diff --git a/DESCRIPTION b/DESCRIPTION
index 74bc19ca5..a457258b1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: aNCA
Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9186
+Version: 0.1.0.9187
Authors@R: c(
person("Ercan", "Suekuer", email = "ercan.suekuer@roche.com", role = "aut",
comment = c(ORCID = "0009-0001-1626-1526")),
diff --git a/NEWS.md b/NEWS.md
index 521d7fc5f..682b63476 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -31,6 +31,14 @@
* Summary tables can filter which stratification values appear: a "Parameters to show" filter on the `pkpt03/07/08` tables and a "Timepoints to show" filter on the `pkct01` tables restrict the rows to the chosen `PARAM`/timepoint values (#1356)
* Summary tables now warn (instead of silently degrading) when a chosen stratification variable is not present in the data — e.g. the "by Dose" concentration tables when a dose-amount column is not carried in the concentration data — so it is clear why a table grouped by fewer variables (#1356)
+### TLG Order & Selection
+* Simplify the TLG Order Details table: the internal `Condition` column is hidden (it stays in `tlg.yaml` as metadata that still auto-selects urine outputs) and the table is trimmed to Type, Dataset, Output, Footnote, Stratification, and Comment (#1335)
+* Urine TLG functions filter to urine specimens internally; when `PCSPEC`/`PPSPEC` is missing, the resulting warning is surfaced as an in-app notification instead of failing silently (#1335)
+* Redesign the "Add TLGs to order" picker as a catalog checklist with dataset tabs (PK Concentrations / PK Parameters), search, CSV/XLSX export, per-column select-all, and a live selection count (#1335)
+* In the "Add TLGs to order" picker, searching now respects the active dataset tab: matches in another dataset surface as a count on that tab's badge instead of appearing under the current tab, so switching tabs reveals them (#1335)
+* In the "Add TLGs to order" picker, the toolbar **Select all** and **Clear all** now act consistently on the whole order — every output across both dataset tabs (limited to the current search when one is active) — while each column's **Select all** stays scoped to that column (#1335)
+* Notify the user when a PK-parameter (ADPP) output is requested before NCA has been run, instead of only showing an empty placeholder (#1335)
+
### Settings & Configuration
* Settings upload auto-restores the full session: mapping, filters, data processing, tab navigation, and auto-runs NCA if previously run. Incompatible settings degrade gracefully with notifications (#1225)
* Settings version control: YAML file stores multiple versions with metadata. Save button in header, version selection on upload, version delete support (#1103)
diff --git a/inst/WORDLIST b/inst/WORDLIST
index 7fab852e7..32b1ea267 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -154,6 +154,7 @@ VSSMDP
WTBL
WTBLU
Walkthrough
+XLSX
XPT
YAML
aNCA's
diff --git a/inst/shiny/app.R b/inst/shiny/app.R
index 37fd78137..23069fbb6 100644
--- a/inst/shiny/app.R
+++ b/inst/shiny/app.R
@@ -79,6 +79,7 @@ ui <- function() {
includeCSS(file.path(assets, "main.css")),
includeScript(file.path(assets, "index.js")),
+ includeScript(file.path(assets, "tlg_add_picker.js")),
sidebar = navset_pill_list(
id = "page",
diff --git a/inst/shiny/functions/tlg_add_picker.R b/inst/shiny/functions/tlg_add_picker.R
new file mode 100644
index 000000000..cd37d0e97
--- /dev/null
+++ b/inst/shiny/functions/tlg_add_picker.R
@@ -0,0 +1,169 @@
+#' Helpers for the "Add TLGs to order" modal (issue #1335).
+#'
+#' The picker was originally a grouped reactable whose Type/Dataset columns were
+#' blank on every selectable row. It is rebuilt as a catalog-style checklist:
+#' dataset tabs (PK Concentrations / PK Parameters) over one column per output
+#' Type (Tables / Listings / Graphs), with a search + download + select-all
+#' toolbar, per-column select-all, and a live count on the confirm button.
+#'
+#' Client-side behaviour lives in `inst/shiny/www/tlg_add_picker.js`
+#' (`window.tlgAdd`); styling lives in
+#' `inst/shiny/www/styles/partials/_tlg_add_modal.scss`. These helpers only
+#' build the server-side UI and translate the checked rows back to `tlg_order()`
+#' ids, keeping `tab_tlg_server()` small enough to stay under the cyclomatic
+#' complexity limit.
+
+# Fixed left-to-right order + icon for the Type columns, and dataset tab order.
+.TLG_TYPE_ORDER <- c("Table", "Listing", "Graph")
+.TLG_TYPE_ICON <- c(Table = "table", Listing = "list-ul", Graph = "chart-line")
+.TLG_DATASET_ORDER <- c("PK Concentrations", "PK Parameters")
+
+#' Escape a string for safe embedding inside a single-quoted JS literal.
+#' @param x Character vector.
+#' @returns Character vector wrapped in single quotes with `'` and `\` escaped.
+#' @noRd
+tlg_js_str <- function(x) paste0("'", gsub("(['\\\\])", "\\\\\\1", x), "'")
+
+#' Build the "Add TLGs" catalog checklist UI.
+#'
+#' @param avail Tibble of not-yet-selected TLGs (rows of `tlg_order()` with
+#' `Selection == FALSE`); must contain `Type`, `Dataset`, `Description`,
+#' `Link`, and `id`.
+#' @param ns Namespace function for the calling module (`session$ns`).
+#' @returns A list with `ui` (the modal body tag) and `group_ids` (the
+#' `checkboxGroupInput` ids created, read back on confirm).
+#' @noRd
+build_add_checklist <- function(avail, ns) {
+ present_types <- intersect(.TLG_TYPE_ORDER, unique(avail$Type))
+ datasets <- c(intersect(.TLG_DATASET_ORDER, unique(avail$Dataset)),
+ setdiff(unique(avail$Dataset), .TLG_DATASET_ORDER))
+
+ pairs <- dplyr::distinct(avail, Type, Dataset)
+ pairs <- pairs[order(match(pairs$Type, .TLG_TYPE_ORDER), pairs$Dataset), ]
+ pairs$input_id <- paste0("modal_check_", seq_len(nrow(pairs)))
+
+ spec_icon_html <- as.character(icon("circle-info"))
+
+ # One dataset block for a Type column: tagged with data-dataset so the tab bar
+ # can show/hide it. The active tab is applied client-side.
+ build_group_ui <- function(type, dataset, input_id) {
+ rows <- dplyr::filter(avail, Type == !!type, Dataset == !!dataset)
+ choice_names <- purrr::map2(rows$Description, rows$Link, function(desc, link) {
+ spec_link <- if (is.na(link)) "" else paste0(
+ "", spec_icon_html, ""
+ )
+ HTML(paste0("", htmltools::htmlEscape(desc), "", spec_link))
+ })
+ div(
+ class = "tlg-ds", `data-dataset` = dataset,
+ checkboxGroupInput(
+ inputId = ns(input_id),
+ label = NULL,
+ choiceNames = choice_names,
+ choiceValues = as.character(rows$id)
+ )
+ )
+ }
+
+ # One flex column per Type (plain flex, not the bootstrap grid, whose negative
+ # row margins would misalign the columns against the toolbar).
+ type_columns <- purrr::map(present_types, function(tp) {
+ tp_pairs <- dplyr::rename(pairs[pairs$Type == tp, ], type = Type, dataset = Dataset)
+ div(
+ class = "tlg-col",
+ div(
+ class = "tlg-col-head",
+ tags$span(
+ class = "tlg-col-title",
+ icon(.TLG_TYPE_ICON[[tp]]), paste0(" ", tp, "s"),
+ tags$span(sum(avail$Type == tp), class = "tlg-col-count")
+ ),
+ tags$button(
+ type = "button", class = "tlg-col-selall",
+ onclick = "window.tlgAdd.colSelect(this)", "Select all"
+ )
+ ),
+ div(
+ class = "tlg-col-body",
+ purrr::pmap(tp_pairs, build_group_ui),
+ div(class = "tlg-col-empty", "None in this view", style = "display: none;")
+ )
+ )
+ })
+
+ # Dataset tab bar; first dataset active by default. data-total feeds the count
+ # badge (restored when the search box is cleared).
+ tab_bar <- div(
+ class = "tlg-tabs",
+ purrr::imap(datasets, function(ds, i) {
+ ds_total <- sum(avail$Dataset == ds)
+ tags$button(
+ type = "button",
+ class = paste("tlg-tab", if (i == 1) "active" else ""),
+ `data-dataset` = ds, `data-total` = ds_total,
+ onclick = paste0("window.tlgAdd.setTab(", tlg_js_str(ds), ", this)"),
+ ds, tags$span(ds_total, class = "tlg-tab-count")
+ )
+ })
+ )
+
+ # Per-open initialisation: pick the first dataset tab and render. Kept inline
+ # (not in tlg_add_picker.js) because it depends on the datasets present now.
+ init_js <- paste0(
+ "window.tlgAdd.tab = ", tlg_js_str(datasets[1]), "; ",
+ "window.tlgAdd.q = ''; window.tlgAdd.render();"
+ )
+
+ # Shared left inset so toolbar, tabs, column headers and checkbox rows all line
+ # up on the same left edge (see --tlg-inset in _tlg_add_modal.scss).
+ ui <- div(
+ class = "tlg-add-modal",
+ div(
+ class = "tlg-toolbar",
+ tags$input(
+ type = "text", class = "form-control tlg-search-input",
+ placeholder = "Search outputs…",
+ oninput = "window.tlgAdd.setQuery(this.value)"
+ ),
+ tags$button(type = "button", class = "btn btn-sm btn-default",
+ title = "Select every output in both tabs (matching the search)",
+ onclick = "window.tlgAdd.selectAll()", "Select all"),
+ tags$button(type = "button", class = "btn btn-sm btn-default",
+ title = "Clear every output in both tabs (matching the search)",
+ onclick = "window.tlgAdd.clearAll()", "Clear all"),
+ div(class = "tlg-toolbar-sep"),
+ downloadButton(ns("modal_dl_csv"), "CSV", class = "btn-sm btn-default"),
+ downloadButton(ns("modal_dl_xlsx"), "XLSX", class = "btn-sm btn-default")
+ ),
+ tab_bar,
+ div(class = "tlg-add-checklist tlg-cols", type_columns),
+ div(class = "tlg-no-matches", "No outputs match your search.", style = "display: none;"),
+ tags$script(HTML(init_js))
+ )
+
+ list(ui = ui, group_ids = pairs$input_id)
+}
+
+#' Ids of the rows checked in the add-picker modal, mapped back to `tlg_order()`.
+#'
+#' @param input The module `input` object.
+#' @param group_ids Character vector of `checkboxGroupInput` ids in the modal.
+#' @returns Integer vector of checked `tlg_order()` ids (empty if none).
+#' @noRd
+checked_tlg_ids <- function(input, group_ids) {
+ as.integer(unlist(lapply(group_ids, function(gid) input[[gid]])))
+}
+
+#' Available-TLG catalog for the modal's CSV / XLSX download.
+#'
+#' @param df The available-TLG tibble (`modal_avail()`), or `NULL`.
+#' @returns A data frame with `Type`, `Dataset`, `PKid`, `Description`.
+#' @noRd
+tlg_modal_dl_data <- function(df) {
+ if (is.null(df) || nrow(df) == 0) {
+ return(data.frame(Type = character(), Dataset = character(),
+ PKid = character(), Description = character()))
+ }
+ dplyr::select(df, Type, Dataset, PKid, Description)
+}
diff --git a/inst/shiny/modules/tab_tlg.R b/inst/shiny/modules/tab_tlg.R
index 89bcd34e5..10240821a 100644
--- a/inst/shiny/modules/tab_tlg.R
+++ b/inst/shiny/modules/tab_tlg.R
@@ -91,6 +91,7 @@ tab_tlg_server <- function(id, data, adpp = reactive(NULL)) {
),
PKid = .x$pkid,
Output = paste0("", .x$description, ""),
+ Link = if (is.null(.x$link)) NA_character_ else .x$link,
Label = .x$label,
Description = .x$description,
Condition = .x$condition,
@@ -122,9 +123,13 @@ tab_tlg_server <- function(id, data, adpp = reactive(NULL)) {
tlg_order(new_tlg_order)
})
+ # Columns shown to the user in the Order Details table. Internal columns
+ # (PKid, Label, Description, Condition) are kept in tlg_order() but hidden:
+ # Condition drives urine auto-preselect above, Label titles the nav panels,
+ # and Description feeds the submit log — none need to be user-facing.
displayed_order <- reactive({
dplyr::filter(tlg_order(), Selection) %>%
- dplyr::select(-id, -Selection)
+ dplyr::select(Type, Dataset, Output, Footnote, Stratification, Comment)
}) %>%
bindEvent(data(), input$confirm_add_tlg, input$remove_tlg)
@@ -136,7 +141,7 @@ tab_tlg_server <- function(id, data, adpp = reactive(NULL)) {
defaultExpanded = TRUE,
wrap = TRUE,
selection = "multiple",
- editable = c("Footnote", "Stratification", "Condition", "Comment"),
+ editable = c("Footnote", "Stratification", "Comment"),
columns = function(df) {
define_cols(df, overrides = list(Output = colDef(html = TRUE)))
}
@@ -145,51 +150,83 @@ tab_tlg_server <- function(id, data, adpp = reactive(NULL)) {
observeEvent(selected_tlg_state()$edit(), {
info <- selected_tlg_state()$edit()
+ # info$column is the display-frame column (reactable.extras reports the
+ # column name; older versions report a positional index). Resolve to a name
+ # and only ever write to an editable column, so a stray edit event can never
+ # overwrite an internal column (id/PKid/Condition/...) of the full frame.
+ editable_cols <- c("Footnote", "Stratification", "Comment")
+ col <- if (is.numeric(info$column)) names(displayed_order())[info$column] else info$column
+ req(col %in% editable_cols)
+
new_tlg_order <- tlg_order()
- new_tlg_order[new_tlg_order$Selection, ][info$row, info$column] <- info$value
+ new_tlg_order[new_tlg_order$Selection, ][info$row, col] <- info$value
tlg_order(new_tlg_order)
})
+ # Issue #1335: the "Add TLGs" picker is a catalog-style checklist -- dataset
+ # tabs (PK Concentrations / PK Parameters) over one column per Type (Tables /
+ # Listings / Graphs), with a search + download + select-all toolbar. The UI
+ # builder and helpers live in inst/shiny/functions/tlg_add_picker.R;
+ # client-side behaviour in inst/shiny/www/tlg_add_picker.js (window.tlgAdd);
+ # styling in inst/shiny/www/styles/partials/_tlg_add_modal.scss.
+ # modal_group_ids -- checkboxGroupInput ids in the current modal (read on confirm)
+ # modal_avail -- the available-TLG tibble backing the CSV/XLSX downloads
+ modal_group_ids <- reactiveVal(character(0))
+ modal_avail <- reactiveVal(NULL)
+
# Show modal when the add_tlg button is pressed
observeEvent(input$add_tlg, {
+ avail <- dplyr::arrange(dplyr::filter(tlg_order(), !Selection), Type, Dataset)
+ modal_avail(avail)
+
+ body <- if (nrow(avail) == 0) {
+ modal_group_ids(character(0))
+ tags$p("All available TLGs are already in the order.")
+ } else {
+ checklist <- build_add_checklist(avail, session$ns)
+ modal_group_ids(checklist$group_ids)
+ checklist$ui
+ }
+
showModal(modalDialog(
title = div(
- "Add TLGs to Order",
+ "Add TLGs to order",
js_close_button,
style = "position: relative;"
),
- reactable_ui(session$ns("modal_tlg_table")),
+ body,
footer = tagList(
modalButton("Close"),
- actionButton(session$ns("confirm_add_tlg"), "Add TLGs to Order")
+ uiOutput(session$ns("modal_confirm_ui"), inline = TRUE)
),
size = "l"
))
})
- modal_tlg_state <- reactable_server(
- "modal_tlg_table",
- reactive({
- dplyr::filter(tlg_order(), !Selection) %>%
- dplyr::select(-id, -Selection, -Footnote, -Stratification, -Condition, -Comment)
- }),
- download_buttons = c("csv", "xlsx"),
- groupBy = c("Type", "Dataset"),
- wrap = TRUE,
- selection = "multiple",
- defaultExpanded = TRUE,
- width = "775px", # fit to the modal width
- columns = function(df) {
- define_cols(df, overrides = list(Output = colDef(html = TRUE)))
- }
+ # Download the available-TLG catalog shown in the modal.
+ output$modal_dl_csv <- downloadHandler(
+ filename = function() "available_tlgs.csv",
+ content = function(file) write.csv(tlg_modal_dl_data(modal_avail()), file, row.names = FALSE)
+ )
+ output$modal_dl_xlsx <- downloadHandler(
+ filename = function() "available_tlgs.xlsx",
+ content = function(file) writexl::write_xlsx(tlg_modal_dl_data(modal_avail()), file)
)
+ # Confirm button with a live count of checked outputs; disabled at zero.
+ output$modal_confirm_ui <- renderUI({
+ n <- length(checked_tlg_ids(input, modal_group_ids()))
+ label <- if (n == 0) "Add to order" else paste0("Add ", n, " to order")
+ btn <- actionButton(session$ns("confirm_add_tlg"), label, class = "btn-primary")
+ if (n == 0) shinyjs::disabled(btn) else btn
+ })
+
# Update the Selection column when the confirm_add_tlg button is pressed
observeEvent(input$confirm_add_tlg, {
- selected_rows <- modal_tlg_state()$selected
- if (length(selected_rows) > 0) {
+ checked_ids <- checked_tlg_ids(input, modal_group_ids())
+ if (length(checked_ids) > 0) {
tlg_order_data <- tlg_order()
- tlg_order_data$Selection[!tlg_order_data$Selection][selected_rows] <- TRUE
+ tlg_order_data$Selection[tlg_order_data$id %in% checked_ids] <- TRUE
tlg_order(tlg_order_data)
}
removeModal()
@@ -252,6 +289,18 @@ tab_tlg_server <- function(id, data, adpp = reactive(NULL)) {
apply_labels(data()$conc$data, type = "ADNCA")
})
adpp_data_all <- reactive({
+ # A PK-parameter (ADPP) output was requested but NCA has not been run, so
+ # ADPP is unavailable. Surface it as a toast (Gero, #1335) in addition to
+ # the inline placeholder, since the empty panel alone reads as a silent
+ # failure.
+ if (is.null(adpp())) {
+ # Fixed id so multiple ADPP panels collapse into one toast rather than
+ # stacking an identical message per output.
+ showNotification(
+ "ADPP data is not available. Run NCA first to view PK parameter outputs.",
+ type = "warning", duration = 10, id = session$ns("adpp_missing")
+ )
+ }
validate(need(
!is.null(adpp()),
"ADPP data is not available. Run NCA first to view PK parameter outputs."
diff --git a/inst/shiny/modules/tab_tlg/tlg_module.R b/inst/shiny/modules/tab_tlg/tlg_module.R
index 5d3c478b6..054b352e3 100644
--- a/inst/shiny/modules/tab_tlg/tlg_module.R
+++ b/inst/shiny/modules/tab_tlg/tlg_module.R
@@ -299,7 +299,19 @@ tlg_module_server <- function(id, data, type, render_list, options = NULL, # nol
# the PKNCA/dplyr pipeline strips column `label` attributes, which breaks
# the `!COLUMN` label-reference syntax in title/subtitle/footnote/axis
# inputs (resolved via parse_annotation).
- do.call(render_list, purrr::list_modify(list(data = data()), !!!list_options))
+ #
+ # Surface warnings from the render function (e.g. urine TLGs warning that
+ # PCSPEC/PPSPEC is absent so no specimen filtering was applied) as app
+ # notifications, then muffle so rendering continues with the result.
+ withCallingHandlers(
+ do.call(render_list, purrr::list_modify(list(data = data()), !!!list_options)),
+ warning = function(w) {
+ showNotification(
+ paste0("Notice: ", conditionMessage(w)), type = "warning", duration = 10
+ )
+ invokeRestart("muffleWarning")
+ }
+ )
},
error = function(e) {
log_error("Error in list rendering:")
diff --git a/inst/shiny/www/main.css b/inst/shiny/www/main.css
index 6c1c76b14..7d924ab72 100644
--- a/inst/shiny/www/main.css
+++ b/inst/shiny/www/main.css
@@ -1187,3 +1187,200 @@ tbody tr:hover td.param-matrix-row-header {
.ratio-adj-factor {
flex-shrink: 0;
}
+
+.tlg-add-modal {
+ --tlg-inset: 0.55em;
+}
+
+.tlg-add-modal .tlg-toolbar {
+ display: flex;
+ align-items: center;
+ gap: 0.5em;
+ flex-wrap: wrap;
+ margin: 0 0 1.25em;
+ padding-left: var(--tlg-inset);
+}
+
+.tlg-add-modal .tlg-search-input {
+ width: 300px;
+ max-width: 100%;
+}
+
+.tlg-add-modal .tlg-toolbar-sep {
+ width: 1px;
+ align-self: stretch;
+ background: #e5e5e5;
+ margin: 0.1em 0.35em;
+}
+
+.tlg-add-modal .tlg-tabs {
+ display: flex;
+ gap: 0.25em;
+ margin: 0 0 1.25em;
+ padding-left: var(--tlg-inset);
+ border-bottom: 1px solid #e5e5e5;
+}
+
+.tlg-tab {
+ background: none;
+ border: none;
+ padding: 0.5em 0.9em;
+ font-weight: 600;
+ color: #7b8794;
+ border-bottom: 2px solid transparent;
+ margin-bottom: -1px;
+ cursor: pointer;
+}
+
+.tlg-tab:hover {
+ color: #21201f;
+}
+
+.tlg-tab.active {
+ color: #007bc2;
+ border-bottom-color: #007bc2;
+}
+
+.tlg-tab-count {
+ color: #8a8f98;
+ font-weight: 600;
+ font-size: 0.8em;
+ margin-left: 0.35em;
+}
+
+.tlg-cols {
+ display: flex;
+ align-items: flex-start;
+ gap: 1.5em;
+}
+
+.tlg-cols .tlg-col {
+ flex: 1 1 0;
+ min-width: 0;
+}
+
+.tlg-cols .tlg-col + .tlg-col {
+ border-left: 1px solid #eee;
+ padding-left: 1.5em;
+}
+
+.tlg-col-body {
+ max-height: 55vh;
+ overflow-y: auto;
+}
+
+.tlg-col-empty {
+ color: #8a8f98;
+ font-style: italic;
+ font-size: 0.85em;
+ padding: 0.6em var(--tlg-inset);
+}
+
+.tlg-add-checklist .tlg-col-head {
+ display: flex;
+ align-items: baseline;
+ margin: 0 0 0.75em;
+ padding: 0 var(--tlg-inset) 0.4em;
+ border-bottom: 2px solid #007bc2;
+}
+
+.tlg-add-checklist .tlg-col-title {
+ flex: 1 1 auto;
+ font-size: 1em;
+ font-weight: 700;
+ color: #21201f;
+}
+
+.tlg-add-checklist .tlg-col-head svg,
+.tlg-add-checklist .tlg-col-head .fa {
+ color: #007bc2;
+ margin-right: 0.3em;
+}
+
+.tlg-add-checklist .tlg-col-count {
+ color: #8a8f98;
+ font-weight: 600;
+ font-size: 0.82em;
+ margin-left: 0.25em;
+}
+
+.tlg-add-checklist .tlg-ds {
+ margin-bottom: 0.5em;
+}
+
+.tlg-add-checklist .checkbox {
+ margin: 0;
+ padding: 0.4em var(--tlg-inset);
+ border-radius: 5px;
+ transition: background 0.1s;
+}
+
+.tlg-add-checklist .checkbox:hover {
+ background: #f2f6fb;
+}
+
+.tlg-add-checklist .checkbox:has(input:checked) {
+ background: #E7ECFA;
+}
+
+.tlg-add-checklist .checkbox label {
+ display: flex;
+ align-items: flex-start;
+ gap: 0.55em;
+ text-align: left;
+ font-weight: normal;
+ line-height: 1.4;
+ padding-left: 0;
+ color: #21201f;
+ cursor: pointer;
+}
+
+.tlg-add-checklist .checkbox label > span {
+ flex: 1 1 auto;
+ display: flex;
+ align-items: flex-start;
+ justify-content: space-between;
+ gap: 0.5em;
+}
+
+.tlg-add-checklist .checkbox input[type="checkbox"] {
+ position: static;
+ margin: 0.22em 0 0;
+ flex: 0 0 auto;
+ width: 15px;
+ height: 15px;
+ accent-color: #007bc2;
+ cursor: pointer;
+}
+
+.tlg-add-checklist .tlg-spec {
+ flex: 0 0 auto;
+ color: #b0b7bf;
+ margin-top: 0.1em;
+}
+
+.tlg-add-checklist .tlg-spec:hover {
+ color: #007bc2;
+}
+
+.tlg-col-selall {
+ flex: 0 0 auto;
+ background: none;
+ border: none;
+ color: #007bc2;
+ font-size: 0.76em;
+ font-weight: 600;
+ cursor: pointer;
+ padding: 0;
+}
+
+.tlg-col-selall:hover {
+ text-decoration: underline;
+}
+
+.tlg-no-matches {
+ color: #8a8f98;
+ font-style: italic;
+ padding: 1em 0.5em;
+ padding-left: var(--tlg-inset);
+}
diff --git a/inst/shiny/www/styles/main.scss b/inst/shiny/www/styles/main.scss
index 3a05ccbe8..37ab40559 100644
--- a/inst/shiny/www/styles/main.scss
+++ b/inst/shiny/www/styles/main.scss
@@ -11,4 +11,5 @@
@import "partials/_loading_spinner";
@import "partials/_non_nca_analysis";
@import "partials/_parameter_matrix";
-@import "partials/_ratio_formula";
\ No newline at end of file
+@import "partials/_ratio_formula";
+@import "partials/_tlg_add_modal";
\ No newline at end of file
diff --git a/inst/shiny/www/styles/partials/_tlg_add_modal.scss b/inst/shiny/www/styles/partials/_tlg_add_modal.scss
new file mode 100644
index 000000000..23e3f002e
--- /dev/null
+++ b/inst/shiny/www/styles/partials/_tlg_add_modal.scss
@@ -0,0 +1,201 @@
+// "Add TLGs to order" modal: catalog checklist (dataset tabs over Type columns).
+// Brand colors come from styles/modules/_colors.scss tokens; the neutral greys
+// are modal-local one-offs with no shared token and are kept as literals.
+.tlg-add-modal {
+ --tlg-inset: 0.55em;
+
+ .tlg-toolbar {
+ display: flex;
+ align-items: center;
+ gap: 0.5em;
+ flex-wrap: wrap;
+ margin: 0 0 1.25em;
+ padding-left: var(--tlg-inset);
+ }
+
+ .tlg-search-input {
+ width: 300px;
+ max-width: 100%;
+ }
+
+ .tlg-toolbar-sep {
+ width: 1px;
+ align-self: stretch;
+ background: #e5e5e5;
+ margin: 0.1em 0.35em;
+ }
+
+ .tlg-tabs {
+ display: flex;
+ gap: 0.25em;
+ margin: 0 0 1.25em;
+ padding-left: var(--tlg-inset);
+ border-bottom: 1px solid #e5e5e5;
+ }
+}
+
+.tlg-tab {
+ background: none;
+ border: none;
+ padding: 0.5em 0.9em;
+ font-weight: 600;
+ color: #7b8794;
+ border-bottom: 2px solid transparent;
+ margin-bottom: -1px;
+ cursor: pointer;
+
+ &:hover {
+ color: $anca-black-2;
+ }
+
+ &.active {
+ color: $anca-blue;
+ border-bottom-color: $anca-blue;
+ }
+}
+
+.tlg-tab-count {
+ color: #8a8f98;
+ font-weight: 600;
+ font-size: 0.8em;
+ margin-left: 0.35em;
+}
+
+.tlg-cols {
+ display: flex;
+ align-items: flex-start;
+ gap: 1.5em;
+
+ .tlg-col {
+ flex: 1 1 0;
+ min-width: 0;
+ }
+
+ .tlg-col + .tlg-col {
+ border-left: 1px solid #eee;
+ padding-left: 1.5em;
+ }
+}
+
+.tlg-col-body {
+ max-height: 55vh;
+ overflow-y: auto;
+}
+
+.tlg-col-empty {
+ color: #8a8f98;
+ font-style: italic;
+ font-size: 0.85em;
+ padding: 0.6em var(--tlg-inset);
+}
+
+.tlg-add-checklist {
+ .tlg-col-head {
+ display: flex;
+ align-items: baseline;
+ margin: 0 0 0.75em;
+ padding: 0 var(--tlg-inset) 0.4em;
+ border-bottom: 2px solid $anca-blue;
+ }
+
+ .tlg-col-title {
+ flex: 1 1 auto;
+ font-size: 1em;
+ font-weight: 700;
+ color: $anca-black-2;
+ }
+
+ .tlg-col-head svg,
+ .tlg-col-head .fa {
+ color: $anca-blue;
+ margin-right: 0.3em;
+ }
+
+ .tlg-col-count {
+ color: #8a8f98;
+ font-weight: 600;
+ font-size: 0.82em;
+ margin-left: 0.25em;
+ }
+
+ .tlg-ds {
+ margin-bottom: 0.5em;
+ }
+
+ .checkbox {
+ margin: 0;
+ padding: 0.4em var(--tlg-inset);
+ border-radius: 5px;
+ transition: background 0.1s;
+
+ &:hover {
+ background: #f2f6fb;
+ }
+
+ &:has(input:checked) {
+ background: $anca-blue-light;
+ }
+
+ label {
+ display: flex;
+ align-items: flex-start;
+ gap: 0.55em;
+ text-align: left;
+ font-weight: normal;
+ line-height: 1.4;
+ padding-left: 0;
+ color: $anca-black-2;
+ cursor: pointer;
+ }
+
+ label > span {
+ flex: 1 1 auto;
+ display: flex;
+ align-items: flex-start;
+ justify-content: space-between;
+ gap: 0.5em;
+ }
+
+ input[type="checkbox"] {
+ position: static;
+ margin: 0.22em 0 0;
+ flex: 0 0 auto;
+ width: 15px;
+ height: 15px;
+ accent-color: $anca-blue;
+ cursor: pointer;
+ }
+ }
+
+ .tlg-spec {
+ flex: 0 0 auto;
+ color: #b0b7bf;
+ margin-top: 0.1em;
+
+ &:hover {
+ color: $anca-blue;
+ }
+ }
+}
+
+.tlg-col-selall {
+ flex: 0 0 auto;
+ background: none;
+ border: none;
+ color: $anca-blue;
+ font-size: 0.76em;
+ font-weight: 600;
+ cursor: pointer;
+ padding: 0;
+
+ &:hover {
+ text-decoration: underline;
+ }
+}
+
+.tlg-no-matches {
+ color: #8a8f98;
+ font-style: italic;
+ padding: 1em 0.5em;
+ padding-left: var(--tlg-inset);
+}
diff --git a/inst/shiny/www/tlg_add_picker.js b/inst/shiny/www/tlg_add_picker.js
new file mode 100644
index 000000000..91e4dd13a
--- /dev/null
+++ b/inst/shiny/www/tlg_add_picker.js
@@ -0,0 +1,123 @@
+// Client-side behaviour for the "Add TLGs to order" modal (see
+// inst/shiny/functions/tlg_add_picker.R). The modal shows dataset tabs
+// (PK Concentrations / PK Parameters) over one column per output Type; this
+// object drives search, tab switching, and the select-all helpers. The
+// per-open initialisation (active tab + first render) is injected inline by the
+// R helper because it depends on the datasets present in the current modal.
+window.tlgAdd = {
+ q: "",
+ tab: null,
+
+ // Toggle checkboxes within `scope`. `mode` standardises what "all" means so
+ // the toolbar buttons behave consistently (issue #1335):
+ // "search" -> every row matching the current search, across BOTH dataset
+ // tabs. A tab is only a view, so the toolbar Select-all /
+ // Clear-all act on the whole order; search is an intentional
+ // filter, so they honour it (rows flagged .tlg-nomatch by
+ // render() are skipped).
+ // "visible" -> only rows currently shown (active tab AND search): used by
+ // the per-column "Select all", the granular scoped tool.
+ _setChecked: function(scope, checked, mode) {
+ var groups = {};
+ scope.querySelectorAll(".checkbox").forEach(function(row) {
+ if (mode === "visible" && row.style.display === "none") return;
+ if (mode === "search" && row.classList.contains("tlg-nomatch")) return;
+ var cb = row.querySelector("input[type=checkbox]");
+ if (!cb) return;
+ cb.checked = checked;
+ var g = cb.closest(".shiny-input-checkboxgroup");
+ if (g) groups[g.id] = g;
+ });
+ Object.keys(groups).forEach(function(id) {
+ var inp = groups[id].querySelector("input[type=checkbox]");
+ if (inp) inp.dispatchEvent(new Event("change", { bubbles: true }));
+ });
+ },
+
+ selectAll: function() {
+ var r = document.querySelector(".tlg-add-checklist");
+ if (r) this._setChecked(r, true, "search");
+ },
+
+ clearAll: function() {
+ var r = document.querySelector(".tlg-add-checklist");
+ if (r) this._setChecked(r, false, "search");
+ },
+
+ colSelect: function(btn) {
+ var c = btn.closest(".tlg-col");
+ if (c) this._setChecked(c, true, "visible");
+ },
+
+ setQuery: function(v) {
+ this.q = v || "";
+ this.render();
+ },
+
+ setTab: function(v, btn) {
+ this.tab = v;
+ document.querySelectorAll(".tlg-tabs .tlg-tab").forEach(function(b) {
+ b.classList.remove("active");
+ });
+ if (btn) btn.classList.add("active");
+ this.render();
+ },
+
+ render: function() {
+ var root = document.querySelector(".tlg-add-checklist");
+ if (!root) return;
+ var q = this.q.trim().toLowerCase();
+ var tab = this.tab;
+ // Per-dataset text-match counts are computed independently of the active
+ // tab (they drive the tab badges), but only the active tab's matches are
+ // shown. This way searching in a term that only matches another dataset
+ // surfaces the count on that tab's badge -- clicking it reveals the match
+ // -- instead of silently showing another dataset's rows under this tab.
+ var dsMatch = {};
+ var totalMatches = 0;
+ root.querySelectorAll(".tlg-ds").forEach(function(ds) {
+ var name = ds.getAttribute("data-dataset");
+ var isActive = name === tab;
+ var anyVisible = false;
+ ds.querySelectorAll(".checkbox").forEach(function(it) {
+ var textMatch = q === "" || it.textContent.toLowerCase().indexOf(q) > -1;
+ // Flag search-match independently of the active tab, so the toolbar
+ // Select-all / Clear-all ("search" mode) can reach matches on the
+ // other dataset tab too (issue #1335).
+ it.classList.toggle("tlg-nomatch", !textMatch);
+ if (textMatch) {
+ dsMatch[name] = (dsMatch[name] || 0) + 1;
+ totalMatches++;
+ }
+ var show = isActive && textMatch;
+ it.style.display = show ? "" : "none";
+ if (show) anyVisible = true;
+ });
+ ds.style.display = anyVisible ? "" : "none";
+ });
+ // Per-column: visible count, empty state, hide select-all when empty.
+ root.querySelectorAll(".tlg-col").forEach(function(col) {
+ var vis = 0;
+ col.querySelectorAll(".checkbox").forEach(function(it) {
+ if (it.style.display !== "none") vis++;
+ });
+ var cnt = col.querySelector(".tlg-col-count");
+ if (cnt) cnt.textContent = vis;
+ var empty = col.querySelector(".tlg-col-empty");
+ if (empty) empty.style.display = vis ? "none" : "";
+ var sa = col.querySelector(".tlg-col-selall");
+ if (sa) sa.style.display = vis ? "" : "none";
+ });
+ // Tab badges: per-dataset match count while searching, dataset total otherwise.
+ document.querySelectorAll(".tlg-tabs .tlg-tab").forEach(function(t) {
+ var badge = t.querySelector(".tlg-tab-count");
+ if (!badge) return;
+ badge.textContent = q === ""
+ ? t.getAttribute("data-total")
+ : (dsMatch[t.getAttribute("data-dataset")] || 0);
+ });
+ // Global "no matches" message only when nothing matches in any dataset.
+ var nm = document.querySelector(".tlg-no-matches");
+ if (nm) nm.style.display = totalMatches === 0 ? "" : "none";
+ }
+};
diff --git a/tests/testthat/test-tab_tlg.R b/tests/testthat/test-tab_tlg.R
index 933e230ba..0d47ec85e 100644
--- a/tests/testthat/test-tab_tlg.R
+++ b/tests/testthat/test-tab_tlg.R
@@ -1,15 +1,20 @@
-# Boundary behaviour of tab_tlg_server. The TLG modules receive an
-# already-exclusion-filtered, label-restored plain data frame; the filtering
-# and label restoration happen here (not inside tlg_module_server).
+# Server-side tests for tab_tlg_server:
+# - add-picker selection, removal, and the Order Details edit write-back (issue #1335)
+# - data boundary: the TLG modules receive an already-exclusion-filtered,
+# label-restored plain data frame; the filtering and label restoration happen
+# here, not inside tlg_module_server (issue #1336 / #1356).
# Source the tab_tlg module and its server-side dependencies.
local({
library(shiny)
+ library(dplyr)
+ library(purrr)
library(logger)
library(reactable)
- library(dplyr)
+ library(reactable.extras)
shiny_dir <- system.file("shiny", package = "aNCA")
for (f in list(
+ c("functions", "tlg_add_picker.R"),
c("modules", "tab_tlg", "tlg_module.R"),
c("modules", "tab_tlg", "tlg_option_select.R"),
c("modules", "common", "reactable.R"),
@@ -20,6 +25,79 @@ local({
},
envir = parent.env(environment()))
+test_data <- reactive(list(conc = list(data = data.frame(
+ USUBJID = c("S1", "S2"),
+ PCSPEC = c("PLASMA", "PLASMA"),
+ AVAL = c(1, 2),
+ stringsAsFactors = FALSE
+))))
+
+describe("tab_tlg_server: add-picker selection", {
+ it("sets Selection = TRUE for exactly the checked ids on confirm", {
+ testServer(tab_tlg_server, args = list(data = test_data), {
+ session$flushReact()
+ target <- head(tlg_order()$id[!tlg_order()$Selection], 2)
+ expect_length(target, 2)
+
+ # The confirm handler reads modal_group_ids() and input[[gid]]; drive it
+ # directly (values not belonging to a real group are simply ignored by the
+ # id %in% checked_ids mapping).
+ modal_group_ids("grp")
+ session$setInputs(grp = as.character(target))
+ session$setInputs(confirm_add_tlg = 1)
+ session$flushReact()
+
+ expect_true(all(tlg_order()$Selection[tlg_order()$id %in% target]))
+ })
+ })
+
+ it("leaves Selection unchanged when nothing is checked", {
+ testServer(tab_tlg_server, args = list(data = test_data), {
+ session$flushReact()
+ before <- tlg_order()$Selection
+ modal_group_ids("grp")
+ session$setInputs(grp = character(0))
+ session$setInputs(confirm_add_tlg = 1)
+ session$flushReact()
+ expect_identical(tlg_order()$Selection, before)
+ })
+ })
+})
+
+describe("tab_tlg_server: Order Details edit write-back", {
+ it("writes an edited Footnote into the matching full-frame row", {
+ testServer(tab_tlg_server, args = list(data = test_data), {
+ session$flushReact()
+ # First selected (displayed) row maps to the first Selection == TRUE row.
+ first_id <- tlg_order()$id[tlg_order()$Selection][1]
+
+ # selected_tlg_state()$edit() is fed by the nested reactable module's
+ # edit_ input; set it through the namespaced id and clear the debounce.
+ session$setInputs(
+ `selected_tlg_table-edit_Footnote` = list(row = 1, column = "Footnote", value = "My note")
+ )
+ session$elapse(800)
+ session$flushReact()
+
+ row <- tlg_order()[tlg_order()$id == first_id, ]
+ expect_equal(row$Footnote, "My note")
+ })
+ })
+
+ it("ignores an edit targeting a non-editable column", {
+ testServer(tab_tlg_server, args = list(data = test_data), {
+ session$flushReact()
+ before <- tlg_order()
+ session$setInputs(
+ `selected_tlg_table-edit_Footnote` = list(row = 1, column = "Type", value = "HACKED")
+ )
+ session$elapse(800)
+ session$flushReact()
+ expect_identical(tlg_order()$Type, before$Type)
+ })
+ })
+})
+
describe("tab_tlg_server: data boundary", {
adnca_df <- data.frame(
USUBJID = c("S1", "S2"), AVAL = c(1, 2),
diff --git a/tests/testthat/test-tlg_add_picker.R b/tests/testthat/test-tlg_add_picker.R
new file mode 100644
index 000000000..1a004d89f
--- /dev/null
+++ b/tests/testthat/test-tlg_add_picker.R
@@ -0,0 +1,67 @@
+# Tests for the "Add TLGs to order" modal helpers (issue #1335).
+local({
+ library(shiny)
+ shiny_dir <- system.file("shiny", package = "aNCA")
+ source(file.path(shiny_dir, "functions", "tlg_add_picker.R"), local = TRUE)
+},
+envir = parent.env(environment()))
+
+avail_fixture <- function() {
+ dplyr::tibble(
+ id = c(2L, 5L, 9L),
+ Type = c("Table", "Listing", "Graph"),
+ Dataset = c("PK Concentrations", "PK Parameters", "PK Concentrations"),
+ PKid = c("pkct01", "pkcl01", "pkpg01"),
+ Description = c("Conc summary table", "Listing of parameters", "Cumulative plot"),
+ Link = c("http://spec/1", NA_character_, "http://spec/3")
+ )
+}
+
+describe("checked_tlg_ids", {
+ it("returns integer ids from the checked group inputs", {
+ input <- list(g1 = c("2", "9"), g2 = character(0))
+ expect_identical(checked_tlg_ids(input, c("g1", "g2")), c(2L, 9L))
+ })
+
+ it("returns an empty integer vector when nothing is checked", {
+ expect_identical(checked_tlg_ids(list(g1 = NULL), "g1"), integer(0))
+ })
+})
+
+describe("tlg_modal_dl_data", {
+ it("selects the catalog columns", {
+ out <- tlg_modal_dl_data(avail_fixture())
+ expect_equal(names(out), c("Type", "Dataset", "PKid", "Description"))
+ expect_equal(nrow(out), 3)
+ })
+
+ it("returns an empty typed frame for NULL or empty input", {
+ for (df in list(NULL, avail_fixture()[0, ])) {
+ empty <- tlg_modal_dl_data(df)
+ expect_equal(names(empty), c("Type", "Dataset", "PKid", "Description"))
+ expect_equal(nrow(empty), 0)
+ }
+ })
+})
+
+describe("build_add_checklist", {
+ it("creates one checkbox group per Type/Dataset pair and returns their ids", {
+ res <- build_add_checklist(avail_fixture(), ns = identity)
+
+ # 3 distinct Type/Dataset pairs -> 3 checkbox groups
+ expect_length(res$group_ids, 3)
+ expect_true(all(grepl("^modal_check_", res$group_ids)))
+
+ html <- as.character(res$ui)
+ # every output description is rendered
+ expect_true(grepl("Conc summary table", html))
+ expect_true(grepl("Listing of parameters", html))
+ expect_true(grepl("Cumulative plot", html))
+ # dataset tab bar + catalog checklist scaffolding present
+ expect_true(grepl("tlg-tabs", html))
+ expect_true(grepl("tlg-add-checklist", html))
+ # spec link only where Link is non-NA
+ expect_true(grepl("http://spec/1", html, fixed = TRUE))
+ expect_true(grepl("http://spec/3", html, fixed = TRUE))
+ })
+})
diff --git a/tests/testthat/test-tlg_module.R b/tests/testthat/test-tlg_module.R
index 474ed92c9..5ee8352a7 100644
--- a/tests/testthat/test-tlg_module.R
+++ b/tests/testthat/test-tlg_module.R
@@ -432,3 +432,48 @@ describe("tlg_module_server", {
)
})
})
+
+# ---------------------------------------------------------------------------
+# tlg_module_server: render-warning surfacing (issue #1335)
+# ---------------------------------------------------------------------------
+
+describe("tlg_module_server: warning surfacing", {
+ test_data <- shiny::reactive(
+ list(conc = list(data = data.frame(
+ NFRLT = 1:3, AVAL = c(5, 4, 3), stringsAsFactors = FALSE
+ )))
+ )
+ # Emits a warning (e.g. a urine TLG reporting PCSPEC/PPSPEC is absent) but
+ # still returns a result.
+ render_list_warns <- function(data, ...) {
+ warning("PCSPEC/PPSPEC not found; specimen filtering skipped")
+ list("plot_a")
+ }
+
+ it("muffles render warnings, notifies with a 'Notice:' prefix, and continues", {
+ notes <- character(0)
+ mockery::stub(
+ tlg_module_server, "showNotification",
+ function(ui, ...) notes[[length(notes) + 1]] <<- ui
+ )
+ shiny::testServer(
+ tlg_module_server,
+ args = list(
+ data = test_data,
+ type = "graph",
+ render_list = render_list_warns,
+ options = list()
+ ),
+ {
+ session$setInputs(entries_per_page = "All")
+ session$elapse(800) # clear the debounce(750)
+ # Muffled: rendering continued and produced the returned list.
+ expect_equal(tlg_list(), list("plot_a"))
+ }
+ )
+ # The warning was surfaced to the user with the friendlier prefix.
+ expect_length(notes, 1)
+ expect_match(notes[[1]], "^Notice: ")
+ expect_match(notes[[1]], "specimen filtering skipped")
+ })
+})