Raw content of BioMart::Configuration::ConfigurationTree
<![CDATA[# $Id: ConfigurationTree.pm,v 1.6 2008/04/09 12:52:33 syed Exp $
#
# BioMart module for BioMart::Configuration::ConfigurationTree
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
BioMart::Configuration::ConfigurationTree
=head1 SYNOPSIS
BioMart::Configuration::ConfigurationTree represent the whole of the
datasetConfig XML recovered from the mart database/server for a
particluar dataset
=head1 DESCRIPTION
BioMart::Configuration::ConfigurationTree is the top level object of
the object hierarchy representing the datasetConfig XML which describes
the attributes, filters available for each dataset.
The ConfigurationTree is a container for BioMart::Configuration::FilterTree
and BioMart::Configuration::AttributeTree objects.
=head1 AUTHOR Arek Kasprzyk, Syed Haider, 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::ConfigurationTree;
use strict;
use warnings;
use base qw(BioMart::Root);
use constant DATASETNAME => "dataSetName";
use constant OPTPARAM => "optional_parameters";
use constant RESTRICTEDPARAM => "primaryKeyRestriction";
use constant DEFDATASET => "default_dataset";
use constant VISIBLEFILTERPAGE => "visibleFilterPage";
use constant TITLES => [ DATASETNAME ];
use constant MARTUSERS => "martUsers";
use constant SOFTWAREVERSION => "softwareVersion";
use constant ENTRYLABEL => "entryLabel";
sub _new {
my ($self, @param) = @_;
$self->SUPER::_new(@param);
$self->addParams(TITLES, @param);
$self->attr('attTs', []);
$self->attr('filtTs', []);
$self->attr(OPTPARAM, undef);
$self->attr(RESTRICTEDPARAM, undef);
$self->attr(DEFDATASET, undef);
$self->attr(VISIBLEFILTERPAGE, undef);
$self->attr(MARTUSERS, 'default');
$self->attr(SOFTWAREVERSION, undef);
$self->attr(ENTRYLABEL, undef);
}
=head2 dataSetName
Usage : my $subName = $ct->dataSetName; $ct->dataSetName($newName);
Description : Gets/Sets the name of the Dataset from which this
ConfigurationTree originates.
Returntype : scalar $name
Exceptions : none
Caller : caller
=cut
sub dataSetName {
my ($self, $name) = @_;
if ($name) {
$self->setParam(DATASETNAME, $name);
}
return $self->getParam(DATASETNAME);
}
=head2 optionalParameters
Usage : my $subName = $ct->optionalParameters;
$ct->optionalParameters($newName);
Description : Gets/Sets the optionalParameters associated with this
configuration. Only used for GenomicSequence processing
at the moment.
Returntype : scalar $optionalParameters
Exceptions : none
Caller : caller
=cut
sub optionalParameters {
my ($self, $param) = @_;
if ($param) {
$self->set(OPTPARAM, $param);
}
return $self->get(OPTPARAM);
}
=head2 mart_Users
Usage : my $subName = $ct->mart_Users;
$ct->mart_Users($newName);
Description : Gets/Sets the mart_Users associated with this
configuration.
Returntype : mart_Users comma separated list
Exceptions : none
Caller : caller
=cut
sub mart_Users {
my ($self, $param) = @_;
if ($param) {
$self->set(MARTUSERS, $param);
}
return $self->get(MARTUSERS);
}
=head2 software_version
Usage : my $subName = $ct->software_version;
$ct->software_version($newName);
Description : Gets/Sets the software_version associated with this
configuration.
Returntype : software_version
Exceptions : none
Caller : caller
=cut
sub software_version {
my ($self, $param) = @_;
if ($param) {
$self->set(SOFTWAREVERSION, $param);
}
return $self->get(SOFTWAREVERSION);
}
=head2 entryLabel
Usage : my $subName = $ct->entryLabel;
$ct->entryLabel($newName);
Description : Gets/Sets the entryLabel associated with this
configuration.
Returntype : entryLabel
Exceptions : none
Caller : caller
=cut
sub entryLabel {
my ($self, $param) = @_;
if ($param) {
$self->set(ENTRYLABEL, $param);
}
return $self->get(ENTRYLABEL);
}
=head2 primaryKeyRestriction
Usage : my $subName = $ct->primaryKeyRestriction;
$ct->primaryKeyRestriction($newName);
Description : Gets/Sets the primaryKeyRestriction associated with this
configuration. Can be used to restict data in the mart
available for querying by certain users
Returntype : scalar $primaryKeyRestriction
Exceptions : none
Caller : caller
=cut
sub primaryKeyRestriction {
my ($self, $param) = @_;
if ($param) {
$self->set(RESTRICTEDPARAM, $param);
}
return $self->get(RESTRICTEDPARAM);
}
=head2 visibleFilterPage
Usage : my $subName = $ct->visibleFilterPage;
$ct->visibleFilterPage($newName);
Description : Gets/Sets the visibleFilterPage associated with this
configuration.
Returntype : scalar $visibleFilterPage
Exceptions : none
Caller : caller
=cut
sub visibleFilterPage {
my ($self, $param) = @_;
if ($param) {
$self->set(VISIBLEFILTERPAGE, $param);
}
return $self->get(VISIBLEFILTERPAGE);
}
=head2 defaultDataset
Usage : my $subName = $ct->defaultDataset;
$ct->defaultDataset($newName);
Description : Gets/Sets the defaultDataset setting. If set to true
the the dataset using this configuration becomes the
default.
Returntype : scalar $defaultDataset
Exceptions : none
Caller : caller
=cut
sub defaultDataset {
my ($self, $param) = @_;
if ($param) {
$self->set(DEFDATASET, $param);
}
return $self->get(DEFDATASET);
}
=head2 addAttributeTree
Usage : $ct->addAttributeTree($atree);
Description: adds an AttributeTree to this ConfigurationTree. The
order of addition of each AttributeTree is maintained.
Returntype : na
Exceptions : none
Caller : caller
=cut
sub addAttributeTree {
my ($self, $attTree) = @_;
my $attTs = $self->get('attTs');
push @{$attTs}, $attTree;
}
=head2 addFilterTree
Usage : $ct->addFilterTree($ag);
Description: adds a FilterTree to this ConfigurationTree. The
order of addition of each FilterTree is maintained.
Returntype : na
Exceptions : none
Caller : caller
=cut
sub addFilterTree {
my ($self, $filtTree) = @_;
my $filtTs = $self->get('filtTs');
push @{$filtTs}, $filtTree;
}
sub getAttributeTreeByName {
my ($self, $name) = @_;
my $retTree;
my $attTs = $self->get('attTs');
foreach my $attT (@{$attTs}) {
if (($attT->name() && $name) && $attT->name() eq $name) {
$retTree = $attT;
last;
}
}
return $retTree;
}
sub getFilterTreeByName {
my ($self, $name) = @_;
my $retTree;
my $filtTs = $self->get('filtTs');
foreach my $filtT (@{$filtTs}) {
if ($filtT->name() eq $name) {
$retTree = $filtT;
last;
}
}
return $retTree;
}
sub getAllAttributeTrees {
my $self = shift;
return $self->get('attTs');
}
sub getAllFilterTrees {
my $self = shift;
return $self->get('filtTs');
}
sub getAttributeByName {
my ($self, $name) = @_;
my $retAtt;
my $attTs = $self->get('attTs');
foreach my $attT (@{$attTs}) {
$retAtt = $attT->getAttributeByName($name);
last if ($retAtt);
}
return $retAtt;
}
sub getAttributeByNameKey {
my ($self, $name, $key) = @_;
my $retAtt;
my $attTs = $self->get('attTs');
foreach my $attT (@{$attTs}) {
$retAtt = $attT->getAttributeByNameKey($name,$key);
last if ($retAtt);
}
return $retAtt;
}
sub getFilterByName {
my ($self, $name) = @_;
my $retFilt;
my $filtTs = $self->get('filtTs');
foreach my $filtT (@{$filtTs}) {
$retFilt = $filtT->getFilterByName($name);
unless ($retFilt) {
#then try option
my $opt = $filtT->getOptionByName($name);
if ($opt) {
$retFilt = $opt->filter;
}
}
last if ($retFilt);
}
return $retFilt if ($retFilt);
# if not found may be a filter in an attributePage
my $attTs = $self->get('attTs');
foreach my $attT (@{$attTs}) {
my $potFilt = $attT->getFilterByName($name);
if ($potFilt && $potFilt->isa("BioMart::Configuration::ValueFilter")){
$retFilt = $potFilt;
last;
}
}
return $retFilt;
}
sub getOptionByName {
my ($self, $name) = @_;
my $retOption;
my $filtTs = $self->get('filtTs');
foreach my $filtT (@{$filtTs}) {
$retOption = $filtT->getOptionByName($name);
last if ($retOption);
}
return $retOption;
}
sub toXML {
my ($self, $xml) = @_;
if ($xml) {
$self->{'datasetConfigXML'}=$xml;
}
return $self->{'datasetConfigXML'};
}
1;
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