tests/testthat/test-s4_helpers.R

In Katsevich-Lab/sceptre: Analysis of Single-Cell CRISPR Screen Data

# `perform_status_check_and_update` is used in each of the main sceptre_object
# functions aside from `import_data`
test_that("perform_status_check_and_update", {
  # `import_data` initializes @functs_called with the "import_data" value
  # at TRUE so we'll never see an all-FALSE @functs_called
  initial_functs_called <- c(
    import_data = TRUE, set_analysis_parameters = FALSE,
    assign_grnas = FALSE, run_qc = FALSE, run_calibration_check = FALSE,
    run_power_check = FALSE, run_discovery_analysis = FALSE
  )

  blank_object <- new("sceptre_object")
  blank_object@functs_called <- initial_functs_called

  ## call `set_analysis_parameters`
  results <- perform_status_check_and_update(blank_object, "set_analysis_parameters")
  expect_equal(results@last_function_called, "set_analysis_parameters")
  expect_equal(results@functs_called |> as.logical(), rep(c(TRUE, FALSE), c(2, 5)))

  ## try to use a function before calling the downstream ones
  expect_error(
    perform_status_check_and_update(blank_object, "run_qc"),
    regex = "The function `assign_grnas\\(\\)` must be called before `run_qc\\(\\)` is called"
  )

  ## chaining some together
  results <- blank_object |>
    perform_status_check_and_update("set_analysis_parameters") |>
    perform_status_check_and_update("assign_grnas") |>
    perform_status_check_and_update("run_qc")
  expect_equal(results@last_function_called, "run_qc")
  expect_equal(results@functs_called |> as.logical(), rep(c(TRUE, FALSE), c(4, 3)))

  ## confirming if we rerun a lower level one after having run a higher level one
  results <- results |> perform_status_check_and_update("assign_grnas")
  expect_equal(results@last_function_called, "assign_grnas")
  expect_false(results@functs_called["run_qc"]) # this was TRUE before
  expect_true(results@functs_called["set_analysis_parameters"]) # this should still be TRUE
})