def __init__(self, patientID):
self.report = dr.DiagnosticReport()
self.phased_rec_map = {}
self.result_ids = []
self.fhir_report = {}
self.obs_contained = []
self.patientID = patientID
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