Commit 31f0121a authored by Andy Yates's avatar Andy Yates
Browse files

Capturing the vague tests and asserting we will return the right kind of warning to the user

parent 81ee91b5
use strict;
use warnings;
BEGIN { $| = 1;
use Test;
plan tests => 94;
}
use Test::More;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Exon;
......@@ -84,12 +82,15 @@ debug( "Links: ".scalar( @$links ));
ok( scalar @$links == 6 );
my $homologies = $gene->get_all_homologous_Genes();
debug( "Homologies: ".scalar( @$homologies ));
ok( scalar @$homologies ?
($homologies->[0][0]->isa("Bio::EnsEMBL::Gene")) : 1 );
SKIP: {
my $compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor('multi', 'compara', 1);
skip 'No comapra database adaptor found', 1 if ! $compara_dba;
my $homologies = $gene->get_all_homologous_Genes();
debug( "Homologies: ".scalar( @$homologies ));
ok( scalar @$homologies ?
($homologies->[0][0]->isa("Bio::EnsEMBL::Gene")) : 1 );
};
# now create a new gene ...
......@@ -459,8 +460,15 @@ ok(scalar @genes == 2);
# Test performance protection (very vague queries return no hits)
debug("Testing vague query protection");
ok(scalar (@{$ga->fetch_all_by_external_name('M%')}) == 0);
ok(scalar (@{$ga->fetch_all_by_external_name('%')}) == 0);
{
my $warnings = q{};
local $SIG{'__WARN__'} = sub {
$warnings .= $_[0];
};
ok(scalar (@{$ga->fetch_all_by_external_name('M%')}) == 0);
ok(scalar (@{$ga->fetch_all_by_external_name('%')}) == 0);
like($warnings, qr/is too vague and will monopolise database/, 'Checking for warnings being emitted by the above methods');
}
#
# test GeneAdaptor::get_Interpro_by_geneid
......@@ -801,3 +809,5 @@ ok($new_gene->canonical_annotation eq 'longest transcript in gene'); #test 86
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('ENSG00000355555');
ok( $species eq 'homo_sapiens' && $object_type eq 'Gene');
done_testing();
\ No newline at end of file
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