Commit 666a547b authored by Magali Ruffier's avatar Magali Ruffier
Browse files

ENSCORESW-308: added tests for is_obsolete

parent 8048b47b
......@@ -30,11 +30,18 @@ my $human = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $human->get_DBAdaptor("core");
debug("Test database instatiated");
ok($db);
my $accession = "GO:0003677";
my $go_adaptor = $odb->get_OntologyTermAdaptor();
my $accession = "GO:0000217";
my $term = $go_adaptor->fetch_by_accession($accession);
ok(!$term->is_root, "Term is not a root");
is($term, undef, "GO:0000217 does not exist in the non obsolete list");
$term = $go_adaptor->fetch_by_accession($accession, 1);
ok($term->is_obsolete, "GO:0003677 is obsolete");
$accession = "GO:0003677";
$term = $go_adaptor->fetch_by_accession($accession, 1);
ok(!$term->is_obsolete, "GO:0003677 is not obsolete");
ok(!$term->is_root, "GO:0003677 is not a root");
my $gene;
my $ga = $db->get_GeneAdaptor();
......@@ -44,7 +51,10 @@ is(@{$genes}, 2, "Genes match the GO term");
my $pattern = '%binding%';
my $terms = $go_adaptor->fetch_all_by_name($pattern);
is(@{$terms}, 138, "Found binding terms");
is(@{$terms}, 134, "Found binding terms");
$terms = $go_adaptor->fetch_all_by_name($pattern, undef, 1);
is(@{$terms}, 138, "Found binding terms, including obsolete ones");
my $roots = $go_adaptor->fetch_all_roots();
is(@{$roots}, 1, "Found roots");
......
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