def test_read_relationship_file(spark_session):
ancestors = with_relationships(
spark_session, create_hierarchies(spark_session),
'tests/resources/SNOMED_RELATIONSHIP_SAMPLE.TXT',
'20160901').get_ancestors()
assert set(ancestors.columns) == EXPECTED_COLUMNS
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_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