def to_fhir(self):
fhir_medication = medication.Medication()
fhir_meta = meta.Meta()
fhir_meta.profile = [self.meta_profile]
fhir_medication.meta = fhir_meta
fhir_medication.ingredient = [self.ingredient.to_fhir()]
return fhir_medication
def add_phased_relationship_obv(self):
patient_reference = reference.FHIRReference(
{"reference": "Patient/" + self.patientID})
self.sequence_rels \
= get_sequence_relation(self.phased_rec_map)
for index in self.sequence_rels.index:
siduid = "sid-" + uuid4().hex[:13]
self.result_ids.append(siduid)
observation_sid = observation.Observation()
observation_sid.resource_type = "Observation"
observation_sid.id = siduid
observation_sid.meta = meta.Meta({
"profile":
[("http://hl7.org/fhir/uv/" + "genomics-reporting/" +
"StructureDefinition/" + "sequence-phase-relationship")]
})
observation_sid.status = "final"
observation_sid.category = [
concept.CodeableConcept({
"coding": [{
"system": ("http://terminology.hl7.org/" +
"CodeSystem/observation-category"),
"code":
"laboratory"
}]
})
]
observation_sid.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "82120-7",
"display": "Allelic phase"
}]
})
observation_sid.subject = patient_reference
observation_sid.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system":
("http://hl7.org/fhir/uv/" + "genomics-reporting/" +
"CodeSystem/seq-phase-relationship"),
"code":
self.sequence_rels.at[index, 'Relation'],
"display":
self.sequence_rels.at[index, 'Relation']
}]
})
self.report.contained.append(observation_sid)
def to_fhir(self) -> procedure.Procedure:
fhir_procedure = procedure.Procedure()
fhir_meta = meta.Meta()
fhir_meta.profile = [self.profile_url]
fhir_procedure.meta = fhir_meta
fhir_procedure.status = self.status
fhir_procedure.category = self.category.to_fhir()
fhir_procedure.code = self.procedure_code.to_fhir()
fhir_procedure.subject = self.pat_reference.to_fhir()
if type(self.performed) == FhirDatetime:
fhir_procedure.performedDateTime = self.performed.to_fhir()
elif type(self.performed) == FhirPeriod:
fhir_procedure.performedPeriod = self.performed.to_fhir()
return fhir_procedure
def initalize_report(self):
patient_reference = reference.FHIRReference(
{"reference": "Patient/" + self.patientID})
self.report.id = "dr-" + uuid4().hex[:13]
self.report.meta = meta.Meta({
"profile": [("http://hl7.org/fhir/uv/genomics-reporting" +
"/StructureDefinition/genomics-report")]
})
self.report.status = "final"
self.report.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "81247-9",
"display": "Master HL7 genetic variant reporting panel"
}]
})
self.report.subject = patient_reference
self.report.issued = date.FHIRDate(get_fhir_date())
self.report.contained = []
def to_fhir(self) -> medicationstatement.MedicationStatement:
fhir_med_statement = medicationstatement.MedicationStatement()
fhir_meta = meta.Meta()
fhir_meta.profile = [self.profile_url]
fhir_med_statement.meta = fhir_meta
fhir_med_statement.status = self.status
# References
# TODO: some of the references may be optional!!
fhir_med_statement.medicationReference = self.med_reference.to_fhir()
fhir_med_statement.subject = self.pat_reference.to_fhir()
fhir_med_statement.partOf = [self.proc_reference.to_fhir()]
if type(self.timestamp) == EffectivePeriod:
fhir_med_statement.effectivePeriod = self.timestamp.to_fhir()
elif type(self.timestamp) == FhirDateTime:
fhir_med_statement.effectiveDateTime = self.timestamp.to_fhir()
fhir_med_statement.dosage = [self.dosage.to_fhir()]
return fhir_med_statement
def meta(self):
return mt.Meta({"profile":
["http://hl7.org/fhir/StructureDefinition/vitalsigns"]})
def add_regionstudied_obv(self, ref_seq, reportable_query_regions,
nocall_regions):
if reportable_query_regions.empty and nocall_regions.empty:
return
patient_reference = reference.FHIRReference(
{"reference": "Patient/" + self.patientID})
contained_uid = "rs-" + uuid4().hex[:13]
self.result_ids.append(contained_uid)
# Region Studied Obeservation
observation_rs = observation.Observation()
contained_rs = observation_rs
contained_rs.id = contained_uid
observation_rs.resource_type = "Observation"
contained_rs.meta = meta.Meta({
"profile": [("http://hl7.org/fhir/uv/" + "genomics-reporting/" +
"StructureDefinition/region-studied")]
})
observation_rs.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "53041-0",
"display": "DNA region of interest panel"
}]
})
observation_rs.status = "final"
observation_rs.category = [
concept.CodeableConcept({
"coding": [{
"system": ("http://terminology.hl7.org/" +
"CodeSystem/observation-category"),
"code":
"laboratory"
}]
})
]
observation_rs.subject = patient_reference
observation_rs_component2 = observation.ObservationComponent()
observation_rs_component2.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "92822-6",
"display": "Genomic coord system"
}]
})
observation_rs_component2\
.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [
{
"system": "http://loinc.org",
"code": "LA30102-0",
"display": "1-based character counting"
}
]
}
)
observation_rs_component3 = observation.ObservationComponent()
observation_rs_component3.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence ID"
}]
})
observation_rs_component3\
.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": ref_seq
}
]
}
)
observation_rs_components = self._get_region_studied_component(
reportable_query_regions, nocall_regions)
observation_rs.component = [
observation_rs_component2, observation_rs_component3
] + observation_rs_components
# Observation structure : described-variants
self.report.contained.append(contained_rs)
def add_variant_obv(self, record, ref_seq, ratio_ad_dp):
# collect all the record with similar position values,
# to utilized later in phased sequence relationship
self._add_phase_records(record)
patient_reference = reference.FHIRReference(
{"reference": "Patient/" + self.patientID})
alleles = get_allelic_state(record, ratio_ad_dp)
dvuid = "dv-" + uuid4().hex[:13]
self.fhir_report.update({str(record.POS): dvuid})
self.result_ids.append(dvuid)
observation_dv = observation.Observation()
observation_dv.resource_type = "Observation"
observation_dv.id = dvuid
observation_dv.meta = meta.Meta({
"profile": [("http://hl7.org/fhir/uv/" +
"genomics-reporting/StructureDefinition/variant")]
})
observation_dv.status = "final"
observation_dv.category = [
concept.CodeableConcept({
"coding": [{
"system": ("http://terminology.hl7.org/" +
"CodeSystem/observation-category"),
"code":
"laboratory"
}]
})
]
observation_dv.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "69548-6",
"display": "Genetic variant assessment"
}]
})
observation_dv.subject = patient_reference
observation_dv.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "present"
}]
})
observation_dv.component = []
observation_dv_component1 = observation.ObservationComponent()
observation_dv_component1.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "62374-4",
"display": "Human reference sequence assembly version"
}]
})
observation_dv_component1\
.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [
{
"system": "http://loinc.org",
"code": "LA14029-5",
"display": "GRCh37"
}
]
}
)
observation_dv.component.append(observation_dv_component1)
observation_dv_component2 = observation.ObservationComponent()
observation_dv_component2.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence ID"
}]
})
observation_dv_component2\
.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": ref_seq
}
]
}
)
observation_dv.component.append(observation_dv_component2)
if alleles['CODE'] != "" or alleles['ALLELE'] != "":
observation_dv_component3 = observation.ObservationComponent()
observation_dv_component3.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "53034-5",
"display": "Allelic state"
}]
})
observation_dv_component3\
.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [
{
"system": "http://loinc.org",
"code": alleles['CODE'],
"display": alleles['ALLELE']
}
]
}
)
observation_dv.component.append(observation_dv_component3)
observation_dv_component4 = observation.ObservationComponent()
observation_dv_component4.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "69547-8",
"display": "Genomic Ref allele [ID]"
}]
})
observation_dv_component4.valueString = record.REF
observation_dv.component.append(observation_dv_component4)
observation_dv_component5 = observation.ObservationComponent()
observation_dv_component5.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "69551-0",
"display": "Genomic Alt allele [ID]"
}]
})
observation_dv_component5.valueString = record.ALT[0].sequence
observation_dv.component.append(observation_dv_component5)
observation_dv_component6 = observation.ObservationComponent()
observation_dv_component6.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "92822-6",
"display": "Genomic coord system"
}]
})
observation_dv_component6\
.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [
{
"system": "http://loinc.org",
"code": "LA30102-0",
"display": "1-based character counting"
}
]
}
)
observation_dv.component.append(observation_dv_component6)
observation_dv_component7 = observation.ObservationComponent()
observation_dv_component7.code = concept.CodeableConcept({
"coding": [{
"system": ("http://hl7.org/fhir/uv/" +
"genomics-reporting/CodeSystem/tbd-codes"),
"code":
"exact-start-end",
"display":
"Variant exact start and end"
}]
})
observation_dv_component7.valueRange = valRange.Range(
{"low": {
"value": int(record.POS)
}})
observation_dv.component.append(observation_dv_component7)
self.report.contained.append(observation_dv)
def getEmptyFhirJSON(patientID, start, end, refSeq, nocall=False):
logging.info("[FHIR: Converting XML to JSON]")
noCallRegion, queryRange = getNoCallableData(NO_CALL_FILE,
QUERY_RANGE_FILE)
nocallRows = len(noCallRegion.index)
start = queryRange.at[0, "START"]
end = queryRange.at[0, "END"]
if not noCallRegion.empty:
if noCallRegion['START'].iloc[0] <= queryRange['START'].iloc[0]:
noCallRegion['START'].iloc[0] = queryRange['START'].iloc[0]
if noCallRegion['END'].iloc[-1] >= queryRange['END'].iloc[0]:
noCallRegion['END'].iloc[-1] = queryRange['END'].iloc[0]
else:
nocall = False
contained_uid = uuid4().hex[:13]
patient_reference = reference.FHIRReference(
{"reference": "Patient/" + patientID})
variant_reference = reference.FHIRReference(
{"reference": "#rs-" + contained_uid})
report = dr.DiagnosticReport()
report.id = "dr-" + uuid4().hex[:13]
report.meta = meta.Meta({
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnosticreport"
]
})
report.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "53041-0",
"display": "DNA region of interest panel"
}]
})
report.status = "final"
report.subject = patient_reference
report.issued = date.FHIRDate(Utilities.getFhirDate())
report.result = [variant_reference]
observation_rs = observation.Observation()
contained_rs = observation_rs
observation_dv = observation.Observation()
contained_dv = observation_dv
observation_sid = observation.Observation()
contained_sid = observation_sid
contained_rs.id = "rs-" + contained_uid
observation_rs.resource_type = "Observation"
contained_rs.meta = meta.Meta({
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-region-studied"
]
})
observation_rs.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "53041-0",
"display": "DNA region of interest panel"
}]
})
observation_rs.status = "final"
observation_rs.category = [
concept.CodeableConcept({
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}]
})
]
observation_rs.subject = patient_reference
observation_rs_component1 = observation.ObservationComponent()
observation_rs_component1.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "51959-5",
"display": "Range(s) of DNA sequence examined"
}]
})
observation_rs_component1.valueRange = valRange.Range({
"low": {
"value": int(start)
},
"high": {
"value": int(end)
}
})
observation_rs_component2 = observation.ObservationComponent()
observation_rs_component2.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "tbd-coordinate system",
"display": "Genomic coordinate system"
}]
})
observation_rs_component2.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system":
"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genetic-coordinate-system",
"code": "1"
}]
})
observation_rs_component3 = observation.ObservationComponent()
observation_rs_component3.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence ID"
}]
})
observation_rs_component3.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": refSeq
}]
})
if nocall:
#component Region-studied (No call region)
nocallComponents = []
for i in range(nocallRows):
nocallComponents.append('observation_rs_component' + str(i + 4))
observation_rs_components = []
for (index, i) in zip(noCallRegion.index, nocallComponents):
i = observation.ObservationComponent()
i.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "TBD-noCallRegion",
"display": "No call region"
}]
})
observation_rs_components.append(i)
if nocall:
observation_rs.component = [
observation_rs_component2, observation_rs_component3
] + observation_rs_components
else:
observation_rs.component = [
observation_rs_component2, observation_rs_component3
]
response = report.as_json()
od = OrderedDict()
od["resourceType"] = response['resourceType']
od["id"] = response['id']
od["meta"] = response['meta']
od["contained"] = response['contained']
od["status"] = response['status']
od["code"] = response['code']
od["subject"] = response['subject']
od["issued"] = response['issued']
od["result"] = response['result']
with open(FHIR_JSON_RESULT + 'fhir.json', 'w') as fp:
json.dump(od, fp, indent=4)
return FHIR_JSON_RESULT
def getFhirJSON(cleanVcf,
nextelem,
patientID,
refSeq,
noCall=False,
gender="M"):
dvuids = {}
siduids = []
alleles = getAllelicState(cleanVcf, nextelem, gender)
sequenceRels = getSequenceRelation(cleanVcf, nextelem)
noCallRegion, queryRange = getNoCallableData(NO_CALL_FILE,
QUERY_RANGE_FILE)
nocallRows = len(noCallRegion.index)
start = queryRange.at[0, "START"]
end = queryRange.at[0, "END"]
if not noCallRegion.empty:
if noCallRegion['START'].iloc[0] <= queryRange['START'].iloc[0]:
noCallRegion['START'].iloc[0] = queryRange['START'].iloc[0]
if noCallRegion['END'].iloc[-1] >= queryRange['END'].iloc[0]:
noCallRegion['END'].iloc[-1] = queryRange['END'].iloc[0]
else:
noCall = False
contained_uid = uuid4().hex[:13]
patient_reference = reference.FHIRReference(
{"reference": "Patient/" + patientID})
variant_reference = reference.FHIRReference(
{"reference": "#rs-" + contained_uid})
report = dr.DiagnosticReport()
report.id = "dr-" + uuid4().hex[:13]
report.meta = meta.Meta({
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"
]
})
report.status = "final"
report.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "81247-9",
"display": "Master HL7 genetic variant reporting panel"
}]
})
report.subject = patient_reference
report.issued = date.FHIRDate(Utilities.getFhirDate())
observation_rs = observation.Observation()
contained_rs = observation_rs
contained_rs.id = "rs-" + contained_uid
observation_rs.resource_type = "Observation"
contained_rs.meta = meta.Meta({
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied"
]
})
observation_rs.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "53041-0",
"display": "DNA region of interest panel"
}]
})
observation_rs.status = "final"
observation_rs.category = [
concept.CodeableConcept({
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}]
})
]
observation_rs.subject = patient_reference
observation_rs_component1 = observation.ObservationComponent()
observation_rs_component1.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "51959-5",
"display": "Range(s) of DNA sequence examined"
}]
})
observation_rs_component1.valueRange = valRange.Range({
"low": {
"value": int(start)
},
"high": {
"value": int(end)
}
})
observation_rs_component2 = observation.ObservationComponent()
observation_rs_component2.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "92822-6",
"display": "Genomic coord system"
}]
})
observation_rs_component2.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "LA30102-0",
"display": "1-based character counting"
}]
})
observation_rs_component3 = observation.ObservationComponent()
observation_rs_component3.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence ID"
}]
})
observation_rs_component3.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": refSeq
}]
})
if noCall:
#component Region-studied (No call region)
nocallComponents = []
for i in range(nocallRows):
nocallComponents.append('observation_rs_component' + str(i + 4))
observation_rs_components = []
for (index, i) in zip(noCallRegion.index, nocallComponents):
i = observation.ObservationComponent()
i.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "TBD-noCallRegion",
"display": "No call region"
}]
})
observation_rs_components.append(i)
observation_rs.component = [
observation_rs_component2, observation_rs_component3
] + observation_rs_components
else:
observation_rs.component = [
observation_rs_component2, observation_rs_component3
]
# Observation structure : described-variants
obsContained = [contained_rs]
for index in alleles.index:
dvuid = uuid4().hex[:13]
dvuids.update({str(alleles.at[index, 'POS']): dvuid})
observation_dv = observation.Observation()
observation_dv.resource_type = "Observation"
observation_dv.id = "dv-" + dvuid
observation_dv.meta = meta.Meta({
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
})
observation_dv.status = "final"
observation_dv.category = [
concept.CodeableConcept({
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}]
})
]
observation_dv.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "69548-6",
"display": "Genetic variant assessment"
}]
})
observation_dv.subject = patient_reference
observation_dv.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "present"
}]
})
observation_dv_component1 = observation.ObservationComponent()
observation_dv_component1.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "62374-4",
"display": "Human reference sequence assembly version"
}]
})
observation_dv_component1.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [{
"system": "http://loinc.org",
"code": "LA14029-5",
"display": "GRCh37"
}]
})
observation_dv_component2 = observation.ObservationComponent()
observation_dv_component2.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence ID"
}]
})
observation_dv_component2.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": refSeq
}]
})
observation_dv_component3 = observation.ObservationComponent()
observation_dv_component3.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "53034-5",
"display": "Allelic state"
}]
})
observation_dv_component3.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [{
"system": "http://loinc.org",
"code": alleles.at[index, 'CODE'],
"display": alleles.at[index, 'ALLELE']
}]
})
observation_dv_component4 = observation.ObservationComponent()
observation_dv_component4.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "69547-8",
"display": "Genomic Ref allele [ID]"
}]
})
observation_dv_component4.valueString = alleles.at[index, 'REF']
observation_dv_component5 = observation.ObservationComponent()
observation_dv_component5.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "69551-0",
"display": "Genomic Alt allele [ID]"
}]
})
observation_dv_component5.valueString = alleles.at[index, 'ALT']
observation_dv_component6 = observation.ObservationComponent()
observation_dv_component6.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "92822-6",
"display": "Genomic coord system"
}]
})
observation_dv_component6.valueCodeableConcept = concept.CodeableConcept(
{
"coding": [{
"system": "http://loinc.org",
"code": "LA30102-0",
"display": "1-based character counting"
}]
})
observation_dv_component7 = observation.ObservationComponent()
observation_dv_component7.code = concept.CodeableConcept({
"coding": [{
"system":
"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code": "exact-start-end",
"display": "Variant exact start and end"
}]
})
observation_dv_component7.valueRange = valRange.Range(
{"low": {
"value": int(alleles.at[index, 'POS'])
}})
observation_dv.component = [
observation_dv_component1, observation_dv_component2,
observation_dv_component3, observation_dv_component4,
observation_dv_component5, observation_dv_component6,
observation_dv_component7
]
obsContained.append(observation_dv)
# Obesrvation structure: sequence-phase relatons
siduids = []
for index in sequenceRels.index:
dvRef1 = dvuids.get(str(sequenceRels.at[index, 'POS1']))
dvRef2 = dvuids.get(str(sequenceRels.at[index, 'POS2']))
siduid = uuid4().hex[:13]
siduids.append(siduid)
observation_sid = observation.Observation()
observation_sid.resource_type = "Observation"
observation_sid.id = "sid-" + siduid
observation_sid.meta = meta.Meta({
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
]
})
observation_sid.status = "final"
observation_sid.category = [
concept.CodeableConcept({
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}]
})
]
observation_sid.code = concept.CodeableConcept({
"coding": [{
"system": "http://loinc.org",
"code": "82120-7",
"display": "Allelic phase"
}]
})
observation_sid.subject = patient_reference
observation_sid.valueCodeableConcept = concept.CodeableConcept({
"coding": [{
"system":
"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/seq-phase-relationship",
"code": sequenceRels.at[index, 'Relation'],
"display": sequenceRels.at[index, 'Relation']
}]
})
obsContained.append(observation_sid)
report.contained = obsContained
reportResult = [variant_reference]
for pos, uid in dvuids.items():
reportResult.append(
reference.FHIRReference({"reference": "#dv-" + uid}))
for uid in siduids:
reportResult.append(
reference.FHIRReference({"reference": "#sid-" + uid}))
report.result = reportResult
response = report.as_json()
od = OrderedDict()
od["resourceType"] = response['resourceType']
od["id"] = response['id']
od["meta"] = response['meta']
od["contained"] = response['contained']
od["status"] = response['status']
od["code"] = response['code']
od["subject"] = response['subject']
od["issued"] = response['issued']
od["result"] = response['result']
odCodeCoding = OrderedDict()
odCodeCoding["system"] = od["code"]["coding"][0]["system"]
odCodeCoding["code"] = od["code"]["coding"][0]["code"]
odCodeCoding["display"] = od["code"]["coding"][0]["display"]
od["code"]["coding"][0] = odCodeCoding
sidIndex = 0
for index, fhirReport in enumerate(od['contained']):
if (fhirReport['id'].startswith('sid-')):
sidIndex = index
break
for index, (sequenceRel, fhirReport) in enumerate(
zip(sequenceRels.index, od['contained'][sidIndex:])):
dvRef1 = dvuids.get(str(sequenceRels.at[index, 'POS1']))
dvRef2 = dvuids.get(str(sequenceRels.at[index, 'POS2']))
if (fhirReport['id'].startswith('sid-')):
derivedFromDV1 = {}
derivedFromDV2 = {}
derivedFromDV1['reference'] = "#dv-" + dvRef1
derivedFromDV2['reference'] = "#dv-" + dvRef2
derivedFrom = [derivedFromDV1, derivedFromDV2]
fhirReport['derivedFrom'] = derivedFrom
for k, i in enumerate(od['contained']):
if (i['category'][0]['coding'][0]):
odCategoryCoding = OrderedDict()
odCategoryCoding["system"] = i['category'][0]['coding'][0][
"system"]
odCategoryCoding["code"] = i['category'][0]['coding'][0]["code"]
od['contained'][k]['category'][0]['coding'][0] = odCategoryCoding
if (i['code']['coding'][0]):
odCodeCoding = OrderedDict()
odCodeCoding["system"] = i['code']['coding'][0]["system"]
odCodeCoding["code"] = i['code']['coding'][0]["code"]
odCodeCoding["display"] = i['code']['coding'][0]["display"]
od['contained'][k]['code']['coding'][0] = odCodeCoding
if 'valueCodeableConcept' in i.keys():
odValueCodeableConceptCoding = OrderedDict()
odValueCodeableConceptCoding["system"] = i['valueCodeableConcept'][
'coding'][0]["system"]
odValueCodeableConceptCoding["code"] = i['valueCodeableConcept'][
'coding'][0]["code"]
odValueCodeableConceptCoding["display"] = i[
'valueCodeableConcept']['coding'][0]["display"]
od['contained'][k]['valueCodeableConcept']['coding'][
0] = odValueCodeableConceptCoding
if ((i['id'].startswith('dv-')) or (i['id'].startswith('rs-'))):
for l, j in enumerate(i['component']):
odComponentCodeCoding = OrderedDict()
if j['code']['coding'][0]["system"]:
odComponentCodeCoding["system"] = j['code']['coding'][0][
"system"]
if j['code']['coding'][0]["code"]:
odComponentCodeCoding["code"] = j['code']['coding'][0][
"code"]
if j['code']['coding'][0]["display"]:
odComponentCodeCoding["display"] = j['code']['coding'][0][
"display"]
if od['contained'][k]['component'][l]['code']['coding'][0]:
od['contained'][k]['component'][l]['code']['coding'][
0] = odComponentCodeCoding
odComponentvalueCodeableConcept = OrderedDict()
if 'valueCodeableConcept' in j.keys():
odComponentvalueCodeableConcept["system"] = j[
'valueCodeableConcept']['coding'][0]["system"]
if 'code' in j['valueCodeableConcept']['coding'][0].keys():
odComponentvalueCodeableConcept["code"] = j[
'valueCodeableConcept']['coding'][0]["code"]
if 'display' in j['valueCodeableConcept']['coding'][
0].keys():
odComponentvalueCodeableConcept["display"] = j[
'valueCodeableConcept']['coding'][0]["display"]
od['contained'][k]['component'][l]['valueCodeableConcept'][
'coding'][0] = odComponentvalueCodeableConcept
if (i['id'].startswith('rs-')):
odRS = OrderedDict()
odRS["resourceType"] = i['resourceType']
odRS["id"] = i['id']
odRS["meta"] = i['meta']
odRS["status"] = i['status']
odRS["category"] = i['category']
odRS["code"] = i['code']
odRS["subject"] = i['subject']
odRS["component"] = i['component']
od['contained'][k] = odRS
if (i['id'].startswith('dv-')):
odDV = OrderedDict()
odDV["resourceType"] = i['resourceType']
odDV["id"] = i['id']
odDV["meta"] = i['meta']
odDV["status"] = i['status']
odDV["category"] = i['category']
odDV["code"] = i['code']
odDV["subject"] = i['subject']
odDV["valueCodeableConcept"] = i['valueCodeableConcept']
odDV["component"] = i['component']
od['contained'][k] = odDV
if (i['id'].startswith('sid-')):
odSID = OrderedDict()
odSID["resourceType"] = i['resourceType']
odSID["id"] = i['id']
odSID["meta"] = i['meta']
odSID["status"] = i['status']
odSID["category"] = i['category']
odSID["code"] = i['code']
odSID["subject"] = i['subject']
odSID["valueCodeableConcept"] = i['valueCodeableConcept']
odSID["derivedFrom"] = i['derivedFrom']
od['contained'][k] = odSID
with open(FHIR_JSON_RESULT + 'fhir.json', 'w') as fp:
json.dump(od, fp, indent=4)
return FHIR_JSON_RESULT
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
