def test_from_fhir(self):
with open(
os.path.join(os.path.dirname(__file__),
'organization-example-f001-burgers.json'),
'r') as fhir_data:
data = json.load(fhir_data)
#prepopuate database with matching locale
Coding.from_fhir({
'code': 'en_AU',
'display': 'Australian English',
'system': "urn:ietf:bcp:47"
})
org = Organization.from_fhir(data)
self.assertEquals(org.addresses[0].line1,
data['address'][0]['line'][0])
self.assertEquals(org.addresses[1].line1,
data['address'][1]['line'][0])
self.assertEquals(org.name, data['name'])
self.assertEquals(org.phone, "022-655 2300")
self.assertTrue(org.use_specific_codings)
self.assertTrue(org.race_codings)
self.assertFalse(org.ethnicity_codings)
self.assertEquals(org.locales.count(), 1)
self.assertEquals(org.default_locale, "en_AU")
def test_codeable_concept_codings(self):
"CodeableConcepts should handle coding changes"
initial_coding1 = Coding(system='sys1', code='ic-1', display='i1')
initial_coding2 = Coding(system='sys2', code='ic-2', display='i2')
cc = CodeableConcept(text='codings change',
codings=[initial_coding1, initial_coding2])
with SessionScope(db):
db.session.add(initial_coding1)
db.session.add(initial_coding2)
db.session.add(cc)
db.session.commit()
initial_coding1 = db.session.merge(initial_coding1)
initial_coding2 = db.session.merge(initial_coding2)
cc = db.session.merge(cc)
# now parse a fhir snippet containing first just a partial set
data = {
"test_concept1": {
"coding": [
{
"system": initial_coding1.system,
"code": initial_coding1.code,
"display": initial_coding1.display
},
],
},
}
cc_parsed = CodeableConcept.from_fhir(data['test_concept1'])
self.assertEquals(cc_parsed.codings, cc.codings)
self.assertEquals(2, len(cc.codings))
self.assertEquals(cc_parsed.text, cc.text)
# and again, but now containing a new coding
data = {
"test_concept2": {
"coding": [
{
"system": initial_coding1.system,
"code": initial_coding1.code,
"display": initial_coding1.display
},
{
"system": 'local',
"code": 'local-1',
"display": 'si-loco'
},
],
"text":
"given two codings"
},
}
cc_parsed = CodeableConcept.from_fhir(data['test_concept2'])
persisted = CodeableConcept.query.get(cc_parsed.id)
self.assertEquals(cc_parsed.codings, persisted.codings)
self.assertEquals(len(persisted.codings), 3)
self.assertEquals(persisted.text, 'given two codings')
def test_cc_format(self):
c1 = Coding(system='http://test.org', code='66.5', display='howdy')
c2 = Coding(system='http://hl7.org', code='5-12', display='grade')
cc = CodeableConcept(text='test text', codings=[c1, c2])
cc_str = "test format: {}".format(cc)
self.assertIn(cc.text, cc_str)
self.assertIn(c1.system, cc_str)
self.assertIn(c1.code, cc_str)
self.assertIn(c1.display, cc_str)
self.assertIn(c2.system, cc_str)
self.assertIn(c2.code, cc_str)
self.assertIn(c2.display, cc_str)
def prep_db_for_clinical(self):
# First push some clinical data into the db for the test user
with SessionScope(db):
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
observation = Observation()
coding = Coding(system='SNOMED-CT',
code='372278000',
display='Gleason score')
cc = CodeableConcept(codings=[
coding,
])
observation.codeable_concept = cc
observation.value_quantity = ValueQuantity(value=2)
performer = Performer(reference_txt=json.dumps(
Reference.patient(TEST_USER_ID).as_fhir()))
observation.performers.append(performer)
db.session.add(observation)
enc = Encounter(status='planned',
auth_method='url_authenticated',
user_id=TEST_USER_ID,
start_time=datetime.utcnow())
db.session.add(enc)
db.session.flush()
db.session.add(
UserObservation(user_id=int(TEST_USER_ID),
observation_id=observation.id,
encounter_id=enc.id,
audit=audit))
db.session.commit()
def add_procedure(self,
code='367336001',
display='Chemotherapy',
system=SNOMED):
"Add procedure data into the db for the test user"
with SessionScope(db):
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
procedure = Procedure(audit=audit)
coding = Coding(system=system, code=code,
display=display).add_if_not_found(True)
code = CodeableConcept(codings=[
coding,
]).add_if_not_found(True)
enc = Encounter(status='planned',
auth_method='url_authenticated',
user_id=TEST_USER_ID,
start_time=datetime.utcnow())
db.session.add(enc)
db.session.commit()
enc = db.session.merge(enc)
procedure.code = code
procedure.user = db.session.merge(self.test_user)
procedure.start_time = datetime.utcnow()
procedure.end_time = datetime.utcnow()
procedure.encounter = enc
db.session.add(procedure)
db.session.commit()
def test_organization_put(self):
self.promote_user(role_name=ROLE.ADMIN)
self.login()
with open(
os.path.join(os.path.dirname(__file__),
'organization-example-f001-burgers.json'),
'r') as fhir_data:
data = json.load(fhir_data)
# remove the id from the file - doesn't play well with ours
data.pop('id')
# Shove a nearly empty org in the db and then update via the api
org = Organization(name='test')
with SessionScope(db):
db.session.add(org)
db.session.commit()
org = db.session.merge(org)
org_id = org.id
#prepopuate database with matching locale
Coding.from_fhir({
'code': 'en_AU',
'display': 'Australian English',
'system': "urn:ietf:bcp:47"
})
rv = self.client.put('/api/organization/{}'.format(org_id),
content_type='application/json',
data=json.dumps(data))
self.assert200(rv)
# Pull the updated db entry
org = Organization.query.get(org_id)
self.assertEquals(org.addresses[0].line1,
data['address'][0]['line'][0])
self.assertEquals(org.addresses[1].line1,
data['address'][1]['line'][0])
self.assertEquals(org.name, data['name'])
self.assertEquals(org.phone, "022-655 2300")
def downgrade():
bind = op.get_bind()
session = Session(bind=bind)
defcode = Coding(system="urn:ietf:bcp:47", display="Default", code="")
session.add(defcode)
session.commit()
defcode = session.merge(defcode)
defcc = CodeableConcept(text="")
defcc.codings.append(defcode)
session.add(defcc)
session.commit()
def test_locale_inheritance(self):
# prepopuate database with matching locale
cd = Coding.from_fhir({'code': 'en_AU', 'display': 'Australian English',
'system': "urn:ietf:bcp:47"})
# create parent with locale
parent_id = 101
parent = Organization(id=parent_id, name='test parent')
ol = OrganizationLocale(organization_id=parent_id, coding_id=cd.id)
# create child org with no locales
org = Organization(id=102, name='test', partOf_id=parent_id)
org.use_specific_codings = False
with SessionScope(db):
db.session.add(parent)
db.session.commit()
db.session.add(ol)
db.session.add(org)
db.session.commit()
org = db.session.merge(org)
self.assertEquals(org.partOf_id, parent_id)
# add child org to user
user = User.query.get(TEST_USER_ID)
user.organizations.append(org)
# test locale inheritance
self.assertEquals(user.locale_display_options,set(['en_AU']))
def test_permanently_delete_user(self):
# created acting user and to-be-deleted user
actor = self.add_user('actor')
deleted = self.add_user('deleted')
deleted, actor = map(db.session.merge, (deleted, actor))
deleted_id, actor_id = deleted.id, actor.id
deleted_email, actor_email = deleted.email, actor.email
self.promote_user(user=actor, role_name=ROLE.ADMIN)
with SessionScope(db):
db.session.commit()
deleted = db.session.merge(deleted)
# create observation and user_observation
audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
observation = Observation()
coding = Coding(system='SNOMED-CT', code='372278000',
display='Gleason score')
cc = CodeableConcept(codings=[coding, ])
observation.codeable_concept = cc
observation.value_quantity = ValueQuantity(value=2)
performer = Performer(reference_txt=json.dumps(
Reference.patient(TEST_USER_ID).as_fhir()))
observation.performers.append(performer)
enc = Encounter(status='planned', auth_method='url_authenticated',
user_id=TEST_USER_ID, start_time=datetime.utcnow())
with SessionScope(db):
db.session.add(observation)
db.session.add(enc)
db.session.commit()
observation, enc = map(db.session.merge, (observation, enc))
observation_id, enc_id = observation.id, enc.id
user_obs = UserObservation(user_id=deleted_id, audit=audit,
observation_id=observation_id,
encounter_id=enc_id)
with SessionScope(db):
db.session.add(user_obs)
db.session.commit()
user_obs = db.session.merge(user_obs)
user_obs_id = user_obs.id
# create user and subject audits
subj_audit = Audit(user_id=TEST_USER_ID, subject_id=deleted_id)
user_audit = Audit(user_id=deleted_id, subject_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(subj_audit)
db.session.add(user_audit)
db.session.commit()
subj_audit, user_audit = map(db.session.merge,
(subj_audit, user_audit))
subj_audit_id, user_audit_id = subj_audit.id, user_audit.id
# create user_consent and audit
consent_org = Organization(name='test org')
consent_audit = Audit(user_id=TEST_USER_ID, subject_id=TEST_USER_ID)
with SessionScope(db):
db.session.add(consent_org)
db.session.add(consent_audit)
db.session.commit()
db.session.add(UserConsent(
user_id=deleted_id,
organization_id=consent_org.id,
audit=consent_audit,
agreement_url='http://example.org',
options=STAFF_EDITABLE_MASK))
db.session.commit()
consent_org, consent_audit = map(db.session.merge,
(consent_org, consent_audit))
co_id, ca_id = consent_org.id, consent_audit.id
# permanently deleted user, check deletion cascades
permanently_delete_user(deleted_email, actor=actor_email)
self.assertFalse(User.query.get(deleted_id))
self.assertFalse(UserObservation.query.get(user_obs_id))
self.assertTrue(Observation.query.get(observation_id))
self.assertFalse(Audit.query.get(subj_audit_id))
self.assertFalse(Audit.query.get(user_audit_id))
self.assertFalse(UserConsent.query.get(co_id))
self.assertFalse(Audit.query.get(ca_id))