_term );
......@@ -343,7 +351,9 @@ ORDER BY closure.distance, child_term.accession);
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, ) );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
}
return \@terms;
......@@ -413,7 +423,9 @@ WHERE relation.child_term_id = ?
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
push( @terms, $parent_term );
push( @{ $term->{'parents'}{$relation} }, $parent_term );
......@@ -541,7 +553,9 @@ ORDER BY closure.distance, parent_term.accession);
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, ) );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
} else {
$sth->finish();
last;
......@@ -684,7 +698,8 @@ sub fetch_by_dbID {
my ( $this, $dbid ) = @_;
my $statement = q(
SELECT term.accession,
SELECT term.term_id,
term.accession,
term.name,
term.definition,
term.subsets,
......@@ -702,7 +717,7 @@ WHERE term.term_id = ?);
my ( $accession, $name, $definition, $subsets, $ontology,
$namespace );
$sth->bind_columns(
\( $accession, $name, $definition, $subsets, $ontology, $namespace
\( $dbid, $accession, $name, $definition, $subsets, $ontology, $namespace
) );
$sth->fetch();
......@@ -776,7 +791,9 @@ WHERE term.term_id IN (%s));
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition, ) );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
}
return \@terms;
......@@ -846,7 +863,10 @@ FROM ontology
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition ) );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
));
}
return \@terms;
......@@ -889,7 +909,9 @@ FROM ontology
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition ) );
'-definition' => $definition,
'-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
) );
}
return \@terms;
......
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