Enhancement: Integrate settings upload in Data tab

inst/shiny/app.R

@@ -152,7 +152,8 @@ server <- function(input, output, session) {
   tab_nca_outputs <- tab_nca_server(
     "nca",
     tab_data_outputs$pknca_data,
-    tab_data_outputs$extra_group_vars
+    tab_data_outputs$extra_group_vars,
+    tab_data_outputs$settings_override
   )
 
   # TLG

inst/shiny/modules/tab_data.R

@@ -120,12 +120,12 @@ tab_data_server <- function(id) {
       updateTabsetPanel(session, "data_navset", selected = step_labels[idx - 1])
     })
     #' Load raw ADNCA data
-    adnca_raw <- data_upload_server("raw_data")
+    uploaded_data <- data_upload_server("raw_data")
 
     # Call the column mapping module
     column_mapping <- data_mapping_server(
       id = "column_mapping",
-      adnca_data = adnca_raw,
+      adnca_data = uploaded_data$adnca_raw,
       trigger = trigger_mapping_submit
     )
     #' Reactive value for the processed dataset
@@ -223,7 +223,8 @@ tab_data_server <- function(id) {
 
     list(
       pknca_data = pknca_data,
-      extra_group_vars = extra_group_vars
+      extra_group_vars = extra_group_vars,
+      settings_override = uploaded_data$settings_override
     )
   })
 }

inst/shiny/modules/tab_data/data_upload.R

@@ -15,7 +15,7 @@ data_upload_ui <- function(id) {
     div(
       class = "upload-container",
       id = ns("upload_container"),
-      p("Upload your PK dataset."),
+      p("Upload your PK dataset and Settings file (optional)."),
       fileInput(
         ns("data_upload"),
         width = "50%",
@@ -41,6 +41,7 @@ data_upload_server <- function(id) {
 
     #' Display file loading error if any issues arise
     file_loading_error <- reactiveVal(NULL)
+    settings_override <- reactiveVal(NULL) # Store loaded settings
 
     output$file_loading_message <- renderUI({
       if (is.null(file_loading_error())) {
@@ -71,27 +72,65 @@ data_upload_server <- function(id) {
           filenames <- input$data_upload$name
         }
 
-        # Iterate over files: Read and classify
+        # Iterate over files: Try reading as Data, then as Settings
         read_results <- purrr::map2(paths, filenames, function(path, name) {
           tryCatch({
             # Attempt to read
             data <- read_pk(path)
             list(status = "success", data = data, name = name, type = "data")
-          }, error = function(e) {
-            # TODO: @Jana, check if settings file is loaded and then create settings override (719)
-            list(status = "error", message = e$message, name = name)
+          }, error = function(e_pk) {
+            # If read_pk fails
+            # check if settings file is loaded and then create settings override
+            tryCatch({
+              # check if error aligns with what we expect for setttings file
+              if (conditionMessage(e_pk) != "Invalid data format.
+                  Data frame was expected, but received list.") {
+                return(list(status = "error", msg = conditionMessage(e_pk), name = name))
+              }
+
+              obj <- readRDS(path)
+              # Check for settings
+              is_settings <- is.list(obj) && "settings" %in% names(obj)
+
+              if (!is_settings) {
+                stop(conditionMessage(e_pk))
+              }
+
+              list(status = "success", type = "settings", content = obj, name = name)
+            }, error = function(e_rds) {
+              list(status = "error", msg = conditionMessage(e_pk), name = name)
+            })
           })
         })
 
         # Process results
-        successful_loads <- purrr::keep(read_results, ~ .x$status == "success")
+        successful_loads <- purrr::keep(read_results, \(x) x$status == "success")
         errors <- purrr::keep(read_results, \(x) x$status == "error") %>%
-          purrr::map(\(x) paste0(x$name, ": ", x$message))
+          purrr::map(\(x) paste0(x$name, ": ", x$msg))
+
+        # Extract and apply settings if any found
+        found_settings <- purrr::keep(successful_loads, \(x) x$type == "settings")
+
+        if (length(found_settings) > 1) {
+          # Error: Too many settings files
+          errors <- append(errors, "Error: Multiple settings files detected.
+                           Please upload only one settings file.")
+          # Do not apply any settings if ambiguous
+          settings_override(NULL)
+
+        } else if (length(found_settings) == 1) {
+          # Success: Single settings file
+          latest <- found_settings[[1]]
+          settings_override(latest$content)
+          log_success("Settings successfully loaded from ", latest$name)
+          showNotification(paste("Settings successfully loaded."), type = "message")
+        }
 
         loaded_data <- DUMMY_DATA
 
+        found_data <- purrr::keep(successful_loads, \(x) x$type == "data")
         # Handle Errors
-        if (length(successful_loads) > 0) {
+        if (length(found_data) > 0) {
           tryCatch({
             loaded_data <- successful_loads %>%
               purrr::map("data") %>%
@@ -127,6 +166,9 @@ data_upload_server <- function(id) {
       style = list(fontSize = "0.75em")
     )
 
-    raw_data
+    list(
+      adnca_raw = raw_data,
+      settings_override = settings_override
+    )
   })
 }

inst/shiny/modules/tab_nca.R

@@ -62,7 +62,7 @@ tab_nca_ui <- function(id) {
   )
 }
 
-tab_nca_server <- function(id, pknca_data, extra_group_vars) {
+tab_nca_server <- function(id, pknca_data, extra_group_vars, settings_override) {
   moduleServer(id, function(input, output, session) {
     ns <- session$ns
 
@@ -74,7 +74,7 @@ tab_nca_server <- function(id, pknca_data, extra_group_vars) {
     adnca_data <- reactive(pknca_data()$conc$data)
 
     # #' NCA Setup module
-    nca_setup <- setup_server("nca_setup", adnca_data, pknca_data)
+    nca_setup <- setup_server("nca_setup", adnca_data, pknca_data, settings_override)
 
     processed_pknca_data <- nca_setup$processed_pknca_data
     settings <- nca_setup$settings

inst/shiny/modules/tab_nca/setup.R

@@ -21,20 +21,9 @@ setup_ui <- function(id) {
     nav_panel(
       "Settings",
       fluidRow(
-        column(6,
-          fileInput(
-            ns("settings_upload"),
-            width = "100%",
-            label = "Upload settings",
-            buttonLabel = list(icon("folder"), "Browse"),
-            accept = ".rds"
-          )
-        ),
-        column(6,
-          downloadButton(
-            ns("settings_download"),
-            label = "Download settings"
-          )
+        downloadButton(
+          ns("settings_download"),
+          label = "Download settings"
         )
       ),
       fluidRow(units_table_ui(ns("units_table"))),
@@ -53,25 +42,20 @@ setup_ui <- function(id) {
   )
 }
 
-setup_server <- function(id, data, adnca_data) {
+setup_server <- function(id, data, adnca_data, settings_override) {
   moduleServer(id, function(input, output, session) {
 
-    imported_settings <- reactive({
-      req(input$settings_upload)
-      readRDS(input$settings_upload$datapath)
-    })
-
-    settings_override <- reactive(imported_settings()$settings)
-    manual_slopes_override <- reactive(imported_settings()$slope_rules)
-    parameters_override <- reactive(imported_settings()$settings$parameter_selections)
-    general_excl_override <- reactive(imported_settings()$settings$general_exclusions)
+    imported_settings <- reactive(settings_override()$settings)
+    imported_slopes <- reactive(settings_override()$slope_rules)
+    imported_params <- reactive(imported_settings()$parameter_selections)
+    general_excl_override <- reactive(imported_settings()$general_exclusions)
 
     # Gather all settings from the appropriate module
     settings <- settings_server(
       "nca_settings",
       data,
       adnca_data,
-      settings_override
+      imported_settings
     )
 
     general_exclusions <- general_exclusions_server("general_exclusions", processed_pknca_data)
@@ -104,7 +88,7 @@ setup_server <- function(id, data, adnca_data) {
     parameters_output <- parameter_selection_server(
       "nca_setup_parameter",
       base_pknca_data,
-      parameters_override
+      imported_params
     )
 
     final_settings <- reactive({
@@ -151,9 +135,9 @@ setup_server <- function(id, data, adnca_data) {
     session$userData$ratio_table <- reactive(ratio_table())
 
     # Automatically update the units table when settings are uploaded.
-    observeEvent(settings_override(), {
-      req(settings_override()$units)
-      session$userData$units_table(settings_override()$units)
+    observeEvent(imported_settings(), {
+      req(imported_settings()$units)
+      session$userData$units_table(imported_settings()$units)
     })
 
     # Parameter unit changes option: Opens a modal message with a units table to edit
@@ -189,7 +173,7 @@ setup_server <- function(id, data, adnca_data) {
     slope_rules <- slope_selector_server(
       "slope_selector",
       slopes_pknca_data,
-      manual_slopes_override
+      imported_slopes
     )
 
     # Handle downloading and uploading settings

inst/shiny/modules/tab_nca/setup/parameter_selection.R

@@ -265,7 +265,6 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       # Validation checks
       if (length(study_type_names) == 0) return(list())
       req(all(study_type_names %in% names(df)))
-
       # Convert from wide to long, filter for selected rows,
       # and then split the result into a list by study_type.
       df %>%