Raw content of BioMart::Configuration::Attribute
<![CDATA[# $Id: Attribute.pm,v 1.4 2008/04/09 12:52:33 syed Exp $
#
# BioMart module for BioMart::Configuration::Attribute
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
BioMart::Configuration::Attribute
=head1 SYNOPSIS
Represents an attribute in a BioMart query
=head1 DESCRIPTION
Attribute objects model the concept of a BioMart attribute ie a column in a
mart ResultTable that can be requested as part of a mart query.
=head1 AUTHOR - Arek Kasprzyk, Syed Haider, Richard Holland, Darin London, Damian Smedley
=head1 CONTACT
This module is part of the BioMart project http://www.biomart.org
Questions can be posted to the mart-dev mailing list:
mart-dev@ebi.ac.uk
=head1 METHODS
=cut
package BioMart::Configuration::Attribute;
use strict;
use warnings;
use Digest::MD5;
use Data::Dumper;
use base qw(BioMart::Root);
use constant NAME => "name";
use constant DISPLAYNAME => "displayName";
use constant DESCRIPTION => "description";
use constant IMAGEURL => "imageURL";
use constant TABLE => "table";
use constant RELATIONALATTRIBUTE => "relational_attribute";
use constant DATASETNAME => "dataSetName";
use constant INTERFACE => "interface";
use constant KEY => "key";
use constant WIDTH => "width";
use constant LINK => "link";
use constant DATASETLINK => "datasetLink";
use constant DEFAULT => "default";
use constant POINTEDFROMDATASET => "pointedFromDataset";
use constant POINTEDFROMATTRIBUTE => "pointedFromAttribute";
use constant POINTEDFROMINTERFACE => "pointedFromInterface";
use constant DEPENDSON => "dependsOn";
use constant DEPENDSONTYPE => "dependsOnType";
use constant ATTRIBUTES => "attributes";
use constant TITLES => [
NAME,
DISPLAYNAME,
DESCRIPTION,
IMAGEURL,
TABLE,
RELATIONALATTRIBUTE,
DATASETNAME,
INTERFACE,
KEY,
WIDTH,
LINK,
DATASETLINK,
DEFAULT,
POINTEDFROMDATASET,
POINTEDFROMINTERFACE ,
POINTEDFROMATTRIBUTE ,
DEPENDSON,
DEPENDSONTYPE,
ATTRIBUTES
];
=head2 _new
Usage : minimal (use setters for name, displayName, etc:
my $att = BioMart::Configuration::Attribute->new;
fully configured:
my $att = BioMart::Configuration::Attribute->new(
'name' => $name,
'displayName' => $dname,
'table' => $table,
'relational_attribute' => $rattribute,
'dataSetName' => $subname
);
Description: creates a new Attribute object.
Returntype : BioMart::Configuration::Attribute
Exceptions : insufficient arguments
Caller : general
=cut
sub _new {
my ($self, @param) = @_;
$self->SUPER::_new(@param);
$self->addParams(TITLES, @param);
$self->attr('dependency', []);
}
#non interface Methods
=head2 name
Usage : my $attName = $att->name; $att->name($newName);
Description: get/set for internal name
Returntype : scalar $name
Exceptions : none
Caller : general
=cut
sub name {
my ($self, $value) = @_;
if ($value){
$self->setParam(NAME, $value);
}
return $self->getParam(NAME);
}
=head2 imageURL
Usage : Arg [1] - (optional) string $imageURL
Description: get/set for imageURL, a relative URL.
This is only used by MartView.
Returntype : string
Exceptions : none
Caller : general
=cut
sub imageURL {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(IMAGEURL, $value);
}
return $self->getParam(IMAGEURL);
}
=head2 attributes
Usage : Arg [1] - (optional) string $attributes
Description: get/set for attributes.
Returntype : string
Exceptions : none
Caller : general
=cut
sub attributes {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(ATTRIBUTES, $value);
}
return $self->getParam(ATTRIBUTES);
}
=head2 displayName
Usage : Arg [1] - (optional) string $display_name
Description: get/set for display name
Returntype : string
Exceptions : none
Caller : general
=cut
sub displayName {
my ($self, $value) = @_;
if ($value){
$self->setParam(DISPLAYNAME, $value);
}
return $self->getParam(DISPLAYNAME);
}
=head2 description
Usage : Arg [1] - (optional) string $description
Description: get/set for description
Returntype : string
Exceptions : none
Caller : general
=cut
sub description {
# stores description
my ($self, $value) = @_;
if ($value){
$self->setParam(DESCRIPTION, $value);
}
return $self->getParam(DESCRIPTION);
}
=head2 dataSetName
Usage : my $subName = $att->dataSetName; $att->dataSetName->($newName);
Description: get/set for the name of the dataSet which hosts this attribute.
Returntype : scalar $name
Exceptions : none
Caller : general
=cut
sub dataSetName {
my ($self, $value) = @_;
if ($value){
$self->setParam(DATASETNAME, $value);
}
return $self->getParam(DATASETNAME);
}
=head2 interface
Usage : my $interface = $att->interface; $att->interface->($newName);
Description: get/set for the name of the interface which
hosts this attribute.
Returntype : scalar $name
Exceptions : none
Caller : general
=cut
sub interface {
my ($self, $value) = @_;
if ($value){
$self->setParam(INTERFACE, $value);
}
return $self->getParam(INTERFACE);
}
=head2 table
Usage : Arg [1] - (optional) string $table
Description: get/set for table
Returntype : string
Exceptions : none
Caller : general
=cut
sub table {
my ($self, $value) = @_;
if ($value){
$self->setParam(TABLE, $value);
}
return $self->getParam(TABLE);
}
=head2 relationalAttribute
Usage : Arg [1] - (optional) string $relational_attribute
Description: get/set for relational attribute
Returntype : string
Exceptions : none
Caller : general
=cut
sub relationalAttribute {
my ($self, $value) = @_;
if ($value){
$self->setParam(RELATIONALATTRIBUTE, $value);
}
return $self->getParam(RELATIONALATTRIBUTE);
}
=head2 key
Usage : Arg [1] - (optional) string $key for table joining
Description: get/set for key
Returntype : string
Exceptions : none
Caller : general
=cut
sub key {
my ($self, $value) = @_;
if ($value){
$self->setParam(KEY, $value);
}
return $self->getParam(KEY);
}
=head2 width
Usage : Arg [1] - (optional) string $width for table joining
Description: get/set for width
Returntype : string
Exceptions : none
Caller : general
=cut
sub width {
my ($self, $value) = @_;
if ($value){
$self->setParam(WIDTH, $value);
}
return $self->getParam(WIDTH);
}
=head2 link
Usage : Arg [1] - (optional) string $link for URL display
Description: get/set for linkURL
Returntype : string
Exceptions : none
Caller : general
=cut
sub link {
my ($self, $value) = @_;
if ($value){
$self->setParam(LINK, $value);
}
return $self->getParam(LINK);
}
=head2 datasetLink
Usage : Arg [1] - (optional) string $datasetLink
Description: get/set for datasetLink
Returntype : string
Exceptions : none
Caller : general
=cut
sub datasetLink {
my ($self, $value) = @_;
if ($value){
$self->setParam(DATASETLINK, $value);
}
return $self->getParam(DATASETLINK);
}
=head2 default
Usage : Arg [1] - (optional) string $default
Description: get/set for default atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub default {
my ($self, $value) = @_;
if ($value){
$self->setParam(DEFAULT, $value);
}
return $self->getParam(DEFAULT);
}
=head2 pointedFromAttribute
Usage : Arg [1] - (optional) string $pointedFromDataset
Description: get/set for pointedFromDataset atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub pointedFromAttribute {
my ($self, $value) = @_;
if ($value){
$self->setParam(POINTEDFROMATTRIBUTE, $value);
}
return $self->getParam(POINTEDFROMATTRIBUTE);
}
=head2 pointedFromDataset
Usage : Arg [1] - (optional) string $pointedFromDataset
Description: get/set for pointedFromDataset atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub pointedFromDataset {
my ($self, $value) = @_;
if ($value){
$self->setParam(POINTEDFROMDATASET, $value);
}
return $self->getParam(POINTEDFROMDATASET);
}
=head2 pointedFromInterface
Usage : Arg [1] - (optional) string $pointedFromInterface
Description: get/set for pointedFromInterface atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub pointedFromInterface {
my ($self, $value) = @_;
if ($value){
$self->setParam(POINTEDFROMINTERFACE, $value);
}
return $self->getParam(POINTEDFROMINTERFACE);
}
=head2 dependsOn
Usage : Arg [1] - (optional) string $dependsOn delimited by commas
Description: get/set for dependsOn atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub dependsOn {
my ($self, $value) = @_;
if ($value){
$self->setParam(DEPENDSON, $value);
}
return $self->getParam(DEPENDSON);
}
=head2 dependsOnType
Usage : Arg [1] - (optional) string $dependsOnType
Description: get/set for dependsOnType - all or any are acceptable.
Returntype : string
Exceptions : none
Caller : general
=cut
sub dependsOnType {
my ($self, $value) = @_;
if ($value){
$self->setParam(DEPENDSONTYPE, $value);
}
return $self->getParam(DEPENDSONTYPE);
}
=head2 addDependency
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub addDependency {
my ($self, $resolvedDependency) = @_;
push @{$self->get('dependency')}, $resolvedDependency;
}
=head2 dependencies
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub dependencies {
my $self = shift;
return $self->get('dependency');
}
=head2 toSQL
Usage : no arguments
Description: returns the SQL stub for the attribute (ie)
table.column
Returntype : string
Exceptions : none
Caller : general
=cut
sub toSQL {
my $self = shift;
return $self->getParam(TABLE).'.'.$self->getParam(RELATIONALATTRIBUTE);
}
sub _hashCode {
my $self = shift;
my $digest = Digest::MD5->new;
# Get uninitialized value in subroutine entry warnings whenever one of
# the below params has been set from an XML::Simple hash ie dataSetName
# is always OK
# investigate keyAttrs setting in XMLIn
$digest->add($self->name) if ($self->name);
$digest->add($self->displayName) if ($self->displayName);
$digest->add($self->dataSetName) if ($self->dataSetName);
$digest->add($self->table) if ($self->table);
$digest->add($self->relationalAttribute) if ($self->relationalAttribute);
$digest->add($self->key) if ($self->key);
return $digest->hexdigest;
}
1;
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