diff --git a/modules/t/attributeAdaptor.t b/modules/t/attributeAdaptor.t index 84d9ef7994ecc530ac51a65952f7beb975781593..6de33880e5df5ed56f69e76989b6d98077a36c41 100644 --- a/modules/t/attributeAdaptor.t +++ b/modules/t/attributeAdaptor.t @@ -224,21 +224,19 @@ $attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -VALUE => 'test_value2'); my $gene = $ga->fetch_by_stable_id($stable_id); +my $gene_id = $gene->dbID(); $aa->store_on_Gene($gene, [$attrib]); # # make sure the seq_region_attrib table was updated # -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0]; - -is($count, 1, "One gene attrib fetched"); +is_rows(1, $db, "gene_attrib", "where gene_id = ? ", [$gene_id]); # # make sure the attrib_type table was updated # -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0]; -is($count, 1, "One attrib_type available"); +is_rows(1, $db, "attrib_type", "where code = ? ", ["test_code2"]); # # test that we can now retrieve this attribute @@ -266,18 +264,14 @@ is($attrib->value, 'test_value2', "Attrib value is test_value2"); # test the removal of this attribute with atrrib code # $aa->remove_from_Gene($gene, "junk"); -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0]; - -is($count, 1, "One gene attrib available"); +is_rows(1, $db, "gene_attrib", "where gene_id = ? ", [$gene_id]); # # test the removal of this attribute # $aa->remove_from_Gene($gene, "test_code2"); -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0]; - -is($count, 0, "Gene attrib has been removed"); +is_rows(0, $db, "gene_attrib", "where gene_id = ? ", [$gene_id]); # # make sure the attribute is no longer retrievable @@ -292,18 +286,14 @@ $aa->store_on_Gene($gene, [$attrib]); # # make sure the seq_region_attrib table was updated # -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0]; - -is($count, 1, "One attrib added for gene"); +is_rows(1, $db, "gene_attrib", "where gene_id = ? ", [$gene_id]); # # make sure the attrib_type table was updated # -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0]; -is($count, 1, "One attrib stored for code test_code2"); +is_rows(1, $db, "attrib_type", "where code = ? ", ["test_code2"]); @attribs = @{$aa->fetch_all_by_Gene($gene)}; -note "attribs: " . scalar(@attribs); is(@attribs, 1, "One attrib for gene"); @attribs = @{$aa->fetch_all_by_Gene(undef)}; @@ -313,9 +303,7 @@ is(@attribs, 1, "One attrib for genes"); # test the removal of this attribute # $aa->remove_from_Gene($gene); -$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0]; - -is($count, 0, "Attrib has been removed from gene"); +is_rows(0, $db, "gene_attrib", "where gene_id = ? ", [$gene_id]); # # test the storage of empty attrib values @@ -330,9 +318,7 @@ is($count, 0, "Attrib has been removed from gene"); cmp_ok($new_rows, '>', $current_rows, 'Asserting the storage of undefined attributes will always store them'); # now remove again $aa->remove_from_Gene($gene); - $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0]; - - is($count, 0, "Attrib has been removed from gene"); + is_rows(0, $db, "gene_attrib", "where gene_id = ? ", [$gene_id]); }