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 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 build_location(ct_loc):
"""
Turn a Location (ct.gov) to a Location (fhir)
:param Location ct_loc: location from ct.gov
"""
l = location.Location()
if not ct_loc.facility.name:
print("Missing facility name: ")
name = "{}-{}".format(ct_loc.facility.address.city,
ct_loc.facility.address.country)
else:
name = ct_loc.facility.name
l.id = quote(name)
l.name = ct_loc.facility.name
a = address.Address(
dict(city=ct_loc.facility.address.city,
country=ct_loc.facility.address.country,
postalCode=ct_loc.facility.address.zip,
type='both'))
l.address = a
return l
def __init__(self):
"""
Creates, validates, and posts an Organization FHIR resource. Currently, using class variables.
:returns: practitioner id created by server
"""
Organization = org.Organization()
Organization.active = True
Organization.name = self.organization_name
Address = a.Address()
Address.line = self.organization_line
Address.city = self.organization_city
Address.postalCode = self.organization_postalCode
Address.state = self.organization_state
Organization.address = [Address]
ContactPoint = cp.ContactPoint()
ContactPoint.system = 'phone'
ContactPoint.value = self.organization_phone
Organization.telecom = [ContactPoint]
self._validate(Organization)
self.response = self.post_resource(Organization)
Organization.id = self._extract_id()
self.Organization = Organization
print(self)
def __init__(self):
"""
Uses fhirclient.models to create and post location resource. Currently, using class variables.
:returns: GenerateLocation object that has Location object as an attribute.
"""
Location = l.Location()
LocationPosition = l.LocationPosition()
Address = a.Address()
Location.status = 'active'
Location.name = self.location_name
Address.line = self.location_line
Address.city = self.location_city
Address.postalCode = self.location_postalCode
Address.state = self.location_state
Location.address = Address
LocationPosition.latitude = self.location_latitude
LocationPosition.longitude = self.location_longitude
Location.position = LocationPosition
# self._validate(Location)
self.response = self.post_resource(Location)
Location.id = self._extract_id()
self.Location = Location
print(self)
def create_fhir_object(self):
"""
method: create_fhir_object()
Create a fhir-client.model.address.Adress object and stores to the self.fhir attribute
:return:
None
"""
# Initialize FHIRclient Address object
# Assign Address object attributes to FHIRclient Address object
fa = fhir_address.Address()
if self.address1:
fa.line = [self.address1]
if self.address2:
fa.line.append(self.address2)
if self.city:
fa.city = self.city
if self.state:
fa.state = self.state
if self.zipcode:
fa.postalCode = self.zipcode
fa.text = self.formatted_address()
if isinstance(self.start_date, date) or isinstance(self.end_date, date):
p = period.Period()
if self.start_date:
fhirdate_start = fhirdate.FHIRDate()
fhirdate_start.date = self.start_date
p.start = fhirdate_start
if self.end_date:
fhirdate_end = fhirdate.FHIRDate()
fhirdate_end.date = self.end_date
p.end = fhirdate_end
fa.period = p
if self.use:
fa.use = self.use.lower()
if self.is_postal and self.is_physical:
fa.type = 'both'
elif self.is_postal:
fa.type = 'postal'
elif self.is_physical:
fa.type = 'physical'
if self.district:
fa.district = self.district
if self.country:
fa.country = self.country
self.fhir = fa
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)
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')