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Wave 4 - tm_t_coxreg shinytests (#1156)
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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_coxreg <- function() {
# TODO: Check if data fabrication is needed for Cox regression
data <- teal.data::teal_data()
data <- within(data, {
ADSL <- teal.data::rADSL
ADTTE <- teal.data::rADTTE
})
datanames <- c("ADSL", "ADTTE")
teal.data::datanames(data) <- datanames
teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]

arm_ref_comp <- list(
ACTARMCD = 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_coxreg(
label = "Cox Reg.",
dataname = "ADTTE",
parentname = "ADSL",
arm_var = teal.transform::choices_selected(c("ARM", "ARMCD", "ACTARMCD"), "ARM"),
arm_ref_comp = arm_ref_comp,
paramcd = teal.transform::choices_selected(
teal.transform::value_choices(data[["ADTTE"]], "PARAMCD", "PARAM"), "OS"
),
strata_var = teal.transform::choices_selected(
c("COUNTRY", "STRATA1", "STRATA2"), "STRATA1"
),
cov_var = teal.transform::choices_selected(
c("AGE", "BMRKR1", "BMRKR2", "REGION1"), "AGE"
),
multivariate = TRUE,
aval_var = teal.transform::choices_selected(
teal.transform::variable_choices(data[["ADTTE"]], "AVAL"), "AVAL",
fixed = TRUE
),
cnsr_var = teal.transform::choices_selected(
teal.transform::variable_choices(data[["ADTTE"]], "CNSR"), "CNSR",
fixed = TRUE
),
na_level = default_na_str(),
conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95,
keep_order =
TRUE
),
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()
)
)
}

testthat::test_that("e2e - tm_t_coxreg: Module initializes in teal without errors and produces table output.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
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_coxreg: Starts with specified label, type, paramcd, arm_var, buckets,
cov_var, strata_var, pval_method, ties, conf_level, combine_comp_arms.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
testthat::expect_equal(
app_driver$get_text("#teal-main_ui-root-active_tab > li.active > a"),
"Cox Reg."
)
testthat::expect_equal(
app_driver$get_active_module_input("type"),
"Multivariate"
)
testthat::expect_equal(
app_driver$get_active_module_input("paramcd-dataset_ADTTE_singleextract-filter1-vals"),
"OS"
)
testthat::expect_equal(
app_driver$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("cov_var-dataset_ADSL_singleextract-select"),
"AGE"
)
testthat::expect_equal(
app_driver$get_active_module_input("strata_var-dataset_ADSL_singleextract-select"),
"STRATA1"
)
testthat::expect_equal(
app_driver$get_active_module_input("pval_method"),
"wald"
)
testthat::expect_equal(
app_driver$get_active_module_input("ties"),
"exact"
)
testthat::expect_equal(
app_driver$get_active_module_input("conf_level"),
"0.95"
)
testthat::expect_false(app_driver$get_active_module_input("combine_comp_arms"))
app_driver$stop()
}
)

testthat::test_that(
"e2e - tm_t_coxreg: Selecting paramcd-level changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("paramcd-dataset_ADTTE_singleextract-filter1-vals", "CRSD")
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_coxreg: Deselection of paramcd-level throws validation error.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
app_driver$set_active_module_input("paramcd-dataset_ADTTE_singleextract-filter1-vals", NULL)
testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
app_driver$expect_validation_error()
testthat::expect_equal(
app_driver$active_module_element_text(
"paramcd-dataset_ADTTE_singleextract-filter1-vals_input .shiny-validation-message"
),
"An endpoint is required"
)
app_driver$stop()
})

testthat::test_that(
"e2e - tm_t_coxreg: Selecting arm_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
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_coxreg: Deselection of arm_var-variable throws validation error.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
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_coxreg: Selecting cov_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("cov_var-dataset_ADSL_singleextract-select", c("BMRKR1", "BMRKR2"))
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_coxreg: Deselection of cov_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("cov_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()
}
)

testthat::test_that(
"e2e - tm_t_coxreg: Selecting strata_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("strata_var-dataset_ADSL_singleextract-select", c("STRATA2", "COUNTRY"))
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_coxreg: Deselection of strata_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_coxreg()
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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