##############################
#
# PValue.t
#
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl PValue.t`
##############################
# C O P Y R I G H T N O T I C E
# Copyright (c) 2001-2006 by:
# * The MicroArray Gene Expression Database Society (MGED)
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
use Carp;
# use blib;
use Test::More tests => 184;
use strict;
use Bio::MAGE;
use Bio::MAGE::Association;
BEGIN { use_ok('Bio::MAGE::QuantitationType::PValue') };
use Bio::MAGE::QuantitationType::ConfidenceIndicator;
use Bio::MAGE::BioAssayData::QuantitationTypeMap;
use Bio::MAGE::Description::OntologyEntry;
use Bio::MAGE::BioAssay::Channel;
use Bio::MAGE::NameValueType;
use Bio::MAGE::AuditAndSecurity::Security;
use Bio::MAGE::AuditAndSecurity::Audit;
use Bio::MAGE::QuantitationType::QuantitationType;
use Bio::MAGE::Description::Description;
# we test the new() method
my $pvalue;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$pvalue = Bio::MAGE::QuantitationType::PValue->new();
}
isa_ok($pvalue, 'Bio::MAGE::QuantitationType::PValue');
# test the package_name class method
is($pvalue->package_name(), q[QuantitationType],
'package');
# test the class_name class method
is($pvalue->class_name(), q[Bio::MAGE::QuantitationType::PValue],
'class_name');
# set the attribute values in the call to new()
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$pvalue = Bio::MAGE::QuantitationType::PValue->new(isBackground => '1',
identifier => '2',
name => '3');
}
#
# testing attribute isBackground
#
# test attribute values can be set in new()
is($pvalue->getIsBackground(), '1',
'isBackground new');
# test getter/setter
$pvalue->setIsBackground('1');
is($pvalue->getIsBackground(), '1',
'isBackground getter/setter');
# test getter throws exception with argument
eval {$pvalue->getIsBackground(1)};
ok($@, 'isBackground getter throws exception with argument');
# test setter throws exception with no argument
eval {$pvalue->setIsBackground()};
ok($@, 'isBackground setter throws exception with no argument');
# test setter throws exception with too many argument
eval {$pvalue->setIsBackground('1', '1')};
ok($@, 'isBackground setter throws exception with too many argument');
# test setter accepts undef
eval {$pvalue->setIsBackground(undef)};
ok((!$@ and not defined $pvalue->getIsBackground()),
'isBackground setter accepts undef');
#
# testing attribute identifier
#
# test attribute values can be set in new()
is($pvalue->getIdentifier(), '2',
'identifier new');
# test getter/setter
$pvalue->setIdentifier('2');
is($pvalue->getIdentifier(), '2',
'identifier getter/setter');
# test getter throws exception with argument
eval {$pvalue->getIdentifier(1)};
ok($@, 'identifier getter throws exception with argument');
# test setter throws exception with no argument
eval {$pvalue->setIdentifier()};
ok($@, 'identifier setter throws exception with no argument');
# test setter throws exception with too many argument
eval {$pvalue->setIdentifier('2', '2')};
ok($@, 'identifier setter throws exception with too many argument');
# test setter accepts undef
eval {$pvalue->setIdentifier(undef)};
ok((!$@ and not defined $pvalue->getIdentifier()),
'identifier setter accepts undef');
#
# testing attribute name
#
# test attribute values can be set in new()
is($pvalue->getName(), '3',
'name new');
# test getter/setter
$pvalue->setName('3');
is($pvalue->getName(), '3',
'name getter/setter');
# test getter throws exception with argument
eval {$pvalue->getName(1)};
ok($@, 'name getter throws exception with argument');
# test setter throws exception with no argument
eval {$pvalue->setName()};
ok($@, 'name setter throws exception with no argument');
# test setter throws exception with too many argument
eval {$pvalue->setName('3', '3')};
ok($@, 'name setter throws exception with too many argument');
# test setter accepts undef
eval {$pvalue->setName(undef)};
ok((!$@ and not defined $pvalue->getName()),
'name setter accepts undef');
# retrieve the list of association meta-data
my %assns = Bio::MAGE::QuantitationType::PValue->associations();
# set the association values in the call to new()
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$pvalue = Bio::MAGE::QuantitationType::PValue->new(dataType => Bio::MAGE::Description::OntologyEntry->new(),
auditTrail => [Bio::MAGE::AuditAndSecurity::Audit->new()],
propertySets => [Bio::MAGE::NameValueType->new()],
channel => Bio::MAGE::BioAssay::Channel->new(),
confidenceIndicators => [Bio::MAGE::QuantitationType::ConfidenceIndicator->new()],
descriptions => [Bio::MAGE::Description::Description->new()],
security => Bio::MAGE::AuditAndSecurity::Security->new(),
scale => Bio::MAGE::Description::OntologyEntry->new(),
targetQuantitationType => Bio::MAGE::QuantitationType::QuantitationType->new(),
quantitationTypeMaps => [Bio::MAGE::BioAssayData::QuantitationTypeMap->new()]);
}
my ($end, $assn);
# testing association dataType
my $datatype_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$datatype_assn = Bio::MAGE::Description::OntologyEntry->new();
}
isa_ok($pvalue->getDataType, q[Bio::MAGE::Description::OntologyEntry]);
is($pvalue->setDataType($datatype_assn), $datatype_assn,
'setDataType returns value');
ok($pvalue->getDataType() == $datatype_assn,
'getDataType fetches correct value');
# test setDataType throws exception with bad argument
eval {$pvalue->setDataType(1)};
ok($@, 'setDataType throws exception with bad argument');
# test getDataType throws exception with argument
eval {$pvalue->getDataType(1)};
ok($@, 'getDataType throws exception with argument');
# test setDataType throws exception with no argument
eval {$pvalue->setDataType()};
ok($@, 'setDataType throws exception with no argument');
# test setDataType throws exception with too many argument
eval {$pvalue->setDataType(1,2)};
ok($@, 'setDataType throws exception with too many argument');
# test setDataType accepts undef
eval {$pvalue->setDataType(undef)};
ok((!$@ and not defined $pvalue->getDataType()),
'setDataType accepts undef');
# test the meta-data for the assoication
$assn = $assns{dataType};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'dataType->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'dataType->self() is a valid Bio::MAGE::Association::End'
);
# testing association auditTrail
my $audittrail_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$audittrail_assn = Bio::MAGE::AuditAndSecurity::Audit->new();
}
ok((UNIVERSAL::isa($pvalue->getAuditTrail,'ARRAY')
and scalar @{$pvalue->getAuditTrail} == 1
and UNIVERSAL::isa($pvalue->getAuditTrail->[0], q[Bio::MAGE::AuditAndSecurity::Audit])),
'auditTrail set in new()');
ok(eq_array($pvalue->setAuditTrail([$audittrail_assn]), [$audittrail_assn]),
'setAuditTrail returns correct value');
ok((UNIVERSAL::isa($pvalue->getAuditTrail,'ARRAY')
and scalar @{$pvalue->getAuditTrail} == 1
and $pvalue->getAuditTrail->[0] == $audittrail_assn),
'getAuditTrail fetches correct value');
is($pvalue->addAuditTrail($audittrail_assn), 2,
'addAuditTrail returns number of items in list');
ok((UNIVERSAL::isa($pvalue->getAuditTrail,'ARRAY')
and scalar @{$pvalue->getAuditTrail} == 2
and $pvalue->getAuditTrail->[0] == $audittrail_assn
and $pvalue->getAuditTrail->[1] == $audittrail_assn),
'addAuditTrail adds correct value');
# test setAuditTrail throws exception with non-array argument
eval {$pvalue->setAuditTrail(1)};
ok($@, 'setAuditTrail throws exception with non-array argument');
# test setAuditTrail throws exception with bad argument array
eval {$pvalue->setAuditTrail([1])};
ok($@, 'setAuditTrail throws exception with bad argument array');
# test addAuditTrail throws exception with no arguments
eval {$pvalue->addAuditTrail()};
ok($@, 'addAuditTrail throws exception with no arguments');
# test addAuditTrail throws exception with bad argument
eval {$pvalue->addAuditTrail(1)};
ok($@, 'addAuditTrail throws exception with bad array');
# test setAuditTrail accepts empty array ref
eval {$pvalue->setAuditTrail([])};
ok((!$@ and defined $pvalue->getAuditTrail()
and UNIVERSAL::isa($pvalue->getAuditTrail, 'ARRAY')
and scalar @{$pvalue->getAuditTrail} == 0),
'setAuditTrail accepts empty array ref');
# test getAuditTrail throws exception with argument
eval {$pvalue->getAuditTrail(1)};
ok($@, 'getAuditTrail throws exception with argument');
# test setAuditTrail throws exception with no argument
eval {$pvalue->setAuditTrail()};
ok($@, 'setAuditTrail throws exception with no argument');
# test setAuditTrail throws exception with too many argument
eval {$pvalue->setAuditTrail(1,2)};
ok($@, 'setAuditTrail throws exception with too many argument');
# test setAuditTrail accepts undef
eval {$pvalue->setAuditTrail(undef)};
ok((!$@ and not defined $pvalue->getAuditTrail()),
'setAuditTrail accepts undef');
# test the meta-data for the assoication
$assn = $assns{auditTrail};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'auditTrail->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'auditTrail->self() is a valid Bio::MAGE::Association::End'
);
# testing association propertySets
my $propertysets_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$propertysets_assn = Bio::MAGE::NameValueType->new();
}
ok((UNIVERSAL::isa($pvalue->getPropertySets,'ARRAY')
and scalar @{$pvalue->getPropertySets} == 1
and UNIVERSAL::isa($pvalue->getPropertySets->[0], q[Bio::MAGE::NameValueType])),
'propertySets set in new()');
ok(eq_array($pvalue->setPropertySets([$propertysets_assn]), [$propertysets_assn]),
'setPropertySets returns correct value');
ok((UNIVERSAL::isa($pvalue->getPropertySets,'ARRAY')
and scalar @{$pvalue->getPropertySets} == 1
and $pvalue->getPropertySets->[0] == $propertysets_assn),
'getPropertySets fetches correct value');
is($pvalue->addPropertySets($propertysets_assn), 2,
'addPropertySets returns number of items in list');
ok((UNIVERSAL::isa($pvalue->getPropertySets,'ARRAY')
and scalar @{$pvalue->getPropertySets} == 2
and $pvalue->getPropertySets->[0] == $propertysets_assn
and $pvalue->getPropertySets->[1] == $propertysets_assn),
'addPropertySets adds correct value');
# test setPropertySets throws exception with non-array argument
eval {$pvalue->setPropertySets(1)};
ok($@, 'setPropertySets throws exception with non-array argument');
# test setPropertySets throws exception with bad argument array
eval {$pvalue->setPropertySets([1])};
ok($@, 'setPropertySets throws exception with bad argument array');
# test addPropertySets throws exception with no arguments
eval {$pvalue->addPropertySets()};
ok($@, 'addPropertySets throws exception with no arguments');
# test addPropertySets throws exception with bad argument
eval {$pvalue->addPropertySets(1)};
ok($@, 'addPropertySets throws exception with bad array');
# test setPropertySets accepts empty array ref
eval {$pvalue->setPropertySets([])};
ok((!$@ and defined $pvalue->getPropertySets()
and UNIVERSAL::isa($pvalue->getPropertySets, 'ARRAY')
and scalar @{$pvalue->getPropertySets} == 0),
'setPropertySets accepts empty array ref');
# test getPropertySets throws exception with argument
eval {$pvalue->getPropertySets(1)};
ok($@, 'getPropertySets throws exception with argument');
# test setPropertySets throws exception with no argument
eval {$pvalue->setPropertySets()};
ok($@, 'setPropertySets throws exception with no argument');
# test setPropertySets throws exception with too many argument
eval {$pvalue->setPropertySets(1,2)};
ok($@, 'setPropertySets throws exception with too many argument');
# test setPropertySets accepts undef
eval {$pvalue->setPropertySets(undef)};
ok((!$@ and not defined $pvalue->getPropertySets()),
'setPropertySets accepts undef');
# test the meta-data for the assoication
$assn = $assns{propertySets};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'propertySets->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'propertySets->self() is a valid Bio::MAGE::Association::End'
);
# testing association channel
my $channel_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$channel_assn = Bio::MAGE::BioAssay::Channel->new();
}
isa_ok($pvalue->getChannel, q[Bio::MAGE::BioAssay::Channel]);
is($pvalue->setChannel($channel_assn), $channel_assn,
'setChannel returns value');
ok($pvalue->getChannel() == $channel_assn,
'getChannel fetches correct value');
# test setChannel throws exception with bad argument
eval {$pvalue->setChannel(1)};
ok($@, 'setChannel throws exception with bad argument');
# test getChannel throws exception with argument
eval {$pvalue->getChannel(1)};
ok($@, 'getChannel throws exception with argument');
# test setChannel throws exception with no argument
eval {$pvalue->setChannel()};
ok($@, 'setChannel throws exception with no argument');
# test setChannel throws exception with too many argument
eval {$pvalue->setChannel(1,2)};
ok($@, 'setChannel throws exception with too many argument');
# test setChannel accepts undef
eval {$pvalue->setChannel(undef)};
ok((!$@ and not defined $pvalue->getChannel()),
'setChannel accepts undef');
# test the meta-data for the assoication
$assn = $assns{channel};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'channel->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'channel->self() is a valid Bio::MAGE::Association::End'
);
# testing association confidenceIndicators
my $confidenceindicators_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$confidenceindicators_assn = Bio::MAGE::QuantitationType::ConfidenceIndicator->new();
}
ok((UNIVERSAL::isa($pvalue->getConfidenceIndicators,'ARRAY')
and scalar @{$pvalue->getConfidenceIndicators} == 1
and UNIVERSAL::isa($pvalue->getConfidenceIndicators->[0], q[Bio::MAGE::QuantitationType::ConfidenceIndicator])),
'confidenceIndicators set in new()');
ok(eq_array($pvalue->setConfidenceIndicators([$confidenceindicators_assn]), [$confidenceindicators_assn]),
'setConfidenceIndicators returns correct value');
ok((UNIVERSAL::isa($pvalue->getConfidenceIndicators,'ARRAY')
and scalar @{$pvalue->getConfidenceIndicators} == 1
and $pvalue->getConfidenceIndicators->[0] == $confidenceindicators_assn),
'getConfidenceIndicators fetches correct value');
is($pvalue->addConfidenceIndicators($confidenceindicators_assn), 2,
'addConfidenceIndicators returns number of items in list');
ok((UNIVERSAL::isa($pvalue->getConfidenceIndicators,'ARRAY')
and scalar @{$pvalue->getConfidenceIndicators} == 2
and $pvalue->getConfidenceIndicators->[0] == $confidenceindicators_assn
and $pvalue->getConfidenceIndicators->[1] == $confidenceindicators_assn),
'addConfidenceIndicators adds correct value');
# test setConfidenceIndicators throws exception with non-array argument
eval {$pvalue->setConfidenceIndicators(1)};
ok($@, 'setConfidenceIndicators throws exception with non-array argument');
# test setConfidenceIndicators throws exception with bad argument array
eval {$pvalue->setConfidenceIndicators([1])};
ok($@, 'setConfidenceIndicators throws exception with bad argument array');
# test addConfidenceIndicators throws exception with no arguments
eval {$pvalue->addConfidenceIndicators()};
ok($@, 'addConfidenceIndicators throws exception with no arguments');
# test addConfidenceIndicators throws exception with bad argument
eval {$pvalue->addConfidenceIndicators(1)};
ok($@, 'addConfidenceIndicators throws exception with bad array');
# test setConfidenceIndicators accepts empty array ref
eval {$pvalue->setConfidenceIndicators([])};
ok((!$@ and defined $pvalue->getConfidenceIndicators()
and UNIVERSAL::isa($pvalue->getConfidenceIndicators, 'ARRAY')
and scalar @{$pvalue->getConfidenceIndicators} == 0),
'setConfidenceIndicators accepts empty array ref');
# test getConfidenceIndicators throws exception with argument
eval {$pvalue->getConfidenceIndicators(1)};
ok($@, 'getConfidenceIndicators throws exception with argument');
# test setConfidenceIndicators throws exception with no argument
eval {$pvalue->setConfidenceIndicators()};
ok($@, 'setConfidenceIndicators throws exception with no argument');
# test setConfidenceIndicators throws exception with too many argument
eval {$pvalue->setConfidenceIndicators(1,2)};
ok($@, 'setConfidenceIndicators throws exception with too many argument');
# test setConfidenceIndicators accepts undef
eval {$pvalue->setConfidenceIndicators(undef)};
ok((!$@ and not defined $pvalue->getConfidenceIndicators()),
'setConfidenceIndicators accepts undef');
# test the meta-data for the assoication
$assn = $assns{confidenceIndicators};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'confidenceIndicators->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'confidenceIndicators->self() is a valid Bio::MAGE::Association::End'
);
# testing association descriptions
my $descriptions_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$descriptions_assn = Bio::MAGE::Description::Description->new();
}
ok((UNIVERSAL::isa($pvalue->getDescriptions,'ARRAY')
and scalar @{$pvalue->getDescriptions} == 1
and UNIVERSAL::isa($pvalue->getDescriptions->[0], q[Bio::MAGE::Description::Description])),
'descriptions set in new()');
ok(eq_array($pvalue->setDescriptions([$descriptions_assn]), [$descriptions_assn]),
'setDescriptions returns correct value');
ok((UNIVERSAL::isa($pvalue->getDescriptions,'ARRAY')
and scalar @{$pvalue->getDescriptions} == 1
and $pvalue->getDescriptions->[0] == $descriptions_assn),
'getDescriptions fetches correct value');
is($pvalue->addDescriptions($descriptions_assn), 2,
'addDescriptions returns number of items in list');
ok((UNIVERSAL::isa($pvalue->getDescriptions,'ARRAY')
and scalar @{$pvalue->getDescriptions} == 2
and $pvalue->getDescriptions->[0] == $descriptions_assn
and $pvalue->getDescriptions->[1] == $descriptions_assn),
'addDescriptions adds correct value');
# test setDescriptions throws exception with non-array argument
eval {$pvalue->setDescriptions(1)};
ok($@, 'setDescriptions throws exception with non-array argument');
# test setDescriptions throws exception with bad argument array
eval {$pvalue->setDescriptions([1])};
ok($@, 'setDescriptions throws exception with bad argument array');
# test addDescriptions throws exception with no arguments
eval {$pvalue->addDescriptions()};
ok($@, 'addDescriptions throws exception with no arguments');
# test addDescriptions throws exception with bad argument
eval {$pvalue->addDescriptions(1)};
ok($@, 'addDescriptions throws exception with bad array');
# test setDescriptions accepts empty array ref
eval {$pvalue->setDescriptions([])};
ok((!$@ and defined $pvalue->getDescriptions()
and UNIVERSAL::isa($pvalue->getDescriptions, 'ARRAY')
and scalar @{$pvalue->getDescriptions} == 0),
'setDescriptions accepts empty array ref');
# test getDescriptions throws exception with argument
eval {$pvalue->getDescriptions(1)};
ok($@, 'getDescriptions throws exception with argument');
# test setDescriptions throws exception with no argument
eval {$pvalue->setDescriptions()};
ok($@, 'setDescriptions throws exception with no argument');
# test setDescriptions throws exception with too many argument
eval {$pvalue->setDescriptions(1,2)};
ok($@, 'setDescriptions throws exception with too many argument');
# test setDescriptions accepts undef
eval {$pvalue->setDescriptions(undef)};
ok((!$@ and not defined $pvalue->getDescriptions()),
'setDescriptions accepts undef');
# test the meta-data for the assoication
$assn = $assns{descriptions};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'descriptions->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'descriptions->self() is a valid Bio::MAGE::Association::End'
);
# testing association security
my $security_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$security_assn = Bio::MAGE::AuditAndSecurity::Security->new();
}
isa_ok($pvalue->getSecurity, q[Bio::MAGE::AuditAndSecurity::Security]);
is($pvalue->setSecurity($security_assn), $security_assn,
'setSecurity returns value');
ok($pvalue->getSecurity() == $security_assn,
'getSecurity fetches correct value');
# test setSecurity throws exception with bad argument
eval {$pvalue->setSecurity(1)};
ok($@, 'setSecurity throws exception with bad argument');
# test getSecurity throws exception with argument
eval {$pvalue->getSecurity(1)};
ok($@, 'getSecurity throws exception with argument');
# test setSecurity throws exception with no argument
eval {$pvalue->setSecurity()};
ok($@, 'setSecurity throws exception with no argument');
# test setSecurity throws exception with too many argument
eval {$pvalue->setSecurity(1,2)};
ok($@, 'setSecurity throws exception with too many argument');
# test setSecurity accepts undef
eval {$pvalue->setSecurity(undef)};
ok((!$@ and not defined $pvalue->getSecurity()),
'setSecurity accepts undef');
# test the meta-data for the assoication
$assn = $assns{security};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'security->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'security->self() is a valid Bio::MAGE::Association::End'
);
# testing association scale
my $scale_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$scale_assn = Bio::MAGE::Description::OntologyEntry->new();
}
isa_ok($pvalue->getScale, q[Bio::MAGE::Description::OntologyEntry]);
is($pvalue->setScale($scale_assn), $scale_assn,
'setScale returns value');
ok($pvalue->getScale() == $scale_assn,
'getScale fetches correct value');
# test setScale throws exception with bad argument
eval {$pvalue->setScale(1)};
ok($@, 'setScale throws exception with bad argument');
# test getScale throws exception with argument
eval {$pvalue->getScale(1)};
ok($@, 'getScale throws exception with argument');
# test setScale throws exception with no argument
eval {$pvalue->setScale()};
ok($@, 'setScale throws exception with no argument');
# test setScale throws exception with too many argument
eval {$pvalue->setScale(1,2)};
ok($@, 'setScale throws exception with too many argument');
# test setScale accepts undef
eval {$pvalue->setScale(undef)};
ok((!$@ and not defined $pvalue->getScale()),
'setScale accepts undef');
# test the meta-data for the assoication
$assn = $assns{scale};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'scale->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'scale->self() is a valid Bio::MAGE::Association::End'
);
# testing association targetQuantitationType
my $targetquantitationtype_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$targetquantitationtype_assn = Bio::MAGE::QuantitationType::QuantitationType->new();
}
isa_ok($pvalue->getTargetQuantitationType, q[Bio::MAGE::QuantitationType::QuantitationType]);
is($pvalue->setTargetQuantitationType($targetquantitationtype_assn), $targetquantitationtype_assn,
'setTargetQuantitationType returns value');
ok($pvalue->getTargetQuantitationType() == $targetquantitationtype_assn,
'getTargetQuantitationType fetches correct value');
# test setTargetQuantitationType throws exception with bad argument
eval {$pvalue->setTargetQuantitationType(1)};
ok($@, 'setTargetQuantitationType throws exception with bad argument');
# test getTargetQuantitationType throws exception with argument
eval {$pvalue->getTargetQuantitationType(1)};
ok($@, 'getTargetQuantitationType throws exception with argument');
# test setTargetQuantitationType throws exception with no argument
eval {$pvalue->setTargetQuantitationType()};
ok($@, 'setTargetQuantitationType throws exception with no argument');
# test setTargetQuantitationType throws exception with too many argument
eval {$pvalue->setTargetQuantitationType(1,2)};
ok($@, 'setTargetQuantitationType throws exception with too many argument');
# test setTargetQuantitationType accepts undef
eval {$pvalue->setTargetQuantitationType(undef)};
ok((!$@ and not defined $pvalue->getTargetQuantitationType()),
'setTargetQuantitationType accepts undef');
# test the meta-data for the assoication
$assn = $assns{targetQuantitationType};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'targetQuantitationType->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'targetQuantitationType->self() is a valid Bio::MAGE::Association::End'
);
# testing association quantitationTypeMaps
my $quantitationtypemaps_assn;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
$quantitationtypemaps_assn = Bio::MAGE::BioAssayData::QuantitationTypeMap->new();
}
ok((UNIVERSAL::isa($pvalue->getQuantitationTypeMaps,'ARRAY')
and scalar @{$pvalue->getQuantitationTypeMaps} == 1
and UNIVERSAL::isa($pvalue->getQuantitationTypeMaps->[0], q[Bio::MAGE::BioAssayData::QuantitationTypeMap])),
'quantitationTypeMaps set in new()');
ok(eq_array($pvalue->setQuantitationTypeMaps([$quantitationtypemaps_assn]), [$quantitationtypemaps_assn]),
'setQuantitationTypeMaps returns correct value');
ok((UNIVERSAL::isa($pvalue->getQuantitationTypeMaps,'ARRAY')
and scalar @{$pvalue->getQuantitationTypeMaps} == 1
and $pvalue->getQuantitationTypeMaps->[0] == $quantitationtypemaps_assn),
'getQuantitationTypeMaps fetches correct value');
is($pvalue->addQuantitationTypeMaps($quantitationtypemaps_assn), 2,
'addQuantitationTypeMaps returns number of items in list');
ok((UNIVERSAL::isa($pvalue->getQuantitationTypeMaps,'ARRAY')
and scalar @{$pvalue->getQuantitationTypeMaps} == 2
and $pvalue->getQuantitationTypeMaps->[0] == $quantitationtypemaps_assn
and $pvalue->getQuantitationTypeMaps->[1] == $quantitationtypemaps_assn),
'addQuantitationTypeMaps adds correct value');
# test setQuantitationTypeMaps throws exception with non-array argument
eval {$pvalue->setQuantitationTypeMaps(1)};
ok($@, 'setQuantitationTypeMaps throws exception with non-array argument');
# test setQuantitationTypeMaps throws exception with bad argument array
eval {$pvalue->setQuantitationTypeMaps([1])};
ok($@, 'setQuantitationTypeMaps throws exception with bad argument array');
# test addQuantitationTypeMaps throws exception with no arguments
eval {$pvalue->addQuantitationTypeMaps()};
ok($@, 'addQuantitationTypeMaps throws exception with no arguments');
# test addQuantitationTypeMaps throws exception with bad argument
eval {$pvalue->addQuantitationTypeMaps(1)};
ok($@, 'addQuantitationTypeMaps throws exception with bad array');
# test setQuantitationTypeMaps accepts empty array ref
eval {$pvalue->setQuantitationTypeMaps([])};
ok((!$@ and defined $pvalue->getQuantitationTypeMaps()
and UNIVERSAL::isa($pvalue->getQuantitationTypeMaps, 'ARRAY')
and scalar @{$pvalue->getQuantitationTypeMaps} == 0),
'setQuantitationTypeMaps accepts empty array ref');
# test getQuantitationTypeMaps throws exception with argument
eval {$pvalue->getQuantitationTypeMaps(1)};
ok($@, 'getQuantitationTypeMaps throws exception with argument');
# test setQuantitationTypeMaps throws exception with no argument
eval {$pvalue->setQuantitationTypeMaps()};
ok($@, 'setQuantitationTypeMaps throws exception with no argument');
# test setQuantitationTypeMaps throws exception with too many argument
eval {$pvalue->setQuantitationTypeMaps(1,2)};
ok($@, 'setQuantitationTypeMaps throws exception with too many argument');
# test setQuantitationTypeMaps accepts undef
eval {$pvalue->setQuantitationTypeMaps(undef)};
ok((!$@ and not defined $pvalue->getQuantitationTypeMaps()),
'setQuantitationTypeMaps accepts undef');
# test the meta-data for the assoication
$assn = $assns{quantitationTypeMaps};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->rank(),
and $end->rank(),
and defined $end->ordered(),
and ($end->ordered() == 0 or $end->ordered() == 1),
and defined $end->class_name(),
and $end->class_name(),
and defined $end->name(),
and $end->name()),
'quantitationTypeMaps->other() is a valid Bio::MAGE::Association::End'
);
$end = $assn->self();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
and defined $end->documentation(),
and defined $end->cardinality(),
and grep {$_ eq $end->cardinality} ('0..1','1','1..N','0..N'),
and defined $end->is_ref(),
and ($end->is_ref() == 0 or $end->is_ref() == 1),
and defined $end->class_name(),
and $end->class_name()),
'quantitationTypeMaps->self() is a valid Bio::MAGE::Association::End'
);
my $confidenceindicator;
{
# silence the abstract class warnings
local $SIG{__WARN__} = sub {'IGNORE'};
# create a superclass
$confidenceindicator = Bio::MAGE::QuantitationType::ConfidenceIndicator->new();
}
# testing superclass ConfidenceIndicator
isa_ok($confidenceindicator, q[Bio::MAGE::QuantitationType::ConfidenceIndicator]);
isa_ok($pvalue, q[Bio::MAGE::QuantitationType::ConfidenceIndicator]);