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kiproping/fhircreator.py

Created October 12, 2017 17:00
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fhircreator.py
#!/bin/python
import csv
firstline = True
def savetofile(file, content):
with open(file, 'w') as file:
file.write(content)
def checkfirst():
global firstline
if firstline:
firstline = False
return True
else:
return False
file = 'PatientInfo.csv'
csvfile = open(file, 'rb');
reader = csv.reader(csvfile)
count = 1
for row in reader:
if checkfirst():
continue
fhir = """\
//Patient
{{
"resourceType": "Patient",
"id": "{count}",
"active": true,
"name": [{{
"use": "official",
"family": "{lastn}",
"given": [
"{firstn}",
"{middlen}"
]
}}],
"gender": "{sex}"
}}
//Hematocrit
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "4544-3",
"display": "Hematocrit"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {hematocrit},
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
}}
}}
//Neutrophils
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "770-8",
"display": "Neutrophils"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {neutrophils},
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
}}
}}
//Sodium
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "2947-0",
"display": "Sodium"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {sodium},
"unit": "mmol/L",
"system": "http://unitsofmeasure.org",
"code": "mmol/L"
}}
}}
//Glucose
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "2339-0",
"display": "Glucose"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {glucose},
"unit": "mmol/L",
"system": "http://unitsofmeasure.org",
"code": "mmol/L"
}}
}}
//Ureanitrogen
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "6299-2",
"display": "Urea nitrogen"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {ureanitrogen},
"unit": "mg/dL ",
"system": "http://unitsofmeasure.org",
"code": "mg/dL "
}}
}}
//Creatinine
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "2160-0",
"display": "Creatinine"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {creatinine},
"unit": "mg/dL",
"system": "http://unitsofmeasure.org",
"code": "mg/dL"
}}
}}
//Body mass index
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "2160-0",
"display": "Body mass index"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {body},
"unit": "kg/m2",
"system": "http://unitsofmeasure.org",
"code": "kg/m2 "
}}
}}
//Heart rate / pulse
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "8867-4",
"display": "Heart rate "
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {heart},
"unit": "beats/min",
"system": "http://unitsofmeasure.org",
"code": "beats/min"
}}
}}
//Respiration
{{
"resourceType": "Observation",
"id": "{count}",
"status": "final",
"code": {{
"coding": [{{
"system": "http://loinc.org",
"code": "9279-1",
"display": "Heart rate "
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"valueQuantity": {{
"value": {respiration},
"unit": "breaths/min",
"system": "http://unitsofmeasure.org",
"code": "breaths/min"
}}
}}
//Encounter
{{
"resourceType": "Encounter",
"id": "{count}",
"status": "finished",
"class": {{
"system": "http://hl7.org/fhir/v3/ActCode",
"code": "IMP",
"display": "inpatient encounter"
}},
"period": {{
"start": "2012-08-29T00:00:00+00:00",
"end": "2012-09-01T00:30:00+00:00"
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}},
"serviceProvider":{{
"reference": "Organization/{org}",
"display": "{org}"
}}
}}
\
"""
if row[7] == '1':
fhir += """\
//dialysisrenalendstage
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "236435004",
"display": "End stage renal failure on dialysis"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[8] == '1':
fhir += """\
//asthma
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "195967001",
"display": "Asthma"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[9] == '1':
fhir += """\
//irondef
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "35240004",
"display": "Iron deficiency"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[10] == '1':
fhir += """\
//pneum
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "233604007",
"display": "Pneumonia"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[11] == '1':
fhir += """\
//substancedependence
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "361055000",
"display": "Misuses drugs"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[12] == '1':
fhir += """\
//phsycholgicaldisordermajor
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "81659004",
"display": "Psychological sign or symptom"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[13] == '1':
fhir += """\
//depress
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "35489007",
"display": "Depressive disorder"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[14] == '1':
fhir += """\
//phsychother
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "81659004",
"display": "Psychological sign or symptom"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[15] == '1':
fhir += """\
//fibriosisandother
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "263756000",
"display": "Fibrosis"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[16] == '1':
fhir += """\
//malnutrition
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "263756000",
"display": "Fibrosis"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
if row[17] == '1':
fhir += """\
//hemo
{{
"resourceType": "Condition",
"id": "1",
"clinicalStatus": "resolved",
"verificationStatus": "confirmed",
"code": {{
"coding": [{{
"system": "http://snomed.info/sct",
"code": "34093004",
"display": "Disorder of hematopoietic system"
}}]
}},
"subject": {{
"reference": "Patient/{count}",
"display": "{firstn}"
}}
}}
\
"""
g = row[6]
if g == 'M':
gender = 'male'
else:
gender = 'female'
fhir = fhir.format(
count=1,
firstn=row[0],
middlen=row[1],
lastn=row[2],
sex=gender,
hematocrit=row[18],
neutrophils=row[19],
sodium=row[20],
glucose=row[21],
ureanitrogen=row[22],
creatinine=row[23],
body=row[24],
heart=row[25],
respiration=row[26],
org=row[29]
);
file = 'files/patient{}.json'.format(count)
savetofile(file, fhir)
count +=1
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