def test_duplicate_identifier(self):
swagger_spec = swagger(self.app)
identifier = Identifier(system='https://unique.org', value='abc123')
data = swagger_spec['definitions']['QuestionnaireResponse']['example']
data['identifier'] = identifier.as_fhir()
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
# Submit a second, with the same identifier, expect error
data2 = swagger_spec['definitions']['QuestionnaireResponse']['example']
data2['identifier'] = identifier.as_fhir()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID), json=data2)
assert response.status_code == 409
self.test_user = db.session.merge(self.test_user)
assert self.test_user.questionnaire_responses.count() == 1
# And a third, with just the id.value changed
data3 = swagger_spec['definitions']['QuestionnaireResponse']['example']
identifier.value = 'do-over'
data3['identifier'] = identifier.as_fhir()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID), json=data3)
assert response.status_code == 200
self.test_user = db.session.merge(self.test_user)
assert self.test_user.questionnaire_responses.count() == 2
def test_organization_identifiers_update(self):
with open(os.path.join(
os.path.dirname(__file__),
'organization-example-gastro.json'), 'r'
) as fhir_data:
data = json.load(fhir_data)
self.promote_user(role_name=ROLE.ADMIN.value)
self.login()
before = Organization.query.count()
response = self.client.post(
'/api/organization', content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
assert Organization.query.count() == before + 1
# the gastro file contains a single identifier - add
# a second one and PUT, expecting we get two total
alias = Identifier(system=SHORTCUT_ALIAS, value='foobar',
use='secondary')
org = Organization.query.filter_by(name='Gastroenterology').one()
data['identifier'].append(alias.as_fhir())
response = self.client.put(
'/api/organization/{}'.format(org.id),
content_type='application/json', data=json.dumps(data))
assert response.status_code == 200
# obtain the org from the db, check the identifiers
org = Organization.query.filter_by(name='Gastroenterology').one()
assert 2 == org.identifiers.count()
def test_questionnaire_serialize(self):
q1 = self.add_questionnaire(name='q1')
data = q1.as_fhir()
assert data['resourceType'] == "Questionnaire"
expected = Identifier(system=TRUENTH_QUESTIONNAIRE_CODE_SYSTEM,
value='q1')
assert Identifier.from_fhir(data['identifier'][0]) == expected
def test_organization_identifiers_update(self):
with open(
os.path.join(os.path.dirname(__file__),
'organization-example-gastro.json'),
'r') as fhir_data:
data = json.load(fhir_data)
self.promote_user(role_name=ROLE.ADMIN.value)
self.login()
before = Organization.query.count()
response = self.client.post('/api/organization',
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
assert Organization.query.count() == before + 1
# the gastro file contains a single identifier - add
# a second one and PUT, expecting we get two total
alias = Identifier(system=SHORTCUT_ALIAS,
value='foobar',
use='secondary')
org = Organization.query.filter_by(name='Gastroenterology').one()
data['identifier'].append(alias.as_fhir())
response = self.client.put('/api/organization/{}'.format(org.id),
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
# obtain the org from the db, check the identifiers
org = Organization.query.filter_by(name='Gastroenterology').one()
assert 2 == org.identifiers.count()
def test_invalid_identifier(self):
swagger_spec = swagger(self.app)
identifier = Identifier(system=None, value='abc-123')
data = swagger_spec['definitions']['QuestionnaireResponse']['example']
data['identifier'] = identifier.as_fhir()
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 == 400
def test_invalid_identifier(self):
swagger_spec = swagger(self.app)
identifier = Identifier(system=None, value='abc-123')
data = swagger_spec['definitions']['QuestionnaireResponse']['example']
data['identifier'] = identifier.as_fhir()
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 == 400
def test_ident_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT)
self.login()
ident = db.session.merge(ident)
rv = self.client.get('/api/patient?identifier={}'.format(
json.dumps(ident.as_fhir())),
follow_redirects=True)
self.assert200(rv)
def test_ident_nomatch_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT)
self.login()
ident = db.session.merge(ident)
# modify the system to mis match
id_str = json.dumps(ident.as_fhir()).replace("example.com",
"wrong-system.com")
rv = self.client.get('/api/patient?identifier={}'.format(id_str),
follow_redirects=True)
self.assert404(rv)
def test_multimatch_search_old_format(self):
second = self.add_user(username='******')
second_id = second.id
self.promote_user(user=second, role_name=ROLE.PATIENT.value)
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
ui2 = UserIdentifier(identifier=ident, user_id=second_id)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.add(ui2)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.promote_user(role_name=ROLE.ADMIN.value) # skip org/staff steps
self.login()
ident = db.session.merge(ident)
response = self.client.get('/api/patient/',
query_string={
'identifier':
'{}|{}'.format(ident.system,
ident.value)
},
follow_redirects=True)
# Multi not supported in old format
assert response.status_code == 400
def test_multimatch_search(self):
second = self.add_user(username='******')
second_id = second.id
self.promote_user(user=second, role_name=ROLE.PATIENT.value)
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
ui2 = UserIdentifier(identifier=ident, user_id=second_id)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.add(ui2)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.promote_user(role_name=ROLE.ADMIN.value) # skip org/staff steps
self.login()
ident = db.session.merge(ident)
response = self.client.get('/api/patient/',
query_string={
'identifier':
'{}|{}'.format(ident.system,
ident.value),
'patch_dstu2':
True
},
follow_redirects=True)
assert response.status_code == 200
assert response.json['resourceType'] == 'Bundle'
assert response.json['total'] == 2
assert response.json['type'] == 'searchset'
def test_identifier_lookup(self):
# setup a minimal communication request
from tests.test_communication import mock_communication_request
from tests.test_assessment_status import mock_tnth_questionnairebanks
from portal.system_uri import TRUENTH_CR_NAME
from portal.models.identifier import Identifier
mock_tnth_questionnairebanks()
cr = mock_communication_request(
'symptom_tracker_recurring', '{"days": 14}')
cr.identifiers.append(
Identifier(value='2 week ST', system=TRUENTH_CR_NAME))
with SessionScope(db):
db.session.add(cr)
db.session.commit()
cr = db.session.merge(cr)
assert cr.identifiers.count() == 1
data = cr.as_fhir()
mp = ModelPersistence(
CommunicationRequest,
sequence_name='communication_requests_id_seq',
lookup_field='identifier')
new_obj = CommunicationRequest.from_fhir(data)
match, field_description = mp.lookup_existing(
new_obj=new_obj, new_data=data)
assert match.name == cr.name
def test_organization_get_by_identifier(self):
org_id_system = "http://test/system"
org_id_value = "testval"
self.login()
org = Organization(name='test', id=999)
ident = Identifier(id=99, system=org_id_system, value=org_id_value)
org_ident = OrganizationIdentifier(organization_id=999,
identifier_id=99)
with SessionScope(db):
db.session.add(org)
db.session.add(ident)
db.session.commit()
db.session.add(org_ident)
db.session.commit()
# use api to obtain FHIR
response = self.client.get(
'/api/organization?system={system}&value={value}'.format(
system=quote_plus(org_id_system), value=org_id_value))
assert response.status_code == 200
assert response.json['total'] == 1
assert response.json['entry'][0]['id'] == 999
# use alternative API to obtain organization
response = self.client.get(
'/api/organization/{value}?system={system}'.format(
system=quote_plus(org_id_system), value=org_id_value))
assert response.status_code == 200
fetched = Organization.from_fhir(response.json)
org = db.session.merge(org)
assert org.id == fetched.id
assert org.name == fetched.name
def test_organization_inheritence_search(self):
# Region at top should apply to leaves
self.deepen_org_tree()
count = Organization.query.count()
assert count > 3
# add region to one mid-level parent org with two children,
# we should get only those three
region = Identifier(value='state:NY', system=PRACTICE_REGION)
with SessionScope(db):
db.session.add(region)
db.session.commit()
region = db.session.merge(region)
oi = OrganizationIdentifier(organization_id=1002,
identifier_id=region.id)
with SessionScope(db):
db.session.add(oi)
db.session.commit()
# use api to obtain FHIR bundle
self.login()
response = self.client.get('/api/organization?state=NY')
assert response.status_code == 200
bundle = response.json
assert bundle['resourceType'] == 'Bundle'
assert len(bundle['entry']) == 3
# add filter to restrict to just the leaves
response = self.client.get('/api/organization?state=NY&filter=leaves')
assert response.status_code == 200
bundle = response.json
assert bundle['resourceType'] == 'Bundle'
assert len(bundle['entry']) == 2
def test_questionnaire_serialize(self):
q1 = self.add_questionnaire(name='q1')
data = q1.as_fhir()
assert data['resourceType'] == "Questionnaire"
expected = Identifier(
system=TRUENTH_QUESTIONNAIRE_CODE_SYSTEM, value='q1')
assert Identifier.from_fhir(data['identifier'][0]) == expected
def test_organization_extension_update(self):
# confirm clearing one of several extensions works
self.promote_user(role_name=ROLE.ADMIN.value)
self.login()
en_AU = LocaleConstants().AustralianEnglish
# Populate db with complete org, and set many fields
org = Organization(name='test',
phone='800-800-5665',
timezone='US/Pacific')
org.identifiers.append(
Identifier(value='state:NY', system=PRACTICE_REGION))
org.locales.append(en_AU)
org.default_locale = 'en_AU'
rp = ResearchProtocol(name='rp1')
with SessionScope(db):
db.session.add(rp)
db.session.add(org)
db.session.commit()
org, rp = map(db.session.merge, (org, rp))
org_id, rp_id = org.id, rp.id
org.research_protocols.append(rp)
data = org.as_fhir()
input = {
k: v
for k, v in data.items() if k in ('name', 'resourceType')
}
# Replace locale extension with null value, copy
# over others.
input['extension'] = [
e for e in data['extension']
if e['url'] != LocaleExtension.extension_url
]
input['extension'].append({'url': LocaleExtension.extension_url})
response = self.client.put('/api/organization/{}'.format(org_id),
content_type='application/json',
data=json.dumps(input))
assert response.status_code == 200
# Pull the updated db entry
org = Organization.query.get(org_id)
en_AU = db.session.merge(en_AU)
# Confirm all the unmentioned entries survived
assert org.phone == '800-800-5665'
assert org.default_locale == 'en_AU'
assert org.locales.count() == 0
assert org.timezone == 'US/Pacific'
assert org.research_protocol(as_of_date=datetime.utcnow()).id == rp_id
# Confirm empty extension isn't included in result
results = response.json
for e in results['extension']:
assert 'url' in e
assert len(e.keys()) > 1
def prep_org_w_identifier(self):
o = Organization(name='test org')
i = Identifier(system=US_NPI, value='123-45')
o.identifiers.append(i)
with SessionScope(db):
db.session.add(o)
db.session.commit()
o = db.session.merge(o)
return o
def add_questionnaire(name):
q = Questionnaire()
i = Identifier(
system=TRUENTH_QUESTIONNAIRE_CODE_SYSTEM, value=name)
q.identifiers.append(i)
with SessionScope(db):
db.session.add(q)
db.session.commit()
return db.session.merge(q)
def test_organization_identifiers(self):
alias = Identifier(use='official',
system='http://www.zorgkaartnederland.nl/',
value='my official alias',
assigner='Organization/1')
shortcut = Identifier(use='secondary',
system=SHORTCUT_ALIAS,
value='shortcut')
self.shallow_org_tree()
org = Organization.query.filter(Organization.id > 0).first()
before = org.identifiers.count()
org.identifiers.append(alias)
org.identifiers.append(shortcut)
with SessionScope(db):
db.session.commit()
org = db.session.merge(org)
assert org.identifiers.count() == before + 2
def test_site_ids(self):
# bless org w/ expected identifier type
wanted_system = 'http://pcctc.org/'
unwanted_system = 'http://other.org/'
self.app.config['REPORTING_IDENTIFIER_SYSTEMS'] = [wanted_system]
id_value = '146-11'
org = Organization.query.filter(
Organization.name == 'metastatic').one()
id1 = Identifier(
system=wanted_system, use='secondary', value=id_value)
id2 = Identifier(
system=unwanted_system, use='secondary', value=id_value)
org.identifiers.append(id1)
org.identifiers.append(id2)
with SessionScope(db):
db.session.commit()
nineback, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=nineback, local_metastatic='metastatic')
instrument_id = 'eortc'
mock_qr(instrument_id=instrument_id)
# add staff user w/ same org association for bundle creation
staff = self.add_user(username='******')
staff.organizations.append(Organization.query.filter(
Organization.name == 'metastatic').one())
self.promote_user(staff, role_name=ROLE.STAFF.value)
staff = db.session.merge(staff)
bundle = aggregate_responses(
instrument_ids=[instrument_id], current_user=staff)
id1 = db.session.merge(id1)
assert 1 == len(bundle['entry'])
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider']))
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider'][0]
['identifier']))
assert (id1.as_fhir() ==
bundle['entry'][0]['subject']['careProvider'][0]
['identifier'][0])
def test_site_ids(self):
# bless org w/ expected identifier type
wanted_system = 'http://pcctc.org/'
unwanted_system = 'http://other.org/'
self.app.config['REPORTING_IDENTIFIER_SYSTEMS'] = [wanted_system]
id_value = '146-11'
org = Organization.query.filter(
Organization.name == 'metastatic').one()
id1 = Identifier(
system=wanted_system, use='secondary', value=id_value)
id2 = Identifier(
system=unwanted_system, use='secondary', value=id_value)
org.identifiers.append(id1)
org.identifiers.append(id2)
with SessionScope(db):
db.session.commit()
nineback, nowish = associative_backdate(
now=now, backdate=relativedelta(months=9, hours=1))
self.bless_with_basics(
setdate=nineback, local_metastatic='metastatic')
instrument_id = 'eortc'
mock_qr(instrument_id=instrument_id)
# add staff user w/ same org association for bundle creation
staff = self.add_user(username='******')
staff.organizations.append(Organization.query.filter(
Organization.name == 'metastatic').one())
self.promote_user(staff, role_name=ROLE.STAFF.value)
staff = db.session.merge(staff)
bundle = aggregate_responses(
instrument_ids=[instrument_id], current_user=staff)
id1 = db.session.merge(id1)
assert 1 == len(bundle['entry'])
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider']))
assert (1 ==
len(bundle['entry'][0]['subject']['careProvider'][0]
['identifier']))
assert (id1.as_fhir() ==
bundle['entry'][0]['subject']['careProvider'][0]
['identifier'][0])
def add_practitioner(
first_name='first', last_name='last', id_value='12345'):
p = Practitioner(first_name=first_name, last_name=last_name)
i = Identifier(system=US_NPI, value=id_value)
p.identifiers.append(i)
with SessionScope(db):
db.session.add(p)
db.session.commit()
p = db.session.merge(p)
return p
def test_delete_identifier(self):
# orgs losing identifiers should delete the orphans
from portal.system_uri import SHORTCUT_ALIAS, TRUENTH_CR_NAME
from portal.models.identifier import Identifier
org = Organization(name='testy')
org.identifiers.append(Identifier(
value='2 week ST', system=TRUENTH_CR_NAME))
org.identifiers.append(Identifier(
value='ohsu', system=SHORTCUT_ALIAS))
with SessionScope(db):
db.session.add(org)
db.session.commit()
mp = ModelPersistence(
Organization, lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Reduce identifiers to one - make sure the other identifier goes away
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'r') as pfile:
data = json.load(pfile)
for i, entry in enumerate(data['entry']):
identifiers = entry['identifier']
keepers = [
identifier for identifier in identifiers
if identifier['system'] == SHORTCUT_ALIAS]
data['entry'][i]['identifier'] = 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 org.identifiers.count() == 1
# Make sure we cleared out the orphan
with pytest.raises(NoResultFound):
Identifier.query.filter_by(
value='2 week ST', system=TRUENTH_CR_NAME).one()
def testPOST(self):
"""Add an existing and fresh identifier - confirm it sticks"""
expected = len(self.test_user.identifiers) + 2
existing = Identifier(system='http://notreal.com', value='unique')
with SessionScope(db):
db.session.add(existing)
db.session.commit()
existing = db.session.merge(existing)
fresh = Identifier(system='http://another.com', value='unique')
data = {'identifier': [i.as_fhir() for i in (existing, fresh)]}
self.login()
response = self.client.post(
'/api/user/{}/identifier'.format(TEST_USER_ID),
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
assert len(response.json['identifier']) == expected
user = User.query.get(TEST_USER_ID)
assert len(user.identifiers) == expected
def test_ident_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
ident = db.session.merge(ident)
response = self.client.get(
'/api/patient/', follow_redirects=True,
query_string={'identifier': json.dumps(ident.as_fhir()),
'patch_dstu2': True})
assert response.status_code == 200
assert response.json['resourceType'] == 'Bundle'
assert response.json['total'] == 1
assert (
response.json['entry'][0]['resource'] ==
Reference.patient(TEST_USER_ID).as_fhir())
def test_duplicate_identifier(self):
swagger_spec = swagger(self.app)
identifier = Identifier(system='https://unique.org', value='abc123')
data = swagger_spec['definitions']['QuestionnaireResponse']['example']
data['identifier'] = identifier.as_fhir()
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
# Submit a second, with the same identifier, expect error
data2 = swagger_spec['definitions']['QuestionnaireResponse']['example']
data2['identifier'] = identifier.as_fhir()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID), json=data2)
assert response.status_code == 409
self.test_user = db.session.merge(self.test_user)
assert self.test_user.questionnaire_responses.count() == 1
# And a third, with just the id.value changed
data3 = swagger_spec['definitions']['QuestionnaireResponse']['example']
identifier.value = 'do-over'
data3['identifier'] = identifier.as_fhir()
response = self.client.post(
'/api/patient/{}/assessment'.format(TEST_USER_ID), json=data3)
assert response.status_code == 200
self.test_user = db.session.merge(self.test_user)
assert self.test_user.questionnaire_responses.count() == 2
def test_shortname(self):
shorty = Identifier(system=SHORTNAME_ID, value='shorty')
self.shallow_org_tree()
org = Organization.query.filter(Organization.id > 0).first()
# prior to adding shortname, should just get org name
assert org.name == org.shortname
org.identifiers.append(shorty)
with SessionScope(db):
db.session.commit()
org = db.session.merge(org)
# after, should get the shortname
assert org.shortname == 'shorty'
def test_ident_nomatch_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
ident = db.session.merge(ident)
# modify the system to mis match
id_str = json.dumps(ident.as_fhir()).replace(
"example.com", "wrong-system.com")
response = self.client.get('/api/patient/', query_string={
'identifier': id_str,
'patch_dstu2': True},
follow_redirects=True)
# expect empty bundle
assert response.status_code == 200
assert response.json['resourceType'] == 'Bundle'
assert response.json['total'] == 0
def test_ident_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
ident = db.session.merge(ident)
response = self.client.get('/api/patient/',
follow_redirects=True,
query_string={
'identifier':
json.dumps(ident.as_fhir()),
'patch_dstu2': True
})
assert response.status_code == 200
assert response.json['resourceType'] == 'Bundle'
assert response.json['total'] == 1
assert (response.json['entry'][0]['resource'] == Reference.patient(
TEST_USER_ID).as_fhir())
def test_ill_formed_ident_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
ident = db.session.merge(ident)
response = self.client.get(
'/api/patient?identifier=system"http://example.com",value="testy"',
follow_redirects=True)
assert response.status_code == 400
def test_unique(self):
"""Try adding a non-unique identifier, expect exception"""
constrained = Identifier(
system='http://us.truenth.org/identity-codes/external-study-id',
value='unique-one')
with SessionScope(db):
db.session.add(constrained)
second_user = self.add_user('second')
constrained = db.session.merge(constrained)
second_user.add_identifier(constrained)
user = db.session.merge(self.test_user)
with pytest.raises(Conflict):
user.add_identifier(constrained)
def test_ident_nomatch_search(self):
ident = Identifier(system='http://example.com', value='testy')
ui = UserIdentifier(identifier=ident, user_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(ident)
db.session.add(ui)
db.session.commit()
self.promote_user(role_name=ROLE.PATIENT.value)
self.login()
ident = db.session.merge(ident)
# modify the system to mis match
id_str = json.dumps(ident.as_fhir()).replace("example.com",
"wrong-system.com")
response = self.client.get('/api/patient/',
query_string={
'identifier': id_str,
'patch_dstu2': True
},
follow_redirects=True)
# expect empty bundle
assert response.status_code == 200
assert response.json['resourceType'] == 'Bundle'
assert response.json['total'] == 0
def test_unique_deleted(self):
"""Try adding a non-unique identifier from deleted user"""
constrained = Identifier(
system='http://us.truenth.org/identity-codes/external-study-id',
value='unique-one')
with SessionScope(db):
db.session.add(constrained)
second_user = self.add_user('second')
constrained = db.session.merge(constrained)
second_user.add_identifier(constrained)
second_user.delete_user(acting_user=self.test_user)
user = db.session.merge(self.test_user)
user.add_identifier(constrained)
assert constrained in user.identifiers
def test_clinc_id(self):
# Create several orgs with identifier
org1 = Organization(name='org1')
org2 = Organization(name='org2')
org3 = Organization(name='org3')
identifier = Identifier(value='pick me', system=DECISION_SUPPORT_GROUP)
for org in (org1, org2, org3):
org.identifiers.append(identifier)
# Add access strategy to the care plan intervention
cp = INTERVENTION.CARE_PLAN
cp.public_access = False # turn off public access to force strategy
cp_id = cp.id
with SessionScope(db):
map(db.session.add, (org1, org2, org3))
db.session.commit()
org1, org2, org3 = map(db.session.merge, (org1, org2, org3))
d = {
'function': 'limit_by_clinic_w_id',
'kwargs': [{
'name': 'identifier_value',
'value': 'pick me'
}]
}
strat = AccessStrategy(name="member of org with identifier",
intervention_id=cp_id,
function_details=json.dumps(d))
with SessionScope(db):
db.session.add(strat)
db.session.commit()
cp = INTERVENTION.CARE_PLAN
user = db.session.merge(self.test_user)
# Prior to associating user with any orgs, shouldn't have access
self.assertFalse(cp.display_for_user(user).access)
# Add association and test again
user.organizations.append(org3)
with SessionScope(db):
db.session.commit()
user, cp = map(db.session.merge, (user, cp))
self.assertTrue(cp.display_for_user(user).access)
def test_organization_get_by_identifier(self):
org_id_system = "testsystem"
org_id_value = "testval"
self.login()
org = Organization(name='test', id=999)
ident = Identifier(id=99, system=org_id_system, value=org_id_value)
org_ident = OrganizationIdentifier(organization_id=999,
identifier_id=99)
with SessionScope(db):
db.session.add(org)
db.session.add(ident)
db.session.commit()
db.session.add(org_ident)
db.session.commit()
# use api to obtain FHIR
rv = self.client.get('/api/organization/{}/{}'.format(
org_id_system, org_id_value))
self.assert200(rv)
def test_organization_put_update(self):
# confirm unmentioned fields persist
self.promote_user(role_name=ROLE.ADMIN.value)
self.login()
en_AU = LocaleConstants().AustralianEnglish
# Populate db with complet org, and set many fields
org = Organization(name='test',
phone='800-800-5665',
timezone='US/Pacific')
org.identifiers.append(
Identifier(value='state:NY', system=PRACTICE_REGION))
org.locales.append(en_AU)
org.default_locale = 'en_AU'
with SessionScope(db):
db.session.add(org)
db.session.commit()
org = db.session.merge(org)
org_id = org.id
data = org.as_fhir()
# Now strip down the representation - confirm a post doesn't
# wipe unmentioned fields
del data['extension']
del data['telecom']
del data['language']
response = self.client.put('/api/organization/{}'.format(org_id),
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
# Pull the updated db entry
org = Organization.query.get(org_id)
en_AU = db.session.merge(en_AU)
# Confirm all the unmentioned entries survived
assert org.phone == '800-800-5665'
assert org.default_locale == 'en_AU'
assert org.locales[0] == en_AU
assert org.timezone == 'US/Pacific'
def test_unique_api(self):
constrained = Identifier(
system='http://us.truenth.org/identity-codes/external-study-id',
value='unique-one')
with SessionScope(db):
db.session.add(constrained)
second_user = self.add_user('second')
constrained = db.session.merge(constrained)
second_user.add_identifier(constrained)
self.login()
response = self.client.get('/api/user/{}/unique'.format(TEST_USER_ID),
query_string={
'identifier':
'|'.join((constrained.system,
constrained.value))
})
assert response.status_code == 200
assert response.json['unique'] is False
def test_demographics_identifier_ref(self):
# referencing careProvider by (unique) external Identifier
self.shallow_org_tree()
org = Organization.query.filter(Organization.id > 0).first()
org_id, org_name = org.id, org.name
# create OrganizationIdentifier and add to org
org_id_system = "testsystem"
org_id_value = "testval"
ident = Identifier(id=99, system=org_id_system, value=org_id_value)
org.identifiers.append(ident)
with SessionScope(db):
db.session.commit()
# create Practitioner and add Identifier
pract = self.add_practitioner(first_name="Indiana",
last_name="Jones",
id_value='practval')
data = {
"careProvider": [{
"reference":
"Organization/{}?system={}".format(org_id_value, org_id_system)
}, {
"reference":
"Practitioner/{}?system={}".format('practval', US_NPI)
}],
"resourceType":
"Patient",
}
self.login()
response = self.client.put('/api/demographics/%s' % TEST_USER_ID,
content_type='application/json',
data=json.dumps(data))
assert response.status_code == 200
user, pract = map(db.session.merge, (self.test_user, pract))
assert len(user.organizations) == 1
assert user.organizations[0].name == org_name
assert user.practitioner_id == pract.id
def test_unicode_value(self):
ex = Identifier(system='http://nonsense.com', value='ascii')
unicode_string = '__invite__justin.emcee\[email protected]'
ex.value = unicode_string
assert ex.value == unicode_string