def test_v1_is_positive_returns_false_all_ct_values_greater_than_30():
identifier = FilteredPositiveIdentifierV1()
sample = positive_sample()
sample[FIELD_CH1_CQ] = Decimal128("40.12345678")
sample[FIELD_CH2_CQ] = Decimal128("41.12345678")
sample[FIELD_CH3_CQ] = Decimal128("42.12345678")
assert identifier.is_positive(sample) is False
def test_v1_is_positive_returns_false_result_not_positive():
identifier = FilteredPositiveIdentifierV1()
# does not conform to regex
sample = positive_sample()
sample[FIELD_RESULT] = " positive"
assert identifier.is_positive(sample) is False
# negative result
sample = positive_sample()
sample[FIELD_RESULT] = "Negative"
assert identifier.is_positive(sample) is False
# void result
sample = positive_sample()
sample[FIELD_RESULT] = "Void"
assert identifier.is_positive(sample) is False
# 'limit of detection' result
sample = positive_sample()
sample[FIELD_RESULT] = LIMIT_OF_DETECTION_RESULT_VALUE
assert identifier.is_positive(sample) is False
def test_v1_is_positive_returns_true_matching_criteria():
identifier = FilteredPositiveIdentifierV1()
# expected positive match
sample = positive_sample()
assert identifier.is_positive(sample) is True
# case invariant positive match
sample = positive_sample()
sample[FIELD_RESULT] = "POSITIVE"
assert identifier.is_positive(sample) is True
# 3x mix of ct values
sample = positive_sample()
sample[FIELD_CH2_CQ] = Decimal128("41.12345678")
sample[FIELD_CH3_CQ] = None
assert identifier.is_positive(sample) is True
sample = positive_sample()
sample[FIELD_CH1_CQ] = None
sample[FIELD_CH3_CQ] = Decimal128("42.12345678")
assert identifier.is_positive(sample) is True
sample = positive_sample()
sample[FIELD_CH1_CQ] = Decimal128("40.12345678")
sample[FIELD_CH2_CQ] = None
assert identifier.is_positive(sample) is True
# all ct values None
sample = positive_sample()
sample[FIELD_CH1_CQ] = None
sample[FIELD_CH2_CQ] = None
sample[FIELD_CH3_CQ] = None
assert identifier.is_positive(sample) is True
# no FIELD_CHX_CQ fields
sample = {FIELD_RESULT: POSITIVE_RESULT_VALUE, FIELD_ROOT_SAMPLE_ID: "MCM001"}
assert identifier.is_positive(sample) is True
def test_v1_is_positive_returns_false_control_sample():
identifier = FilteredPositiveIdentifierV1()
sample = positive_sample()
sample[FIELD_ROOT_SAMPLE_ID] = "CBIQA_MCM001"
assert identifier.is_positive(sample) is False
def test_v1_version():
identifier = FilteredPositiveIdentifierV1()
assert identifier.version == FILTERED_POSITIVE_VERSION_1
from crawler.filtered_positive_identifier import (
FILTERED_POSITIVE_VERSION_0,
FILTERED_POSITIVE_VERSION_1,
FILTERED_POSITIVE_VERSION_2,
FilteredPositiveIdentifierV0,
FilteredPositiveIdentifierV1,
FilteredPositiveIdentifierV2,
)
from migrations import update_legacy_filtered_positives
start_date_input = "201209_0000"
end_date_input = "201217_0000"
identifier_v0 = FilteredPositiveIdentifierV0()
identifier_v1 = FilteredPositiveIdentifierV1()
identifier_v2 = FilteredPositiveIdentifierV2()
@pytest.fixture
def mock_helper_database_updates():
with patch(
"migrations.update_legacy_filtered_positives.update_mongo_filtered_positive_fields"
) as mock_update_mongo:
with patch(
"migrations.update_legacy_filtered_positives.update_mlwh_filtered_positive_fields_batched"
) as mock_update_mlwh:
yield mock_update_mongo, mock_update_mlwh
@pytest.fixture