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))
crv_id = crv.id
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)
with SessionScope(db):
db.session.add(bank)
db.session.commit()
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv_id)
self.test_user = db.session.merge(self.test_user)
# test user with status = 'Expired' (should not show up)
a_s = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert a_s.overall_status == OverallStatus.expired
ostats = self.get_ostats()
assert len(ostats) == 0
# test user with status = 'Overdue' (should show up)
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))
invalidate_users_QBT(self.test_user.id)
a_s = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert a_s.overall_status == OverallStatus.overdue
ostats = self.get_ostats()
assert len(ostats) == 1
assert ostats[(crv.id, crv.name)] == [(15, TEST_USER_ID)]
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))
crv_id = crv.id
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)
with SessionScope(db):
db.session.add(bank)
db.session.commit()
self.test_user = db.session.merge(self.test_user)
self.test_user.organizations.append(crv)
self.consent_with_org(org_id=crv_id)
self.test_user = db.session.merge(self.test_user)
# test user with status = 'Expired' (should not show up)
a_s = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert a_s.overall_status == OverallStatus.expired
ostats = self.get_ostats()
assert len(ostats) == 0
# test user with status = 'Overdue' (should show up)
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))
invalidate_users_QBT(self.test_user.id)
a_s = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert a_s.overall_status == OverallStatus.overdue
ostats = self.get_ostats()
assert len(ostats) == 1
assert ostats[(crv.id, crv.name)] == [(15, TEST_USER_ID)]
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 add_user(
self, username, first_name="", last_name="", image_url=None,
password=DEFAULT_PASSWORD, email=None):
"""Create a user and add to test db, and return it"""
# Hash the password
password = self.app.user_manager.hash_password(password)
test_user = User(
username=username, first_name=first_name, last_name=last_name,
image_url=image_url, password=password)
if email is not None:
test_user.email = email
with SessionScope(db):
db.session.add(test_user)
db.session.commit()
test_user = db.session.merge(test_user)
# Avoid testing cached/stale data
invalidate_users_QBT(test_user.id)
return test_user
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_st_undone(self):
# Symptom Tracker QB with incompleted should generate communication
mock_communication_request('symptom_tracker', '{"days": 30}')
self.app.config['NO_CHALLENGE_WO_DATA'] = False
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
self.add_required_clinical_data(backdate=relativedelta(days=31))
self.test_user = db.session.merge(self.test_user)
self.test_user.birthdate = '1969-07-16'
# Confirm test user qualifies for ST QB
qstats = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert qstats.enrolled_in_classification('baseline')
# With most q's undone, should generate a message
mock_qr(instrument_id='epic26')
invalidate_users_QBT(TEST_USER_ID)
self.test_user = db.session.merge(self.test_user)
qstats = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert OverallStatus.in_progress == qstats.overall_status
update_patient_loop(update_cache=False, queue_messages=True)
expected = Communication.query.first()
assert expected
def test_st_undone(self):
# Symptom Tracker QB with incompleted should generate communication
mock_communication_request('symptom_tracker', '{"days": 30}')
self.app.config['NO_CHALLENGE_WO_DATA'] = False
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
self.add_required_clinical_data(backdate=relativedelta(days=31))
self.test_user = db.session.merge(self.test_user)
self.test_user.birthdate = '1969-07-16'
# Confirm test user qualifies for ST QB
qstats = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert qstats.enrolled_in_classification('baseline')
# With most q's undone, should generate a message
mock_qr(instrument_id='epic26')
invalidate_users_QBT(TEST_USER_ID)
self.test_user = db.session.merge(self.test_user)
qstats = QB_Status(self.test_user, as_of_date=datetime.utcnow())
assert OverallStatus.in_progress == qstats.overall_status
update_patient_loop(update_cache=False, queue_messages=True)
expected = Communication.query.first()
assert expected
def patch_deceased_user_consents(uid):
user = User.query.get(uid)
user_consents = UserConsent.query.filter(
UserConsent.user_id == uid).order_by(UserConsent.id).all()
# if no user_consents exist for user, we're done
if not user_consents:
return
# acquire the deceased date
dd = user.deceased.timestamp
# if the most recent consent looks correct, assume we're done
if user_consents[-1].status == 'suspended' and not (
user_consents[-1].options & SEND_REMINDERS_MASK):
return
admin = User.query.filter_by(email='__system__').first()
log.info("Patching broken consents for {}, with deceased date {}".format(
user, dd))
keeper = user_consents.pop(0)
log.info(" keeping original user_consent {} {} {} {}".format(
keeper.id, keeper.status, keeper.options, keeper.acceptance_date))
obsolete_audits, obsolete_consents = [], []
for uc in user_consents:
log.info(" deleting user_consent {} {} {} {}".format(
uc.id, uc.status, uc.options, uc.acceptance_date))
a = Audit.query.get(uc.audit_id)
log.info(" and the related {}".format(a))
obsolete_audits.append(a.id)
obsolete_consents.append(uc.id)
# out of loop, delete the unwanted
db.session.query(UserConsent).filter(
UserConsent.id.in_(obsolete_consents)).delete(
synchronize_session=False)
db.session.query(Audit).filter(
Audit.id.in_(obsolete_audits)).delete(synchronize_session=False)
db.session.commit()
# now add back in the corrected consent, from the initial
deceased_options = STAFF_EDITABLE_MASK | INCLUDE_IN_REPORTS_MASK
deceased_consent = UserConsent(user_id=uid,
organization_id=keeper.organization_id,
agreement_url=keeper.agreement_url,
acceptance_date=dd,
options=deceased_options,
status='suspended')
user.update_consents(consent_list=[deceased_consent], acting_user=admin)
# The updated consent may have altered the cached assessment
# status - invalidate this user's data at this time.
invalidate_users_QBT(user_id=user.id)
db.session.commit()
log.info(" Done, results:")
for uc in UserConsent.query.filter(UserConsent.user_id == uid):
log.info(" {} {} {} {}".format(uc, uc.acceptance_date, uc.status,
uc.options))
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'])
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 patch_deceased_user_consents(uid):
user = User.query.get(uid)
user_consents = UserConsent.query.filter(
UserConsent.user_id == uid).order_by(UserConsent.id).all()
# if no user_consents exist for user, we're done
if not user_consents:
return
# acquire the deceased date
dd = user.deceased.timestamp
# if the most recent consent looks correct, assume we're done
if user_consents[-1].status == 'suspended' and not(
user_consents[-1].options & SEND_REMINDERS_MASK):
return
admin = User.query.filter_by(email='__system__').first()
log.info("Patching broken consents for {}, with deceased date {}".format(
user, dd))
keeper = user_consents.pop(0)
log.info(" keeping original user_consent {} {} {} {}".format(
keeper.id, keeper.status, keeper.options, keeper.acceptance_date))
obsolete_audits, obsolete_consents = [], []
for uc in user_consents:
log.info(" deleting user_consent {} {} {} {}".format(
uc.id, uc.status, uc.options, uc.acceptance_date))
a = Audit.query.get(uc.audit_id)
log.info(" and the related {}".format(a))
obsolete_audits.append(a.id)
obsolete_consents.append(uc.id)
# out of loop, delete the unwanted
db.session.query(UserConsent).filter(UserConsent.id.in_(
obsolete_consents)).delete(synchronize_session=False)
db.session.query(Audit).filter(Audit.id.in_(
obsolete_audits)).delete(synchronize_session=False)
db.session.commit()
# now add back in the corrected consent, from the initial
deceased_options = STAFF_EDITABLE_MASK | INCLUDE_IN_REPORTS_MASK
deceased_consent = UserConsent(
user_id=uid,
organization_id=keeper.organization_id,
agreement_url=keeper.agreement_url,
acceptance_date=dd,
options=deceased_options,
status='suspended')
user.update_consents(
consent_list=[deceased_consent], acting_user=admin)
# The updated consent may have altered the cached assessment
# status - invalidate this user's data at this time.
invalidate_users_QBT(user_id=user.id)
db.session.commit()
log.info(" Done, results:")
for uc in UserConsent.query.filter(UserConsent.user_id == uid):
log.info(" {} {} {} {}".format(
uc, uc.acceptance_date, uc.status, uc.options))
def upgrade():
# Tricky task to locate the errors. One time expensive process,
# loop through patients identifying problems.
admin = admin_id()
qb_map = qb_pairs_by_rp()
if not qb_map:
return # nothing to do on systems w/o RP changes
fix_map = dict()
for patient in active_patients(include_test_role=True).order_by(User.id):
qnrs = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == patient.id).order_by(
QuestionnaireResponse.authored)
if not qnrs.count():
# Only care if the user submitted QNRs:
continue
for qnr in qnrs:
# Obtain qb_timeline row at the time of QNR.authored
as_of_date = qnr.authored
qbt = QBT.query.filter(QBT.user_id == patient.id).filter(
QBT.at <= as_of_date).order_by(
QBT.at.desc(), QBT.id.desc()).first()
if qnr.questionnaire_bank_id is None:
print(
"qnr {} user_id {} authored {} {}"
" with NO qb_id set".format(
qnr.id, patient.id, as_of_date,
qnr.document['questionnaire']['reference']))
continue
if qbt and qbt.status != OverallStatus.withdrawn:
recorded_qb = QuestionnaireBank.query.get(
qnr.questionnaire_bank_id)
qbd = qbt.qbd()
expected_qb = qbd.questionnaire_bank
if recorded_qb.classification == 'indefinite':
# indefinite case is handled differently...
qb_status = QB_Status(patient, as_of_date)
expected_qb = QuestionnaireBank.query.get(
qb_status._current_indef.qb_id)
if recorded_qb != expected_qb:
replacement = qb_map.get(recorded_qb.id)
if replacement == expected_qb.id:
# retain the change request, as altering it inline
# interrupts the iteration
patched_qbd = QBD(
relative_start=qbd.relative_start, iteration=qbd.iteration,
recur=qbd.recur, qb_id=replacement)
fix_map[qnr.id] = (expected_qb.id, visit_name(patched_qbd))
print(
"qnr {} replacing incorrect qb_id {} with {} "
"for user {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
patient.id))
else:
print(
"qnr {} PROBLEM: recorded qb_id {}, "
"expected {} doesn't match replacement {} "
"for user_id {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
replacement, patient.id))
for qnr_id, row in fix_map.items():
qb_id, visit = row
qnr = QuestionnaireResponse.query.get(qnr_id)
comment = (
"Migration correct qnr.id {} ({}) questionnaire_bank_id"
" from {} to {}".format(
qnr.id, visit, qnr.questionnaire_bank_id, qb_id))
audit = Audit(
user_id=admin, subject_id=qnr.subject_id,
context='assessment', comment=comment)
db.session.add(audit)
qnr.questionnaire_bank_id = qb_id
# clear out cached qb_timeline data for user as it
# needs to be recalculated given the change
invalidate_users_QBT(qnr.subject_id)
db.session.commit()
def upgrade():
# Tricky task to locate the errors. One time expensive process,
# loop through patients identifying problems.
admin = admin_id()
qb_map = qb_pairs_by_rp()
if not qb_map:
return # nothing to do on systems w/o RP changes
fix_map = dict()
raise RuntimeError(
"Unsupported migration; code has changed - not maintained")
for patient in active_patients(include_test_role=True).order_by(User.id):
qnrs = QuestionnaireResponse.query.filter(
QuestionnaireResponse.subject_id == patient.id).order_by(
QuestionnaireResponse.authored)
if not qnrs.count():
# Only care if the user submitted QNRs:
continue
for qnr in qnrs:
# Obtain qb_timeline row at the time of QNR.authored
as_of_date = qnr.authored
qbt = QBT.query.filter(QBT.user_id == patient.id).filter(
QBT.at <= as_of_date).order_by(
QBT.at.desc(), QBT.id.desc()).first()
if qnr.questionnaire_bank_id is None:
print(
"qnr {} user_id {} authored {} {}"
" with NO qb_id set".format(
qnr.id, patient.id, as_of_date,
qnr.document['questionnaire']['reference']))
continue
if qbt and qbt.status != OverallStatus.withdrawn:
recorded_qb = QuestionnaireBank.query.get(
qnr.questionnaire_bank_id)
qbd = qbt.qbd()
expected_qb = qbd.questionnaire_bank
if recorded_qb.classification == 'indefinite':
# indefinite case is handled differently...
qb_status = QB_Status(patient, as_of_date)
expected_qb = QuestionnaireBank.query.get(
qb_status._current_indef.qb_id)
if recorded_qb != expected_qb:
replacement = qb_map.get(recorded_qb.id)
if replacement == expected_qb.id:
# retain the change request, as altering it inline
# interrupts the iteration
patched_qbd = QBD(
relative_start=qbd.relative_start, iteration=qbd.iteration,
recur=qbd.recur, qb_id=replacement)
fix_map[qnr.id] = (expected_qb.id, visit_name(patched_qbd))
print(
"qnr {} replacing incorrect qb_id {} with {} "
"for user {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
patient.id))
else:
print(
"qnr {} PROBLEM: recorded qb_id {}, "
"expected {} doesn't match replacement {} "
"for user_id {}".format(
qnr.id, recorded_qb.id, expected_qb.id,
replacement, patient.id))
for qnr_id, row in fix_map.items():
qb_id, visit = row
qnr = QuestionnaireResponse.query.get(qnr_id)
comment = (
"Migration correct qnr.id {} ({}) questionnaire_bank_id"
" from {} to {}".format(
qnr.id, visit, qnr.questionnaire_bank_id, qb_id))
audit = Audit(
user_id=admin, subject_id=qnr.subject_id,
context='assessment', comment=comment)
db.session.add(audit)
qnr.questionnaire_bank_id = qb_id
# clear out cached qb_timeline data for user as it
# needs to be recalculated given the change
invalidate_users_QBT(qnr.subject_id)
db.session.commit()
