def test_qb_pre_retired(self):
# Confirm backdating returns the correct QB
weekago = now - timedelta(days=7)
org, rpv3, rpv3_id = self.setup_org_n_rp(rp_name='v3')
org, rpv2, rpv2_id = self.setup_org_n_rp(org=org,
rp_name='v2',
retired_as_of=weekago)
qn3 = self.add_questionnaire(name='epic26-v3')
qn2 = self.add_questionnaire(name='epic26-v2')
qb3 = QuestionnaireBank(name='Test Questionnaire Bank v3',
classification='baseline',
research_protocol_id=rpv3_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"days": 90}')
qbq3 = QuestionnaireBankQuestionnaire(questionnaire=qn3, rank=0)
qb3.questionnaires.append(qbq3)
qb2 = QuestionnaireBank(name='Test Questionnaire Bank v2',
classification='baseline',
research_protocol_id=rpv2_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"days": 90}')
qbq2 = QuestionnaireBankQuestionnaire(questionnaire=qn2, rank=0)
qb2.questionnaires.append(qbq2)
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=org,
audit=audit,
agreement_url='http://no.com')
with SessionScope(db):
map(db.session.add, (qb2, qb3))
db.session.add(audit)
db.session.add(uc)
db.session.commit()
user, org, qb2, qb3 = map(db.session.merge,
(self.test_user, org, qb2, qb3))
# w/o backdating, should get current QB
self.assertEqual(
qb3,
QuestionnaireBank.most_current_qb(
user, as_of_date=now).questionnaire_bank)
# backdate prior to retirement of previous, should get the previous QB
pre_retirement = weekago - timedelta(days=1)
self.assertEqual(
qb2,
QuestionnaireBank.most_current_qb(
user, as_of_date=pre_retirement).questionnaire_bank)
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()
# User associated with INTV intervention should generate appropriate
# questionnaires
self.test_user = db.session.merge(self.test_user)
qb = QuestionnaireBank.most_current_qb(
self.test_user, as_of_date=now).questionnaire_bank
results = list(qb.questionnaires)
self.assertEqual(2, len(results))
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.organizations.append(crv)
self.consent_with_org(org_id=crv.id)
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)
qb = QuestionnaireBank.most_current_qb(
self.test_user, as_of_date=now).questionnaire_bank
results = list(qb.questionnaires)
self.assertEqual(3, len(results))
# confirm rank sticks
self.assertEqual(results[0].name, 'epic26')
self.assertEqual(results[2].name, 'comorb')
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_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 mock_qr(instrument_id,
status='completed',
timestamp=None,
qb=None,
doc_id=None,
iteration=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=TEST_USER_ID,
start_time=timestamp)
with SessionScope(db):
db.session.add(enc)
db.session.commit()
enc = db.session.merge(enc)
qb = qb or QuestionnaireBank.most_current_qb(get_user(TEST_USER_ID),
timestamp).questionnaire_bank
qr = QuestionnaireResponse(subject_id=TEST_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_assessment_status_cache(TEST_USER_ID)
def upgrade():
bind = op.get_bind()
session = Session(bind=bind)
for qnr in QuestionnaireResponse.query.all():
if ("questionnaire" in qnr.document) and qnr.subject:
qn_ref = qnr.document.get("questionnaire").get("reference")
qn_name = qn_ref.split("/")[-1] if qn_ref else None
qn = Questionnaire.query.filter_by(name=qn_name).first()
qbd = QuestionnaireBank.most_current_qb(
qnr.subject, as_of_date=qnr.authored)
qb = qbd.questionnaire_bank
ic = qbd.iteration
if qb and qn and (qn.id in [qbq.questionnaire.id for qbq in
qb.questionnaires]):
ic = ic or 'NULL'
session.execute(
'UPDATE questionnaire_responses SET '
'questionnaire_bank_id = {}, qb_iteration = {} WHERE '
'id = {}'.format(qb.id, ic, qnr.id))
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=None)
self.test_user = db.session.merge(self.test_user)
obs = self.test_user.observations.first()
self.assertEqual(obs.codeable_concept.codings[0].display, 'biopsy')
self.assertEqual(qb.trigger_date(self.test_user), obs.issued)
# add mock in-process QB - confirm most_current_qb still returns one
mock_qr('q', 'in-progress', qb=qb)
self.test_user, qb = map(db.session.merge, (self.test_user, qb))
self.assertEqual(
qb.most_current_qb(self.test_user,
as_of_date=now).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)
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')
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='epic_26',
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 = QuestionnaireBank.most_current_qb(
self.test_user, as_of_date=now).questionnaire_bank
self.assertEqual(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 = QuestionnaireBank.most_current_qb(
self.test_user, as_of_date=now).questionnaire_bank
self.assertEqual(qb.name, 'Test Questionnaire Bank')
self.assertEqual(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='epic_26',
status='completed',
timestamp=now,
qb=qb)
self.test_user = db.session.merge(self.test_user)
qb = QuestionnaireBank.most_current_qb(
self.test_user, as_of_date=now).questionnaire_bank
self.assertEqual(qb.name, 'Test Questionnaire Bank')