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Wave 4 - tm_t_binary_outcome shinytests (#1155)
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Part of #1108

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Co-authored-by: unknown <[email protected]>
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@vedhav @kartikeyakirar
vedhav and kartikeyakirar authored May 7, 2024
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app_driver_tm_t_binary_outcome <- function() {
data <- teal.data::teal_data() %>%
within({
library(dplyr)
ADSL <- teal.data::rADSL
ADRS <- teal.data::rADRS %>%
mutate(
AVALC = d_onco_rsp_label(AVALC) %>%
with_label("Character Result/Finding")
) %>%
filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
})

datanames <- c("ADSL", "ADRS")
teal.data::datanames(data) <- datanames
teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]

arm_ref_comp <- list(
ARMCD = list(ref = "ARM B", comp = c("ARM A", "ARM C")),
ARM = list(ref = "B: Placebo", comp = c("A: Drug X", "C: Combination"))
)

init_teal_app_driver(
data = data,
modules = tm_t_binary_outcome(
label = "Responders",
dataname = "ADRS",
parentname = "ADSL",
arm_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices(data[["ADRS"]], c("ARM", "ARMCD", "ACTARMCD")),
selected = "ARM"
),
arm_ref_comp = arm_ref_comp,
paramcd = teal.transform::choices_selected(
choices = teal.transform::value_choices(data[["ADRS"]], "PARAMCD", "PARAM"),
selected = "BESRSPI"
),
strata_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices(data[["ADRS"]], c("SEX", "BMRKR2", "RACE")),
selected = "RACE"
),
aval_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices(
data[["ADRS"]], c("AVALC", "SEX")
),
selected = "AVALC",
fixed = FALSE
),
conf_level = teal.transform::choices_selected(
c(2, 0.95, 0.9, 0.8), 0.95,
keep_order = TRUE
),
default_responses = list(
BESRSPI = list(
rsp = c("Complete Response (CR)", "Partial Response (PR)"),
levels = c(
"Complete Response (CR)", "Partial Response (PR)",
"Stable Disease (SD)", "Progressive Disease (PD)"
)
),
INVET = list(
rsp = c("Stable Disease (SD)", "Not Evaluable (NE)"),
levels = c(
"Complete Response (CR)", "Not Evaluable (NE)", "Partial Response (PR)",
"Progressive Disease (PD)", "Stable Disease (SD)"
)
),
OVRINV = list(
rsp = c("Progressive Disease (PD)", "Stable Disease (SD)"),
levels = c("Progressive Disease (PD)", "Stable Disease (SD)", "Not Evaluable (NE)")
)
),
rsp_table = FALSE,
control = list(global = list(
method = "waldcc",
conf_level = 0.95
), unstrat = list(
method_ci = "waldcc",
method_test = "schouten", odds = TRUE
), strat = list(
method_ci = "cmh", method_test =
"cmh"
)),
add_total = FALSE,
total_label = default_total_label(),
na_level = default_na_str(),
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()
)
)
}

testthat::test_that("e2e - tm_t_binary_outcome: Module initializes in teal without errors and produces table output.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
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_binary_outcome: Starts with specified label, paramcd, responders, arm_var,
buckets, u_diff_ci, u_diff_test, strata_var, s_diff_ci, prop_ci_method, conf_level,
aval_var, compare_arms, combine_comp_arms, u_odds_ratio, show_rsp_cat.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()

testthat::expect_equal(
app_driver$get_text("#teal-main_ui-root-active_tab > li.active > a"),
"Responders"
)
testthat::expect_equal(
app_driver$get_active_module_input("paramcd-dataset_ADRS_singleextract-filter1-vals"),
"BESRSPI"
)
testthat::expect_equal(
app_driver$get_active_module_input("responders"),
c("Complete Response (CR)", "Partial Response (PR)")
)
testthat::expect_equal(
app_driver$get_active_module_input("arm_var-dataset_ADSL_singleextract-select"),
"ARM"
)
testthat::expect_equal(
app_driver$get_active_module_input("buckets"),
list(
Ref = list("B: Placebo"),
Comp = list("A: Drug X", "C: Combination")
)
)
testthat::expect_equal(
app_driver$get_active_module_input("u_diff_ci"),
"waldcc"
)
testthat::expect_equal(
app_driver$get_active_module_input("u_diff_test"),
"schouten"
)
testthat::expect_equal(
app_driver$get_active_module_input("strata_var-dataset_ADSL_singleextract-select"),
"RACE"
)
testthat::expect_equal(
app_driver$get_active_module_input("s_diff_ci"),
"cmh"
)
testthat::expect_equal(
app_driver$get_active_module_input("prop_ci_method"),
"waldcc"
)
testthat::expect_equal(
app_driver$get_active_module_input("conf_level"),
"0.95"
)
testthat::expect_equal(
app_driver$get_active_module_input("aval_var-dataset_ADRS_singleextract-select"),
"AVALC"
)
testthat::expect_true(app_driver$get_active_module_input("compare_arms"))
testthat::expect_false(app_driver$get_active_module_input("combine_comp_arms"))
testthat::expect_true(app_driver$get_active_module_input("u_odds_ratio"))
testthat::expect_false(app_driver$get_active_module_input("show_rsp_cat"))
app_driver$stop()
}
)

testthat::test_that(
"e2e - tm_t_binary_outcome: Selecting paramcd-level changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("paramcd-dataset_ADRS_singleextract-filter1-vals", "INVET")
testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
app_driver$expect_no_validation_error()
app_driver$stop()
}
)

testthat::test_that("e2e - tm_t_binary_outcome: Deselection of paramcd-level throws validation error.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
app_driver$set_active_module_input("paramcd-dataset_ADRS_singleextract-filter1-vals", NULL)
testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
app_driver$expect_validation_error()
testthat::expect_equal(
app_driver$active_module_element_text(
"paramcd-dataset_ADRS_singleextract-filter1-vals_input .shiny-validation-message"
),
"Please select a filter."
)
app_driver$stop()
})

testthat::test_that(
"e2e - tm_t_binary_outcome: Selecting responders changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("responders", c("Stable Disease (SD)", "Progressive Disease (PD)"))
testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
app_driver$expect_no_validation_error()
app_driver$stop()
}
)

testthat::test_that("e2e - tm_t_binary_outcome: Deselection of responders throws validation error.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
app_driver$set_active_module_input("responders", NULL)
testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
app_driver$expect_validation_error()
testthat::expect_equal(
app_driver$get_text("#teal-main_ui-root-responders .shiny-validation-message"),
"`Responders` field is empty"
)
app_driver$stop()
})

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

testthat::test_that("e2e - tm_t_binary_outcome: Deselection of arm_var-variable throws validation error.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
app_driver$set_active_module_input("arm_var-dataset_ADSL_singleextract-select", NULL)
testthat::expect_identical(app_driver$get_active_module_tws_output("table"), 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"),
"Treatment variable must be selected"
)
app_driver$stop()
})

testthat::test_that(
"e2e - tm_t_binary_outcome: Selecting strata_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("strata_var-dataset_ADSL_singleextract-select", "SEX")

testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
app_driver$expect_no_validation_error()
app_driver$stop()
}
)

testthat::test_that(
"e2e - tm_t_binary_outcome: Deselection of strata_var-variable changes the table and does not throw validation errors.", # nolint line_length_linter
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_binary_outcome()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("strata_var-dataset_ADSL_singleextract-select", NULL)
testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
app_driver$expect_no_validation_error()
app_driver$stop()
}
)

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