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# $Id$
#
# BioPerl module for Bio::DB::BioSQL::OntologyAdaptor
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2003.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::BioSQL::OntologyAdaptor - DB Adaptor for Ontology objects
=head1 SYNOPSIS
# don't use directly
=head1 DESCRIPTION
DB adaptor for Bio::Ontology::OntologyI compliant objects.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bio.perl.org
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.open-bio.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::BioSQL::OntologyAdaptor;
use vars qw(@ISA);
use strict;
# Object preamble
use Bio::DB::BioSQL::BasePersistenceAdaptor;
use Bio::DB::PersistentObjectI;
use Bio::Ontology::Ontology;
@ISA = qw(Bio::DB::BioSQL::BasePersistenceAdaptor);
=head2 new
Title : new
Usage :
Function: Instantiates the persistence adaptor.
Example :
Returns :
Args :
=cut
sub new{
my ($class,@args) = @_;
# we want to enable object caching
push(@args, "-cache_objects", 1) unless grep { /cache_objects/i; } @args;
my $self = $class->SUPER::new(@args);
return $self;
}
=head2 get_persistent_slots
Title : get_persistent_slots
Usage :
Function: Get the slots of the object that map to attributes in its respective
entity in the datastore.
Slots should be methods callable without an argument.
Example :
Returns : an array of method names constituting the serializable slots
Args : the object about to be inserted or updated
=cut
sub get_persistent_slots{
my ($self,@args) = @_;
return ("name", "definition");
}
=head2 get_persistent_slot_values
Title : get_persistent_slot_values
Usage :
Function: Obtain the values for the slots returned by get_persistent_slots(),
in exactly that order.
Example :
Returns : A reference to an array of values for the persistent slots of this
object. Individual values may be undef.
Args : The object about to be serialized.
A reference to an array of foreign key objects if not retrievable
from the object itself.
=cut
sub get_persistent_slot_values {
my ($self,$obj,$fkobjs) = @_;
my @vals = ($obj->name(),
$obj->definition()
);
return \@vals;
}
=head2 remove_children
Title : remove_children
Usage :
Function: This method is to cascade deletes in maintained objects.
We just return TRUE here.
Example :
Returns : TRUE on success and FALSE otherwise
Args : The persistent object that was just removed from the database.
Additional (named) parameter, as passed to remove().
=cut
sub remove_children{
return 1;
}
=head2 instantiate_from_row
Title : instantiate_from_row
Usage :
Function: Instantiates the class this object is an adaptor for, and populates
it with values from columns of the row.
This implementation call populate_from_row() to do the real job.
Example :
Returns : An object, or undef, if the row contains no values
Args : A reference to an array of column values. The first column is the
primary key, the other columns are expected to be in the order
returned by get_persistent_slots().
Optionally, the object factory to be used for instantiating the
proper class. The adaptor must be able to instantiate a default
class if this value is undef.
=cut
sub instantiate_from_row{
my ($self,$row,$fact) = @_;
my $obj;
if($row && @$row) {
if($fact) {
$obj = $fact->create_object();
} else {
$obj = Bio::Ontology::Ontology->new();
}
$self->populate_from_row($obj, $row);
}
return $obj;
}
=head2 populate_from_row
Title : populate_from_row
Usage :
Function: Instantiates the class this object is an adaptor for, and populates
it with values from columns of the row.
Example :
Returns : An object, or undef, if the row contains no values
Args : The object to be populated.
A reference to an array of column values. The first column is the
primary key, the other columns are expected to be in the order
returned by get_persistent_slots().
=cut
sub populate_from_row{
my ($self,$obj,$rows) = @_;
if(! ref($obj)) {
$self->throw("\"$obj\" is not an object. Probably internal error.");
}
if($rows && @$rows) {
$obj->name($rows->[1]) if $rows->[1];
$obj->definition($rows->[2]) if $rows->[2];
if($obj->isa("Bio::DB::PersistentObjectI")) {
$obj->primary_key($rows->[0]);
}
return $obj;
}
return undef;
}
=head2 get_unique_key_query
Title : get_unique_key_query
Usage :
Function: Obtain the suitable unique key slots and values as determined by the
attribute values of the given object and the additional foreign
key objects, in case foreign keys participate in a UK.
Example :
Returns : One or more references to hash(es) where each hash
represents one unique key, and the keys of each hash
represent the names of the object's slots that are part of
the particular unique key and their values are the values
of those slots as suitable for the key.
Args : The object with those attributes set that constitute the chosen
unique key (note that the class of the object will be suitable for
the adaptor).
A reference to an array of foreign key objects if not retrievable
from the object itself.
=cut
sub get_unique_key_query{
my ($self,$obj,$fkobjs) = @_;
my $uk_h = {};
# UK for ontology is its name
if($obj->name()) {
$uk_h->{'name'} = $obj->name();
}
return $uk_h;
}
=head1 Methods overriden from BasePersistenceAdaptor
=cut
=head2 create_persistent
Title : create_persistent
Usage :
Function: Takes the given object and turns it onto a
PersistentObjectI implementing object. Returns the
result. Does not actually create the object in a database.
Calling this method is expected to have a recursive effect
such that all children of the object, i.e., all slots that
are objects themselves, are made persistent objects, too.
We override this method here because we need to temporarily
break the cycle between ontology and its term and
relationship objects.
Example :
Returns : A Bio::DB::PersistentObjectI implementing object wrapping the
passed object.
Args : An object to be made into a PersistentObjectI object (the class
will be suitable for this adaptor).
Optionally, the class which actually implements wrapping the object
to become a PersistentObjectI.
=cut
sub create_persistent{
my ($self,$obj,$pwrapper) = @_;
return unless $obj;
my $engine;
if($obj->can('engine')) {
$engine = $obj->engine();
$obj->engine(undef);
}
my $pobj = $self->SUPER::create_persistent($obj,$pwrapper);
# restore engine
$pobj->engine($engine) if $engine;
return $pobj;
}
=head1 Methods specific to this adaptor
=cut
=head2 compute_transitive_closure
Title : compute_transitive_closure
Usage :
Function: Compute the transitive closure over a given ontology
and populate the respective path table in the relational
schema.
There are options that allow one to create certain
necessary relationships between predicates on-the-fly. Read
below.
Example :
Returns : TRUE on success, and FALSE otherwise
Args : The ontology over which to create the transitive closure
(a Bio::Ontology::OntologyI compliant object).
In addition, named parameters. Currently, the following are
recognized.
-truncate If assigned a true value, will cause an existing
transitive closure for the ontology be deleted
from the path table. Usually, this option should
be enabled.
-predicate_superclass A Bio::Ontology::TermI compliant object
that specifies a common ancestor predicate
for all predicates in the ontology. If this
is specified, the method will create and
serialize relationships between all
predicates in the ontology and the ancestor
predicate, where the ancestor predicate is
the object, the predicate is either the one
given by -subclass_predicate or the term
'subclasses', and the ontology is the
ontology referenced by the ancestor
predicate.
If this is not provided, the aforementioned
relationships should be present in an
ontology in the database already, unless the
ontology over which to compute the transitive
closure has only one predicate, or if paths
over mixed predicates are void. Otherwise the
transitive closure will not be complete for
mixed predicate paths.
-subclass_predicate A Bio::Ontology::TermI compliant object
that represents the predicate for the
relationship between predicate A and
predicate B if predicate A can be considered
to subclass predicate B.
-identity_predicate A Bio::Ontology::TermI compliant object
that represents the predicate for the
identity of a predicate with itself. If
provided, the method will create
relationships for all predicates in the
ontology, where subject and object are the
predicate of the ontology, the predicate is
the supplied identity predicate, and the
ontology is the ontology referenced by the
supplied term object.
If this is not provided, the aforementioned
relationships should be present in an
ontology in the database already. Otherwise the
transitive closure will be incomplete.
The predicate will also be used for
indicating identity between a term and itself
for the paths of distance zero between a term
and itself. If undef the zero distance paths
will not be created.
=cut
sub compute_transitive_closure{
my $self = shift;
# the main implementation actually sits in the path adaptor
my $pathadp = $self->db->get_object_adaptor("Bio::Ontology::PathI");
return $pathadp->compute_transitive_closure(@_);
}
1;
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