From d7d9bdac272dc6b997df5d72cd95428208acf4de Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 11 Jun 2012 11:09:01 +0000
Subject: [PATCH] Classificaiton was not working as expected
---
modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm | 5 +++--
modules/t/metaContainer.t | 6 ++++++
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt | 1 +
3 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
index ccbe61232c..51c41c4fae 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
@@ -262,8 +262,9 @@ sub get_genebuild {
sub get_classification {
my ($self) = @_;
my $classification = $self->list_value_by_key('species.classification');
- splice(@{$classification}, 0, 2); # remove the sapiens, Homo from the backing array
- return $classification;
+ my $copy = [@{$classification}];
+ splice(@{$copy}, 0, 1); # remove the Homo sapiens
+ return $copy;
}
diff --git a/modules/t/metaContainer.t b/modules/t/metaContainer.t
index d909702e80..f392648503 100644
--- a/modules/t/metaContainer.t
+++ b/modules/t/metaContainer.t
@@ -63,6 +63,12 @@ $mc->store_key_value('species.division',$divname);
$div = $mc->get_division();
ok($div eq $divname);
+#
+# classification
+#
+my $classification = [ qw/Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota/ ];
+is_deeply($mc->get_classification(), $classification, 'Checking classification as expected');
+
#
# Testing get_Species()
#
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 37fe516d07..0b6bfa7229 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -9,6 +9,7 @@
27 1 species.classification Hominidae
34 1 species.classification Metazoa
35 1 species.classification Eukaryota
+26 1 species.classification Homo sapiens
36 1 species.common_name Human
70 1 species.scientific_name Homo sapiens
3 1 species.taxonomy_id 9606
--
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