added tests for new AttributeAdaptor

modules/t/attributeAdaptor.t

+use strict;
+
+use lib 't';
+use TestUtils qw(test_getter_setter debug);
+
+BEGIN { $| = 1;
+	use Test;
+	plan tests => 11;
+}
+
+use MultiTestDB;
+use Bio::EnsEMBL::Attribute;
+
+our $verbose = 0;
+
+my $multi = MultiTestDB->new;
+
+# get a core DBAdaptor
+my $db = $multi->get_DBAdaptor("core");
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+my $mfa           = $db->get_MiscFeatureAdaptor();
+
+
+#
+# Test get_AttributeAdaptor works
+#
+my $aa = $db->get_AttributeAdaptor();
+
+ok($aa && ref($aa) && $aa->isa('Bio::EnsEMBL::DBSQL::AttributeAdaptor'));
+
+
+# hide the contents of the attrib_type, misc_attrib, seq_region_attrib tables
+# so we can test storing etc. with a clean slate
+$multi->hide('core', 'misc_attrib', 'seq_region_attrib', 'attrib_type');
+
+
+##############
+# MiscFeature functionality tests
+#
+
+my $attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name',
+                                          -CODE => 'test_code',
+                                          -DESC => 'test_desc',
+                                          -VALUE => 'test_value');
+
+
+my $mf = $mfa->fetch_by_dbID(1);
+$aa->store_on_MiscFeature($mf, [$attrib]);
+
+#
+# make sure the misc_attrib table was updated
+#
+my $count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM misc_attrib " .
+   "WHERE misc_feature_id = 1")->[0]->[0];
+
+ok($count == 1);
+
+#
+# make sure the attrib_type table was updated
+#
+$count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM attrib_type " .
+   "WHERE code = 'test_code'")->[0]->[0];
+ok($count == 1);
+
+#
+# test that we can now retrieve this attribute
+#
+my @attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
+
+ok(@attribs == 1);
+
+$attrib = $attribs[0];
+
+ok($attrib->name eq 'test_name');
+ok($attrib->code eq 'test_code');
+ok($attrib->desc eq 'test_desc');
+ok($attrib->value eq 'test_value');
+
+
+#
+# test the removal of this attribute
+#
+$aa->remove_from_MiscFeature($mf);
+
+#
+# make sure the misc_attrib table was updated
+#
+my $count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM misc_attrib " .
+   "WHERE misc_feature_id = 1")->[0]->[0];
+
+ok($count == 0);
+
+#
+# make sure the attribute is no longer retrievable
+#
+my @attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
+ok(@attribs == 0);
+
+
+
+#################
+# Slice functionality tests
+#
+
+
+my $attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
+                                          -CODE => 'test_code2',
+                                          -DESC => 'test_desc2',
+                                          -VALUE => 'test_value2');
+
+
+my $slice = $slice_adaptor->fetch_by_region('chromosome', '20');
+
+$aa->store_on_Slice($slice, [$attrib]);
+
+#
+# make sure the seq_region_attrib table was updated
+#
+my $count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM seq_region_attrib " .
+   "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
+
+ok($count == 1);
+
+#
+# make sure the attrib_type table was updated
+#
+$count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM attrib_type " .
+   "WHERE code = 'test_code2'")->[0]->[0];
+ok($count == 1);
+
+#
+# test that we can now retrieve this attribute
+#
+my @attribs = @{$aa->fetch_all_by_Slice($slice)};
+
+ok(@attribs == 1);
+
+$attrib = $attribs[0];
+
+ok($attrib->name eq 'test_name2');
+ok($attrib->code eq 'test_code2');
+ok($attrib->desc eq 'test_desc2');
+ok($attrib->value eq 'test_value2');
+
+
+#
+# test the removal of this attribute
+#
+$aa->remove_from_Slice($slice);
+
+#
+# make sure the seq_region_attrib table was updated
+#
+my $count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM seq_region_attrib " .
+   "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
+
+ok($count == 0);
+
+#
+# make sure the attribute is no longer retrievable
+#
+my @attribs = @{$aa->fetch_all_by_Slice($slice)};
+ok(@attribs == 0);
+
+
+
+#
+# try to add an attribute with an already existing code
+#
+
+$aa->store_on_Slice($slice, [$attrib]);
+#
+# make sure the seq_region_attrib table was updated
+#
+my $count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM seq_region_attrib " .
+   "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
+
+ok($count == 1);
+
+#
+# make sure the attrib_type table was updated
+#
+$count = $db->db_handle->selectall_arrayref
+  ("SELECT count(*) FROM attrib_type " .
+   "WHERE code = 'test_code2'")->[0]->[0];
+ok($count == 1);
+
+my @attribs = @{$aa->fetch_all_by_Slice($slice)};
+ok(@attribs == 1);
+
+
+$multi->restore('core', 'misc_attrib', 'seq_region_attrib', 'attrib_type');