import petl as etl
from fhir_petl.util import preprocess, resolve, mkdirp
import random
mkdirp(resolve('work'))
selection = etl.io.csv.fromtsv(resolve('sa1cases.txt')).columns()['STUDYID']
selection = set(random.sample(selection, 1000))
preprocess(
etl.io.csv.fromcsv(resolve('case_demog_27065.csv')).selectin(
'STUDYID', selection), 'STUDYID').tocsv(resolve('work/Patient.csv'))
preprocess(
etl.io.csv.fromtsv(resolve('dx_case_inst.txt')).selectin(
'STUDYID', selection),
'STUDYID',
).tocsv(resolve('work/Condition.csv'))
preprocess(
etl.io.csv.fromtsv(resolve('lab_case_inst.txt')).selectin(
'STUDYID', selection),
'STUDYID').tocsv(resolve('work/Observation.csv'))
preprocess(
etl.io.csv.fromtsv(resolve('med_case_inst_gpi.txt')).selectin(
'CASE_ID', selection),
'CASE_ID').tocsv(resolve('work/MedicationDispense.csv'))
preprocess(
etl.io.csv.fromtsv(resolve('order_case_inst_gpi.txt')).selectin(
'subject': 'subject'
}, True))
def medications2(rec):
group = rec['DRUG_GROUP'].strip('*')
clazz = rec['DRUG_CLASS'].strip('*')
return [
('http://hl7.org/fhir/sid/ndc', rec['NDC'], rec['ORDER_NAME']),
('urn:oid:2.16.840.1.113883.6.68', rec['GPI'], rec['ORDER_NAME']),
('drug-class', clazz, clazz),
('drug-group', group, group)
]
med_requests = (etl.io.csv.fromcsv(resolve('work/MedicationRequest.csv'))
.hashjoin(index, lkey='STUDYID', rkey='STUDYID')
.fieldmap({
'id': 'ID',
'date': lambda rec: rec['index_date'] + timedelta(int(rec['DAYS_ORDER_INDEX'])),
'medication': medications2,
'subject': 'subject'
}, True))
mkdirp(resolve('fhir'))
to_json(patients, 'Patient', resolve('fhir/Patient.json'))
to_json(procedures, 'Procedure', resolve('fhir/Procedure.json'))
to_json(conditions, 'Condition', resolve('fhir/Condition.json'))
to_json(observations, 'Observation', resolve('fhir/Observation.json'))
to_json(med_dispenses, 'MedicationDispense', resolve('fhir/MedicationDispense.json'))
to_json(med_requests, 'MedicationRequest', resolve('fhir/MedicationRequest.json'))
# ),
# # "route": ("ROUTE", map_rx_route),
# "subject": "subject",
# # # "status": (
# # "ONGOING",
# # lambda active: "active"
# # if active == "TRUE"
# # else "completed"
# # if active == "FALSE"
# # else None,
# # ),
# # "note": "STATUS_REASON",
# "start_date": ("START_DATE", parse_date),
# # "indication": ("INDICATION", map_indication),
# # "end_date": ("END_DATE", date),
# # "nct": ("NCT"),
# },
# True,
# )
# )
mkdirp(resolve("fhir"))
# to_json(patients, "Patient", resolve("fhir/Patient_ktb_updated.json"))
# to_json(procedures, 'Procedure', resolve('fhir/Procedure.json'))
to_json(observations, "Observation", resolve("fhir/Observation_bmi_gs.json"))
# to_json(conditions, "Condition", resolve("fhir/Condition_ktb.json"))
# to_json(med_requests, 'MedicationRequest', resolve('fhir/MedicationRequest.json'))
# to_json(
# med_statements, "MedicationStatement", resolve("fhir/MedicationStatement_ktb.json")
# )