def main(
country=None,
site_name=None,
assignment=None,
slots=None,
write_header=None,
filename=None,
assignment_map=None,
):
"""
Adds slots to a dummy `randomisation` list file where all assignments are the same
for each slot.
"""
assignment_map = assignment_map or ["intervention", "control"]
if assignment not in assignment_map:
raise ValueError(f"Invalid assignment. Got {assignment}")
# get site ID and write the file
site_id = get_site_id(site_name, sites=all_sites[country])
with open(filename, "a+", newline="") as f:
writer = csv.DictWriter(
f, fieldnames=["sid", "assignment", "site_name", "country"])
if write_header:
writer.writeheader()
for j in range(1, int(slots)):
sid = str(j).zfill(len(slots))
writer.writerow(
dict(
sid=f"{site_id}{sid}",
assignment=assignment,
site_name=site_name,
country=country,
))
print(f"(*) Added {slots} slots for {site_name}.")
additional=False),
Requisition(show_order=100,
panel=plasma_buffycoat_panel,
required=True,
additional=False),
Requisition(show_order=120,
panel=qpcr_blood_panel,
required=True,
additional=False),
Requisition(
show_order=125,
panel=qpcr24_blood_panel,
required=True,
additional=False,
site_ids=[
get_site_id("blantyre", sites=ambition_sites),
get_site_id("gaborone", sites=ambition_sites),
get_site_id("harare", sites=ambition_sites),
get_site_id("kampala", sites=ambition_sites),
get_site_id("lilongwe", sites=ambition_sites),
get_site_id("mbarara", sites=ambition_sites),
],
),
Requisition(
show_order=200,
panel=wb_paxgene_panel,
required=True,
additional=False,
site_ids=[
get_site_id("blantyre", sites=ambition_sites),
get_site_id("gaborone", sites=ambition_sites),
def test_all(self):
self.assertEqual(get_site_id("reviewer", sites=meta_sites), 1)
self.assertEqual(get_site_id("hindu_mandal", sites=meta_sites), 10)
self.assertEqual(get_site_id("amana", sites=meta_sites), 20)
class TestPredicates(AmbitionTestCaseMixin, TestCase):
app_label = "ambition_subject"
import_randomization_list = True
reference_helper_cls = ReferenceTestHelper
reference_model = "edc_reference.reference"
visit_model = "ambition_subject.subjectvisit"
@classmethod
def setUpClass(cls):
add_or_update_django_sites(apps=django_apps,
sites=ambition_sites,
fqdn=fqdn)
return super().setUpClass()
def update_randomization_list(self, arm):
site = Site.objects.get_current()
RandomizationList.objects.update(site_name=site.name,
subject_identifier=None)
rando = (RandomizationList.objects.filter(
site_name=site.name, assignment=arm).order_by("sid").first())
rando.subject_identifier = self.subject_identifier
rando.save()
def setUp(self):
self.subject_identifier = "111111111"
self.reference_helper = self.reference_helper_cls(
visit_model=self.visit_model,
subject_identifier=self.subject_identifier)
report_datetime = Arrow.fromdatetime(datetime(2017, 7, 7)).datetime
self.reference_helper.create_visit(
report_datetime=report_datetime,
visit_schedule_name="visit_schedule",
schedule_name="schedule",
visit_code=DAY1,
timepoint=Decimal("1.0"),
)
self.reference_helper.create_visit(
report_datetime=report_datetime + relativedelta(days=3),
visit_schedule_name="visit_schedule",
schedule_name="schedule",
visit_code=DAY3,
timepoint=Decimal("1.0"),
)
self.reference_helper.create_visit(
report_datetime=report_datetime + relativedelta(days=5),
visit_schedule_name="visit_schedule",
schedule_name="schedule",
visit_code=DAY5,
timepoint=Decimal("1.0"),
)
@property
def subject_visits(self):
return LongitudinalRefsets(
subject_identifier=self.subject_identifier,
visit_model=self.visit_model,
name=self.visit_model,
reference_model_cls=self.reference_model,
).order_by("report_datetime")
def test_cd4_requisition_required(self):
pc = Predicates()
self.reference_helper.create_for_model(
report_datetime=self.subject_visits[0].report_datetime,
reference_name=f"{self.app_label}.patienthistory",
visit_schedule_name=self.subject_visits[0].visit_schedule_name,
schedule_name=self.subject_visits[0].schedule_name,
visit_code=self.subject_visits[0].visit_code,
timepoint=self.subject_visits[0].timepoint,
cd4_date=(self.subject_visits[0].report_datetime -
relativedelta(months=4)).date(),
)
self.assertTrue(pc.func_require_cd4(self.subject_visits[0]))
def test_cd4_requisition_not_required(self):
pc = Predicates()
self.reference_helper.create_for_model(
report_datetime=self.subject_visits[0].report_datetime,
reference_name=f"{self.app_label}.patienthistory",
visit_schedule_name=self.subject_visits[0].visit_schedule_name,
schedule_name=self.subject_visits[0].schedule_name,
visit_code=self.subject_visits[0].visit_code,
timepoint=self.subject_visits[0].timepoint,
cd4_date=(self.subject_visits[0].report_datetime).date(),
)
self.assertFalse(pc.func_require_cd4(self.subject_visits[0]))
def test_vl_requisition_required(self):
pc = Predicates()
self.reference_helper.create_for_model(
report_datetime=self.subject_visits[0].report_datetime,
reference_name=f"{self.app_label}.patienthistory",
visit_schedule_name=self.subject_visits[0].visit_schedule_name,
schedule_name=self.subject_visits[0].schedule_name,
visit_code=self.subject_visits[0].visit_code,
timepoint=self.subject_visits[0].timepoint,
viral_load_date=(self.subject_visits[0].report_datetime -
relativedelta(months=4)).date(),
)
self.assertTrue(pc.func_require_vl(self.subject_visits[0]))
def test_vl_requisition_not_required(self):
pc = Predicates()
self.reference_helper.create_for_model(
report_datetime=self.subject_visits[0].report_datetime,
reference_name=f"{self.app_label}.patienthistory",
visit_schedule_name=self.subject_visits[0].visit_schedule_name,
schedule_name=self.subject_visits[0].schedule_name,
visit_code=self.subject_visits[0].visit_code,
timepoint=self.subject_visits[0].timepoint,
viral_load_date=(self.subject_visits[0].report_datetime).date(),
)
self.assertFalse(pc.func_require_vl(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("blantyre", sites=ambition_sites))
def test_pkpd_site_eq_blantyre(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("harare", sites=ambition_sites))
def test_pkpd_site_eq_harare(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("gaborone", sites=ambition_sites))
def test_pkpd_site_eq_gaborone(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("capetown", sites=ambition_sites))
def test_pkpd_site_eq_capetown(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("lilongwe", sites=ambition_sites))
def test_pkpd_site_eq_lilongwe(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("kampala", sites=ambition_sites))
def test_pkpd_site_eq_kampala(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(pc.func_require_pkpd_stopcm(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("gaborone", sites=ambition_sites))
def test_qpcr_requisition_site_eq_gaborone(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertTrue(
pc.func_require_qpcr_requisition(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertTrue(
pc.func_require_qpcr_requisition(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("harare", sites=ambition_sites))
def test_qpcr_requisition_site_eq_harare(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertFalse(
pc.func_require_qpcr_requisition(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertFalse(
pc.func_require_qpcr_requisition(self.subject_visits[0]))
@override_settings(SITE_ID=get_site_id("capetown", sites=ambition_sites))
def test_qpcr_24_requisition_site_eq_cape_town(self):
pc = Predicates()
self.update_randomization_list(CONTROL)
self.assertTrue(
pc.func_require_qpcr_requisition(self.subject_visits[0]))
self.update_randomization_list(SINGLE_DOSE)
self.assertTrue(
pc.func_require_qpcr_requisition(self.subject_visits[0]))
APP_NAME = env.str("DJANGO_APP_NAME")
LIVE_SYSTEM = env.str("DJANGO_LIVE_SYSTEM")
ETC_DIR = env.str("DJANGO_ETC_FOLDER")
TEST_DIR = os.path.join(BASE_DIR, APP_NAME, "tests")
ALLOWED_HOSTS = ["*"] # env.list('DJANGO_ALLOWED_HOSTS')
ENFORCE_RELATED_ACTION_ITEM_EXISTS = False
# get site ID from more familiar town name
TOWN = env.str("DJANGO_TOWN")
if TOWN:
SITE_ID = get_site_id(TOWN, sites=inte_sites)
else:
SITE_ID = env.int("DJANGO_SITE_ID")
DEFAULT_APPOINTMENT_TYPE = "hospital"
REVIEWER_SITE_ID = env.int("DJANGO_REVIEWER_SITE_ID")
LOGIN_REDIRECT_URL = env.str("DJANGO_LOGIN_REDIRECT_URL")
SENTRY_ENABLED = env("SENTRY_ENABLED")
INSTALLED_APPS = [
"django.contrib.admin",
"django.contrib.auth",
"django.contrib.contenttypes",
def test_all(self):
self.assertEqual(get_site_id("reviewer", sites=inte_sites), 1)
self.assertEqual(get_site_id("kinoni", sites=inte_sites), 100)
self.assertEqual(get_site_id("bugamba", sites=inte_sites), 110)
self.assertEqual(get_site_id("bwizibwera", sites=inte_sites), 120)
self.assertEqual(get_site_id("ruhoko", sites=inte_sites), 140)
self.assertEqual(get_site_id("kyazanga", sites=inte_sites), 150)
self.assertEqual(get_site_id("bukulula", sites=inte_sites), 160)
self.assertEqual(get_site_id("kojja", sites=inte_sites), 170)
self.assertEqual(get_site_id("mpigi", sites=inte_sites), 180)
self.assertEqual(get_site_id("namayumba", sites=inte_sites), 190)
self.assertEqual(get_site_id("buwambo", sites=inte_sites), 200)
self.assertEqual(get_site_id("kajjansi", sites=inte_sites), 210)
self.assertEqual(get_site_id("tikalu", sites=inte_sites), 220)
self.assertEqual(get_site_id("namulonge", sites=inte_sites), 230)
self.assertEqual(get_site_id("kasanje", sites=inte_sites), 240)
self.assertEqual(get_site_id("kasangati", sites=inte_sites), 250)
if SENTRY_ENABLED:
import sentry_sdk
from sentry_sdk.integrations.django import DjangoIntegration
sentry_sdk.init(dsn=SENTRY_DSN,
integrations=[DjangoIntegration()],
send_default_pii=True)
else:
if env("DJANGO_LOGGING_ENABLED"):
from .logging.standard import LOGGING # noqa
# read SITE specific variables from separate .env file
env.read_env(os.path.join(BASE_DIR, ".env-site"))
COUNTRY = env.str("DJANGO_COUNTRY")
# get site ID from more familiar town name
DJANGO_SITE_NAME = env.str("DJANGO_SITE_NAME")
if DJANGO_SITE_NAME:
SITE_ID = get_site_id(DJANGO_SITE_NAME, sites=inte_sites)
else:
SITE_ID = env.int("DJANGO_SITE_ID")
# if running tests ...
if "test" in sys.argv or "runtests" in sys.argv:
ETC_DIR = os.path.join(BASE_DIR, "inte_edc", "tests", "etc")
KEY_PATH = os.path.join(BASE_DIR, "inte_edc", "tests", "etc")
DJANGO_CRYPTO_FIELDS_TEMP_PATH = env("DJANGO_CRYPTO_FIELDS_TEMP_PATH")
MIGRATION_MODULES = DisableMigrations()
PASSWORD_HASHERS = ("django.contrib.auth.hashers.MD5PasswordHasher", )
DEFAULT_FILE_STORAGE = "inmemorystorage.InMemoryStorage"
if env.str("DJANGO_ETC_FOLDER"):
ETC_DIR = env.str("DJANGO_ETC_FOLDER")
else:
ETC_DIR = BASE_DIR
TEST_DIR = os.path.join(BASE_DIR, APP_NAME, "tests")
ALLOWED_HOSTS = ["*"] # env.list('DJANGO_ALLOWED_HOSTS')
ENFORCE_RELATED_ACTION_ITEM_EXISTS = False
# get site ID from more familiar town name
TOWN = env.str("DJANGO_TOWN")
if TOWN:
SITE_ID = get_site_id(TOWN, sites=ambition_sites)
else:
SITE_ID = env.int("DJANGO_SITE_ID")
DEFAULT_APPOINTMENT_TYPE = "hospital"
REVIEWER_SITE_ID = env.int("DJANGO_REVIEWER_SITE_ID")
LOGIN_REDIRECT_URL = env.str("DJANGO_LOGIN_REDIRECT_URL")
SENTRY_ENABLED = env("SENTRY_ENABLED")
INSTALLED_APPS = [
"django.contrib.admin",
"django.contrib.auth",
"django.contrib.contenttypes",