def test_remove_cherrypicked_samples_returns_input_samples_with_none_cp_samples_df(
config, testing_samples):
with patch(
"migrations.helpers.update_filtered_positives_helper.get_cherrypicked_samples",
return_value=None):
with pytest.raises(Exception):
remove_cherrypicked_samples(config, testing_samples)
def test_remove_cherrypicked_samples_throws_for_error_getting_cherrypicked_samples(
config, testing_samples):
with patch(
"migrations.helpers.update_filtered_positives_helper.get_cherrypicked_samples",
side_effect=Exception("Boom!")):
with pytest.raises(Exception):
remove_cherrypicked_samples(config, testing_samples)
def test_remove_cherrypicked_samples_throws_for_error_removing_cp_samples(
config, testing_samples):
cp_samples_df = MagicMock()
type(cp_samples_df).empty = PropertyMock(return_value=False)
with patch(
"migrations.helpers.update_filtered_positives_helper.get_cherrypicked_samples",
return_value=cp_samples_df):
with patch(
"migrations.helpers.update_filtered_positives_helper.remove_cp_samples",
side_effect=Exception("Boom!")):
with pytest.raises(Exception):
remove_cherrypicked_samples(config, testing_samples)
def test_remove_cherrypicked_samples_returns_input_samples_with_empty_cp_samples_df(
config, testing_samples):
cp_samples_df = MagicMock()
type(cp_samples_df).empty = PropertyMock(return_value=True)
with patch(
"migrations.helpers.update_filtered_positives_helper.get_cherrypicked_samples",
return_value=cp_samples_df):
result = remove_cherrypicked_samples(config, testing_samples)
assert result == testing_samples
# 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:
logger.warning("No pending plates found in DART")
if num_pos_samples := len(samples):
logger.info(
f"{num_pos_samples} matching positive samples found in Mongo")
# Filter out cherrypicked samples
logger.info("Filtering out cherrypicked samples...")
non_cp_pos_pending_samples = remove_cherrypicked_samples(
config, samples)
if num_non_cp_pos_samples := len(non_cp_pos_pending_samples):
logger.info(
f"{num_non_cp_pos_samples} non-cherrypicked matching positive samples found"
)
filtered_positive_identifier = current_filtered_positive_identifier(
)
version = filtered_positive_identifier.version
update_timestamp = datetime.utcnow()
logger.info("Updating filtered positives...")
update_filtered_positive_fields(
filtered_positive_identifier,
non_cp_pos_pending_samples,
version,
update_timestamp,