From 6ba7997030b8689f372bcad4f197c9097a652389 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Wed, 11 Sep 2013 14:16:43 +0000
Subject: [PATCH] Tests for the public method translate.
---
modules/t/sequenceOntologyMapper.t | 78 ++++++++++++++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/modules/t/sequenceOntologyMapper.t b/modules/t/sequenceOntologyMapper.t
index 2d14c230f1..839a38bd28 100644
--- a/modules/t/sequenceOntologyMapper.t
+++ b/modules/t/sequenceOntologyMapper.t
@@ -8,10 +8,88 @@
use strict;
use warnings;
+use Data::Dumper;
use Test::More;
+use Test::Exception;
+
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Utils::Scalar qw ( assert_ref );
+use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Utils::SequenceOntologyMapper;
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Gene;
+use Bio::EnsEMBL::Transcript;
+use Bio::EnsEMBL::Exon;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::SimpleFeature;
+use Bio::EnsEMBL::MiscFeature;
+use Bio::EnsEMBL::RepeatFeature;
+use Bio::EnsEMBL::Variation::VariationFeature;
+use Bio::EnsEMBL::Variation::StructuralVariationFeature;
+use Bio::EnsEMBL::Compara::ConstrainedElement;
+use Bio::EnsEMBL::Funcgen::RegulatoryFeature;
+
+# Module compiles
ok(1, 'Bio::EnsEMBL::Utils::SequenceOntologyMapper compiles');
+#
+# Test constructor
+#
+throws_ok { new Bio::EnsEMBL::Utils::SequenceOntologyMapper() }
+ qr /No ontology term adaptor/, "constructor with no argument raises exception";
+throws_ok { new Bio::EnsEMBL::Utils::SequenceOntologyMapper(bless({}, 'Someclass')) }
+ qr /Argument is not/, "constructor with object not of class OntologyTermAdaptor raises exception";
+
+# my $registry = 'Bio::EnsEMBL::Registry';
+# Bio::EnsEMBL::Registry->no_version_check(1);
+# Bio::EnsEMBL::Registry->no_cache_warnings(1);
+
+# $registry->load_registry_from_db(-host => '127.0.0.1',
+# -port => 33061,
+# -db_version => 73,
+# -user => 'ensro',
+# -no_cache => 1);
+
+# my $oa = $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
+# assert_ref($oa, 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor');
+
+my $omulti = Bio::EnsEMBL::Test::MultiTestDB->new('ontology');
+my $odb = $omulti->get_DBAdaptor('ontology');
+my $oa = $odb->get_OntologyTermAdaptor();
+
+my $mapper = Bio::EnsEMBL::Utils::SequenceOntologyMapper->new($oa);
+isa_ok($mapper, 'Bio::EnsEMBL::Utils::SequenceOntologyMapper');
+
+#
+# Test translate method
+#
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
+my $db = $multi->get_DBAdaptor('core');
+
+my $mappings =
+ [
+ { obj => Bio::EnsEMBL::Feature->new, term => 'region' },
+ { obj => Bio::EnsEMBL::Gene->new, term => 'gene' },
+ { obj => Bio::EnsEMBL::Transcript->new, term => 'transcript' },
+ { obj => Bio::EnsEMBL::Exon->new, term => 'exon' },
+ { obj => $db->get_SliceAdaptor->fetch_by_region('chromosome', '20', 30_270_000, 31_200_000), term => 'region' },
+ { obj => Bio::EnsEMBL::SimpleFeature->new(), term => 'biological_region' },
+ { obj => Bio::EnsEMBL::MiscFeature->new(), term => 'biological_region' },
+ { obj => Bio::EnsEMBL::RepeatFeature->new(), term => 'repeat_region' },
+ { obj => Bio::EnsEMBL::Variation::VariationFeature->new(), term => 'sequence_variant' },
+ { obj => Bio::EnsEMBL::Variation::StructuralVariationFeature->new(), term => 'structural_variant' },
+ { obj => Bio::EnsEMBL::Compara::ConstrainedElement->new(), term => 'DNA_constraint_sequence' }
+
+ # 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' => 'regulatory_region'
+ ];
+
+throws_ok { $mapper->translate( bless({}, 'Someclass')) }
+ qr /not found/, "translate method raises exception";
+
+map {
+ print ref($_->{obj}) and is($mapper->translate($_->{obj}), $_->{term}, sprintf "%s translates as assumed", ref($_->{obj})) }
+ @{$mappings};
+
done_testing();
--
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