def test_with_disjoint_value_sets_from_directory(spark_session): spark_session.sql("CREATE DATABASE IF NOT EXISTS disjoint_value_sets_db") create_value_sets(spark_session) \ .with_value_sets_from_directory("tests/resources/valuesets") \ .write_to_database("disjoint_value_sets_db") reloaded = get_value_sets(spark_session, "disjoint_value_sets_db") \ .with_disjoint_value_sets_from_directory("tests/resources/valuesets", "disjoint_value_sets_db") assert reloaded.get_values("urn:cerner:bunsen:valueset:married_maritalstatus", "0.0.1") \ .count() == 1
def test_with_value_sets_from_directory(spark_session): value_sets = create_value_sets(spark_session) \ .with_value_sets_from_directory("tests/resources/valuesets") assert value_sets.get_values("urn:cerner:bunsen:valueset:married_maritalstatus", "0.0.1") \ .count() == 1
def test_isa_custom(spark_session, bundles): observations = extract_entry(spark_session, bundles, 'observation') observations.registerTempTable('observations') blood_pressure = {'blood_pressure': [('http://loinc.org', '8462-4')]} spark_session.sql('create database custom_ontologies') create_value_sets(spark_session).write_to_database('custom_ontologies') create_hierarchies(spark_session).write_to_database('custom_ontologies') push_valuesets(spark_session, blood_pressure, database='custom_ontologies') results = spark_session.sql("SELECT subject.reference, " + "effectiveDateTime, " + "valueQuantity.value " + "FROM observations " + "WHERE in_valueset(code, 'blood_pressure')") assert get_current_valuesets(spark_session) == blood_pressure assert results.count() == 14
def test_isa_snomed(spark_session): spark_session.sql('create database isa_snomed_ontologies') with_relationships( spark_session, create_hierarchies(spark_session), 'tests/resources/SNOMED_RELATIONSHIP_SAMPLE.TXT', '20160901') \ .write_to_database('isa_snomed_ontologies') create_value_sets(spark_session).write_to_database('isa_snomed_ontologies') push_valuesets(spark_session, {'diabetes': isa_snomed('73211009')}, database='isa_snomed_ontologies') expected = { 'diabetes': [('http://snomed.info/sct', '73211009'), ('http://snomed.info/sct', '44054006')] } assert get_current_valuesets(spark_session) == expected
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
def test_add_valueset(spark_session): value_sets = create_value_sets(spark_session) values = [('urn:cerner:system1', 'urn:code:a'), ('urn:cerner:system1', 'urn:code:b'), ('urn:cerner:system2', 'urn:code:1')] appended = value_sets.with_new_value_set( url='urn:cerner:test:valuesets:testvalueset', version='0.1', values=values) assert appended.get_value_sets().count() == 1 assert appended.get_values().count() == 3
def test_get_value_set_as_xml(spark_session): value_sets = create_value_sets(spark_session) values = [('urn:cerner:system1', 'urn:code:a'), ('urn:cerner:system1', 'urn:code:b'), ('urn:cerner:system2', 'urn:code:1')] appended = value_sets.with_new_value_set( url='urn:cerner:test:valuesets:testvalueset', version='0.1', values=values) # this test fails because version is null on line 778 of ValueSets.java xml_str = appended.get_value_set_as_xml( 'urn:cerner:test:valuesets:testvalueset', '0.1') root = ET.fromstring(xml_str) assert root.tag == '{http://hl7.org/fhir}ValueSet'