#!/usr/bin/env perl
#
# Copyright 2008-2010 Tim Rayner
#
# This file is part of Bio::MAGETAB.
#
# Bio::MAGETAB is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# Bio::MAGETAB is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Bio::MAGETAB. If not, see <http://www.gnu.org/licenses/>.
#
# $Id: 003_array_design.t 333 2010-06-02 16:41:31Z tfrayner $
use strict;
use warnings;
use Test::More qw(no_plan);
BEGIN {
use_ok( 'Bio::MAGETAB::ArrayDesign' );
}
INIT {
use lib 't/testlib';
use CommonTests qw(test_class);
}
require Bio::MAGETAB::ControlledTerm;
require Bio::MAGETAB::Comment;
require Bio::MAGETAB::Reporter;
require Bio::MAGETAB::CompositeElement;
my $ct = Bio::MAGETAB::ControlledTerm->new( category => 1, value => 2 );
my @co = Bio::MAGETAB::Comment->new( name => 1, value => 2 );
my @de;
for ( 1..3 ) {
push @de, Bio::MAGETAB::Reporter->new( name => "test $_" );
}
use Bio::MAGETAB::TermSource;
my $ts = Bio::MAGETAB::TermSource->new( name => 'test term source' );
my %required_attr = (
name => 'test array design',
);
my %optional_attr = (
accession => 'A-TEST-1111',
termSource => $ts,
version => '1.21b',
uri => 'http://dummy.com/array_design.txt',
technologyType => $ct,
surfaceType => $ct,
substrateType => $ct,
sequencePolymerType => $ct,
printingProtocol => 'test text here',
provider => 'simple string provider',
designElements => \@de,
comments => \@co,
);
my %bad_attr = (
name => [],
accession => [],
termSource => 'test',
version => [],
uri => [],
technologyType => 'test',
surfaceType => 'test',
substrateType => 'test',
sequencePolymerType => 'test',
printingProtocol => [],
provider => [],
designElements => [qw(1 2 3)],
comments => 'test',
);
my $ct2 = Bio::MAGETAB::ControlledTerm->new( category => 2, value => 3 );
my @co2 = Bio::MAGETAB::Comment->new( name => 2, value => 3 );
my @de2;
for ( 1..3 ) {
push @de2, Bio::MAGETAB::CompositeElement->new( name => "test 2 $_" );
}
my $ts2 = Bio::MAGETAB::TermSource->new( name => 'test term source 2' );
my %secondary_attr = (
name => 'test array design 2',
accession => 'A-TEST-1112',
termSource => $ts2,
version => '1.23b',
uri => 'http://dummy.com/array_design2.txt',
technologyType => $ct2,
surfaceType => $ct2,
substrateType => $ct2,
sequencePolymerType => $ct2,
printingProtocol => 'test text here 2',
provider => 'simple string provider 2',
designElements => \@de2,
comments => \@co2,
);
my $obj = test_class(
'Bio::MAGETAB::ArrayDesign',
\%required_attr,
\%optional_attr,
\%bad_attr,
\%secondary_attr,
);
ok( $obj->isa('Bio::MAGETAB::DatabaseEntry'), 'object has correct superclass' );