tests/testthat/test-shinytest2-tm_t_pp_laboratory.R

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

app_driver_tm_t_pp_laboratory <- function() {
  data <- teal.data::teal_data()
  data <- within(data, {
    ADSL <- teal.data::rADSL
    ADLB <- teal.data::rADLB
  })
  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]

  init_teal_app_driver(
    data = data,
    modules = tm_t_pp_laboratory(
      label = "Vitals",
      dataname = "ADLB",
      parentname = "ADSL",
      patient_col = "USUBJID",
      paramcd = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], c("PARAMCD", "STUDYID")),
        selected = "PARAMCD"
      ),
      param = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], c("PARAM", "SEX")),
        selected = "PARAM"
      ),
      timepoints = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], c("ADY", "AGE")),
        selected = "ADY"
      ),
      anrind = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], c("ANRIND", "AGEU")),
        selected = "ANRIND"
      ),
      aval_var = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], c("AVAL", "AGE")),
        selected = "AVAL"
      ),
      avalu_var = teal.transform::choices_selected(
        choices = teal.transform::variable_choices(data[["ADLB"]], c("AVALU", "SEX")),
        selected = "AVALU"
      ),
      pre_output = NULL,
      post_output = NULL
    )
  )
}

testthat::test_that("e2e - tm_t_pp_laboratory: Module initializes in teal without errors and produces table output.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$expect_no_shiny_error()
  app_driver$expect_no_validation_error()
  testthat::expect_true(
    app_driver$is_visible(app_driver$active_module_element("lab_values_table"))
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Starts with specified label, patient_id, paramcd, param,
  timepoints, aval_var, avalu_var, anrind, round_value.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()

    testthat::expect_equal(
      app_driver$get_text("#teal-teal_modules-active_tab > li.active > a"),
      "Vitals"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("patient_id"),
      "AB12345-CHN-3-id-128"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("paramcd-dataset_ADLB_singleextract-select"),
      "PARAMCD"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("param-dataset_ADLB_singleextract-select"),
      "PARAM"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("timepoints-dataset_ADLB_singleextract-select"),
      "ADY"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("aval_var-dataset_ADLB_singleextract-select"),
      "AVAL"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("avalu_var-dataset_ADLB_singleextract-select"),
      "AVALU"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("anrind-dataset_ADLB_singleextract-select"),
      "ANRIND"
    )
    testthat::expect_equal(
      app_driver$get_active_module_input("round_value"),
      "4"
    )
    app_driver$stop()
  }
)

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting patient_id changes the table and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("patient_id", "AB12345-USA-1-id-261")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_pp_laboratory: Deselection of patient_id throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$set_active_module_input("patient_id", NULL)
  testthat::expect_false(
    app_driver$is_visible(
      app_driver$active_module_element("lab_values_table"),
      visibility_property = TRUE
    )
  )
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("patient_id_input .shiny-validation-message"),
    "Please select a patient"
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting paramcd changes the table
  and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("paramcd-dataset_ADLB_singleextract-select", "STUDYID")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_pp_laboratory: Deselection of paramcd throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$set_active_module_input("paramcd-dataset_ADLB_singleextract-select", NULL)
  testthat::expect_false(
    app_driver$is_visible(
      app_driver$active_module_element("lab_values_table"),
      visibility_property = TRUE
    )
  )
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("paramcd-dataset_ADLB_singleextract-select_input .shiny-validation-message"),
    "Please select PARAMCD variable."
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting param changes the table
  and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("param-dataset_ADLB_singleextract-select", "SEX")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Deselection of param throws validation error.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    app_driver$set_active_module_input("param-dataset_ADLB_singleextract-select", NULL)
    testthat::expect_false(
      app_driver$is_visible(
        app_driver$active_module_element("lab_values_table"),
        visibility_property = TRUE
      )
    )
    app_driver$expect_validation_error()
    testthat::expect_equal(
      app_driver$active_module_element_text("param-dataset_ADLB_singleextract-select_input .shiny-validation-message"),
      "Please select PARAM variable."
    )
    app_driver$stop()
  }
)

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting timepoints changes the table
  and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("timepoints-dataset_ADLB_singleextract-select", "AGE")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_pp_laboratory: Deselection of timepoints throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$set_active_module_input("timepoints-dataset_ADLB_singleextract-select", NULL)
  testthat::expect_false(
    app_driver$is_visible(
      app_driver$active_module_element("lab_values_table"),
      visibility_property = TRUE
    )
  )
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text(
      "timepoints-dataset_ADLB_singleextract-select_input .shiny-validation-message"
    ),
    "Please select timepoints variable."
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting avalu changes the table
  and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("avalu_var-dataset_ADLB_singleextract-select", "SEX")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_pp_laboratory: Deselection of avalu throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$set_active_module_input("avalu_var-dataset_ADLB_singleextract-select", NULL)
  testthat::expect_false(
    app_driver$is_visible(
      app_driver$active_module_element("lab_values_table"),
      visibility_property = TRUE
    )
  )
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text(
      "avalu_var-dataset_ADLB_singleextract-select_input .shiny-validation-message"
    ),
    "Please select AVALU variable."
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting aval_var changes the table
  and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("aval_var-dataset_ADLB_singleextract-select", "AGE")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_pp_laboratory: Deselection of aval_var throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$set_active_module_input("aval_var-dataset_ADLB_singleextract-select", NULL)
  testthat::expect_false(
    app_driver$is_visible(
      app_driver$active_module_element("lab_values_table"),
      visibility_property = TRUE
    )
  )
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("aval_var-dataset_ADLB_singleextract-select_input .shiny-validation-message"),
    "Please select AVAL variable."
  )
  app_driver$stop()
})

testthat::test_that(
  "e2e - tm_t_pp_laboratory: Selecting arind changes the table
  and does not throw validation errors.",
  {
    skip_if_too_deep(5)
    app_driver <- app_driver_tm_t_pp_laboratory()
    table_before <- app_driver$get_active_module_table_output("lab_values_table", which = 2)
    app_driver$set_active_module_input("anrind-dataset_ADLB_singleextract-select", "AGEU")
    testthat::expect_false(
      identical(
        table_before,
        app_driver$get_active_module_table_output("lab_values_table", which = 2)
      )
    )
    app_driver$expect_no_validation_error()
    app_driver$stop()
  }
)

testthat::test_that("e2e - tm_t_pp_laboratory: Deselection of arind throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_t_pp_laboratory()
  app_driver$set_active_module_input("anrind-dataset_ADLB_singleextract-select", NULL)
  testthat::expect_false(
    app_driver$is_visible(
      app_driver$active_module_element("lab_values_table"),
      visibility_property = TRUE
    )
  )
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("anrind-dataset_ADLB_singleextract-select_input .shiny-validation-message"),
    "Please select ANRIND variable."
  )
  app_driver$stop()
})