def test_withdrawn(self):
# qbs should halt beyond withdrawal
crv = self.setup_org_qbs()
crv_id = crv.id
# consent 17 months in past
backdate = datetime.utcnow() - relativedelta(months=17)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv_id, setdate=backdate)
# withdraw user now, which should provide result
# in QBs prior to 17 months.
user = db.session.merge(self.test_user)
withdraw_consent(user=user,
org_id=crv_id,
acting_user=user,
acceptance_date=datetime.utcnow())
gen = ordered_qbs(user=user)
# expect each in order despite overlapping nature
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
for n in (3, 6, 9, 15):
assert visit_name(next(gen)) == 'Month {}'.format(n)
with pytest.raises(StopIteration):
next(gen)
def test_withdrawn(self):
# qbs should halt beyond withdrawal
crv = self.setup_org_qbs()
crv_id = crv.id
# consent 17 months in past
backdate = datetime.utcnow() - relativedelta(months=17)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv_id, setdate=backdate)
# withdraw user now, which should provide result
# in QBs prior to 17 months.
user = db.session.merge(self.test_user)
withdraw_consent(
user=user, org_id=crv_id, acting_user=user,
acceptance_date=datetime.utcnow())
gen = ordered_qbs(user=user)
# expect each in order despite overlapping nature
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
for n in (3, 6, 9, 15):
assert visit_name(next(gen)) == 'Month {}'.format(n)
with pytest.raises(StopIteration):
next(gen)
def test_empty(self):
# Basic case, without org, empty list
self.setup_org_qbs()
user = db.session.merge(self.test_user)
gen = ordered_qbs(user=user)
with pytest.raises(StopIteration):
next(gen)
def test_change_before_start_rp(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(
now=now, backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(rp_name='v2', retired_as_of=back14)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.consent_with_org(org_id=org_id, setdate=back7)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user)
# expect everything in v3
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
assert (
expect_baseline.questionnaire_bank.research_protocol.name == 'v3')
for n in (3, 6, 9, 15, 18, 21, 30):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v3'
with pytest.raises(StopIteration):
next(gen)
def test_indef_change_before_start_rp_w_result(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(now=now,
backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(rp_name='v2',
retired_as_of=back14,
include_indef=True)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3', include_indef=True)
self.consent_with_org(org_id=org_id, setdate=back7)
# submit a mock response for indef QB on old RP
# which should result in v2
qb_name = "indef_v2"
i_v2 = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
mock_qr("irondemog_v2", qb=i_v2, iteration=None)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user, classification='indefinite')
# expect only v2 given submission
expect_v2 = next(gen)
assert (expect_v2.questionnaire_bank.research_protocol.name == 'v2')
with pytest.raises(StopIteration):
next(gen)
def test_change_before_start_rp_w_result(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(now=now,
backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(rp_name='v2', retired_as_of=back14)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.consent_with_org(org_id=org_id, setdate=back7)
# submit a mock response for baseline QB on old RP
# which should result in v2 for baseline and v3 thereafter
qb_name = "CRV Baseline v2"
baseline = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
mock_qr('epic_26_v2', qb=baseline, iteration=None)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user)
# expect everything in v3 post baseline
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
assert (
expect_baseline.questionnaire_bank.research_protocol.name == 'v2')
for n in (3, 6, 9, 15, 18, 21, 30):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v3'
with pytest.raises(StopIteration):
next(gen)
def test_change_before_start_rp(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(now=now,
backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(rp_name='v2', retired_as_of=back14)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.consent_with_org(org_id=org_id, setdate=back7)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user)
# expect everything in v3
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
assert (
expect_baseline.questionnaire_bank.research_protocol.name == 'v3')
for n in (3, 6, 9, 15, 18, 21, 30):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v3'
with pytest.raises(StopIteration):
next(gen)
def test_empty(self):
# Basic case, without org, empty list
self.setup_org_qbs()
user = db.session.merge(self.test_user)
gen = ordered_qbs(user=user)
with pytest.raises(StopIteration):
next(gen)
def test_indef_change_before_start_rp_w_result(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(
now=now, backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(
rp_name='v2', retired_as_of=back14, include_indef=True)
org_id = org.id
self.setup_org_qbs(
org=org, rp_name='v3', include_indef=True)
self.consent_with_org(org_id=org_id, setdate=back7)
# submit a mock response for indef QB on old RP
# which should result in v2
qb_name = "indef_v2"
i_v2 = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
mock_qr("irondemog_v2", qb=i_v2, iteration=None)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user, classification='indefinite')
# expect only v2 given submission
expect_v2 = next(gen)
assert (
expect_v2.questionnaire_bank.research_protocol.name == 'v2')
with pytest.raises(StopIteration):
next(gen)
def test_change_before_start_rp_w_result(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(
now=now, backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(rp_name='v2', retired_as_of=back14)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.consent_with_org(org_id=org_id, setdate=back7)
# submit a mock response for baseline QB on old RP
# which should result in v2 for baseline and v3 thereafter
qb_name = "CRV Baseline v2"
baseline = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
mock_qr('epic_26_v2', qb=baseline, iteration=None)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user)
# expect everything in v3 post baseline
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
assert (
expect_baseline.questionnaire_bank.research_protocol.name == 'v2')
for n in (3, 6, 9, 15, 18, 21, 30):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v3'
with pytest.raises(StopIteration):
next(gen)
def test_full_list(self):
crv = self.setup_org_qbs()
self.bless_with_basics() # pick up a consent, etc.
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
gen = ordered_qbs(user=self.test_user)
# expect each in order despite overlapping nature
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
for n in (3, 6, 9, 15, 18, 21, 30):
assert visit_name(next(gen)) == 'Month {}'.format(n)
with pytest.raises(StopIteration):
next(gen)
def test_full_list(self):
crv = self.setup_org_qbs()
self.bless_with_basics() # pick up a consent, etc.
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
gen = ordered_qbs(user=self.test_user)
# expect each in order despite overlapping nature
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
for n in (3, 6, 9, 15, 18, 21, 30):
assert visit_name(next(gen)) == 'Month {}'.format(n)
with pytest.raises(StopIteration):
next(gen)
def test_indef_change_before_start_rp(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(now=now,
backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(rp_name='v2',
retired_as_of=back14,
include_indef=True)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3', include_indef=True)
self.consent_with_org(org_id=org_id, setdate=back7)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user, classification='indefinite')
# expect only v3
expect_v3 = next(gen)
assert (expect_v3.questionnaire_bank.research_protocol.name == 'v3')
with pytest.raises(StopIteration):
next(gen)
def test_intervention_list(self):
self.setup_intervention_qbs()
self.bless_with_basics() # pick up a consent, etc.
# user with biopsy should return biopsy date
self.login()
user = db.session.merge(self.test_user)
user.save_observation(
codeable_concept=CC.BIOPSY, value_quantity=CC.TRUE_VALUE,
audit=Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID),
status='', issued=None)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user=user)
# expect all intervention QBs - baseline then every 3mos
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
for n in (3, 9, 15, 21, 27):
assert visit_name(next(gen)) == 'Month {}'.format(n)
with pytest.raises(StopIteration):
next(gen)
def test_indef_change_before_start_rp(self):
now = datetime.utcnow()
back7, nowish = associative_backdate(
now=now, backdate=relativedelta(months=7))
back14, nowish = associative_backdate(
now=now, backdate=relativedelta(months=14))
org = self.setup_org_qbs(
rp_name='v2', retired_as_of=back14, include_indef=True)
org_id = org.id
self.setup_org_qbs(
org=org, rp_name='v3', include_indef=True)
self.consent_with_org(org_id=org_id, setdate=back7)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user, classification='indefinite')
# expect only v3
expect_v3 = next(gen)
assert (
expect_v3.questionnaire_bank.research_protocol.name == 'v3')
with pytest.raises(StopIteration):
next(gen)
def test_change_midstream_results_rp(self):
now = datetime.utcnow()
back1, nowish = associative_backdate(now=now,
backdate=relativedelta(months=1))
back10, nowish = associative_backdate(
now=now, backdate=relativedelta(months=10))
org = self.setup_org_qbs(rp_name='v2', retired_as_of=back1)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.consent_with_org(org_id=org_id, setdate=back10)
# submit a mock response for 9 month QB on old RP
# which should result in v2 for up to 9 month and v3 thereafter
qb_name = "CRV_recurring_3mo_period v2"
nineMo = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
mock_qr('epic_26_v2', qb=nineMo, iteration=1)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user)
# expect baseline and 3 month in v2, rest in v3
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
assert (
expect_baseline.questionnaire_bank.research_protocol.name == 'v2')
for n in (3, 6, 9):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v2'
for n in (15, 18, 21, 30):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v3'
with pytest.raises(StopIteration):
next(gen)
def test_change_midstream_results_rp(self):
now = datetime.utcnow()
back1, nowish = associative_backdate(
now=now, backdate=relativedelta(months=1))
back10, nowish = associative_backdate(
now=now, backdate=relativedelta(months=10))
org = self.setup_org_qbs(rp_name='v2', retired_as_of=back1)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.consent_with_org(org_id=org_id, setdate=back10)
# submit a mock response for 9 month QB on old RP
# which should result in v2 for up to 9 month and v3 thereafter
qb_name = "CRV_recurring_3mo_period v2"
nineMo = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
mock_qr('epic_26_v2', qb=nineMo, iteration=1)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user)
# expect baseline and 3 month in v2, rest in v3
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
assert (
expect_baseline.questionnaire_bank.research_protocol.name == 'v2')
for n in (3, 6, 9):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v2'
for n in (15, 18, 21, 30):
qbd = next(gen)
assert visit_name(qbd) == 'Month {}'.format(n)
assert qbd.questionnaire_bank.research_protocol.name == 'v3'
with pytest.raises(StopIteration):
next(gen)
def test_intervention_list(self):
self.setup_intervention_qbs()
self.bless_with_basics() # pick up a consent, etc.
# user with biopsy should return biopsy date
self.login()
user = db.session.merge(self.test_user)
user.save_observation(codeable_concept=CC.BIOPSY,
value_quantity=CC.TRUE_VALUE,
audit=Audit(user_id=TEST_USER_ID,
subject_id=TEST_USER_ID),
status='',
issued=None)
user = db.session.merge(self.test_user)
gen = ordered_qbs(user=user)
# expect all intervention QBs - baseline then every 3mos
expect_baseline = next(gen)
assert visit_name(expect_baseline) == 'Baseline'
for n in (3, 9, 15, 21, 27):
assert visit_name(next(gen)) == 'Month {}'.format(n)
with pytest.raises(StopIteration):
next(gen)