tests/testthat/test-shinytest2-tm_t_abnormality.R

In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

app_driver_tm_t_abnormality <- function() {
  data <- teal.data::teal_data()
  data <- within(data, {
    library(dplyr)

    ADSL <- teal.data::rADSL
    ADLB <- teal.data::rADLB %>%
      mutate(
        ONTRTFL = case_when(
          AVISIT %in% c("SCREENING", "BASELINE") ~ "",
          TRUE ~ "Y"
        ) %>% with_label("On Treatment Record Flag")
      )
  })
  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]

  init_teal_app_driver(
    data = data,
    modules = tm_t_abnormality(
      label = "Abnormality Table",
      dataname = "ADLB",
      parentname = "ADSL",
      arm_var = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADSL"]], subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      add_total = FALSE,
      by_vars = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], subset = c("LBCAT", "PARAM", "AVISIT")),
        selected = c("LBCAT", "PARAM"),
        keep_order = TRUE
      ),
      baseline_var = teal.transform::choices_selected(
        teal.transform::variable_choices(data[["ADLB"]], subset = "BNRIND"),
        selected = "BNRIND", fixed = TRUE
      ),
      grade = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      abnormal = list(low = "LOW", high = "HIGH"),
      id_var = teal.transform::choices_selected(
        teal.transform::variable_choices(data[["ADLB"]], subset = "USUBJID"),
        selected = "USUBJID", fixed = TRUE
      ),
      exclude_base_abn = FALSE,
      treatment_flag_var = teal.transform::choices_selected(
        teal.transform::variable_choices(data[["ADLB"]], subset = "ONTRTFL"),
        selected = "ONTRTFL", fixed = TRUE
      ),
      treatment_flag = teal.transform::choices_selected("Y"),
      total_label = default_total_label(),
      drop_arm_levels = TRUE,
      pre_output = NULL,
      post_output = NULL,
      na_level = default_na_str(),
      basic_table_args = teal.widgets::basic_table_args()
    )
  )
}

testthat::test_that("e2e - tm_t_abnormality: Module initializes in teal without errors and produces table output.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_abnormality()
  app_driver$expect_no_shiny_error()
  app_driver$expect_no_validation_error()

  testthat::expect_true(
    app_driver$is_visible(app_driver$active_module_element("table-table-with-settings"))
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_abnormality: Starts with specified label, arm_var, by_vars,
  add_total, exclude_base_abn, drop_arm_levels.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_abnormality()

    testthat::expect_equal(
      app_driver$get_text("#teal-teal_modules-active_tab > li.active > a"),
      "Abnormality Table"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("arm_var-dataset_ADSL_singleextract-select"),
      "ARM"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("by_vars-dataset_ADLB_singleextract-select"),
      c("LBCAT", "PARAM")
    )
    testthat::expect_false(app_driver$get_active_module_input("add_total"))
    testthat::expect_false(app_driver$get_active_module_input("exclude_base_abn"))
    testthat::expect_true(app_driver$get_active_module_input("drop_arm_levels"))
    testthat::expect_equal(
      app_driver$get_active_module_input("baseline_var-dataset_ADLB_singleextract-select"),
      "BNRIND"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("grade-dataset_ADLB_singleextract-select"),
      "ANRIND"
    )
    app_driver$stop()
  }
)

testthat::test_that(
  "e2e - tm_t_abnormality: Selecting arm_var changes the table and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_abnormality()
    table_before <- app_driver$get_active_module_table_output("table-table-with-settings")
    app_driver$set_active_module_input("arm_var-dataset_ADSL_singleextract-select", "ARMCD")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("table-table-with-settings")
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - arm_var: Deselection of arm_var throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_abnormality()
  app_driver$set_active_module_input("arm_var-dataset_ADSL_singleextract-select", NULL)
  testthat::expect_identical(app_driver$get_active_module_table_output("table-table-with-settings"), data.frame())
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("arm_var-dataset_ADSL_singleextract-select_input .shiny-validation-message"),
    "Please select a treatment variable."
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_abnormality: Selecting by_vars changes the table and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_abnormality()
    table_before <- app_driver$get_active_module_table_output("table-table-with-settings")
    app_driver$set_active_module_input("by_vars-dataset_ADLB_singleextract-select", "AVISIT")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("table-table-with-settings")
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_abnormality: Deselection of by_vars throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_abnormality()
  app_driver$set_active_module_input("by_vars-dataset_ADLB_singleextract-select", NULL)
  testthat::expect_identical(app_driver$get_active_module_table_output("table-table-with-settings"), data.frame())
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("by_vars-dataset_ADLB_singleextract-select_input .shiny-validation-message"),
    "Please select a Row By Variable."
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_abnormality: Changing add_total changes the table and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_abnormality()
    table_before <- app_driver$get_active_module_table_output("table-table-with-settings")
    app_driver$set_active_module_input("add_total", TRUE)
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("table-table-with-settings")
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that(
  "e2e - tm_t_abnormality: Changing exclude_base_abn changes the table and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_abnormality()
    table_before <- app_driver$get_active_module_table_output("table-table-with-settings")
    app_driver$set_active_module_input("exclude_base_abn", TRUE)
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("table-table-with-settings")
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that(
  "e2e - tm_t_abnormality: Changing drop_arm_levels does not change the table and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_abnormality()
    table_before <- app_driver$get_active_module_table_output("table-table-with-settings")
    app_driver$set_active_module_input("drop_arm_levels", FALSE)
    testthat::expect_true(
      identical(
        table_before,
        app_driver$get_active_module_table_output("table-table-with-settings")
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)