def test_filters(self):
from fhirtordf.rdfsupport.fhirgraphutils import codeable_concept_code
from fhirtordf.rdfsupport.fhirgraphutils import CodeableConcept
g = Graph()
g.load(os.path.join(self.base_dir, "patient-example-f201-roel.ttl"), format="turtle")
codes = sorted(codeable_concept_code(g, URIRef(FHIR['Patient/f201']), FHIR.Patient.maritalStatus,
"http://snomed.info/sct"))
self.assertEqual([CodeableConcept("http://snomed.info/sct", "36629006",
URIRef("http://snomed.info/id/36629006"))], codes)
codes = sorted(codeable_concept_code(g, URIRef(FHIR['Patient/f201']), FHIR.Patient.maritalStatus,
"http://loinc.org"))
self.assertEqual([], codes)
def test_empty(self):
from fhirtordf.rdfsupport.fhirgraphutils import codeable_concept_code
g = Graph()
g.load(os.path.join(self.base_dir, "patient-example-f201-roel-edited.ttl"), format="turtle")
codes = sorted(codeable_concept_code(g, URIRef(FHIR['Patient/f201']), FHIR.Patient.maritalStatus))
self.assertEqual([], codes)
def add_patient_information(self, g: Graph, patient: URIRef) -> None:
"""
Add additional information to the patient
:param g: Graph carrying additional facts about the patient
:param patient: URI of the actual patient
"""
if not g.value(patient,
FHIR.Patient.animal): # i2b2 doesn't do animals
# gender
gender = value(g, patient, FHIR.Patient.gender)
if gender == "male":
self.patient_dimension_entry._sex_cd = 'M'
elif gender == "female":
self.patient_dimension_entry._sex_cd = 'F'
elif gender == "other":
self.patient_dimension_entry._sex_cd = 'U'
# deceased.deceasedBoolean --> vital_status_code.deathInd
isdeceased = value(g, patient, FHIR.Patient.deceasedBoolean)
if isdeceased is not None:
self.patient_dimension_entry._vital_status_cd = VitalStatusCd.dd_deceased if isdeceased \
else VitalStatusCd.dd_living
# deceased.deceasedDateTime --> deathcode / death_date
self.deathdate = value(g, patient, FHIR.Patient.deceasedDateTime,
True)
# birthdate - must be processed after deceased, as deceased goes into age calculation
bd = g.value(patient, FHIR.Patient.birthDate)
birthdate = None
if bd:
birthdate = extension(
g,
bd,
"http://hl7.org/fhir/StructureDefinition/patient-birthTime",
asLiteral=True)
if not birthdate:
birthdate = value(g,
patient,
FHIR.Patient.birthDate,
asLiteral=True)
self.birthdate = birthdate
# address -- use == home / period.end is empty or past deathcode date
addresses = g.objects(patient, FHIR.Patient.address)
for address in addresses:
address_use = value(g, address, FHIR.Address.use)
if address_use is None or address_use == "home":
period = g.value(address, FHIR.Address.period)
if not period or (period and value(
g, period, FHIR.Period.end) is None):
city = value(g, address, FHIR.Address.city)
state = value(g, address, FHIR.Address.state)
zipcode = value(g, address, FHIR.Address.postalCode)
if zipcode:
self.patient_dimension_entry._zip_cd = zipcode
if city and state:
self.patient_dimension_entry._statecityzip_path = \
'Zip codes\\' + state + '\\' + city + '\\' + zipcode + '\\'
# maritalStatus --> map to 'single', 'married', 'divorced', 'widow', other?
marital_stati = codeable_concept_code(g, patient,
FHIR.Patient.maritalStatus)
for ms in marital_stati:
if ms.system == str(V3.MaritalStatus):
self._marital_status = marital_stati[0]
msc = self._marital_status.code
if msc != 'UNK':
self.patient_dimension_entry._marital_status_cd = \
'divorced' if msc in ['A', 'D'] else \
'married' if msc in ['L', 'M', 'P'] else \
'widow' if msc in ['W'] else \
'single'
break
else:
msuri = concept_uri(g, patient, FHIR.Patient.maritalStatus,
SNOMEDCT)
if msuri:
# TODO: figure out what to do with SNOMED id's (terminology service, anyone?)
pass
# language
communications = list(
g.objects(patient, FHIR.Patient.communication))
language = None
for communication in communications:
pref = value(g, communication,
FHIR.Patient.communication.preferred)
if pref or (pref is None and len(communications) == 1):
languages = codeable_concept_code(
g, communication, FHIR.Patient.communication.language)
if languages:
language = languages[0]
break
if language is not None:
self._language = language.code