Created

modules/t/canonicalDBAdaptor.t

+use strict;
+use warnings;
+
+use lib 't';
+
+BEGIN { $| = 1;
+	use Test;
+	plan tests => 41;
+}
+
+
+use TestUtils qw(debug test_getter_setter);
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor;
+
+my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new( -user   => 'ensro',
+					      -dbname => 'homo_sapiens_core_14_31',
+					      -host   => '127.0.0.1',
+					      -port   => '5000',
+					      -driver => 'mysql');
+
+# Check DBAdaptor
+ok($db);
+
+# Should get meaningful type back
+my $test_adaptor = $db->get_ArchiveStableIdAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor"));
+$test_adaptor = $db->get_QtlFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor"));
+$test_adaptor = $db->get_QtlAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlAdaptor"));
+$test_adaptor = $db->get_ProteinFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor"));
+$test_adaptor = $db->get_ProteinAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinAdaptor"));
+#$test_adaptor = $db->get_SNPAdaptor();
+#ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProxySNPAdaptor"));
+#$test_adaptor = $db->get_BlastAdaptor();
+#ok($test_adaptor->isa("Bio::EnsEMBL::External::BlastAdaptor"));
+$test_adaptor = $db->get_MapFragAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::MapFragAdaptor"));
+$test_adaptor = $db->get_CloneAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::CloneAdaptor"));
+$test_adaptor = $db->get_PredictionTranscriptAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor"));
+$test_adaptor = $db->get_SequenceAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::SequenceAdaptor"));
+$test_adaptor = $db->get_GeneAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProxyGeneAdaptor"));
+$test_adaptor = $db->get_ExonAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ExonAdaptor"));
+$test_adaptor = $db->get_TranscriptAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::TranscriptAdaptor"));
+$test_adaptor = $db->get_TranslationAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::TranslationAdaptor"));
+$test_adaptor = $db->get_RawContigAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::RawContigAdaptor"));
+$test_adaptor = $db->get_SliceAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::SliceAdaptor"));
+$test_adaptor = $db->get_AnalysisAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::AnalysisAdaptor"));
+$test_adaptor = $db->get_SimpleFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor"));
+$test_adaptor = $db->get_RepeatConsensusAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor"));
+$test_adaptor = $db->get_RepeatFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProxyRepeatFeatureAdaptor"));
+$test_adaptor = $db->get_ProteinAlignFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor"));
+$test_adaptor = $db->get_DnaAlignFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProxyDnaAlignFeatureAdaptor"));
+$test_adaptor = $db->get_AssemblyMapperAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor"));
+$test_adaptor = $db->get_DBEntryAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::DBEntryAdaptor"));
+$test_adaptor = $db->get_KaryotypeBandAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor"));
+$test_adaptor = $db->get_ChromosomeAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ChromosomeAdaptor"));
+$test_adaptor = $db->get_SupportingFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor"));
+$test_adaptor = $db->get_MarkerFeatureAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor"));
+$test_adaptor = $db->get_MarkerAdaptor();
+ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor"));
+
+# Should get an error if we ask for something non-existent
+eval { $db->get_adaptor("SomeNonExistentType") };
+ok($@);
+
+# Check setting module with good values
+ok($db->set_adaptor("ArchiveStableId", "Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor" ));
+
+# Setting an unknown data type should give an error
+eval { $db->set_adaptor("SomeNonExistentType", "Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor") };
+ok($@);
+
+# Setting to a non-subclass of the default should give an error
+eval { $db->set_adaptor("ArchiveStableId", "Bio::EnsEMBL::DBSQL::GeneAdaptor") };
+ok($@);
+
+# Generic adaptors
+
+# Should work OK with subclasses of BaseFeatureAdaptor
+my $rfa = Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor->new($db);
+my $sfa = Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor->new($db);
+ok($db->add_GenericFeatureAdaptor("Repeat", $rfa));
+ok($db->add_GenericFeatureAdaptor("Simple", $sfa));
+
+
+# Check get-ing the above
+# by name ...
+my %generic_adaptors = $db->get_GenericFeatureAdaptors("Simple", "Repeat");
+ok(%generic_adaptors);
+ok(exists(%generic_adaptors->{'Simple'}));
+
+# no arg should return all
+%generic_adaptors = $db->get_GenericFeatureAdaptors();
+my $size = keys(%generic_adaptors);
+ok($size == 2);
+ok(%generic_adaptors->{"Simple"});
+ok(%generic_adaptors->{"Repeat"});
+
+# requesting one that hasn't been added should throw
+eval { my %generic_adpators = $db->get_GenericFeatureAdaptors("Mickey") };
+ok($@);
+