def test_error_condition2(self):
"""Assert raises if randomization_list_model_cls not updated correctly.
"""
self.populate_list()
site = Site.objects.get_current()
randomization_list_model_cls = site_randomizers.get(
"ambition").model_cls()
randomization_list_model_cls.objects.update(site_name=site.name)
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
rando = site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
rando.registered_subject.sid = None
rando.registered_subject.save()
with self.assertRaises(AlreadyRandomized) as cm:
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
self.assertEqual(cm.exception.code,
randomization_list_model_cls._meta.label_lower)
def test_error_condition3(self):
"""Assert raises if randomization_list_model_cls not updated correctly.
"""
self.populate_list()
site = Site.objects.get(name="gaborone")
randomization_list_model_cls = site_randomizers.get(
"ambition").model_cls()
randomization_list_model_cls.objects.update(site_name=site.name)
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", site=site, user_created="erikvw")
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
randomization_list_model_cls.objects.update(subject_identifier=None)
with self.assertRaises(AlreadyRandomized) as cm:
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
self.assertEqual(cm.exception.code,
"edc_registration.registeredsubject")
def test_for_sites(self):
"""Assert that allocates by site correctly.
"""
randomization_list_model_cls = site_randomizers.get(
"ambition").model_cls()
randomization_list_model_cls.objects.all().delete()
self.populate_list(site_names=self.site_names, per_site=5)
site_names = [
obj.site_name
for obj in randomization_list_model_cls.objects.all()
]
shuffle(site_names)
assert len(site_names) == len(self.site_names * 5)
# consent and randomize 5 for each site
for index, site_name in enumerate(site_names):
site = Site.objects.get(name=site_name)
subject_consent = SubjectConsent.objects.create(
subject_identifier=f"12345{index}",
site=site,
user_created="erikvw")
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
# assert consented subjects were allocated SIDs in the
# correct order per site.
for site_name in site_names:
randomized_subjects = [
(obj.subject_identifier, str(obj.sid))
for obj in randomization_list_model_cls.objects.filter(
allocated_site__name=site_name,
subject_identifier__isnull=False).order_by("sid")
]
for index, obj in enumerate(
SubjectConsent.objects.filter(
site__name=site_name).order_by("consent_datetime")):
rs = RegisteredSubject.objects.get(
subject_identifier=obj.subject_identifier)
self.assertEqual(obj.subject_identifier,
randomized_subjects[index][0])
self.assertEqual(rs.sid, randomized_subjects[index][1])
# clear out any unallocated
randomization_list_model_cls.objects.filter(
subject_identifier__isnull=True).delete()
# assert raises on next attempt to randomize
subject_consent = SubjectConsent.objects.create(
subject_identifier=f"ABCDEF", site=site, user_created="erikvw")
self.assertRaises(
AllocationError,
site_randomizers.get("ambition"),
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
def assignment(self):
randomization_list_model_cls = site_randomizers.get(
self.randomizer_name).model_cls()
subject_identifier = self.cleaned_data.get("subject_identifier")
obj = randomization_list_model_cls.objects.get(
subject_identifier=subject_identifier)
return site_randomizers.get(self.randomizer_name).get_assignment(
{"assignment": obj.assignment})
def test_with_consent_ok(self):
self.populate_list()
site = Site.objects.get_current()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", site=site, user_created="erikvw")
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
def test_str(self):
self.populate_list()
site = Site.objects.get(name="gaborone")
RandomizationList.objects.update(site_name=site.name)
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", site=site, user_created="erikvw")
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
obj = RandomizationList.objects.all().first()
self.assertTrue(str(obj))
def test_with_list_selects_first(self):
self.populate_list()
randomization_list_model_cls = site_randomizers.get(
"ambition").model_cls()
site = Site.objects.get_current()
randomization_list_model_cls.objects.update(site_name=site.name)
first_obj = randomization_list_model_cls.objects.all().first()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
rando = site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
self.assertEqual(rando.sid, first_obj.sid)
def test_with_gender_and_consent(self):
class RandomizerWithGender(Randomizer):
def __init__(self, gender=None, **kwargs):
self.gender = gender
super().__init__(**kwargs)
@property
def extra_required_attrs(self):
return dict(gender=self.gender)
randomizer = site_randomizers.get("default")
randomizer.import_list()
site = Site.objects.get_current()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345",
site=site,
gender=FEMALE,
user_created="erikvw")
try:
RandomizerWithGender(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
gender=FEMALE,
user=subject_consent.user_created,
)
except Exception as e:
self.fail(f"Exception unexpectedly raised. Got {str(e)}.")
class CrfDfHandler(BaseCrfDfHandler):
column_handler_cls = ColumnHandler
na_value = "."
visit_tbl = get_visit_tracking_model().replace(".", "_")
enrollment_tbl = "ambition_screening_subjectscreening"
rando_tbl = site_randomizers.get("default").model.replace(".", "_")
sort_by = ["subject_identifier", "visit_datetime"]
def test_subject_does_not_exist(self):
self.populate_list()
site = Site.objects.get(name="gaborone")
randomization_list_model_cls = site_randomizers.get(
"ambition").model_cls()
randomization_list_model_cls.objects.update(site_name=site.name)
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", site=site, user_created="erikvw")
RegisteredSubject.objects.all().delete()
self.assertRaises(
RandomizationError,
site_randomizers.get("ambition"),
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
def save(self, *args, **kwargs):
self.registered_subject = RegisteredSubject.objects.get(
subject_identifier=self.subject_identifier)
if self.randomizer_name:
randomizer = site_randomizers.get(self.randomizer_name)
self.rando_sid = (randomizer.model_cls().objects.get(
subject_identifier=self.subject_identifier).sid)
super().save(*args, **kwargs)
def test_updates_registered_subject(self):
self.populate_list()
site = Site.objects.get_current()
RandomizationList.objects.update(site_name=site.name)
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
first_obj = RandomizationList.objects.all().first()
rs = RegisteredSubject.objects.get(subject_identifier="12345")
self.assertEqual(rs.subject_identifier, first_obj.subject_identifier)
self.assertEqual(rs.sid, str(first_obj.sid))
self.assertEqual(rs.randomization_datetime,
first_obj.allocated_datetime)
def populate_list(self, site_names=None, per_site=None):
make_test_list(
site_names=site_names or self.site_names,
per_site=per_site,
full_path=os.path.join(
settings.EDC_RANDOMIZATION_LIST_PATH,
site_randomizers.get("ambition").filename,
),
)
RandomizationListImporter(name="ambition", overwrite=True)
def test_cannot_overwrite(self):
site_randomizers._registry = {}
site_randomizers.register(MyRandomizer)
make_test_list(
full_path=MyRandomizer.get_randomization_list_fullpath(),
site_names=self.site_names,
count=5,
)
randomizer = site_randomizers.get(MyRandomizer.name)
randomizer.import_list()
self.assertRaises(RandomizationListImportError, randomizer.import_list)
def test_invalid_sid(self):
# change to a different starting SID
RandomizationListImporter(name="ambition")
randomization_list_model_cls = site_randomizers.get(
"ambition").model_cls()
obj = randomization_list_model_cls.objects.all().order_by(
"sid").first()
obj.sid = 100
obj.save()
with self.assertRaises(RandomizationListError) as cm:
RandomizationListVerifier(randomizer_name="ambition")
self.assertIn("Randomization list has invalid SIDs", str(cm.exception))
def test_with_consent_no_site(self):
self.populate_list()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
self.assertRaises(
RandomizationError,
site_randomizers.get("ambition"),
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=None,
user=subject_consent.user_created,
)
def test_with_consent_insufficient_data(self):
randomizer = site_randomizers.get("default")
randomizer.import_list()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
self.assertRaises(
RandomizationError,
Randomizer,
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=None,
)
def test_updates_list_obj_as_allocated(self):
self.populate_list()
site = Site.objects.get_current()
RandomizationList.objects.update(site_name=site.name)
RandomizationList.objects.all().first()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
first_obj = RandomizationList.objects.all().first()
self.assertEqual(first_obj.subject_identifier, "12345")
self.assertTrue(first_obj.allocated)
self.assertIsNotNone(first_obj.allocated_user)
self.assertEqual(first_obj.allocated_user,
subject_consent.user_created)
self.assertEqual(first_obj.allocated_datetime,
subject_consent.consent_datetime)
self.assertGreater(first_obj.modified, subject_consent.modified)
def test_cannot_rerandomize(self):
self.populate_list()
site = Site.objects.get_current()
RandomizationList.objects.update(site_name=site.name)
first_obj = RandomizationList.objects.all().first()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", user_created="erikvw")
rando = site_randomizers.get("ambition")(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
self.assertEqual(rando.sid, first_obj.sid)
self.assertRaises(
AlreadyRandomized,
site_randomizers.get("ambition"),
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
def test_can_overwrite_explicit(self):
site_randomizers._registry = {}
site_randomizers.register(MyRandomizer)
make_test_list(
full_path=MyRandomizer.get_randomization_list_fullpath(),
site_names=self.site_names,
count=5,
)
randomizer = site_randomizers.get(MyRandomizer.name)
try:
randomizer.import_list(overwrite=True)
except RandomizationListImportError:
self.fail("RandomizationListImportError unexpectedly raised")
def get_subject_by_assignment(self, assignment):
randomization_list_model_cls = site_randomizers.get(
self.randomizer_name
).model_cls()
for _ in range(0, 4):
subject_identifier = self.create_subject()
obj = randomization_list_model_cls.objects.get(
subject_identifier=subject_identifier
)
if Randomizer.get_assignment({"assignment": obj.assignment}) == assignment:
return subject_identifier
raise ValueError(
f"Subject identifier cannot be None. Git assignment={assignment}"
)
def subject_consent_on_post_save(sender, instance, raw, created, **kwargs):
"""Creates an onschedule instance for this consented subject, if
it does not exist.
"""
if not raw:
if not created:
_, schedule = site_visit_schedules.get_by_onschedule_model(
"ambition_prn.onschedule"
)
schedule.refresh_schedule(subject_identifier=instance.subject_identifier)
else:
subject_screening = SubjectScreening.objects.get(
screening_identifier=instance.screening_identifier
)
subject_screening.subject_identifier = instance.subject_identifier
subject_screening.consented = True
subject_screening.save_base(
update_fields=["subject_identifier", "consented"]
)
# randomize
Randomizer = site_randomizers.get("ambition")
Randomizer(
subject_identifier=instance.subject_identifier,
report_datetime=instance.consent_datetime,
site=instance.site,
user=instance.user_created,
)
# put subject on schedule
_, schedule = site_visit_schedules.get_by_onschedule_model(
"ambition_prn.onschedule"
)
schedule.put_on_schedule(
subject_identifier=instance.subject_identifier,
onschedule_datetime=instance.consent_datetime,
)
# create / delete action for reconsent
if instance.completed_by_next_of_kin == YES:
ReconsentAction(subject_identifier=instance.subject_identifier)
else:
try:
delete_action_item(
action_cls=ReconsentAction,
subject_identifier=instance.subject_identifier,
)
except ActionItemDeleteError:
pass
def test_invalid_assignment(self):
# change to a different assignments
assignments = [100, 101]
make_test_list(
full_path=os.path.join(
settings.EDC_RANDOMIZATION_LIST_PATH,
site_randomizers.get("ambition").filename,
),
site_names=self.site_names,
assignments=assignments,
count=5,
)
self.assertRaises(InvalidAssignment,
RandomizationListImporter,
name="ambition")
def test_with_consent(self):
randomizer = site_randomizers.get("default")
randomizer.import_list()
site = Site.objects.get_current()
subject_consent = SubjectConsent.objects.create(
subject_identifier="12345", site=site, user_created="erikvw")
try:
Randomizer(
subject_identifier=subject_consent.subject_identifier,
report_datetime=subject_consent.consent_datetime,
site=subject_consent.site,
user=subject_consent.user_created,
)
except Exception as e:
self.fail(f"Exception unexpectedly raised. Got {str(e)}.")
def populate_list(self,
randomizer_name=None,
site_names=None,
per_site=None,
overwrite_site=None):
randomizer = site_randomizers.get(randomizer_name)
make_test_list(
full_path=randomizer.get_randomization_list_fullpath(),
site_names=site_names or self.site_names,
per_site=per_site,
)
randomizer.import_list(overwrite=True)
if overwrite_site:
site = Site.objects.get_current()
randomizer.model_cls().objects.update(site_name=site.name)
def assignment_description(self):
Randomizer = site_randomizers.get(self.randomizer_name)
subject_identifier = is_subject_identifier_or_raise(
self.kwargs.get("subject_identifier"))
try:
obj = Randomizer.model_cls().objects.get(
subject_identifier=subject_identifier)
except ObjectDoesNotExist as e:
current_site = Site.objects.get_current()
total = (Randomizer.model_cls().objects.filter(
site_name=current_site.name).count())
available = (Randomizer.model_cls().objects.filter(
site_name=current_site.name, allocated=False).count())
raise RandomizationError(
f"Subject {subject_identifier}. "
f"Found {available}/{total} available records for {current_site}. Got {e}"
)
return obj.assignment_description
def __init__(self, randomizer_name=None, fieldnames=None):
self.messages = []
self.randomizer = site_randomizers.get(randomizer_name)
if not self.randomizer:
raise RandomizationListError(
f"Randomizer not registered. Got `{randomizer_name}`")
self.fieldnames = fieldnames or self.default_fieldnames
try:
self.count = self.randomizer.model_cls().objects.all().count()
except (ProgrammingError, OperationalError) as e:
self.messages.append(str(e))
else:
if self.count == 0:
self.messages.append(
"Randomization list has not been loaded. "
"Run the 'import_randomization_list' management command "
"to load before using the system. "
"Resolve this issue before using the system.")
else:
if not self.randomizer.get_randomization_list_path(
) or not os.path.exists(
self.randomizer.get_randomization_list_path()):
self.messages.append(
f"Randomization list file does not exist but SIDs "
f"have been loaded. Expected file "
f"{self.randomizer.get_randomization_list_path()}. "
f"Resolve this issue before using the system.")
else:
message = self.verify_list()
if message:
self.messages.append(message)
if self.messages:
if ("migrate" not in sys.argv and "makemigrations" not in sys.argv
and "import_randomization_list" not in sys.argv):
raise RandomizationListError(", ".join(self.messages))
class RandomizationList(RandomizationListModelMixin, BaseUuidModel):
randomizer_cls = site_randomizers.get("ambition")
assignment = EncryptedTextField(choices=((SINGLE_DOSE, SINGLE_DOSE_NAME),
(CONTROL, CONTROL_NAME)), )
allocation = EncryptedTextField(verbose_name="Original integer allocation",
null=True)
@property
def assignment_description(self):
if self.assignment == CONTROL:
assignment_description = CONTROL_NAME
elif self.assignment == SINGLE_DOSE:
assignment_description = SINGLE_DOSE_NAME
else:
raise RandomizationError(
f"Invalid assignment. Expected one of [{CONTROL}, {SINGLE_DOSE}]. "
f"Got `{self.assignment}`")
return assignment_description
class Meta(RandomizationListModelMixin.Meta):
pass
def test_(self):
randomizer = site_randomizers.get("default")
randomizer.import_list()
