def test_rp_as_json(self):
rp = ResearchProtocol(name="test_rp")
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
rp_json = rp.as_json()
assert rp_json['name'] == 'test_rp'
assert rp_json['created_at']
assert rp_json['display_name'] == 'Test Rp'
def test_submit_assessment_for_qb(self):
swagger_spec = swagger(self.app)
data = swagger_spec['definitions']['QuestionnaireResponse']['example']
rp = ResearchProtocol(name='proto')
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
rp_id = rp.id
qn = self.add_questionnaire(name='epic26')
org = Organization(name="testorg")
org.research_protocols.append(rp)
with SessionScope(db):
db.session.add(qn)
db.session.add(org)
db.session.commit()
qn, org = map(db.session.merge, (qn, org))
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)
test_user = get_user(TEST_USER_ID)
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(test_user)
db.session.add(audit)
db.session.add(uc)
db.session.commit()
qb = db.session.merge(qb)
self.login()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID),
content_type='application/json',
data=json.dumps(data),
)
assert response.status_code == 200
test_user = get_user(TEST_USER_ID)
assert test_user.questionnaire_responses.count() == 1
assert test_user.questionnaire_responses[0].questionnaire_bank_id ==\
qb.id
def test_rp_from_json(self):
# test from_fhir for new RP
data = {"name": "test_rp"}
rp = ResearchProtocol.from_json(data)
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
self.assertTrue(rp.id)
self.assertTrue(rp.created_at)
def test_rp_from_json(self):
# test from_fhir for new RP
data = {"name": "test_rp"}
rp = ResearchProtocol.from_json(data)
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
assert rp.id
assert rp.created_at
def test_overdue_stats(self):
self.promote_user(user=self.test_user, role_name=ROLE.PATIENT.value)
rp = ResearchProtocol(name='proto')
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
rp_id = rp.id
crv = Organization(name='CRV')
crv.research_protocols.append(rp)
epic26 = self.add_questionnaire(name='epic26')
with SessionScope(db):
db.session.add(crv)
db.session.commit()
crv, epic26 = map(db.session.merge, (crv, epic26))
bank = QuestionnaireBank(name='CRV',
research_protocol_id=rp_id,
start='{"days": 1}',
overdue='{"days": 2}',
expired='{"days": 90}')
qbq = QuestionnaireBankQuestionnaire(questionnaire_id=epic26.id,
rank=0)
bank.questionnaires.append(qbq)
self.test_user = db.session.merge(self.test_user)
# test user with status = 'Expired' (should not show up)
a_s = AssessmentStatus(self.test_user, as_of_date=datetime.utcnow())
self.assertEqual(a_s.overall_status, 'Expired')
ostats = self.get_ostats()
self.assertEqual(len(ostats), 0)
# test user with status = 'Overdue' (should show up)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv.id, backdate=relativedelta(days=18))
with SessionScope(db):
db.session.add(bank)
db.session.commit()
crv, self.test_user = map(db.session.merge, (crv, self.test_user))
a_s = AssessmentStatus(self.test_user, as_of_date=datetime.utcnow())
self.assertEqual(a_s.overall_status, 'Overdue')
ostats = self.get_ostats()
self.assertEqual(len(ostats), 1)
self.assertEqual(ostats[crv], [15])
def test_multiple_rps_in_fhir(self):
yesterday = datetime.utcnow() - timedelta(days=1)
lastyear = datetime.utcnow() - timedelta(days=365)
org = Organization(name='Testy')
rp1 = ResearchProtocol(name='rp1')
rp2 = ResearchProtocol(name='yesterday')
rp3 = ResearchProtocol(name='last year')
with SessionScope(db):
map(db.session.add, (org, rp1, rp2, rp3))
db.session.commit()
org, rp1, rp2, rp3 = map(db.session.merge, (org, rp1, rp2, rp3))
o_rp1 = OrganizationResearchProtocol(research_protocol=rp1,
organization=org)
o_rp2 = OrganizationResearchProtocol(research_protocol=rp2,
organization=org,
retired_as_of=yesterday)
o_rp3 = OrganizationResearchProtocol(research_protocol=rp3,
organization=org,
retired_as_of=lastyear)
with SessionScope(db):
map(db.session.add, (o_rp1, o_rp2, o_rp3))
db.session.commit()
org, rp1, rp2, rp3 = map(db.session.merge, (org, rp1, rp2, rp3))
data = org.as_fhir()
assert org.name == data['name']
rps = [
extension for extension in data['extension']
if extension['url'] == ResearchProtocolExtension.extension_url
]
assert len(rps) == 1
assert len(rps[0]['research_protocols']) == 3
# confirm the order is descending in the custom accessor method
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert [(rp1, None), (rp2, yesterday), (rp3, lastyear)] == results
def test_org_rp_reference(self):
rp = ResearchProtocol(name="test_rp")
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
org_data = {"name": "test_org",
"extension": [
{"url": TRUENTH_RP_EXTENSION,
"research_protocols": [{'name': "test_rp"}]}
]}
org = Organization.from_fhir(org_data)
self.assertEqual(1, len(org.research_protocols))
self.assertEqual(org.research_protocols[0].id, rp.id)
def migrate_to_rp(org_id, rp_name):
bind = op.get_bind()
session = Session(bind=bind)
org = session.query(Organization).get(org_id)
if org:
rp = ResearchProtocol(name=rp_name)
session.add(rp)
session.commit()
rp = session.merge(rp)
rp_id = rp.id
session.execute('UPDATE organizations '
'SET research_protocol_id = {} '
'WHERE id = {}'.format(rp_id, org_id))
session.execute('UPDATE questionnaire_banks '
'SET research_protocol_id = {} '
'WHERE organization_id = {}'.format(rp_id, org_id))
def test_rp_inheritance(self):
rp = ResearchProtocol(name="test_rp")
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
parent = Organization(name='parent', id=101)
parent.research_protocols.append(rp)
child = Organization(name='child', partOf_id=101)
with SessionScope(db):
db.session.add(parent)
db.session.add(child)
db.session.commit()
parent, child, rp = map(db.session.merge, (parent, child, rp))
self.assertEqual(1, len(parent.research_protocols))
self.assertEqual(parent.research_protocols[0].id, rp.id)
self.assertEqual(0, len(child.research_protocols))
self.assertEqual(child.research_protocol(as_of_date=datetime.utcnow()).id, rp.id)
def setup_org_n_rp(org=None,
org_name='org',
rp_name='proto',
retired_as_of=None):
"""Create simple test org with RP, return (org, rp, rp_id)"""
if not org:
org = Organization(name=org_name)
rp = ResearchProtocol(name=rp_name)
with SessionScope(db):
db.session.add(org)
db.session.add(rp)
db.session.commit()
org, rp = map(db.session.merge, (org, rp))
if not retired_as_of:
org.research_protocols.append(rp)
else:
o_rp = OrganizationResearchProtocol(research_protocol=rp,
organization=org,
retired_as_of=retired_as_of)
with SessionScope(db):
db.session.add(o_rp)
db.session.commit()
org, rp = map(db.session.merge, (org, rp))
return (org, rp, rp.id)
def test_questionnaire_banks_recurs(self):
# only one recurrence per qb allowed at this time
initial_recur = Recur(start='{"days": 90}',
cycle_length='{"days": 90}',
termination='{"days": 720}')
every_six_thereafter = Recur(start='{"days": 720}',
cycle_length='{"days": 180}')
rp = ResearchProtocol(name='proto')
with SessionScope(db):
db.session.add(rp)
db.session.commit()
rp = db.session.merge(rp)
rp_id = rp.id
metastatic_org = Organization(name='metastatic')
metastatic_org.research_protocols.append(rp)
questionnaire = self.add_questionnaire(name='test_q')
with SessionScope(db):
db.session.add(initial_recur)
db.session.add(every_six_thereafter)
db.session.add(metastatic_org)
db.session.add(questionnaire)
db.session.commit()
initial_recur = db.session.merge(initial_recur)
every_six_thereafter = db.session.merge(every_six_thereafter)
# with bits in place, setup a recurring QB
recurs = [initial_recur, every_six_thereafter]
mr_qb = QuestionnaireBank(name='metastatic_recurring',
classification='recurring',
research_protocol_id=rp_id,
start='{"days": 0}',
overdue='{"days": 1}',
expired='{"days": 30}',
recurs=recurs)
questionnaire = db.session.merge(questionnaire)
qbq = QuestionnaireBankQuestionnaire(questionnaire=questionnaire,
rank=1)
mr_qb.questionnaires.append(qbq)
with SessionScope(db):
db.session.add(mr_qb)
db.session.commit()
mr_qb, initial_recur, every_six_thereafter = map(
db.session.merge, (mr_qb, initial_recur, every_six_thereafter))
# confirm persistence of this questionnaire bank includes the bits
# added above
results = mr_qb.as_json()
copy = QuestionnaireBank.from_json(results)
assert copy.name == mr_qb.name
assert copy.recurs == [initial_recur, every_six_thereafter]
# now, modify the persisted form, remove one recur and add another
new_recur = Recur(start='{"days": 900}',
cycle_length='{"days": 180}',
termination='{"days": 1800}')
results['recurs'] = [initial_recur.as_json(), new_recur.as_json()]
updated_copy = QuestionnaireBank.from_json(results)
assert ([r.as_json() for r in updated_copy.recurs
] == [r.as_json() for r in (initial_recur, new_recur)])
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 mock_eproms_questionnairebanks():
# Define base ResearchProtocols
localized_protocol = ResearchProtocol(name='localized_protocol')
metastatic_protocol = ResearchProtocol(name='metastatic_protocol')
with SessionScope(db):
db.session.add(localized_protocol)
db.session.add(metastatic_protocol)
db.session.commit()
localized_protocol = db.session.merge(localized_protocol)
metastatic_protocol = db.session.merge(metastatic_protocol)
locpro_id = localized_protocol.id
metapro_id = metastatic_protocol.id
# Define test Orgs and QuestionnaireBanks for each group
localized_org = Organization(name='localized')
localized_org.research_protocols.append(localized_protocol)
metastatic_org = Organization(name='metastatic')
metastatic_org.research_protocols.append(metastatic_protocol)
# from https://docs.google.com/spreadsheets/d/\
# 1oJ8HKfMHOdXkSshjRlr8lFXxT4aUHX5ntxnKMgf50wE/edit#gid=1339608238
three_q_recur = Recur(start='{"months": 3}',
cycle_length='{"months": 6}',
termination='{"months": 24}')
four_q_recur1 = Recur(start='{"months": 6}',
cycle_length='{"years": 1}',
termination='{"months": 21}')
four_q_recur2 = Recur(start='{"months": 30}',
cycle_length='{"years": 1}',
termination='{"months": 33}')
six_q_recur = Recur(start='{"years": 1}',
cycle_length='{"years": 1}',
termination='{"years": 3, "months": 3}')
for name in (localized_instruments.union(
*(metastatic_baseline_instruments,
metastatic_indefinite_instruments, metastatic_3, metastatic_4,
metastatic_6))):
TestCase.add_questionnaire(name=name)
with SessionScope(db):
db.session.add(localized_org)
db.session.add(metastatic_org)
db.session.add(three_q_recur)
db.session.add(four_q_recur1)
db.session.add(four_q_recur2)
db.session.add(six_q_recur)
db.session.commit()
localized_org, metastatic_org = map(db.session.merge,
(localized_org, metastatic_org))
three_q_recur = db.session.merge(three_q_recur)
four_q_recur1 = db.session.merge(four_q_recur1)
four_q_recur2 = db.session.merge(four_q_recur2)
six_q_recur = db.session.merge(six_q_recur)
# Localized baseline
l_qb = QuestionnaireBank(name='localized',
classification='baseline',
research_protocol_id=locpro_id,
start='{"days": 0}',
overdue='{"days": 7}',
expired='{"months": 3}')
for rank, instrument in enumerate(localized_instruments):
q = Questionnaire.find_by_name(name=instrument)
qbq = QuestionnaireBankQuestionnaire(questionnaire=q, rank=rank)
l_qb.questionnaires.append(qbq)
# Metastatic baseline
mb_qb = QuestionnaireBank(name='metastatic',
classification='baseline',
research_protocol_id=metapro_id,
start='{"days": 0}',
overdue='{"days": 30}',
expired='{"months": 3}')
for rank, instrument in enumerate(metastatic_baseline_instruments):
q = Questionnaire.find_by_name(name=instrument)
qbq = QuestionnaireBankQuestionnaire(questionnaire=q, rank=rank)
mb_qb.questionnaires.append(qbq)
# Metastatic indefinite
mi_qb = QuestionnaireBank(name='metastatic_indefinite',
classification='indefinite',
research_protocol_id=metapro_id,
start='{"days": 0}',
expired='{"years": 50}')
for rank, instrument in enumerate(metastatic_indefinite_instruments):
q = Questionnaire.find_by_name(name=instrument)
qbq = QuestionnaireBankQuestionnaire(questionnaire=q, rank=rank)
mi_qb.questionnaires.append(qbq)
# Metastatic recurring 3
mr3_qb = QuestionnaireBank(name='metastatic_recurring3',
classification='recurring',
research_protocol_id=metapro_id,
start='{"days": 0}',
overdue='{"days": 30}',
expired='{"months": 3}',
recurs=[three_q_recur])
for rank, instrument in enumerate(metastatic_3):
q = Questionnaire.find_by_name(name=instrument)
qbq = QuestionnaireBankQuestionnaire(questionnaire=q, rank=rank)
mr3_qb.questionnaires.append(qbq)
# Metastatic recurring 4
mr4_qb = QuestionnaireBank(name='metastatic_recurring4',
classification='recurring',
research_protocol_id=metapro_id,
recurs=[four_q_recur1, four_q_recur2],
start='{"days": 0}',
overdue='{"days": 30}',
expired='{"months": 3}')
for rank, instrument in enumerate(metastatic_4):
q = Questionnaire.find_by_name(name=instrument)
qbq = QuestionnaireBankQuestionnaire(questionnaire=q, rank=rank)
mr4_qb.questionnaires.append(qbq)
# Metastatic recurring 6
mr6_qb = QuestionnaireBank(name='metastatic_recurring6',
classification='recurring',
research_protocol_id=metapro_id,
recurs=[six_q_recur],
start='{"days": 0}',
overdue='{"days": 30}',
expired='{"months": 3}')
for rank, instrument in enumerate(metastatic_6):
q = Questionnaire.find_by_name(name=instrument)
qbq = QuestionnaireBankQuestionnaire(questionnaire=q, rank=rank)
mr6_qb.questionnaires.append(qbq)
with SessionScope(db):
db.session.add(l_qb)
db.session.add(mb_qb)
db.session.add(mi_qb)
db.session.add(mr3_qb)
db.session.add(mr4_qb)
db.session.add(mr6_qb)
db.session.commit()