def test_swagger_keyfile():
keyfile = KeyFileFactory()
as_dict = keyfile.to_dict()
reconstructed = KeyFile.from_dict(as_dict)
assert reconstructed.pseudonym_template == keyfile.pseudonym_template
assert reconstructed.description == keyfile.description
assert reconstructed.name == keyfile.name
assert reconstructed.key == keyfile.key
def test_pimsconnection(mock_pims_session):
connection = PIMSConnection(session=mock_pims_session)
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_CREATE_JSONOUTPUT_TRUE)
connection.pseudonymize(key_file=KeyFileFactory(),
identifiers=[IdentifierFactory()])
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.KEYFILES_PSEUDONYMS_REIDENTIFY_RESPONSE)
connection.reidentify(key_file=KeyFileFactory(),
pseudonyms=[PseudonymFactory()])
def test_deidentify(mock_pims_session):
connection = PIMSConnection(session=mock_pims_session)
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_CREATE_JSONOUTPUT_TRUE)
identifiers = [IdentifierFactory(), IdentifierFactory()]
keys = connection.pseudonymize(key_file=KeyFileFactory(),
identifiers=identifiers)
assert len(keys) == 2
assert str(keys[0].identifier) == str(identifiers[0])
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_CREATE_JSONOUTPUT_TRUE_INVALID)
with pytest.raises(PIMSSwaggerException) as e:
connection.pseudonymize(key_file=KeyFileFactory(),
identifiers=identifiers)
def test_keyfiles_get_users(mock_pims_session):
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.GET_USERS_FOR_KEYFILE_RESPONSE)
entrypoint = KeyFiles(mock_pims_session)
users = entrypoint.get_users(key_file=KeyFileFactory())
assert len(users) == 2
assert users[1].key == 22
def test_set_keys(mock_pims_session, some_patient_id_keys):
"""Add an pseudonym-identifier pair"""
connection = PIMSConnection(session=mock_pims_session)
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.
KEYFILES_PSEUDONYMS_REIDENTIFY_NON_EXISTENT_RESPONSE)
# keys need to be patientID to match mocked response above
connection.set_keys(key_file=KeyFileFactory(), keys=some_patient_id_keys)
def test_keyfiles_reidentify_chunked(mock_pims_session):
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.KEYFILES_PSEUDONYMS_REIDENTIFY_RESPONSE
)
entrypoint = KeyFiles(mock_pims_session)
_ = entrypoint.reidentify(
key_file=KeyFileFactory(), pseudonyms=[PseudoPatientIDFactory() for _ in range(2000)]
)
reidentified_items = mock_pims_session.session.requests_mock.post.mock_calls[0][2]['params']['items']
assert len(reidentified_items) <= 501
def test_set_keys_existing_pseudonym(mock_pims_session, some_patient_id_keys):
"""Setting a pseudonym that is already used for a different identifier should
fail
"""
connection = PIMSConnection(session=mock_pims_session)
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_FAILED_TO_INSERT)
# keys need to be patientID to match mocked response above
with pytest.raises(PIMSServerException):
connection.set_keys(key_file=KeyFileFactory(),
keys=some_patient_id_keys)
def test_set_keys_existing_identity(mock_pims_session, some_patient_id_keys):
"""I want to add an pseudonym-identifier pair, but the identifier already
exists
"""
connection = PIMSConnection(session=mock_pims_session)
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.
KEYFILES_PSEUDONYMS_REIDENTIFY_EXISTENT_RESPONSE)
# keys need to be patientID to match mocked response above
with pytest.raises(PIMSServerException):
connection.set_keys(key_file=KeyFileFactory(),
keys=some_patient_id_keys)
def mock_project_requests(requests_mock):
"""Mock project that simulates actual requests.post calls. Will
raise PIMSServerException for invalid return values, but allows checking what
is sent to server
"""
mock_session = Mock()
project = Project(
key_file_id=1,
connection=PIMSConnection(
session=PIMSSession(mock_session, base_url="/test")),
)
project.get_key_file = lambda: KeyFileFactory() # make sure this passes
return project
def test_keyfiles_pseudonymize(mock_pims_session):
"""Get a pseudonym, mock server response"""
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_CREATE_JSONOUTPUT_TRUE)
entrypoint = KeyFiles(mock_pims_session)
keys = entrypoint.pseudonymize(
key_file=KeyFileFactory(),
identifiers=[
Identifier(value="Jack de Boer", source="Test"),
Identifier(value="Chris van Os", source="Test"),
],
)
assert len(keys) == 2
assert keys[0].identifier.value == "Jack de Boer"
def test_keyfiles_pseudonymize_chunk_size(mock_pims_session):
"""In live testing the PIMS server was found not to be able to handle API requests with more then 1000 items
Check the chunking system to work around this"""
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_CREATE_JSONOUTPUT_TRUE
)
entrypoint = KeyFiles(mock_pims_session)
_ = entrypoint.pseudonymize(
key_file=KeyFileFactory(),
identifiers=[PatientIDFactory() for _ in range(2000)],
)
values_posted = mock_pims_session.session.requests_mock.post.mock_calls[0][2]['json'][0]['values']
assert len(values_posted) <= 1001
def test_keyfiles_pseudonymize_different_sources(mock_pims_session):
"""Get a pseudonym, mock server response. Two different sources should yield separate calls for each source"""
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.DEIDENTIFY_CREATE_JSONOUTPUT_TRUE
)
entrypoint = KeyFiles(mock_pims_session)
keys = entrypoint.pseudonymize(
key_file=KeyFileFactory(),
identifiers=[
Identifier(value="Jack de Boer", source="Test"),
Identifier(value="Sarah Toh", source="Test_2"),
],
)
assert mock_pims_session.session.requests_mock.post.call_count == 2
def test_keyfiles_reidentify(mock_pims_session):
mock_pims_session.session.set_response_tuple(
RequestsMockResponseExamples.KEYFILES_PSEUDONYMS_REIDENTIFY_RESPONSE
)
entrypoint = KeyFiles(mock_pims_session)
keys = entrypoint.reidentify(
key_file=KeyFileFactory(), pseudonyms=[
PseudoPatientID(value='test'),
PseudoPatientID(value='test2')]
)
assert len(keys) == 2
assert keys[0].identifier.source == "PatientID"