def test_json_bundles_from_df(spark_session):
json_bundles = spark_session.sparkContext.wholeTextFiles(
'tests/resources/bundles/json').toDF()
bundles = from_json(json_bundles, '_2')
assert extract_entry(spark_session, bundles, 'Condition').count() == 5
def test_valueset_from_bundle(spark_session):
bundles = load_from_directory(spark_session,
'tests/resources/bundles/json', 1)
vs = extract_entry(spark_session, bundles, 'ValueSet')
value_sets = create_value_sets(spark_session) \
.with_value_sets(vs)
assert value_sets.get_values("http://hl7.org/fhir/ValueSet/example-extensional", "20150622") \
.count() == 4
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')]}
push_valuesets(spark_session, blood_pressure)
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_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, " +
"effective.dateTime, " +
"value.quantity.value " +
"FROM observations " +
"WHERE in_valueset(code, 'blood_pressure')")
assert get_current_valuesets(spark_session) == blood_pressure
assert results.count() == 14
def test_to_bundle(spark_session, bundles):
conditions = extract_entry(spark_session, bundles, 'Condition')
assert to_bundle(spark_session, conditions) != None
def test_extract_entry(spark_session, bundles):
assert extract_entry(spark_session, bundles, 'Condition').count() == 5
