Bio::DB::BioSQL SimpleValueAdaptor
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Summary
Bio::DB::BioSQL::SimpleValueAdaptor - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::Annotation::SimpleValue
Bio::DB::BioSQL::BasePersistenceAdaptor
Bio::DB::BioSQL::TermAdaptor
Bio::DB::PersistentObjectI
Bio::Ontology::Ontology
Bio::Ontology::Term
Inherit
Bio::DB::BioSQL::TermAdaptor
Synopsis
Give standard usage here
Description
SimpleValue DB adaptor
Methods
get_persistent_slotsDescriptionCode
get_persistent_slot_valuesDescriptionCode
get_foreign_key_objectsDescriptionCode
attach_foreign_key_objectsDescriptionCode
store_childrenDescriptionCode
attach_childrenDescriptionCode
remove_childrenDescriptionCode
instantiate_from_rowDescriptionCode
populate_from_rowDescriptionCode
get_unique_key_queryDescriptionCode
removeDescriptionCode
add_associationDescriptionCode
find_by_associationDescriptionCode
find_by_primary_keyDescriptionCode
_ontology_fkDescriptionCode
Methods description
get_persistent_slotscode    nextTop
 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. 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().
store_childrencodeprevnextTop
 Title   : store_children
Usage :
Function: Inserts or updates the child entities of the given object in the
datastore.
Usually, those child objects will reference the given object as a foreign key. We override this here from the ontology term adaptor because there is no synonyms or dbxrefs for SimpleValue tags. I.e., we revert to the default behaviour of doing nothing. Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent. A reference to an array of foreign key values, in the order of foreign keys returned by get_foreign_key_objects().
attach_childrencodeprevnextTop
 Title   : attach_children
Usage :
Function: Possibly retrieve and attach child objects of the given object.
This is needed when whole object trees are supposed to be built when a base object is queried for and returned. An example would be Bio::SeqI objects and all the annotation objects that hang off of it. This is called by the find_by_XXXX() methods once the base object has been built. We override this here from the ontology term adaptor because there is no synonyms or dbxrefs for SimpleValue tags. I.e., we revert to the default behaviour of doing nothing. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child 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.
removecodeprevnextTop
 Title   : remove
Usage : $objectstoreadp->remove($persistent_obj, @params)
Function: Removes the persistent object from the datastore.
Example :
Returns : TRUE on success and FALSE otherwise
Args : The object to be removed, and optionally additional (named)
parameters.
add_associationcodeprevnextTop
 Title   : add_assocation
Usage :
Function: Stores the association between given objects in the datastore.
We override this here to make sure the value slot gets stored in associations. Example : Returns : TRUE on success and FALSE otherwise Args : Named parameters. At least the following must be recognized: -objs a reference to an array of objects to be associated with each other -values a reference to a hash the keys of which are abstract column names and the values are values of those columns. These columns are generally those other than the ones for foreign keys to the entities to be associated Caveats: Make sure you *always* give the objects to be associated in the same order.
find_by_associationcodeprevnextTop
 Title   : find_by_association
Usage :
Function: Locates those records associated between a SimpleValue
annotation and another object.
We override this here in order to be able to constrain by the ontology of a term (which is the category of the tag). Example : Returns : A Bio::DB::Query::QueryResultI implementing object Args : Named parameters. At least the following must be recognized: -objs a reference to an array of objects to be associated with each other -obj_factory the factory to use for instantiating object from the found rows -constraints a reference to an array of additional Bio::DB::Query::QueryConstraint objects
-values the values to bind to the constraint clauses,
as a hash reference keyed by the constraints
Caveats: Make sure you *always* give the objects to be associated in the same order.
find_by_primary_keycodeprevnextTop
 Title   : find_by_primary_key
Usage : $objectstoreadp->find_by_primary_key($pk)
Function: Locates the entry associated with the given primary key and
initializes a persistent object with that entry.
SimpleValues are not identifiable by primary key. It is suspicious if someone calls this method, so we throw an exception until we know better. Example : Returns : An instance of the class this adaptor adapts, represented by an object implementing Bio::DB::PersistentObjectI, or undef if no matching entry was found. Args : The primary key. Optionally, the Bio::Factory::ObjectFactoryI compliant object factory to be used for instantiating the proper class. If the object does not implement Bio::Factory::ObjectFactoryI, it is assumed to be the object to be populated with the query results.
_ontology_fkcodeprevnextTop
 Title   : _ontology_fk
Usage : $obj->_ontology_fk($svann)
Function: Get/set the ontology foreign key constant.
This is a private method. Example : Returns : value of _ontology_fk (a Bio::Ontology::OntologyI compliant object) Args : the Bio::Annotation::SimpleValue object for which
to return the ontology
new value (a Bio::Ontology::OntologyI compliant object, optional)
Methods code
get_persistent_slotsdescriptionprevnextTop
sub get_persistent_slots {
    my ($self,@args) = @_;

    return ("tagname", "value", "rank");
}
get_persistent_slot_valuesdescriptionprevnextTop
sub get_persistent_slot_values {
    my ($self,$obj,$fkobjs) = @_;
    my @vals = ($obj->tagname(),
		$obj->value(),
                $obj->can('rank') ? $obj->rank() : undef,
		);
    return\@ vals;
}
get_foreign_key_objectsdescriptionprevnextTop
sub get_foreign_key_objects {
    my ($self,$obj,$fkobjs) = @_;
    my $ont;

    if(ref($obj)) {
	$ont = $self->_ontology_fk($obj);
    } else {
	$ont = "Bio::Ontology::OntologyI";
    }
    return ($ont);
}
attach_foreign_key_objectsdescriptionprevnextTop
sub attach_foreign_key_objects {
    my ($self,$obj,$fks) = @_;
    my $ok = 1;

    # we don't need to attach an ontology here, since it's a constant ...
return $ok;
}
store_childrendescriptionprevnextTop
sub store_children {
    return 1;
}
attach_childrendescriptionprevnextTop
sub attach_children {
    return 1;
}
remove_childrendescriptionprevnextTop
sub remove_children {
    return 1;
}
instantiate_from_rowdescriptionprevnextTop
sub instantiate_from_row {
    my ($self,$row,$fact) = @_;
    my $obj;

    if($row && @$row) {
	if($fact) {
	    $obj = $fact->create_object();
	} else {
	    $obj = Bio::Annotation::SimpleValue->new();
	}
        # in order to store rank we need a persistent object - sooner or later
# it will be turned into one anyway
if (!$obj->isa("Bio::DB::PersistentObjectI")) { $obj = $self->create_persistent($obj); } # now populate
$self->populate_from_row($obj, $row); } return $obj;
}
populate_from_rowdescriptionprevnextTop
sub populate_from_row {
    my ($self,$obj,$row) = @_;

    if(! ref($obj)) {
	$self->throw("\"$obj\" is not an object. Probably internal error.");
    }
    if($row && @$row) {
	$obj->tagname($row->[1]) if $row->[1];
	$obj->value($row->[2]) if defined($row->[2]);
        $obj->rank($row->[3]) if $row->[3] && $obj->can('rank');
	if($obj->isa("Bio::DB::PersistentObjectI")) {
	    $obj->primary_key($row->[0]);
	}
	return $obj;
    }
    return undef;
}
get_unique_key_querydescriptionprevnextTop
sub get_unique_key_query {
    my ($self,$obj,$fkobjs) = @_;
    my $uk_h = {};

    # UK for the tag of tag/value is the tag plus its namespace (ontology)
if($obj->tagname()) { $uk_h->{'tagname'} = $obj->tagname(); my $ont = $self->_ontology_fk($obj); if($ont && $ont->primary_key) { $uk_h->{'ontology'} = $ont->primary_key(); } } return $uk_h;
}
removedescriptionprevnextTop
sub remove {
    my ($self,$obj,@args) = @_;

    $self->throw("remove() not yet implemented in SimpleValueAdaptor()");
}
add_associationdescriptionprevnextTop
sub add_association {
    my ($self,@args) = @_;
    my ($i);

    # get arguments
my ($objs, $values) = $self->_rearrange([qw(OBJS VALUES)], @args); # have we been called in error? If so, be graceful and return an error.
return undef unless $objs && @$objs; # figure out which one of the objects is the simple value annotation
my $obj; my $svidx = 0; while($svidx < @$objs) { if($objs->[$svidx]->isa("Bio::Annotation::SimpleValue")) { $obj = $objs->[$svidx]; last; } $svidx++; } # make sure we include the value for the association
if (defined($obj)) { # if there wasn't -values already we push it onto the arguments
if(! defined($values)) { $values = {}; push(@args, '-values', $values); } $values->{'value'} = $obj->value(); if(! $obj->primary_key()) { # this may happen as SimpleValue objects are sometimes created
# on the fly from more light-weight tag/value pairs
my $svobj = $self->find_by_unique_key($obj); $obj->primary_key($svobj->primary_key()) if $svobj; } } else { $self->warn("unable to figure out the Bio::Annotation::SimpleValue ". "object to associate with something, expect problems"); } # pass on to the inherited implementation
return $self->SUPER::add_association(@args);
}
find_by_associationdescriptionprevnextTop
sub find_by_association {
    my ($self,@args) = @_;
    my $i;

    # get arguments
my ($objs,$constraints,$values) = $self->_rearrange([qw(OBJS CONSTRAINTS VALUES)], @args); # have we been called in error? If so, be graceful and return an error.
return undef unless $objs && @$objs; # figure out which one of the objects is the simple value annotation
my ($obj) = grep { ref($_) && $_->isa("Bio::Annotation::SimpleValue"); } @$objs; # constrain by the ontology (there is a default if there is no live
# annotation object)
my $cat = $self->_ontology_fk($obj); if (defined($cat)) { if(! $cat->primary_key()) { $cat = $cat->adaptor->find_by_unique_key($cat); } # if there wasn't -constraints already we push it onto the arguments
if(! defined($constraints)) { $constraints = []; $values = {}; push(@args, '-constraints', $constraints, '-values', $values); } # add a constraint for the ontology
my $constraint = Bio::DB::Query::QueryConstraint->new( "Bio::Annotation::SimpleValue::ontology = ?"); push(@$constraints, $constraint); $values->{$constraint} = $cat ? $cat->primary_key() : undef; } # pass on to the inherited implementation
return $self->SUPER::find_by_association(@args);
}
find_by_primary_keydescriptionprevnextTop
sub find_by_primary_key {
    my ($self,$dbid,$fact) = @_;

    $self->throw("SimpleValue annotations don't have a primary key.");
}
_ontology_fkdescriptionprevnextTop
sub _ontology_fk {
    my ($self,$svann,$ont) = @_;

    # if the tag is in fact an ontology term, we simply return its ontology
if(ref($svann) && $svann->tag_term()) { $ont = $svann->tag_term->ontology(); if(! $ont->isa("Bio::DB::PersistentObjectI")) { $ont = $self->db()->create_persistent($ont); } } else { # otherwise we create and cache a default
if( defined $ont) { $self->{'_ontology_fk'} = $ont; } else { if(! exists($self->{'_ontology_fk'})) { $ont = Bio::Ontology::Ontology->new(-name=>"Annotation Tags"); } else { $ont = $self->{'_ontology_fk'}; } if(! $ont->isa("Bio::DB::PersistentObjectI")) { $ont = $self->db()->create_persistent($ont); $self->{'_ontology_fk'} = $ont; } } } return $ont; } 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@bio.perl.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
Internal methodsTop
 These are mostly private or 'protected.' Methods which are in the
latter class have this explicitly stated in their
documentation. 'Protected' means you may call these from derived
classes, but not from outside.
Most of these methods cache certain adaptors or otherwise reduce call path and object creation overhead. There's no magic here.