Raw content of BioMart::FormatterI
<![CDATA[# $Id: FormatterI.pm,v 1.4 2008/04/09 12:52:33 syed Exp $
#
# BioMart module for BioMart::FormatterI
#
# You may distribute this module under the same terms as perl
# itself.
# POD documentation - main docs before the code.
=head1 NAME
BioMart::FormatterI
=head1 SYNOPSIS
TODO: Synopsis here.
=head1 DESCRIPTION
An abstract class for Formatters
=head1 AUTHOR - Arek Kasprzyk, Syed Haider, Richard Holland, Damian Smedley, Gudmundur Arni Thorisson
=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::FormatterI;
use strict;
use warnings;
# Extends BioMart::Root
use base qw(BioMart::Root);
use BioMart::Web::SiteDefs;
sub _new {
my ($self) = @_;
$self->SUPER::_new();
$self->attr('query',undef);
$self->attr('original_attributes',undef);
$self->attr('result_table',undef);
$self->attr('attribute_positions',undef);# for hyperlink processing
$self->attr('attribute_url_positions',undef);# for hyperlink processing
$self->attr('attribute_url',undef);# for hyperlink processing
$self->attr('dataset1_end',undef);#for result table color highlighting
}
# must be implemented for every formatter implementation
sub processQuery {
my $self = shift;
$self->unimplemented_method();
}
# must be implemented for every formatter implementation
sub nextRow {
my $self = shift;
$self->unimplemented_method();
}
# must be implemented for every formatter implementation
sub getDisplayNames {
my $self = shift;
$self->unimplemented_method();
}
# can be implemented in formatter implementations
sub getFooterText {
return undef;
}
sub resultTable {
my ($self,$result_table) = @_;
if ($result_table){
$self->set('result_table',$result_table);
}
return $self->get('result_table');
}
sub getTextDisplayNames {
my ($self,$separator) = @_;
my $original_attributes = $self->get('original_attributes');
my $final_dataset_order = $self->get('query')->finalDatasetOrder;
my @attribute_display_names;
my @original_dataset_attributes;
foreach my $dataset(reverse @$final_dataset_order){
foreach (@{$original_attributes}){
push @original_dataset_attributes,$_
if ($_->dataSetName eq $dataset);
}
}
foreach my $original_attribute(@original_dataset_attributes){
push @attribute_display_names, $original_attribute->displayName;
}
return @attribute_display_names;
}
sub setHTMLAttributes {
my ($self, $query) = @_;
# add extra url attributes on query if required (eg) for HTML, XLS
if($query->getAllAttributes())
{
my $registry = $query->getRegistry;
my $attributes = [@{$query->getAllAttributes()}];
foreach my $attribute (@$attributes){
if ($attribute->link){
my @link = split(/\|/,$attribute->link);
if (@link > 2){# multi attribute link
for (my $i = 2; $i < @link; $i++){
next if ($link[$i] eq $attribute->name);
# skip broken hyperlink URL templates for now
# use long winded method call to avoid exception throwing
next if (!$query->getRegistry
->getDatasetByName($query->virtualSchema, $attribute->dataSetName)
->getConfigurationTree($attribute->interface)
->getAttributeByName($link[$i]));
if($query->get('currentDS') ne $attribute->dataSetName)
{
my $tempDS = $query->get('currentDS');
$query->setDataset($attribute->dataSetName);
$query->addAttribute($link[$i], $attribute->interface);
$query->setDataset($tempDS);
}
else
{
$query->addAttribute($link[$i], $attribute->interface);
}
}
}
}
}
# set @attribute_positions, @attribute_url_positions and and @attribute_url
# so nextRow can process hyperlinks
my $final_dataset_order = $query->finalDatasetOrder;
# establish the position of attributes and URL-only attributes in
# final ResultTable
my $original_attributes = $self->get('original_attributes');
my @attribute_positions;
my @attribute_url_positions;
my @attribute_url;
my $att_counter = 0;
my $extra_att_counter = 0;
my $dataset_start = 0;
my $extra_att_start = 0;
foreach my $dataset(reverse @$final_dataset_order){
my @original_dataset_attributes;
foreach (@{$original_attributes}){
push @original_dataset_attributes,$_
if ($_->dataSetName eq $dataset);
}
$dataset_start = $extra_att_start + $extra_att_counter;
$extra_att_start = $dataset_start + @original_dataset_attributes;
$att_counter = 0;
$extra_att_counter = 0;
foreach my $original_attribute(@original_dataset_attributes){
my @url_positions;
my @link;
if ($original_attribute->link){
@link = split(/\|/,$original_attribute->link);
if (@link > 2){# multi attribute link
for (my $i = 2; $i < @link; $i++){
# skip any that had broken links as above
next if (!$query->getRegistry
->getDatasetByName($query->virtualSchema,
$original_attribute->dataSetName)
->getConfigurationTree($original_attribute->interface)
->getAttributeByName($link[$i]));
if ($link[$i] eq $original_attribute->name){
push @url_positions, $dataset_start+$att_counter;
}
else{
push @url_positions,
$extra_att_start+$extra_att_counter;
$extra_att_counter++;
}
}
}
else{
push @url_positions,$dataset_start+$att_counter;
}
}
else{
push @url_positions,$dataset_start+$att_counter;
}
push @attribute_url_positions, \@url_positions;
push @attribute_positions, $dataset_start+$att_counter;
# Check $link[0] to find out what kind of link
# this is. Then, look up the prefix for links of that kind
# in SiteDefs.pm. If found, prefix it. If not, leave as-is.
#my %prefixes = BioMart::Web::SiteDefs->getSettings('urlPrefixes');
my %prefixes;
my $mart_registry = $query->getRegistry();
my $hash = $mart_registry->settingsParams();
foreach(keys %$hash) {
if($_ eq "urlPrefixes") {
%prefixes = %{$hash->{$_}};
}
}
my $resolvedLink =
$link[1]
? (
(substr($link[1],0,1) eq '/')
? $prefixes{$link[0]} . $link[1]
: $link[1]
)
: $link[0];
push @attribute_url, $resolvedLink;
$att_counter++;
}
}
$self->set('attribute_positions',\@attribute_positions);
$self->set('attribute_url_positions',\@attribute_url_positions);
$self->set('attribute_url',\@attribute_url);
# set dataset1_end
#my $original_attributes = $self->get('original_attributes');
my @original_dataset_attributes;
foreach my $dataset(reverse @$final_dataset_order){
foreach (@{$original_attributes}){
push @original_dataset_attributes,$_
if ($_->dataSetName eq $dataset);
}
}
my ($first_dataset,$dataset1_end);
foreach my $original_attribute(@original_dataset_attributes){
my $dataset_name = $original_attribute->pointedFromDataset ||
$original_attribute->dataSetName;
if ($first_dataset && $first_dataset ne $dataset_name){
$self->set('dataset1_end',$dataset1_end-1);
last;
}
$dataset1_end++;
$self->set('dataset1_end',$dataset1_end-1);
$first_dataset = $dataset_name;
}
}
return $query;
}
sub getMimeType {
return 'text/plain';
}
sub getFileType {
return 'txt';
}
sub getFormatterDisplayName {
return undef;
}
sub isBinary {
return 0;
}
sub isSpecial {
return 0;
}
1;
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