Bio::DB::BioSQL RelationshipAdaptor
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Summary
Bio::DB::BioSQL::RelationshipAdaptor - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::DB::BioSQL::BasePersistenceAdaptor
Bio::DB::PersistentObjectI
Bio::Ontology::Relationship
Inherit
Bio::DB::BioSQL::BasePersistenceAdaptor
Synopsis
Give standard usage here
Description
Bio::Ontology::RelationshipI DB adaptor
Methods
newDescriptionCode
get_persistent_slotsDescriptionCode
get_persistent_slot_valuesDescriptionCode
get_foreign_key_objectsDescriptionCode
attach_foreign_key_objectsDescriptionCode
remove_childrenDescriptionCode
instantiate_from_rowDescriptionCode
populate_from_rowDescriptionCode
get_unique_key_queryDescriptionCode
remove_all_relationshipsDescriptionCode
_ont_adaptorDescriptionCode
_term_adaptorDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage :
Function: Instantiates the persistence adaptor.
Example :
Returns :
Args :
get_persistent_slotscodeprevnextTop
 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
get_persistent_slot_valuescodeprevnextTop
 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.
get_foreign_key_objectscodeprevnextTop
 Title   : get_foreign_key_objects
Usage :
Function: Gets the objects referenced by this object, and which therefore need
to be referenced as foreign keys in the datastore.
Note that the objects are expected to implement Bio::DB::PersistentObjectI. An implementation needs to make sure that the order of foreign key objects returned is always the same. Example : Returns : an array of Bio::DB::PersistentObjectI implementing objects Args : The object about to be inserted or updated, or undef if the call is for a SELECT query. In the latter case return class or interface names that are mapped to the foreign key tables. Optionally, additional named parameters. A common parameter will be -fkobjs, with a reference to an array of foreign key objects that are not retrievable from the persistent object itself.
attach_foreign_key_objectscodeprevnextTop
 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().
remove_childrencodeprevnextTop
 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().
instantiate_from_rowcodeprevnextTop
 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.
populate_from_rowcodeprevnextTop
 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().
get_unique_key_querycodeprevnextTop
 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.
remove_all_relationshipscodeprevnextTop
 Title   : remove_all_relationships
Usage :
Function: Removes all relationships within a given ontology.
This is mostly a convenience method for calling remove_association() with the appropriate arguments. Example : Returns : TRUE on success and FALSE otherwise Args : the ontology as an Bio::Ontology::OntologyI compliant object
_ont_adaptorcodeprevnextTop
 Title   : _ont_adaptor
Usage : $obj->_ont_adaptor($newval)
Function: Get/set the ontology persistence adaptor.
Example :
Returns : value of _ont_adaptor (a Bio::DB::PersistenceAdaptorI object)
Args : on set, new value (a Bio::DB::PersistenceAdaptorI object
or undef, optional)
_term_adaptorcodeprevnextTop
 Title   : _term_adaptor
Usage : $obj->_term_adaptor($newval)
Function: Get/set the ontology term persistence adaptor.
Example :
Returns : value of _term_adaptor (a Bio::DB::PersistenceAdaptorI object)
Args : on set, new value (a Bio::DB::PersistenceAdaptorI object
or undef, optional)
Methods code
newdescriptionprevnextTop
sub new {
   my ($class,@args) = @_;

   # we want to enable object caching
#well I'm not sure about this
#push(@args, "-cache_objects", 1) unless grep { /cache_objects/i; } @args;
my $self = $class->SUPER::new(@args); return $self;
}
get_persistent_slotsdescriptionprevnextTop
sub get_persistent_slots {
    my ($self,@args) = @_;

    return ();
}
get_persistent_slot_valuesdescriptionprevnextTop
sub get_persistent_slot_values {
    my ($self,$obj,$fkobjs) = @_;
    my @vals = ();
    return\@ vals;
}
get_foreign_key_objectsdescriptionprevnextTop
sub get_foreign_key_objects {
    my ($self,$obj,$fkobjs) = @_;
    my ($subj_term,$pred_term,$obj_term,$ont);

    # initialize with defaults
if(ref($obj)) { $subj_term = $obj->subject_term(); $pred_term = $obj->predicate_term(); $obj_term = $obj->object_term(); # make sure the contexts are set
$subj_term->foreign_key_slot(ref($self) ."::subject"); $obj_term->foreign_key_slot(ref($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,$ont);
}
attach_foreign_key_objectsdescriptionprevnextTop
sub attach_foreign_key_objects {
    my ($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 $ok;
}
remove_childrendescriptionprevnextTop
sub remove_children {
    return 1;
}
instantiate_from_rowdescriptionprevnextTop
sub instantiate_from_row {
    my ($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 $obj;
}
populate_from_rowdescriptionprevnextTop
sub populate_from_row {
    my ($self,$obj,$rows) = @_;

    if(! ref($obj)) {
	$self->throw("\"$obj\" is not an object. Probably internal error.");
    }
    if($rows && @$rows) {
	if($obj->isa("Bio::DB::PersistentObjectI")) {
	    $obj->primary_key($rows->[0]);
	}
	return $obj;
    }
    return undef;
}
get_unique_key_querydescriptionprevnextTop
sub get_unique_key_query {
    my ($self,$obj,$fkobjs) = @_;
    my $uk_h = {};

    # UK for a relationship is the tuple of all its foreign keys:
# (subject,predicate,object,ontology)
if(ref($obj)) { my $tadp = $self->_term_adaptor; my %name_map = ("subject_term" => "subject", "object_term" => "object", "predicate_term" => "predicate"); foreach my $meth (keys %name_map) { my $term = $obj->$meth; if($term && (!$term->isa("Bio::DB::PersistentObjectI"))) { $term = $tadp->find_by_unique_key($term); } $uk_h->{$name_map{$meth}} = $term ? $term->primary_key : undef; } my $ont = $obj->ontology(); if($ont && (!$ont->isa("Bio::DB::PersistentObjectI"))) { $ont = $self->_ont_adaptor->find_by_unique_key($ont); } $uk_h->{"ontology"} = $ont ? $ont->primary_key : undef; } return $uk_h;
}
remove_all_relationshipsdescriptionprevnextTop
sub remove_all_relationships {
    my ($self,$ont) = @_;

    if (! ($ont && ref($ont) && $ont->isa("Bio::Ontology::OntologyI"))) {
        $self->throw("argument must be an OntologyI-compliant object");
    }
    if (! ($ont->isa("Bio::DB::PersistentObjectI") && $ont->primary_key)) {
        # to avoid side effects like clobbering this ontology's
# properties with possibly older ones from the database we'll
# need an object factory
$ont = $ont->obj() if $ont->isa("Bio::DB::PeristentObjectI"); my $ontfact = Bio::Factory::ObjectFactory->new(-type => ref($ont)); my $adp = $self->_ont_adaptor(); $ont = $adp->find_by_unique_key($ont, '-obj_factory' => $ontfact); } return ref($ont) ? # note that having the persistent object in the -objs array
# will constrain by the foreign key to that object
$self->remove_association(-objs => ["Bio::Ontology::TermI", "Bio::Ontology::TermI", "Bio::Ontology::TermI", $ont] ) # if the ontology couldn't be found, there can't be relationships
# for it either
: 1;
}
_ont_adaptordescriptionprevnextTop
sub _ont_adaptor {
    my $self = shift;

    return $self->{'_ont_adaptor'} = shift if @_;
    if(! exists($self->{'_ont_adaptor'})) {
	$self->{'_ont_adaptor'} =
	    $self->db->get_object_adaptor("Bio::Ontology::OntologyI");
    }
    return $self->{'_ont_adaptor'};
}
_term_adaptordescriptionprevnextTop
sub _term_adaptor {
    my $self = shift;

    return $self->{'_term_adaptor'} = shift if @_;
    if(! exists($self->{'_term_adaptor'})) {
	$self->{'_term_adaptor'} =
	    $self->db->get_object_adaptor("Bio::Ontology::TermI");
    }
    return $self->{'_term_adaptor'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
 
Please direct usage questions or support issues to the mailing list:

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.
Reporting BugsTop
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/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Methods overriden from BasePersistenceAdaptorTop
Private methodsTop
 These are mostly convenience and/or short-hand methods.