def test_lookup_with_intervention(self):
intv = Intervention(name='TEST', description='Test Intervention')
epic26 = self.add_questionnaire(name='epic26')
eproms_add = self.add_questionnaire(name='eproms_add')
with SessionScope(db):
db.session.add(intv)
db.session.commit()
intv, epic26, eproms_add = map(db.session.merge,
(intv, epic26, eproms_add))
bank = QuestionnaireBank(name='CRV',
intervention_id=intv.id,
start='{"days": 7}',
expired='{"days": 90}')
for rank, q in enumerate((epic26, eproms_add)):
qbq = QuestionnaireBankQuestionnaire(questionnaire_id=q.id,
rank=rank)
bank.questionnaires.append(qbq)
self.test_user.interventions.append(intv)
self.login()
self.add_required_clinical_data()
with SessionScope(db):
db.session.add(bank)
db.session.commit()
# Patient associated with INTV intervention should generate appropriate
# questionnaires as of start date
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
qb_status = QB_Status(self.test_user,
as_of_date=now + relativedelta(days=8))
qb = qb_status.current_qbd().questionnaire_bank
results = list(qb.questionnaires)
assert len(results) == 2
def test_intervention_in_progress(self):
# testing intervention-based QBs
q = self.add_questionnaire('q')
interv = Intervention(name='interv', description='test')
with SessionScope(db):
db.session.add(interv)
db.session.commit()
q, interv, self.test_user = map(db.session.merge,
(q, interv, self.test_user))
qb = QuestionnaireBank(
name='qb', intervention_id=interv.id, classification='baseline',
start='{"days": 0}', expired='{"days": 2}')
qbq = QuestionnaireBankQuestionnaire(rank=0, questionnaire=q)
qb.questionnaires.append(qbq)
# user with biopsy should return biopsy date
self.login()
self.test_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=now)
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
obs = self.test_user.observations.first()
assert obs.codeable_concept.codings[0].display == 'biopsy'
assert trigger_date(self.test_user, qb) == obs.issued
# add mock in-process QB - confirm current qb is still correct
mock_qr('q', 'in-progress', qb=qb)
self.test_user, qb = map(db.session.merge, (self.test_user, qb))
qb_stat = QB_Status(user=self.test_user, as_of_date=now)
assert qb_stat.current_qbd().questionnaire_bank == qb
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_lookup_for_user(self):
crv, rp, rp_id = self.setup_org_n_rp(org_name='CRV')
epic26 = self.add_questionnaire(name='epic26')
eproms_add = self.add_questionnaire(name='eproms_add')
comorb = self.add_questionnaire(name='comorb')
crv, epic26, eproms_add, comorb = map(
db.session.merge, (crv, epic26, eproms_add, comorb))
bank = QuestionnaireBank(
name='CRV', research_protocol_id=rp_id,
start='{"days": 7}',
expired='{"days": 90}')
for rank, q in enumerate((epic26, eproms_add, comorb)):
qbq = QuestionnaireBankQuestionnaire(
questionnaire_id=q.id,
rank=rank)
bank.questionnaires.append(qbq)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv.id, setdate=now)
self.promote_user(role_name=ROLE.PATIENT.value)
with SessionScope(db):
db.session.add(bank)
db.session.commit()
# User associated with CRV org should generate appropriate
# questionnaires
self.test_user = db.session.merge(self.test_user)
# Doesn't start for 7 days, initially shouldn't get any
qb_stat = QB_Status(user=self.test_user, as_of_date=now)
assert qb_stat.current_qbd() is None
qb_stat = QB_Status(
user=self.test_user, as_of_date=now + relativedelta(days=7))
qb = qb_stat.current_qbd().questionnaire_bank
results = list(qb.questionnaires)
assert len(results) == 3
# confirm rank sticks
assert results[0].name == 'epic26'
assert results[2].name == 'comorb'
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_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_lookup_for_user(self):
crv, rp, rp_id = self.setup_org_n_rp(org_name='CRV')
epic26 = self.add_questionnaire(name='epic26')
eproms_add = self.add_questionnaire(name='eproms_add')
comorb = self.add_questionnaire(name='comorb')
crv, epic26, eproms_add, comorb = map(
db.session.merge, (crv, epic26, eproms_add, comorb))
bank = QuestionnaireBank(name='CRV',
research_protocol_id=rp_id,
start='{"days": 7}',
expired='{"days": 90}')
for rank, q in enumerate((epic26, eproms_add, comorb)):
qbq = QuestionnaireBankQuestionnaire(questionnaire_id=q.id,
rank=rank)
bank.questionnaires.append(qbq)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv.id, setdate=now)
self.promote_user(role_name=ROLE.PATIENT.value)
with SessionScope(db):
db.session.add(bank)
db.session.commit()
# User associated with CRV org should generate appropriate
# questionnaires
self.test_user = db.session.merge(self.test_user)
# Doesn't start for 7 days, initially shouldn't get any
qb_stat = QB_Status(user=self.test_user, as_of_date=now)
assert qb_stat.current_qbd() is None
qb_stat = QB_Status(user=self.test_user,
as_of_date=now + relativedelta(days=7))
qb = qb_stat.current_qbd().questionnaire_bank
results = list(qb.questionnaires)
assert len(results) == 3
# confirm rank sticks
assert results[0].name == 'epic26'
assert results[2].name == 'comorb'
def test_no_start_date(self):
# W/O a biopsy (i.e. event start date), no questionnaries
self.promote_user(role_name=ROLE.PATIENT.value)
# toggle default setup - set biopsy false for test user
self.login()
self.test_user = db.session.merge(self.test_user)
self.test_user.save_observation(
codeable_concept=CC.BIOPSY, value_quantity=CC.FALSE_VALUE,
audit=Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID),
status='final', issued=now)
qstats = QB_Status(self.test_user, now)
assert not qstats.current_qbd()
assert not qstats.enrolled_in_classification("baseline")
def test_no_start_date(self):
# W/O a biopsy (i.e. event start date), no questionnaries
self.promote_user(role_name=ROLE.PATIENT.value)
# toggle default setup - set biopsy false for test user
self.login()
self.test_user = db.session.merge(self.test_user)
self.test_user.save_observation(
codeable_concept=CC.BIOPSY, value_quantity=CC.FALSE_VALUE,
audit=Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID),
status='final', issued=now)
qstats = QB_Status(self.test_user, now)
assert not qstats.current_qbd()
assert not qstats.enrolled_in_classification("baseline")
def test_completed_older_rp(self):
"""If current qb completed on older rp, should show as done"""
fourmonthsago = now - timedelta(days=120)
weekago = now - timedelta(weeks=1)
twoweeksago = now - timedelta(weeks=2)
org = self.setup_org_qbs(rp_name='v2', retired_as_of=weekago)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(org)
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
uc = UserConsent(user_id=TEST_USER_ID,
organization_id=org_id,
audit=audit,
agreement_url='http://no.com',
acceptance_date=fourmonthsago)
with SessionScope(db):
db.session.add(audit)
db.session.add(uc)
db.session.commit()
user = db.session.merge(self.test_user)
# Now, should still be rp v3, 3mo recurrence
a_s = QB_Status(user=user, as_of_date=now)
assert (a_s.current_qbd().questionnaire_bank.name ==
'CRV_recurring_3mo_period v3')
assert a_s.instruments_needing_full_assessment() == [
'epic26_v3', 'eortc_v3'
]
# Complete the questionnaire from the 3mo v2 QB
v2qb = QuestionnaireBank.query.filter(
QuestionnaireBank.name == 'CRV_recurring_3mo_period v2').one()
mock_qr('epic26_v2', timestamp=twoweeksago, qb=v2qb, iteration=0)
mock_qr('eortc_v2', timestamp=twoweeksago, qb=v2qb, iteration=0)
# Two weeks ago, should be completed
user = db.session.merge(user)
a_s = QB_Status(user=user, as_of_date=twoweeksago)
assert a_s.overall_status == OverallStatus.completed
# Current should also be completed, even tho protocol changed
a_s = QB_Status(user=user, as_of_date=now)
assert a_s.overall_status == OverallStatus.completed
def mock_qr(
instrument_id, status='completed', timestamp=None, qb=None,
doc_id=None, iteration=None, user_id=TEST_USER_ID, entry_method=None):
if not doc_id:
doc_id = ''.join(choice(ascii_letters) for _ in range(10))
timestamp = timestamp or datetime.utcnow()
qr_document = {
"questionnaire": {
"display": "Additional questions",
"reference":
"https://{}/api/questionnaires/{}".format(
'SERVER_NAME', instrument_id)},
"identifier": {
"use": "official",
"label": "cPRO survey session ID",
"value": doc_id,
"system": "https://stg-ae.us.truenth.org/eproms-demo"}
}
enc = Encounter(
status='planned', auth_method='url_authenticated', user_id=user_id,
start_time=timestamp)
if entry_method:
enc.type.append(entry_method.codings[0])
with SessionScope(db):
db.session.add(enc)
db.session.commit()
enc = db.session.merge(enc)
if not qb:
qstats = QB_Status(get_user(user_id), timestamp)
qbd = qstats.current_qbd()
qb, iteration = qbd.questionnaire_bank, qbd.iteration
qr = QuestionnaireResponse(
subject_id=user_id,
status=status,
authored=timestamp,
document=qr_document,
encounter_id=enc.id,
questionnaire_bank=qb,
qb_iteration=iteration)
with SessionScope(db):
db.session.add(qr)
db.session.commit()
invalidate_users_QBT(user_id=user_id)
def test_completed_older_rp(self):
"""If current qb completed on older rp, should show as done"""
fourmonthsago = now - timedelta(days=120)
weekago = now - timedelta(weeks=1)
twoweeksago = now - timedelta(weeks=2)
org = self.setup_org_qbs(rp_name='v2', retired_as_of=weekago)
org_id = org.id
self.setup_org_qbs(org=org, rp_name='v3')
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(org)
audit = Audit(
user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
uc = UserConsent(
user_id=TEST_USER_ID, organization_id=org_id,
audit=audit, agreement_url='http://no.com',
acceptance_date=fourmonthsago)
with SessionScope(db):
db.session.add(audit)
db.session.add(uc)
db.session.commit()
user = db.session.merge(self.test_user)
# Now, should still be rp v3, 3mo recurrence
a_s = QB_Status(user=user, as_of_date=now)
assert (a_s.current_qbd().questionnaire_bank.name
== 'CRV_recurring_3mo_period v3')
assert a_s.instruments_needing_full_assessment() == [
'epic26_v3', 'eortc_v3']
# Complete the questionnaire from the 3mo v2 QB
v2qb = QuestionnaireBank.query.filter(
QuestionnaireBank.name == 'CRV_recurring_3mo_period v2').one()
mock_qr('epic26_v2', timestamp=twoweeksago, qb=v2qb, iteration=0)
mock_qr('eortc_v2', timestamp=twoweeksago, qb=v2qb, iteration=0)
# Two weeks ago, should be completed
user = db.session.merge(user)
a_s = QB_Status(user=user, as_of_date=twoweeksago)
assert a_s.overall_status == OverallStatus.completed
# Current should also be completed, even tho protocol changed
a_s = QB_Status(user=user, as_of_date=now)
assert a_s.overall_status == OverallStatus.completed
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 mock_qr(
instrument_id, status='completed', timestamp=None, qb=None,
doc_id=None, iteration=None, user_id=TEST_USER_ID):
if not doc_id:
doc_id = ''.join(choice(ascii_letters) for _ in range(10))
timestamp = timestamp or datetime.utcnow()
qr_document = {
"questionnaire": {
"display": "Additional questions",
"reference":
"https://{}/api/questionnaires/{}".format(
'SERVER_NAME', instrument_id)},
"identifier": {
"use": "official",
"label": "cPRO survey session ID",
"value": doc_id,
"system": "https://stg-ae.us.truenth.org/eproms-demo"}
}
enc = Encounter(
status='planned', auth_method='url_authenticated', user_id=user_id,
start_time=timestamp)
with SessionScope(db):
db.session.add(enc)
db.session.commit()
enc = db.session.merge(enc)
if not qb:
qstats = QB_Status(get_user(user_id), timestamp)
qbd = qstats.current_qbd()
qb, iteration = qbd.questionnaire_bank, qbd.iteration
qr = QuestionnaireResponse(
subject_id=user_id,
status=status,
authored=timestamp,
document=qr_document,
encounter_id=enc.id,
questionnaire_bank=qb,
qb_iteration=iteration)
with SessionScope(db):
db.session.add(qr)
db.session.commit()
invalidate_users_QBT(user_id=user_id)
def test_lookup_with_intervention(self):
intv = Intervention(name='TEST', description='Test Intervention')
epic26 = self.add_questionnaire(name='epic26')
eproms_add = self.add_questionnaire(name='eproms_add')
with SessionScope(db):
db.session.add(intv)
db.session.commit()
intv, epic26, eproms_add = map(
db.session.merge, (intv, epic26, eproms_add))
bank = QuestionnaireBank(
name='CRV', intervention_id=intv.id,
start='{"days": 7}',
expired='{"days": 90}')
for rank, q in enumerate((epic26, eproms_add)):
qbq = QuestionnaireBankQuestionnaire(
questionnaire_id=q.id,
rank=rank)
bank.questionnaires.append(qbq)
self.test_user.interventions.append(intv)
self.login()
self.add_required_clinical_data()
with SessionScope(db):
db.session.add(bank)
db.session.commit()
# Patient associated with INTV intervention should generate appropriate
# questionnaires as of start date
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
qb_status = QB_Status(
self.test_user,
as_of_date=now+relativedelta(days=8))
qb = qb_status.current_qbd().questionnaire_bank
results = list(qb.questionnaires)
assert len(results) == 2
def test_intervention_in_progress(self):
# testing intervention-based QBs
q = self.add_questionnaire('q')
interv = Intervention(name='interv', description='test')
with SessionScope(db):
db.session.add(interv)
db.session.commit()
q, interv, self.test_user = map(db.session.merge,
(q, interv, self.test_user))
qb = QuestionnaireBank(name='qb',
intervention_id=interv.id,
classification='baseline',
start='{"days": 0}',
expired='{"days": 2}')
qbq = QuestionnaireBankQuestionnaire(rank=0, questionnaire=q)
qb.questionnaires.append(qbq)
# user with biopsy should return biopsy date
self.login()
self.test_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=now)
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
obs = self.test_user.observations.first()
assert obs.codeable_concept.codings[0].display == 'biopsy'
assert trigger_date(self.test_user, qb) == obs.issued
# add mock in-process QB - confirm current qb is still correct
mock_qr('q', 'in-progress', qb=qb)
self.test_user, qb = map(db.session.merge, (self.test_user, qb))
qb_stat = QB_Status(user=self.test_user, as_of_date=now)
assert qb_stat.current_qbd().questionnaire_bank == qb
def test_outdated_inprogress_qb(self):
# create base QB/RP
org, rp, rp_id = self.setup_org_n_rp(org_name='testorg')
qn = self.add_questionnaire(name='epic26')
qn, org, self.test_user = map(db.session.merge,
(qn, org, self.test_user))
org_id = org.id
qb = QuestionnaireBank(name='Test Questionnaire Bank',
classification='baseline',
research_protocol_id=rp_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"days": 90}')
qbq = QuestionnaireBankQuestionnaire(questionnaire=qn, rank=0)
qb.questionnaires.append(qbq)
self.test_user.organizations.append(org)
self.promote_user(role_name=ROLE.PATIENT.value)
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
uc = UserConsent(user_id=TEST_USER_ID,
organization=org,
audit=audit,
agreement_url='http://no.com',
acceptance_date=now)
with SessionScope(db):
db.session.add(qb)
db.session.add(self.test_user)
db.session.add(audit)
db.session.add(uc)
db.session.commit()
qb = db.session.merge(qb)
# create in-progress QNR for User/QB/RP
mock_qr(instrument_id='epic26',
status='in-progress',
timestamp=now,
qb=qb)
# User associated with CRV org should generate appropriate
# questionnaires
self.test_user = db.session.merge(self.test_user)
qb_stat = QB_Status(self.test_user, now)
qb = qb_stat.current_qbd().questionnaire_bank
assert qb.research_protocol.name == 'proto'
# Pointing the User's org to a new QB/RP
# marking the old RP as retired as of yesterday
old_rp = OrganizationResearchProtocol.query.filter(
OrganizationResearchProtocol.organization_id == org_id,
OrganizationResearchProtocol.research_protocol_id == rp_id).one()
old_rp.retired_as_of = now - timedelta(days=1)
rp2 = ResearchProtocol(name='new_proto')
qn2 = self.add_questionnaire(name='epic27')
with SessionScope(db):
db.session.add(rp2)
db.session.commit()
rp2 = db.session.merge(rp2)
rp2_id = rp2.id
qn2, org = map(db.session.merge, (qn2, org))
qb2 = QuestionnaireBank(name='Test Questionnaire Bank 2',
classification='baseline',
research_protocol_id=rp2_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"days": 90}')
qbq2 = QuestionnaireBankQuestionnaire(questionnaire=qn2, rank=0)
qb2.questionnaires.append(qbq2)
org.research_protocols.append(rp2)
with SessionScope(db):
db.session.add(qb2)
db.session.add(org)
db.session.commit()
qb2 = db.session.merge(qb2)
# outdated QB/RP should be used as long as User has in-progress QNR
self.test_user = db.session.merge(self.test_user)
qb_stat = QB_Status(self.test_user, now)
qb = qb_stat.current_qbd().questionnaire_bank
assert qb.name == 'Test Questionnaire Bank'
assert qb.research_protocol.name == 'proto'
# completing QNR should result in completed status
# shouldn't pick up new protocol till next iteration
mock_qr(instrument_id='epic26',
status='completed',
timestamp=now,
qb=qb)
self.test_user = db.session.merge(self.test_user)
invalidate_users_QBT(TEST_USER_ID)
qb_stat = QB_Status(self.test_user, now)
qb = qb_stat.current_qbd().questionnaire_bank
assert qb.name == 'Test Questionnaire Bank'
assert qb_stat.overall_status == OverallStatus.completed
def test_outdated_done_indef(self):
"""Confirm completed indefinite counts after RP switch"""
# boiler plate to create baseline and indef with retired RP
yesterday = now - timedelta(days=1)
weekago = now - timedelta(weeks=1)
org, rp2, rp2_id = self.setup_org_n_rp(
org_name='testorg', rp_name='v2', retired_as_of=yesterday)
org, rp3, rp3_id = self.setup_org_n_rp(org=org, rp_name='v3')
org_id = org.id
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(org)
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
uc = UserConsent(
user_id=TEST_USER_ID, organization_id=org_id,
audit=audit, agreement_url='http://no.com',
acceptance_date=weekago)
with SessionScope(db):
db.session.add(audit)
db.session.add(uc)
db.session.commit()
self.setup_qb(
questionnaire_name='epic23', qb_name='baseline v2',
classification='baseline', rp_id=rp2_id)
self.setup_qb(
questionnaire_name='epic26', qb_name='baseline v3',
classification='baseline', rp_id=rp3_id)
qb2_indef = self.setup_qb(
questionnaire_name='irondemog', qb_name='indef v2',
classification='indefinite', rp_id=rp2_id)
self.setup_qb(
questionnaire_name='irondemog_v3', qb_name='indef v3',
classification='indefinite', rp_id=rp3_id)
# for today, should get the v3 baseline
user = db.session.merge(self.test_user)
a_s = QB_Status(user=user, as_of_date=now)
assert (['epic26', 'irondemog_v3'] ==
a_s.instruments_needing_full_assessment(classification='all'))
# create done QNR for indefinite dated prior to rp transition
# belonging to older qb - confirm that clears indef work as of then
mock_qr('irondemog', timestamp=weekago, qb=qb2_indef)
user = db.session.merge(self.test_user)
invalidate_users_QBT(user_id=TEST_USER_ID)
a_s = QB_Status(user=user, as_of_date=weekago)
assert (a_s.instruments_needing_full_assessment(
classification='indefinite') == [])
# move forward in time; user should no longer need indefinite, even
# tho RP changed
qb2_indef = db.session.merge(qb2_indef)
a_s = QB_Status(user=user, as_of_date=now)
assert qb2_indef == a_s.current_qbd(
classification='indefinite').questionnaire_bank
assert (a_s.instruments_needing_full_assessment(
classification='indefinite') == [])
assert (a_s.instruments_needing_full_assessment(
classification='all') == ['epic26'])
def test_outdated_inprogress_qb(self):
# create base QB/RP
org, rp, rp_id = self.setup_org_n_rp(org_name='testorg')
qn = self.add_questionnaire(name='epic26')
qn, org, self.test_user = map(
db.session.merge, (qn, org, self.test_user))
org_id = org.id
qb = QuestionnaireBank(
name='Test Questionnaire Bank',
classification='baseline',
research_protocol_id=rp_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"days": 90}')
qbq = QuestionnaireBankQuestionnaire(questionnaire=qn, rank=0)
qb.questionnaires.append(qbq)
self.test_user.organizations.append(org)
self.promote_user(role_name=ROLE.PATIENT.value)
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
uc = UserConsent(
user_id=TEST_USER_ID, organization=org,
audit=audit, agreement_url='http://no.com',
acceptance_date=now)
with SessionScope(db):
db.session.add(qb)
db.session.add(self.test_user)
db.session.add(audit)
db.session.add(uc)
db.session.commit()
qb = db.session.merge(qb)
# create in-progress QNR for User/QB/RP
mock_qr(
instrument_id='epic26', status='in-progress',
timestamp=now, qb=qb)
# User associated with CRV org should generate appropriate
# questionnaires
self.test_user = db.session.merge(self.test_user)
qb_stat = QB_Status(self.test_user, now)
qb = qb_stat.current_qbd().questionnaire_bank
assert qb.research_protocol.name == 'proto'
# Pointing the User's org to a new QB/RP
# marking the old RP as retired as of yesterday
old_rp = OrganizationResearchProtocol.query.filter(
OrganizationResearchProtocol.organization_id == org_id,
OrganizationResearchProtocol.research_protocol_id == rp_id).one()
old_rp.retired_as_of = now - timedelta(days=1)
rp2 = ResearchProtocol(name='new_proto')
qn2 = self.add_questionnaire(name='epic27')
with SessionScope(db):
db.session.add(rp2)
db.session.commit()
rp2 = db.session.merge(rp2)
rp2_id = rp2.id
qn2, org = map(db.session.merge, (qn2, org))
qb2 = QuestionnaireBank(
name='Test Questionnaire Bank 2',
classification='baseline',
research_protocol_id=rp2_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"days": 90}')
qbq2 = QuestionnaireBankQuestionnaire(questionnaire=qn2, rank=0)
qb2.questionnaires.append(qbq2)
org.research_protocols.append(rp2)
with SessionScope(db):
db.session.add(qb2)
db.session.add(org)
db.session.commit()
qb2 = db.session.merge(qb2)
# outdated QB/RP should be used as long as User has in-progress QNR
self.test_user = db.session.merge(self.test_user)
qb_stat = QB_Status(self.test_user, now)
qb = qb_stat.current_qbd().questionnaire_bank
assert qb.name == 'Test Questionnaire Bank'
assert qb.research_protocol.name == 'proto'
# completing QNR should result in completed status
# shouldn't pick up new protocol till next iteration
mock_qr(
instrument_id='epic26', status='completed',
timestamp=now, qb=qb)
self.test_user = db.session.merge(self.test_user)
invalidate_users_QBT(TEST_USER_ID)
qb_stat = QB_Status(self.test_user, now)
qb = qb_stat.current_qbd().questionnaire_bank
assert qb.name == 'Test Questionnaire Bank'
assert qb_stat.overall_status == OverallStatus.completed
def test_outdated_done_indef(self):
"""Confirm completed indefinite counts after RP switch"""
# boiler plate to create baseline and indef with retired RP
yesterday = now - timedelta(days=1)
weekago = now - timedelta(weeks=1)
org, rp2, rp2_id = self.setup_org_n_rp(org_name='testorg',
rp_name='v2',
retired_as_of=yesterday)
org, rp3, rp3_id = self.setup_org_n_rp(org=org, rp_name='v3')
org_id = org.id
self.promote_user(role_name=ROLE.PATIENT.value)
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(org)
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
uc = UserConsent(user_id=TEST_USER_ID,
organization_id=org_id,
audit=audit,
agreement_url='http://no.com',
acceptance_date=weekago)
with SessionScope(db):
db.session.add(audit)
db.session.add(uc)
db.session.commit()
self.setup_qb(questionnaire_name='epic23',
qb_name='baseline v2',
classification='baseline',
rp_id=rp2_id)
self.setup_qb(questionnaire_name='epic26',
qb_name='baseline v3',
classification='baseline',
rp_id=rp3_id)
qb2_indef = self.setup_qb(questionnaire_name='irondemog',
qb_name='indef v2',
classification='indefinite',
rp_id=rp2_id)
self.setup_qb(questionnaire_name='irondemog_v3',
qb_name='indef v3',
classification='indefinite',
rp_id=rp3_id)
# for today, should get the v3 baseline
user = db.session.merge(self.test_user)
a_s = QB_Status(user=user, as_of_date=now)
assert ([
'epic26', 'irondemog_v3'
] == a_s.instruments_needing_full_assessment(classification='all'))
# create done QNR for indefinite dated prior to rp transition
# belonging to older qb - confirm that clears indef work as of then
mock_qr('irondemog', timestamp=weekago, qb=qb2_indef)
user = db.session.merge(self.test_user)
invalidate_users_QBT(user_id=TEST_USER_ID)
a_s = QB_Status(user=user, as_of_date=weekago)
assert (a_s.instruments_needing_full_assessment(
classification='indefinite') == [])
# move forward in time; user should no longer need indefinite, even
# tho RP changed
qb2_indef = db.session.merge(qb2_indef)
a_s = QB_Status(user=user, as_of_date=now)
assert qb2_indef == a_s.current_qbd(
classification='indefinite').questionnaire_bank
assert (a_s.instruments_needing_full_assessment(
classification='indefinite') == [])
assert (a_s.instruments_needing_full_assessment(
classification='all') == ['epic26'])