def fhir_specimen_collection(obj):
""" Converts Procedure to FHIR Specimen collection. """
collection = s.SpecimenCollection()
collection.id = str(obj['id'])
collection.method = fhir_codeable_concept(obj['code'])
if 'body_site' in obj.keys():
collection.bodySite = fhir_codeable_concept(obj['body_site'])
return collection.as_json()
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 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()