From 25756817263a4b576f5951721ad0a6abde9a644d Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Mon, 15 Dec 2025 13:12:50 +0100
Subject: [PATCH 01/25] feat: settings upload v1 not working because settings
 file wrong

---
 inst/shiny/app.R                          |  3 +-
 inst/shiny/modules/tab_data.R             |  7 +--
 inst/shiny/modules/tab_data/data_upload.R | 55 ++++++++++++++++++++---
 inst/shiny/modules/tab_nca.R              |  4 +-
 inst/shiny/modules/tab_nca/setup.R        |  2 +-
 5 files changed, 57 insertions(+), 14 deletions(-)

diff --git a/inst/shiny/app.R b/inst/shiny/app.R
index 2ef02386a..1c26d4bc4 100644
--- a/inst/shiny/app.R
+++ b/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
diff --git a/inst/shiny/modules/tab_data.R b/inst/shiny/modules/tab_data.R
index 008558c68..f054ad787 100644
--- a/inst/shiny/modules/tab_data.R
+++ b/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
     )
   })
 }
diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 7a9ceda07..75d10c0b8 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -41,7 +41,8 @@ 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$file_loading_message <- renderUI({
       if (is.null(file_loading_error())) {
         p("")
@@ -71,22 +72,59 @@ data_upload_server <- function(id) {
           filenames <- input$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) {
+          }, error = function(e_pk) {
             # If read_pk fails
-            # TODO: @Jana, check if settings file is loaded and then create settings override (719)
-            list(status = "error", message = e$message, name = name)
+            # check if settings file is loaded and then create settings override
+            tryCatch({
+              obj <- readRDS(path)
+
+              # Check for settings
+              is_settings <- is.list(obj) && "settings" %in% names(obj)
+              
+              final_settings <- if (is_settings) obj else NULL
+              
+              if (!is.null(final_settings)) {
+                list(status = "success", type = "settings", content = final_settings, name = name)
+              } else {
+                # Not a settings file either, return original PK error
+                stop(e_pk$message)
+              }
+            }, error = function(e_rds) {
+              # Return the original read_pk error to the user
+              list(status = "error", msg = e_pk$message, name = name)
+            })
           })
         })
 
         # Process results
         successful_loads <- purrr::keep(read_results, ~ .x$status == "success")
         errors <- purrr::keep(read_results, ~ .x$status == "error")
+        
+        # Extract and apply settings if any found
+        found_settings <- purrr::keep(successful_loads, ~ .x$type == "settings")
+        
+        if (length(found_settings) > 1) {
+          # Error: Too many settings files
+          msg <- "Error: Multiple settings files detected. Please upload only one settings file."
+          prev_msgs <- if (length(errors) > 0) paste(purrr::map_chr(errors, ~ paste0(.x$name, ": ", .x$msg)), collapse = "<br>") else ""
+          file_loading_error(paste(c(prev_msgs, msg), collapse = "<br>"))
+          
+          # Do not apply any settings if ambiguous
+          settings_override(NULL)
+          
+        } else if (length(found_settings) == 1) {
+          # Success: Single settings file
+          latest <- found_settings[[1]]
+          settings_override(latest$content)
+          log_success("Settings successfully loaded from ", latest$name)
+          showNotification(paste("Settings successfully loaded."), type = "message")
+        }
 
         # Handle Errors
         if (length(successful_loads) == 0) {
@@ -105,7 +143,7 @@ data_upload_server <- function(id) {
             if (length(errors) > 0) {
               error_msgs <- purrr::map_chr(errors, ~ paste0(.x$name, ": ", .x$msg))
               file_loading_error(paste(error_msgs, collapse = "<br>"))
-              log_warning("Some files failed to load: ", paste(error_msgs, collapse = "; "))
+              log_warn("Some files failed to load: ", paste(error_msgs, collapse = "; "))
             } else {
               log_success("All user data loaded successfully.")
             }
@@ -141,6 +179,9 @@ data_upload_server <- function(id) {
       style = list(fontSize = "0.75em")
     )
 
-    raw_data
+    list(
+      adnca_raw = raw_data,
+      settings_override = settings_override
+    )
   })
 }
diff --git a/inst/shiny/modules/tab_nca.R b/inst/shiny/modules/tab_nca.R
index cbd861e8a..fcd5feb1c 100644
--- a/inst/shiny/modules/tab_nca.R
+++ b/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
diff --git a/inst/shiny/modules/tab_nca/setup.R b/inst/shiny/modules/tab_nca/setup.R
index ecaa904a9..482b41355 100644
--- a/inst/shiny/modules/tab_nca/setup.R
+++ b/inst/shiny/modules/tab_nca/setup.R
@@ -52,7 +52,7 @@ 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({

From a4e82f17269d08f2bbc36bdee12245b4c9c65386 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Wed, 24 Dec 2025 14:10:52 +0100
Subject: [PATCH 02/25] feat: settings override

---
 inst/shiny/modules/tab_nca/setup.R            | 29 ++++++++++++-------
 .../tab_nca/setup/parameter_selection.R       |  2 +-
 inst/shiny/modules/tab_nca/setup/settings.R   |  4 +--
 3 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup.R b/inst/shiny/modules/tab_nca/setup.R
index 994b9a4da..112046876 100644
--- a/inst/shiny/modules/tab_nca/setup.R
+++ b/inst/shiny/modules/tab_nca/setup.R
@@ -56,20 +56,27 @@ 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$datapath)
+      req(settings_override())
+      settings_override()$settings
+    })
+    
+    imported_slopes <- reactive({
+      req(settings_override())
+      settings_override()$slope_rules
+    })
+    
+    imported_params <- reactive({
+      req(imported_settings())
+      imported_settings()$parameter_selections
     })
 
-    settings_override <- reactive(imported_settings()$settings)
-    manual_slopes_override <- reactive(imported_settings()$slope_rules)
-    parameters_override <- reactive(imported_settings()$settings$parameter_selections)
 
     # Gather all settings from the appropriate module
     settings <- settings_server(
       "nca_settings",
       data,
       adnca_data,
-      settings_override
+      imported_settings
     )
 
     # Create processed data object with applied settings.
@@ -99,7 +106,7 @@ setup_server <- function(id, data, adnca_data, settings_override) {
     parameters_output <- parameter_selection_server(
       "nca_setup_parameter",
       base_pknca_data,
-      parameters_override
+      imported_params
     )
 
     final_settings <- reactive({
@@ -145,9 +152,9 @@ setup_server <- function(id, data, adnca_data, settings_override) {
     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
@@ -183,7 +190,7 @@ setup_server <- function(id, data, adnca_data, settings_override) {
     slope_rules <- slope_selector_server(
       "slope_selector",
       slopes_pknca_data,
-      manual_slopes_override
+      imported_slopes
     )
 
     # Handle downloading and uploading settings
diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index d34f7b3f5..57dd231d7 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -259,7 +259,7 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       study_type_names <- unique(study_types_df()$type)
 
       if (length(study_type_names) == 0) return(list())
-
+browser()
       # Convert from wide to long, filter for selected rows,
       # and then split the result into a list by study_type.
       df %>%
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 360f66e58..ae24f7184 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -136,9 +136,9 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     conc_data <- reactive(adnca_data()$conc$data)
 
     # File Upload Handling
-    observeEvent(settings_override(), {
+    observeEvent(c(settings_override(), data()), {
       settings <- settings_override()
-
+browser()
       log_debug_list("User settings override:", settings)
 
       not_compatible <- c()

From 1d44c0f0b7d05d313fc240c3343337504ab426a7 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Wed, 24 Dec 2025 14:17:29 +0100
Subject: [PATCH 03/25] temp: param selection settings working

---
 inst/shiny/modules/tab_nca/setup/parameter_selection.R | 1 -
 inst/shiny/modules/tab_nca/setup/settings.R            | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 57dd231d7..97ba4e706 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -259,7 +259,6 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       study_type_names <- unique(study_types_df()$type)
 
       if (length(study_type_names) == 0) return(list())
-browser()
       # Convert from wide to long, filter for selected rows,
       # and then split the result into a list by study_type.
       df %>%
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index ae24f7184..4d17c25dd 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -138,7 +138,7 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     # File Upload Handling
     observeEvent(c(settings_override(), data()), {
       settings <- settings_override()
-browser()
+
       log_debug_list("User settings override:", settings)
 
       not_compatible <- c()

From dadce3e0fb35aea3101dd40f6837f7a53db9fce9 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Mon, 29 Dec 2025 12:47:48 +0100
Subject: [PATCH 04/25] fix: settings upload works in data tab

---
 inst/shiny/modules/tab_nca/setup/settings.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 4d17c25dd..a0393fcbb 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -136,7 +136,9 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     conc_data <- reactive(adnca_data()$conc$data)
 
     # File Upload Handling
-    observeEvent(c(settings_override(), data()), {
+    observeEvent(c(data(), settings_override()), priority = 0, {
+      req(data())
+      
       settings <- settings_override()
 
       log_debug_list("User settings override:", settings)
@@ -230,7 +232,7 @@ settings_server <- function(id, data, adnca_data, settings_override) {
 
 
     # Choose data to be analyzed
-    observeEvent(data(), priority = -1, {
+    observeEvent(data(), priority = 1, {
       req(data())
 
       choices <- unique(data()$PARAM) %>%

From bda831dff7be479251a5901fc0d1752a197304de Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Wed, 31 Dec 2025 14:36:40 +0100
Subject: [PATCH 05/25] lint

---
 inst/shiny/modules/tab_data/data_upload.R   | 20 +++++++++++---------
 inst/shiny/modules/tab_nca/setup.R          |  4 ++--
 inst/shiny/modules/tab_nca/setup/settings.R |  2 +-
 3 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index efb11a6ec..958b5e461 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -42,7 +42,7 @@ 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$file_loading_message <- renderUI({
       if (is.null(file_loading_error())) {
         p("")
@@ -85,9 +85,9 @@ data_upload_server <- function(id) {
               obj <- readRDS(path)
               # Check for settings
               is_settings <- is.list(obj) && "settings" %in% names(obj)
-              
+
               final_settings <- if (is_settings) obj else NULL
-              
+
               if (!is.null(final_settings)) {
                 list(status = "success", type = "settings", content = final_settings, name = name)
               } else {
@@ -105,21 +105,23 @@ data_upload_server <- function(id) {
         successful_loads <- purrr::keep(read_results, ~ .x$status == "success")
         errors <- purrr::keep(read_results, \(x) x$status == "error") %>%
           purrr::map(\(x) paste0(x$name, ": ", x$message))
-        
+
         # Extract and apply settings if any found
         found_settings <- purrr::keep(successful_loads, ~ .x$type == "settings")
-        
+
         if (length(found_settings) > 1) {
           # Error: Too many settings files
           msg <- "Error: Multiple settings files detected. Please upload only one settings file."
-          prev_msgs <- if (length(errors) > 0){
+          prev_msgs <- if (length(errors) > 0) {
             paste(purrr::map_chr(errors, ~ paste0(.x$name, ": ", .x$msg)), collapse = "<br>")
-          } else ""
+          } else {
+            ""
+          }
           file_loading_error(paste(c(prev_msgs, msg), collapse = "<br>"))
-          
+
           # Do not apply any settings if ambiguous
           settings_override(NULL)
-          
+
         } else if (length(found_settings) == 1) {
           # Success: Single settings file
           latest <- found_settings[[1]]
diff --git a/inst/shiny/modules/tab_nca/setup.R b/inst/shiny/modules/tab_nca/setup.R
index 112046876..b248e40cc 100644
--- a/inst/shiny/modules/tab_nca/setup.R
+++ b/inst/shiny/modules/tab_nca/setup.R
@@ -59,12 +59,12 @@ setup_server <- function(id, data, adnca_data, settings_override) {
       req(settings_override())
       settings_override()$settings
     })
-    
+
     imported_slopes <- reactive({
       req(settings_override())
       settings_override()$slope_rules
     })
-    
+
     imported_params <- reactive({
       req(imported_settings())
       imported_settings()$parameter_selections
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index a0393fcbb..9ee18ff38 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -138,7 +138,7 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     # File Upload Handling
     observeEvent(c(data(), settings_override()), priority = 0, {
       req(data())
-      
+
       settings <- settings_override()
 
       log_debug_list("User settings override:", settings)

From 87795928abd1646dd02b13722051855abd167c1e Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Tue, 6 Jan 2026 17:05:10 +0100
Subject: [PATCH 06/25] fix: update slope selector settings

---
 .../modules/tab_nca/setup/slope_selector.R    | 22 +++++++------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 540b7ab6e..621e301f9 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -340,25 +340,19 @@ slope_selector_server <- function( # nolint
     })
 
     #' If any settings are uploaded by the user, overwrite current rules
-    observeEvent(manual_slopes_override(), {
-      req(manual_slopes_override())
+    observeEvent(list(manual_slopes_override(), plot_data()), {
+      req(manual_slopes_override(), plot_data())
 
       if (nrow(manual_slopes_override()) == 0) return(NULL)
 
       log_debug_list("Manual slopes override:", manual_slopes_override())
 
-      override_valid <- apply(manual_slopes_override(), 1, function(r) {
-        dplyr::filter(
-          plot_data()$conc$data,
-          PCSPEC == r["PCSPEC"],
-          USUBJID == r["USUBJID"],
-          PARAM == r["PARAM"],
-          ATPTREF == r["ATPTREF"],
-          DOSNOA == r["DOSNOA"]
-        ) %>%
-          NROW() != 0
-      }) %>%
-        all()
+      allowed_keys <- c("PCSPEC", "USUBJID", "PARAM", "ATPTREF", "DOSNOA")
+      use_keys <- intersect(allowed_keys, names(manual_slopes_override()))
+      
+      override_valid <- manual_slopes_override() %>%
+        dplyr::semi_join(plot_data()$conc$data, by = use_keys) %>%
+        nrow() == nrow(manual_slopes_override())
 
       if (!override_valid) {
         msg <- "Manual slopes not compatible with current data, leaving as default."

From e6ef26c6f265a9eee06bee77323e1a089abd351c Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Tue, 6 Jan 2026 17:28:45 +0100
Subject: [PATCH 07/25] fix: settings within if null statement

---
 inst/shiny/modules/tab_nca/setup.R          |  3 -
 inst/shiny/modules/tab_nca/setup/settings.R | 99 +++++++++++----------
 2 files changed, 50 insertions(+), 52 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup.R b/inst/shiny/modules/tab_nca/setup.R
index b248e40cc..4c2b9fde8 100644
--- a/inst/shiny/modules/tab_nca/setup.R
+++ b/inst/shiny/modules/tab_nca/setup.R
@@ -56,17 +56,14 @@ setup_server <- function(id, data, adnca_data, settings_override) {
   moduleServer(id, function(input, output, session) {
 
     imported_settings <- reactive({
-      req(settings_override())
       settings_override()$settings
     })
 
     imported_slopes <- reactive({
-      req(settings_override())
       settings_override()$slope_rules
     })
 
     imported_params <- reactive({
-      req(imported_settings())
       imported_settings()$parameter_selections
     })
 
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 73ed7a6f4..fc35d312c 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -163,6 +163,55 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         if (!all(settings$pcspec %in% data()$PCSPEC)) {
           not_compatible <- c(not_compatible, "Dose Specimen")
         }
+        
+        # Additional settings (PCSPEC and ATPTREF handled later)
+        updateSelectInput(session, inputId = "method", selected = settings$method)
+        
+        if (!is.null(settings$bioavailability))
+          updateSelectInput(session, inputId = "bioavailability", selected = settings$bioavailability)
+        
+        # Data imputation #
+        update_switch("should_impute_c0", value = settings$data_imputation$impute_c0)
+        
+        # Partial AUCs #
+        auc_data(settings$partial_aucs)
+        refresh_reactable(refresh_reactable() + 1)
+        
+        # Flags #
+        .update_rule_input(
+          session,
+          "R2ADJ",
+          settings$flags$R2ADJ$is.checked,
+          settings$flags$R2ADJ$threshold
+        )
+        
+        .update_rule_input(
+          session,
+          "R2",
+          settings$flags$R2$is.checked,
+          settings$flags$R2$threshold
+        )
+        
+        .update_rule_input(
+          session,
+          "AUCPEO",
+          settings$flags$AUCPEO$is.checked,
+          settings$flags$AUCPEO$threshold
+        )
+        
+        .update_rule_input(
+          session,
+          "AUCPEP",
+          settings$flags$AUCPEP$is.checked,
+          settings$flags$AUCPEP$threshold
+        )
+        
+        .update_rule_input(
+          session,
+          "LAMZSPN",
+          settings$flags$LAMZSPN$is.checked,
+          settings$flags$LAMZSPN$threshold
+        )
       }
       
       if (length(not_compatible) > 0) {
@@ -173,60 +222,12 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       }
       
       updatePickerInput(session, "select_analyte", choices = choices, selected = selected)
-      
-      # Additional settings (PCSPEC and ATPTREF handled later)
-      updateSelectInput(session, inputId = "method", selected = settings$method)
-      
-      if (!is.null(settings$bioavailability))
-        updateSelectInput(session, inputId = "bioavailability", selected = settings$bioavailability)
-      
-      # Data imputation #
-      update_switch("should_impute_c0", value = settings$data_imputation$impute_c0)
-      
-      # Partial AUCs #
-      auc_data(settings$partial_aucs)
-      refresh_reactable(refresh_reactable() + 1)
-      
-      # Flags #
-      .update_rule_input(
-        session,
-        "R2ADJ",
-        settings$flags$R2ADJ$is.checked,
-        settings$flags$R2ADJ$threshold
-      )
-      
-      .update_rule_input(
-        session,
-        "R2",
-        settings$flags$R2$is.checked,
-        settings$flags$R2$threshold
-      )
-      
-      .update_rule_input(
-        session,
-        "AUCPEO",
-        settings$flags$AUCPEO$is.checked,
-        settings$flags$AUCPEO$threshold
-      )
-      
-      .update_rule_input(
-        session,
-        "AUCPEP",
-        settings$flags$AUCPEP$is.checked,
-        settings$flags$AUCPEP$threshold
-      )
-      
-      .update_rule_input(
-        session,
-        "LAMZSPN",
-        settings$flags$LAMZSPN$is.checked,
-        settings$flags$LAMZSPN$threshold
-      )
     })
     
     # Update Downstream Inputs (Profile & Specimen)
     observeEvent(input$select_analyte, {
       req(data())
+
       settings <- settings_override()
       
       # Filter data based on Analyte

From faf9e232837fb3b7cf08024f9f8175ad5b344e59 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Tue, 6 Jan 2026 17:31:38 +0100
Subject: [PATCH 08/25] remove test settings file

---
 tests/testthat/data/settings.rds | Bin 744 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 tests/testthat/data/settings.rds

diff --git a/tests/testthat/data/settings.rds b/tests/testthat/data/settings.rds
deleted file mode 100644
index 3ea3f54d997109ced5e431f215981e494ade5eac..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 744
zcmV<E0vG)siwFP!000002F+DVbJH*o_9IT~^aaz-aLpgUlui!}my))DX$MkI(lC@u
zMzQ5aAU}}gHthv|3qOuCzo15rwT|t!7Y+=b*wTK|zBjv{I+~`LTFW#w(~?`w8lS&?
z{z}t~ZAlnv%`ZKXudcN;TdsC5Li9%9-It969RNcC)_8a_=qsY_Qp7{l;Mt-i>ZZvH
z8eew(_&So%ozkl--For1j0&3-p%C+?VI)jafhXQ>A;nZ)Xq#$XJl}uk-<6+$zqx4Q
zHBB~)uN}~~ku&^|pDfGnii>*IaN6bqF)=}@r+^h4`3th)f+ynvE|?G`F{KkfP?RYt
zwe9#wASYnbkV=TGWva?hY05GE;8(DC9<j4SxZ};R_Z9nKxtKA`XEF6FD*mD94Yl9-
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zI(w#&4dj1un8UxNh?VwsWYLl+aN;R1ua$`7N1$GUvXn)ID<_v1)+CbPxu^(Q2Pj#p
zYkRbE!!CqWSV~|ix#fju4rb*0<&ix@G;k;h!0A<r!l{p(TSY$w+KHSbCXoO|+vR~E
zA$9`7O5avPCY*||D>+@U`CbHhf+B|@L1IX+sIa%h(){+-?Ltz$r8V+WFBxbWoBg@R
zu+$NCk7buo=+1~lmlSvVbHUIR;$BJ-gRZO2PCj-IW18{@>akO1x9IjjCM*sJ1+txZ
zJi*ZE+94LR7@Xgll2|Gx6io>w;s)TnlT8+_I*$wFYdw)&lOURRN{FWwP;^-mX++8#
z?a14*6$;EI98>J&f|M7gYK*lwK0JK%<^;24BxN{qtLg{l{_FjwNG@jb_sHM4?H-NX
z{t-lNJQ^RKo*YBo&o5jUi`K9=cvsHIVZS#z8x%5)Osh|vtia8zVadJO@L)e$<yZ)r
ab_n4br*VQOETxOlcJ~L_I8n?E2mk;zV{4!Q


From c16cab1e6a042b2d92119cff8818adeeef945bba Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Tue, 6 Jan 2026 17:44:10 +0100
Subject: [PATCH 09/25] lint

---
 inst/shiny/modules/tab_nca/setup/settings.R   | 114 +++++++++---------
 .../modules/tab_nca/setup/slope_selector.R    |   2 +-
 2 files changed, 56 insertions(+), 60 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index fc35d312c..3f49ce772 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -135,27 +135,26 @@ settings_server <- function(id, data, adnca_data, settings_override) {
 
     conc_data <- reactive(adnca_data()$conc$data)
 
-    
     # File Upload Handling
     observeEvent(c(data(), settings_override()), {
       req(data())
       # Initialize Analyte + Global Validation
       choices <- unique(data()$PARAM) %>% na.omit()
       settings <- settings_override()
-      
+
       # Defaults
       selected <- choices
       not_compatible <- c()
-      
+
       # if settings exist, update analyte picker input and check compatibility
       if (!is.null(settings)) {
-        
+
         if (all(settings$analyte %in% choices)) {
           selected <- settings$analyte
         } else {
           not_compatible <- c(not_compatible, "Analyte")
         }
-        
+
         # We check raw data here just to see if the settings exist
         if (!all(settings$profile %in% data()$ATPTREF)) {
           not_compatible <- c(not_compatible, "Profile")
@@ -163,20 +162,21 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         if (!all(settings$pcspec %in% data()$PCSPEC)) {
           not_compatible <- c(not_compatible, "Dose Specimen")
         }
-        
+
         # Additional settings (PCSPEC and ATPTREF handled later)
         updateSelectInput(session, inputId = "method", selected = settings$method)
-        
+
         if (!is.null(settings$bioavailability))
-          updateSelectInput(session, inputId = "bioavailability", selected = settings$bioavailability)
-        
+          updateSelectInput(session, inputId = "bioavailability",
+                            selected = settings$bioavailability)
+
         # Data imputation #
         update_switch("should_impute_c0", value = settings$data_imputation$impute_c0)
-        
+
         # Partial AUCs #
         auc_data(settings$partial_aucs)
         refresh_reactable(refresh_reactable() + 1)
-        
+
         # Flags #
         .update_rule_input(
           session,
@@ -184,28 +184,28 @@ settings_server <- function(id, data, adnca_data, settings_override) {
           settings$flags$R2ADJ$is.checked,
           settings$flags$R2ADJ$threshold
         )
-        
+
         .update_rule_input(
           session,
           "R2",
           settings$flags$R2$is.checked,
           settings$flags$R2$threshold
         )
-        
+
         .update_rule_input(
           session,
           "AUCPEO",
           settings$flags$AUCPEO$is.checked,
           settings$flags$AUCPEO$threshold
         )
-        
+
         .update_rule_input(
           session,
           "AUCPEP",
           settings$flags$AUCPEP$is.checked,
           settings$flags$AUCPEP$threshold
         )
-        
+
         .update_rule_input(
           session,
           "LAMZSPN",
@@ -213,56 +213,69 @@ settings_server <- function(id, data, adnca_data, settings_override) {
           settings$flags$LAMZSPN$threshold
         )
       }
-      
+
       if (length(not_compatible) > 0) {
-        msg <- paste0(paste0(not_compatible, collapse = ", "), 
+        msg <- paste0(paste0(not_compatible, collapse = ", "),
                       " settings not found in data. Reverting to defaults.")
         log_warn(msg)
         showNotification(msg, type = "warning", duration = 10)
       }
-      
+
       updatePickerInput(session, "select_analyte", choices = choices, selected = selected)
     })
-    
+
     # Update Downstream Inputs (Profile & Specimen)
     observeEvent(input$select_analyte, {
       req(data())
 
       settings <- settings_override()
-      
+
       # Filter data based on Analyte
       filtered_data <- data() %>%
         filter(PARAM %in% input$select_analyte, !is.na(PCSPEC), !is.na(ATPTREF))
-      
+
       profile_choices <- sort(unique(filtered_data$ATPTREF))
       pcspec_choices  <- unique(filtered_data$PCSPEC)
-      
+
       # PROFILE
       current_profile <- isolate(input$select_profile)
-      
-      if (!is.null(settings) && all(settings$profile %in% profile_choices)) {
-        target_profile <- settings$profile
-      } else if (length(intersect(current_profile, profile_choices)) > 0) {
-        target_profile <- current_profile # Keep current if valid
-      } else {
-        target_profile <- profile_choices[1] # Default
-      }
-
       # SPECIMEN
       current_pcspec <- isolate(input$select_pcspec)
-      
-      if (!is.null(settings) && all(settings$pcspec %in% pcspec_choices)) {
-        target_pcspec <- settings$pcspec
-      } else if (length(intersect(current_pcspec, pcspec_choices)) > 0) {
-        target_pcspec <- current_pcspec # Keep current if valid
+
+      if (!is.null(settings)) {
+        if (all(settings$profile %in% profile_choices)) {
+          target_profile <- settings$profile
+        }
+        if (all(settings$pcspec %in% pcspec_choices)) {
+          target_pcspec <- settings$pcspec
+        }
       } else {
-        # Smart Default (Plasma/Serum)
-        plasma_serum <- grep("^plasma$|^serum$", pcspec_choices, value = TRUE, ignore.case = TRUE)
-        target_pcspec <- if(length(plasma_serum) > 0) plasma_serum else pcspec_choices
+        if (length(intersect(current_profile, profile_choices)) > 0) {
+          target_profile <- current_profile # Keep current if valid
+        } else {
+          target_profile <- profile_choices[1]
+        }
+        if (length(intersect(current_pcspec, pcspec_choices)) > 0) {
+          target_pcspec <- current_pcspec # Keep current if valid
+        } else {
+          # Smart Default (Plasma/Serum)
+          plasma_serum <- grep("^plasma$|^serum$", pcspec_choices, value = TRUE, ignore.case = TRUE)
+          target_pcspec <- if (length(plasma_serum) > 0) plasma_serum else pcspec_choices
+        }
       }
-      
-      updatePickerInput(session, "select_profile", choices = profile_choices, selected = target_profile)
-      updatePickerInput(session, "select_pcspec",  choices = pcspec_choices,  selected = target_pcspec)
+
+      updatePickerInput(
+        session,
+        "select_profile",
+        choices = profile_choices,
+        selected = target_profile
+      )
+      updatePickerInput(
+        session,
+        "select_pcspec",
+        choices = pcspec_choices,
+        selected = target_pcspec
+      )
     })
 
     # Include keyboard limits for the settings GUI display
@@ -273,23 +286,6 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "AUCPEP_threshold", max = 100, min = 0, lab = "AUCPEP")
     limit_input_value(input, session, "LAMZSPN_threshold", min = 0, lab = "LAMZSPN")
 
-
-    # Choose data to be analyzed
-    observeEvent(data(), priority = 1, {
-      req(data())
-
-      choices <- unique(data()$PARAM) %>%
-        na.omit()
-
-      updatePickerInput(
-        session,
-        inputId = "select_analyte",
-        choices = choices,
-        selected = choices
-      )
-
-    })
-
     # Reactive value to store the AUC data table
     auc_data <- reactiveVal(
       tibble(start_auc = rep(NA_real_, 2), end_auc = rep(NA_real_, 2))
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 621e301f9..bca69c777 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -349,7 +349,7 @@ slope_selector_server <- function( # nolint
 
       allowed_keys <- c("PCSPEC", "USUBJID", "PARAM", "ATPTREF", "DOSNOA")
       use_keys <- intersect(allowed_keys, names(manual_slopes_override()))
-      
+
       override_valid <- manual_slopes_override() %>%
         dplyr::semi_join(plot_data()$conc$data, by = use_keys) %>%
         nrow() == nrow(manual_slopes_override())

From 1118307ba56c3de7ec900dba4df7bc1b4155dd35 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Wed, 14 Jan 2026 11:29:29 +0100
Subject: [PATCH 10/25] fix: issue w type mismatch in slope selector

---
 inst/shiny/modules/tab_nca/setup/slope_selector.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index bca69c777..deb07985c 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -351,7 +351,9 @@ slope_selector_server <- function( # nolint
       use_keys <- intersect(allowed_keys, names(manual_slopes_override()))
 
       override_valid <- manual_slopes_override() %>%
-        dplyr::semi_join(plot_data()$conc$data, by = use_keys) %>%
+        mutate(across(all_of(use_keys), as.character)) %>% # mutate incase of type issues
+        semi_join(plot_data()$conc$data %>% 
+                    mutate(across(all_of(use_keys), as.character)), by = use_keys) %>%
         nrow() == nrow(manual_slopes_override())
 
       if (!override_valid) {

From 1c1a4f3c6ab6d02d3c5c37a30bba7c6f2bde7aab Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Thu, 15 Jan 2026 11:50:07 +0100
Subject: [PATCH 11/25] rm settings upload button in nca tab

---
 inst/shiny/modules/tab_nca/setup.R | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup.R b/inst/shiny/modules/tab_nca/setup.R
index 2a42c1f4a..6b8c78e12 100644
--- a/inst/shiny/modules/tab_nca/setup.R
+++ b/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"))),

From e22b4d1ac609ac673273de3581c092a01358dc33 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Thu, 15 Jan 2026 11:56:58 +0100
Subject: [PATCH 12/25] refactor: update widget text to specify settings upload

---
 inst/shiny/modules/tab_data/data_upload.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 958b5e461..691ea45b5 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/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%",

From 463220d8e51bf66c583520c76d23debafd521311 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Thu, 15 Jan 2026 12:10:31 +0100
Subject: [PATCH 13/25] lint

---
 inst/shiny/modules/tab_nca/setup/slope_selector.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index deb07985c..6557ee932 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -352,7 +352,7 @@ slope_selector_server <- function( # nolint
 
       override_valid <- manual_slopes_override() %>%
         mutate(across(all_of(use_keys), as.character)) %>% # mutate incase of type issues
-        semi_join(plot_data()$conc$data %>% 
+        semi_join(plot_data()$conc$data %>%
                     mutate(across(all_of(use_keys), as.character)), by = use_keys) %>%
         nrow() == nrow(manual_slopes_override())
 

From f2a861a0c9162e6a3d53f0bcda0b0c126f9da1a6 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Thu, 15 Jan 2026 15:45:55 +0100
Subject: [PATCH 14/25] style: use anaonymous functions in purrr

---
 inst/shiny/modules/tab_data/data_upload.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 691ea45b5..748b32272 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -102,12 +102,12 @@ data_upload_server <- function(id) {
         })
 
         # 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))
 
         # Extract and apply settings if any found
-        found_settings <- purrr::keep(successful_loads, ~ .x$type == "settings")
+        found_settings <- purrr::keep(successful_loads, \(x) x$type == "settings")
 
         if (length(found_settings) > 1) {
           # Error: Too many settings files

From dc77c8b063407ffbd9c160e330635cec2afec197 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Mon, 19 Jan 2026 09:32:24 +0100
Subject: [PATCH 15/25] refactor: anonymous functinos

---
 inst/shiny/modules/tab_data/data_upload.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 748b32272..e6aeb520c 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -113,7 +113,7 @@ data_upload_server <- function(id) {
           # Error: Too many settings files
           msg <- "Error: Multiple settings files detected. Please upload only one settings file."
           prev_msgs <- if (length(errors) > 0) {
-            paste(purrr::map_chr(errors, ~ paste0(.x$name, ": ", .x$msg)), collapse = "<br>")
+            paste(purrr::map_chr(errors, \(x) paste0(x$name, ": ", x$msg)), collapse = "<br>")
           } else {
             ""
           }
@@ -132,7 +132,7 @@ data_upload_server <- function(id) {
 
         loaded_data <- DUMMY_DATA
 
-        found_data <- purrr::keep(successful_loads, ~ .x$type == "data")
+        found_data <- purrr::keep(successful_loads, \(x) x$type == "data")
         # Handle Errors
         if (length(found_data) > 0) {
           tryCatch({

From bc408ebae767f9bec0e0078122aee9ee00063a4d Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Mon, 19 Jan 2026 09:50:22 +0100
Subject: [PATCH 16/25] refactor: settings upload handling refactor

---
 inst/shiny/modules/tab_data/data_upload.R | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index e6aeb520c..db4b28df7 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -82,21 +82,22 @@ data_upload_server <- function(id) {
             # 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)
 
-              final_settings <- if (is_settings) obj else NULL
-
-              if (!is.null(final_settings)) {
-                list(status = "success", type = "settings", content = final_settings, name = name)
-              } else {
-                # Not a settings file either, return original PK error
-                stop(e_pk$message)
+              if (!is_settings) {
+                stop(conditionMessage(e_pk))
               }
+
+              list(status = "success", type = "settings", content = obj, name = name)
             }, error = function(e_rds) {
-              # Return the original read_pk error to the user
-              list(status = "error", msg = e_pk$message, name = name)
+              list(status = "error", msg = conditionMessage(e_pk), name = name)
             })
           })
         })
@@ -104,7 +105,7 @@ data_upload_server <- function(id) {
         # Process results
         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")

From 72857d76fe8ff177b624899b0a9a855840ac5ae6 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Mon, 19 Jan 2026 09:52:43 +0100
Subject: [PATCH 17/25] refactor: settings file error messages

---
 inst/shiny/modules/tab_data/data_upload.R | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index db4b28df7..d6558c547 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -112,14 +112,7 @@ data_upload_server <- function(id) {
 
         if (length(found_settings) > 1) {
           # Error: Too many settings files
-          msg <- "Error: Multiple settings files detected. Please upload only one settings file."
-          prev_msgs <- if (length(errors) > 0) {
-            paste(purrr::map_chr(errors, \(x) paste0(x$name, ": ", x$msg)), collapse = "<br>")
-          } else {
-            ""
-          }
-          file_loading_error(paste(c(prev_msgs, msg), collapse = "<br>"))
-
+          errors <- append(errors, "Error: Multiple settings files detected. Please upload only one settings file.")
           # Do not apply any settings if ambiguous
           settings_override(NULL)
 

From ed4d82226062a9b26a9934430b0ba6c130cf27ac Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Mon, 19 Jan 2026 09:53:57 +0100
Subject: [PATCH 18/25] lint

---
 inst/shiny/modules/tab_data/data_upload.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index d6558c547..ed7597876 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -83,10 +83,11 @@ data_upload_server <- function(id) {
             # 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.") {
+              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)
@@ -112,7 +113,8 @@ data_upload_server <- function(id) {
 
         if (length(found_settings) > 1) {
           # Error: Too many settings files
-          errors <- append(errors, "Error: Multiple settings files detected. Please upload only one settings file.")
+          errors <- append(errors, "Error: Multiple settings files detected.
+                           Please upload only one settings file.")
           # Do not apply any settings if ambiguous
           settings_override(NULL)
 

From 89085900e05a7bfee065d942b1a36667c6ce6df8 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 13:52:28 +0100
Subject: [PATCH 19/25] fix: slope rules export for both settinsg downloads

---
 inst/shiny/modules/tab_nca.R                  |  9 +++----
 inst/shiny/modules/tab_nca/setup.R            |  2 +-
 .../modules/tab_nca/setup/slope_selector.R    | 24 ++++++++++---------
 3 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/inst/shiny/modules/tab_nca.R b/inst/shiny/modules/tab_nca.R
index 025b37b9d..59130d999 100644
--- a/inst/shiny/modules/tab_nca.R
+++ b/inst/shiny/modules/tab_nca.R
@@ -81,9 +81,10 @@ tab_nca_server <- function(id, pknca_data, extra_group_vars, settings_override)
 
     ratio_table <- nca_setup$ratio_table
     slope_rules <- nca_setup$slope_rules
+
     session$userData$settings <- list(
       settings =  settings,
-      slope_rules = slope_rules$manual_slopes
+      slope_rules = slope_rules
     ) # This will be saved in the results zip folder
 
     reactable_server("manual_slopes", slope_rules$manual_slopes)
@@ -127,9 +128,9 @@ tab_nca_server <- function(id, pknca_data, extra_group_vars, settings_override)
         res <- withCallingHandlers({
           processed_pknca_data %>%
             filter_slopes(
-              slope_rules$manual_slopes(),
-              slope_rules$profiles_per_subject(),
-              slope_rules$slopes_groups(),
+              slope_rules()$manual_slopes,
+              slope_rules()$profiles_per_subject,
+              slope_rules()$slopes_groups,
               check_reasons = TRUE
             ) %>%
             # Perform PKNCA parameter calculations
diff --git a/inst/shiny/modules/tab_nca/setup.R b/inst/shiny/modules/tab_nca/setup.R
index 97e528c78..b8a4d4949 100644
--- a/inst/shiny/modules/tab_nca/setup.R
+++ b/inst/shiny/modules/tab_nca/setup.R
@@ -187,7 +187,7 @@ setup_server <- function(id, data, adnca_data, extra_group_vars, settings_overri
         paste0(session$userData$project_name(), "_settings_", Sys.Date(), ".rds")
       },
       content = function(con) {
-        saveRDS(list(settings = final_settings(), slope_rules = slope_rules$manual_slopes()), con)
+        saveRDS(list(settings = final_settings(), slope_rules = slope_rules()), con)
       }
     )
 
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 6557ee932..784730d7c 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -343,18 +343,18 @@ slope_selector_server <- function( # nolint
     observeEvent(list(manual_slopes_override(), plot_data()), {
       req(manual_slopes_override(), plot_data())
 
-      if (nrow(manual_slopes_override()) == 0) return(NULL)
+      if (nrow(manual_slopes_override()$manual_slopes) == 0) return(NULL)
 
-      log_debug_list("Manual slopes override:", manual_slopes_override())
+      log_debug_list("Manual slopes override:", manual_slopes_override()$manual_slopes)
 
       allowed_keys <- c("PCSPEC", "USUBJID", "PARAM", "ATPTREF", "DOSNOA")
-      use_keys <- intersect(allowed_keys, names(manual_slopes_override()))
+      use_keys <- intersect(allowed_keys, names(manual_slopes_override()$manual_slopes))
 
-      override_valid <- manual_slopes_override() %>%
+      override_valid <- manual_slopes_override()$manual_slopes %>%
         mutate(across(all_of(use_keys), as.character)) %>% # mutate incase of type issues
         semi_join(plot_data()$conc$data %>%
                     mutate(across(all_of(use_keys), as.character)), by = use_keys) %>%
-        nrow() == nrow(manual_slopes_override())
+        nrow() == nrow(manual_slopes_override()$manual_slopes)
 
       if (!override_valid) {
         msg <- "Manual slopes not compatible with current data, leaving as default."
@@ -363,14 +363,16 @@ slope_selector_server <- function( # nolint
         return(NULL)
       }
 
-      manual_slopes(manual_slopes_override())
+      manual_slopes(manual_slopes_override()$manual_slopes)
     })
 
     #' return reactive with slope exclusions data to be displayed in Results -> Exclusions tab
-    list(
-      manual_slopes = manual_slopes,
-      profiles_per_subject = profiles_per_subject,
-      slopes_groups = slopes_groups
-    )
+    reactive({
+      list(
+        manual_slopes = manual_slopes(),
+        profiles_per_subject = profiles_per_subject(),
+        slopes_groups = slopes_groups()
+      )
+    })
   })
 }

From c3c099e513da09fe7c3ea3f05f130191c35ca16f Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 13:54:49 +0100
Subject: [PATCH 20/25] lint

---
 inst/shiny/modules/tab_data/data_upload.R | 2 +-
 inst/shiny/modules/tab_nca.R              | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 1af216c78..6b95b04c0 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -83,7 +83,7 @@ data_upload_server <- function(id) {
             # check if settings file is loaded and then create settings override
             tryCatch({
               # check if error aligns with what we expect for settings file
-              if (conditionMessage(e_pk) != "Invalid data format. Data frame was expected, but received list.") {
+              if (conditionMessage(e_pk) != "Invalid data format. Data frame was expected, but received list.") { #nolint
                 return(list(status = "error", msg = conditionMessage(e_pk), name = name))
               }
 
diff --git a/inst/shiny/modules/tab_nca.R b/inst/shiny/modules/tab_nca.R
index 59130d999..8f77859d5 100644
--- a/inst/shiny/modules/tab_nca.R
+++ b/inst/shiny/modules/tab_nca.R
@@ -74,7 +74,13 @@ tab_nca_server <- function(id, pknca_data, extra_group_vars, settings_override)
     adnca_data <- reactive(pknca_data()$conc$data)
 
     # #' NCA Setup module
-    nca_setup <- setup_server("nca_setup", adnca_data, pknca_data, extra_group_vars, settings_override)
+    nca_setup <- setup_server(
+      "nca_setup",
+      adnca_data,
+      pknca_data,
+      extra_group_vars,
+      settings_override
+    )
 
     processed_pknca_data <- nca_setup$processed_pknca_data
     settings <- nca_setup$settings

From 4f972215fd8bd8d5ab103be8d0a8e30157025a44 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 14:15:00 +0100
Subject: [PATCH 21/25] update PR template

---
 .github/PULL_REQUEST_TEMPLATE.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index ad5f31524..d8b26aaf8 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -22,6 +22,7 @@ How to test features not covered by unit tests.
 - [ ] App or package changes are reflected in NEWS
 - [ ] Package version is incremented
 - [ ] R script works with the new implementation (if applicable)
+- [ ] Settings upload works with the new implementation (if applicable)
 
 ## Notes to reviewer
 

From 7b909ae2b6bd008be58871ce4d0ff851b1cce08c Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 14:16:24 +0100
Subject: [PATCH 22/25] update description and news

---
 DESCRIPTION | 2 +-
 NEWS.md     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d10fb1978..8e65df0c1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: aNCA
 Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9043
+Version: 0.1.0.9044
 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 b9b2497a6..bb12d1588 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -16,6 +16,7 @@
 * CMAX automatically selected in box plots if available (#890)
 * Allow user to select additional `grouping variables` (chosen in the mapping) for ratio calculations (#868)
 * General button at top page to save all NCA results, settings & draft slides as a ZIP file (#638)
+* Settings are now uploaded on initial opening of the app in the data tab, and applied to the next steps (#860)
 
 
 ## Bugs fixed

From 72ea2e401acb44ecf30408c8df1710c6b974ac69 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 16:18:12 +0100
Subject: [PATCH 23/25] update rscript data to raw_data()

---
 inst/shiny/modules/tab_data/data_upload.R | 5 +++++
 inst/shiny/modules/tab_nca/zip.R          | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 294ce75a1..7d4382c9c 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -162,6 +162,11 @@ data_upload_server <- function(id) {
       }) %>%
         bindEvent(input$data_upload, ignoreNULL = FALSE)
     )
+    
+    observeEvent(raw_data(), {
+      session$userData$raw_data <- raw_data()
+      }
+    )
 
     reactable_server(
       "data_display",
diff --git a/inst/shiny/modules/tab_nca/zip.R b/inst/shiny/modules/tab_nca/zip.R
index 25f3d33fa..39623c3dd 100644
--- a/inst/shiny/modules/tab_nca/zip.R
+++ b/inst/shiny/modules/tab_nca/zip.R
@@ -189,7 +189,7 @@ zip_server <- function(id, res_nca, settings, grouping_vars) {
               # Save input dataset used
               data_tmpdir <- file.path(output_tmpdir, "data")
               dir.create(data_tmpdir, recursive = TRUE)
-              data <- read_pk(session$userData$data_path)
+              data <- session$userData$raw_data
               saveRDS(data, paste0(data_tmpdir, "/data.rds"))
 
               # Save a code R script template for the session

From adadea936a229d42424435ce2a3133f350e860f4 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 16:19:14 +0100
Subject: [PATCH 24/25] lint

---
 inst/shiny/modules/tab_data/data_upload.R | 9 +--------
 inst/shiny/modules/tab_nca/zip.R          | 2 +-
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index 7d4382c9c..ad477b12d 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -52,13 +52,6 @@ data_upload_server <- function(id) {
     })
 
     datapath <- getOption("aNCA.datapath", NULL)
-    observe({
-      if (!is.null(input$data_upload$datapath)) {
-        session$userData$data_path <- input$data_upload$datapath
-      } else {
-        session$userData$data_path <- system.file("shiny/data/example-ADNCA.csv", package = "aNCA")
-      }
-    })
 
     raw_data <- (
       reactive({
@@ -162,7 +155,7 @@ data_upload_server <- function(id) {
       }) %>%
         bindEvent(input$data_upload, ignoreNULL = FALSE)
     )
-    
+  
     observeEvent(raw_data(), {
       session$userData$raw_data <- raw_data()
       }
diff --git a/inst/shiny/modules/tab_nca/zip.R b/inst/shiny/modules/tab_nca/zip.R
index 39623c3dd..2d6e06483 100644
--- a/inst/shiny/modules/tab_nca/zip.R
+++ b/inst/shiny/modules/tab_nca/zip.R
@@ -183,7 +183,7 @@ zip_server <- function(id, res_nca, settings, grouping_vars) {
                   slope_rules = session$userData$slope_rules()
                 )
                 saveRDS(settings_to_save, paste0(setts_tmpdir, "/settings.rds"))
-                
+
               }
 
               # Save input dataset used

From e9d8d3efa7738c71f4c732473191c3180b856682 Mon Sep 17 00:00:00 2001
From: Jana Spinner <spinnerjana@gmail.com>
Date: Fri, 23 Jan 2026 16:20:19 +0100
Subject: [PATCH 25/25] lint

---
 inst/shiny/modules/tab_data/data_upload.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/inst/shiny/modules/tab_data/data_upload.R b/inst/shiny/modules/tab_data/data_upload.R
index ad477b12d..d661d3735 100644
--- a/inst/shiny/modules/tab_data/data_upload.R
+++ b/inst/shiny/modules/tab_data/data_upload.R
@@ -155,11 +155,10 @@ data_upload_server <- function(id) {
       }) %>%
         bindEvent(input$data_upload, ignoreNULL = FALSE)
     )
-  
+
     observeEvent(raw_data(), {
       session$userData$raw_data <- raw_data()
-      }
-    )
+    })
 
     reactable_server(
       "data_display",