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_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(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_aggregate_response_timepoints(self):
# generate a few mock qr's from various qb iterations, confirm
# time points.
nineback, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=nineback, local_metastatic='metastatic')
instrument_id = 'eortc'
for months_back in (0, 3, 6, 9):
backdate, _ = associative_backdate(
now=now, backdate=relativedelta(months=months_back))
mock_qr(instrument_id=instrument_id, timestamp=backdate)
# add staff user w/ same org association for bundle creation
staff = self.add_user(username='******')
staff.organizations.append(Organization.query.filter(
Organization.name == 'metastatic').one())
self.promote_user(staff, role_name=ROLE.STAFF.value)
staff = db.session.merge(staff)
bundle = aggregate_responses(
instrument_ids=[instrument_id], current_user=staff)
expected = {'Baseline', 'Month 3', 'Month 6', 'Month 9'}
found = [i['timepoint'] for i in bundle['entry']]
assert set(found) == expected
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_aggregate_response_timepoints(self):
# generate a few mock qr's from various qb iterations, confirm
# time points.
nineback, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=nineback, local_metastatic='metastatic')
instrument_id = 'eortc'
for months_back in (0, 3, 6, 9):
backdate, _ = associative_backdate(
now=now, backdate=relativedelta(months=months_back))
mock_qr(instrument_id=instrument_id, timestamp=backdate)
# add staff user w/ same org association for bundle creation
staff = self.add_user(username='******')
staff.organizations.append(Organization.query.filter(
Organization.name == 'metastatic').one())
self.promote_user(staff, role_name=ROLE.STAFF.value)
staff = db.session.merge(staff)
bundle = aggregate_responses(
instrument_ids=[instrument_id], current_user=staff)
expected = {'Baseline', 'Month 3', 'Month 6', 'Month 9'}
found = [i['timepoint'] for i in bundle['entry']]
assert set(found) == expected
def test_permissions(self):
"""Shouldn't get results from orgs outside view permissions"""
# Generate a few patients from different orgs
org1_name, org2_name = 'test_org1', 'test_org2'
org1 = Organization(name=org1_name)
org2 = Organization(name=org2_name)
with SessionScope(db):
db.session.add(org1)
db.session.add(org2)
db.session.commit()
org1 = db.session.merge(org1)
org1_id = org1.id
self.setup_org_qbs(org1)
org2 = db.session.merge(org2)
self.setup_org_qbs(org2)
user2 = self.add_user('user2')
user3 = self.add_user('user3')
user4 = self.add_user('user4')
with SessionScope(db):
db.session.add(user2)
db.session.add(user3)
db.session.add(user4)
db.session.commit()
user2 = db.session.merge(user2)
user3 = db.session.merge(user3)
user4 = db.session.merge(user4)
now = datetime.utcnow()
back15, nowish = associative_backdate(now, relativedelta(days=15))
back45, nowish = associative_backdate(now, relativedelta(days=45))
back115, nowish = associative_backdate(now, relativedelta(days=115))
self.bless_with_basics(user=user2,
setdate=back15,
local_metastatic=org1_name)
self.bless_with_basics(user=user3,
setdate=back45,
local_metastatic=org1_name)
self.bless_with_basics(user=user4,
setdate=back115,
local_metastatic=org2_name)
self.test_user = db.session.merge(self.test_user)
self.promote_user(role_name=ROLE.STAFF.value)
self.login()
response = self.client.get("/api/report/questionnaire_status")
assert response.status_code == 200
# with zero orgs in common, should see empty result set
assert response.json['total'] == 0
# Add org to staff to see results from matching patiens (2&3)
self.consent_with_org(org_id=org1_id)
response = self.client.get("/api/report/questionnaire_status")
assert response.status_code == 200
assert response.json['total'] == 2
def test_permissions(self):
"""Shouldn't get results from orgs outside view permissions"""
# Generate a few patients from different orgs
org1_name, org2_name = 'test_org1', 'test_org2'
org1 = Organization(name=org1_name)
org2 = Organization(name=org2_name)
with SessionScope(db):
db.session.add(org1)
db.session.add(org2)
db.session.commit()
org1 = db.session.merge(org1)
org1_id = org1.id
self.setup_org_qbs(org1)
org2 = db.session.merge(org2)
self.setup_org_qbs(org2)
user2 = self.add_user('user2')
user3 = self.add_user('user3')
user4 = self.add_user('user4')
with SessionScope(db):
db.session.add(user2)
db.session.add(user3)
db.session.add(user4)
db.session.commit()
user2 = db.session.merge(user2)
user3 = db.session.merge(user3)
user4 = db.session.merge(user4)
now = datetime.utcnow()
back15, nowish = associative_backdate(now, relativedelta(days=15))
back45, nowish = associative_backdate(now, relativedelta(days=45))
back115, nowish = associative_backdate(now, relativedelta(days=115))
self.bless_with_basics(
user=user2, setdate=back15, local_metastatic=org1_name)
self.bless_with_basics(
user=user3, setdate=back45, local_metastatic=org1_name)
self.bless_with_basics(
user=user4, setdate=back115, local_metastatic=org2_name)
self.test_user = db.session.merge(self.test_user)
self.promote_user(role_name=ROLE.STAFF.value)
self.login()
response = self.client.get("/api/report/questionnaire_status")
assert response.status_code == 200
# with zero orgs in common, should see empty result set
assert response.json['total'] == 0
# Add org to staff to see results from matching patiens (2&3)
self.consent_with_org(org_id=org1_id)
response = self.client.get("/api/report/questionnaire_status")
assert response.status_code == 200
assert response.json['total'] == 2
def test_user_current_qb(self):
crv = self.setup_org_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3))
self.bless_with_basics(setdate=backdate)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.login()
resp = self.client.get('/api/user/{}/'
'questionnaire_bank'.format(TEST_USER_ID))
assert resp.status_code == 200
assert (resp.json['questionnaire_bank']['name']
== 'CRV_recurring_3mo_period v2')
dt = (nowish - relativedelta(months=2)).strftime('%Y-%m-%d')
resp2 = self.client.get('/api/user/{}/questionnaire_bank?as_of_date='
'{}'.format(TEST_USER_ID, dt))
assert resp2.status_code == 200
assert (resp2.json['questionnaire_bank']['name']
== 'CRV Baseline v2')
# User's trigger was only 3 months ago. At 4 months should
# return a valid empty
dt = (nowish - relativedelta(months=4)).strftime('%Y-%m-%d')
resp3 = self.client.get('/api/user/{}/questionnaire_bank?as_of_date='
'{}'.format(TEST_USER_ID, dt))
assert resp3.status_code == 200
assert not resp3.json['questionnaire_bank']
def test_localized_as_of_date(self):
# backdating consent beyond expired and the status lookup date
# within a valid window should show available assessments.
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3))
self.bless_with_basics(setdate=backdate)
self.mark_localized()
# backdate so the baseline q's have expired
mock_qr(instrument_id='epic26',
status='in-progress',
doc_id='doc-26',
timestamp=backdate)
self.test_user = db.session.merge(self.test_user)
as_of_date = backdate + relativedelta(days=2)
a_s = AssessmentStatus(user=self.test_user, as_of_date=as_of_date)
assert a_s.overall_status == "In Progress"
# with only epic26 started, should see results for both
# instruments_needing_full_assessment and insturments_in_progress
assert \
{'eproms_add', 'comorb'} ==\
set(a_s.instruments_needing_full_assessment())
assert ['doc-26'] == a_s.instruments_in_progress()
def test_user_current_qb(self):
crv = self.setup_org_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3))
self.bless_with_basics(setdate=backdate)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.login()
resp = self.client.get('/api/user/{}/'
'questionnaire_bank'.format(TEST_USER_ID))
assert resp.status_code == 200
assert (resp.json['questionnaire_bank']['name'] ==
'CRV_recurring_3mo_period v2')
dt = (nowish - relativedelta(months=2)).strftime('%Y-%m-%d')
resp2 = self.client.get('/api/user/{}/questionnaire_bank?as_of_date='
'{}'.format(TEST_USER_ID, dt))
assert resp2.status_code == 200
assert (resp2.json['questionnaire_bank']['name'] == 'CRV Baseline v2')
# User's trigger was only 3 months ago. At 4 months should
# return a valid empty
dt = (nowish - relativedelta(months=4)).strftime('%Y-%m-%d')
resp3 = self.client.get('/api/user/{}/questionnaire_bank?as_of_date='
'{}'.format(TEST_USER_ID, dt))
assert resp3.status_code == 200
assert not resp3.json['questionnaire_bank']
def test_user_current_qb(self):
crv = self.setup_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3))
self.bless_with_basics(setdate=backdate)
self.test_user.organizations.append(crv)
self.test_user = db.session.merge(self.test_user)
self.login()
resp = self.client.get('/api/user/{}/'
'questionnaire_bank'.format(TEST_USER_ID))
self.assert200(resp)
self.assertEqual(resp.json['questionnaire_bank']['name'],
'CRV_recurring_3mo_period v2')
dt = (nowish - relativedelta(months=2)).strftime('%Y-%m-%d')
resp2 = self.client.get('/api/user/{}/questionnaire_bank?as_of_date='
'{}'.format(TEST_USER_ID, dt))
self.assert200(resp2)
self.assertEqual(resp2.json['questionnaire_bank']['name'],
'CRV Baseline v2')
dt = (nowish - relativedelta(months=4)).strftime('%Y-%m-%d')
resp3 = self.client.get('/api/user/{}/questionnaire_bank?as_of_date='
'{}'.format(TEST_USER_ID, dt))
self.assert200(resp3)
self.assertFalse(resp3.json['questionnaire_bank'])
def test_initial_recur_baseline_done(self):
# backdate to be within the first recurrence window
backdate, nowish = associative_backdate(now=now,
backdate=relativedelta(
months=3, days=2))
self.bless_with_basics(setdate=backdate)
self.mark_metastatic()
# add baseline QNRs, as if submitted nearly 3 months ago, during
# baseline window
backdated = nowish - relativedelta(months=2, days=25)
baseline = QuestionnaireBank.query.filter_by(name='metastatic').one()
for instrument in metastatic_baseline_instruments:
mock_qr(instrument, qb=baseline, timestamp=backdated)
self.test_user = db.session.merge(self.test_user)
# Check status during baseline window
a_s_baseline = AssessmentStatus(user=self.test_user,
as_of_date=backdated)
assert a_s_baseline.overall_status == "Completed"
assert not a_s_baseline.instruments_needing_full_assessment()
# Whereas "current" status for the initial recurrence show due.
a_s = AssessmentStatus(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == "Due"
# in the initial window w/ no questionnaires submitted
# should include all from initial recur
assert set(a_s.instruments_needing_full_assessment()) == metastatic_3
def test_initial_recur_baseline_done(self):
# backdate to be within the first recurrence window
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3, days=2))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
# add baseline QNRs, as if submitted nearly 3 months ago, during
# baseline window
backdated = nowish - relativedelta(months=2, days=25)
baseline = QuestionnaireBank.query.filter_by(
name='metastatic').one()
for instrument in metastatic_baseline_instruments:
mock_qr(instrument, qb=baseline, timestamp=backdated)
self.test_user = db.session.merge(self.test_user)
# Check status during baseline window
a_s_baseline = QB_Status(
user=self.test_user, as_of_date=backdated)
assert a_s_baseline.overall_status == OverallStatus.completed
assert not a_s_baseline.instruments_needing_full_assessment()
# Whereas "current" status for the initial recurrence show due.
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.due
# in the initial window w/ no questionnaires submitted
# should include all from initial recur
assert set(a_s.instruments_needing_full_assessment()) == metastatic_3
def test_boundary_overdue(self):
self.login()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3, hours=-1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.overdue
def test_boundary_overdue(self):
self.login()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3, hours=-1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.overdue
def test_visit_9mo(self):
crv = self.setup_org_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9))
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, nowish + timedelta(hours=1))
qbd = qstats.current_qbd()
assert visit_name(qbd) == "Month 9"
def test_boundary_expired(self):
"At expired, should be expired"
self.login()
backdate, nowish = associative_backdate(now=now,
backdate=relativedelta(
months=3, hours=1))
self.bless_with_basics(setdate=backdate)
self.mark_localized()
self.test_user = db.session.merge(self.test_user)
a_s = AssessmentStatus(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == 'Expired'
def test_visit_9mo(self):
crv = self.setup_org_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9))
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, nowish + timedelta(hours=1))
qbd = qstats.current_qbd()
assert visit_name(qbd) == "Month 9"
def test_visit_9mo(self):
crv = self.setup_qbs()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9))
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 9", visit_name(qbd))
def test_boundary_in_progress_expired(self):
self.login()
backdate, nowish = associative_backdate(now=now,
backdate=relativedelta(
months=3, hours=1))
self.bless_with_basics(setdate=backdate)
self.mark_localized()
for instrument in localized_instruments:
mock_qr(instrument_id=instrument, status='in-progress')
self.test_user = db.session.merge(self.test_user)
a_s = AssessmentStatus(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == 'Partially Completed'
def test_boundary_in_progress_expired(self):
self.login()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
for instrument in localized_instruments:
mock_qr(
instrument_id=instrument, status='in-progress',
timestamp=nowish-relativedelta(days=1))
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.partially_completed
def test_boundary_in_progress_expired(self):
self.login()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
for instrument in localized_instruments:
mock_qr(
instrument_id=instrument, status='in-progress',
timestamp=nowish-relativedelta(days=1))
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.partially_completed
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_boundary_recurring_in_progress(self):
self.login()
backdate, nowish = associative_backdate(now=now,
backdate=relativedelta(
months=6, hours=-1))
self.bless_with_basics(setdate=backdate)
self.mark_metastatic()
for instrument in metastatic_3:
mock_qr(instrument_id=instrument,
status='in-progress',
iteration=0)
self.test_user = db.session.merge(self.test_user)
a_s = AssessmentStatus(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == 'In Progress'
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_secondary_recur_due(self):
# backdate so baseline q's have expired, and we are within the
# second recurrence window
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.due
# w/ no questionnaires submitted
# should include all from second recur
assert set(a_s.instruments_needing_full_assessment()) == metastatic_4
def test_secondary_recur_due(self):
# backdate so baseline q's have expired, and we are within the
# second recurrence window
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.due
# w/ no questionnaires submitted
# should include all from second recur
assert set(a_s.instruments_needing_full_assessment()) == metastatic_4
def test_all_expired_old_tx(self):
self.login()
# backdate outside of baseline window (which uses consent date)
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=4, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
# provide treatment date outside of all recurrences
tx_date = datetime(2000, 3, 12, 0, 0, 00, 000000)
self.add_procedure(code='7', display='Focal therapy',
system=ICHOM, setdate=tx_date)
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.expired
def test_all_expired_old_tx(self):
self.login()
# backdate outside of baseline window (which uses consent date)
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=4, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
# provide treatment date outside of all recurrences
tx_date = datetime(2000, 3, 12, 0, 0, 00, 000000)
self.add_procedure(code='7', display='Focal therapy',
system=ICHOM, setdate=tx_date)
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.expired
def test_boundary_recurring_in_progress(self):
self.login()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6, hours=-1))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
mr3_qb = QuestionnaireBank.query.filter_by(
name='metastatic_recurring3').first()
for instrument in metastatic_3:
mock_qr(
instrument_id=instrument, status='in-progress',
qb=mr3_qb, timestamp=nowish, iteration=0)
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.in_progress
def test_boundary_recurring_in_progress(self):
self.login()
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=6, hours=-1))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
mr3_qb = QuestionnaireBank.query.filter_by(
name='metastatic_recurring3').first()
for instrument in metastatic_3:
mock_qr(
instrument_id=instrument, status='in-progress',
qb=mr3_qb, timestamp=nowish, iteration=0)
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.in_progress
def test_2nd_recur_due(self):
# backdate so baseline q's have expired, and we within the 2nd
# recurrence window
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.due
# in the initial window w/ no questionnaires submitted
# should include all from initial recur
assert set(a_s.instruments_needing_full_assessment()) == metastatic_3
# however, we should be looking at iteration 2 (zero index)!
assert a_s.current_qbd().iteration == 1
def test_2nd_recur_due(self):
# backdate so baseline q's have expired, and we within the 2nd
# recurrence window
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='metastatic')
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.due
# in the initial window w/ no questionnaires submitted
# should include all from initial recur
assert set(a_s.instruments_needing_full_assessment()) == metastatic_3
# however, we should be looking at iteration 2 (zero index)!
assert a_s.current_qbd().iteration == 1
def test_site_ids(self):
# bless org w/ expected identifier type
wanted_system = 'http://pcctc.org/'
unwanted_system = 'http://other.org/'
self.app.config['REPORTING_IDENTIFIER_SYSTEMS'] = [wanted_system]
id_value = '146-11'
org = Organization.query.filter(
Organization.name == 'metastatic').one()
id1 = Identifier(
system=wanted_system, use='secondary', value=id_value)
id2 = Identifier(
system=unwanted_system, use='secondary', value=id_value)
org.identifiers.append(id1)
org.identifiers.append(id2)
with SessionScope(db):
db.session.commit()
nineback, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=nineback, local_metastatic='metastatic')
instrument_id = 'eortc'
mock_qr(instrument_id=instrument_id)
# add staff user w/ same org association for bundle creation
staff = self.add_user(username='******')
staff.organizations.append(Organization.query.filter(
Organization.name == 'metastatic').one())
self.promote_user(staff, role_name=ROLE.STAFF.value)
staff = db.session.merge(staff)
bundle = aggregate_responses(
instrument_ids=[instrument_id], current_user=staff)
id1 = db.session.merge(id1)
assert 1 == len(bundle['entry'])
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider']))
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider'][0]
['identifier']))
assert (id1.as_fhir() ==
bundle['entry'][0]['subject']['careProvider'][0]
['identifier'][0])
def test_site_ids(self):
# bless org w/ expected identifier type
wanted_system = 'http://pcctc.org/'
unwanted_system = 'http://other.org/'
self.app.config['REPORTING_IDENTIFIER_SYSTEMS'] = [wanted_system]
id_value = '146-11'
org = Organization.query.filter(
Organization.name == 'metastatic').one()
id1 = Identifier(
system=wanted_system, use='secondary', value=id_value)
id2 = Identifier(
system=unwanted_system, use='secondary', value=id_value)
org.identifiers.append(id1)
org.identifiers.append(id2)
with SessionScope(db):
db.session.commit()
nineback, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=nineback, local_metastatic='metastatic')
instrument_id = 'eortc'
mock_qr(instrument_id=instrument_id)
# add staff user w/ same org association for bundle creation
staff = self.add_user(username='******')
staff.organizations.append(Organization.query.filter(
Organization.name == 'metastatic').one())
self.promote_user(staff, role_name=ROLE.STAFF.value)
staff = db.session.merge(staff)
bundle = aggregate_responses(
instrument_ids=[instrument_id], current_user=staff)
id1 = db.session.merge(id1)
assert 1 == len(bundle['entry'])
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider']))
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider'][0]
['identifier']))
assert (id1.as_fhir() ==
bundle['entry'][0]['subject']['careProvider'][0]
['identifier'][0])
def test_metastatic_as_of_date(self):
# backdating consent beyond expired and the status lookup date
# within a valid window should show available assessments.
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3))
self.bless_with_basics(setdate=backdate, local_metastatic='metastatic')
# backdate so the baseline q's have expired
mock_qr(instrument_id='epic23', status='in-progress', doc_id='doc-23',
timestamp=backdate)
self.test_user = db.session.merge(self.test_user)
as_of_date = backdate + relativedelta(days=2)
a_s = QB_Status(user=self.test_user, as_of_date=as_of_date)
assert a_s.overall_status == OverallStatus.in_progress
# with only epic26 started, should see results for both
# instruments_needing_full_assessment and instruments_in_progress
assert ['doc-23'] == a_s.instruments_in_progress()
assert a_s.instruments_needing_full_assessment()
def test_localized_overdue(self):
# if the user completed something on time, and nothing else
# is due, should see the thank you message.
backdate, nowish = associative_backdate(now=now,
backdate=relativedelta(
months=3, hours=1))
self.bless_with_basics(setdate=backdate)
self.mark_localized()
# backdate so the baseline q's have expired
mock_qr(instrument_id='epic26', status='in-progress')
self.test_user = db.session.merge(self.test_user)
a_s = AssessmentStatus(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == "Partially Completed"
# with all q's expired,
# instruments_needing_full_assessment and instruments_in_progress
# should be empty
assert not a_s.instruments_needing_full_assessment()
assert not a_s.instruments_in_progress()
def test_metastatic_as_of_date(self):
# backdating consent beyond expired and the status lookup date
# within a valid window should show available assessments.
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3))
self.bless_with_basics(setdate=backdate, local_metastatic='metastatic')
# backdate so the baseline q's have expired
mock_qr(instrument_id='epic23', status='in-progress', doc_id='doc-23',
timestamp=backdate)
self.test_user = db.session.merge(self.test_user)
as_of_date = backdate + relativedelta(days=2)
a_s = QB_Status(user=self.test_user, as_of_date=as_of_date)
assert a_s.overall_status == OverallStatus.in_progress
# with only epic26 started, should see results for both
# instruments_needing_full_assessment and instruments_in_progress
assert ['doc-23'] == a_s.instruments_in_progress()
assert a_s.instruments_needing_full_assessment()
def test_initial_recur_due(self):
# backdate so baseline q's have expired, and we within the first
# recurrence window
backdate, nowish = associative_backdate(now=now,
backdate=relativedelta(
months=3, hours=1))
self.bless_with_basics(setdate=backdate)
self.mark_metastatic()
self.test_user = db.session.merge(self.test_user)
a_s = AssessmentStatus(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == "Due"
# in the initial window w/ no questionnaires submitted
# should include all from initial recur
assert \
set(a_s.instruments_needing_full_assessment()) ==\
metastatic_3
# confirm iteration 0
assert a_s.qb_data.qbd.iteration == 0
def test_localized_overdue(self):
# if the user completed something on time, and nothing else
# is due, should see the thank you message.
backdate, nowish = associative_backdate(
now=now, backdate=relativedelta(months=3, hours=1))
self.bless_with_basics(
setdate=backdate, local_metastatic='localized')
# backdate so the baseline q's have expired
mock_qr(
instrument_id='epic26', status='in-progress', timestamp=backdate)
self.test_user = db.session.merge(self.test_user)
a_s = QB_Status(user=self.test_user, as_of_date=nowish)
assert a_s.overall_status == OverallStatus.partially_completed
# with all q's expired,
# instruments_needing_full_assessment and instruments_in_progress
# should be empty
assert not a_s.instruments_needing_full_assessment()
assert not a_s.instruments_in_progress()
def test_results(self):
from portal.system_uri import TRUENTH_EXTERNAL_STUDY_SYSTEM
# Generate a few patients with differing results
org = self.setup_org_qbs()
org_id, org_name = org.id, org.name
user2 = self.add_user('user2')
user3 = self.add_user('user3')
user4 = self.add_user('user4')
with SessionScope(db):
db.session.add(user2)
db.session.add(user3)
db.session.add(user4)
db.session.commit()
user2 = db.session.merge(user2)
user3 = db.session.merge(user3)
user4 = db.session.merge(user4)
user4_id = user4.id
self.add_user_identifier(
user=user2, system=TRUENTH_EXTERNAL_STUDY_SYSTEM,
value='study user 2')
self.add_user_identifier(
user=user3, system=TRUENTH_EXTERNAL_STUDY_SYSTEM,
value='study user 3')
now = datetime.utcnow()
back15, nowish = associative_backdate(now, relativedelta(days=15))
back45, nowish = associative_backdate(now, relativedelta(days=45))
back115, nowish = associative_backdate(now, relativedelta(days=115))
self.bless_with_basics(
user=user2, setdate=back15, local_metastatic=org_name)
self.bless_with_basics(
user=user3, setdate=back45, local_metastatic=org_name)
self.bless_with_basics(
user=user4, setdate=back115, local_metastatic=org_name)
# submit a mock response for all q's in 3 mo qb
# which should result in completed status for user4
qb_name = "CRV_recurring_3mo_period v2"
threeMo = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
for q in threeMo.questionnaires:
q = db.session.merge(q)
mock_qr(
q.name, qb=threeMo, iteration=0, user_id=user4_id,
timestamp=back15, entry_method=EC.INTERVIEW_ASSISTED)
self.test_user = db.session.merge(self.test_user)
self.promote_user(role_name=ROLE.STAFF.value)
self.consent_with_org(org_id=org_id)
self.login()
response = self.client.get("/api/report/questionnaire_status")
assert response.status_code == 200
# expect baseline for each plus 3 mo for user4
assert response.json['total'] == 4
expect = {'Due', 'Overdue', 'Completed', 'Expired'}
found = set([item['status'] for item in response.json['entry']])
assert expect == found
# the one done should have entry method set above
for item in response.json['entry']:
if item['status'] == 'Completed':
assert item['entry_method'] == 'interview_assisted'
else:
assert 'entry_method' not in item
def test_results(self):
from portal.system_uri import TRUENTH_EXTERNAL_STUDY_SYSTEM
# Generate a few patients with differing results
org = self.setup_org_qbs()
org_id, org_name = org.id, org.name
user2 = self.add_user('user2')
user3 = self.add_user('user3')
user4 = self.add_user('user4')
with SessionScope(db):
db.session.add(user2)
db.session.add(user3)
db.session.add(user4)
db.session.commit()
user2 = db.session.merge(user2)
user3 = db.session.merge(user3)
user4 = db.session.merge(user4)
user4_id = user4.id
self.add_user_identifier(user=user2,
system=TRUENTH_EXTERNAL_STUDY_SYSTEM,
value='study user 2')
self.add_user_identifier(user=user3,
system=TRUENTH_EXTERNAL_STUDY_SYSTEM,
value='study user 3')
now = datetime.utcnow()
back15, nowish = associative_backdate(now, relativedelta(days=15))
back45, nowish = associative_backdate(now, relativedelta(days=45))
back115, nowish = associative_backdate(now, relativedelta(days=115))
self.bless_with_basics(user=user2,
setdate=back15,
local_metastatic=org_name)
self.bless_with_basics(user=user3,
setdate=back45,
local_metastatic=org_name)
self.bless_with_basics(user=user4,
setdate=back115,
local_metastatic=org_name)
# submit a mock response for all q's in 3 mo qb
# which should result in completed status for user4
qb_name = "CRV_recurring_3mo_period v2"
threeMo = QuestionnaireBank.query.filter(
QuestionnaireBank.name == qb_name).one()
for q in threeMo.questionnaires:
q = db.session.merge(q)
mock_qr(q.name,
qb=threeMo,
iteration=0,
user_id=user4_id,
timestamp=back15)
self.test_user = db.session.merge(self.test_user)
self.promote_user(role_name=ROLE.STAFF.value)
self.consent_with_org(org_id=org_id)
self.login()
response = self.client.get("/api/report/questionnaire_status")
assert response.status_code == 200
# expect baseline for each plus 3 mo for user4
assert response.json['total'] == 4
expect = {'Due', 'Overdue', 'Completed', 'Expired'}
found = set([item['status'] for item in response.json['entry']])
assert expect == found
