def test_default_init(monkeypatch):
def requests_mock(*args, **kwargs):
response = requests.models.Response()
response.status_code = 200
return response
monkeypatch.setattr(
requests, "get",
requests_mock) # apply the monkeypatch for requests.get to mock_get
rubrix._client = None
if "RUBRIX_API_URL" in os.environ:
del os.environ["RUBRIX_API_URL"]
if "RUBRIX_API_KEY" in os.environ:
del os.environ["RUBRIX_API_KEY"]
rubrix.init()
assert isinstance(rubrix._client._client, Client)
assert rubrix._client._client.base_url == "http://localhost:6900"
expected_token = "blablabla"
rubrix.init(api_key=expected_token)
assert isinstance(rubrix._client._client, AuthenticatedClient)
assert rubrix._client._client.token == expected_token
def main(config):
rb.init(api_url=config["rubrix_uri"], api_key=config["rubrix_api_key"])
rb.set_workspace(config["rubrix_workspace"])
connection_uri = config["connection_uri"]
engine = sa.create_engine(connection_uri)
result_list = []
with engine.connect() as connection:
# Long Covid Patients; notes 1 month after DX or test, Outpatient physician notes
query = """
select pn.*, e.service_delivery_location from sbm_covid19_documents.physician_notes pn
join sbm_covid19_hi.PH_F_Encounter e on pn.encounter_id = e.encounter_number
where document_id in (
select distinct document_id from sbm_covid19_documents.physician_notes p
join sbm_covid19_analytics_build.pui_covid_result_overview pcro
on p.patient_id = pcro.mrn
join sbm_covid19_hi_cdm_build.map2_condition_occurrence co on pcro.person_id = co.person_id
and co.condition_source_concept_code = 'U09.9'
where p.document_datetime >= pcro.positive_datetime + interval '1 month' and pcro.positive_datetime is not null)
and document_type not in ('Ambulatory Patient Summary')
and e.classification_display = 'Outpatient'
"""
cursor = connection.execute(query)
report_list = []
for row in cursor:
result_list += [row["file_text"]]
meta_data_dict = {}
columns = ["patient_id", "mapped_document_type", "document_type", "service_delivery_location", "patient_id",
"encounter_id"]
for column in columns:
meta_data_dict[column] = row[column]
rb_obj = rb.TextClassificationRecord(inputs={"text": row["file_text"]}, metadata=meta_data_dict,
id=row["document_id"], multi_label=True)
report_list += [rb_obj]
reports_to_commit = []
for i in range(len(report_list)):
reports_to_commit += [report_list[i]]
if i > 0 and i % 50 == 0:
rb.log(records=reports_to_commit, name="long_covid_with_metadata")
reports_to_commit = []
else:
pass
if len(reports_to_commit):
rb.log(records=reports_to_commit, name="long_covid_with_metadata")
def test_init_token_auth_fail(mock_response_token_401):
"""Testing initalization with failed authentication
It checks an Exception is raised with the correct message.
Parameters
----------
mock_response_401
Mocked correct http response
"""
rubrix._client = None # assert empty client
with pytest.raises(Exception,
match="Authentification error: invalid credentials."):
rubrix.init(api_url="fake_url", api_key="422")
def test_init_token_correct(mock_response_200):
"""Testing correct token initalization
It checks if the _client created is a RubrixClient object.
Parameters
----------
mock_response_200
Mocked correct http response
"""
rubrix._client = None # assert empty client
rubrix.init(api_key="fjkjdf333")
assert isinstance(rubrix._client, RubrixClient)
def test_init_correct(mock_response_200):
"""Testing correct default initalization
It checks if the _client created is a RubrixClient object.
Parameters
----------
mock_response_200
Mocked correct http response
"""
rubrix.init()
assert isinstance(rubrix._client, RubrixClient)
def test_init_token_incorrect(mock_response_500):
"""Testing incorrect token initalization
It checks an Exception is raised with the correct message.
Parameters
----------
mock_response_500
Mocked correct http response
"""
rubrix._client = None # assert empty client
with pytest.raises(Exception,
match="Unidentified error, it should not get here."):
rubrix.init(api_key="422")
def test_init_token_incorrect(mock_response_500):
"""Testing incorrect token initalization
It checks an Exception is raised with the correct message.
Parameters
----------
mock_response_500
Mocked correct http response
"""
rubrix._client = None # assert empty client
with pytest.raises(
Exception,
match=
"Connection error: Indetermined error connecting to Rubrix Server. The API answered with a 500 code: b",
):
rubrix.init(api_key="422")
def test_default_init(mock_response_200):
rubrix._client = None
if "RUBRIX_API_URL" in os.environ:
del os.environ["RUBRIX_API_URL"]
if "RUBRIX_API_KEY" in os.environ:
del os.environ["RUBRIX_API_KEY"]
rubrix.init()
assert isinstance(rubrix._client._client, Client)
assert rubrix._client._client.base_url == "http://localhost:6900"
expected_token = "blablabla"
rubrix.init(api_key=expected_token)
assert isinstance(rubrix._client._client, AuthenticatedClient)
assert rubrix._client._client.token == expected_token
def test_init_evironment_no_url_token(token_env_var, mock_response_200):
"""Testing initalization with token provided via environment variable and api_url via args
It checks a non-secured Client is created
Parameters
----------
token_env_var
Fixture to set the fake token in the env variable
mock_response_200
Mocked correct http response
"""
rubrix._client = None # assert empty client
rubrix.init(api_url="http://anotherfakeurl.com")
assert isinstance(rubrix._client, RubrixClient)
assert isinstance(rubrix._client._client, Client)
assert rubrix._client._client.base_url == "http://anotherfakeurl.com"
def test_init_evironment_url(api_url_env_var, mock_response_200):
"""Testing initalization with api_url provided via environment variable
It checks the url in the environment variable gets passed to client.
Parameters
----------
api_url_env_var
Fixture to set the fake url in the env variable
mock_response_200
Mocked correct http response
"""
rubrix._client = None # assert empty client
rubrix.init()
assert isinstance(rubrix._client, RubrixClient)
assert isinstance(rubrix._client._client, Client)
assert rubrix._client._client.base_url == "http://fakeurl.com"
def test_trailing_slash(api_url_env_var_trailing_slash, mock_response_200):
"""Testing initalization with provided api_url via environment variable and argument
It checks the trailing slash is removed in all cases
Parameters
----------
api_url_env_var
Fixture to set the fake url in the env variable, with trailing slash
mock_response_200
Mocked correct http response
"""
rubrix._client = None # assert empty client
# Environment variable case
rubrix.init(api_url="http://anotherfakeurl.com/")
assert rubrix._client._client.base_url == "http://anotherfakeurl.com"
rubrix._client = None # assert empty client
# Argument case
rubrix.init()
assert rubrix._client._client.base_url == "http://fakeurl.com"
