def test_bulk_insert_should_throw_error_if_file_does_not_exist(self):
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
self.assertRaises(
IOError, Clonotype.import_adaptive, s, '/fake/path/to/fake/file')
def validate(self, data):
validated_data = super(PatientForm).validate(data)
validated_data['inclusion_code'] = Patient.hash(
validated_data['inclusion_code'])
validated_data['inclusion_nb'] = Patient.hash(
validated_data['inclusion_nb'])
return validated_data
def create_profile_for_new_user(sender, created, instance, **kwargs):
# TODO - use this signal to create blank patient profile
if created:
owner1 = User.objects.get(id = 1)
profile = Patient(user=instance)
profile.save()
pass
def managePatients(self, force, patientNumber):
if (Patient.objects.all().count() != 0):
self.stdout.write("\tPatients already exist in the system\n")
if not force:
return None
self.stdout.write("\tDeleting all the Patients in the system\n")
Patient.objects.all().delete()
self.stdout.write("\tCreating the random Patients\n")
first_names = ('Afonso', 'Alexandre', 'André', 'Artur', 'António',
'Ângelo', 'Mateus', 'Matias', 'Martim', 'Miguel',
'Marco', 'Mário', 'Micael', 'Jaime', 'José', 'João',
'Joaquim', 'Jorge', 'Joel', 'Isaac', 'Ivo', 'Ezequiel',
'Adolfo', 'Ianis', 'Teodoro', 'Salomão', 'Elvis')
last_names = ('Silva', 'Santos', 'Ferreira', 'Pereira', 'Oliveira',
'Costa', 'Rodrigues', 'Martins', 'Jesus', 'Sousa',
'Fernandes', 'Gonçalves', 'Gomes', 'Lopes', 'Marques',
'Alves', 'Almeida', 'Ribeiro', 'Pinto', 'Carvalho',
'Teixeira', 'Moreira', 'Correia', 'Mendes', 'Nunes',
'Soares', 'Vieira', 'Monteiro', 'Cardoso', 'Rocha',
'Raposo', 'Neves', 'Coelho', 'Cruz', 'Cunha', 'Pires',
'Ramos', 'Reis', 'Simões', 'Antunes')
for x in range(patientNumber / 2):
fname = random.choice(first_names)
lname = random.choice(last_names)
Patient(first_name=fname + " " + random.choice(first_names),
last_name=random.choice(last_names) + " " + lname,
status=Patient.DISCHARGED,
gender="M",
birthdate=self.dateRandom("1960-01-01", "2000-01-01",
'%Y-%m-%d'),
phone="234" + str(random.randint(100, 999)) +
str(random.randint(100, 999)),
email=(fname + "." + lname + "@mail.com").lower()).save()
first_names = ('Pérola', 'Lua', 'Josiane', 'Chloe', 'Giulia', 'Perla',
'Teresa', 'Joana', 'Juliana', 'Júlia', 'Luísa',
'Leonor', 'Letícia', 'Sofia', 'Luana', 'Liliana',
'Lara', 'Maria', 'Margarida', 'Marta', 'Tânia',
'Matilde', 'Nádia', 'Olívia', 'Pilar', 'Rafaela',
'Rita', 'Sara')
for x in range(patientNumber / 2):
fname = random.choice(first_names)
lname = random.choice(last_names)
Patient(first_name=fname + " " + random.choice(first_names),
last_name=random.choice(last_names) + " " + lname,
status=Patient.DISCHARGED,
gender="F",
birthdate=self.dateRandom("1960-01-01", "2000-01-01",
'%Y-%m-%d'),
phone="234" + str(random.randint(100, 999)) +
str(random.randint(100, 999)),
email=fname + "." + lname + "@mail.com").save()
def test_import_adaptive_data_to_database(self):
# Make a test sample
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
# Model can read in a file
Clonotype.import_adaptive(s, 'clonotypes/tests/data/test_adaptive.tsv')
all_clonotypes = Clonotype.objects.all()
self.assertEquals(len(all_clonotypes), 100)
def test_blank_true_for_non_required_fields(self, patientd):
"""
mixer don't autopopulate blank fields
"""
d = {i: patientd[i] for i in ['name', 'firstname', 'birthdate']}
a = Patient(name=d['name'],
firstname=d['firstname'],
birthdate=d['birthdate'])
a.save()
b = Patient.objects.get(id=a.id)
assert a == b
def test_patient_has_disease(self):
all_patients_in_db = Patient.objects.all()
self.assertEquals(len(all_patients_in_db), 0)
# can create a patient that is male
man = Patient()
man.disease = "Ankylosing Spondylitis"
man.save()
# check db to see if patient exists
man_in_db = Patient.objects.get(disease=man.disease)
self.assertEquals(man.disease, man_in_db.disease)
def test_import_miTCR_to_database(self):
# Make a test sample
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
# Model can read in a file
Clonotype.import_mitcr(s, 'clonotypes/tests/data/test_mitcr.txt')
all_clonotypes = Clonotype.objects.all()
self.assertEquals(len(all_clonotypes), 100)
self.fail('todo')
def test_patient_has_name(self):
# first check that db is empty
all_patients_in_db = Patient.objects.all()
self.assertEquals(len(all_patients_in_db), 0)
# can create a patient that is male
man = Patient()
man.name = "Vernon Davis"
man.save()
# check db to see if patient exists
man_in_db = Patient.objects.get(name=man.name)
self.assertEquals(man.name, man_in_db.name)
def test_patient_has_birthday(self):
all_patients_in_db = Patient.objects.all()
self.assertEquals(len(all_patients_in_db), 0)
# can create a patient that is male
man = Patient()
# man.birthday = timezone.now()
man.birthday = datetime.date(2011, 11, 11)
man.save()
# check db to see if patient exists
man_in_db = Patient.objects.get(birthday=man.birthday)
self.assertEquals(man.birthday, man_in_db.birthday)
def consult(request):
if request.method == "POST":
form = request.POST
consult = Consultation()
pat_name = Patient()
pat_name.name = form['patient_id']
consult.medical_history = form['medical_history']
consult.admission = form['admission']
consult.test_types = form['test_types']
consult.notes = form['notes']
consult.prescription = form['prescription']
consult.save() #insert in database
#give us a new id of the recorded item
return redirect('patient:detail', patient.pk)
return render(request, 'consultations/consult.html')
def index(request):
try:
dept = get_object_or_404(Department, pk = request.user.profile.department.pk)
except:
return HttpResponse('You are not assigned to any departments')
# queues = dept.get_queues()
queues = Queue.get_all_queues_of_hospital(dept.hospital)
# patients_visited_today = Patient.total_number_of_patients_today()
first_queue = dept.queue_set.first()
if first_queue:
average_wait_time =first_queue.get_waittime()
else:
average_wait_time = 0
active_patients = VirtualQueue.get_active_patients()
bounce_rate = VirtualQueue.get_bounce_rate()
unique_patients = Patient.get_total_number_of_patients()
context={
'queues': queues,
'department': dept,
'average_wait_time' : average_wait_time,
'active_patients' : active_patients,
'unique_patients' : unique_patients,
'bounce_rate' : bounce_rate,
# 'patients_visited_today' : patients_visited_today,
}
return render(request, 'queues/index.html', context)
def Add_patient(request):
if request.method =="POST":
form =request.POST
#print(form)
patient= Patient()
patient.name = form['name']
patient.mobile = form['mobile']
patient.id_number = form['id_number']
patient.address = form['address']
patient.age = form['age']
patient.gender = form['gender']
#patient.address = form['address']
patient.save() #insert in database
#give us a new id of the recorded item
return redirect ('patients:detail', patient.pk)
return render(request, 'patients/add_patient.html')
def test_create_clonotypes_for_a_sample(self):
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
r = RecombinationFactory()
c = Clonotype(
sample=s,
recombination=r,
frequency=9.336458E-6,
count=2,
)
c.save()
# Get all clonotypes from database
all_clonotypes = Clonotype.objects.all()
self.assertEqual(all_clonotypes[0], c)
def create(self, validated_data):
user = self.context.get('request').user
if user.is_authenticated:
# hospital = get_user_hospital(user)
# if hospital is None:
# raise serializers.ValidationError('Unknown hospital')
# validated_data['hospital'] = hospital
user = get_user_profile(user)
assigned_caregivers = validated_data.pop("assigned_caregivers",
None)
bed_id = validated_data.pop("bed", None)
start_date = validated_data.pop("stay_start_date", None)
validated_data.pop("stay_id", None)
patient = Patient(**validated_data)
if bed_id:
bed = Bed.objects.filter(id=bed_id).first()
if bed is None:
raise serializers.ValidationError('Bed id (' + bed_id +
') was not found')
rea = bed.unit.reanimation_service if bed.unit else None
if rea is None: # should never happen
raise serializers.ValidationError(
f'Bed id ({bed_id}) does not belong to a Reanimation service'
)
if rea not in user.authorized_reanimation_services.all():
raise serializers.ValidationError(
f'The bed is in Reanimation {bed_id}, and the user can\'t manage it'
)
if bed.is_unusable:
raise serializers.ValidationError(
f'The bed {bed.unit_index} in Reanimation {bed_id} is not usable'
)
if get_current_unit_stay(bed):
raise serializers.ValidationError(
f'The bed {bed.unit_index} in Reanimation {bed_id} is already occupied'
)
patient.current_reanimation_service = rea
patient.save()
patient.assigned_caregivers.set(assigned_caregivers)
UnitStay.objects.create(created_by=user,
patient=patient,
bed=bed,
start_date=start_date)
else:
patient.save()
patient.assigned_caregivers.set(assigned_caregivers)
return patient
else:
raise PermissionDenied
class PatientCVsViewSet(viewsets.ModelViewSet):
queryset = Patient.all(active=True)
serializer_class = PatientSerializer
def retrieve(self, request, *args, **kwargs):
patient = self.get_object()
return self.buildResponse(patient)
#Refactor this URGENT
def buildResponse(self, patient):
headers = CVGroup.all()
headerSerialized = CVGroupSerializer(headers, many=True)
results = []
for group in headers:
obj = {"group": group.title}
cvs = CVPatient.all(patient=patient, group=group)
content = []
cvsSplitedByDate = [
list(grp)
for i, grp in groupby(sorted(cvs.values()),
key=lambda item: item["measure_date"])
]
# These nested fors hurts my soul, but i don't know a better solution
for cvsInThatDate in cvsSplitedByDate:
cvToAddInResponse = {
"measure_date":
cvsInThatDate[0]["measure_date"].strftime("%Y-%m-%d %H:%M")
}
for cv in cvsInThatDate:
cvName = ClinicalVariable.objects.get(
id=cv["variable_id"]).variable
cvToAddInResponse[cvName] = cv["value"]
content += [cvToAddInResponse]
obj["content"] = content
results += [obj]
return Response({"headers": headerSerialized.data, "results": results})
@list_route(methods=['post'])
@transaction.atomic
def addVariables(self, request, *args, **kwargs):
measure_date = timezone.now()
group = CVGroup.objects.get(title=request.data["group"])
patient = Patient.objects.get(id=request.data["patient"])
for cv in request.data:
if (cv != "group" and cv != "patient"):
variable = cv
value = request.data[cv]
CVPatient.new(patient, group, variable, value, measure_date)
return self.buildResponse(patient)
def add_patient(request,room_name):
if request.method == 'POST':
form = AdminPatientRegistrationForm(request.POST)
if form.is_valid():
patient = Patient(
first_name=form.cleaned_data['first_name'],
last_name=form.cleaned_data['last_name'],
email=form.cleaned_data.get('email'),
phone_number = form.cleaned_data.get('phone_number'),
age = form.cleaned_data['age'],
gender = form.cleaned_data['gender'],
verified=True,
added_by = request.user
)
patient.save()
queue = Queue.get_queue_by_name(name=room_name)
inqueue = VirtualQueue(patient=patient, queue=queue)
inqueue.save()
send_update_notification(room_name)
return redirect('queues:room', room_name)
def get_patients_qs(self):
samples = set()
node_ids = [n.pk for n in self.analysisnode_ptr.get_roots()]
roots = AnalysisNode.objects.filter(
pk__in=node_ids).select_subclasses()
for node in roots:
samples.update(node.get_samples())
return Patient.filter_for_user(
self.analysis.user).filter(sample__in=samples)
def create_patient_match_phenotypes(self, phenotype):
patient = Patient(phenotype=phenotype)
patient.save(phenotype_matcher=self.phenotype_matcher)
patient.process_phenotype_if_changed(
phenotype_matcher=self.phenotype_matcher)
return patient.patient_text_phenotype.phenotype_description.get_results(
)
def _update_patient(self, patient, row, new=False):
patient.unique_id = row["Patient Number"]
patient.government_id = row["State Patient Number"]
patient.diagnosed_date = datetime.strptime(row["Date Announced"],
"%d/%m/%Y")
if row["Age Bracket"].strip():
patient.age = int(row["Age Bracket"])
if row["Gender"] == "M":
patient.gender = Gender.MALE
elif row["Gender"] == "F":
patient.gender = Gender.FEMALE
elif row["Gender"]:
patient.gender = Gender.OTHERS
else:
patient.gender = Gender.UNKNOWN
city = row.get("Detected City", None).strip()
patient.detected_city = city
patient.detected_district = row["Detected District"]
state = row.get("Detected State", None).strip()
patient.detected_state = state
if new or patient.detected_city != city:
patient.detected_city_pt = Patient.get_point_for_location(
city=city, state=state)
patient.current_location_pt = patient.detected_city_pt
patient.nationality = ""
if row["Current Status"] in PatientStatus.CHOICES:
patient.current_status = row["Current Status"]
patient.status_change_date = self._safe_parse_datetime(
row["Status Change Date"])
patient.notes = row["Notes"]
if row["Backup Notes"].strip() and row["Backup Notes"] != row["Notes"]:
patient.notes += ".\n" + row["Backup Notes"]
patient.nationality = row["Nationality"]
patient.save()
links = row["Contracted from which Patient (Suspected)"].split(",")
if new or patient.contacts.count() != len(links):
self._add_contacts(patient, links)
sources = [
row[s] for s in ["Source_1", "Source_2", "Source_3"]
if row.get(s, "").strip()
]
if new or patient.source_set.count() != len(sources):
self._add_sources(patient, sources)
def create(self, request):
try:
result = ''
data = request.POST.dict().get('data')
try:
data = json.loads(data)
except Exception as e:
print(e)
pass
patient = data.get('patient')
patient_name = patient.get('name').strip()
patients = Patient.objects.filter(name=patient_name)
if len(patients) > 0:
return HttpResponse(status=400)
p = Patient()
p.name = patient_name
p.age = patient.get('age').strip()
p.phone = patient.get('phone').strip()
p.gender = patient.get('gender').strip()
p.save()
treatments = data.get('treatments')
for treatment in treatments:
pictures = treatment.get('pictures')
t = Treatment()
t.name = treatment.get('name').strip()
t.detail = treatment.get('detail')
t.patient = p
t.save()
for picture in pictures:
pic = Picture()
pic.treatment = t
pic.name = picture.get('name').strip()
pic.data = picture.get('data')
pic.save()
return HttpResponse(status=201)
except Exception as e:
return HttpResponse(status=500)
def test_patient_objects_are_named_after_their_name(self):
p = Patient()
p.name = "Lady Gaga"
self.assertEquals(unicode(p), "Lady Gaga")
def test_patient_has_gender(self):
# first check that db is empty
all_patients_in_db = Patient.objects.all()
self.assertEquals(len(all_patients_in_db), 0)
# can create a patient that is male
man = Patient()
man.gender = "M"
man.save()
# check db to see if patient exists
men_in_db = Patient.objects.filter(gender="M")
self.assertEquals(len(men_in_db), 1)
# can create a patient that is female
woman = Patient()
woman.gender = "F"
woman.save()
women_in_db = Patient.objects.filter(gender="F")
self.assertEquals(len(women_in_db), 1)
# can create a patient with unknown gender
person = Patient()
person.save()
androgynous_people_in_db = Patient.objects.filter(gender="")
self.assertEquals(len(androgynous_people_in_db), 1)
def test_patient_correpted_data(ss):
"should not fail with corrupted date, because of readonly schema"
a = Patient(name="ùlùlù#", firstname="mkljlij", birthdate="1234-12-12")
a.save()
patients_detail(ss, a.id)
patients_list(ss)
def listAdmitted(self, request, *args, **kwargs):
'''
Return a list of active patients that are admitted in the hospital
'''
self.queryset = Patient.all(status=Patient.ADMITTED)
return super(PatientViewSet, self).list(request, *args, **kwargs)
def populate():
hosp1 = Hospital(name='Strong')
hosp2 = Hospital(name='Rochester General')
hosp1.save()
hosp2.save()
user_content = ContentType.objects.get_for_model(User)
patientPerm = Permission.objects.create(codename='patient',
name='Is Patient',
content_type=user_content)
doctorPerm = Permission.objects.create(codename='doctor',
name='Is Doctor',
content_type=user_content)
nursePerm = Permission.objects.create(codename='nurse',
name='Is Nurse',
content_type=user_content)
patientPerm.save()
doctorPerm.save()
nursePerm.save()
patientuser1 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
patientuser1.first_name = 'Test'
patientuser1.last_name = 'Patient'
patientuser1.user_permissions.add(patientPerm)
patientuser1.save()
patient1 = Patient(firstName= 'Test',\
lastName= 'Patient', \
hospital=hosp1, \
userNameField='test_patient', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='test road.', \
phone='(888) 888-8888', \
insuranceID= '001', \
insuranceName='testcare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient1.save()
patientuser2 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
patientuser2.first_name = 'Richard'
patientuser2.last_name = 'Posterior'
patientuser2.user_permissions.add(patientPerm)
patientuser2.save()
patient2 = Patient(firstName= 'Richard',\
lastName= 'Posterior', \
hospital=hosp1, \
userNameField='richard', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='007 Bond st.', \
phone='(888) 999-8888', \
insuranceID= '002', \
insuranceName='apathetiCare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient2.save()
patientuser3 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
patientuser3.first_name = 'Bill'
patientuser3.last_name = 'Gates'
patientuser3.user_permissions.add(patientPerm)
patientuser3.save()
patient3 = Patient(firstName= 'Bill',\
lastName= 'Gates', \
hospital=hosp2, \
userNameField='bill', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='010 Silicon Val.', \
phone='(888) 777-8888', \
insuranceID= '003', \
insuranceName='apathetiCare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient3.save()
patientuser4 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
patientuser4.first_name = 'Rick'
patientuser4.last_name = 'Astley'
patientuser4.user_permissions.add(patientPerm)
patientuser4.save()
patient4 = Patient(firstName= 'Rick',\
lastName= 'Astley', \
hospital=hosp2, \
userNameField='rastley', \
email='*****@*****.**', \
city='You', \
state='Down.', \
address1='Gunna 137.', \
phone='(YOU) 11P-N3V4', \
insuranceID= '004', \
insuranceName='notGunnaHurtYou', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient4.save()
doctorUser1 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
doctorUser1.first_name = 'Test'
doctorUser1.last_name = 'Doctor'
doctorUser1.user_permissions.add(doctorPerm)
doctorUser1.save()
doctor1 = Doctor(userNameField= 'test_doctor',\
firstName= 'Test',\
lastName= 'Doctor',\
phone= '(333) 333-3333')
doctor1.save()
doctorUser2 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
doctorUser2.first_name = 'Test'
doctorUser2.last_name = 'Doctor'
doctorUser2.user_permissions.add(doctorPerm)
doctorUser2.save()
doctor2 = Doctor(userNameField= 'mister',\
firstName= 'Mister',\
lastName= 'Labotamy',\
phone= '(585) 315-6030')
doctor2.save()
nurseUser1 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
nurseUser1.first_name = 'Test'
nurseUser1.last_name = 'Nurse'
nurseUser1.user_permissions.add(nursePerm)
nurseUser1.save()
nurse1 = Nurse(userNameField = 'test_nurse',\
firstName = 'Test',\
lastName = 'Nurse',\
phone = '(555) 555-5555',\
hospital = hosp1)
nurse1.save()
nurseUser2 = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
nurseUser2.first_name = 'Amy'
nurseUser2.last_name = 'Nursington'
nurseUser2.user_permissions.add(nursePerm)
nurseUser2.save()
nurse2 = Nurse(userNameField = 'amy',\
firstName = 'Amy',\
lastName = 'Nursington',\
phone = '(444) 444-4444',\
hospital = hosp2)
nurse2.save()
admin = User.objects.create_superuser(username='******',
password='******',
email='*****@*****.**')
admin.first_name = 'Test'
admin.last_name = 'Admin'
admin.save()
def populate():
hosp = Hospital(name = 'Test Hospital')
hosp.save()
user_content = ContentType.objects.get_for_model(User)
patientPerm = Permission.objects.create(codename='patient',\
name='Is Patient',\
content_type=user_content)
doctorPerm = Permission.objects.create(codename='doctor',\
name='Is Doctor',\
content_type=user_content)
nursePerm = Permission.objects.create(codename='nurse',\
name='Is Nurse',\
content_type=user_content)
patientPerm.save()
doctorPerm.save()
nursePerm.save()
u1 = User.objects.create_user(username='******',\
email='*****@*****.**',\
password = '******')
u1.first_name = 'Test'
u1.last_name = 'Patient'
u1.user_permissions.add(patientPerm)
u1.save()
u2 = User.objects.create_user(username='******',\
email='*****@*****.**',\
password = '******')
u2.first_name = 'Test'
u2.last_name = 'Doctor'
u2.user_permissions.add(doctorPerm)
u2.save()
u3 = User.objects.create_user(username='******',\
email='*****@*****.**',\
password = '******')
u3.first_name = 'Test'
u3.last_name = 'Nurse'
u3.user_permissions.add(nursePerm)
u3.save()
p1 = Patient(firstName= 'Test',\
lastName= 'Patient', \
hospital=hosp, \
userNameField='test_patient', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='test road.', \
phone='(888) 888-8888', \
insuranceID= '001', \
insuranceName='testcare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
p1.save()
doc = Doctor(userNameField= 'test_doctor',\
firstName= 'Test',\
lastName= 'Doctor',\
phone= '(555) 555-5555')
doc.save()
nur = Nurse(userNameField = 'test_nurse',\
firstName = 'Test',\
lastName = 'Nurse',\
phone = '(555) 555-5555',\
hospital = hosp)
nur.save()
from datetime import date
Patient.objects.all().delete()
with open('Patients.csv', encoding='cp1251') as file:
reader = DictReader(file)
patients = []
for row in reader:
day, month, year = (int(x) for x in row['DateReceiving'].split('.'))
if row['LastName']=='':
log.warn('Empty last name for %s', row['PatientNumber'])
row['LastName']='!!{}!!'.format(row['PatientNumber'])
patients += [Patient(
id = row['PatientNumber'],
last_name = row['LastName'],
first_name = row['FirstName'],
middle_name = row['MiddleName'],
registration_date = date(year, month, day),
years = row['Years'] or None ,
months = row['Months'] or None,
attending_doctor = row['Director'])]
Patient.objects.bulk_create(patients)
Patient.analyzes.through.objects.all().delete()
with open('Analyses.csv', encoding='cp1251') as file:
reader = DictReader(file)
analyzes = {}
for row in reader:
if row['Appendix']!='+':
log.warn('Strange appendix for (%s, %s)', row['PatientNumber'], row['AllergenNumber'])
if row['OD']!='':
def patients_qs_for_ontology_term(user, ontology_term):
return Patient.filter_for_user(user).filter(
**{
PATIENT_ONTOLOGY_TERM_PATH: ontology_term
}).order_by("id")
def get_patient_form(request):
return Response(Patient.get_react_description())
def _create_new_patient(self, row):
print(f"Adding patient {row['Patient Number']}")
patient = Patient()
self._update_patient(patient, row, new=True)
def _create_new_patient(row):
print(f"Adding patient {row['Patient number']}")
patient = Patient()
patient.unique_id = row["Patient number"]
patient.diagnosed_date = datetime.strptime(row["Date Announced"],
"%d/%m/%Y")
patient.status_change_date = datetime.strptime(
row["Status Change Date"], "%d/%m/%Y")
if row["Age Bracket"].strip():
patient.age = int(row["Age Bracket"])
if row["Gender"] == "M":
patient.gender = Gender.MALE
elif row["Gender"] == "F":
patient.gender = Gender.FEMALE
elif row["Gender"]:
patient.gender = Gender.OTHERS
else:
patient.gender = Gender.UNKNOWN
city = row.get("Detected City", None).strip()
patient.detected_city = city
patient.detected_district = row["Detected District"]
state = row.get("Detected State", None).strip()
patient.detected_state = state
patient.detected_city_pt = Patient.get_point_for_location(city=city,
state=state)
patient.current_location_pt = patient.detected_city_pt
patient.nationality = ""
if row["Current Status"] in PatientStatus.CHOICES:
patient.current_status = row["Current Status"]
patient.notes = row["Notes"]
patient.source = "\n".join(
[row["Source_1"], row["Source_2"], row["Source_3"]]).strip()
patient.nationality = row["Nationality"]
patient.save()
def _create_new_patient(row):
print(f"Adding patient {row['Patient number']}")
patient = Patient()
patient.unique_id = row["Patient number"]
patient.government_id = row["State Patient Number"]
patient.diagnosed_date = datetime.strptime(row["Date Announced"],
"%d/%m/%Y")
if row["Age Bracket"].strip():
patient.age = int(row["Age Bracket"])
if row["Gender"] == "M":
patient.gender = Gender.MALE
elif row["Gender"] == "F":
patient.gender = Gender.FEMALE
elif row["Gender"]:
patient.gender = Gender.OTHERS
else:
patient.gender = Gender.UNKNOWN
city = row.get("Detected City", None).strip()
patient.detected_city = city
patient.detected_district = row["Detected District"]
state = row.get("Detected State", None).strip()
patient.detected_state = state
patient.detected_city_pt = Patient.get_point_for_location(city=city,
state=state)
patient.current_location_pt = patient.detected_city_pt
patient.nationality = ""
if row["Current Status"] in PatientStatus.CHOICES:
patient.current_status = row["Current Status"]
patient.status_change_date = datetime.strptime(
row["Status Change Date"], "%d/%m/%Y")
patient.notes = row["Notes"]
if row["Backup Notes"].strip() and row["Backup Notes"] != row["Notes"]:
patient.notes += ".\n" + row["Backup Notes"]
patient.nationality = row["Nationality"]
patient.save()
links = row["Contracted from which Patient (Suspected)"].split(",")
for link in links:
link = link.strip().strip("P")
try:
contact = Patient.objects.get(unique_id=link)
patient.contacts.add(contact)
except Patient.DoesNotExist:
continue
patient.save()
for source in ["Source_1", "Source_2", "Source_3"]:
text = row.get(source, "")
if not text:
continue
if text.startswith("http") or text.startswith("www"):
patient.source_set.create(url=text, is_verified=True)
else:
patient.source_set.create(description=text, is_verified=True)
def listDischarged(self, request, *args, **kwargs):
'''
Return a list of active patients that are discharged from the hospital
'''
self.queryset = Patient.all(status=Patient.DISCHARGED)
return super(PatientViewSet, self).list(request, *args, **kwargs)
def gen_patient(self, mrn):
patient = Patient()
patient.mrn = mrn
if randint(0, 1):
patient.gender = 'male'
patient.first_name = self._factory.first_name_male()
patient.middle_name = self._factory.first_name_male()
else:
patient.gender = 'female'
patient.first_name = self._factory.first_name_female()
patient.middle_name = self._factory.first_name_female()
patient.last_name = self._factory.last_name()
offset = timedelta(days=randint(28, 67) * 365)
patient.birthdate = (self._factory.date_time_this_century() - offset)
# Values are in centimeters
patient.height = randint(140, 180)
# Values are in kg
patient.weight = randint(60, 90) + round(random(), 2)
patient.is_sample = True
return patient
# Start making the object
for index, item in df.iterrows():
print(index)
p = Patient(
case_number = item['Case #'],
sex = item['Sex'],
age = item['Age'],
nationality = item['Nationality'],
overseas_travel = overseas(item['OverseasTravelHistory']),
country_visited_0 = item['Country1Visited'],
country_visited_1 = item['Country2Visited'],
country_visited_2 = '',
exposure = item['Exposure'],
# exposure_link = '',
# symptoms = symptoms(item['Symptoms']),
onset_date = date_helper(item['OnsetMonth'],item['OnsetDate']),
admission_date = date_helper(item['AdmissionMonth'],item['AdmissionDate']),
lab_confirmation_date = date_helper(item['LabConfirmMonth'],item['LabConfirmDate']),
admitted_to = hospital(item['HospitalID']),
residence_city_mun = item['ResidenceCityMun'],
city_mun_psgc = item['PSGC_MUNI'],
residence_prov = item['ResidenceProv'],
prov_psgc = item['PSGC_PROV'],
status = item['Status'],
death_date = date_helper(item['DeathMonth'],item['DeathDate']),
death_cause = item['DeathCause'],
remarks = item['Remarks']
)
p.save()
symptoms(p,item['Symptoms'])
def populate():
hosp = Hospital(name='Test Hospital')
hosp.save()
user_content = ContentType.objects.get_for_model(User)
patientPerm = Permission.objects.create(codename='patient',\
name='Is Patient',\
content_type=user_content)
doctorPerm = Permission.objects.create(codename='doctor',\
name='Is Doctor',\
content_type=user_content)
nursePerm = Permission.objects.create(codename='nurse',\
name='Is Nurse',\
content_type=user_content)
patientPerm.save()
doctorPerm.save()
nursePerm.save()
u1 = User.objects.create_user(username='******',\
email='*****@*****.**',\
password = '******')
u1.first_name = 'Test'
u1.last_name = 'Patient'
u1.user_permissions.add(patientPerm)
u1.save()
u2 = User.objects.create_user(username='******',\
email='*****@*****.**',\
password = '******')
u2.first_name = 'Test'
u2.last_name = 'Doctor'
u2.user_permissions.add(doctorPerm)
u2.save()
u3 = User.objects.create_user(username='******',\
email='*****@*****.**',\
password = '******')
u3.first_name = 'Test'
u3.last_name = 'Nurse'
u3.user_permissions.add(nursePerm)
u3.save()
p1 = Patient(firstName= 'Test',\
lastName= 'Patient', \
hospital=hosp, \
userNameField='test_patient', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='test road.', \
phone='(888) 888-8888', \
insuranceID= '001', \
insuranceName='testcare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
p1.save()
doc = Doctor(userNameField= 'test_doctor',\
firstName= 'Test',\
lastName= 'Doctor',\
phone= '(555) 555-5555')
doc.save()
nur = Nurse(userNameField = 'test_nurse',\
firstName = 'Test',\
lastName = 'Nurse',\
phone = '(555) 555-5555',\
hospital = hosp)
nur.save()
def populate():
hosp1 = Hospital(name = 'Strong')
hosp2 = Hospital(name = 'Rochester General')
hosp1.save()
hosp2.save()
user_content = ContentType.objects.get_for_model(User)
patientPerm = Permission.objects.create(codename='patient',name='Is Patient',content_type=user_content)
doctorPerm = Permission.objects.create(codename='doctor',name='Is Doctor',content_type=user_content)
nursePerm = Permission.objects.create(codename='nurse',name='Is Nurse',content_type=user_content)
patientPerm.save()
doctorPerm.save()
nursePerm.save()
patientuser1 = User.objects.create_user(username='******',email='*****@*****.**',password = '******')
patientuser1.first_name = 'Test'
patientuser1.last_name = 'Patient'
patientuser1.user_permissions.add(patientPerm)
patientuser1.save()
patient1 = Patient(firstName= 'Test',\
lastName= 'Patient', \
hospital=hosp1, \
userNameField='test_patient', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='test road.', \
phone='(888) 888-8888', \
insuranceID= '001', \
insuranceName='testcare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient1.save()
patientuser2 = User.objects.create_user(username='******',email='*****@*****.**',password = '******')
patientuser2.first_name = 'Richard'
patientuser2.last_name = 'Posterior'
patientuser2.user_permissions.add(patientPerm)
patientuser2.save()
patient2 = Patient(firstName= 'Richard',\
lastName= 'Posterior', \
hospital=hosp1, \
userNameField='richard', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='007 Bond st.', \
phone='(888) 999-8888', \
insuranceID= '002', \
insuranceName='apathetiCare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient2.save()
patientuser3 = User.objects.create_user(username='******',email='*****@*****.**',password = '******')
patientuser3.first_name = 'Bill'
patientuser3.last_name = 'Gates'
patientuser3.user_permissions.add(patientPerm)
patientuser3.save()
patient3 = Patient(firstName= 'Bill',\
lastName= 'Gates', \
hospital=hosp2, \
userNameField='bill', \
email='*****@*****.**', \
city='Rochester', \
state='New York', \
address1='010 Silicon Val.', \
phone='(888) 777-8888', \
insuranceID= '003', \
insuranceName='apathetiCare', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient3.save()
patientuser4 = User.objects.create_user(username='******',email='*****@*****.**',password = '******')
patientuser4.first_name = 'Rick'
patientuser4.last_name = 'Astley'
patientuser4.user_permissions.add(patientPerm)
patientuser4.save()
patient4 = Patient(firstName= 'Rick',\
lastName= 'Astley', \
hospital=hosp2, \
userNameField='rastley', \
email='*****@*****.**', \
city='You', \
state='Down.', \
address1='Gunna 137.', \
phone='(YOU) 11P-N3V4', \
insuranceID= '004', \
insuranceName='notGunnaHurtYou', \
emergencyContactEmail='*****@*****.**', \
emergencyContactFirstName='Stuart', \
emergencyContactLastName='Burtner', \
emergencyContactPhone='(555) 555-5555', \
medicalInformation='nothing')
patient4.save()
doctorUser1 = User.objects.create_user(username='******',email='*****@*****.**', password = '******')
doctorUser1.first_name = 'Test'
doctorUser1.last_name = 'Doctor'
doctorUser1.user_permissions.add(doctorPerm)
doctorUser1.save()
doctor1 = Doctor(userNameField= 'test_doctor',\
firstName= 'Test',\
lastName= 'Doctor',\
phone= '(333) 333-3333')
doctor1.save()
doctorUser2 = User.objects.create_user(username='******',email='*****@*****.**', password = '******')
doctorUser2.first_name = 'Test'
doctorUser2.last_name = 'Doctor'
doctorUser2.user_permissions.add(doctorPerm)
doctorUser2.save()
doctor2 = Doctor(userNameField= 'mister',\
firstName= 'Mister',\
lastName= 'Labotamy',\
phone= '(585) 315-6030')
doctor2.save()
nurseUser1 = User.objects.create_user(username='******',email='*****@*****.**',password = '******')
nurseUser1.first_name = 'Test'
nurseUser1.last_name = 'Nurse'
nurseUser1.user_permissions.add(nursePerm)
nurseUser1.save()
nurse1 = Nurse(userNameField = 'test_nurse',\
firstName = 'Test',\
lastName = 'Nurse',\
phone = '(555) 555-5555',\
hospital = hosp1)
nurse1.save()
nurseUser2 = User.objects.create_user(username='******',email='*****@*****.**',password = '******')
nurseUser2.first_name = 'Amy'
nurseUser2.last_name = 'Nursington'
nurseUser2.user_permissions.add(nursePerm)
nurseUser2.save()
nurse2 = Nurse(userNameField = 'amy',\
firstName = 'Amy',\
lastName = 'Nursington',\
phone = '(444) 444-4444',\
hospital = hosp2)
nurse2.save()
admin = User.objects.create_superuser(username='******',password='******',email='*****@*****.**')
admin.first_name='Test'
admin.last_name='Admin'
admin.save()