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'