def test_microsecond_truncation():
"""Microseconds should be rounded in FHIR output"""
sample = datetime.utcnow()
sample = sample.replace(tzinfo=pytz.utc)
if sample.microsecond == 0:
sample = sample.replace(microsecond=1234567890)
assert sample.isoformat() != FHIR_datetime.as_fhir(sample)
expected = sample.replace(microsecond=0)
assert expected.isoformat() == FHIR_datetime.as_fhir(sample)
def test_microsecond_truncation():
"""Microseconds should be rounded in FHIR output"""
sample = datetime.utcnow()
sample = sample.replace(tzinfo=pytz.utc)
if sample.microsecond == 0:
sample = sample.replace(microsecond=1234567890)
assert sample.isoformat() != FHIR_datetime.as_fhir(sample)
expected = sample.replace(microsecond=0)
assert expected.isoformat() == FHIR_datetime.as_fhir(sample)
def test_get_user_documents(self):
"""tests get the list of user documents for a user"""
now = datetime.utcnow()
ud1 = UserDocument(
document_type="TestFile", uploaded_at=now,
filename="test_file_1.txt", filetype="txt", uuid="012345")
ud2 = UserDocument(
document_type="AlternateTestFile", uploaded_at=now,
filename="test_file_2.txt", filetype="txt", uuid="098765")
self.test_user.documents.append(ud1)
self.test_user.documents.append(ud2)
with SessionScope(db):
db.session.commit()
self.test_user = db.session.merge(self.test_user)
self.login()
response = self.client.get(
'/api/user/{}/user_documents'.format(TEST_USER_ID))
assert response.status_code == 200
assert len(response.json['user_documents']) == 2
# tests document_type filter
response = self.client.get(
'/api/user/{}/user_documents?document_type=TestFile'.format(
TEST_USER_ID))
assert response.status_code == 200
assert len(response.json['user_documents']) == 1
assert (response.json['user_documents'][0]['uploaded_at']
== FHIR_datetime.as_fhir(now))
def test_get_user_documents(self):
"""tests get the list of user documents for a user"""
now = datetime.utcnow()
ud1 = UserDocument(document_type="TestFile",
uploaded_at=now,
filename="test_file_1.txt",
filetype="txt",
uuid="012345")
ud2 = UserDocument(document_type="AlternateTestFile",
uploaded_at=now,
filename="test_file_2.txt",
filetype="txt",
uuid="098765")
self.test_user.documents.append(ud1)
self.test_user.documents.append(ud2)
with SessionScope(db):
db.session.commit()
self.test_user = db.session.merge(self.test_user)
self.login()
rv = self.client.get(
'/api/user/{}/user_documents'.format(TEST_USER_ID))
self.assert200(rv)
self.assertEqual(len(rv.json['user_documents']), 2)
# tests document_type filter
rv = self.client.get(
'/api/user/{}/user_documents?document_type=TestFile'.format(
TEST_USER_ID))
self.assert200(rv)
self.assertEqual(len(rv.json['user_documents']), 1)
self.assertEqual(rv.json['user_documents'][0]['uploaded_at'],
FHIR_datetime.as_fhir(now))
def test_tz_aware_output():
"""FHIR_datetime.as_fhir() should always be tz aware (UTC)"""
unaware = datetime(2016, 7, 15, 9, 20, 37, 0)
# generate fhir - expect UTC tz info at end
isostring = FHIR_datetime.as_fhir(unaware)
assert isostring[-6:] == '+00:00'
def test_tz_aware_output():
"""FHIR_datetime.as_fhir() should always be tz aware (UTC)"""
unaware = datetime(2016, 7, 15, 9, 20, 37, 0)
# generate fhir - expect UTC tz info at end
isostring = FHIR_datetime.as_fhir(unaware)
assert isostring[-6:] == '+00:00'
def test_rp_alteration(self):
# orgs with old rp should migrate to multiple w/ updated retired
from portal.system_uri import SHORTCUT_ALIAS, TRUENTH_CR_NAME
from portal.models.identifier import Identifier
rp1 = ResearchProtocol(name='initial')
rp2 = ResearchProtocol(name='replacement')
org = Organization(name='testy')
org.research_protocols.append(rp1)
with SessionScope(db):
db.session.add(rp2)
db.session.add(org)
db.session.commit()
mp = ModelPersistence(Organization,
lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Add second rp, mark old as retired
with open(os.path.join(self.tmpdir, 'Organization.json'),
'r') as pfile:
data = json.load(pfile)
now = datetime.utcnow().replace(microsecond=0)
updated = {
'url':
ResearchProtocolExtension.extension_url,
'research_protocols': [{
"name": 'replacement'
}, {
"name": 'initial',
"retired_as_of": FHIR_datetime.as_fhir(now)
}]
}
for i, entry in enumerate(data['entry']):
if entry['name'] != 'testy':
continue
extensions = entry['extension']
keepers = [
ext for ext in extensions
if ext['url'] != ResearchProtocolExtension.extension_url
]
keepers.append(updated)
data['entry'][i]['extension'] = keepers
with open(os.path.join(self.tmpdir, 'Organization.json'),
'w') as pfile:
pfile.write(json.dumps(data))
mp.import_(keep_unmentioned=False)
org = Organization.query.filter(Organization.name == 'testy').one()
assert len(org.research_protocols) == 2
# Make sure retired_as_of was set properly on old
rp1, rp2 = map(db.session.merge, (rp1, rp2))
expected = [(rp2, None), (rp1, now)]
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert results == expected
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)
authored = FHIR_datetime.parse(data['authored'])
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=authored)
with SessionScope(db):
db.session.add(qb)
db.session.add(test_user)
db.session.add(audit)
db.session.add(uc)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID), json=data)
assert response.status_code == 200
test_user = get_user(TEST_USER_ID)
qb = db.session.merge(qb)
assert test_user.questionnaire_responses.count() == 1
assert (
test_user.questionnaire_responses[0].questionnaire_bank_id
== qb.id)
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)
authored = FHIR_datetime.parse(data['authored'])
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=authored)
with SessionScope(db):
db.session.add(qb)
db.session.add(test_user)
db.session.add(audit)
db.session.add(uc)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID), json=data)
assert response.status_code == 200
test_user = get_user(TEST_USER_ID)
qb = db.session.merge(qb)
assert test_user.questionnaire_responses.count() == 1
assert (test_user.questionnaire_responses[0].questionnaire_bank_id ==
qb.id)
def test_tz_aware_conversion():
eastern = pytz.timezone('US/Eastern')
aware = datetime(2016, 7, 15, 9, 20, 37, 0, eastern)
parsed = FHIR_datetime.parse(aware.strftime("%Y-%m-%dT%H:%M:%S%z"))
# FHIR_datetime converts to UTC and strips the tzinfo
# for safe comparisons with other tz unaware strings
assert parsed.tzinfo is None
# Add it back in to confirm values match
parsed = parsed.replace(tzinfo=pytz.utc)
assert aware == parsed
def test_tz_aware_conversion():
eastern = pytz.timezone('US/Eastern')
aware = datetime(2016, 7, 15, 9, 20, 37, 0, eastern)
parsed = FHIR_datetime.parse(aware.strftime("%Y-%m-%dT%H:%M:%S%z"))
# FHIR_datetime converts to UTC and strips the tzinfo
# for safe comparisons with other tz unaware strings
assert parsed.tzinfo is None
# Add it back in to confirm values match
parsed = parsed.replace(tzinfo=pytz.utc)
assert aware == parsed
def test_rp_alteration(self):
# orgs with old rp should migrate to multiple w/ updated retired
from portal.system_uri import SHORTCUT_ALIAS, TRUENTH_CR_NAME
from portal.models.identifier import Identifier
rp1 = ResearchProtocol(name='initial')
rp2 = ResearchProtocol(name='replacement')
org = Organization(name='testy')
org.research_protocols.append(rp1)
with SessionScope(db):
db.session.add(rp2)
db.session.add(org)
db.session.commit()
mp = ModelPersistence(
Organization, lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Add second rp, mark old as retired
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'r') as pfile:
data = json.load(pfile)
now = datetime.utcnow().replace(microsecond=0)
updated = {
'url': ResearchProtocolExtension.extension_url,
'research_protocols': [
{"name": 'replacement'},
{"name": 'initial', "retired_as_of": FHIR_datetime.as_fhir(
now)}]}
for i, entry in enumerate(data['entry']):
if entry['name'] != 'testy':
continue
extensions = entry['extension']
keepers = [
ext for ext in extensions
if ext['url'] != ResearchProtocolExtension.extension_url]
keepers.append(updated)
data['entry'][i]['extension'] = keepers
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'w') as pfile:
pfile.write(json.dumps(data))
mp.import_(keep_unmentioned=False)
org = Organization.query.filter(Organization.name == 'testy').one()
assert len(org.research_protocols) == 2
# Make sure retired_as_of was set properly on old
rp1, rp2 = map(db.session.merge, (rp1, rp2))
expected = [(rp2, None), (rp1, now)]
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert results == expected
def test_deceased(self):
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
now = FHIR_datetime.as_fhir(datetime.utcnow())
data = {'deceasedDateTime': now}
response = self.client.post(
'/api/patient/{}/deceased'.format(TEST_USER_ID),
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
user = User.query.get(TEST_USER_ID)
assert user.deceased
def test_deceased(self):
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
now = FHIR_datetime.as_fhir(datetime.utcnow())
data = {'deceasedDateTime': now}
response = self.client.post(
'/api/patient/{}/deceased'.format(TEST_USER_ID),
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
user = User.query.get(TEST_USER_ID)
assert user.deceased
def test_post_user_future_consent_date(self):
"""Shouldn't allow future consent date"""
self.shallow_org_tree()
org1 = Organization.query.filter(Organization.id > 0).first()
acceptance_date = datetime.utcnow() + relativedelta(days=1)
data = {'organization_id': org1.id,
'agreement_url': self.url,
'acceptance_date': FHIR_datetime.as_fhir(acceptance_date)}
self.login()
response = self.client.post(
'/api/user/{}/consent'.format(TEST_USER_ID),
json=data,
)
assert response.status_code == 400
def test_int_date(self):
# integer value shouldn't generate parser error
acceptance_date = 1394413200000
with pytest.raises(BadRequest) as e:
dt = FHIR_datetime.parse(acceptance_date, 'acceptance date')
assert 'acceptance date' in str(e)
def test_tz_unaware_conversion():
unaware = datetime(2016, 7, 15, 9, 20, 37, 0)
parsed = FHIR_datetime.parse(unaware.strftime("%Y-%m-%dT%H:%M:%S"))
assert unaware == parsed
def test_int_date(self):
# integer value shouldn't generate parser error
acceptance_date = 1394413200000
with pytest.raises(BadRequest) as e:
dt = FHIR_datetime.parse(acceptance_date, 'acceptance date')
assert 'acceptance date' in str(e)
def test_tz_unaware_conversion():
unaware = datetime(2016, 7, 15, 9, 20, 37, 0)
parsed = FHIR_datetime.parse(unaware.strftime("%Y-%m-%dT%H:%M:%S"))
assert unaware == parsed