def _questionnaire_response_item_answer(value):
# Create the item
answer = QuestionnaireResponseItemAnswer()
# Check type
if type(value) is str:
answer.valueString = str(value)
elif type(value) is bool:
answer.valueBoolean = value
elif type(value) is int:
answer.valueInteger = value
elif type(value) is datetime.datetime:
answer.valueDateTime = FHIRDate(value.isoformat())
elif type(value) is datetime.date:
answer.valueDate = FHIRDate(value.isoformat())
else:
logger.warning('Unhandled answer type: {} - {}'.format(
type(value), value))
# Cast it as string
answer.valueString = str(value)
return answer
def _related_contract(patient, date, patient_name, related_person,
related_person_name, related_person_signature,
questionnaire_response):
# Build it
contract = Contract()
contract.status = 'executed'
contract.issued = FHIRDate(date)
contract.id = uuid.uuid4().urn
# Signer
contract_signer = ContractSigner()
contract_signer.type = FHIR._coding(
'http://hl7.org/fhir/ValueSet/contract-signer-type', 'CONSENTER',
'Consenter')
contract_signer.party = FHIR._reference_to(related_person)
# Signature
signature = Signature()
signature.type = [
FHIR._coding('http://hl7.org/fhir/ValueSet/signature-type',
'1.2.840.10065.1.12.1.7', 'Consent Signature')
]
signature.when = FHIRDate(date)
signature.contentType = 'text/plain'
signature.blob = FHIR._blob(related_person_signature)
signature.whoReference = FHIR._reference_to(related_person)
signature.whoReference.display = related_person_name
# Refer to the patient
patient_reference = FHIRReference({
'reference':
'{}/{}'.format(patient.resource_type, patient.id),
'display':
patient_name
})
signature.onBehalfOfReference = patient_reference
# Add references
contract_signer.signature = [signature]
contract.signer = [contract_signer]
contract.bindingReference = FHIR._reference_to(questionnaire_response)
return contract
def _qr_item_answer(self) -> QuestionnaireResponseItemAnswer:
"""
Returns a QuestionnaireResponseItemAnswer.
"""
# Look things up
raw_answer = self.answer
answer_type = self.answer_type
# Convert the value
if raw_answer is None:
# Deal with null values first, otherwise we will get
# mis-conversion, e.g. str(None) == "None", bool(None) == False.
fhir_answer = None
elif answer_type == FHIRAnswerType.BOOLEAN:
fhir_answer = bool(raw_answer)
elif answer_type == FHIRAnswerType.DATE:
fhir_answer = FHIRDate(
format_datetime(raw_answer, DateFormat.FHIR_DATE)).as_json()
elif answer_type == FHIRAnswerType.DATETIME:
fhir_answer = FHIRDate(raw_answer.isoformat()).as_json()
elif answer_type == FHIRAnswerType.DECIMAL:
fhir_answer = float(raw_answer)
elif answer_type == FHIRAnswerType.INTEGER:
fhir_answer = int(raw_answer)
elif answer_type == FHIRAnswerType.QUANTITY:
fhir_answer = Quantity(
jsondict={
Fc.VALUE: float(raw_answer)
# More sophistication is possible -- units, for example.
}).as_json()
elif answer_type == FHIRAnswerType.STRING:
fhir_answer = str(raw_answer)
elif answer_type == FHIRAnswerType.TIME:
fhir_answer = FHIRDate(
format_datetime(raw_answer, DateFormat.FHIR_TIME)).as_json()
elif answer_type == FHIRAnswerType.URI:
fhir_answer = str(raw_answer)
else:
raise NotImplementedError(
f"Don't know how to handle FHIR answer type {answer_type}")
# Build the FHIR object
return QuestionnaireResponseItemAnswer(
jsondict={answer_type.value: fhir_answer})
def _contract(patient,
date,
patient_name,
patient_signature,
questionnaire_response=None):
# Build it
contract = Contract()
contract.status = 'executed'
contract.issued = FHIRDate(date)
contract.id = uuid.uuid4().urn
# Signer
signer = ContractSigner()
signer.type = FHIR._coding(
'http://hl7.org/fhir/ValueSet/contract-signer-type', 'CONSENTER',
'Consenter')
signer.party = FHIR._reference_to(patient)
# Signature
signature = Signature()
signature.type = [
FHIR._coding('http://hl7.org/fhir/ValueSet/signature-type',
'1.2.840.10065.1.12.1.7', 'Consent Signature')
]
signature.when = FHIRDate(date)
signature.contentType = 'text/plain'
signature.blob = FHIR._blob(patient_signature)
signature.whoReference = FHIR._reference_to(patient)
signature.whoReference.display = patient_name
# Add references
signer.signature = [signature]
contract.signer = [signer]
# Add questionnaire if passed
if questionnaire_response:
contract.bindingReference = FHIR._reference_to(
questionnaire_response)
return contract
def _consent(patient, date, exceptions=[], related_person=None):
# Make it
consent = Consent()
consent.status = 'proposed'
consent.id = uuid.uuid4().urn
consent.dateTime = FHIRDate(date)
consent.patient = FHIR._reference_to(patient)
# Policy
policy = ConsentPolicy()
policy.authority = 'HMS-DBMI'
policy.uri = 'https://hms.harvard.edu'
consent.policy = [policy]
# Check for a related person consenting
if related_person:
# Add them
consent.consentingParty = [FHIR._reference_to(related_person)]
# Period
period = Period()
period.start = FHIRDate(date)
# Add items
consent.period = period
consent.purpose = [
FHIR._coding('http://hl7.org/fhir/v3/ActReason', 'HRESCH',
'healthcare research')
]
# Add exceptions
consent.except_fhir = exceptions
return consent
def _composition(patient, date, text, resources=[]):
# Build it
composition = Composition()
composition.id = uuid.uuid4().urn
composition.status = 'final'
composition.subject = FHIR._reference_to(patient)
composition.date = FHIRDate(date)
composition.title = 'Signature'
composition.author = [
FHIRReference({'reference': 'Device/hms-dbmi-ppm-consent'})
]
# Composition type
coding = Coding()
coding.system = 'http://loinc.org'
coding.code = '83930-8'
coding.display = 'Research Consent'
# Convoluted code property
code = CodeableConcept()
code.coding = [coding]
# Combine
composition.type = code
# Add sections
composition.section = []
# Add text
narrative = Narrative()
narrative.div = text
narrative.status = 'additional'
text_section = CompositionSection()
text_section.text = narrative
composition.section.append(text_section)
# Add related section resources
for resource in resources:
# Add consent
consent_section = CompositionSection()
consent_section.entry = [FHIR._reference_to(resource)]
composition.section.append(consent_section)
return composition
def get_fhir_resource(self, resource: str, *args, **kwargs):
if resource != CapabilityStatement.resource_type:
... # throw an error
cs: CapabilityStatement = CapabilityStatement()
cs.fhirVersion = '4.0.0'
cs.status = 'active'
cs.acceptUnknown = 'false'
cs.format = ['json']
cs.kind = 'json'
date = FHIRDate()
date.date = datetime.today()
cs.date = date
rest: CapabilityStatementRest = CapabilityStatementRest()
cs.rest = [rest]
rest.mode = "server"
rest.resource = []
for rule in current_app.url_map.iter_rules():
print(rule)
return cs
def _questionnaire_response(questionnaire,
patient,
date=datetime.datetime.utcnow().isoformat(),
answers={},
author=None):
# Build the response
response = QuestionnaireResponse()
response.id = uuid.uuid4().urn
response.questionnaire = FHIR._reference_to(questionnaire)
response.source = FHIR._reference_to(patient)
response.status = 'completed'
response.authored = FHIRDate(date)
response.author = FHIR._reference_to(author if author else patient)
# Collect response items flattened
response.item = FHIR._questionnaire_response_items(
questionnaire, answers)
# Set it on the questionnaire
return response