Tests for the public method translate.

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();