From a8c0902e361b289e628c8508c42303acbb0de368 Mon Sep 17 00:00:00 2001
From: Carlos Vega <carlos.vega@lih.lu>
Date: Thu, 29 Aug 2024 14:02:46 +0200
Subject: [PATCH] moved redcap test instance token and url to settings
---
smash/smash/settings.py | 5 +
smash/web/tests/functions.py | 308 ++++++++++++++++++++---------------
2 files changed, 185 insertions(+), 128 deletions(-)
diff --git a/smash/smash/settings.py b/smash/smash/settings.py
index 53366991..5d3a28ae 100644
--- a/smash/smash/settings.py
+++ b/smash/smash/settings.py
@@ -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
diff --git a/smash/web/tests/functions.py b/smash/web/tests/functions.py
index 51d91ea3..60eddf74 100644
--- a/smash/web/tests/functions.py
+++ b/smash/web/tests/functions.py
@@ -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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