def patient_to_individual(obj):
""" FHIR Patient to Individual. """
patient = p.Patient(obj)
individual = {"id": patient.id}
if patient.identifier:
individual["alternate_ids"] = [
alternate_id.value for alternate_id in patient.identifier
]
gender_to_sex = {
"male": "MALE",
"female": "FEMALE",
"other": "OTHER_SEX",
"unknown": "UNKNOWN_SEX"
}
if patient.gender:
individual["sex"] = gender_to_sex[patient.gender]
if patient.birthDate:
individual["date_of_birth"] = patient.birthDate.isostring
if patient.active:
individual["active"] = patient.active
if patient.deceasedBoolean:
individual["deceased"] = patient.deceasedBoolean
individual["extra_properties"] = patient.as_json()
return individual
def create_patient(base_url, project_id, cloud_region, dataset_id,
fhir_store_id):
"""Creates a new Patient resource in a FHIR store."""
url = "{}/projects/{}/locations/{}".format(base_url, project_id,
cloud_region)
fhir_store_path = "{}/datasets/{}/fhirStores/{}/fhir/Patient".format(
url, dataset_id, fhir_store_id)
# Make an authenticated API request
session = get_session()
headers = {"Content-Type": "application/fhir+json;charset=utf-8"}
patient = p.Patient({'id': 'patient-1'})
# body = {
# "name": [{"use": "official", "family": "Smith", "given": ["Darcy"]}],
# "gender": "female",
# "birthDate": "1970-01-01",
# "resourceType": "Patient",
# }
body = patient.as_json()
response = session.post(fhir_store_path, headers=headers, json=body)
response.raise_for_status()
resource = response.json()
print("Created Patient resource with ID {}".format(resource["id"]))
return response
def patient_list():
start = request.args.get('start', 0)
length = request.args.get('length', 100)
start = int(start)
length = int(length)
count = db.engine.execute("select count(*) from T_Patients").scalar()
result = db.engine.execute("select * from T_Patients limit %d, %d" %
(start, length))
plist = []
total = count
for row in result:
patient = p.Patient({'id': row['pat_id']})
name = hn.HumanName()
name.given = [row['pat_first']]
name.family = row['pat_last']
patient.name = [name]
address = addr.Address()
address.city = row['pat_city']
address.state = row['pat_state']
address.postalCode = row['pat_zip']
address.district = row['pat_address']
patient.address = [address]
patient.gender = row['pat_gender']
patient.birthDate = fd.FHIRDate(
datetime.strftime(row['pat_birthdate'], "%Y-%m-%d"))
# patient.maritalStatus = row['pat_marital']
plist.append(patient.as_json())
return jsonify(results=plist, total=total)
def patient(id):
# https://{FHIR Base URL}/Patient/{id}?
# name={name}&
# family={family name}&
# gender={gender}&
# _format=json
# TODO: query params
name = request.args.get('name', None)
family = request.args.get('family', None)
gender = request.args.get('gender', None)
# TODO: connect to database to search patient
result = db.engine.execute("select * from T_Patients limit 1")
names = []
for row in result:
patient = p.Patient({'id': row['pat_id']})
name = hn.HumanName()
name.given = [row['pat_first']]
name.family = row['pat_last']
patient.name = [name]
address = addr.Address()
address.city = row['pat_city']
address.state = row['pat_state']
address.postalCode = row['pat_zip']
address.district = row['pat_address']
patient.address = [address]
patient.gender = row['pat_gender']
patient.birthDate = fd.FHIRDate(
datetime.strftime(row['pat_birthdate'], "%Y-%m-%d"))
patient.maritalStatus = row['pat_marital']
return jsonify(result=patient.as_json())
def addPatientToServer(self, given_name, family_name):
patient = p.Patient()
name = hn.HumanName()
name.given = [given_name]
name.family = [family_name]
patient.name = [name]
result_json = patient.create(self.smart.server)
patient.id = self.getCreatedId(result_json)
return patient.id
def fhir():
import fhirclient.models.patient as p
import fhirclient.models.humanname as hn
patient = p.Patient({'id': 'patient-1'})
print(patient.id)
# prints `patient-1`
name = hn.HumanName()
name.given = ['Peter']
name.family = 'Parker'
patient.name = [name]
print(mongodb)
print(patient.as_json())
dict01 = patient.as_json()
ret = mongodb.a.insert_one(dict01)
print(ret)
ret = mongodb.a.find()
for i in ret:
print(i)
print('111111111111111111')
import json
import fhirclient.models.patient as p
with open('/home/python/Desktop/odk/patient-example.json', 'r') as h:
pjs = json.load(h)
patient = p.Patient(pjs)
dict02 = patient.as_json()
ret = mongodb.a.insert_one(dict02)
print(ret)
ret = mongodb.a.find()
for i in ret:
print(i)
print('2222222222222222')
print(patient.name[0].given)
print(patient.name)
print(patient.gender)
print(patient.photo)
print(patient.address)
print("-------------------------")
# prints patient's given name array in the first `name` property
return ret_data(200, '请求成功', 1000)
def read_json_patient(path):
"""
INPUTS:
path:
path to example json file
OUTPUT:
the patient object
"""
with open(path) as data_file:
return patient.Patient(json.load(data_file))
def individual_to_fhir(obj):
"""Converts Individual to FHIR Patient.
:param obj: Individual json
:return: FHIR Patient json
"""
# first validate if phenopackets object is well-formed
schema_path = os.path.join(SCHEMA_PATH, 'individual_schema.json')
try:
validate_schema(schema_path, obj)
except jsonschema.exceptions.ValidationError:
raise Exception("The individual object is not valid.")
patient = p.Patient()
patient.id = obj['id']
patient.birthDate = fhirdate.FHIRDate(obj.get('dateOfBirth', None))
patient.gender = obj.get('sex', None)
patient.active = obj.get('active', None)
patient.deceasedBoolean = obj.get('deceased', None)
patient.extension = list()
# age
if 'age' in obj:
age_extension = age_to_fhir(
obj, PHENOPACKETS_ON_FHIR_MAPPING['individual']['age'], 'age')
patient.extension.append(age_extension)
# karyotypic_sex
if 'karyotypicSex' in obj:
karyotypic_sex_extension = extension.Extension()
karyotypic_sex_extension.url = PHENOPACKETS_ON_FHIR_MAPPING[
'individual']['karyotypicSex']['url']
karyotypic_sex_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
karyotypic_sex_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('karyotypicSex', None)
coding.code = obj.get('karyotypicSex', None)
coding.system = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'karyotypicSex']['system']
karyotypic_sex_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(karyotypic_sex_extension)
# taxonomy
if 'taxonomy' in obj:
taxonomy_extension = extension.Extension()
taxonomy_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'taxonomy']
taxonomy_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
taxonomy_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('taxonomy', None).get('label', None)
coding.code = obj.get('taxonomy', None).get('id', None)
taxonomy_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(taxonomy_extension)
return patient.as_json()
def import_patient(self, res, options):
"""Import a single patient"""
verbosity = options['verbosity']
strict = options['strict']
force = options['force']
f_patient = pat.Patient(res, strict=strict)
# OC: Normal logging for progress. Do not write to stdout or stderr as some sample code for manage commands does.
logger.info(f'Importing {f_patient}')
official_name = [x for x in f_patient.name if x.use == 'official'][0] # pylint: disable=E1133
# TODO: Pull type code from settings
primary_identifier = [
x for x in f_patient.identifier if self.hastypecode(x, 'MR')
][0] # pylint: disable=E1133
d_patient = Patient(id=f_patient.id,
identifier=primary_identifier.value,
name=self.get_humanname(official_name),
gender=f_patient.gender,
birth_date=f_patient.birthDate.isostring)
# TODO: This is currently not working as it should. Problems with updating existing entries and created_at NOT NULL constraints
# Do I need to .create() the object first, before saving it???
try:
d_patient.full_clean(validate_unique=False)
except ValidationError as err:
# OC: Error logging with exceptions will also be sent to telemetry
logger.error('Validation failed', exc_info=True)
try:
d_patient.save()
except IntegrityError as err:
logger.error('Saving to database failed', exc_info=True)
# TODO: This should use bulk_create
for f_patid in f_patient.identifier:
d_patid = PatientIdentifier(type_code=self.get_codeableconcept(
f_patid.type),
system=f_patid.system,
value=f_patid.value,
subject_id=f_patient.id)
try:
d_patid.save()
except IntegrityError as err:
logger.error('Saving patient identifier to database failed',
exc_info=True)
def mkpatient():
"""
make a Patient resource using the data model
"""
import fhirclient.models.patient as p
import fhirclient.models.humanname as hn
patient = p.Patient()
# patient.id = 'patient-1'
# print(patient.id)
# prints `patient-1`
name = hn.HumanName()
name.given = ['Peter']
name.family = 'Parker'
patient.name = [name]
# print(json.dumps(patient.as_json(), indent=4))
patient.uuid = uuid.uuid4().urn
print(patient.uuid)
return (patient)
def to_fhir_obj(self):
patient = p.Patient()
identifier = p.identifier.Identifier()
identifier.value = self.id
patient.identifier = [identifier]
name = hn.HumanName()
name.given = [self.first_name]
name.family = self.last_name
patient.name = [name]
patient.gender = self.sex
patient.birthDate = fd.FHIRDate(str(datetime.utcnow().date()))
# prints patient's JSON representation, now with id and name
address = a.Address()
address.state = self.state
address.district = self.district
patient.address = [address]
json = patient.as_json()
return patient
def fhir_patient(obj):
""" Converts Individual to FHIR Patient. """
patient = p.Patient()
patient.id = obj['id']
patient.birthDate = fhirdate.FHIRDate(obj.get('date_of_birth', None))
patient.gender = obj.get('sex', None)
patient.active = obj.get('active', None)
patient.deceasedBoolean = obj.get('deceased', None)
patient.extension = list()
# age
if 'age' in obj.keys():
age_extension = fhir_age(
obj, PHENOPACKETS_ON_FHIR_MAPPING['individual']['age'], 'age')
patient.extension.append(age_extension)
# karyotypic_sex
karyotypic_sex_extension = extension.Extension()
karyotypic_sex_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'karyotypic_sex']['url']
karyotypic_sex_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
karyotypic_sex_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('karyotypic_sex', None)
coding.code = obj.get('karyotypic_sex', None)
coding.system = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'karyotypic_sex']['system']
karyotypic_sex_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(karyotypic_sex_extension)
# taxonomy
if 'taxonomy' in obj.keys():
taxonomy_extension = extension.Extension()
taxonomy_extension.url = PHENOPACKETS_ON_FHIR_MAPPING['individual'][
'taxonomy']
taxonomy_extension.valueCodeableConcept = codeableconcept.CodeableConcept(
)
taxonomy_extension.valueCodeableConcept.coding = list()
coding = c.Coding()
coding.display = obj.get('taxonomy', None).get('label', None)
coding.code = obj.get('taxonomy', None).get('id', None)
taxonomy_extension.valueCodeableConcept.coding.append(coding)
patient.extension.append(taxonomy_extension)
return patient.as_json()
def PatientCreate(client):
print("PatCreate")
jsondict = {
"resourceType": "Patient",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Ryan</div>"
},
"active": True,
"name": [{
"use": "official",
"family": "Murky",
"given": ["Ryan"]
}],
"gender": "male",
"birthDate": "1974-12-25",
"deceasedBoolean": False
}
return P.Patient(jsondict, strict=False).create(client.server)
from fhirclient import client
settings = {'app_id': 'test_app', 'api_base': 'http://test.fhir.org/r4/'}
## REMOVE ID FIELD
gen_json = {
"resourceType": "Patient",
"name": [{
"use": "official",
"given": ["Peter"],
"family": "Man"
}],
"gender": "male"
}
smart = client.FHIRClient(settings=settings)
import fhirclient.models.patient as p
patient_gen = p.Patient(gen_json)
#Change gender to female
patient_gen.gender = "female"
print("Preview resource as JSON\n")
print(patient_gen.as_json())
print("\n")
print("Return from FHIR test server\n")
pt1_created = patient_gen.create(smart.server)
print(pt1_created)
def read_patient(data: dict) -> patient.Patient:
return patient.Patient(data, False)
def _generate_patient_fhir_object(self):
"""Creates a test patient using fhirclient.models."""
Patient = p.Patient()
HumanName = hn.HumanName()
HumanName.family = [self.name_last]
HumanName.given = [self.name_first]
Patient.name = [HumanName]
Patient.gender = self.gender
birthDay = fd.FHIRDate()
birthDay.date = self.bday
Patient.birthDate = birthDay
Address = a.Address()
Address.country = 'USA'
Address.postalCode = self.zipcode
Address.state = self.state
Address.city = self.city
Address.line = [f'{self.address_number} {self.address_street}']
Address.use = 'home'
Address.type = 'postal'
Patient.active = True
Patient.address = [Address]
PatientCommunication = p.PatientCommunication()
PatientCommunication.language = self._create_FHIRCodeableConcept(
'en-US', 'urn:ietf:bcp:47', 'English')
# PatientCommunication.language = self._create_FHIRCodeableConcept('en-US','http://hl7.org/fhir/ValueSet/languages','English')
PatientCommunication.preferred = True
Patient.communication = [PatientCommunication]
race = e.Extension()
race.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race'
us_core = e.Extension()
us_core.url = 'ombCategory'
us_core.valueCoding = self._create_FHIRCoding(
self.race_code, 'urn:oid:2.16.840.1.113883.6.238',
self.race_description)
race_detailed = e.Extension()
race_detailed.url = 'detailed'
race_detailed.valueCoding = self._create_FHIRCoding(
self.race_code, 'urn:oid:2.16.840.1.113883.6.238',
self.race_description)
race_text = e.Extension()
race_text.url = 'text'
race_text.valueString = self.race_description
race.extension = [us_core, race_detailed, race_text]
ethnicity = e.Extension()
ethnicity.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'
us_core = e.Extension()
us_core.url = 'ombCategory'
us_core.valueCoding = self._create_FHIRCoding(
self.ethnicity_code, 'urn:oid:2.16.840.1.113883.6.238',
self.ethnicity_description)
ethnicity_text = e.Extension()
ethnicity_text.url = 'text'
ethnicity_text.valueString = self.ethnicity_description
ethnicity.extension = [us_core, ethnicity_text]
Patient.extension = [race, ethnicity]
Patient.managingOrganization = self._create_FHIRReference(
self.Organization)
self._validate(Patient)
self.response = self.post_resource(Patient)
Patient.id = self._extract_id()
self.Patient = Patient
print(self)
df_a['date_of_birth'] = pd.to_datetime(df_a['date_of_birth'], errors='coerce')
# now back into str or fhirdate will complain
df_a['date_of_birth'] = df_a['date_of_birth'].apply(
lambda x: x.strftime('%Y-%m-%d') if not pd.isnull(x) else '')
print(df_a.head())
# In[6]:
# default server/path
server = "https://localhost:3000/Patient"
# 3 records, modify if more are required
limit = 100
for index, row in itertools.islice(df_a.iterrows(), limit):
# for index, row in df_a.iterrows():
patient = p.Patient() # not using rec_id as pandas id, leaving empty
patient.gender = row['sex']
name = hn.HumanName()
name.given = [row['given_name']]
name.family = row['surname']
name.use = 'official'
patient.name = [name]
phone = cp.ContactPoint()
phone.system = 'phone'
phone.value = row['phone_number']
patient.telecom = [phone]
patient.birthDate = fd.FHIRDate(row['date_of_birth'])
emr = ident.Identifier()
emr.system = 'http://clientregistry.org/openmrs'
emr.value = row['rec_id']
art = ident.Identifier()
message=
'Program can\'t run without a server URL. Are you sure you want to continue?'
)
if warning:
flag = False
exit()
else:
flag = False
else:
flag = False
# Post example patient and get ID
with open('Patient-example.json', 'r') as f:
data = json.load(f)
fhir_pat = patient.Patient(data)
low_val_col = 'Einheit_Wert_min'
high_val_col = 'Einheit_Wert_max'
numerical_cols = [low_val_col, high_val_col]
col_names = ['ASK_Substanz_allg']
coding_col_names = [
'UNII_Substanz_allg', 'ASK_Substanz_allg', 'CAS_Substanz_allg'
]
coding_display_col = 'Substanz_allg_engl_INN_oder_sonst'
route_code_col = 'Routes and Methods of Administration - Concept Code'
route_display_col = 'Routes and Methods of Administration - Term'
ops_text_col = 'opsText'
unit_code_col = 'UCUM-Code'
unit_col = 'UCUM-Description'
ops_code_col = 'opsCode'
import fhirclient.models.patient as patient_model
import json
if __name__ == '__main__':
patient_json = json.load(open('patient.json'))
patient = patient_model.Patient(patient_json)
def get_dashboard_FHIR_current_data():
settings = {
'app_id': 'LGBTQCovidReporting',
'api_base': 'https://r4.smarthealthit.org'
}
smart = client.FHIRClient(settings=settings)
covid_historic_county_data_url = 'https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv'
lgbt_population_data_url = 'https://raw.githubusercontent.com/PatrickGood/lgbt-covid-data/main/lgbt_populations.csv'
state_abbr_data_url = 'https://raw.githubusercontent.com/PatrickGood/lgbt-covid-data/main/state_abbreviations.csv'
covid_historic_county_data = pd.read_csv(covid_historic_county_data_url, dtype={"fips": str})
yesterday_date = str((pd.datetime.utcnow() - timedelta(2)).date())
# latest_covid_historic_county_data = covid_historic_county_data[covid_historic_county_data['date'] == yesterday_date]
lgbt_population_data = pd.read_csv(lgbt_population_data_url, thousands=',')[["STATE", "LGBT POPULATION DENSITY"]]
state_abbreviations = pd.read_csv(state_abbr_data_url)
covid_historic_county_data['state_lower'] = covid_historic_county_data['state'].str.lower()
lgbt_population_data['state_lower'] = lgbt_population_data['STATE'].str.lower()
lgbt_covid_data_history = pd.merge(covid_historic_county_data, lgbt_population_data, how='inner', on='state_lower')
lgbt_covid_data_history['lgbt_cases'] = lgbt_covid_data_history['cases'] * lgbt_covid_data_history[
'LGBT POPULATION DENSITY'] // 100
lgbt_covid_data_history['lgbt_deaths'] = lgbt_covid_data_history['deaths'] * lgbt_covid_data_history[
'LGBT POPULATION DENSITY'] // 100
lgbt_covid_data_history.dropna(inplace=True)
lgbt_covid_data_history = lgbt_covid_data_history.astype(({'lgbt_cases': 'int32', 'lgbt_deaths': 'int32'}))
lgbt_covid_data_history = pd.merge(lgbt_covid_data_history, state_abbreviations, how="inner", on='state')
current_columns = ['state', 'county', 'abbreviation', 'fips', 'cases', 'lgbt_cases', 'deaths', 'lgbt_deaths',
'LGBT POPULATION DENSITY']
final_lgbt_covid_data_current = lgbt_covid_data_history[lgbt_covid_data_history['date'] == yesterday_date]
final_lgbt_covid_data_current = final_lgbt_covid_data_current[current_columns].sort_values(by=['fips'])
final_current_columns = ['state', 'county', 'abbreviation', 'fips', 'lgbt_cases', 'cases']
final_lgbt_covid_data_current = final_lgbt_covid_data_current[final_current_columns].sort_values(by=['fips'])
fip_list =[]
fip_data_url="https://raw.githubusercontent.com/plotly/datasets/master/geojson-counties-fips.json"
# python 3.x
r = requests.get(fip_data_url)
for item in r.json()['features']:
item_properties = item['properties']
fip_list.append([item['id'], item_properties['STATE'], item_properties['COUNTY'], item_properties['NAME']])
fip_data_pd = pd.DataFrame(fip_list, columns=['id', 'state_id', 'county_id', 'county'])
fips_state_data_url = 'https://raw.githubusercontent.com/PatrickGood/lgbt-covid-data/main/fips_state.csv'
fips_state_data_df = pd.read_csv(fips_state_data_url, dtype={"fips_code": str}, error_bad_lines=False)
fips_df = pd.merge(fip_data_pd, fips_state_data_df, 'inner', left_on='state_id', right_on='fips_code')
fips_df['lookup_key'] = fips_df['state'] + fips_df['county']
query_url ='/Patient?_has:Condition:patient:code=http://snomed.info/sct|840539006&_has:Condition:patient:verification-status=http://terminology.hl7.org/CodeSystem/condition-ver-status|confirmed&_has:Observation:patient:code=http://loinc.org|76690-7&_has:Observation:patient:value-string=Other,Homosexual,Bisexual&_count=250'
result = smart.server.request_json(query_url)
fhir_positive_lgbt_cases_df = pd.DataFrame(columns=['key', 'count'])
fhir_positive_lgbt_cases_lst = []
#p.Patient(smart.server.request_json(bundle_url_next)['entry'][000]['resource'])
if result is not None and 'entry' in result.keys():
for entry in result['entry']:
if entry['resource']['resourceType'] == 'Patient':
patient = p.Patient(entry['resource'])
state = None
district = None
if patient.address is not None and len(patient.address) > 0:
address = patient.address[0]
if address.state:
state = address.state
if address.district:
district = address.district
key = state + district
fhir_positive_lgbt_cases_lst.append([key, 1])
while(any(obj['relation'] == 'next' for obj in result['link']) and len(fhir_positive_lgbt_cases_lst) < 1000):
query_url = result['link'][-1]['url']
result = smart.server.request_json(query_url)
if result is not None and 'entry' in result.keys():
for entry in result['entry']:
if entry['resource']['resourceType'] == 'Patient':
patient = p.Patient(entry['resource'])
state = None
district = None
if patient.address is not None and len(patient.address) > 0:
address = patient.address[0]
if address.state:
state = address.state
if address.district:
district = address.district
key = state + district
fhir_positive_lgbt_cases_lst.append([key, 1])
fhir_positive_lgbt_cases_df = pd.DataFrame(fhir_positive_lgbt_cases_lst, columns=['key', 'count'])
fhir_positive_lgbt_cases_fips_df = pd.merge(fhir_positive_lgbt_cases_df, fips_df, how='inner',
left_on='key', right_on='lookup_key')
final_stats = fhir_positive_lgbt_cases_fips_df.groupby('id')['count'].sum()
final_stats_states = pd.merge(final_stats, fips_df, how='inner', on='id')
final_stats_states = final_stats_states[['id', 'count', 'fips_code', 'post_code', 'lookup_key']]
final_stats_states_population = pd.merge(final_stats_states, final_lgbt_covid_data_current, how='inner',
left_on='id', right_on='fips')
final_data_frame = final_stats_states_population[
['fips', 'state', 'county', 'post_code', 'count', 'cases', 'lgbt_cases']]
return final_data_frame
else:
return pd.DataFrame(columns=[['fips', 'state', 'county', 'post_code', 'count', 'cases', 'lgbt_cases']])
def patient():
user = get_jwt_identity()
print("user:"******"name_given"]]
name.family = request.form["name_family"]
patient.name = [name]
# 设置性别 只能是male或者female
patient.gender = request.form["gender"] if request.form[
"gender"] == "男" or request.form["女"] == "female" else ""
# 设置生日
patient.birthDate = fdate.FHIRDate().with_json(
request.form["birthDate"])
# 设置逻辑删除
patient.active = True
# 设置地址
patient.address = [ad.Address({"city": request.form["city"]})]
ret = mongodb.basic_information.insert_one(patient.as_json())
print(ret)
return ret_data(200, '请求成功', 1003)
else:
return ret_data(200, "请求成功", 2008)
elif request.method == 'GET':
dict01 = mongodb.basic_information.find_one({
'id': str(user),
'active': True
})
if dict01 is None:
return ret_data(200, '请求成功', 2011)
dict02 = {}
del dict01['_id']
dict02['city'] = dict01['address'][0]['city']
dict02['birthDate'] = dict01['birthDate']
dict02['gender'] = dict01['gender']
dict02['name'] = str(dict01['name'][0]['family']) + str(
dict01['name'][0]['given'][0])
return ret_data(200, '请求成功', 1005, **dict02)
elif request.method == 'DELETE':
count = 0
for i in patientList:
print(i['active'])
if i['active'] is True:
count += 1
if count >= 1:
mongodb.basic_information.update_one(
{
'id': str(user),
'active': True
}, {'$set': {
'active': False
}})
# mongodb.basic_information.delete_one({'id':str(user)})
return ret_data(200, '请求成功', 1004)
else:
return ret_data(200, '请求成功', 2010)
elif request.method == 'PUT':
count = 0
for i in patientList:
print(i['active'])
if i['active'] is True:
count += 1
if count == 1:
patient = p.Patient({'id': str(user)})
# 设置名字
name = hn.HumanName()
name.given = [request.form["name_given"]]
name.family = request.form["name_family"]
patient.name = [name]
# 设置性别 只能是male或者female
patient.gender = request.form["gender"] if request.form[
"gender"] == "男" or request.form["女"] == "female" else ""
# 设置生日
patient.birthDate = fdate.FHIRDate().with_json(
request.form["birthDate"])
# 设置逻辑删除
patient.active = True
# 设置地址
patient.address = [ad.Address({"city": request.form["city"]})]
mongodb.basic_information.update_one({'id': str(user)},
{'$set': patient.as_json()})
return ret_data(200, '请求成功', 1006)
else:
return ret_data(200, '请求成功', 2009)
return ret_data(200, '请求成功', 1000, test='hello world')
# Make an authenticated API request
session = get_session()
headers = {"Content-Type": "application/fhir+json;charset=utf-8"}
patient = p.Patient({'id': 'patient-1'})
# body = {
# "name": [{"use": "official", "family": "Smith", "given": ["Darcy"]}],
# "gender": "female",
# "birthDate": "1970-01-01",
# "resourceType": "Patient",
# }
body = patient.as_json()
response = session.post(fhir_store_path, headers=headers, json=body)
response.raise_for_status()
resource = response.json()
print("Created Patient resource with ID {}".format(resource["id"]))
return response
patient = p.Patient({'id': 'patient-1'})
print(patient.as_json())
create_patient(_BASE_URL, PROJECT_ID, CLOUD_REGION, DATASET_ID, FHIR_STORE)
from fhirclient import client
settings = {'app_id': 'test_app', 'api_base': 'http://test.fhir.org/r4/'}
smart = client.FHIRClient(settings=settings)
import fhirclient.models.patient as p
import fhirclient.models.humanname as hn
import fhirclient.models.contactpoint as cp
patient1 = p.Patient()
contact = cp.ContactPoint()
contact.system = 'phone'
contact.value = '00999811119'
patient1.telecom = [contact]
name = hn.HumanName()
name.given = ['Peter2']
name.family = 'Man'
patient1.name = [name]
patient1.gender = 'male'
#This won't show as it's not part of the FHIR spec
patient1.gender2 = 'male'
print("Preview resource as JSON\n")
print(patient1.as_json())
print("\n")
print("Return from FHIR test server\n")
pt1_created = patient1.create(smart.server)
def createPatient(dohmpifield, record):
#extract fields from dohmpi from database
field = []
for i in range(len(dohmpifield)):
f1, = dohmpifield[i] # dohmpi loads from db as a list of onetuples.
field.append(f1) # we make a traditional list to refer to.
fnamei = field.index('provider_first')
lnamei = field.index('provider_last')
genderi = field.index('provider_gender_cd')
deathyi = field.index('deathccyy')
deathmi = field.index('deathmm')
deathdi = field.index('deathdd')
birthi = field.index('provider_dob_dob')
provi = field.index('provider_license_no')
# record is one record from the postgres db
import fhirclient.models.patient as p
# set patient id as provider licence numberS
pid = record[provi]
p = p.Patient({})
import fhirclient.models.identifier as idf
identifier = idf.Identifier()
identifier.value = pid
p.identifier = [identifier]
# resolve name
import fhirclient.models.humanname as hn
name = hn.HumanName()
name.given = [record[fnamei]]
name.family = [record[lnamei]]
p.name = [name]
#[name.family, name.given]
# resolve gender
if (record[genderi] == "1"):
p.gender = 'male'
elif (record[genderi] == "2"):
p.gender = 'female'
else:
p.gender = 'unknown'
# build and resolve birthdate
birthdate = record[birthi]
bsep1 = birthdate.index("/")
bsep2 = birthdate.index("/", bsep1 + 1)
year = birthdate[-4:]
month = birthdate[0:bsep1]
if (len(month) < 2):
month = "0%s" % month
date = birthdate[bsep1 + 1:bsep2]
if (len(date) < 2):
date = "0%s" % date
birthdate = year + "-" + month + "-" + date
p.birthDate = fhirclient.models.fhirdate.FHIRDate(birthdate)
# build and resolve death date
tt = "12:00:00" #Setting time to noon
yyyy = record[deathyi]
mm = record[deathmi]
if (len(mm) < 2):
mm = "0%s" % mm
dd = record[deathdi]
if (len(dd) < 2):
dd = "0%s" % dd
deathdate = "%s-%s-%sT%s" % (yyyy, mm, dd, tt)
deathdate = fhirclient.models.fhirdate.FHIRDate(deathdate)
# Create period
import fhirclient.models.period as per
per = per.Period()
per.start = deathdate
p.deceasedBoolean = True
p.deceasedDateTime = deathdate
return p
def postPatient(name):
pat = p.Patient({"name": [{"use": name}]})
result = p.Patient.create(
pat, smart.server)['issue'][0]['diagnostics'].split('/')[1]
return 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
