def test_families(self): """ to check if mutations are correctly retrieved """ self.init_test(self.current_func_name) abs_fam_db = self.__create_db_instance() test_file = os.path.join(self.data_dir, self.current_func_name + ".txt") fam_db = FamilyDB() fam_db.open_db(test_file) abs_fam_db.add_connector(fam_db) families = abs_fam_db.families # *************** test keys ****************** self.assertEqual(len(families.keys()), 7, "Incorrect number of families keys") self.assertTrue("8" in families, "Incorrect families key") self.assertTrue("231" in families, "Incorrect families key") self.assertTrue("347" not in families, "Incorrect families key") # *************** test contents ****************** test_family = families["425"] self.assertEqual(len(test_family.patient_codes), 3, "Incorrect number of members") self.assertEqual(test_family.type2, "RECTAL", "Incorrect family type2") self.assertEqual(test_family.type3, "", "Incorrect family type3") self.assertEqual(test_family.type4, "CAFAM", "Incorrect family type4") patient_codes = test_family.patient_codes self.assertEqual(len(patient_codes), 3, "Incorrect number of patient codes being read") self.assertEqual(patient_codes[0], "Co1458", "Incorrect patient code") self.assertEqual(patient_codes[1], "Co1595", "Incorrect patient code") self.assertEqual(patient_codes[2], "Co866", "Incorrect patient code")
def test_group_members_count(self): """ to check if number of members in each group are correctly counted """ self.init_test(self.current_func_name) abs_fam_db = self.__create_db_instance() test_file = os.path.join(self.data_dir, self.current_func_name + ".txt") fam_db = FamilyDB() fam_db.open_db(test_file) abs_fam_db.add_connector(fam_db) test_group_members_count = abs_fam_db.group_members_count # *************** test group members count ****************** self.assertEqual(test_group_members_count[TYPE1_ALL], 76, "Invaild number of members in group: " + TYPE1_ALL) self.assertEqual( test_group_members_count[TYPE2_RECTAL], 37, "Invaild number of members in group: " + TYPE2_RECTAL ) self.assertEqual( test_group_members_count[TYPE2_NON_RECTAL], 39, "Invaild number of members in group: " + TYPE2_NON_RECTAL ) self.assertEqual( test_group_members_count[TYPE3_COLON], 21, "Invaild number of members in group: " + TYPE3_COLON ) self.assertEqual( test_group_members_count[TYPE3_NON_COLON], 55, "Invaild number of members in group: " + TYPE3_NON_COLON ) self.assertEqual( test_group_members_count[TYPE4_CAFAM], 37, "Invaild number of members in group: " + TYPE4_CAFAM ) self.assertEqual( test_group_members_count[TYPE4_NON_CAFAM], 39, "Invaild number of members in group: " + TYPE4_NON_CAFAM )
def __connect_family_db(self, family_db_file): self.info("creating family db connection to " + family_db_file) fam_db = FamilyDB() fam_db.open_db(family_db_file) self.__abs_fam_db.add_connector(fam_db)