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_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_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_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_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_visit_6mo(self):
crv = self.setup_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6))
self.bless_with_basics(setdate=backdate)
self.test_user.organizations.append(crv)
self.test_user = db.session.merge(self.test_user)
qbd = QuestionnaireBank.most_current_qb(self.test_user,
as_of_date=nowish +
timedelta(hours=1))
self.assertEqual("Month 6", visit_name(qbd))
qbd_i2 = qbd._replace(iteration=1)
self.assertEqual("Month 18", visit_name(qbd_i2))
def test_visit_6mo(self):
crv = self.setup_org_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6))
self.bless_with_basics(setdate=backdate)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
qstats = QB_Status(self.test_user,
as_of_date=nowish + timedelta(hours=1))
qbd = qstats.current_qbd()
assert visit_name(qbd) == "Month 6"
qbd.iteration = 1
assert visit_name(qbd) == "Month 18"
def test_visit_6mo(self):
crv = self.setup_org_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6))
self.bless_with_basics(setdate=backdate)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
qstats = QB_Status(
self.test_user, as_of_date=nowish + timedelta(hours=1))
qbd = qstats.current_qbd()
assert visit_name(qbd) == "Month 6"
qbd.iteration = 1
assert visit_name(qbd) == "Month 18"
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_recurring_starts(self):
# should get full list of QBDs for recurring qb
self.setup_org_qbs()
td = datetime.utcnow().replace(month=1, day=1)
sixMoQB = QuestionnaireBank.query.filter(
QuestionnaireBank.name == 'CRV_recurring_6mo_period v2').one()
results = sixMoQB.recurring_starts(trigger_date=td)
# Expect in order, 6mo, 18mo, 30mo
expect6 = next(results)
assert visit_name(expect6) == 'Month 6'
expect18 = next(results)
assert visit_name(expect18) == 'Month 18'
expect30 = next(results)
assert visit_name(expect30) == 'Month 30'
with pytest.raises(StopIteration):
next(results)
def test_recurring_starts(self):
# should get full list of QBDs for recurring qb
self.setup_org_qbs()
td = datetime.utcnow().replace(month=1, day=1)
sixMoQB = QuestionnaireBank.query.filter(
QuestionnaireBank.name == 'CRV_recurring_6mo_period v2').one()
results = sixMoQB.recurring_starts(trigger_date=td)
# Expect in order, 6mo, 18mo, 30mo
expect6 = next(results)
assert visit_name(expect6) == 'Month 6'
expect18 = next(results)
assert visit_name(expect18) == 'Month 18'
expect30 = next(results)
assert visit_name(expect30) == 'Month 30'
with pytest.raises(StopIteration):
next(results)
def test_visit_baseline(self):
crv = self.setup_qbs()
self.bless_with_basics() # pick up a consent, etc.
self.test_user.organizations.append(crv)
self.test_user = db.session.merge(self.test_user)
qbd = QuestionnaireBank.most_current_qb(self.test_user, as_of_date=now)
self.assertEqual("Baseline", visit_name(qbd))
def test_visit_baseline(self):
crv = self.setup_org_qbs()
self.bless_with_basics(setdate=now) # pick up a consent, etc.
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
qstats = QB_Status(self.test_user, now)
qbd = qstats.current_qbd()
assert visit_name(qbd) == "Baseline"
def test_visit_baseline(self):
crv = self.setup_org_qbs()
self.bless_with_basics(setdate=now) # pick up a consent, etc.
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
qstats = QB_Status(self.test_user, now)
qbd = qstats.current_qbd()
assert visit_name(qbd) == "Baseline"
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_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)
def upgrade():
# Tricky task to locate the errors. One time expensive process,
# loop through patients identifying problems.
admin = admin_id()
qb_map = qb_pairs_by_rp()
if not qb_map:
return # nothing to do on systems w/o RP changes
fix_map = dict()
raise RuntimeError(
"Unsupported migration; code has changed - not maintained")
for patient in active_patients(include_test_role=True).order_by(User.id):
qnrs = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == patient.id).order_by(
QuestionnaireResponse.authored)
if not qnrs.count():
# Only care if the user submitted QNRs:
continue
for qnr in qnrs:
# Obtain qb_timeline row at the time of QNR.authored
as_of_date = qnr.authored
qbt = QBT.query.filter(QBT.user_id == patient.id).filter(
QBT.at <= as_of_date).order_by(
QBT.at.desc(), QBT.id.desc()).first()
if qnr.questionnaire_bank_id is None:
print(
"qnr {} user_id {} authored {} {}"
" with NO qb_id set".format(
qnr.id, patient.id, as_of_date,
qnr.document['questionnaire']['reference']))
continue
if qbt and qbt.status != OverallStatus.withdrawn:
recorded_qb = QuestionnaireBank.query.get(
qnr.questionnaire_bank_id)
qbd = qbt.qbd()
expected_qb = qbd.questionnaire_bank
if recorded_qb.classification == 'indefinite':
# indefinite case is handled differently...
qb_status = QB_Status(patient, as_of_date)
expected_qb = QuestionnaireBank.query.get(
qb_status._current_indef.qb_id)
if recorded_qb != expected_qb:
replacement = qb_map.get(recorded_qb.id)
if replacement == expected_qb.id:
# retain the change request, as altering it inline
# interrupts the iteration
patched_qbd = QBD(
relative_start=qbd.relative_start, iteration=qbd.iteration,
recur=qbd.recur, qb_id=replacement)
fix_map[qnr.id] = (expected_qb.id, visit_name(patched_qbd))
print(
"qnr {} replacing incorrect qb_id {} with {} "
"for user {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
patient.id))
else:
print(
"qnr {} PROBLEM: recorded qb_id {}, "
"expected {} doesn't match replacement {} "
"for user_id {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
replacement, patient.id))
for qnr_id, row in fix_map.items():
qb_id, visit = row
qnr = QuestionnaireResponse.query.get(qnr_id)
comment = (
"Migration correct qnr.id {} ({}) questionnaire_bank_id"
" from {} to {}".format(
qnr.id, visit, qnr.questionnaire_bank_id, qb_id))
audit = Audit(
user_id=admin, subject_id=qnr.subject_id,
context='assessment', comment=comment)
db.session.add(audit)
qnr.questionnaire_bank_id = qb_id
# clear out cached qb_timeline data for user as it
# needs to be recalculated given the change
invalidate_users_QBT(qnr.subject_id)
db.session.commit()
def upgrade():
# Tricky task to locate the errors. One time expensive process,
# loop through patients identifying problems.
admin = admin_id()
qb_map = qb_pairs_by_rp()
if not qb_map:
return # nothing to do on systems w/o RP changes
fix_map = dict()
for patient in active_patients(include_test_role=True).order_by(User.id):
qnrs = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == patient.id).order_by(
QuestionnaireResponse.authored)
if not qnrs.count():
# Only care if the user submitted QNRs:
continue
for qnr in qnrs:
# Obtain qb_timeline row at the time of QNR.authored
as_of_date = qnr.authored
qbt = QBT.query.filter(QBT.user_id == patient.id).filter(
QBT.at <= as_of_date).order_by(
QBT.at.desc(), QBT.id.desc()).first()
if qnr.questionnaire_bank_id is None:
print(
"qnr {} user_id {} authored {} {}"
" with NO qb_id set".format(
qnr.id, patient.id, as_of_date,
qnr.document['questionnaire']['reference']))
continue
if qbt and qbt.status != OverallStatus.withdrawn:
recorded_qb = QuestionnaireBank.query.get(
qnr.questionnaire_bank_id)
qbd = qbt.qbd()
expected_qb = qbd.questionnaire_bank
if recorded_qb.classification == 'indefinite':
# indefinite case is handled differently...
qb_status = QB_Status(patient, as_of_date)
expected_qb = QuestionnaireBank.query.get(
qb_status._current_indef.qb_id)
if recorded_qb != expected_qb:
replacement = qb_map.get(recorded_qb.id)
if replacement == expected_qb.id:
# retain the change request, as altering it inline
# interrupts the iteration
patched_qbd = QBD(
relative_start=qbd.relative_start, iteration=qbd.iteration,
recur=qbd.recur, qb_id=replacement)
fix_map[qnr.id] = (expected_qb.id, visit_name(patched_qbd))
print(
"qnr {} replacing incorrect qb_id {} with {} "
"for user {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
patient.id))
else:
print(
"qnr {} PROBLEM: recorded qb_id {}, "
"expected {} doesn't match replacement {} "
"for user_id {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
replacement, patient.id))
for qnr_id, row in fix_map.items():
qb_id, visit = row
qnr = QuestionnaireResponse.query.get(qnr_id)
comment = (
"Migration correct qnr.id {} ({}) questionnaire_bank_id"
" from {} to {}".format(
qnr.id, visit, qnr.questionnaire_bank_id, qb_id))
audit = Audit(
user_id=admin, subject_id=qnr.subject_id,
context='assessment', comment=comment)
db.session.add(audit)
qnr.questionnaire_bank_id = qb_id
# clear out cached qb_timeline data for user as it
# needs to be recalculated given the change
invalidate_users_QBT(qnr.subject_id)
db.session.commit()
