def fhir_condition(obj):
""" Converts Disease to FHIR Condition. """
condition = cond.Condition()
condition.id = str(obj['id'])
condition.code = fhir_codeable_concept(obj['term'])
# subject is required by Pheno-FHIR mapping Guide and by FHIR, set to 'unknown'
condition.subject = fhirreference.FHIRReference()
condition.subject.reference = 'unknown'
condition.extension = []
# only adds disease-onset if it's ontology term
# NOTE it is required element by Pheno-FHIR mapping guide but not Phenopackets
if check_disease_onset(obj):
onset_extension = extension.Extension()
onset_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['disease']['onset']
onset_extension.valueCodeableConcept = fhir_codeable_concept(
obj['onset']['age'])
condition.extension.append(onset_extension)
if 'disease_stage' in obj.keys():
for item in obj['disease_stage']:
disease_stage_extension = extension.Extension()
disease_stage_extension.url = PHENOPACKETS_ON_FHIR_MAPPING[
'disease']['disease_stage']
disease_stage_extension.valueCodeableConcept = fhir_codeable_concept(
item)
condition.extension.append(disease_stage_extension)
return condition.as_json()
def __init__(self, Patient=None):
"""
Uses fhirclient.models to create, validate, and post a Condition FHIR resource.
:returns: GenerateCondition object which has Condition object as an attribute.
"""
if Patient == None:
self.Patient = generatepatient.GeneratePatient().Patient
else:
self.Patient = Patient
self._generate_icd_code()
Condition = cond.Condition()
Condition.clinicalStatus = 'active'
Condition.verificationStatus = 'confirmed'
# Condition.verificationStatus = 'active'
# Condition.category = self._create_FHIRCodeableConcept(code='problem', system='urn:oid:2.16.840.1.113883.4.642.3.153', display='Problem List Item')
Condition.code = self._create_FHIRCodeableConcept(
code=self.icd_code,
system='urn:oid:2.16.840.1.113883.6.3',
display=self.icd_description)
Condition.patient = self._create_FHIRReference(self.Patient)
self._validate(Condition)
self.response = self.post_resource(Condition)
Condition.id = self._extract_id()
self.Condition = Condition
self.Condition.Patient = self.Patient
print(self)
def condition_to_disease(obj):
""" FHIR Condition to Phenopackets Disease. """
condition = cond.Condition(obj)
codeable_concept = condition.code # CodeableConcept
disease = {
"term": {
# id is an integer AutoField, legacy id can be a string
# "id": condition.id,
"id":
f"{codeable_concept.coding[0].system}:{codeable_concept.coding[0].code}",
"label": codeable_concept.coding[0].display
# TODO collect system info in metadata
},
"extra_properties": condition.as_json()
}
# condition.stage.type is only in FHIR 4.0.0 version
return disease
def import_condition(self, res, options):
"""Import a single condition"""
verbosity = options['verbosity']
strict = options['strict']
force = options['force']
f_condition = cond.Condition(res, strict=strict)
logger.info(f'Importing {f_condition}')
d_condition = Condition(
code=self.get_codeableconcept(f_condition.code),
onset_datetime=f_condition.onsetDateTime.date,
subject_id=f_condition.subject.reference[
9:] # Remove urn:uuid: prefix
)
try:
d_condition.save()
except IntegrityError as err:
logger.error('Saving condition to database failed', exc_info=True)
def disease_to_fhir(obj):
"""Converts Disease to FHIR Condition.
:param obj: Disease json
:return: FHIR Condition json
"""
schema_path = os.path.join(SCHEMA_PATH, 'disease_schema.json')
try:
validate_schema(schema_path, obj)
except jsonschema.exceptions.ValidationError:
raise Exception("The disease object is not valid.")
condition = cond.Condition()
if 'id' in obj:
condition.id = str(obj['id'])
condition.code = fhir_codeable_concept(obj['term'])
# subject is required by Pheno-FHIR mapping Guide and by FHIR, set to 'unknown'
condition.subject = fhirreference.FHIRReference()
condition.subject.reference = 'unknown'
condition.extension = []
# only adds disease-onset if it's ontology term
# NOTE it is required element by Phenopackets IG but not Phenopackets
# what do to if it's AGE string?
if check_disease_onset(obj):
onset_extension = extension.Extension()
onset_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['disease']['onset']
onset_extension.valueCodeableConcept = fhir_codeable_concept(
obj['onset']['age'])
condition.extension.append(onset_extension)
if 'diseaseStage' in obj:
for item in obj['diseaseStage']:
disease_stage_extension = extension.Extension()
disease_stage_extension.url = PHENOPACKETS_ON_FHIR_MAPPING[
'disease']['disease_stage']
disease_stage_extension.valueCodeableConcept = fhir_codeable_concept(
item)
condition.extension.append(disease_stage_extension)
return condition.as_json()
def to_fhir_obj(self):
condition = c.Condition(base_condition)
#observation.subject_reference = self.subject_reference
condition.subject.reference = self.subject_reference
return condition