def test_positive_result_samples_from_mongo_throws_for_error_creating_db(
config):
with patch(
"migrations.helpers.update_filtered_positives_helper.get_mongo_db"
) as mongo_db:
mongo_db.side_effect = NotImplementedError("Boom!")
with pytest.raises(NotImplementedError):
positive_result_samples_from_mongo(config, [])
def test_positive_result_samples_from_mongo_returns_expected_samples(
config, testing_samples):
plate_barcodes = ["123"]
expected_samples = testing_samples[:
1] # only the first sample is positive, with matching plate barcode
result = positive_result_samples_from_mongo(config, plate_barcodes)
assert result == expected_samples
def run(settings_module: str = "", omit_dart: bool = False) -> None:
"""Updates filtered positive values for all positive samples in pending plates
Arguments:
settings_module {str} -- settings module from which to generate the app config
omit_dart {bool} -- whether to omit DART queries/updates from the process
"""
config, settings_module = get_config(settings_module)
logging.config.dictConfig(config.LOGGING)
logger.info("-" * 80)
logger.info("STARTING FILTERED POSITIVES UPDATE")
logger.info(f"Time start: {datetime.now()}")
num_pending_plates = 0
num_pos_samples = 0
num_non_cp_pos_samples = 0
mongo_updated = False
mlwh_updated = False
dart_updated = False
try:
samples = []
if omit_dart:
# Get positive result samples from Mongo
logger.warning("Omitting DART from this update")
samples = positive_result_samples_from_mongo(config)
else:
# Get barcodes of pending plates in DART
logger.info("Selecting pending plates from DART...")
pending_plate_barcodes = pending_plate_barcodes_from_dart(config)
if num_pending_plates := len(pending_plate_barcodes):
logger.info(
f"{num_pending_plates} pending plates found in DART")
# Get positive result samples from Mongo in these pending plates
logger.info(
"Selecting postive samples in pending plates from Mongo..."
)
samples = positive_result_samples_from_mongo(
config, pending_plate_barcodes)
else:
def test_positive_result_samples_from_mongo_returns_expected_samples_no_plate_barcodes(config, testing_samples):
expected_samples = [testing_samples[0], testing_samples[-1]] # only the first and last samples are positive
result = positive_result_samples_from_mongo(config)
assert result == expected_samples
def test_positive_result_samples_from_mongo_throws_for_error_finding_samples(config, mock_mongo_collection):
mock_mongo_collection().aggregate.side_effect = Exception("Boom!")
with pytest.raises(Exception):
positive_result_samples_from_mongo(config, [])
def test_positive_result_samples_from_mongo_throws_for_error_getting_collection(config, mock_mongo_collection):
mock_mongo_collection.side_effect = ValueError("Boom!")
with pytest.raises(ValueError):
positive_result_samples_from_mongo(config, [])
def test_positive_result_samples_from_mongo_throws_for_errors_creating_client(config, mock_mongo_client):
mock_mongo_client.side_effect = Exception("Boom!")
with pytest.raises(Exception):
positive_result_samples_from_mongo(config, [])