def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
service_request_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/serviceRequest.json'
).json()
row_parser = RowParser(values[0])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
service_request_row = row_parser.as_dict(row)
service_request = copy.deepcopy(service_request_model)
service_request['id'] = service_request_row['id']
service_request['status'] = service_request_row['status']
service_request['authoredOn'] = service_request_row[
'authoredOn']
service_request['code']['text'] = service_request_row[
'code.text']
service_request['subject'][
'reference'] = f"Patient/{service_request_row['subject']}"
service_request['requester'][
'reference'] = f"PractitionerRole/{service_request_row['requester']}"
service_request['specimen'][0][
'reference'] = f"Specimen/{service_request_row['specimen']}"
service_request['extension'][0]['valueReference']['reference'] = \
f"ClinicalImpression/{service_request_row['extension.valueReference']}"
service_request_json = json.dumps(service_request,
ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into servicerequest (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query,
(service_request['id'], service_request_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
study_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/researchStudy.json').json()
row_parser = RowParser(values[0])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
study_row = row_parser.as_dict(row)
study = copy.deepcopy(study_model)
study['id'] = study_row['id']
study['status'] = study_row['status']
study['title'] = study_row['title']
study['description'] = study_row['description']
study['sponsor']['reference'] = f"Organization/{study_row['sponsor']}"
study['principalInvestigator']['reference'] = f"Practitioner/{study_row['principalInvestigator']}"
study['enrollment'][0]['reference'] = f"Group/{study_row['enrolement']}"
study['period']['start'] = study_row['period.start']
study['period']['end'] = study_row['period.end']
study_json = json.dumps(study, ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into researchstudy (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query, (study['id'], study_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
fmh_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/familyMemberHistory.json'
).json()
row_parser = RowParser(values[0])
for row in values[1:]:
fmh_row = row_parser.as_dict(row)
fmh = copy.deepcopy(fmh_model)
fmh['id'] = fmh_row['id']
fmh['status'] = fmh_row['status']
fmh['patient']['reference'] = f"Patient/{fmh_row['patient']}"
fmh['date'] = fmh_row['date']
fmh['note'][0]['text'] = fmh_row['note']
fmh_json = json.dumps(fmh)
response = requests.put(
f"{args.url}/fhir/FamilyMemberHistory/{fmh['id']}",
data=fmh_json,
headers={
'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"
})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nfmh={fmh_json}'
)
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
specimen_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/specimen.json'
).json()
specimen_model.pop('parent')
row_parser = RowParser(values[0])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
specimen_row = row_parser.as_dict(row)
specimen = copy.deepcopy(specimen_model)
specimen['id'] = specimen_row['id']
specimen['status'] = specimen_row['status']
specimen['subject'][
'reference'] = f"Patient/{specimen_row['subject']}"
specimen['request'][0][
'reference'] = f"ServiceRequest/{specimen_row['request']}"
specimen['container'][0]['identifier'][0][
'value'] = specimen_row['container.identifier.value']
specimen_json = json.dumps(specimen, ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into specimen (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query, (specimen['id'], specimen_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
study_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/researchStudy.json').json()
row_parser = RowParser(values[0])
for row in values[1:]:
study_row = row_parser.as_dict(row)
study = copy.deepcopy(study_model)
study['id'] = study_row['id']
study['status'] = study_row['status']
study['title'] = study_row['title']
study['description'] = study_row['description']
study['sponsor']['reference'] = f"Organization/{study_row['sponsor']}"
study['principalInvestigator']['reference'] = f"Practitioner/{study_row['principalInvestigator']}"
study['enrollment'][0]['reference'] = f"Group/{study_row['enrolement']}"
study['period']['start'] = study_row['period.start']
study['period']['end'] = study_row['period.end']
study_json = json.dumps(study)
response = requests.put(f"{args.url}/fhir/ResearchStudy/{study['id']}", data=study_json,
headers={'Authorization': f"Basic {args.token}", "Content-Type": "application/json"})
if response.status_code not in (201, 200):
raise Exception(f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nstudy={study_json}')
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
service_request_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/serviceRequest.json'
).json()
row_parser = RowParser(values[0])
for row in values[1:]:
service_request_row = row_parser.as_dict(row)
service_request = copy.deepcopy(service_request_model)
service_request['id'] = service_request_row['id']
service_request['status'] = service_request_row['status']
service_request['authoredOn'] = service_request_row['authoredOn']
service_request['code']['text'] = service_request_row['code.text']
service_request['subject'][
'reference'] = f"Patient/{service_request_row['subject']}"
service_request['requester'][
'reference'] = f"PractitionerRole/{service_request_row['requester']}"
service_request['specimen'][0][
'reference'] = f"Specimen/{service_request_row['specimen']}"
service_request['extension'][0]['valueReference']['reference'] = \
f"ClinicalImpression/{service_request_row['extension.valueReference']}"
service_request_json = json.dumps(service_request)
response = requests.put(
f"{args.url}/fhir/ServiceRequest/{service_request['id']}",
data=service_request_json,
headers={
'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"
})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nservice_request={service_request_json}'
)
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
practitioner_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/practitioner.json'
).json()
row_parser = RowParser(values[0][0:6])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
practitioner_row = row_parser.as_dict(row[0:6])
practitioner = copy.deepcopy(practitioner_model)
practitioner['id'] = practitioner_row['id']
name = practitioner['name'][0]
name['family'] = practitioner_row['name.family']
name['prefix'] = [practitioner_row['name.prefix']]
md = practitioner_row['MD']
if md != 'null':
practitioner['identifier'][0]['value'] = md
else:
practitioner['identifier'].pop(0)
practitioner_json = json.dumps(practitioner,
ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into practitioner (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query,
(practitioner['id'], practitioner_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
practitioner_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/practitionerRole.json'
).json()
row_parser = RowParser(values[0][0:6])
for row in values[1:]:
practitioner_role_row = row_parser.as_dict(row[0:6])
practitioner_role = copy.deepcopy(practitioner_model)
practitioner_role['id'] = practitioner_role_row['id']
practitioner_role['practitioner']['reference'] = \
f"Practitioner/{practitioner_role_row['practitioner']}"
practitioner_role['organization']['reference'] = \
f"Organization/{practitioner_role_row['organization']}"
code = practitioner_role['code'][0]
code['coding'][0]['code'] = practitioner_role_row[
'code.coding.code']
code['coding'][0]['display'] = practitioner_role_row[
'code.coding.display']
code['text'] = practitioner_role_row['code.text']
practitioner_role_json = json.dumps(practitioner_role)
response = requests.put(
f"{args.url}/fhir/PractitionerRole/{practitioner_role['id']}",
data=practitioner_role_json,
headers={
'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"
})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nparticipant={practitioner_role_json}'
)
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
specimen_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/specimen.json'
).json()
specimen_model.pop('parent')
row_parser = RowParser(values[0])
for row in values[1:]:
specimen_row = row_parser.as_dict(row)
specimen = copy.deepcopy(specimen_model)
specimen['id'] = specimen_row['id']
specimen['status'] = specimen_row['status']
specimen['subject'][
'reference'] = f"Patient/{specimen_row['subject']}"
specimen['request'][0][
'reference'] = f"ServiceRequest/{specimen_row['request']}"
specimen['container'][0]['identifier'][0]['value'] = specimen_row[
'container.identifier.value']
specimen_json = json.dumps(specimen)
response = requests.put(
f"{args.url}/fhir/Specimen/{specimen['id']}",
data=specimen_json,
headers={
'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"
})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nspecimen={specimen_json}'
)
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
practitioner_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/practitioner.json'
).json()
row_parser = RowParser(values[0][0:6])
for row in values[1:]:
practitioner_row = row_parser.as_dict(row[0:6])
practitioner = copy.deepcopy(practitioner_model)
practitioner['id'] = practitioner_row['id']
name = practitioner['name'][0]
name['family'] = practitioner_row['name.family']
name['prefix'] = [practitioner_row['name.prefix']]
md = practitioner_row['MD']
if md != 'null':
practitioner['identifier'][0]['value'] = md
else:
practitioner['identifier'].pop(0)
practitioner_json = json.dumps(practitioner)
response = requests.put(
f"{args.url}/fhir/Practitioner/{practitioner['id']}",
data=practitioner_json,
headers={
'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"
})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nparticipant={practitioner_json}'
)
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
practitioner_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/practitionerRole.json'
).json()
row_parser = RowParser(values[0][0:6])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
practitioner_role_row = row_parser.as_dict(row[0:6])
practitioner_role = copy.deepcopy(practitioner_model)
practitioner_role['id'] = practitioner_role_row['id']
practitioner_role['practitioner']['reference'] = \
f"Practitioner/{practitioner_role_row['practitioner']}"
practitioner_role['organization']['reference'] = \
f"Organization/{practitioner_role_row['organization']}"
code = practitioner_role['code'][0]
code['coding'][0]['code'] = practitioner_role_row[
'code.coding.code']
code['coding'][0]['display'] = practitioner_role_row[
'code.coding.display']
code['text'] = practitioner_role_row['code.text']
practitioner_role_json = json.dumps(practitioner_role,
ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into practitionerRole (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(
insert_query,
(practitioner_role['id'], practitioner_role_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
clinical_impression_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/clinicalImpression.json'
).json()
clinical_impression_model.pop('meta')
row_parser = RowParser(values[0])
for row in values[1:]:
clinical_impression_row = row_parser.as_dict(row)
clinical_impression = copy.deepcopy(clinical_impression_model)
clinical_impression['id'] = clinical_impression_row['id']
clinical_impression['effectiveDateTime'] = clinical_impression_row[
'effectiveDateTime']
clinical_impression['subject'][
'reference'] = f"Patient/{clinical_impression_row['subject']}"
clinical_impression['assessor'][
'reference'] = f"PractitionerRole/{clinical_impression_row['assessor']}"
clinical_impression['extension'][0]['valueAge']['value'] = int(
clinical_impression_row['valueAge'])
clinical_impression['investigation'][0]['item'] = []
for r in row[5:9]:
clinical_impression['investigation'][0]['item'].extend([{
'reference':
r
}])
clinical_impression_json = json.dumps(clinical_impression)
response = requests.put(
f"{args.url}/fhir/ClinicalImpression/{clinical_impression['id']}",
data=clinical_impression_json,
headers={
'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"
})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nclinical_impression={clinical_impression_json}'
)
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
organization_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/organization.json').json()
row_parser = RowParser(values[0])
for row in values[1:]:
organization_row = row_parser.as_dict(row)
organization = copy.deepcopy(organization_model)
organization['id'] = organization_row['id']
organization['name'] = organization_row['name']
organization['alias'] = [organization_row['alias']]
organization_json = json.dumps(organization)
response = requests.put(f"{args.url}/fhir/Organization/{organization['id']}", data=organization_json,
headers={'Authorization': f"Basic {args.token}",
"Content-Type": "application/json"})
if response.status_code not in (201, 200):
raise Exception(
f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \norg={organization_json}')
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
fmh_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/familyMemberHistory.json'
).json()
row_parser = RowParser(values[0])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
fmh_row = row_parser.as_dict(row)
fmh = copy.deepcopy(fmh_model)
fmh['id'] = fmh_row['id']
fmh['status'] = fmh_row['status']
fmh['patient']['reference'] = f"Patient/{fmh_row['patient']}"
fmh['date'] = fmh_row['date']
fmh['note'][0]['text'] = fmh_row['note']
fmh_json = json.dumps(fmh, ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into familymemberhistory (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query, (fmh['id'], fmh_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
observation_pheno = requests.get('https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/observation_exemple_de_pheno.json').json()
observation_notes = requests.get('https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/observation_exemple_de_notes.json').json()
row_parser = RowParser(values[0])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
observation_row = row_parser.as_dict(row)
is_pheno = observation_row['code.text'] == 'phenotype observation'
observation = copy.deepcopy(observation_pheno) if is_pheno else copy.deepcopy(observation_notes)
observation['id'] = observation_row['id']
observation['effectiveDateTime'] = observation_row['effectiveDateTime']
observation['subject']['reference'] = f"Patient/{observation_row['subject']}"
observation['performer'][0]['reference'] = f"PractitionerRole/{observation_row['performer']}"
row_note = observation_row.get('note')
if row_note:
observation['note'][0]['text'] = row_note
else:
observation.pop('note')
if is_pheno:
(code, display) = observation_row['valueCodeableConcept.code et .display'].split(', ')
coding = observation['valueCodeableConcept']['coding'][0]
coding['code'] = code
coding['display'] = display
coding['system'] = observation_row['valueCodableConcept.coding.system']
interpretation_coding = observation['interpretation'][0]['coding'][0]
interpretation_coding['code'] = observation_row['interpretation.coding.code']
interpretation_coding['display'] = observation_row['interpretation.coding.display']
observation['interpretation'][0]['text'] = observation_row['interpretation.text']
observation_json = json.dumps(observation, ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into observation (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query, (observation['id'], observation_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
observation_pheno = requests.get('https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/observation_exemple_de_pheno.json').json()
observation_notes = requests.get('https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/observation_exemple_de_notes.json').json()
row_parser = RowParser(values[0])
for row in values[1:]:
observation_row = row_parser.as_dict(row)
is_pheno = observation_row['code.text'] == 'phenotype observation'
observation = copy.deepcopy(observation_pheno) if is_pheno else copy.deepcopy(observation_notes)
observation['id'] = observation_row['id']
observation['effectiveDateTime'] = observation_row['effectiveDateTime']
observation['subject']['reference'] = f"Patient/{observation_row['subject']}"
observation['performer'][0]['reference'] = f"Practitioner/{observation_row['performer']}"
row_note = observation_row.get('note')
if row_note:
observation['note'][0]['text'] = row_note
else:
observation.pop('note')
if is_pheno:
(code, display) = observation_row['valueCodeableConcept.code et .display'].split(', ')
coding = observation['valueCodeableConcept']['coding'][0]
coding['code'] = code
coding['display'] = display
coding['system'] = observation_row['valueCodableConcept.coding.system']
interpretation_coding = observation['interpretation'][0]['coding'][0]
interpretation_coding['code'] = observation_row['interpretation.coding.code']
interpretation_coding['display'] = observation_row['interpretation.coding.display']
observation['interpretation'][0]['text'] = observation_row['interpretation.text']
observation_json = json.dumps(observation)
response = requests.put(f"{args.url}/fhir/Observation/{observation['id']}", data=observation_json,
headers={'Authorization': f"Basic {args.token}", "Content-Type": "application/json"})
if response.status_code not in (201, 200):
raise Exception(f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nobservation={observation_json}')
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
clinical_impression_model = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/clinicalImpression.json'
).json()
row_parser = RowParser(values[0])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
clinical_impression_row = row_parser.as_dict(row)
clinical_impression = copy.deepcopy(clinical_impression_model)
clinical_impression['id'] = clinical_impression_row['id']
clinical_impression['status'] = clinical_impression_row[
'status']
clinical_impression[
'effectiveDateTime'] = clinical_impression_row[
'effectiveDateTime']
clinical_impression['subject'][
'reference'] = f"Patient/{clinical_impression_row['subject']}"
clinical_impression['assessor'][
'reference'] = f"PractitionerRole/{clinical_impression_row['assessor']}"
clinical_impression['extension'][0]['valueAge'][
'value'] = clinical_impression_row['valueAge']
clinical_impression['investigation'][0]['item'] = []
for r in row[5:9]:
clinical_impression['investigation'][0]['item'].extend([{
'reference':
r
}])
clinical_impression_json = json.dumps(clinical_impression,
ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into clinicalImpression (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(
insert_query,
(clinical_impression['id'], clinical_impression_json))
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
patient_mother = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/patient_exemple_mother.json').json()
patient_proband = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/patient_exemple_proband.json').json()
patient_proband['link'].pop(2) # No brothers or sisters
row_parser = RowParser(values[0][0:19])
for row in values[1:]:
participant_row = row_parser.as_dict(row[0:19])
is_proband = participant_row['isProband'] == 'true'
participant = copy.deepcopy(patient_proband) if is_proband else copy.deepcopy(patient_mother)
participant['id'] = participant_row['id']
for identifier in participant['identifier']:
if identifier['type']['coding'][0]['code'] == 'MR':
identifier['value'] = participant_row['MR']
if identifier['type']['coding'][0]['code'] == 'JHN':
identifier['value'] = participant_row['JHN']
birth_date = datetime.strptime(participant_row['birthdate'], '%y-%m-%d')
participant['birthDate'] = birth_date.strftime('%Y-%m-%d')
participant['active'] = bool(participant_row['active'])
participant['gender'] = participant_row['gender']
name = participant['name'][0]
name['use'] = participant_row['name.use']
name['family'] = participant_row['name.family']
name['given'] = [participant_row['name.given']]
participant['managingOrganization']['reference'] = \
f"Organization/{participant_row['managingOrganization']}"
participant['generalPractitioner'][0]['reference'] = \
f"PractitionerRole/{participant_row['generalPractitioner']}"
for extension in participant['extension'][0]['extension']:
if extension['url'] == 'familyId':
extension['valueId'] = participant_row['familyId']
if extension['url'] == 'ethnicity':
extension['valueCode'] = participant_row['ethnicity']
if extension['url'] == 'familyComposition':
extension['valueCode'] = participant_row['familyComposition']
if extension['url'] == 'isProband':
extension['valueBoolean'] = is_proband
if is_proband:
father = participant['link'][0]
mother = participant['link'][1]
if participant_row['FTH']:
father['other']['reference'] = f"Patient/{participant_row['FTH']}"
else:
participant['link'].remove(father)
if participant_row['MTH']:
mother['other']['reference'] = f"Patient/{participant_row['MTH']}"
else:
participant['link'].remove(mother)
participant_json = json.dumps(participant)
response = requests.put(f"{args.url}/fhir/Patient/{participant['id']}", data=participant_json,
headers={'Authorization': f"Basic {args.token}", "Content-Type": "application/json"})
if response.status_code not in (201, 200):
raise Exception(f'Aidobox did not return status code 201, status={response.status_code} \ntext={response.text} \nparticipant={participant_json}')
def main(args):
with spreadsheet(SAMPLE_SPREADSHEET_ID, SAMPLE_RANGE_NAME) as values:
patient_mother = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/patient_exemple_mother.json'
).json()
patient_proband = requests.get(
'https://raw.githubusercontent.com/cr-ste-justine/clin-FHIR/master/patient_exemple_proband.json'
).json()
patient_proband['link'].pop(2) # No brothers or sisters
row_parser = RowParser(values[0][0:19])
connection = get_connection(args)
with db_transaction(connection):
for row in values[1:]:
participant_row = row_parser.as_dict(row[0:19])
is_proband = participant_row['isProband'] == 'true'
participant = copy.deepcopy(
patient_proband) if is_proband else copy.deepcopy(
patient_mother)
participant['id'] = participant_row['id']
for identifier in participant['identifier']:
if identifier['type']['coding'][0]['code'] == 'MR':
identifier['value'] = participant_row['MR']
if identifier['type']['coding'][0]['code'] == 'JHN':
identifier['value'] = participant_row['JHN']
birth_date = datetime.strptime(participant_row['birthdate'],
'%y-%m-%d')
participant['birthDate'] = birth_date.strftime('%Y-%m-%d')
participant['active'] = participant_row['active']
participant['gender'] = participant_row['gender']
participant['name']['use'] = participant_row['name.use']
participant['name']['family'] = participant_row['name.family']
participant['name']['given'] = [participant_row['name.given']]
participant['managingOrganization']['reference'] = \
f"Organization/{participant_row['managingOrganization']}"
participant['generalPractitioner'][0]['reference'] = \
f"PractitionerRole/{participant_row['generalPractitioner']}"
for extension in participant['extension'][0]['extension']:
if extension['url'] == 'familyId':
extension['valueId'] = participant_row['familyId']
if extension['url'] == 'ethnicity':
extension['valueCode'] = participant_row['ethnicity']
if extension['url'] == 'familyComposition':
extension['valueCode'] = participant_row[
'familyComposition']
if extension['url'] == 'isProband':
extension['valueBoolean'] = participant_row[
'isProband']
if is_proband:
father = participant['link'][0]
mother = participant['link'][1]
if participant_row['FTH']:
father['other'][
'reference'] = f"Patient/{participant_row['FTH']}"
else:
participant['link'].remove(father)
if participant_row['MTH']:
mother['other'][
'reference'] = f"Patient/{participant_row['MTH']}"
else:
participant['link'].remove(mother)
participant_json = json.dumps(participant, ensure_ascii=False)
cursor = connection.cursor()
insert_query = "insert into patient (id, txid, resource, status) values (%s, 0, %s, 'created')"
cursor.execute(insert_query,
(participant['id'], participant_json))
