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 __init__(self, Organization=None):
"""
Uses fhirclient.models to create and post practitoner resource. Currently, using class variables.
:param smart: fhirclient.client.FHIRClient object.
:returns: practitioner id created by server
"""
if Organization is None:
self.Organization = generateorganization.GenerateOrganization(
).Organization
else:
self.Organization = Organization
Practitioner = pr.Practitioner()
PractitionerQualification = pr.PractitionerQualification()
CodeableConcept = cc.CodeableConcept()
Coding = c.Coding()
Coding.code = random.choice(['MD', 'DO'])
Coding.system = 'https://www.hl7.org/fhir/v2/0360/2.7/index.html'
CodeableConcept.coding = [Coding]
PractitionerQualification.code = CodeableConcept
Practitioner.qualification = [PractitionerQualification]
name = hn.HumanName()
self.family, self.given, Practitioner.gender = self._generate_person()
name.family = [self.family]
name.given = [self.given]
Practitioner.name = name
self._validate(Practitioner)
self.response = self.post_resource(Practitioner)
Practitioner.id = self._extract_id()
self.Practitioner = Practitioner
print(self)
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 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 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 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 fhir_gen_humanname(use='official', first_name=None, last_name=None, middle_name=None, suffix=None, prefix=None):
"""
Helper function to generate a fhirclient HumanName class object from standard person attributes
:param use:
:param first_name:
String representation of person first name
:param last_name:
String representation of person last name
:param middle_name:
String representation of person middle name
:param suffix:
String representation of name suffix
:param prefix:
String representation of name prefix
:return:
fhirclient HumanName class object
"""
hn = humanname.HumanName()
if use:
hn.use = use
hn.family = last_name
given_name = []
if first_name:
given_name.append(first_name)
if middle_name:
given_name.append(middle_name)
if given_name:
hn.given = given_name
if suffix:
hn.suffix = [suffix]
if prefix:
hn.prefix = [prefix]
hn.text = '{}{}{}{}'.format(last_name + ',' if last_name else '',
' ' + first_name if first_name else '',
' ' + middle_name if middle_name else '',
' ' + suffix if suffix else '')
return hn
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()
art.system = 'http://system1/artnumber'
art.value = row['art_number']
def createPractitioner(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.practitioner as p
# set practitioner id as provider licence numberS
p = p.Practitioner({'id': record[provi]})
# resolve name
import fhirclient.models.humanname as hn
name = hn.HumanName()
name.given = [record[fnamei]]
name.family = [record[lnamei]]
p.name = name
# 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)
birthdate = birthdate[-4:] + "-" + birthdate[0:bsep1] + "-" + birthdate[
bsep1 + 1:bsep2]
p.birthDate = fhirclient.models.fhirdate.FHIRDate(birthdate)
# build and resolve death date
tz = "00:00:00-0600" # Utah is in the Mountain Time Zone, setting time as midnight.
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, tz)
deathdate = fhirclient.models.fhirdate.FHIRDate(deathdate)
# Create period
import fhirclient.models.period as per
per = per.Period()
per.start = deathdate
import fhirclient.models.fhirreference as ref
location = ref.FHIRReference()
location.reference = 'http://fhir.ehoth.net/deceased'
location.display = 'deceased'
# Create role
import fhirclient.models.practitioner as r
role = r.PractitionerPractitionerRole()
role.healthcareservice = 'deceased'
role.location = [location]
role.period = per
role.managingOrganization = location
#print role.as_json()
p.practitionerRole = [role]
# return practitioner.
return p
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 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 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')