def test_with_disjoint_maps_from_directory(spark_session):
spark_session.sql("CREATE DATABASE IF NOT EXISTS disjoint_maps_db")
create_concept_maps(spark_session) \
.with_maps_from_directory("tests/resources/conceptmaps") \
.write_to_database("disjoint_maps_db")
reloaded = get_concept_maps(spark_session, "disjoint_maps_db") \
.with_disjoint_maps_from_directory("tests/resources/conceptmaps", "disjoint_maps_db")
assert reloaded.get_mappings("urn:cerner:poprec:fhir:conceptmap:demographics:gender", "0.0.1") \
.count() == 5
def test_with_maps_from_directory(spark_session):
concept_maps = create_concept_maps(spark_session) \
.with_maps_from_directory("tests/resources/conceptmaps")
assert concept_maps.get_mappings("urn:cerner:poprec:fhir:conceptmap:demographics:gender", "0.0.1") \
.count() == 5
def test_write_maps(spark_session):
concept_maps = create_concept_maps(spark_session)
snomed_to_loinc = [('http://snomed.info/sct', '75367002', 'http://loinc.org', '55417-0', 'equivalent'), # Blood pressure
('http://snomed.info/sct', '271649006', 'http://loinc.org', '8480-6', 'equivalent'), # Systolic BP
('http://snomed.info/sct', '271650006', 'http://loinc.org', '8462-4', 'equivalent')] # Diastolic BP
appended = concept_maps.with_new_map(url='urn:cerner:test:snomed-to-loinc',
version='0.1',
source='urn:cerner:test:valueset',
target='http://hl7.org/fhir/ValueSet/observation-code',
mappings=snomed_to_loinc)
spark_session.sql('create database if not exists ontologies')
spark_session.sql('drop table if exists ontologies.mappings')
spark_session.sql('drop table if exists ontologies.ancestors')
spark_session.sql('drop table if exists ontologies.conceptmaps')
appended.write_to_database('ontologies')
# Check that the maps were written by reloading and inspecting them.
reloaded = get_concept_maps(spark_session)
assert reloaded.get_maps().count() == 1
assert reloaded.get_mappings().where(col('conceptmapuri') == 'urn:cerner:test:snomed-to-loinc').count() == 3
def test_add_mappings(spark_session):
concept_maps = create_concept_maps(spark_session)
original = [('http://snomed.info/sct', '75367002', 'http://loinc.org',
'55417-0', 'equivalent')]
added = [
('http://snomed.info/sct', '271649006', 'http://loinc.org', '8480-6',
'equivalent'), # Systolic BP
('http://snomed.info/sct', '271650006', 'http://loinc.org', '8462-4',
'equivalent')
] # Diastolic BP
appended = concept_maps.with_new_map(url='urn:cerner:test:snomed-to-loinc',
version='0.1',
source='urn:cerner:test:valueset',
target='http://hl7.org/fhir/ValueSet/observation-code',
mappings=original) \
.add_mappings(url='urn:cerner:test:snomed-to-loinc',
version='0.1',
new_version='0.2',
mappings=added)
assert appended.get_maps().count() == 2
assert appended.get_mappings() \
.where(col('conceptmapuri') == 'urn:cerner:test:snomed-to-loinc') \
.where(col('conceptmapversion') == '0.1') \
.count() == 1
assert appended.get_mappings() \
.where(col('conceptmapuri') == 'urn:cerner:test:snomed-to-loinc') \
.where(col('conceptmapversion') == '0.2') \
.count() == 3
def test_latest_concept_map_version(spark_session):
concept_maps = create_concept_maps(spark_session)
added = concept_maps.with_new_map(url='urn:cerner:test:snomed-to-loinc',
version='0.1',
source='urn:cerner:test:valueset',
target='http://hl7.org/fhir/ValueSet/observation-code',
mappings=[]) \
.with_new_map(url='urn:cerner:test:snomed-to-loinc',
version='0.2',
source='urn:cerner:test:valueset',
target='http://hl7.org/fhir/ValueSet/observation-code',
mappings=[])
assert added.latest_version('urn:cerner:test:snomed-to-loinc') == '0.2'
def test_get_map_as_xml(spark_session):
concept_maps = create_concept_maps(spark_session)
snomed_to_loinc = [('http://snomed.info/sct', '75367002', 'http://loinc.org', '55417-0', 'equivalent'), # Blood pressure
('http://snomed.info/sct', '271649006', 'http://loinc.org', '8480-6', 'equivalent'), # Systolic BP
('http://snomed.info/sct', '271650006', 'http://loinc.org', '8462-4', 'equivalent')] # Diastolic BP
appended = concept_maps.with_new_map(url='urn:cerner:test:snomed-to-loinc',
version='0.1',
source='urn:cerner:test:valueset',
target='http://hl7.org/fhir/ValueSet/observation-code',
mappings=snomed_to_loinc)
xml_str = appended.get_map_as_xml('urn:cerner:test:snomed-to-loinc', '0.1')
root = ET.fromstring(xml_str)
assert root.tag == '{http://hl7.org/fhir}ConceptMap'