def test_read_hierarchy_file(spark_session): ancestors = with_loinc_hierarchy( spark_session, create_hierarchies(spark_session), 'tests/resources/LOINC_HIERARCHY_SAMPLE.CSV', '2.56').get_ancestors() assert set(ancestors.columns) == EXPECTED_COLUMNS
def test_isa_loinc(spark_session): spark_session.sql('create database isa_loinc_ontologies') with_loinc_hierarchy( spark_session, create_hierarchies(spark_session), 'tests/resources/LOINC_HIERARCHY_SAMPLE.CSV', '2.56') \ .write_to_database('isa_loinc_ontologies') create_value_sets(spark_session).write_to_database('isa_loinc_ontologies') push_valuesets(spark_session, {'leukocytes' : isa_loinc('LP14738-6')}, database='isa_loinc_ontologies') expected = {'leukocytes' : [('http://loinc.org', '5821-4'), ('http://loinc.org', 'LP14738-6'), ('http://loinc.org', 'LP14419-3')]} assert get_current_valuesets(spark_session) == expected