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"
)
'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")
class GraphManager:
"""Create a FHIR object to retrieve patient data """
def __init__(self):
self.FHIR = FHIR()
def get_patients(self, page_number: int = 0) -> List[Patient]:
if page_number == 0:
return self.FHIR.get_all_patients()
else:
return self.FHIR.get_patient_page(page_number)
def characteristic_is_observation_type(self, characteristic: str) -> bool:
non_observation_types = ['language', 'marital status', 'city', 'country', 'state', 'family name', 'age']
if non_observation_types.__contains__(characteristic):
return False
return True
def get_latest_obeservation_with_characteristic(self, patient: Patient, characteristic: str):
observations = self.FHIR.get_patient_observations_page(patient.uuid, 3)
latest_observation_value = 0
latest_time = datetime(1,1,1)
found_first_observation = False
for observation in observations:
for observation_component in observation.components:
if observation_component.display == characteristic:
if found_first_observation == False:
found_first_observation = True
latest_time = observation.effective_datetime
latest_observation_value = observation_component.value
elif observation.effective_datetime > latest_time:
latest_time = observation.effective_datetime
latest_observation_value = observation_component.value
return latest_observation_value
def get_data(self, characteristic: str, page_number: int = 0):
characteristic_values = {}
patients = self.get_patients(page_number)
if self.characteristic_is_observation_type(characteristic) == True:
for patient in patients:
data_point = self.get_latest_obeservation_with_characteristic(patient, characteristic)
if str(data_point) in characteristic_values:
characteristic_values[str(data_point)] += 1
else:
characteristic_values[str(data_point)] = 1
else:
for patient in patients:
if characteristic == 'language':
for language in patient.communications.languages:
characteristic_values.update({language: characteristic_values.get(language, 0) + 1})
if characteristic == 'marital status':
if str(patient.marital_status) in characteristic_values:
characteristic_values[str(patient.marital_status)] += 1
else:
characteristic_values[str(patient.marital_status)] = 1
if characteristic == 'city':
if patient.addresses[0].city in characteristic_values:
characteristic_values[str(patient.addresses[0].city)] += 1
else:
characteristic_values[str(patient.addresses[0].city)] = 1
if characteristic == 'country':
if patient.addresses[0].country in characteristic_values:
characteristic_values[str(patient.addresses[0].country)] += 1
else:
characteristic_values[str(patient.addresses[0].country)] = 1
if characteristic == 'state':
if patient.addresses[0].state in characteristic_values:
characteristic_values[str(patient.addresses[0].state)] += 1
else:
characteristic_values[str(patient.addresses[0].state)] = 1
if characteristic == 'family name':
if patient.name.family in characteristic_values:
characteristic_values[str(patient.name.family)] += 1
else:
characteristic_values[str(patient.name.family)] = 1
if characteristic == 'age':
if floor(patient.age()) in characteristic_values:
characteristic_values[str(floor(patient.age()))] += 1
else:
characteristic_values[str(floor(patient.age()))] = 1
return collections.OrderedDict(sorted(characteristic_values.items()))
def graph_single_characteristic(self, characteristic: str, page_number: int = 0, graph_type: str = 'x_y_plot'):
data = self.get_data(characteristic, page_number)
plt.title('Values of the ' + str(characteristic) + ' in the first ' + str(page_number) + ' pages in the patients record')
if graph_type == 'bar chart':
plt.bar(range(len(data)), list(data.values()), align='center')
plt.xticks(range(len(data)), list(data.keys()), rotation='vertical')
elif graph_type == 'pie chart':
plt.pie(data.values(), labels=data.keys(), autopct='%1.1f%%',
shadow=True, startangle=90)
plt.axis('equal')
elif graph_type == 'x_y_plot':
plt.plot(list(data.keys()), list(data.values()))
def graph_multiple_characteristics(self, characteristics: List[str], page_number: int = 0, graph_type: str = 'x_y_plot'):
for characteristic in characteristics:
plt.figure()
self.graph_single_characteristic(characteristic, page_number, graph_type)
def show_figures(self):
plt.show()