def get_smart(self):
state = self.request.session.get('state')
if state:
return client.FHIRClient(state=state, save_func=self.save_state)
else:
return client.FHIRClient(settings=smart_defaults,
save_func=self.save_state)
def _get_smart():
state = session.get('state')
if state:
return client.FHIRClient(state=state, save_func=_save_state)
else:
return client.FHIRClient(settings=smart_defaults,
save_func=_save_state)
def _get_epic():
state = session.get('epic_state')
if state:
return client.FHIRClient(state=state, save_func=_save_epic_state)
else:
return client.FHIRClient(settings=epic_defaults,
save_func=_save_epic_state)
def launch(request):
iss = request.GET.get('iss')
if iss:
_ENDPOINT.update({
'api_base': iss,
'auth_type': 'oauth2',
'patient_id': None,
'launch_token': request.GET.get('launch'),
'redirect_uri': _ENDPOINT['app_base'] + "authorize.html"
})
smart = client.FHIRClient(settings=_ENDPOINT)
auth_url = smart.authorize_url
request.session['client_state'] = smart.state # TO DO: encrypt the state to protect app secrets
return redirect(auth_url)
fhirServiceUrl = request.GET.get('fhirServiceUrl')
if fhirServiceUrl:
_ENDPOINT['api_base'] = fhirServiceUrl
_ENDPOINT['patient_id'] = request.GET.get('patientId')
_ENDPOINT['auth_type'] = 'none'
smart = client.FHIRClient(settings=_ENDPOINT)
redirect_url = _ENDPOINT['app_base'] + "index.html"
request.session['client_state'] = smart.state # TO DO: encrypt the state to protect app secrets
return redirect(redirect_url)
def _get_smart(new_settings={}):
state = session.get('state')
settings = smart_defaults #the global defaults
settings.update(new_settings) #specific overriding defaults
if state:
return client.FHIRClient(state=state, save_func=_save_state)
else:
return client.FHIRClient(settings=smart_defaults,
save_func=_save_state)
def __init__(self, request):
self.request = request
state = self.request.session.get('state')
if state:
self.smart = client.FHIRClient(state=state,
save_func=self.save_state)
print('state is: {0}'.format(state))
else:
self.smart = client.FHIRClient(settings=self.smart_defaults,
save_func=self.save_state)
print('no state, create new connection')
def patient(id):
helloval = request.args.get('hello')
output = "<p>"
smart = client.FHIRClient(settings=settings)
smart.prepare()
smart = client.FHIRClient(settings=settings)
import fhirclient.models.patient as p
try:
import fhirclient.models.patient as p
patient = p.Patient.read(id, smart.server)
output = "<h2>" + id + "</h2><p>" + patient.name[0].given[
0] + " " + patient.name[0].family + "</p>"
except:
output = "Cannot find a patient based on the ID provided."
return output
def get_patient_info(patient_id):
settings = {
'app_id': 'LGBTQCovidReporting',
'api_base': 'https://r4.smarthealthit.org'
}
smart = client.FHIRClient(settings=settings)
patient = p.Patient.read(patient_id, smart.server)
patient_name = get_patient_name(patient)
patient_address = get_patient_address(patient)
patient_birthdate = str(patient.birthDate.date)
patient_gender = patient.gender
tested_positive = False
bundle = p.Patient.where({'_id': str(patient_id),
'_has:Condition:patient:code':'http://snomed.info/sct|840539006',
'_has:Condition:patient:verification-status':'http://terminology.hl7.org/CodeSystem/condition-ver-status|confirmed'},
).perform(smart.server)
if bundle.entry:
if len(bundle.entry) > 0:
tested_positive = True
sexuality = "I choose not to answer"
bundle = o.Observation.where({'subject': str(patient_id),
'code':'http://loinc.org|76690-7',
'_sort':'-date',
'_count':'1'}
).perform(smart.server)
if bundle.entry:
if len(bundle.entry) > 0:
sexuality = bundle.entry[0].resource.valueString
return [patient_id, patient_name, patient_gender, patient_birthdate, patient_address, tested_positive, sexuality]
def form():
if request.method == 'GET':
return '''
<form method="post">
Search for a Name: <input type="text" name="text1" />
<input type="submit" name="Search" value="Search" />
</form>
'''
else:
# return 'You entered:'+request.form.get('text1');
smart = client.FHIRClient(settings=settings)
smart.prepare()
import fhirclient.models.patient as p
search = p.Patient.where({'name': request.form.get('text1')})
patients = search.perform_resources(smart.server)
serializablepatientarray = []
output = "<table>"
for patient in patients:
output = output + "<tr>"
output = output + "<td><a href='/patient/" + patient.id + "'>" + patient.name[
0].given[0] + "</a></td>"
output = output + "<td><a href='/patient/" + patient.id + "'>" + patient.name[
0].family + "</a></td>"
output = output + "</tr>"
output = output + "</table>"
return render_template('search.html', output=Markup(output))
def __init__(self, questionnaire_id, *args, **kwargs):
super(FHIRQuestionnaireForm, self).__init__(*args, **kwargs)
try:
# Prepare the client
fhir = client.FHIRClient(settings={'app_id': settings.FHIR_APP_ID, 'api_base': settings.FHIR_URL})
# Get the questionnaire
questionnaire = Questionnaire.read(questionnaire_id, fhir.server)
# Retain it
self.questionnaire_id = questionnaire_id
self.questionnaire = questionnaire
except FHIRNotFoundException:
raise FHIR.QuestionnaireDoesNotExist
# Get fields
self.fields = self._get_form_fields(questionnaire, questionnaire_id)
self.fields['questionnaire_id'] = forms.CharField(empty_value=questionnaire_id, widget=forms.HiddenInput)
# Create the crispy helper
self.helper = FormHelper(self)
self.helper.form_method = 'POST'
# Set the layout
self.helper.layout = self._get_form_layout(self.questionnaire.item)
# Add a submit button
self.helper.layout.append(ButtonHolder(Submit('submit', 'Submit', css_class='btn btn-primary')))
def get_patient_info(pat_id):
"""
Queries a FHIR server for patient information
Args:
param1: FHIR patient ID
Returns:
A dictionary that includes a patient's name, ID, date of birth, age, and gender
"""
smart = client.FHIRClient(settings=SETTINGS)
import fhirclient.models.patient as p
patient = p.Patient.read(pat_id, smart.server)
name = patient.name[0].given[0] + ' ' + patient.name[0].family
dob = patient.birthDate.isostring #yyyy-mm-dd
age = calculate_age(patient.birthDate.date)
gender = patient.gender
return {
'name': name,
'id': pat_id,
'dob': dob,
'age': age,
'gender': gender
}
def get_procedure_info(proc_id):
"""
Queries a FHIR server for procedure information. The procedure text might be in a TIU database,
so it's currently just part of the template.
Args:
param1: FHIR procedure ID
Returns:
A dictionary that includes the procedure ID, exam type (name), indications, and an array
of associated diagnostic codes/descriptions. The array type works well with JS and Python.
"""
smart = client.FHIRClient(settings=SETTINGS)
import fhirclient.models.procedure as p
proc = p.Procedure.read(proc_id, smart.server)
exam_type = proc.code.coding[0].display
indications = proc.reasonCode[0].text
cond_code_desc = []
for cond in proc.reasonReference:
cond_json = json.loads(urllib.request.urlopen(SETTINGS['api_base'] + '/Condition/' + \
cond.reference.split('/')[1]).read())
cond_code_desc.append([cond_json['code']['coding'][0]["code"], \
cond_json['code']['coding'][0]['display']])
return {
'proc_id': proc_id,
'exam_type': exam_type,
'indications': indications,
'condition': cond_code_desc
}
def get_patient_aggregate_data(patient_id='212',
window_secs=72000,
interval_secs=600,
calc_cnt=40):
settings = {
'app_id': 'my_web_app',
'api_base': "http://35.192.2.85:8080/baseDstu2/",
'count': '500'
}
smart = client.FHIRClient(settings=settings)
pd = pat_dat(patient_id, smart)
pat_ag_dat = {}
for obn in pd.observation_list:
pat_ag_dat[obn] = np.zeros(0)
pat_ag_dat['dt'] = np.zeros(0)
end_tm = pd.get_min_max_dts()['max']
for i in range(calc_cnt):
start_tm = end_tm - datetime.timedelta(seconds=window_secs)
new_vals = pd.get_aggragation_for_dates(start_tm, end_tm)
pat_ag_dat['dt'] = np.append(pat_ag_dat['dt'], end_tm)
for obn in pd.observation_list:
pat_ag_dat[obn] = np.append(pat_ag_dat[obn], new_vals[obn])
end_tm = end_tm - datetime.timedelta(seconds=interval_secs)
pat_ag_dat['dt'] = pat_ag_dat['dt'][::-1]
for obn in pd.observation_list:
pat_ag_dat[obn] = pat_ag_dat[obn][::-1]
pat_ag_dat[obn] = ff_and_bf(pat_ag_dat[obn])
return pat_ag_dat
def getPatient():
'''
This method shows how to use the fhirclient's Patient model to get FHIR data from a server.
This example returns the ID, name, and birth year for all females over 45 years old.
'''
settings = {
'app_id': 'python_FHIR_app',
'api_base': 'http://sqlonfhir-stu3.azurewebsites.net/fhir/'
}
server = client.FHIRClient(settings=settings).server
#Query to FHIR server for all female patients
search = p.Patient.where(struct={'gender': 'female'})
results = search.perform_resources(server)
count = 0
data = ''
#For each female Patient resource returned, extract the birth year to determine age
for r in results:
try:
birthyear = int(r.as_json()['birthDate'].split('-')[0])
if birthyear < 1973:
data += r.as_json()['id'] + '\n' + \
r.as_json()['name'][0]['given'][0] + ' ' + r.as_json()['name'][0]['family'] + '\n' + \
'Born: ' + str(birthyear) + '\n\n'
count += 1
except:
continue
#Return this information to app.py to include in the HTML rendering
return 'ID, name, and birth year for each female over 45 years old in the ' + settings['api_base'] + \
' FHIR server.\n\nTotal: ' + str(count) + '\n\n' + data
def SumAuditType(server, bundle): #include rest summary
key = {}
smart = client.FHIRClient(settings={'app_id':'audit_app','api_base':server})
while bundle is not None and bundle.entry:
for entry in bundle.entry:
if not entry.resource.type.code == "rest":
if entry.resource.type.code in key:
key[entry.resource.type.code] += 1
else:
key[entry.resource.type.code] = 1
else:
if not "rest" in key:
key["rest"] = {}
if not entry.resource.subtype:
try:
key["rest"]['null'] += 1
except KeyError:
key["rest"]['null'] = 1
else:
for subtype in entry.resource.subtype:
if not subtype.code:
try:
key["rest"]['null'] += 1
except KeyError:
key["rest"]['null'] = 1
else:
try:
key["rest"][subtype.code] += 1
except KeyError:
key["rest"][subtype.code] = 1
bundle = NextBundle(smart, bundle)
return key
def bootstrap():
settings = {
'app_id': 'my_web_app',
'api_base': "http://35.184.247.92:8080/baseDstu2/",
'count':'500'
}
smart = client.FHIRClient(settings=settings)
# this will run a query that returns all observations
search = p.Patient.where ( struct=None)
# This will put a bundle into the variable obs with the first 10 results as entries
obs = search.perform(smart.server)
lastUrl = ""
jsonArray = []
lastObject = obs.as_json()
# Print it out -
while 1 == 1:
nex = lastObject
lastUrl = nex['link'][1]['url']
r = requests.get(lastUrl)
if nex['link'][1]['relation'] == 'previous':
break
jsonArray.append(r.json())
lastObject = r.json()
#print lastUrl
nameArray = []
for record in jsonArray:
for rec2 in (record['entry']):
try:
nameArray.append(str(rec2['resource']['name'][0]['use']))
except:
pass
print str(nameArray)
return render_template('bootstrap/startbootstrap-sb-admin-gh-pages/index.html', option_list=nameArray)
def smart():
settings = {
"app_id": "integrationtest",
"api_base": os.environ["FHIR_SERVER_URL"]
}
smart = client.FHIRClient(settings=settings)
return smart
def setup():
client_instance = client.FHIRClient(
settings={
'app_id': 'epidurio',
'api_base': API_BASES['cerner-open'],
}
)
return client_instance
def connect(self, **kwargs):
""" Connect to the rest api service / data storage.
:param kwargs: key based arguments
"""
self.fhir_client = client.FHIRClient(settings=self.settings)
self.fhir_client.prepare()
self.server = self.fhir_client.server
def index(request):
indexpage = get_template('index.html')
# Declare global variables that may be modified here
global Global_PATIENT_ID
global Global_ADHERE_VARS
smart = client.FHIRClient(state=request.session['client_state'])
record_change_p = True
patientID = smart.patient_id
# Get the medication dispenses for this context
dispenses = MedicationDispense.where({'patient': patientID}).perform(smart.server)
pills = []
if dispenses.entry:
for dispense in dispenses.entry:
d = dispense.resource
name = d.medicationCodeableConcept.coding[0].display
assert d.status == 'completed'
quant = d.daysSupply.value
when = d.whenHandedOver.isostring
pills.append((None,name,quant,when))
birthday, patient_name = get_birthday_name(smart)
drug = 'all'
# We only want to call the adherence_check once for a specific patient
if Global_PATIENT_ID == patientID:
meds_flags, gaps, refill_data, refill_day = Global_ADHERE_VARS
else:
tests = adherenceTests.AdherenceTests()
meds_flags, gaps, refill_data, refill_day = tests.allTests(pills, drug, birthday)
Global_ADHERE_VARS = [meds_flags, gaps, refill_data, refill_day] # save the data for future needs
Global_PATIENT_ID = patientID
# Medication information will be displayed by drug class. Here we
# sort all the patient's medications into drug classes defined
# in this application.
drug_class_array = {}
for n in range(len(meds_flags)):
drug_class_array[meds_flags[n][5]] = 1
sorted_drug_class_list = sorted(drug_class_array.keys())
# Send these variables to the page for rendering
variables = Context({
'head_title': u'Medication Adherence Monitor',
'patientID': patientID,
'meds_flags': meds_flags, # Contains all the data needed for tables and plotting
'media_root': settings.MEDIA_ROOT,
'patient_name': patient_name,
'drug_class_array': sorted_drug_class_list,
})
output = indexpage.render(variables)
response = HttpResponse(output)
return response
def getsmart():
"""
set setting, and return smart server
"""
settings = {
'app_id': 'my_web_app',
'api_base': 'http://fhirtest.b12x.org/baseDstu3'
}
smart = client.FHIRClient(settings=settings)
return smart
def update_patients_sexuality(patient_id, sexual_orientation):
base_observation = {
"resourceType": "Observation",
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "social-history",
"display": "social-history"
}
]
}
],
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "76690-7",
"display": "Sexual orientation"
}
],
"text": "Sexual orientation"
},
"subject": {
"reference": ""
},
"performer": [{"reference": ""}],
"valueString": ""
}
settings = {
'app_id': 'LGBTQCovidReporting',
'api_base': 'https://r4.smarthealthit.org'
}
smart = client.FHIRClient(settings=settings)
#id = str(datetime.utcnow().date()) + "pgood7userobservation" + "1"
subject_reference = "Patient/" + patient_id
#date = datetime.utcnow().isoformat()
#sexual_orientations = ['Bisexual', 'Heterosexual', 'Homosexual', 'Other', 'Asked but unknown', 'Unknown']
observation = o.Observation(base_observation)
#observation.subject_reference = subject_reference
observation.subject.reference = subject_reference
observation.performer[0].reference = subject_reference
observation.effectiveDateTime = fd.FHIRDate(str(datetime.utcnow().isoformat()))
observation.issued = fd.FHIRDate(str(datetime.utcnow().isoformat()))
observation.valueString = sexual_orientation
new_observation = observation.create(smart.server)
if(new_observation):
return 200
else:
return 400
def demo_fhir_server():
""" Builds a SMART server against Cerner's open playground for querying.
See http://fhir.cerner.com/millennium/dstu2/#open-sandbox.
Returns:
A SMART server that requires no auth tokens to use.
"""
return client.FHIRClient(settings={
'app_id': "example",
'api_base': 'https://fhir-open.sandboxcerner.com/dstu2/0b8a0111-e8e6-4c26-a91c-5069cbc6b1ca'
}).server
def fhirclient(self):
''' Make a client.
'''
fhirclient = client.FHIRClient({
'app_id': self.client_id,
'app_secret': self.client_secret,
'api_base': self.fhir_url,
'redirect_uri': self.redirect_uri,
'scope': self.scope,
})
return fhirclient
def home_view(request):
if not request.user.is_authenticated:
return redirect('/')
settings = {
'app_id': 'faircare',
'api_base': 'https://launch.smarthealthit.org/v/r3/fhir'
}
smart = client.FHIRClient(settings=settings)
search = med.Medication.where(struct={'_include': '*'})
medications = search.perform_resources(smart.server)
for m in medications:
m.as_json()
# Medication.objects.create(medicine_name=m.code.text)
template = loader.get_template('home.html')
medication_submit_form = MedicationDataSubmitForm()
if request.method == 'POST':
medication_submit_form = MedicationDataSubmitForm(request.POST)
if medication_submit_form.is_valid():
medication_submit = MedicationPrice(
medicine_name=medication_submit_form.cleaned_data.get(
'medication'),
price=medication_submit_form.cleaned_data.get(
'medication_price'),
state=medication_submit_form.cleaned_data.get(
'medication_state'))
messages.success(request,
'Medication Data Submitted Successfully.')
medication_submit.save()
medication_view_form = MedicationViewForm()
medication_view = ""
if request.method == 'POST' and 'medication_view' in request.POST:
medication_view_form = MedicationViewForm(request.POST)
if medication_view_form.is_valid():
medication_view = medication_view_form['medication_view'].value()
context = {
'medications': medications,
'medication_submit_form': medication_submit_form,
'medication_view_form': medication_view_form,
'medication_view': medication_view,
}
return HttpResponse(template.render(context, request))
def test_000_something(self):
settings = {
'app_id': 'my_web_app',
'api_base': 'http://fhirtest.b12x.org/r3'
}
smart = client.FHIRClient(settings=settings)
gfefhir = GfeFHIR(smart=smart)
self.assertIsInstance(gfefhir, GfeFHIR)
gfefhir.annotate('6289')
#for ids in ['6227','6228','6229','6234','6235','6236','6241','6242','6243',]:
# gfefhir.annotate(ids)
# print("--------------")
pass
def create_data_if_FHIR_Server_returns_none():
settings = {
'app_id': 'LGBTQCovidReporting',
'api_base': 'https://r4.smarthealthit.org'
}
smart = client.FHIRClient(settings=settings)
bundle = b.Bundle.read_from(
'/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',
smart.server)
if bundle.entry is None or len(bundle.entry) < 1:
create_data(smart)
def fhirclient(self):
''' Returns a FHIRClient object from the current state.
'''
def save_func(state): # pylint: disable=missing-docstring
self._fhirclient = json.dumps(state)
if not self._fhirclient:
fhirclient = self.provider.fhirclient
fhirclient.prepare()
state = fhirclient.state
else:
state = json.loads(self._fhirclient)
return client.FHIRClient(state=state, save_func=save_func)
def query():
fhirServer = client.FHIRClient(settings=settings).server
#Will print the first names of all males in the server
search = p.Patient.where(struct={'gender': 'male'})
results = search.perform_resources(fhirServer)
for r in results:
print(r.as_json()['name'][0]['given'][0])
#Will print patient ID's for all patients with a recorded systolic BP
search = o.Observation.where(struct={'code-value-concept': '8480-6'})
results = search.perform_resources(fhirServer)
for r in results:
print(r.as_json()['subject']['reference'])
def runCohortCounter(endpointUrl, endpointToken):
#connect to FHIR server
smart = client.FHIRClient(settings={
'app_id': endpointToken,
'api_base': endpointUrl
})
urlBase = endpointUrl
#Patients diagnosed with diabetes
print('Patient cohort for Diabetes')
search_str = 'Condition?_include=Condition:patient&code:below=http://snomed.info/sct|73211009'
# print('Patient cohort for asthma')
#search_str = 'Condition?_include=Condition:patient&code=195917001'
cohort = perform_in(search_str, smart.server, urlBase)
results = len(cohort)
cohortSize = int(results / 2)
print("Retrieved cohort size %s" % cohortSize)
ageSum = 0
def calculate_age(born):
# convert str to datetime format
dob = datetime.strptime(born, "%Y-%m-%d")
today = date.today()
return today.year - dob.year - ((today.month, today.day) <
(dob.month, dob.day))
# Loop over all patients in bundle
for patients in cohort:
entry = patients.as_json()
if 'birthDate' in entry.keys():
dob = entry['birthDate']
age_i = calculate_age(dob)
ageSum = ageSum + age_i
else:
results = results - 1
print("Cohort size after eliminating patients with no age data: %s" %
results)
# Calculate mean age
meanAge = None
if cohortSize > 0:
meanAge = ageSum / results
print("Mean age in cohort: %s" % meanAge)
return {'cohortCount': results, 'meanAge': meanAge}
