def test_tag_feature_to_all_diseases(self): config = IniParser().read_ini(MY_INI_FILE) section = "is_gene_in_mhc" feature_id = 'ENSG00000229281' result = Criteria.tag_feature_to_all_diseases(feature_id, section, config, {}) result_diseases = sorted(list(result['ENSG00000229281'].keys())) (core_disease, other_disease) = CriteriaManager.get_available_diseases() available_diseases = sorted(core_disease + other_disease) self.assertEqual(result_diseases, available_diseases) section = "is_marker_in_mhc" feature_id = 'rs6679677' result = Criteria.tag_feature_to_all_diseases(feature_id, section, config, {}) result_diseases = sorted(list(result['rs6679677'].keys())) (core_disease, other_disease) = CriteriaManager.get_available_diseases() available_diseases = sorted(core_disease + other_disease) self.assertEqual(result_diseases, available_diseases)
def test_get_available_diseases(self): (main, other) = utils.Disease.get_site_diseases() self.assertEqual(12, len(main), "12 main diseases found when searching for all diseases") self.assertEqual(8, len(other), "8 other diseases found when searching for all diseases") (main_dis_code, other_dis_code) = CriteriaManager.get_available_diseases() self.assertIn("T1D", main_dis_code) self.assertIn("AA", other_dis_code)
def test_criteria_mappings(self, idx, idx_types): (main_codes, other_codes) = CriteriaManager.get_available_diseases() site_enabled_diseases = main_codes + other_codes elastic_url = ElasticSettings.url() for idx_type in idx_types: url = idx + '/' + idx_type + '/_mapping' response = Search.elastic_request(elastic_url, url, is_post=False) elastic_type_mapping = json.loads(response.content.decode("utf-8")) property_keys = list(elastic_type_mapping[idx]['mappings'][idx_type]['properties'].keys()) '''check if score and disease_tags and qid are there in mapping''' self.assertIn('score', property_keys) self.assertIn('disease_tags', property_keys) self.assertIn('qid', property_keys) '''check if all the enabled diseases are there''' for disease in site_enabled_diseases: self.assertIn(disease, property_keys)