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lib/Bio/DB/BioSQL/RelationshipAdaptor.pm  view on Meta::CPAN

	$obj_term->foreign_key_slot(ref($self) ."::object");
	$pred_term->foreign_key_slot(ref($self) ."::predicate");
	# and the ontology FK
	$ont = $obj->ontology();
    } 
    $ont = "Bio::Ontology::OntologyI" unless $ont;
    $subj_term = "Bio::Ontology::TermI::subject" unless $subj_term;
    $pred_term = "Bio::Ontology::TermI::predicate" unless $pred_term;
    $obj_term = "Bio::Ontology::TermI::object" unless $obj_term;
    return ($subj_term,$pred_term,$obj_term,$ont);
}

=head2 attach_foreign_key_objects

 Title   : attach_foreign_key_objects
 Usage   :
 Function: Attaches foreign key objects to the given object as far as
           necessary.

           This method is called after find_by_XXX() queries, not for INSERTs
           or UPDATEs.

 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The object to which to attach foreign key objects.
           A reference to an array of foreign key values, in the order of
           foreign keys returned by get_foreign_key_objects().


=cut

sub attach_foreign_key_objects{
    my ($self,$obj,$fks) = @_;
    my $ok = 1;
    
    if($fks && @$fks) {
	# we expect to find 4 foreign keys: subject, predicate, object, and
	# namespace (ontology)
	my $i = 0;
	foreach my $meth ("subject_term", "predicate_term", "object_term") {
	    next unless $fks->[$i]; # this actually always be defined
	    my $term = $self->_term_adaptor->find_by_primary_key($fks->[$i]);
	    $ok = defined($term) && $ok;
	    $obj->$meth($term) if $term;
	    $i++;
	}
	# foreign key to ontology 
	if($fks->[$i]) {
	    my $ont = $self->_ont_adaptor->find_by_primary_key($fks->[$i]);
	    $ok = defined($ont) && $ok;
	    $obj->ontology($ont) if $ont;
	}
    }
    return $ok;
}

=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::Relationship->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.