def test_get_after_withdrawal_fails(self):
self.insert_codes()
p = Participant(participantId=1, biobankId=2)
self.participant_dao.insert(p)
self._setup_questionnaire()
qr = QuestionnaireResponse(questionnaireResponseId=1,
questionnaireId=1,
questionnaireVersion=1,
participantId=1,
resource=QUESTIONNAIRE_RESPONSE_RESOURCE)
qr.answers.extend(self._names_and_email_answers())
self.questionnaire_response_dao.insert(qr)
p.withdrawalStatus = WithdrawalStatus.NO_USE
self.participant_dao.update(p)
with self.assertRaises(Forbidden):
self.questionnaire_response_dao.get(qr.questionnaireResponseId)
def test_update_withdraw(self):
p = Participant()
time = datetime.datetime(2016, 1, 1)
with random_ids([1, 2]):
with FakeClock(time):
self.dao.insert(p)
p.version = 1
p.withdrawalStatus = WithdrawalStatus.NO_USE
time2 = datetime.datetime(2016, 1, 2)
with FakeClock(time2):
self.dao.update(p)
p2 = self.dao.get(1)
expected_participant = self._participant_with_defaults(
participantId=1,
version=2,
biobankId=2,
lastModified=time2,
signUpTime=time,
withdrawalStatus=WithdrawalStatus.NO_USE,
withdrawalTime=time2)
self.assertEquals(expected_participant.asdict(), p2.asdict())
p.version = 2
p.providerLink = make_primary_provider_link_for_name('PITT')
p.withdrawalTime = None
time3 = datetime.datetime(2016, 1, 3)
with FakeClock(time3):
self.dao.update(p)
# Withdrawal time should get copied over.
p2 = self.dao.get(1)
expected_participant = self._participant_with_defaults(
participantId=1,
version=3,
biobankId=2,
lastModified=time3,
signUpTime=time,
withdrawalStatus=WithdrawalStatus.NO_USE,
withdrawalTime=time2,
hpoId=PITT_HPO_ID,
providerLink=p2.providerLink)
self.assertEquals(expected_participant.asdict(), p2.asdict())
def test_update_withdrawn_status_fails(self):
p = Participant(withdrawalStatus=WithdrawalStatus.NO_USE)
time = datetime.datetime(2016, 1, 1)
with random_ids([1, 2]):
with FakeClock(time):
self.dao.insert(p)
expected_participant = self._participant_with_defaults(
participantId=1,
version=1,
biobankId=2,
lastModified=time,
signUpTime=time,
withdrawalStatus=WithdrawalStatus.NO_USE)
self.assertEquals(expected_participant.asdict(), p.asdict())
p2 = self.dao.get(1)
self.assertEquals(p.asdict(), p2.asdict())
p.version = 1
p.withdrawalStatus = WithdrawalStatus.NOT_WITHDRAWN
with self.assertRaises(Forbidden):
self.dao.update(p)
def _create_data(self):
HPODao().insert(HPO(hpoId=AZ_HPO_ID + 1, name='AZ_TUCSON_2'))
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 4, name='TEST'))
SqlTestBase.setup_codes(
ANSWER_FIELD_TO_QUESTION_CODE.values() + [EHR_CONSENT_QUESTION_CODE],
code_type=CodeType.QUESTION)
SqlTestBase.setup_codes(
FIELD_TO_QUESTIONNAIRE_MODULE_CODE.values(), code_type=CodeType.MODULE)
# Import codes for white and female, but not male or black.
SqlTestBase.setup_codes(
[
RACE_WHITE_CODE, CONSENT_PERMISSION_YES_CODE,
RACE_NONE_OF_THESE_CODE, PMI_PREFER_NOT_TO_ANSWER_CODE,
CONSENT_PERMISSION_NO_CODE, 'female', 'PIIState_VA'
],
code_type=CodeType.ANSWER)
participant_dao = ParticipantDao()
questionnaire_id = self.create_questionnaire('questionnaire3.json')
questionnaire_id_2 = self.create_questionnaire('questionnaire4.json')
questionnaire_id_3 = self.create_questionnaire(
'all_consents_questionnaire.json')
with FakeClock(TIME):
participant = self._participant_with_defaults(
participantId=1,
version=2,
biobankId=2,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant)
self.send_consent('P1', email='*****@*****.**')
# Participant 2 starts out unpaired; later gets paired automatically when their physical
# measurements come in.
participant2 = Participant(participantId=2, biobankId=3)
participant_dao.insert(participant2)
self.send_consent('P2', email='*****@*****.**')
# Test HPO affiliation; this test participant is ignored.
participant3 = Participant(
participantId=3,
biobankId=4,
providerLink=make_primary_provider_link_for_name('TEST'))
participant_dao.insert(participant3)
self.send_consent('P3', email='*****@*****.**')
# example.com e-mail; this test participant is ignored, too.
participant4 = Participant(
participantId=4,
biobankId=5,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant4)
self.send_consent('P4', email='*****@*****.**')
participant5 = Participant(
participantId=5,
biobankId=6,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant5)
self.send_consent('P5', email='*****@*****.**')
# A withdrawn participant should be excluded from metrics.
participant6 = Participant(
participantId=6,
biobankId=7,
providerLink=make_primary_provider_link_for_name('PITT')
)
participant_dao.insert(participant6)
self.send_consent('P6', email='*****@*****.**')
participant6.withdrawalStatus=WithdrawalStatus.NO_USE
participant_dao.update(participant6)
self.send_post('Participant/P2/PhysicalMeasurements',
load_measurement_json(2))
self.send_post('Participant/P2/BiobankOrder', load_biobank_order_json(2))
self.submit_questionnaire_response('P1', questionnaire_id,
RACE_WHITE_CODE, 'female', None,
datetime.date(1980, 1, 2))
self.submit_questionnaire_response(
'P2', questionnaire_id, PMI_PREFER_NOT_TO_ANSWER_CODE, 'male', None,
datetime.date(1920, 1, 3))
self.submit_questionnaire_response('P2', questionnaire_id_2, None, None,
'PIIState_VA', None)
self.submit_questionnaire_response('P5', questionnaire_id, None, None,
None, datetime.date(1970, 1, 2))
self.submit_consent_questionnaire_response('P1', questionnaire_id_3,
CONSENT_PERMISSION_NO_CODE)
self.submit_consent_questionnaire_response('P2', questionnaire_id_3,
CONSENT_PERMISSION_YES_CODE)
sample_dao = BiobankStoredSampleDao()
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='abc',
biobankId=2,
biobankOrderIdentifier='KIT',
test='test',
confirmed=TIME))
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='def',
biobankId=3,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME))
# Required to update the HPO linkage (and test filtering for P3).
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='xyz',
biobankId=4,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME))
def _create_data(self):
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 1, name='AZ_TUCSON_2'))
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 4, name='TEST'))
SqlTestBase.setup_codes(ANSWER_FIELD_TO_QUESTION_CODE.values() +
[EHR_CONSENT_QUESTION_CODE],
code_type=CodeType.QUESTION)
SqlTestBase.setup_codes(FIELD_TO_QUESTIONNAIRE_MODULE_CODE.values(),
code_type=CodeType.MODULE)
# Import codes for white and female, but not male or black.
SqlTestBase.setup_codes([
RACE_WHITE_CODE, CONSENT_PERMISSION_YES_CODE,
RACE_NONE_OF_THESE_CODE, PMI_PREFER_NOT_TO_ANSWER_CODE,
CONSENT_PERMISSION_NO_CODE, 'female', 'PIIState_VA', PMI_SKIP_CODE
],
code_type=CodeType.ANSWER)
participant_dao = ParticipantDao()
questionnaire_id = self.create_questionnaire('questionnaire3.json')
questionnaire_id_2 = self.create_questionnaire('questionnaire4.json')
questionnaire_id_3 = self.create_questionnaire(
'all_consents_questionnaire.json')
pl_tucson = make_primary_provider_link_for_name('AZ_TUCSON')
pl_test = make_primary_provider_link_for_name('TEST')
pl_pitt = make_primary_provider_link_for_name('PITT')
with FakeClock(TIME):
participant = Participant(participantId=1,
biobankId=2,
providerLink=pl_tucson)
participant_dao.insert(participant)
self.send_consent('P1', email='*****@*****.**')
# Participant 2 starts out unpaired; later gets paired automatically when their physical
# measurements come in.
participant2 = Participant(participantId=2, biobankId=3)
participant_dao.insert(participant2)
self.send_consent('P2', email='*****@*****.**')
# Test HPO affiliation; this test participant is ignored.
participant3 = Participant(participantId=3,
biobankId=4,
providerLink=pl_test)
participant_dao.insert(participant3)
self.send_consent('P3', email='*****@*****.**')
# example.com e-mail; this test participant is ignored, too.
participant4 = Participant(participantId=4,
biobankId=5,
providerLink=pl_pitt)
participant_dao.insert(participant4)
self.send_consent('P4', email='*****@*****.**')
participant5 = Participant(participantId=5,
biobankId=6,
providerLink=pl_tucson)
participant_dao.insert(participant5)
self.send_consent('P5', email='*****@*****.**')
participant6 = Participant(participantId=6,
biobankId=7,
providerLink=pl_tucson)
participant_dao.insert(participant6)
self.send_consent('P6', email='*****@*****.**')
# Participant that starts at PITT but winds up in TEST; should be ignored.
participant7 = Participant(participantId=7,
biobankId=8,
providerLink=pl_pitt)
participant_dao.insert(participant7)
self.send_consent('P7', email='*****@*****.**')
# Participant that re-pairs and then withdraws; should be ignored.
participant8 = Participant(participantId=8,
biobankId=9,
providerLink=pl_pitt)
participant_dao.insert(participant8)
self.send_consent('P8', email='*****@*****.**')
# Participant that has cancelled biobank order should not have order in metrics.
participant9 = Participant(participantId=9,
biobankId=10,
providerLink=pl_pitt)
participant_dao.insert(participant9)
self.send_consent('P9', email='*****@*****.**')
with FakeClock(TIME_2):
# FIXME: The test passes, but the following "update" doesn't actually make much sense. The
# providerlink is not changed but the HPO ID actually is (at this point in time
# `participant.hpoId` evaluates to 4, which is the value given in `unit_test_util.AZ_HPO_ID`).
# The original intent of the test is not clear.
# This update to participant has no effect, as the HPO ID didn't change.
participant = self._participant_with_defaults(
participantId=1,
version=1,
biobankId=2,
hpoId=3, # <<<< Had to add hpoId here, default is UNSET_HPO_ID
providerLink=pl_tucson)
participant_dao.update(participant)
participant8.providerLink = pl_tucson
participant_dao.update(participant8)
self.submit_questionnaire_response('P1',
questionnaire_id,
race_code=RACE_WHITE_CODE,
gender_code='male',
state=PMI_SKIP_CODE,
date_of_birth=datetime.date(
1980, 1, 2))
self.submit_questionnaire_response(
'P2',
questionnaire_id,
race_code=RACE_NONE_OF_THESE_CODE,
gender_code=None,
state=None,
date_of_birth=None)
self.submit_questionnaire_response('P5',
questionnaire_id,
race_code=PMI_SKIP_CODE,
gender_code=PMI_SKIP_CODE,
state=None,
date_of_birth=None)
self.submit_questionnaire_response('P6',
questionnaire_id,
race_code=PMI_SKIP_CODE,
gender_code=PMI_SKIP_CODE,
state=None,
date_of_birth=None)
self.submit_questionnaire_response('P9',
questionnaire_id,
race_code=PMI_SKIP_CODE,
gender_code=PMI_SKIP_CODE,
state=None,
date_of_birth=None)
with FakeClock(TIME_3):
t3 = TIME_3.strftime(TIME_FORMAT)
# Re-pair the original participant
participant.version = 2
participant.providerLink = pl_pitt
participant_dao.update(participant)
participant7.providerLink = pl_test
participant_dao.update(participant7)
participant8.withdrawalStatus = WithdrawalStatus.NO_USE
participant8.withdrawalReason = WithdrawalReason.TEST
participant8.withdrawalReasonJustification = 'test account'
participant_dao.update(participant8)
self.send_post('Participant/P2/PhysicalMeasurements',
load_measurement_json(2, t3))
self.send_post('Participant/P2/BiobankOrder',
load_biobank_order_json(2))
self.submit_questionnaire_response('P1',
questionnaire_id,
race_code='black',
gender_code='female',
state=None,
date_of_birth=datetime.date(
1980, 1, 3))
self.submit_questionnaire_response(
'P2',
questionnaire_id,
race_code=None,
gender_code=PMI_PREFER_NOT_TO_ANSWER_CODE,
state=None,
date_of_birth=None)
self.submit_questionnaire_response('P2',
questionnaire_id_2,
race_code=None,
gender_code=None,
state='PIIState_VA',
date_of_birth=None)
self.submit_questionnaire_response('P6',
questionnaire_id_2,
race_code=None,
gender_code=None,
state='PIIState_VA',
date_of_birth=None)
self.submit_consent_questionnaire_response(
'P1', questionnaire_id_3, CONSENT_PERMISSION_NO_CODE)
self.submit_consent_questionnaire_response(
'P2', questionnaire_id_3, CONSENT_PERMISSION_YES_CODE)
self.submit_consent_questionnaire_response(
'P6', questionnaire_id_3, CONSENT_PERMISSION_YES_CODE)
path = 'Participant/P9/BiobankOrder'
new_order = self.send_post(path, load_biobank_order_json(9))
path = path + '/' + new_order['id']
self.send_get(path)
self.send_patch(path,
request_data=cancel_biobank_order(),
headers={'If-Match': 'W/"1"'})
sample_dao = BiobankStoredSampleDao()
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId='abc',
biobankId=2,
biobankOrderIdentifier='KIT',
test='test',
confirmed=TIME_2))
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId='def',
biobankId=3,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME_2))
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId='xyz',
biobankId=4,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME_2))
# participant 6 withdrawl shouldn't be in csv's.
participant6.withdrawalStatus = WithdrawalStatus.NO_USE
participant_dao.update(participant6)
def setUp(self, **kwargs):
super(MetricsEhrMultiEndpointTest, self).setUp(**kwargs)
#
# insert some test data
#
for date in iter_dates(
datetime.date(2017, 12, 30),
datetime.date(2018, 2, 1)
):
calendar_day = Calendar(day=date)
CalendarDao().insert(calendar_day)
# noinspection PyArgumentList
participant_1 = Participant(participantId=1, biobankId=1)
summary_1 = self._make_participant(
participant_1, 'Alice', 'Aardvark', self.hpo_foo, self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_study=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4)
)
self._update_ehr(
summary_1,
update_time=datetime.datetime(2018, 1, 5)
)
# noinspection PyArgumentList
participant_2 = Participant(participantId=2, biobankId=2)
summary_2 = self._make_participant(
participant_2, 'Bo', 'Badger', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
self._update_ehr(
summary_2,
update_time=datetime.datetime(2018, 1, 6)
)
# noinspection PyArgumentList
participant_3 = Participant(participantId=3, biobankId=3)
self._make_participant(
participant_3, 'Cheryl', 'Caterpillar', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
participant_3.withdrawalStatus = WithdrawalStatus.NO_USE
self.dao.update(participant_3)
# noinspection PyArgumentList
participant_4 = Participant(participantId=4, biobankId=4)
self._make_participant(
participant_4, 'Dan', 'Donkey', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
participant_4.isGhostId = True
self.dao.update(participant_4)
# noinspection PyArgumentList
participant_5 = Participant(participantId=5, biobankId=5)
self._make_participant(
participant_5, 'Elia', 'Elephant', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
# noinspection PyArgumentList
participant_6 = Participant(participantId=6, biobankId=6)
self._make_participant(
participant_6, 'Elia', 'Elephant', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
