def test_update_filtered_positives_omitting_dart_outputs_success(
mock_helper_imports, mock_filter_out_cherrypicked_samples, mock_update_positives, mock_helper_database_updates
):
_, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock a successful update
mock_get_positive_samples.return_value = [{"plate_barcode": "123"}, {"plate_barcode": "456"}]
non_cp_samples = [{"plate_barcode": "123"}]
mock_filter_out_cherrypicked_samples.return_value = non_cp_samples
mock_update_mongo.return_value = True
mock_update_mlwh.return_value = True
mock_update_dart.return_value = True
version = "v2.3"
mock_pos_id = MagicMock()
type(mock_pos_id).version = PropertyMock(return_value=version)
with patch("migrations.update_filtered_positives.current_filtered_positive_identifier", return_value=mock_pos_id):
with patch("migrations.update_filtered_positives.datetime") as mock_datetime:
timestamp = datetime.utcnow()
mock_datetime.utcnow.return_value = timestamp
# call the migration
update_filtered_positives.run("crawler.config.integration", True)
# ensure expected database calls
config, _ = get_config("crawler.config.integration")
mock_update_mongo.assert_called_once()
mock_update_mongo.assert_called_with(config, non_cp_samples, version, timestamp)
mock_update_mlwh.assert_called_once()
mock_update_mlwh.assert_called_with(config, non_cp_samples)
mock_update_dart.assert_not_called()
def test_update_filtered_positives_catches_aborts_failing_updating_samples_in_dart(
mock_helper_imports, mock_remove_cherrypicked, mock_update_positives,
mock_helper_database_updates):
mock_get_plate_barcodes, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock updating the samples in dart to fail
mock_get_plate_barcodes.return_value = ["123", "456"]
mock_get_positive_samples.return_value = [{
"plate_barcode": "123"
}, {
"plate_barcode": "456"
}]
mock_remove_cherrypicked.return_value = [{"plate_barcode": "123"}]
mock_update_mongo.return_value = True
mock_update_mlwh.return_value = True
mock_update_dart.return_value = False
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure expected database calls
mock_update_mongo.assert_called_once()
mock_update_mlwh.assert_called_once()
mock_update_dart.assert_called_once()
def test_update_filtered_positives_aborts_with_no_pending_plate_barcodes(
mock_helper_imports, mock_helper_database_updates):
mock_get_plate_barcodes, _ = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock to return no pending plate barcodes
mock_get_plate_barcodes.return_value = []
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_catches_error_fetching_pending_plate_barcodes(
mock_helper_imports, mock_helper_database_updates):
mock_get_plate_barcodes, _ = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock fetching pending plate barcodes to throw
mock_get_plate_barcodes.side_effect = ValueError("Boom!")
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_omitting_dart_aborts_with_no_positive_samples_fetched_from_mongo(
mock_helper_imports, mock_helper_database_updates):
_, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock no positive samples
mock_get_positive_samples.return_value = []
# call the migration
update_filtered_positives.run("crawler.config.integration", True)
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_omitting_dart_catches_error_pending_positive_samples(
mock_helper_imports, mock_helper_database_updates):
_, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock getting positive samples to throw
mock_get_positive_samples.side_effect = NotImplementedError("Boom!")
# call the migration
update_filtered_positives.run("crawler.config.integration", True)
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_catches_error_pending_positive_samples(
mock_helper_imports, mock_helper_database_updates):
mock_get_plate_barcodes, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock a pending plate, but getting associated positive samples to throw
mock_get_plate_barcodes.return_value = ["ABC123"]
mock_get_positive_samples.side_effect = NotImplementedError("Boom!")
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_aborts_with_no_positive_samples_fetched_from_mongo(
mock_helper_imports, mock_helper_database_updates):
mock_get_plate_barcodes, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock a pending plate, but no associated positive samples
mock_get_plate_barcodes.return_value = ["barcode with no matching sample"]
mock_get_positive_samples.return_value = []
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_aborts_with_no_non_cherrypicked_samples(
mock_helper_imports, mock_filter_out_cherrypicked_samples, mock_helper_database_updates
):
mock_get_plate_barcodes, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock removing cherrypicked samples to throw
mock_get_plate_barcodes.return_value = ["123", "456"]
mock_get_positive_samples.return_value = [{"plate_barcode": "123"}, {"plate_barcode": "456"}]
mock_filter_out_cherrypicked_samples.return_value = []
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_catches_error_updating_samples_in_mongo(
mock_helper_imports, mock_filter_out_cherrypicked_samples, mock_update_positives, mock_helper_database_updates
):
mock_get_plate_barcodes, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock updating the samples in mongo to throw
mock_get_plate_barcodes.return_value = ["123", "456"]
mock_get_positive_samples.return_value = [{"plate_barcode": "123"}, {"plate_barcode": "456"}]
mock_filter_out_cherrypicked_samples.return_value = [{"plate_barcode": "123"}]
mock_update_mongo.side_effect = NotImplementedError("Boom!")
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure expected database calls
mock_update_mongo.assert_called_once()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def test_update_filtered_positives_catches_error_determining_filtered_positive_results(
mock_helper_imports, mock_filter_out_cherrypicked_samples, mock_update_positives, mock_helper_database_updates
):
mock_get_plate_barcodes, mock_get_positive_samples = mock_helper_imports
mock_update_mongo, mock_update_mlwh, mock_update_dart = mock_helper_database_updates
# mock determining the filtered positive fields to throw
mock_get_plate_barcodes.return_value = ["123", "456"]
mock_get_positive_samples.return_value = [{"plate_barcode": "123"}, {"plate_barcode": "456"}]
mock_filter_out_cherrypicked_samples.return_value = [{"plate_barcode": "123"}]
mock_update_positives.side_effect = NotImplementedError("Boom!")
# call the migration
update_filtered_positives.run("crawler.config.integration")
# ensure that no databases are updated
mock_update_mongo.assert_not_called()
mock_update_mlwh.assert_not_called()
mock_update_dart.assert_not_called()
def migration_update_filtered_positives():
print("Running update_filtered_positives migration")
omit_dart = sys.argv[2] == "omit_dart" if 2 < len(sys.argv) else False
update_filtered_positives.run(omit_dart=omit_dart)
