Bio-MAGETAB

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t/004_magetab.t  view on Meta::CPAN

# Bio::MAGETAB::BaseClass (should really do them all, FIXME?).
my $db1;
lives_ok( sub{ $db1 = Bio::MAGETAB::DatabaseEntry->new( accession => 1234 ) },
          'knows how to create a DatabaseEntry object' );
ok( $db1->isa('Bio::MAGETAB::DatabaseEntry'), 'of the correct class' );

# Confirm that there's no container set for this instance.
ok( ! defined $db1->get_ClassContainer(), 'and with no container object set' );

# Create our MAGETAB container object.
dies_ok( sub{ Bio::MAGETAB->new( not_a_real_attribute => 1 ) },
         'object instantiation with unrecognised attribute fails' ); 
my $obj;
lives_ok( sub{ $obj = Bio::MAGETAB->new() }, 'can create a MAGETAB object' );
ok( $obj->isa('Bio::MAGETAB'), 'of the correct class' );
ok( ! $obj->has_databaseEntries(), 'with no associated DatabaseEntry objects' );

# Evaluated in scalar context, this gives zero for an empty array..
is( $obj->get_databaseEntries(), 0, 'and get_databaseEntries agrees' );

# Now create a new object that will associate with this container automatically.

t/013_sdrf.t  view on Meta::CPAN

$sdrf = test_parse( $sdrf_reader );

my $assay = $sdrf_reader->get_builder()->get_assay({ name => 'Assay 1' });
my $ad = $assay->get_arrayDesign();
is( $ad->get_name(), 'Design 1', 'Assay Array Design correctly linked' );
is( join(";", map { $_->get_value } $ad->get_comments()), 'Comment 1',
    'Array Design commented correctly');

__DATA__
Source Name	Provider	Characteristics[ OrganismPart ]	Characteristics[DiseaseState]	Term Source REF:test namespace	Term Accession Number	Material Type	Description	Comment[MyNVT]	Sample Name	Characteristics[Age]	Unit[TimeUnit]	Term Source REF	Material ...
my source	the guy in the next room	root	hemophilia	NCI META	CL:111111	organism_part	description_text	mycomment	my sample	6	hours	MO	cell	sample comment value	EXTPRTCL10654	the guy in the next room	total RNA	2007-02-21	This did not happen. I was not h...
my source	the guy in the next room	root	hemophilia	NCI META	CL:111111	organism_part	description_text	mycomment	my sample	6	hours	MO	cell	sample comment value	EXTPRTCL10654	the guy in the next room	total RNA	2007-02-21	This did not happen. I was not h...
sparse source 1			normal		blah blah ignore me										EXTPRTCL10654		polyA RNA					sparse LE Cy5			Cy5		P-XMPL-11	ArrayExpress	sparse hyb		A-TEST-1			sparse scan1	testing.jpg		Data3.txt		TRANPRTCL10656	norm 3		NormData3.txt	pained expression			10	mM...
sparse source 2			normal												EXTPRTCL10654		polyA RNA					sparse LE Cy3			Cy3		P-XMPL-11	ArrayExpress	sparse hyb		A-TEST-1			sparse scan2			Data4.txt		TRANPRTCL10656	norm 3		NormData3.txt	pregnant pause					
sparse source 3			normal												EXTPRTCL10654		polyA RNA					sparse LE biotin			biotin		P-XMPL-11	ArrayExpress	sparse hyb b		A-TEST-1		scanning protocol	sparse scan3	imagefile2.TIFF	a bit blurry			TRANPRTCL10656	norm 4		NormData4.txt	preternatura...

t/015_dbloader.t  view on Meta::CPAN

                  'TermSource created' );
        ok( UNIVERSAL::isa( $ts, 'Bio::MAGETAB::TermSource' ), 'of the correct class' );
    }

    my $oid;
    {
        my $ts;
        lives_ok( sub { $ts = $loader->get_term_source({ name => 'test_term_source' }) },
                  'TermSource retrieved' );
        ok( UNIVERSAL::isa( $ts, 'Bio::MAGETAB::TermSource' ), 'of the correct class' );        
        dies_ok( sub { $ts = $loader->get_term_source({ name => 'not_the_correct_name' }) },
                 'non-existent TermSource is not retrieved' );
        $oid = $loader->id( $ts );
    }

    {
        my $ts;
        lives_ok( sub { $ts = $loader->find_or_create_term_source({ name    => 'test_term_source',
                                                                    version => 0.9 }) },
                  'old TermSource find_or_created' );
        ok( UNIVERSAL::isa( $ts, 'Bio::MAGETAB::TermSource' ), 'of the correct class' );

t/testlib/CommonTests.pm  view on Meta::CPAN

    lives_ok( sub { $obj = instantiate( $class, $required ) },
              "instantiation with all required args succeeds" );

    # Check predicate method behaviour - before opt attr setting.
    while ( my ( $key, $value ) = each %{ $optional } ) {
        my $predicate = "has_$key";
        ok( ! $obj->$predicate, qq{and optional "$key" attribute predicate method agrees} );
    }

    # Required attributes with an unrecognised impostor; should fail.
    my %with_unrecognised = ( 'this_is_not_a_recognised_attribute' => 1, %{ $required } );
    dies_ok( sub { $obj = instantiate( $class, \%with_unrecognised ) },
              "instantiation with an unrecognised arg fails" );

    # Construct a full instance as our return value.
    my $all = { %{ $optional }, %{ $required } };
    lives_ok( sub { $obj = instantiate( $class, $all      ) },
              "instantiation with all required and optional args succeeds" );

    # Check our fully-constructed object.
    ok( defined $obj,        'and returns an object' );



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