def test_split_mongo_samples_by_version_error_raises_exception(
mock_filtered_positive_fields_set,
mock_helper_database_updates,
mock_query_helper_functions,
mock_extract_required_cp_info,
mock_split_mongo_samples_by_version,
):
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
mock_mongo_samples_by_date, mock_get_cherrypicked_samples_by_date = mock_query_helper_functions
mock_filtered_positive_fields_set.return_value = False
mock_mongo_samples_by_date.return_value = [{"plate_barcode": "1"}]
mock_extract_required_cp_info.return_value = [["id_1"],
["plate_barcode_1"]]
mock_get_cherrypicked_samples_by_date.return_value = pd.DataFrame(
{"id": ["s1", "s2"]})
mock_split_mongo_samples_by_version.side_effect = Exception("Boom!")
with pytest.raises(Exception):
update_legacy_filtered_positives.run("crawler.config.integration",
start_date_input, end_date_input)
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
def test_update_legacy_filtered_positives_returns_early_start_datetime_after_end_datetime(
config, mock_helper_database_updates):
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
start_datetime = "201017_1200"
end_datetime = "201016_1600"
update_legacy_filtered_positives.run("crawler.config.integration",
start_datetime, end_datetime)
# ensure no database connections/updates are made
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
def test_update_legacy_filtered_positives_exception_raised_if_user_enters_invalid_input(
mock_user_input, mock_helper_database_updates,
filtered_positive_testing_samples):
mock_user_input.return_value = "invalid_input"
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
update_legacy_filtered_positives.run("crawler.config.integration",
start_date_input, end_date_input)
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
def migration_update_legacy_filtered_positives():
if not len(sys.argv) == 4:
print(
"Please add both start and end datetime range arguments for this migration "
"(format YYMMDD_HHmm e.g. 200115_1200, inclusive), aborting")
return
s_start_datetime = sys.argv[2]
s_end_datetime = sys.argv[3]
print("Running update_legacy_filtered_positives migration")
update_legacy_filtered_positives.run(s_start_datetime=s_start_datetime,
s_end_datetime=s_end_datetime)
def test_update_legacy_filtered_positives_catches_error_connecting_to_mongo(
mock_helper_database_updates, mock_filtered_positive_fields_set):
mock_filtered_positive_fields_set.return_value = False
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
mock_update_mongo.side_effect = Exception("Boom!")
with pytest.raises(Exception):
update_legacy_filtered_positives.run("crawler.config.integration",
start_date_input, end_date_input)
mock_update_mongo.assert_called_once()
mock_update_mlwh.assert_not_called()
def test_update_legacy_filtered_positives_returns_early_datetime_post_fields_set_date(
config, mock_helper_database_updates):
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
start_datetime = "201016_1600"
end_datetime = "201217_1600"
mock_valid_datetime_string.return_value = True # type: ignore
update_legacy_filtered_positives.run("crawler.config.integration",
start_datetime, end_datetime)
# ensure no database connections/updates are made
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
def test_update_legacy_filtered_positives_returns_early_invalid_end_datetime(
config, mock_helper_database_updates):
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
start_datetime = "201016_1600"
end_datetime = "not a real datetime"
mock_valid_datetime_string.side_effect = [True, False] # type: ignore
update_legacy_filtered_positives.run("crawler.config.integration",
start_datetime, end_datetime)
# ensure no database connections/updates are made
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
def test_update_legacy_filtered_positives_successful_if_user_chooses_to_continue(
config,
freezer,
mock_user_input,
mock_filtered_positive_fields_set,
mock_helper_database_updates,
mock_query_helper_functions,
mock_extract_required_cp_info,
mock_split_mongo_samples_by_version,
mock_filtered_positive_identifier_by_version,
mock_update_filtered_positive_fields,
):
update_timestamp = datetime.now()
v0_samples = [{"plate_barcode": "0"}]
v1_samples = [{"plate_barcode": "1"}]
v2_samples = [{"plate_barcode": "2"}]
mock_update_mongo, mock_update_mlwh = mock_helper_database_updates
mock_mongo_samples_by_date, mock_get_cherrypicked_samples_by_date = mock_query_helper_functions
mock_split_mongo_samples_by_version = mock_split_mongo_samples_by_version
mock_filtered_positive_fields_set.return_value = True
mock_user_input.return_value = "yes"
mock_mongo_samples_by_date.return_value = [{"plate_barcode": "1"}]
mock_extract_required_cp_info.return_value = [["id_1"],
["plate_barcode_1"]]
mock_get_cherrypicked_samples_by_date.return_value = pd.DataFrame(
{"id": ["s1", "s2"]})
mock_split_mongo_samples_by_version.return_value = {
FILTERED_POSITIVE_VERSION_0: v0_samples,
FILTERED_POSITIVE_VERSION_1: v1_samples,
FILTERED_POSITIVE_VERSION_2: v2_samples,
}
mock_filtered_positive_identifier_by_version.side_effect = [
identifier_v0, identifier_v1, identifier_v2
]
mock_update_mongo.return_value = True
mock_update_mlwh.return_value = True
update_legacy_filtered_positives.run("crawler.config.test",
start_date_input, end_date_input)
assert mock_update_filtered_positive_fields.call_count == 3
mock_update_filtered_positive_fields.assert_any_call(
identifier_v0, v0_samples, FILTERED_POSITIVE_VERSION_0,
update_timestamp) # noqa: E501
mock_update_filtered_positive_fields.assert_any_call(
identifier_v1, v1_samples, FILTERED_POSITIVE_VERSION_1,
update_timestamp) # noqa: E501
mock_update_filtered_positive_fields.assert_any_call(
identifier_v2, v2_samples, FILTERED_POSITIVE_VERSION_2,
update_timestamp) # noqa: E501
assert mock_update_mongo.call_count == 3
mock_update_mongo.assert_any_call(config, v0_samples,
FILTERED_POSITIVE_VERSION_0,
update_timestamp)
mock_update_mongo.assert_any_call(config, v1_samples,
FILTERED_POSITIVE_VERSION_1,
update_timestamp)
mock_update_mongo.assert_any_call(config, v2_samples,
FILTERED_POSITIVE_VERSION_2,
update_timestamp)
assert mock_update_mlwh.call_count == 3
mock_update_mlwh.assert_any_call(config, v0_samples,
FILTERED_POSITIVE_VERSION_0,
update_timestamp)
mock_update_mlwh.assert_any_call(config, v1_samples,
FILTERED_POSITIVE_VERSION_1,
update_timestamp)
mock_update_mlwh.assert_any_call(config, v2_samples,
FILTERED_POSITIVE_VERSION_2,
update_timestamp)
