def test_empty_database(real_adapter): ## GIVEN an empty database adapter = real_adapter ## WHEN asking for data data = get_dashboard_info(adapter) ## THEN assert that the data is empty assert data.get("total_cases") == 0
def test_empty_database(real_adapter): ## GIVEN an empty database adapter = real_adapter ## WHEN asking for data data = get_dashboard_info(adapter) ## THEN assert that the data is empty assert data.get('total_cases') == 0
def test_one_case(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) ## WHEN asking for data data = get_dashboard_info(adapter) ## THEN assert there is one case in the data for group in data["cases"]: if group["status"] == "all": assert group["count"] == 1 elif group["status"] == case_obj["status"]: assert group["count"] == 1
def test_one_case(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) ## WHEN asking for data data = get_dashboard_info(adapter) ## THEN assert there is one case in the data for group in data['cases']: if group['status'] == 'all': assert group['count'] == 1 elif group['status'] == case_obj['status']: assert group['count'] == 1
def test_one_causative(real_adapter, case_obj): ## GIVEN an database with two cases where one has a causative adapter = real_adapter adapter._add_case(case_obj) case_obj["causatives"] = ["a variant"] case_obj["_id"] = "test1" adapter._add_case(case_obj) ## WHEN asking for data institute_id = case_obj["owner"] data = get_dashboard_info(adapter, institute_id=institute_id) ## THEN assert there is one case in the causative information for info in data["overview"]: if info["title"] == "Causative variants": assert info["count"] == 1 else: assert info["count"] == 0
def test_one_causative(real_adapter, case_obj): ## GIVEN an database with two cases where one has a causative adapter = real_adapter adapter._add_case(case_obj) case_obj['causatives'] = ['a variant'] case_obj['_id'] = 'test1' adapter._add_case(case_obj) ## WHEN asking for data institute_id = case_obj['owner'] data = get_dashboard_info(adapter, institute_id=institute_id) ## THEN assert there is one case in the causative information for info in data['overview']: if info['title'] == 'Causative variants': assert info['count'] == 1 else: assert info['count'] == 0
def test_one_causative(real_adapter, case_obj): ## GIVEN an database with two cases where one has a causative adapter = real_adapter adapter._add_case(case_obj) case_obj['causatives'] = ['a variant'] case_obj['_id'] = 'test1' adapter._add_case(case_obj) ## WHEN asking for data institute_id = case_obj['owner'] data = get_dashboard_info(adapter, institute_id=institute_id) ## THEN assert there is one case in the causative information for info in data['overview']: if info['title'] == 'Causative variants': assert info['count'] == 1 else: assert info['count'] == 0
def test_with_slice_query(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) ## WHEN asking for data case_display_id = case_obj["display_name"] institute_id = case_obj["owner"] slice_query = f"case:{case_display_id}" data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query) ## THEN assert there is one case in the data for group in data["cases"]: if group["status"] == "all": assert group["count"] == 1 elif group["status"] == case_obj["status"]: assert group["count"] == 1
def test_with_slice_query(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) ## WHEN asking for data case_display_id = case_obj['display_name'] institute_id = case_obj['owner'] slice_query = case_display_id data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query) ## THEN assert there is one case in the data for group in data['cases']: if group['status'] == 'all': assert group['count'] == 1 elif group['status'] == case_obj['status']: assert group['count'] == 1
def test_with_slice_query(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) ## WHEN asking for data case_display_id = case_obj['display_name'] institute_id = case_obj['owner'] slice_query = case_display_id data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query) ## THEN assert there is one case in the data for group in data['cases']: if group['status'] == 'all': assert group['count'] == 1 elif group['status'] == case_obj['status']: assert group['count'] == 1
def test_with_phenotype_group_query(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) phenotype = {"phenotype_id": "HP:0000001", "feature": "Bioterm"} ## WITH a phenotype set for one case case_obj["phenotype_groups"] = [phenotype] case_obj["_id"] = "test1" adapter._add_case(case_obj) ## WHEN querying for cases with that phenotype id institute_id = case_obj["owner"] slice_query = "pheno_group:HP:0000001" data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query) ## THEN assert there is one case in the data for group in data["cases"]: if group["status"] == "all": assert group["count"] == 1 elif group["status"] == case_obj["status"]: assert group["count"] == 1
def test_with_phenotype_group_query(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) phenotype = {'phenotype_id': 'HP:0000001' , 'feature':'Bioterm'} ## WITH a phenotype set for one case case_obj['phenotype_groups'] = [ phenotype ] case_obj['_id'] = 'test1' adapter._add_case(case_obj) ## WHEN querying for cases with that phenotype id institute_id = case_obj['owner'] slice_query = 'PG:0000001' data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query) ## THEN assert there is one case in the data for group in data['cases']: if group['status'] == 'all': assert group['count'] == 1 elif group['status'] == case_obj['status']: assert group['count'] == 1
def test_with_phenotype_group_query(real_adapter, case_obj): ## GIVEN an database with one case adapter = real_adapter adapter._add_case(case_obj) phenotype = {'phenotype_id': 'HP:0000001', 'feature': 'Bioterm'} ## WITH a phenotype set for one case case_obj['phenotype_groups'] = [phenotype] case_obj['_id'] = 'test1' adapter._add_case(case_obj) ## WHEN querying for cases with that phenotype id institute_id = case_obj['owner'] slice_query = 'PG:0000001' data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query) ## THEN assert there is one case in the data for group in data['cases']: if group['status'] == 'all': assert group['count'] == 1 elif group['status'] == case_obj['status']: assert group['count'] == 1