def test_composite_key(self):
known_coding = Coding(
system=SNOMED, code='26294005',
display='Radical prostatectomy (nerve-sparing)').add_if_not_found(
True)
mp = ModelPersistence(
Coding, sequence_name='codings_id_seq',
lookup_field=('system', 'code'))
data = known_coding.as_fhir()
# Modify only the `display` - composite keys should still match
modified_data = data.copy()
modified_data['display'] = 'Radical prostatectomy'
modified = Coding.from_fhir(data)
match, _ = mp.lookup_existing(
new_obj=modified, new_data=modified_data)
assert data == match.as_fhir()
# Import and see the change
updated = mp.update(modified_data)
assert modified == updated
# Export and verify
serial = mp.serialize()
assert modified_data in serial
def test_organization_put(self):
self.promote_user(role_name=ROLE.ADMIN.value)
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
# prepopulate database with matching locale
Coding.from_fhir({
'code': 'en_AU',
'display': 'Australian English',
'system': "urn:ietf:bcp:47"})
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)
assert org.addresses[0].line1 == data['address'][0]['line'][0]
assert org.addresses[1].line1 == data['address'][1]['line'][0]
assert org.name == data['name']
assert org.phone == "022-655 2300"
def test_organization_put(self):
self.promote_user(role_name=ROLE.ADMIN.value)
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
# prepopulate database with matching locale
Coding.from_fhir({
'code': 'en_AU',
'display': 'Australian English',
'system': "urn:ietf:bcp:47"
})
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)
assert org.addresses[0].line1 == data['address'][0]['line'][0]
assert org.addresses[1].line1 == data['address'][1]['line'][0]
assert org.name == data['name']
assert org.phone == "022-655 2300"
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)
# prepopulate database with matching locale
Coding.from_fhir({
'code': 'en_AU',
'display': 'Australian English',
'system': IETF_LANGUAGE_TAG
})
org = Organization.from_fhir(data)
assert org.addresses[0].line1 == data['address'][0]['line'][0]
assert org.addresses[1].line1 == data['address'][1]['line'][0]
assert org.name == data['name']
assert org.phone == "022-655 2300"
assert org.use_specific_codings
assert org.race_codings
assert not org.ethnicity_codings
assert org.locales.count() == 1
assert org.default_locale == "en_AU"
assert org._timezone == "US/Pacific"
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)
# prepopulate database with matching locale
Coding.from_fhir(
{'code': 'en_AU', 'display': 'Australian English',
'system': IETF_LANGUAGE_TAG})
org = Organization.from_fhir(data)
assert org.addresses[0].line1 == data['address'][0]['line'][0]
assert org.addresses[1].line1 == data['address'][1]['line'][0]
assert org.name == data['name']
assert org.phone == "022-655 2300"
assert org.use_specific_codings
assert org.race_codings
assert not org.ethnicity_codings
assert org.locales.count() == 1
assert org.default_locale == "en_AU"
assert org._timezone == "US/Pacific"
def add_procedure(self, code='367336001', display='Chemotherapy',
system=SNOMED, setdate=None):
"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 = setdate or datetime.utcnow()
procedure.end_time = datetime.utcnow()
procedure.encounter = enc
db.session.add(procedure)
db.session.commit()
def test_display_lookup(self):
# example used: Coding(system=SNOMED, code='707266006',
# display='Androgen deprivation therapy').add_if_not_found(True)
display = Coding.display_lookup(system=SNOMED, code='707266006')
assert 'Androgen deprivation therapy' == display
def test_display_lookup(self):
# example used: Coding(system=SNOMED, code='707266006',
# display='Androgen deprivation therapy').add_if_not_found(True)
display = Coding.display_lookup(system=SNOMED, code='707266006')
assert 'Androgen deprivation therapy' == display