From 666a547b020f6fdcc1d53c210818570e1c5e91fb Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 5 Apr 2013 09:29:01 +0000
Subject: [PATCH] ENSCORESW-308: added tests for is_obsolete
---
modules/t/ontologyTerm.t | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/modules/t/ontologyTerm.t b/modules/t/ontologyTerm.t
index dd504df66b..59b3dfb0ec 100644
--- a/modules/t/ontologyTerm.t
+++ b/modules/t/ontologyTerm.t
@@ -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is_obsolete, "GO:0003677 is obsolete");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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