def get_report(request, uid):
fhir = FHIR('https://localhost:5001/api/', verify_ssl=False)
if request.method == 'GET':
try:
patient = fhir.get_patient(uid)
fbcReqAttributes = ("laboratory", [2, 13, 5, 3, 15, 16, 17, 6])
bpReqAttributes = ("vital-signs", [3, 4, 5])
otherReqAttributes = ("laboratory",
[22, 23, 24, 25, 26, 27, 28, 33, 55])
fbcAttributes = getAttributes(uid, fbcReqAttributes[0],
fbcReqAttributes[1])
bpAttributes = getAttributes(uid, bpReqAttributes[0],
bpReqAttributes[1])
otherAttributes = getAttributes(uid, otherReqAttributes[0],
otherReqAttributes[1])
myDict = {
'UID': patient.uuid,
'Name': patient.name.full_name,
'Address': str(patient.addresses[0]),
'Full-Blood Count Attributes': makeDict(fbcAttributes),
'Blood Pressure Values': makeDict(bpAttributes),
'Other blood readings': makeDict(otherAttributes)
}
response = json.dumps(myDict)
return HttpResponse(response, content_type='text/json')
except ConnectionError:
response = json.dumps([{'Error': 'No patient found'}])
return HttpResponse(response, content_type='text/json')
def getPatient(patientID):
fhir = FHIR('https://localhost:5001/api/', verify_ssl=False)
try:
patient = fhir.get_patient(patientID)
except:
patient = None
return patient
def patient(id):
fhir = FHIR()
patient = fhir.get_patient(id)
observations = fhir.get_patient_observations(id)
return render_template('patientinfo.html',
observations=observations,
patient=patient)
def getaverageage():
fhir = FHIR()
patients = fhir.get_all_patients()
ages = []
for patient in patients:
ages.append(patient.age())
return str(sum(ages) / len(ages))
def observations(id):
fhir = FHIR()
patient = fhir.get_patient(id)
observations = fhir.get_patient_observations(id)
spreadSheet = {
'bodyWeight': [],
'BMI': [],
'dBP': [],
'sBP': [],
'pain': [],
'latestObs': {
'uuid': "",
'latestDate': "",
'type': "",
'status': "",
'weight': "",
'sBP': "",
'BMI': ""
}
}
for i in observations:
components = i.components
for i2 in components:
value = i2.value
if value == None: continue
date = i.effective_datetime
dateStr = str(date.day) + "/" + str(date.month) + "/" + str(
date.year)
display = i2.display
if display == "Body Weight":
spreadSheet['bodyWeight'].append((dateStr, value))
elif display == "Diastolic Blood Pressure":
spreadSheet['dBP'].append((dateStr, value))
elif display == "Systolic Blood Pressure":
spreadSheet['sBP'].append((dateStr, value))
elif display == "Body Mass Index":
spreadSheet['BMI'].append((dateStr, value))
elif "Pain severity" in display:
spreadSheet['pain'].append((dateStr, value))
dictItemsToBeSorted = [
spreadSheet['bodyWeight'], spreadSheet['BMI'], spreadSheet['dBP'],
spreadSheet['sBP'], spreadSheet['pain']
]
sortTime(dictItemsToBeSorted)
spreadSheet['latestObs']['uuid'] = observations[-1].uuid
tmp = observations[-1].effective_datetime
spreadSheet['latestObs']['latestDate'] = str(tmp.day) + "/" + str(
tmp.month) + "/" + str(tmp.year)
spreadSheet['latestObs']['type'] = observations[-1].type
spreadSheet['latestObs']['status'] = observations[-1].status
spreadSheet['latestObs']['weight'] = spreadSheet['bodyWeight'][-1][-1]
spreadSheet['latestObs']['sBP'] = spreadSheet['sBP'][-1][-1]
spreadSheet['latestObs']['BMI'] = spreadSheet['BMI'][-1][-1]
return render_template("observations.html",
obsData=spreadSheet,
patient=patient)
def __init__(self, patients_object: Patients):
fhir = FHIR()
self.patients = patients_object
self.patients_uuid_list = self.patients.get_uuid() # List
if type(self.patients_uuid_list
) is not list: # type is str when only patient is given
self.patients_uuid_list = [self.patients_uuid_list]
self.get_patient_observations_by_uuid = lambda x: fhir.get_patient_observations(
x)
def __init__(self):
self.fhir = FHIR()
self.patients = self.fhir.get_all_patients()
self.num_examples = len(self.patients)
self.num_features = 11
self.patient_record_columns = [
"UUID", "Name", "Gender", "Birthdate", "MaritalStatus",
"MultipleBirth", "CoreRace", "CoreEthnicity", "Birthsex",
"disabilityAdjLifeYears", "QualAdjLifeYears"
]
def surname(text):
fhir = FHIR()
patients = fhir.get_all_patients()
number_of_patients = 0
for i in patients:
number_of_patients = number_of_patients + 1
for index in range(0, number_of_patients):
patient = patients[index]
if text == patient.name.family:
return index
return -1
def unique_identifier(text):
fhir = FHIR()
patients = fhir.get_all_patients()
number_of_patients = 0
for i in patients:
number_of_patients = number_of_patients + 1
for index in range(0, number_of_patients):
patient = patients[index]
if text == patient.uuid:
return index
return -1
def getAttributes(uuid, obType, requiredAttributes):
fhir = FHIR('https://localhost:5001/api/', verify_ssl=False)
obs = fhir.get_patient_observations(uuid)
count = 0
attribList = []
for ob in obs:
if ob.type == obType:
for i in ob.components:
if count in requiredAttributes:
attribList.append(str(i))
count += 1
return attribList
def graph_by_states():
fhir = FHIR()
patients = fhir.get_all_patients()
states = {}
for patient in patients:
for addressArr in patient.addresses:
states.update({addressArr.state: states.get(addressArr.state, 0) + 1})
plt.bar(range(len(states)), list(states.values()), align='center')
plt.xticks(range(len(states)), list(states.keys()), rotation='vertical')
plt.show()
def __init__(self, page=None, patient_uuid=None):
fhir = FHIR()
self.uuid_presented = False
self.patients = fhir.get_all_patients()
if patient_uuid is not None:
self.uuid_presented = True
self.specific_patient = fhir.get_patient(patient_uuid)
if page is not None:
try:
assert patient_uuid is None
self.patients = fhir.get_patient_page(page)
except AssertionError:
sys.exit(
"Error: patients page and patient uuid cannot be initialised at the same time"
)
def graph_by_cities():
fhir = FHIR()
patients = fhir.get_all_patients()
cities = {}
for patient in patients:
for addressArr in patient.addresses:
cities.update({addressArr.city: cities.get(addressArr.city, 0) + 1})
plt.bar(range(len(cities)), list(cities.values()), align='center')
plt.xticks(range(len(cities)), list(cities.keys()), rotation='vertical')
# fig = plt.figure()
# fig.savefig('plot.png')
plt.show()
# need to think of what can we graph from the observation data
# def graph_by_diseases():
# fhir = FHIR()
# patients = fhir.get_all_patients()
# problems = {}
# count = 0
# for patient in patients:
# count = count + 1
# if count == 4:
# break
# print("YOOOO THIS IS THR FKING ID" + patient.uuid)
# try:
# observations = fhir.get_patient_observations(patient.uuid)
# except:
# continue
# for observation in observations:
# print("observation 1")
# components = observation.components
# for component in components:
# print(component.display)
# print(component.value)
# problems.update({component.display: problems.get(component.display, 0) + 1})
# plt.bar(range(len(problems)), list(problems.values()), align = 'center')
# plt.xticks(range(len(problems)),list(problems.keys()), rotation = 'vertical' )
# plt.show();
# def graph_by_diseases():
# def graph_by_certain_age(age):
def graph_languages_spoken():
fhir = FHIR()
patients = fhir.get_all_patients()
languages = {}
for patient in patients:
for language in patient.communications.languages:
languages.update({language: languages.get(language, 0) + 1})
plt.bar(range(len(languages)), list(languages.values()), align='center')
plt.xticks(range(len(languages)), list(languages.keys()), rotation='vertical')
fig1 = plt.gcf()
plt.draw()
number = random.randint(1, 1000)
fig1.savefig('plot'+str(number)+'.png', dpi=100)
return number
def graph_marital_status():
fhir = FHIR()
patients = fhir.get_all_patients()
marital_status = {}
for patient in patients:
if str(patient.marital_status) in marital_status:
marital_status[str(patient.marital_status)] += 1
else:
marital_status[str(patient.marital_status)] = 1
plt.bar(range(len(marital_status)), list(marital_status.values()), align='center')
plt.xticks(range(len(marital_status)), list(marital_status.keys()))
fig1 = plt.gcf()
plt.draw()
number = random.randint(1, 1000)
fig1.savefig('plot'+str(number)+'.png', dpi=100)
return number
def graph_by_age_groups():
fhir = FHIR()
patients = fhir.get_all_patients()
ageGroups = {'<10': 0, '10-20': 0, '20-30':0, '30-40':0, '40-50':0, '50-60':0, '60-70': 0, '70-80':0, '80-90':0, '90+':0}
for patient in patients:
birth = patient.birth_date
patientAge = calculate_age(birth)
if(patientAge < 10):
ageGroups['<10'] += 1
elif( 10 <= patientAge < 20):
ageGroups['10-20'] += 1
elif( 20 <=patientAge < 30):
ageGroups['20-30'] += 1
elif( 30 <=patientAge < 40):
ageGroups['30-40'] += 1
elif( 40 <=patientAge< 50):
ageGroups['40-50'] += 1
elif( 50 <=patientAge < 60):
ageGroups['50-60'] += 1
elif( 60 <patientAge < 70 ):
ageGroups['60-70'] += 1
elif( 70 <patientAge < 80 ):
ageGroups['70-80'] += 1
elif( 80 <patientAge < 90 ):
ageGroups['80-90'] += 1
elif( 90 <=patientAge ):
ageGroups['90+'] += 1
plt.bar(range(len(ageGroups)), list(ageGroups.values()), align='center')
plt.xticks(range(len(ageGroups)), list(ageGroups.keys()), rotation='vertical')
fig1 = plt.gcf()
plt.draw()
number = random.randint(1, 1000)
fig1.savefig('plot'+str(number)+'.png', dpi=100)
return number
def __getSkypePrefixURI(self, patientUUIDs: List[str]):
url = "skype:"
for index, patientUUID in enumerate(patientUUIDs):
if index == 9:
break
patient = FHIR().get_patient(patientUUID)
url += "+1" + str(patient.telecoms[0].number).replace("-", "")
url += ";"
if (url[-1] == ';'):
url = url[:-1]
return url
def observationstats():
fhir = FHIR()
patients = fhir.get_all_patients()
observations = []
for patient in patients:
observations.extend(fhir.get_patient_observations(patient.uuid))
total_obsv = len(observations)
observation_types = [observation.type for observation in observations]
most_frequent_observation_type = max(set(observation_types),
key=observation_types.count)
observation_components = []
for observation in observations:
observation_components.extend(observation.components)
total_obsv_components = len(observation_components)
observation_component_types = [
observation_component.display
for observation_component in observation_components
]
most_frequent_observation_component_type = max(set(observation_types),
key=observation_types.count)
obsvstats_dictionary = {
"totalObsv": total_obsv,
"mfObservationType": most_frequent_observation_type,
"totalObsvComp": total_obsv_components,
"mfObsvCompType": most_frequent_observation_component_type
}
response = jsonify(obsvstats_dictionary)
return response
class Main:
def __init__(self):
self.fhir = FHIR('https://localhost:5001/api/', verify_ssl=False)
self.patients = self.fhir.get_all_patients()
def print_patients_in_range(self, limit, lower, upper, sender_name, sender_ref, app_url):
i = 0
patients_list = []
for patient in self.patients:
dict = {}
if not i < limit:
# print(patients_list)
return patients_list
id = patient.uuid
name = patient.full_name()
age = patient.age()
if age >= lower and age < upper:
telecoms = patient.telecoms
phone = telecoms[len(telecoms) - 1].number
# print(phone)
msg = "Hi " + name + ",\n" + "Are you a carer? If so, we've built an app just for you! You can download our app for carers here: " + app_url + "\nUse this reference code to set up your app: " + sender_ref + "\nTake Care,\n" + sender_name
# print(msg)
# print(id)
# print(name)
# print(age)
# print()
dict["phone"] = phone
dict["msg"] = msg
patients_list.append(dict)
i += 1
# main = Main()
# list = main.print_patients_in_range(3, 55, 65, "Paul", "UCL-FHIR-Hack", "appdownload.com")
# patient = fhir.get_patient('8f789d0b-3145-4cf2-8504-13159edaa747')
# name = patient.full_name()
# print(patient)
# list = fhir.get_all_patients()
from fhir_parser import FHIR
import matplotlib.pyplot as plt
import pandas as pd
fhir = FHIR(endpoint='https://fhir.compositegrid.com:5001/api/')
patients = fhir.get_all_patients()
genders = []
ages = []
for patient in patients:
if patient.gender == 'male':
genders.append(0)
else:
genders.append(1)
ages.append(patient.age())
data = {'sex': genders, 'age': ages}
df = pd.DataFrame(data)
df.groupby('sex')['age'].plot(title='Age Distribution By Gender', kind='kde')
plt.show()
def index():
fhir = FHIR()
patients = fhir.get_all_patients()
return render_template('patients.html', patients=patients)
def getstatistics(id):
fhir = FHIR()
patient = fhir.get_patient(id)
observations = fhir.get_patient_observations(id)
bp_dict = {"date": [], "dbp": [], "sbp": []}
hr_dict = {"date": [], "hr": []}
rr_dict = {"date": [], "rr": []}
bw_dict = {"date": [], "bw": []}
bh_dict = {"date": [], "bh": []}
bmi_dict = {"date": [], "bmi": []}
bmip_dict = {"date": [], "bmip": []}
ps_dict = {"date": [], "ps": []}
temp_bp_dates = []
bp_observations = []
temp_hr_dates = []
hr_observations = []
temp_rr_dates = []
rr_observations = []
temp_bw_dates = []
bw_observations = []
temp_bh_dates = []
bh_observations = []
temp_bmi_dates = []
bmi_observations = []
temp_bmip_dates = []
bmip_observations = []
temp_ps_dates = []
ps_observations = []
for observation in observations:
if observation.components[0].display == "Blood Pressure":
bp_observations.append(observation)
temp_bp_dates.append(observation.effective_datetime)
if observation.components[0].display == "Heart rate":
hr_observations.append(observation)
temp_hr_dates.append(observation.effective_datetime)
if observation.components[0].display == "Respiratory rate":
rr_observations.append(observation)
temp_rr_dates.append(observation.effective_datetime)
if observation.components[0].display == "Body Weight":
bw_observations.append(observation)
temp_bw_dates.append(observation.effective_datetime)
if observation.components[0].display == "Body Height":
bh_observations.append(observation)
temp_bh_dates.append(observation.effective_datetime)
if observation.components[0].display == "Body Mass Index":
bmi_observations.append(observation)
temp_bmi_dates.append(observation.effective_datetime)
if observation.components[
0].display == "Body mass index (BMI) [Percentile] Per age and gender":
bmip_observations.append(observation)
temp_bmip_dates.append(observation.effective_datetime)
if observation.components[
0].display == "Pain severity - 0-10 verbal numeric rating [Score] - Reported":
ps_observations.append(observation)
temp_ps_dates.append(observation.effective_datetime)
temp_hr_dates.sort()
temp_bp_dates.sort()
temp_rr_dates.sort()
temp_bw_dates.sort()
temp_bh_dates.sort()
temp_bmi_dates.sort()
temp_bmip_dates.sort()
temp_ps_dates.sort()
for i in range(0, len(temp_bp_dates)):
for observation in bp_observations:
if temp_bp_dates[i] == observation.effective_datetime:
bp_dict["date"].append(
int(time.mktime(temp_bp_dates[i].timetuple())) * 1000)
bp_dict["dbp"].append(observation.components[1].value)
bp_dict["sbp"].append(observation.components[2].value)
break
for i in range(0, len(temp_hr_dates)):
for observation in hr_observations:
if temp_hr_dates[i] == observation.effective_datetime:
hr_dict["date"].append(
int(time.mktime(temp_hr_dates[i].timetuple())) * 1000)
hr_dict["hr"].append(observation.components[0].value)
break
for i in range(0, len(temp_rr_dates)):
for observation in rr_observations:
if temp_rr_dates[i] == observation.effective_datetime:
rr_dict["date"].append(
int(time.mktime(temp_rr_dates[i].timetuple())) * 1000)
rr_dict["rr"].append(observation.components[0].value)
break
for i in range(0, len(temp_bw_dates)):
for observation in bw_observations:
if temp_bw_dates[i] == observation.effective_datetime:
bw_dict["date"].append(
int(time.mktime(temp_bw_dates[i].timetuple())) * 1000)
bw_dict["bw"].append(observation.components[0].value)
break
for i in range(0, len(temp_bh_dates)):
for observation in bh_observations:
if temp_bh_dates[i] == observation.effective_datetime:
bh_dict["date"].append(
int(time.mktime(temp_bh_dates[i].timetuple())) * 1000)
bh_dict["bh"].append(observation.components[0].value)
break
for i in range(0, len(temp_bmi_dates)):
for observation in bmi_observations:
if temp_bmi_dates[i] == observation.effective_datetime:
bmi_dict["date"].append(
int(time.mktime(temp_bmi_dates[i].timetuple())) * 1000)
bmi_dict["bmi"].append(observation.components[0].value)
break
for i in range(0, len(temp_bmip_dates)):
for observation in bmip_observations:
if temp_bmip_dates[i] == observation.effective_datetime:
bmip_dict["date"].append(
int(time.mktime(temp_bmip_dates[i].timetuple())) * 1000)
bmip_dict["bmip"].append(observation.components[0].value)
break
for i in range(0, len(temp_ps_dates)):
for observation in ps_observations:
if temp_ps_dates[i] == observation.effective_datetime:
ps_dict["date"].append(
int(time.mktime(temp_ps_dates[i].timetuple())) * 1000)
ps_dict["ps"].append(observation.components[0].value)
break
return render_template('statistics.html',
patient=patient,
bp_dict=bp_dict,
hr_dict=hr_dict,
rr_dict=rr_dict,
bw_dict=bw_dict,
bh_dict=bh_dict,
bmi_dict=bmi_dict,
bmip_dict=bmip_dict,
ps_dict=ps_dict)
from fhir_parser import FHIR
import pdfkit
fhir = FHIR()
def showOptions():
print("Please select what you want to do:\n")
print("1. Generate documents\n")
print("2. Return to last page\n")
def getPatient(patient_id):
return fhir.get_patient(patient_id)
def getObservation(patient_id):
return fhir.get_patient_observations(patient_id)
def patientDocument():
result = "Patient Name: " + patient.full_name() + "<br>"
result += "<br>"
result += "Id: " + patient.uuid + "<br>"
result += "<br>"
result += "Age: " + str(patient.age()) + "<br>"
result += "<br>"
result += "Gender: " + patient.gender + "<br>"
result += "<br>"
result += "Addresses: <br>"
for x in patient.addresses:
class Model:
fhir = FHIR()
patients = fhir.get_all_patients()
patient_lists = []
def __init__(self):
self.patient_lists = self.get_all_patient_lists()
def get_all_patient_lists(self):
files = glob.glob("saved_lists/*")
l = []
for file in files:
file = file.replace("saved_lists/", "")
file = file.replace(".pickle", "")
file = file.replace("_", " ")
l.append(file)
return l
#
# def get_patient_details_from_name(self, firstname, surname):
# patients_with_name = []
# self.patients = self.fhir.get_all_patients()
# for patient in self.patients:
# if patient.name.given.lower() == firstname.lower() and patient.name.given.lower() == surname.lower():
# patients_with_name.append(patient)
#
# return patients_with_name
#
def update_complete(self, filename, uuid):
patient_list = self.fetch_patient_list(filename)
i = 0
for i, patient in enumerate(patient_list):
if patient[0].uuid == uuid:
break
if patient_list[i][1]:
patient_list[i][1] = False
else:
patient_list[i][1] = True
self.delete_patient_list(filename)
self.save_patient_list(patient_list, filename)
def save_patient_list(self, list, filename):
files = glob.glob("saved_lists/*")
for file in files:
if os.path.join("saved_lists", filename + "." + "pickle") == file:
return False
with open("saved_lists/" + filename + ".pickle", 'wb') as handle:
pickle.dump(list, handle, protocol=pickle.HIGHEST_PROTOCOL)
return True
def fetch_patient_list(self, filename):
path = os.path.join("saved_lists", filename + "." + "pickle")
return self.get_pickle(path)
def get_pickle(self, path):
try:
with open(path, 'rb') as handle:
p = pickle.load(handle)
return p
except FileNotFoundError:
return []
def delete_patient_list(self, filename):
try:
os.remove(os.path.join("saved_lists", filename + "." + "pickle"))
except FileNotFoundError:
return False
return True
def get_patient_details_from_query(self, query):
patients = []
# todo fix this shitty code
for patient in self.patients:
patient_dict = self.generate_patient_dict(patient)
passed = True
for key in query:
info = str(query[key][0])
contains_or_exact = query[key][1].lower()
p_dict = str(patient_dict[key])
try:
if contains_or_exact == "contains":
if info not in p_dict:
passed = False
break
if contains_or_exact == "exact":
if not p_dict == info:
passed = False
break
if contains_or_exact == "less":
if not int(p_dict) < int(info):
passed = False
break
if contains_or_exact == "greater":
if not int(p_dict) > int(info):
passed = False
break
except TypeError:
passed = False
break
if passed:
patients.append([patient, False])
return patients
def generate_patient_dict(self, p):
today = datetime.date.today()
return {
'uuid':
p.uuid,
'first_name':
''.join([i for i in p.name.given if not i.isdigit()]),
'last_name':
''.join([i for i in p.name.family if not i.isdigit()]),
'gender':
p.gender,
'birth_year':
p.birth_date.year,
'birth_month':
p.birth_date.month,
'birth_day':
p.birth_date.day,
'age':
today.year - p.birth_date.year -
((today.month, today.day) <
(p.birth_date.month, p.birth_date.day)),
'house':
p.addresses[0].lines[0],
'city':
p.addresses[0].city,
'state':
p.addresses[0].state,
'postal_code':
p.addresses[0].postal_code,
'country':
p.addresses[0].country,
'marital_status':
p.marital_status.marital_status,
'language':
p.communications.languages[0]
}
def save_doc(text, dropdown):
# Full list of patients
fhir = FHIR()
patients = fhir.get_all_patients()
document = Document()
new_line = " "
# Find number of patients
number_of_patients = 0
for i in patients:
number_of_patients = number_of_patients + 1
# Index of Patient
if dropdown == "Forename":
result = forename(text)
elif dropdown == "Surname":
result = surname(text)
else:
result = unique_identifier(text)
patient = patients[result]
# Address of Patient
address = patient.addresses[0]
communications = patient.communications
# Date Today
today = date.today()
# Marital Status
marital_status_patient = patient.marital_status.marital_status
# Age
age = today.year - patient.birth_date.year - (
(today.month, today.day) <
(patient.birth_date.month, patient.birth_date.day))
# Records of patients
patient_data = {"Unique Identifier": patient.uuid.upper(), "Surname": patient.name.family,
"Forename": patient.name.given, "Gender": patient.gender.capitalize(),
"Birthday": str(patient.birth_date.day) + "." + str(patient.birth_date.month) + "." \
+ str(patient.birth_date.year), "Age": str(age),
"Marital Status": str(marital_status_patient), "Address": address.full_address,
"Languages Spoken": communications.languages}
# Records of a patient
observations = fhir.get_patient_observations(
patient_data["Unique Identifier"].lower())
# Number of observations for 1 Patient
count = 0
for i in observations:
count = count + 1
# NHS Image
LOGO = "1280px-NHS-Logo.svg.png"
logo = document.add_picture(LOGO, width=Inches(1.50))
document.add_heading(patient.name.full_name, 1)
document.add_heading(new_line, 1)
# Adding general information about a patient in a word document
for data in patient_data:
p = document.add_paragraph()
p.add_run(data + ": ").bold = True
p.add_run(patient_data[data])
document.add_heading(new_line, 1)
# Creating a table
table = document.add_table(rows=1, cols=8)
hdr_cells = table.rows[0].cells
hdr_cells[0].text = 'Observation(s) '
hdr_cells[1].text = 'Number'
hdr_cells[2].text = 'Type'
hdr_cells[3].text = 'Status '
hdr_cells[5].text = 'Issued Date'
hdr_cells[6].text = 'Code'
hdr_cells[7].text = 'Result'
# Adding data into the table
for i in range(0, count):
row_cells = table.add_row().cells
row_cells[0].text = str(i + 1)
row_cells[1].text = observations[i].uuid.upper()
row_cells[2].text = observations[i].type.capitalize()
row_cells[3].text = observations[i].status.capitalize()
row_cells[5].text = str(observations[i].issued_datetime)
for component in observations[i].components:
row_cells[6].text = component.code
row_cells[7].text = component.display + ": " + component.quantity()
# Save the document
document.save(
str(patient.name.given[0]) + "." + str(patient.name.family) + "." +
str(age) + '.docx')
def setVariables(searchField, searchCriteria):
searchF = searchField
searchC = searchCriteria
fhir = FHIR()
global patients
patients = fhir.get_all_patients()
from fhir_parser import FHIR
from docxtpl import DocxTemplate
from fhir_patient_summary.renderTemplate import *
from fhir_patient_summary.createObservationDictionary import *
from fhir_patient_summary.convertDocxToPDF import convertDocxToPDF
import shutil
import tempfile
fhir = FHIR()
def createPatientSummaryDocumentFromPatientIDList(patientIDList,
format: str,
destinationDir: str,
zipFile=False):
if zipFile is True:
with tempfile.TemporaryDirectory() as dirpath:
createDocuments(patientIDList, format, dirpath)
shutil.make_archive(destinationDir + "/patientSummaryDocuments",
'zip', dirpath)
return destinationDir + "/patientSummaryDocuments.zip"
else:
createDocuments(patientIDList, format, destinationDir)
return destinationDir
def createDocuments(patientIDList, format: str, destinationDir: str):
for counter, patientID in enumerate(patientIDList):
if counter > 100: # limit number of patients to 100
break
createPatientSummaryDocument(patientID, format, destinationDir)
from flask import Flask, render_template, url_for, redirect, request
from fhir_parser import FHIR, Patient, Observation
from forms import IdentifyForm, HeartRateForm, ChooseForm, BloodPressureForm
from access import Connect
from datetime import datetime
import requests
app = Flask(__name__)
app.config["SECRET_KEY"] = "password"
fhir = FHIR("https://*****:*****@app.route("/", methods=["GET", "POST"])
def home():
patient = None
form = IdentifyForm()
if form.validate_on_submit():
patient_name = search_patient(form.patientID.data)
return redirect(url_for("usr_page", name=patient_name))
else:
return render_template("home.html", title="form", form=form)
@app.route("/patient/<name>", methods=["POST", "GET"])
def usr_page(name):
import matplotlib.pyplot as plt
from fhir_parser import FHIR
import math
fhir = FHIR()
patients = fhir.get_all_patients()
def getLanguageData():
languages = {}
for patient in patients:
for language in patient.communications.languages:
languages.update({language: languages.get(language, 0) + 1})
print(languages)
return languages
def getMaritalStatus():
maritalStatus = {}
for patient in patients:
maritalStatus.update({
str(patient.marital_status):
maritalStatus.get(str(patient.marital_status), 0) + 1
})
return maritalStatus
def getAge():
ages = {}
for patient in patients:
# print(math.floor(patient.age()))
'patient_prefix': patient_info[4],
'patient_surname': patient_info[5],
'doctors_phone_number': doctor_info[0],
'doctors_address1': doctor_info[1],
'doctors_address2': doctor_info[2],
'dr_name': doctor_info[3],
'day': appointment_info[0],
'month': appointment_info[1],
'year': appointment_info[2],
'time': appointment_info[3],
'clinic_type': appointment_info[4],
'signature': signature
}
save_path = "generated/" + patient_info[6] + patient_info[5] + ".docx"
tpl.render(context)
tpl.save(save_path)
if __name__ == "__main__":
doctorJB = Dr.Doctor("Backwell", "Gastroenterology",
["123 Street", "W1 456"], "0123456789",
"Guy's Hospital")
appointment1 = appt.Appointment("1st", "January", "2020", "12:00",
"Gastro Clinic",
"8f789d0b-3145-4cf2-8504-13159edaa747")
fhir = FHIR('https://localhost:5001/api/', verify_ssl=False)
patients = fhir.get_patient_page(5)
for patient in patients:
generateApptLetterDocX(patient.uuid, doctorJB, appointment1,
"templates/doctorAppointment.docx")