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Wave 5 - tm_t_events_summary shinytests (#1160)
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Part of #1108

---------

Signed-off-by: Vedha Viyash <[email protected]>
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_events_summary <- function() {
data <- teal.data::teal_data()
data <- within(data, {
library(dplyr)
ADSL <- teal.data::rADSL %>%
mutate(
DTHFL = case_when(
!is.na(DTHDT) ~ "Y",
TRUE ~ ""
) %>% with_label("Subject Death Flag")
)
ADAE <- teal.data::rADAE

add_event_flags <- function(dat) {
dat <- dat %>%
dplyr::mutate(
TMPFL_SER = AESER == "Y",
TMPFL_REL = AEREL == "Y",
TMPFL_GR5 = AETOXGR == "5",
TMP_SMQ01 = !is.na(SMQ01NAM),
TMP_SMQ02 = !is.na(SMQ02NAM),
TMP_CQ01 = !is.na(CQ01NAM)
)
column_labels <- list(
TMPFL_SER = "Serious AE",
TMPFL_REL = "Related AE",
TMPFL_GR5 = "Grade 5 AE",
TMP_SMQ01 = tern::aesi_label(dat[["SMQ01NAM"]], dat[["SMQ01SC"]]),
TMP_SMQ02 = tern::aesi_label("Y.9.9.9.9/Z.9.9.9.9 AESI"),
TMP_CQ01 = tern::aesi_label(dat[["CQ01NAM"]])
)
col_labels(dat)[names(column_labels)] <- as.character(column_labels)
dat
}

ADAE <- ADAE %>% add_event_flags()

ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), "TMPFL_")]
aesi_vars <- names(ADAE)[startsWith(names(ADAE), "TMP_")]
})

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

init_teal_app_driver(
data = data,
modules = tm_t_events_summary(
label = "Adverse Events Summary",
dataname = "ADAE",
parentname = "ADSL",
arm_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices("ADSL", c("ARM", "ARMCD")),
selected = "ARM"
),
flag_var_anl = teal.transform::choices_selected(
choices = teal.transform::variable_choices("ADAE", data[["ae_anl_vars"]]),
selected = data[["ae_anl_vars"]][1],
keep_order = TRUE,
fixed = FALSE
),
flag_var_aesi = teal.transform::choices_selected(
choices = teal.transform::variable_choices("ADAE", data[["aesi_vars"]]),
selected = data[["aesi_vars"]][1],
keep_order = TRUE,
fixed = FALSE
),
dthfl_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices(data[["ADSL"]], "DTHFL"),
selected = "DTHFL", fixed = TRUE
),
dcsreas_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices(data[["ADSL"]], "DCSREAS"),
selected = "DCSREAS", fixed = TRUE
),
llt = teal.transform::choices_selected(
choices = teal.transform::variable_choices(data[["ADAE"]], "AEDECOD"),
selected = "AEDECOD", fixed = TRUE
),
aeseq_var = teal.transform::choices_selected(
choices = teal.transform::variable_choices(data[["ADAE"]], "AESEQ"),
selected = "AESEQ", fixed = TRUE
),
add_total = TRUE,
total_label = default_total_label(),
na_level = default_na_str(),
count_subj = TRUE,
count_pt = TRUE,
count_events = TRUE,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()
)
)
}

testthat::test_that("e2e - tm_t_events_summary: Module initializes in teal without errors and produces table output.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
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_events_summary: Starts with specified label, arm_var, flag_var_anl, flag_var_aesi,
add_total, count_subj, count_pt, count_events",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
testthat::expect_equal(
app_driver$get_text("#teal-main_ui-root-active_tab > li.active > a"),
"Adverse Events Summary"
)
testthat::expect_equal(
app_driver$get_active_module_input("arm_var-dataset_ADSL_singleextract-select"),
"ARM"
)
testthat::expect_equal(
app_driver$get_active_module_input("flag_var_anl-dataset_ADAE_singleextract-select"),
"TMPFL_SER"
)
testthat::expect_equal(
app_driver$get_active_module_input("flag_var_aesi-dataset_ADAE_singleextract-select"),
"TMP_SMQ01"
)
testthat::expect_true(app_driver$get_active_module_input("add_total"))
testthat::expect_true(app_driver$get_active_module_input("count_subj"))
testthat::expect_true(app_driver$get_active_module_input("count_pt"))
testthat::expect_true(app_driver$get_active_module_input("count_events"))
app_driver$stop()
}
)

testthat::test_that(
"e2e - tm_t_events_summary: Selecting arm_var-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
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_events_summary: Deselection of arm_var-variable throws validation error.", {
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
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"),
"Please select exactly 1 or 2 treatment variables"
)
app_driver$stop()
})

testthat::test_that(
"e2e - tm_t_events_summary: Selecting flag_var_anl-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("flag_var_anl-dataset_ADAE_singleextract-select", c("TMPFL_REL", "TMPFL_GR5"))
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_events_summary: Deselection of flag_var_anl-variable changes the table
and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("flag_var_anl-dataset_ADAE_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_events_summary: Selecting flag_var_aesi-variable changes the table and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("flag_var_aesi-dataset_ADAE_singleextract-select", c("TMP_SMQ02", "TMP_CQ01"))
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_events_summary: Deselection of flag_var_aesi-variable changes the table
and does not throw validation errors.",
{
skip_if_too_deep(5)
app_driver <- app_driver_tm_t_events_summary()
table_before <- app_driver$get_active_module_tws_output("table")
app_driver$set_active_module_input("flag_var_aesi-dataset_ADAE_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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