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 individual_to_fhir(obj):
"""Converts Individual to FHIR Patient.
:param obj: Individual json
:return: FHIR Patient json
"""
# first validate if phenopackets object is well-formed
schema_path = os.path.join(SCHEMA_PATH, 'individual_schema.json')
try:
validate_schema(schema_path, obj)
except jsonschema.exceptions.ValidationError:
raise Exception("The individual object is not valid.")
patient = p.Patient()
patient.id = obj['id']
patient.birthDate = fhirdate.FHIRDate(obj.get('dateOfBirth', None))
patient.gender = obj.get('sex', None)
patient.active = obj.get('active', None)
patient.deceasedBoolean = obj.get('deceased', None)
patient.extension = list()
# age
if 'age' in obj:
age_extension = age_to_fhir(
obj, PHENOPACKETS_ON_FHIR_MAPPING['individual']['age'], 'age')
patient.extension.append(age_extension)
# karyotypic_sex
if 'karyotypicSex' in obj:
karyotypic_sex_extension = extension.Extension()
karyotypic_sex_extension.url = PHENOPACKETS_ON_FHIR_MAPPING[
'individual']['karyotypicSex']['url']
karyotypic_sex_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
karyotypic_sex_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('karyotypicSex', None)
coding.code = obj.get('karyotypicSex', None)
coding.system = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'karyotypicSex']['system']
karyotypic_sex_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(karyotypic_sex_extension)
# taxonomy
if 'taxonomy' in obj:
taxonomy_extension = extension.Extension()
taxonomy_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'taxonomy']
taxonomy_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
taxonomy_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('taxonomy', None).get('label', None)
coding.code = obj.get('taxonomy', None).get('id', None)
taxonomy_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(taxonomy_extension)
return patient.as_json()
def fhir_document_reference(obj):
""" Converts HTS file to FHIR DocumentReference. """
doc_ref = documentreference.DocumentReference()
doc_ref.type = fhir_codeable_concept({
"label": obj['hts_format'],
"id": obj['hts_format']
})
# GA4GH requires status with the fixed value
doc_ref.status = PHENOPACKETS_ON_FHIR_MAPPING['hts_file']['status']
doc_ref.content = []
doc_content = documentreference.DocumentReferenceContent()
doc_content.attachment = attachment.Attachment()
doc_content.attachment.url = obj['uri']
if 'description' in obj.keys():
doc_content.attachment.title = obj.get('description', None)
doc_ref.content.append(doc_content)
doc_ref.indexed = fhirdate.FHIRDate()
# check what date it should be - when it's retrieved or created
doc_ref.indexed.date = datetime.now()
doc_ref.extension = []
genome_assembly = extension.Extension()
genome_assembly.url = PHENOPACKETS_ON_FHIR_MAPPING['hts_file'][
'genome_assembly']
genome_assembly.valueString = obj['genome_assembly']
doc_ref.extension.append(genome_assembly)
return doc_ref.as_json()
def hts_file_to_fhir(obj):
"""Converts HTS file to FHIR DocumentReference.
:param obj: HTS file json
:return: FHIR DocumentReference json
"""
schema_path = os.path.join(SCHEMA_PATH, 'hts_file_schema.json')
try:
validate_schema(schema_path, obj)
except jsonschema.exceptions.ValidationError:
raise Exception("The hts file object is not valid.")
doc_ref = documentreference.DocumentReference()
doc_ref.type = fhir_codeable_concept({
"label": obj['htsFormat'],
"id": obj['htsFormat']
})
# GA4GH requires status with the fixed value
doc_ref.status = PHENOPACKETS_ON_FHIR_MAPPING['htsFile']['status']
doc_ref.content = []
doc_content = documentreference.DocumentReferenceContent()
doc_content.attachment = attachment.Attachment()
doc_content.attachment.url = obj['uri']
if 'description' in obj:
doc_content.attachment.title = obj['description']
doc_ref.content.append(doc_content)
doc_ref.indexed = fhirdate.FHIRDate()
doc_ref.indexed.date = datetime.now()
doc_ref.extension = []
genome_assembly = extension.Extension()
genome_assembly.url = PHENOPACKETS_ON_FHIR_MAPPING['htsFile'][
'genomeAssembly']
genome_assembly.valueString = obj['genomeAssembly']
doc_ref.extension.append(genome_assembly)
return doc_ref.as_json()
def get_responseperiod_x(start,end):
responseperiod_x = Ext.Extension()
responseperiod_x.url = 'http://fhir.org/guides/argonaut-questionnaire/StructureDefinition/extension-responsePeriod'
responseperiod_x.valuePeriod = P.Period()
responseperiod_x.valuePeriod.start = FD.FHIRDate(start)
responseperiod_x.valuePeriod.end = FD.FHIRDate(end)
return responseperiod_x
def QuestionnaireExtension(questionnaire=questionnaire.Questionnaire):
from fhirclient.models import extension
extension = extension.Extension()
extension.url = 'http://hl7.org/fhir/StructureDefinition/servicerequest-questionnaireRequest'
reference = fhirreference.FHIRReference()
reference.reference = f'Questionnaire/{questionnaire.id}'
extension.valueReference = reference
return extension
def fhir_specimen(obj):
""" Converts biosample to FHIR Specimen. """
specimen = s.Specimen()
specimen.identifier = []
# id
identifier = fhir_indentifier.Identifier()
identifier.value = obj['id']
specimen.identifier.append(identifier)
# individual - subject property in FHIR is mandatory for a specimen
specimen.subject = fhirreference.FHIRReference()
specimen.subject.reference = obj.get('individual', 'unknown')
# sampled_tissue
specimen.type = codeableconcept.CodeableConcept()
specimen.type.coding = []
coding = c.Coding()
coding.code = obj['sampled_tissue']['id']
coding.display = obj['sampled_tissue']['label']
specimen.type.coding.append(coding)
# description
if 'description' in obj.keys():
specimen.note = []
annotation = a.Annotation()
annotation.text = obj.get('description', None)
specimen.note.append(annotation)
# procedure
specimen.collection = s.SpecimenCollection()
specimen.collection.method = fhir_codeable_concept(
obj['procedure']['code'])
if 'body_site' in obj['procedure'].keys():
specimen.collection.bodySite = fhir_codeable_concept(
obj['procedure']['body_site'])
# Note on taxonomy from phenopackets specs:
# Individuals already contain a taxonomy attribute so this attribute is not needed.
# extensions
specimen.extension = []
# individual_age_at_collection
if 'individual_age_at_collection' in obj.keys():
ind_age_at_collection_extension = fhir_age(
obj, PHENOPACKETS_ON_FHIR_MAPPING['biosample']
['individual_age_at_collection'], 'individual_age_at_collection')
specimen.extension.append(ind_age_at_collection_extension)
concept_extensions = codeable_concepts_fields([
'histological_diagnosis', 'tumor_progression', 'tumor_grade',
'diagnostic_markers'
], 'biosample', obj)
for concept in concept_extensions:
specimen.extension.append(concept)
if 'is_control_sample' in obj.keys():
control_extension = extension.Extension()
control_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['biosample'][
'is_control_sample']
control_extension.valueBoolean = obj['is_control_sample']
specimen.extension.append(control_extension)
# TODO 2m extensions - references
return specimen.as_json()
def fhir_patient(obj):
""" Converts Individual to FHIR Patient. """
patient = p.Patient()
patient.id = obj['id']
patient.birthDate = fhirdate.FHIRDate(obj.get('date_of_birth', None))
patient.gender = obj.get('sex', None)
patient.active = obj.get('active', None)
patient.deceasedBoolean = obj.get('deceased', None)
patient.extension = list()
# age
if 'age' in obj.keys():
age_extension = fhir_age(
obj, PHENOPACKETS_ON_FHIR_MAPPING['individual']['age'], 'age')
patient.extension.append(age_extension)
# karyotypic_sex
karyotypic_sex_extension = extension.Extension()
karyotypic_sex_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'karyotypic_sex']['url']
karyotypic_sex_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
karyotypic_sex_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('karyotypic_sex', None)
coding.code = obj.get('karyotypic_sex', None)
coding.system = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'karyotypic_sex']['system']
karyotypic_sex_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(karyotypic_sex_extension)
# taxonomy
if 'taxonomy' in obj.keys():
taxonomy_extension = extension.Extension()
taxonomy_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'taxonomy']
taxonomy_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
taxonomy_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('taxonomy', None).get('label', None)
coding.code = obj.get('taxonomy', None).get('id', None)
taxonomy_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(taxonomy_extension)
return patient.as_json()
def to_fhir(self) -> extension.Extension:
fhir_extension = extension.Extension()
fhir_extension.url = self.extension_url
fhir_coding = coding.Coding()
fhir_coding.system = self.system
fhir_coding.code = self.code
fhir_coding.display = self.display
fhir_extension.valueCoding = fhir_coding
return fhir_extension
def to_fhir(self) -> extension.Extension:
ingredient_extension = extension.Extension()
ingredient_extension.url = self.url
extension_coding = coding.Coding()
extension_coding.system = self.coding_system
extension_coding.code = self.coding_code
extension_coding.display = self.coding_display
ingredient_extension.valueCoding = extension_coding
return ingredient_extension
def codeable_concepts_fields(field_list, profile, obj):
""" Converts a list of fields to FHIR CodeableConcepts and returns a list of extensions. """
concept_extensions = []
for field in field_list:
if field in obj.keys():
codeable_concepts_extension = extension.Extension()
codeable_concepts_extension.url = PHENOPACKETS_ON_FHIR_MAPPING[
profile][field]
codeable_concepts_extension.valueCodeableConcept = fhir_codeable_concept(
obj[field])
concept_extensions.append(codeable_concepts_extension)
return concept_extensions
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 fhir_age(obj, mapping, field):
""" Generic function to convert Age or AgeRange to FHIR Age. """
age_extension = extension.Extension()
age_extension.url = mapping
if isinstance(obj[field]['age'], dict):
age_extension.valueRange = range.Range()
age_extension.valueRange.low = quantity.Quantity()
age_extension.valueRange.low.unit = obj[field]['age']['start']['age']
age_extension.valueRange.high = quantity.Quantity()
age_extension.valueRange.high.unit = obj[field]['age']['end']['age']
else:
age_extension.valueAge = age.Age()
age_extension.valueAge.unit = obj[field]['age']
return age_extension
def fhir_age(obj, mapping, field):
""" Generic function to convert Age or AgeRange to FHIR Age. """
age_extension = extension.Extension()
age_extension.url = mapping
if "start" in obj[field]: # Is an age range
age_extension.valueRange = range_.Range()
age_extension.valueRange.low = quantity.Quantity()
age_extension.valueRange.low.unit = obj[field]['start']['age']
age_extension.valueRange.high = quantity.Quantity()
age_extension.valueRange.high.unit = obj[field]['end']['age']
else: # Is a precise age
age_extension.valueAge = age.Age()
age_extension.valueAge.unit = obj[field]['age']
return age_extension
def codeable_concepts_fields(field_list, profile, obj):
"""Converts a list of fields to FHIR CodeableConcepts and returns a list of extensions.
:param field_list: fields to convert to codeable concepts
:param profile: name of an object in phenopackets mappings
:param obj: object to which fields belong to
:return: list of extensions
"""
concept_extensions = []
for field in field_list:
if field in obj:
codeable_concepts_extension = extension.Extension()
codeable_concepts_extension.url = PHENOPACKETS_ON_FHIR_MAPPING[
profile][field]
codeable_concepts_extension.valueCodeableConcept = fhir_codeable_concept(
obj[field])
concept_extensions.append(codeable_concepts_extension)
return concept_extensions
def age_to_fhir(obj, mapping, field):
"""Generic function to convert Phenopackets Age or AgeRange to FHIR Age.
:param obj: object to which field Age or AgeRange belongs to
:param mapping: mapping from PHENOPACKETS_ON_FHIR
:param field: name of the field that stores age
:return: age extension object
"""
age_extension = extension.Extension()
age_extension.url = mapping
if isinstance(obj[field]['age'], dict):
age_extension.valueRange = range.Range()
age_extension.valueRange.low = quantity.Quantity()
age_extension.valueRange.low.unit = obj[field]['age']['start']['age']
age_extension.valueRange.high = quantity.Quantity()
age_extension.valueRange.high.unit = obj[field]['age']['end']['age']
else:
age_extension.valueAge = age.Age()
age_extension.valueAge.unit = obj[field]['age']
return age_extension
def getextension(url, valuetype, value): # fhirextension
ext = Ext.Extension({'url': url, valuetype: value})
return (ext) # note this returning as a list!! TODO fix this
def biosample_to_fhir(obj):
"""Converts Biosample to FHIR Specimen.
:param obj: Biosample json
:return: FHIR Specimen json
"""
schema_path = os.path.join(SCHEMA_PATH, 'biosample_schema.json')
try:
validate_schema(schema_path, obj)
except jsonschema.exceptions.ValidationError:
raise Exception("The biosample object is not valid.")
specimen = s.Specimen()
specimen.identifier = []
# id
identifier = fhir_indentifier.Identifier()
identifier.value = obj['id']
specimen.identifier.append(identifier)
# individual - subject property in FHIR is mandatory for a specimen
specimen.subject = fhirreference.FHIRReference()
specimen.subject.reference = obj.get('individual', 'unknown')
# sampled_tissue
specimen.type = codeableconcept.CodeableConcept()
specimen.type.coding = []
coding = c.Coding()
coding.code = obj['sampledTissue']['id']
coding.display = obj['sampledTissue']['label']
specimen.type.coding.append(coding)
# description
if 'description' in obj:
specimen.note = []
annotation = a.Annotation()
annotation.text = obj.get('description', None)
specimen.note.append(annotation)
# procedure
specimen.collection = s.SpecimenCollection()
specimen.collection.method = fhir_codeable_concept(
obj['procedure']['code'])
if 'bodySite' in obj['procedure']:
specimen.collection.bodySite = fhir_codeable_concept(
obj['procedure']['bodySite'])
# Note on taxonomy from phenopackets specs:
# Individuals already contain a taxonomy attribute so this attribute is not needed.
# extensions
specimen.extension = []
# individual_age_at_collection
if 'individualAgeAtCollection' in obj:
ind_age_at_collection_extension = age_to_fhir(
obj, PHENOPACKETS_ON_FHIR_MAPPING['biosample']
['individualAgeAtCollection'], 'individualAgeAtCollection')
specimen.extension.append(ind_age_at_collection_extension)
concept_extensions = codeable_concepts_fields([
'histologicalDiagnosis', 'tumorProgression', 'tumorGrade',
'diagnosticMarkers'
], 'biosample', obj)
for concept in concept_extensions:
specimen.extension.append(concept)
if 'isControlSample' in obj:
control_extension = extension.Extension()
control_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['biosample'][
'isControlSample']
control_extension.valueBoolean = obj['isControlSample']
specimen.extension.append(control_extension)
# TODO 2m extensions - references
return specimen.as_json()
def fhir_observation(obj):
""" Converts phenotypic feature to FHIR Observation. """
observation = obs.Observation()
if 'description' in obj.keys():
observation.note = []
annotation = a.Annotation()
annotation.text = obj.get('description', None)
observation.note.append(annotation)
observation.code = fhir_codeable_concept(obj['type'])
# required by FHIR specs but omitted by phenopackets, for now set for unknown
observation.status = 'unknown'
if 'negated' in obj.keys():
observation.interpretation = fhir_codeable_concept({
"label": "Positive",
"id": "POS"
})
else:
observation.interpretation = fhir_codeable_concept({
"label": "Negative",
"id": "NEG"
})
observation.extension = []
concept_extensions = codeable_concepts_fields(
['severity', 'modifier', 'onset'], 'phenotypic_feature', obj)
for c in concept_extensions:
observation.extension.append(c)
if 'evidence' in obj.keys():
evidence = extension.Extension()
evidence.url = PHENOPACKETS_ON_FHIR_MAPPING['phenotypic_feature'][
'evidence']['url']
evidence.extension = []
evidence_code = extension.Extension()
evidence_code.url = PHENOPACKETS_ON_FHIR_MAPPING['phenotypic_feature'][
'evidence']['evidence_code']
evidence_code.valueCodeableConcept = fhir_codeable_concept(
obj['evidence']['evidence_code'])
evidence.extension.append(evidence_code)
if 'reference' in obj['evidence'].keys():
evidence_reference = extension.Extension()
evidence_reference.url = PHENOPACKETS_ON_FHIR_MAPPING[
'external_reference']['url']
evidence_reference.extension = []
evidence_reference_id = extension.Extension()
evidence_reference_id.url = PHENOPACKETS_ON_FHIR_MAPPING[
'external_reference']['id_url']
# GA$GH guide requires valueURL but there is no such property
evidence_reference_id.valueUri = obj['evidence']['reference']['id']
evidence_reference.extension.append(evidence_reference_id)
if 'description' in obj['evidence']['reference'].keys():
evidence_reference_desc = extension.Extension()
evidence_reference_desc.url = PHENOPACKETS_ON_FHIR_MAPPING[
'external_reference']['description_url']
evidence_reference_desc.valueString = obj['evidence'][
'reference'].get('description', None)
evidence_reference.extension.append(evidence_reference_desc)
evidence.extension.append(evidence_reference)
observation.extension.append(evidence)
if 'biosample' in obj.keys():
observation.specimen = fhirreference.FHIRReference()
observation.specimen.reference = obj.get('biosample', None)
return observation.as_json()
def to_fhir(self) -> extension.Extension:
fhir_extension = extension.Extension()
fhir_extension.url = self.extention_url
fhir_extension.valueDateTime = self.recorded_datetime.to_fhir()
return fhir_extension
def phenotypic_feature_to_fhir(obj):
"""Converts Phenotypic feature to FHIR Observation.
:param obj: PhenotypicFeature json
:return: FHIR Observation json
"""
schema_path = os.path.join(SCHEMA_PATH, 'phenotypic_feature_schema.json')
try:
validate_schema(schema_path, obj)
except jsonschema.exceptions.ValidationError:
raise Exception("The phenotypic feature object is not valid.")
observation = obs.Observation()
if 'description' in obj:
observation.note = []
annotation = a.Annotation()
annotation.text = obj.get('description', None)
observation.note.append(annotation)
observation.code = fhir_codeable_concept(obj['type'])
# required by FHIR specs but omitted by phenopackets, for now set for unknown
observation.status = 'unknown'
if 'negated' in obj:
observation.interpretation = fhir_codeable_concept({
"label": "Positive",
"id": "POS"
})
else:
observation.interpretation = fhir_codeable_concept({
"label": "Negative",
"id": "NEG"
})
observation.extension = []
concept_extensions = codeable_concepts_fields(
['severity', 'modifier', 'onset'], 'phenotypicFeature', obj)
for c in concept_extensions:
observation.extension.append(c)
if 'evidence' in obj:
evidence = extension.Extension()
evidence.url = PHENOPACKETS_ON_FHIR_MAPPING['phenotypicFeature'][
'evidence']['url']
evidence.extension = []
evidence_code = extension.Extension()
evidence_code.url = PHENOPACKETS_ON_FHIR_MAPPING['phenotypicFeature'][
'evidence']['evidenceCode']
evidence_code.valueCodeableConcept = fhir_codeable_concept(
obj['evidence']['evidenceCode'])
evidence.extension.append(evidence_code)
if 'reference' in obj['evidence']:
evidence_reference = extension.Extension()
evidence_reference.url = PHENOPACKETS_ON_FHIR_MAPPING[
'externalReference']['url']
evidence_reference.extension = []
evidence_reference_id = extension.Extension()
evidence_reference_id.url = PHENOPACKETS_ON_FHIR_MAPPING[
'externalReference']['idUrl']
evidence_reference_id.valueUri = obj['evidence']['reference']['id']
evidence_reference.extension.append(evidence_reference_id)
if 'description' in obj['evidence']['reference']:
evidence_reference_desc = extension.Extension()
evidence_reference_desc.url = PHENOPACKETS_ON_FHIR_MAPPING[
'externalReference']['descriptionUrl']
evidence_reference_desc.valueString = obj['evidence'][
'reference'].get('description', None)
evidence_reference.extension.append(evidence_reference_desc)
evidence.extension.append(evidence_reference)
observation.extension.append(evidence)
if 'biosample' in obj:
observation.specimen = fhirreference.FHIRReference()
observation.specimen.reference = obj.get('biosample', None)
return observation.as_json()
def create_fhir_object(self):
"""
Generate a fhirclient.Patient class object and store in the protected attribute _fhir
:return:
None
"""
# Patient object must be persistent to generate FHIR attributes
ins = inspect(self)
if ins.persistent:
# Initialize Patient resource
fhir_pt = fhir_patient.Patient()
# Set resource logical identifier
fhir_pt.id = self.get_url()
# Build and assign Meta resource for Patient object
fhir_meta = meta.Meta()
fhir_meta.lastUpdated = fhir_gen_datetime(value=self.updated_at, error_out=False, to_date=False)
fhir_meta.versionId = str(self.version_number)
fhir_meta.profile = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']
fhir_pt.meta = fhir_meta
# Patient name represented as HumanName resource
fhir_pt.name = []
fhir_pt.name.append(fhir_gen_humanname(use='usual', first_name=self.first_name, last_name=self.last_name,
middle_name=self.middle_name, suffix=self.suffix,
prefix=self.prefix))
# Display MRN as identifier codeable concept = Patient.identifier.codeableconcept.coding
# Initialize Identifier resource
id_mrn = identifier.Identifier()
id_mrn.use = 'usual'
id_mrn.system = 'http://unkani.com'
id_mrn.value = str(self.uuid)
# Initialize CodeableConcept resource
mrn_cc = codeableconcept.CodeableConcept()
mrn_cc.text = 'Medical Record Number'
# Initialize Coding resource
mrn_coding = coding.Coding()
mrn_coding.system = 'http://hl7.org/fhir/v2/0203'
mrn_coding.code = 'MR'
mrn_coding.display = 'Medical Record Number'
# Assign Coding resource to CodeableConcept
mrn_cc.coding = [mrn_coding]
# Assign CodeableConcept to Identifier
id_mrn.type = mrn_cc
# Assign CodeableConcept to Patient
fhir_pt.identifier = [id_mrn]
# Display SSN as identifier codeable concept = Patient.identifier.codeableconcept.coding
if self.ssn:
# Initialize Identifier resource
id_ssn = identifier.Identifier()
id_ssn.use = 'usual'
id_ssn.system = 'http://hl7.org/fhir/sid/us-ssn'
id_ssn.value = self.ssn
# Initialize CodeableConcept resource
ssn_cc = codeableconcept.CodeableConcept()
ssn_cc.text = 'Social Security Number'
# Initialize Coding resource
ssn_coding = coding.Coding()
ssn_coding.system = 'http://hl7.org/fhir/v2/0203'
ssn_coding.code = 'SS'
ssn_coding.display = 'Social Security Number'
# Assign Coding resource to CodeableConcept
ssn_cc.coding = [ssn_coding]
# Assign CodeableConcept to Identifier
id_ssn.type = ssn_cc
# Assign CodeableConcept to Patient
fhir_pt.identifier.append(id_ssn)
if self.marital_status:
marital_status_cc = codeableconcept.CodeableConcept()
marital_status_url = 'http://hl7.org/fhir/ValueSet/marital-status'
marital_status_concept = ValueSet.get_valueset_concept(marital_status_url, self.marital_status)
if marital_status_concept:
marital_status_cc.text = getattr(marital_status_concept, 'display')
marital_status_coding = coding.Coding()
marital_status_coding.code = self.marital_status
marital_status_coding.system = marital_status_url
marital_status_coding.display = marital_status_cc.text
marital_status_cc.coding = [marital_status_coding]
fhir_pt.maritalStatus = marital_status_cc
if self.race:
ext_race = extension.Extension()
ext_race.url = 'http://hl7.org/fhir/StructureDefinition/us-core-race'
race_url = 'http://hl7.org/fhir/us/core/ValueSet/omb-race-category'
cc_race = codeableconcept.CodeableConcept()
race_concept = ValueSet.get_valueset_concept(race_url, self.race)
if race_concept:
cc_race.text = getattr(race_concept, 'display')
coding_race = coding.Coding()
coding_race.system = race_url
coding_race.code = self.race
coding_race.display = cc_race.text
cc_race.coding = [coding_race]
ext_race.valueCodeableConcept = cc_race
try:
fhir_pt.extension.append(ext_race)
except AttributeError:
fhir_pt.extension = [ext_race]
if self.ethnicity:
ext_ethnicity = extension.Extension()
ext_ethnicity.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'
cc_ethnicity = codeableconcept.CodeableConcept()
cc_ethnicity.text = ethnicity_dict.get(self.ethnicity)[0].capitalize()
coding_ethnicity = coding.Coding()
coding_ethnicity.system = 'http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity-category'
coding_ethnicity.code = self.race
coding_ethnicity.display = cc_ethnicity.text
cc_ethnicity.coding = [coding_ethnicity]
ext_ethnicity.valueCodeableConcept = cc_ethnicity
try:
fhir_pt.extension.append(ext_ethnicity)
except AttributeError:
fhir_pt.extension = [ext_ethnicity]
if self.sex:
sex_dict = {"administrativeGender": {"M": "male", "F": "female", "u": "unknown", "o": "other"},
"usCoreBirthSex": {"M": "M", "F": "F", "U": "UNK", "O": "UNK"}}
fhir_pt.gender = sex_dict['administrativeGender'][str(self.sex).upper()]
ext_birth_sex = extension.Extension()
ext_birth_sex.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex'
ext_birth_sex.valueCode = sex_dict['usCoreBirthSex'][str(self.sex).upper()]
try:
fhir_pt.extension.append(ext_birth_sex)
except AttributeError:
fhir_pt.extension = [ext_birth_sex]
if self.dob:
fhir_pt.birthDate = fhir_gen_datetime(value=self.dob, to_date=True)
fhir_pt.active = self.active
fhir_pt.deceasedBoolean = self.deceased
if self.deceased_date:
fhir_pt.deceasedDateTime = fhir_gen_datetime(value=self.deceased_date, to_date=False)
if self.preferred_language:
fhir_comm = fhir_patient.PatientCommunication()
fhir_comm.preferred = True
fhir_lang_cc = codeableconcept.CodeableConcept()
fhir_lang_coding = coding.Coding()
fhir_lang_coding.code = self.preferred_language
fhir_lang_url = 'http://hl7.org/fhir/ValueSet/languages'
fhir_lang_coding.system = fhir_lang_url
fhir_lang_concept = ValueSet.get_valueset_concept(fhir_lang_url, self.preferred_language)
if fhir_lang_concept:
fhir_lang_coding.display = fhir_lang_concept.display
fhir_lang_cc.text = fhir_lang_coding.display
fhir_lang_cc.coding = [fhir_lang_coding]
fhir_comm.language = fhir_lang_cc
fhir_pt.communication = [fhir_comm]
contact_point_list = []
phone_list = self.phone_numbers.all()
if phone_list:
for ph in phone_list:
contact_point_list.append(ph.fhir)
email_list = self.email_addresses.all()
if email_list:
for em in email_list:
contact_point_list.append(em.fhir)
if contact_point_list:
fhir_pt.telecom = contact_point_list
address_list = self.addresses.all()
if address_list:
fhir_pt.address = []
for addr in address_list:
fhir_pt.address.append(addr.fhir)
xhtml = render_template('fhir/patient.html', fhir_patient=fhir_pt, patient=self)
fhir_pt.text = narrative.Narrative()
fhir_pt.text.status = 'generated'
fhir_pt.text.div = xhtml
self._fhir = fhir_pt
def _generate_patient_fhir_object(self):
"""Creates a test patient using fhirclient.models."""
Patient = p.Patient()
HumanName = hn.HumanName()
HumanName.family = [self.name_last]
HumanName.given = [self.name_first]
Patient.name = [HumanName]
Patient.gender = self.gender
birthDay = fd.FHIRDate()
birthDay.date = self.bday
Patient.birthDate = birthDay
Address = a.Address()
Address.country = 'USA'
Address.postalCode = self.zipcode
Address.state = self.state
Address.city = self.city
Address.line = [f'{self.address_number} {self.address_street}']
Address.use = 'home'
Address.type = 'postal'
Patient.active = True
Patient.address = [Address]
PatientCommunication = p.PatientCommunication()
PatientCommunication.language = self._create_FHIRCodeableConcept(
'en-US', 'urn:ietf:bcp:47', 'English')
# PatientCommunication.language = self._create_FHIRCodeableConcept('en-US','http://hl7.org/fhir/ValueSet/languages','English')
PatientCommunication.preferred = True
Patient.communication = [PatientCommunication]
race = e.Extension()
race.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race'
us_core = e.Extension()
us_core.url = 'ombCategory'
us_core.valueCoding = self._create_FHIRCoding(
self.race_code, 'urn:oid:2.16.840.1.113883.6.238',
self.race_description)
race_detailed = e.Extension()
race_detailed.url = 'detailed'
race_detailed.valueCoding = self._create_FHIRCoding(
self.race_code, 'urn:oid:2.16.840.1.113883.6.238',
self.race_description)
race_text = e.Extension()
race_text.url = 'text'
race_text.valueString = self.race_description
race.extension = [us_core, race_detailed, race_text]
ethnicity = e.Extension()
ethnicity.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'
us_core = e.Extension()
us_core.url = 'ombCategory'
us_core.valueCoding = self._create_FHIRCoding(
self.ethnicity_code, 'urn:oid:2.16.840.1.113883.6.238',
self.ethnicity_description)
ethnicity_text = e.Extension()
ethnicity_text.url = 'text'
ethnicity_text.valueString = self.ethnicity_description
ethnicity.extension = [us_core, ethnicity_text]
Patient.extension = [race, ethnicity]
Patient.managingOrganization = self._create_FHIRReference(
self.Organization)
self._validate(Patient)
self.response = self.post_resource(Patient)
Patient.id = self._extract_id()
self.Patient = Patient
print(self)
