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Restore behavior of tm_t_abnormality_by_wrong as it was before migration #1539

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Merged
averissimo merged 4 commits into from
Jun 26, 2026
Merged

Restore behavior of tm_t_abnormality_by_wrong as it was before migration #1539

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9cfae18
refactor: allow for multiple values for worst_flag_indicator
osenan May 31, 2026
6ba963c
chore: fix lintr
osenan May 31, 2026
9bd2e66
fix: change the way we extract the input value due to usage of teal.w…
osenan Jun 1, 2026
714fd08
Fixes validation and case when worst flag does not exist (#1543)
averissimo Jun 26, 2026
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72 changes: 45 additions & 27 deletions R/tm_t_abnormality_by_worst_grade.R
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Original file line number Diff line number Diff line change
Expand Up @@ -221,6 +221,7 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint: object_len

y$table <- substitute(
expr = {
stopifnot("No common arm levels in data, please check input." = nrow(parent) > 0)
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent)
},
env = list(parent = as.name(parentname))
Expand Down Expand Up @@ -359,9 +360,6 @@ tm_t_abnormality_by_worst_grade <- function(label, # nolint: object_length.
worst_high_flag_var <- migrate_choices_selected_to_variables(worst_high_flag_var)
worst_low_flag_var <- migrate_choices_selected_to_variables(worst_low_flag_var)
worst_flag_indicator <- migrate_choices_selected_to_values(worst_flag_indicator)
worst_flag_value <- as.character(worst_flag_indicator$selected)
checkmate::assert_character(worst_flag_value, min.len = 1L, .var.name = "worst_flag_indicator$selected")
worst_flag_value <- worst_flag_value[[1]]

checkmate::assert_string(label)
checkmate::assert_string(dataname)
Expand Down Expand Up @@ -399,7 +397,7 @@ ui_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
atoxgr_var,
worst_high_flag_var,
worst_low_flag_var,
worst_flag_value,
worst_flag_indicator,
add_total,
drop_arm_levels,
id_var,
Expand Down Expand Up @@ -444,9 +442,13 @@ ui_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
),
tags$div(
tags$label("Value Indicating Worst Grade"),
tags$p(
class = "tm-abnormality-worst-grade-worst-flag-value text-muted mb-0",
worst_flag_value
teal.widgets::optionalSelectInput(
ns("worst_flag_indicator"),
label = NULL,
choices = worst_flag_indicator$choices,
selected = if (is.function(worst_flag_indicator$selected)) NULL else worst_flag_indicator$selected,
multiple = FALSE,
fixed = teal.picks::is_pick_fixed(worst_flag_indicator)
)
),
checkboxInput(
Expand All @@ -471,7 +473,6 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
arm_var,
paramcd,
atoxgr_var,
worst_flag_value,
worst_low_flag_var,
worst_high_flag_var,
add_total,
Expand Down Expand Up @@ -522,26 +523,40 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
anl_q <- merged_adsl_anl$data

validate_checks <- reactive({
input_arm <- anl_selectors$arm_var()$variables$selected
validate(
need(length(input_arm) == 1L, "Please select a treatment variable.")
teal::need_input(
inputId = "arm_var-variables-selected",
condition = length(anl_selectors$arm_var()$variables$selected) == 1L,
message = "Please select a treatment variable."
)
)
validate(
need(
length(anl_selectors$id_var()$variables$selected) >= 1L,
"Please select a Subject Identifier."
teal::need_input(
inputId = "id_var-variables-selected",
condition = length(anl_selectors$id_var()$variables$selected) >= 1L,
message = "Please select a Subject Identifier."
),
need(
length(anl_selectors$atoxgr_var()$variables$selected) >= 1L,
"Please select Analysis Toxicity Grade variable."
teal::need_input(
inputId = "atoxgr_var-variables-selected",
condition = length(anl_selectors$atoxgr_var()$variables$selected) >= 1L,
message = "Please select Analysis Toxicity Grade variable."
),
need(
length(anl_selectors$worst_low_flag_var()$variables$selected) >= 1L,
"Please select the Worst Low Grade flag variable."
teal::need_input(
inputId = "worst_low_flag_var-variables-selected",
condition = length(anl_selectors$worst_low_flag_var()$variables$selected) >= 1L,
message = "Please select the Worst Low Grade flag variable."
),
need(
length(anl_selectors$worst_high_flag_var()$variables$selected) >= 1L,
"Please select the Worst High Grade flag variable."
teal::need_input(
inputId = "worst_high_flag_var-variables-selected",
condition = length(anl_selectors$worst_high_flag_var()$variables$selected) >= 1L,
message = "Please select the Worst High Grade flag variable."
)
)
validate(
teal::need_input(
inputId = "worst_flag_indicator",
condition = !is.null(input$worst_flag_indicator),
message = "Please select a value indicating the worst grade."
)
)

Expand All @@ -552,9 +567,10 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
pcd$values$selected
}
validate(
need(
length(pcd_vals) >= 1L,
"Please select at least one Laboratory parameter."
teal::need_input(
inputId = "paramcd-values-selected",
condition = length(pcd_vals) >= 1L,
message = "Please select at least one Laboratory parameter."
)
)

Expand Down Expand Up @@ -632,7 +648,7 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
atoxgr_var = as.vector(anl_selectors$atoxgr_var()$variables$selected),
worst_high_flag_var = as.vector(anl_selectors$worst_high_flag_var()$variables$selected),
worst_low_flag_var = as.vector(anl_selectors$worst_low_flag_var()$variables$selected),
worst_flag_indicator = worst_flag_value,
worst_flag_indicator = input$worst_flag_indicator,
add_total = input$add_total,
total_label = total_label,
drop_arm_levels = input$drop_arm_levels,
Expand All @@ -641,7 +657,9 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.

obj <- anl_q()
teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "### Table")
teal.code::eval_code(obj, as.expression(unlist(my_calls)))
obj <- teal.code::eval_code(obj, as.expression(unlist(my_calls)))
validate(need(!inherits(obj, "qenv.error"), obj$message))
obj
})

decorated_table_q <- teal::srv_transform_teal_data(
Expand Down
2 changes: 1 addition & 1 deletion R/tm_t_binary_outcome.R
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Original file line number Diff line number Diff line change
Expand Up @@ -827,7 +827,7 @@ srv_t_binary_outcome <- function(id,
paramcd_pick$values$selected
}

if (c(any(!is.data.frame(anl), nrow(anl) == 0L, length(aval_var) == 0L, length(paramcd_sel) == 0L))){
if (c(any(!is.data.frame(anl), nrow(anl) == 0L, length(aval_var) == 0L, length(paramcd_sel) == 0L))) {
return(invisible(NULL))
}

Expand Down
8 changes: 6 additions & 2 deletions R/tm_t_summary_by.R
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Expand Up @@ -404,7 +404,11 @@ template_summary_by <- function(parentname,
#' by_vars = variables(choices = c("PARAM", "AVISIT"), selected = "AVISIT"),
#' summarize_vars = variables(choices = c("AVAL", "CHG"), selected = "AVAL"),
#' useNA = "ifany",
#' paramcd = variables(choices = "PARAMCD")
#' paramcd = picks(
#' variables(choices = "PARAMCD"),
#' values(selected = "ALT"),
#' check_dataset = FALSE
#' )
#' )
#' )
#' )
Expand Down Expand Up @@ -444,7 +448,7 @@ tm_t_summary_by <- function(label,
summarize_vars <- migrate_choices_selected_to_variables(summarize_vars)
id_var <- migrate_choices_selected_to_variables(id_var)
denominator <- migrate_choices_selected_to_values(denominator)
if (!is.null(paramcd)) paramcd <- migrate_value_choices_to_picks(paramcd, multiple = FALSE)
if (!is.null(paramcd)) paramcd <- migrate_value_choices_to_picks(paramcd, multiple = TRUE)

checkmate::assert_string(label)
checkmate::assert_string(dataname)
Expand Down
10 changes: 7 additions & 3 deletions man/tm_t_summary_by.Rd
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4 changes: 4 additions & 0 deletions tests/testthat/_snaps/tm_t_abnormality_by_worst_grade.md
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,8 @@

$table
{
stopifnot(`No common arm levels in data, please check input.` = nrow(adsl) >
0)
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl)
}

Expand Down Expand Up @@ -88,6 +90,8 @@

$table
{
stopifnot(`No common arm levels in data, please check input.` = nrow(myadsl) >
0)
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = myadsl)
}

Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R
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Expand Up @@ -94,7 +94,7 @@ testthat::test_that(
"WGRLOFL"
)
testthat::expect_equal(
app_driver$get_text(".tm-abnormality-worst-grade-worst-flag-value"),
app_driver$get_active_module_input("worst_flag_indicator"),
"Y"
)
}
Expand Down
11 changes: 9 additions & 2 deletions tests/testthat/test-tm_t_summary_by.R
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Expand Up @@ -112,9 +112,16 @@ testthat::describe("template_summary_by rtables output for different statistics"
parentname = "ADSL",
arm_var = teal.picks::variables(choices = "ARM", selected = "ARM", fixed = TRUE),
by_vars = teal.picks::variables(choices = "AVISIT", selected = "AVISIT", fixed = TRUE),
summarize_vars = teal.picks::variables(choices = "AVALC", selected = "AVALC", fixed = TRUE),
summarize_vars = teal.picks::variables(choices = "AVALC", selected = "AVALC", fixed = TRUE, multiple = TRUE),
categorical_stats = "count",
paramcd = teal.picks::variables(choices = "PARAMCD")
paramcd = suppressWarnings(
teal.picks::picks(
teal.picks::variables(choices = "PARAMCD", selected = "PARAMCD"),
teal.picks::values(selected = "ALT", multiple = TRUE),
check_dataset = FALSE
),
classes = "pick_delayed"
)
)

it("adds 'fraction' to the statistics", {
Expand Down
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