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Commit a8c0902e authored by Carlos Vega's avatar Carlos Vega
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moved redcap test instance token and url to settings

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smash/smash/settings.py
+ 5
− 0
View file @ a8c0902e
......@@ -23,6 +23,11 @@ PROJECT_PATH = os.path.abspath(os.path.dirname(__file__))
# Quick-start development settings - unsuitable for production
# See https://docs.djangoproject.com/en/1.10/howto/deployment/checklist/
# To run the unit tests we need a redcap instance.
# UL
REDCAP_TEST_API_TOKEN = "5DC21D45E3A2E068659F11046EA88734"
REDCAP_TEST_URL = "https://luxparktest.lcsb.uni.lu/redcap/"
COPYRIGHT_NOTE = "2024 Bioinformatics Core, Luxembourg Centre for Systems Biomedicine"
DEBUG = True
......
smash/web/tests/functions.py
+ 180
− 128
View file @ a8c0902e
......@@ -6,14 +6,46 @@ from typing import Union
from django.contrib.auth.models import Permission
from django.contrib.auth import get_user_model
from django.utils.timezone import make_aware, is_aware
from web.models import Location, AppointmentType, StudySubject, Worker, Visit, Appointment, ConfigurationItem, \
Language, ContactAttempt, FlyingTeam, Availability, Subject, Study, StudyColumns, StudyNotificationParameters, \
VoucherType, VoucherTypePrice, Voucher, Room, Item, WorkerStudyRole, StudyRedCapColumns, EtlColumnMapping, \
SubjectImportData, SubjectType
from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, REDCAP_BASE_URL_CONFIGURATION_TYPE, \
SEX_CHOICES_MALE, CONTACT_TYPES_PHONE, \
MONDAY_AS_DAY_OF_WEEK, COUNTRY_AFGHANISTAN_ID, VOUCHER_STATUS_NEW, GLOBAL_STUDY_ID, DEFAULT_LOCALE_NAME
from django.conf import settings
from web.models import (
Location,
AppointmentType,
StudySubject,
Worker,
Visit,
Appointment,
ConfigurationItem,
Language,
ContactAttempt,
FlyingTeam,
Availability,
Subject,
Study,
StudyColumns,
StudyNotificationParameters,
VoucherType,
VoucherTypePrice,
Voucher,
Room,
Item,
WorkerStudyRole,
StudyRedCapColumns,
EtlColumnMapping,
SubjectImportData,
SubjectType,
)
from web.models.constants import (
REDCAP_TOKEN_CONFIGURATION_TYPE,
REDCAP_BASE_URL_CONFIGURATION_TYPE,
SEX_CHOICES_MALE,
CONTACT_TYPES_PHONE,
MONDAY_AS_DAY_OF_WEEK,
COUNTRY_AFGHANISTAN_ID,
VOUCHER_STATUS_NEW,
GLOBAL_STUDY_ID,
DEFAULT_LOCALE_NAME,
)
from web.models.worker_study_role import ROLE_CHOICES_DOCTOR, WORKER_VOUCHER_PARTNER
from web.redcap_connector import RedcapSubject
from web.views.notifications import get_today_midnight_date
......@@ -37,10 +69,12 @@ def create_voucher_type():
def create_voucher_type_price():
return VoucherTypePrice.objects.create(voucher_type=create_voucher_type(),
price=12.34,
start_date=get_today_midnight_date(),
end_date=get_today_midnight_date())
return VoucherTypePrice.objects.create(
voucher_type=create_voucher_type(),
price=12.34,
start_date=get_today_midnight_date(),
end_date=get_today_midnight_date(),
)
def create_empty_study_columns():
......@@ -68,8 +102,9 @@ def create_study(name="test"):
study_columns = StudyColumns.objects.create()
notification_parameters = StudyNotificationParameters.objects.create()
redcap_columns = StudyRedCapColumns.objects.create()
return Study.objects.create(name=name, columns=study_columns, notification_parameters=notification_parameters,
redcap_columns=redcap_columns)
return Study.objects.create(
name=name, columns=study_columns, notification_parameters=notification_parameters, redcap_columns=redcap_columns
)
TEST_ID_COUNTER = 0
......@@ -90,14 +125,16 @@ def create_voucher(study_subject=None, partner=None, worker=None):
if worker is None:
worker = create_worker()
number = str(get_test_id())
return Voucher.objects.create(number=number,
study_subject=study_subject,
issue_date=get_today_midnight_date(),
expiry_date=get_today_midnight_date(),
voucher_type=create_voucher_type(),
usage_partner=partner,
issue_worker=worker,
status=VOUCHER_STATUS_NEW)
return Voucher.objects.create(
number=number,
study_subject=study_subject,
issue_date=get_today_midnight_date(),
expiry_date=get_today_midnight_date(),
voucher_type=create_voucher_type(),
usage_partner=partner,
issue_worker=worker,
status=VOUCHER_STATUS_NEW,
)
def create_empty_notification_parameters():
......@@ -158,7 +195,7 @@ def get_test_study() -> Study:
return create_study("test-study")
def create_appointment_type(code='C', default_duration=10, description='test'):
def create_appointment_type(code="C", default_duration=10, description="test"):
return AppointmentType.objects.create(
code=code,
default_duration=default_duration,
......@@ -172,26 +209,25 @@ def create_contact_attempt(subject=None, worker=None):
if worker is None:
worker = create_worker()
return ContactAttempt.objects.create(subject=subject,
worker=worker,
type=CONTACT_TYPES_PHONE,
datetime_when=get_today_midnight_date(),
success=True,
comment="Successful contact attempt",
)
return ContactAttempt.objects.create(
subject=subject,
worker=worker,
type=CONTACT_TYPES_PHONE,
datetime_when=get_today_midnight_date(),
success=True,
comment="Successful contact attempt",
)
def create_subject():
return Subject.objects.create(
first_name="Piotr",
last_name="Gawron",
sex=SEX_CHOICES_MALE,
country_id=COUNTRY_AFGHANISTAN_ID
first_name="Piotr", last_name="Gawron", sex=SEX_CHOICES_MALE, country_id=COUNTRY_AFGHANISTAN_ID
)
def create_study_subject(subject_id: int = 1, subject: Subject = None, nd_number: str = 'ND0001',
study: Study = None) -> StudySubject:
def create_study_subject(
subject_id: int = 1, subject: Subject = None, nd_number: str = "ND0001", study: Study = None
) -> StudySubject:
if study is None:
study = get_test_study()
if subject is None:
......@@ -201,7 +237,7 @@ def create_study_subject(subject_id: int = 1, subject: Subject = None, nd_number
type=get_control_subject_type(),
screening_number="piotr's number" + str(subject_id),
study=study,
subject=subject
subject=subject,
)
if nd_number is not None: # null value in column "nd_number" violates not-null constraint
study_subject.nd_number = nd_number
......@@ -211,11 +247,11 @@ def create_study_subject(subject_id: int = 1, subject: Subject = None, nd_number
def get_control_subject_type() -> SubjectType:
return SubjectType.objects.filter(name='CONTROL').first()
return SubjectType.objects.filter(name="CONTROL").first()
def get_patient_subject_type() -> SubjectType:
return SubjectType.objects.filter(name='PATIENT').first()
return SubjectType.objects.filter(name="PATIENT").first()
def create_study_subject_with_multiple_screening_numbers(subject_id=1, subject=None, screening_number=None):
......@@ -223,13 +259,13 @@ def create_study_subject_with_multiple_screening_numbers(subject_id=1, subject=N
subject = create_subject()
if screening_number is None:
screening_number = f'E-00{subject_id}; L-00{subject_id}'
screening_number = f"E-00{subject_id}; L-00{subject_id}"
return StudySubject.objects.create(
default_location=get_test_location(),
type=get_control_subject_type(),
screening_number=screening_number,
study=get_test_study(),
subject=subject
subject=subject,
)
......@@ -239,15 +275,12 @@ def create_red_cap_subject():
return result
def create_user(username: str = None, password: str = None, email: str = 'jacob@bla') -> get_user_model():
def create_user(username: str = None, password: str = None, email: str = "jacob@bla") -> get_user_model():
if username is None:
username = 'piotr'
username = "piotr"
if password is None:
password = 'top_secret'
user = get_user_model().objects.create_user(
username=username,
email=email,
password=password)
password = "top_secret"
user = get_user_model().objects.create_user(username=username, email=email, password=password)
create_worker(user)
return user
......@@ -262,49 +295,48 @@ def add_permissions_to_worker(worker, codenames):
def create_worker(user=None, with_test_location=False):
worker = Worker.objects.create(
first_name='piotr',
first_name="piotr",
last_name="gawron",
email='jacob@bla.com',
email="jacob@bla.com",
user=user,
specialization="spec",
unit="LCSB",
phone_number="0123456789"
phone_number="0123456789",
)
if with_test_location:
worker.locations.set([get_test_location()])
worker.save()
WorkerStudyRole.objects.create(
worker=worker, study_id=GLOBAL_STUDY_ID, name=ROLE_CHOICES_DOCTOR)
WorkerStudyRole.objects.create(worker=worker, study_id=GLOBAL_STUDY_ID, name=ROLE_CHOICES_DOCTOR)
return worker
def create_voucher_partner():
worker = Worker.objects.create(
first_name='piotr',
first_name="piotr",
last_name="gawron",
email='jacob@bla.com',
email="jacob@bla.com",
specialization="spec",
unit="LCSB",
phone_number="0123456789"
phone_number="0123456789",
)
WorkerStudyRole.objects.create(
worker=worker, study_id=GLOBAL_STUDY_ID, name=WORKER_VOUCHER_PARTNER)
WorkerStudyRole.objects.create(worker=worker, study_id=GLOBAL_STUDY_ID, name=WORKER_VOUCHER_PARTNER)
return worker
def create_availability(worker=None, available_from=None, available_till=None, day_number=MONDAY_AS_DAY_OF_WEEK):
if available_from is None:
available_from = '8:00'
available_from = "8:00"
if available_till is None:
available_till = '18:00'
available_till = "18:00"
if worker is None:
worker = create_worker()
availability = Availability.objects.create(person=worker,
day_number=day_number,
available_from=available_from,
available_till=available_till,
)
availability = Availability.objects.create(
person=worker,
day_number=day_number,
available_from=available_from,
available_till=available_till,
)
return availability
......@@ -315,10 +347,9 @@ def create_visit(subject: StudySubject = None, datetime_begin=None, datetime_end
datetime_begin = get_today_midnight_date() + datetime.timedelta(days=-31)
if datetime_end is None:
datetime_end = get_today_midnight_date() + datetime.timedelta(days=31)
return Visit.objects.create(datetime_begin=datetime_begin,
datetime_end=datetime_end,
subject=subject,
is_finished=False)
return Visit.objects.create(
datetime_begin=datetime_begin, datetime_end=datetime_end, subject=subject, is_finished=False
)
def create_appointment(visit=None, when=None, length=30) -> Appointment:
......@@ -339,15 +370,14 @@ def create_appointment(visit=None, when=None, length=30) -> Appointment:
length=length,
location=get_test_location(),
status=Appointment.APPOINTMENT_STATUS_SCHEDULED,
datetime_when=when_datetime)
datetime_when=when_datetime,
)
def create_appointment_without_visit(when=None, length=30):
return Appointment.objects.create(
length=length,
location=get_test_location(),
status=Appointment.APPOINTMENT_STATUS_SCHEDULED,
datetime_when=when)
length=length, location=get_test_location(), status=Appointment.APPOINTMENT_STATUS_SCHEDULED, datetime_when=when
)
def create_configuration_item():
......@@ -366,19 +396,24 @@ def create_flying_team(place=None):
return result
def create_item(name='Test item', is_fixed=False, disposable=False):
def create_item(name="Test item", is_fixed=False, disposable=False):
item = Item(name=name, is_fixed=is_fixed, disposable=disposable)
item.save()
return item
def create_room(owner='Test owner', city='Test city',
address='Test address', equipment=None,
floor=1, is_vehicle=False, room_number=1):
def create_room(
owner="Test owner",
city="Test city",
address="Test address",
equipment=None,
floor=1,
is_vehicle=False,
room_number=1,
):
if equipment is None:
equipment = []
room = Room(owner=owner, city=city, address=address,
floor=floor, is_vehicle=is_vehicle, room_number=room_number)
room = Room(owner=owner, city=city, address=address, floor=floor, is_vehicle=is_vehicle, room_number=room_number)
room.save()
room.equipment.set(equipment) # Cannot be made in constructor/with single save
room.save()
......@@ -392,14 +427,14 @@ def create_language(name="French", locale=DEFAULT_LOCALE_NAME) -> Language:
def get_resource_path(filename):
return os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', filename)
return os.path.join(os.path.dirname(os.path.realpath(__file__)), "data", filename)
def format_form_field(value):
if isinstance(value, datetime.date):
return value.strftime('%Y-%m-%d')
return value.strftime("%Y-%m-%d")
elif isinstance(value, datetime.datetime):
return value.strftime('%Y-%m-%d %H:%M')
return value.strftime("%Y-%m-%d %H:%M")
elif value is None:
return ""
else:
......@@ -409,14 +444,12 @@ def format_form_field(value):
def prepare_test_redcap_connection():
Language.objects.create(name="Finnish").save()
Language.objects.create(name="Italian").save()
token_item = ConfigurationItem.objects.filter(
type=REDCAP_TOKEN_CONFIGURATION_TYPE)[0]
token_item = ConfigurationItem.objects.filter(type=REDCAP_TOKEN_CONFIGURATION_TYPE)[0]
# noinspection SpellCheckingInspection
token_item.value = "5DC21D45E3A2E068659F11046EA88734"
token_item.value = settings.REDCAP_TEST_API_TOKEN
token_item.save()
url_item = ConfigurationItem.objects.filter(
type=REDCAP_BASE_URL_CONFIGURATION_TYPE)[0]
url_item.value = "https://luxparktest.lcsb.uni.lu/redcap/"
url_item = ConfigurationItem.objects.filter(type=REDCAP_BASE_URL_CONFIGURATION_TYPE)[0]
url_item.value = settings.REDCAP_TEST_URL
url_item.save()
......@@ -427,49 +460,68 @@ def datetimeify_date(date: Union[datetime.date, str, bytes]) -> datetime.datetim
else:
return make_aware(date)
if isinstance(date, bytes): # If it's bytes, then convert to string and carry on...
date = date.decode('utf8')
date = date.decode("utf8")
if isinstance(date, str): # If it's string, convert to datetime with timezone support
return make_aware(datetime.datetime.strptime(date, '%Y-%m-%d'))
return make_aware(datetime.datetime.strptime(date, "%Y-%m-%d"))
actual_type = str(type(date))
raise TypeError(
f"Date should be either a subclass of 'datetime.date', string or bytes! But is: {actual_type} instead")
f"Date should be either a subclass of 'datetime.date', string or bytes! But is: {actual_type} instead"
)
def create_tns_column_mapping(subject_import_data: SubjectImportData):
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="nd_number",
csv_column_name="donor_id",
table_name=StudySubject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="comments",
csv_column_name="treatingphysician",
table_name=StudySubject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="first_name",
csv_column_name="firstname",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="first_name",
csv_column_name="sig_firstname",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="last_name",
csv_column_name="lastname",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="last_name",
csv_column_name="sig_lastname",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="phone_number",
csv_column_name="phonenr",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="date_born",
csv_column_name="dateofbirth",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(etl_data=subject_import_data,
column_name="next_of_kin_name",
csv_column_name="representative",
table_name=Subject._meta.db_table)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="nd_number",
csv_column_name="donor_id",
table_name=StudySubject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="comments",
csv_column_name="treatingphysician",
table_name=StudySubject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="first_name",
csv_column_name="firstname",
table_name=Subject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="first_name",
csv_column_name="sig_firstname",
table_name=Subject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="last_name",
csv_column_name="lastname",
table_name=Subject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="last_name",
csv_column_name="sig_lastname",
table_name=Subject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="phone_number",
csv_column_name="phonenr",
table_name=Subject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="date_born",
csv_column_name="dateofbirth",
table_name=Subject._meta.db_table,
)
EtlColumnMapping.objects.create(
etl_data=subject_import_data,
column_name="next_of_kin_name",
csv_column_name="representative",
table_name=Subject._meta.db_table,
)
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