[Review view] SDTM Phase 3: Shiny app integration

.lintr

@@ -11,4 +11,4 @@ linters:
     seq_linter = seq_linter()
   )
 encoding: "UTF-8"
-exclusions: list("R/PKNCA_extra_parameters.R", "tests/testthat/test-PKNCA_extra_parameters.R", "inst/www/templates/script_template.R")
+exclusions: list("R/PKNCA_extra_parameters.R", "tests/testthat/test-PKNCA_extra_parameters.R", "inst/www/templates/script_template.R", "inst/www/templates/script_template_sdtm.R")

R/get_session_code.R

@@ -213,10 +213,21 @@ get_settings_code <- function(
   settings_file_path,
   data_path,
   output_path = "settings_code.R",
-  template_path = system.file("www/templates/script_template.R", package = "aNCA")
+  template_path = NULL
 ) {
   settings <- read_settings(settings_file_path)
 
+  # Auto-select template based on input_mode if not explicitly provided
+  if (is.null(template_path)) {
+    mode <- settings[["input_mode"]] %||% "adnca"
+    template_file <- if (identical(mode, "sdtm")) {
+      "www/templates/script_template_sdtm.R"
+    } else {
+      "www/templates/script_template.R"
+    }
+    template_path <- system.file(template_file, package = "aNCA")
+  }
+
   session <- list(
     settings = settings[["settings"]],
     slope_rules = settings[["slope_rules"]],
@@ -228,7 +239,8 @@ get_settings_code <- function(
     extra_vars_to_keep = c(
       settings[["mapping"]][["Grouping_Variables"]], "DOSEA", "ATPTREF", "ROUTE"
     ),
-    time_duplicate_rows = settings[["time_duplicate_keys"]]
+    time_duplicate_rows = settings[["time_duplicate_keys"]],
+    sdtm_metabolites = settings[["sdtm_metabolites"]]
   )
 
   get_code(

inst/shiny/functions/zip-utils.R

@@ -435,7 +435,19 @@ prepare_export_files <- function(target_dir,
     if ("r_script" %in% input$res_tree) {
       progress$set(message = "Creating exports...",
                    detail = "Saving R script...")
-      saveRDS(session$userData$raw_data, file.path(target_dir, "input_data.rds"))
+      mode <- session$userData$input_mode %||% "adnca"
+      if (mode == "sdtm") {
+        sdtm <- session$userData$sdtm_raw
+        if (!is.null(sdtm)) {
+          saveRDS(sdtm$pc, file.path(target_dir, "input_pc.rds"))
+          saveRDS(sdtm$ex, file.path(target_dir, "input_ex.rds"))
+          if (!is.null(sdtm$dm)) {
+            saveRDS(sdtm$dm, file.path(target_dir, "input_dm.rds"))
+          }
+        }
+      } else {
+        saveRDS(session$userData$raw_data, file.path(target_dir, "input_data.rds"))
+      }
       .export_script(target_dir, session)
     }
   } else {
@@ -569,9 +581,15 @@ prepare_export_files <- function(target_dir,
     slope_rules = session$userData$slope_rules(),
     filters = session$userData$applied_filters,
     time_duplicate_keys = session$userData$time_duplicate_keys,
-    nca_ran = isTRUE(session$userData$nca_ran)
+    nca_ran = isTRUE(session$userData$nca_ran),
+    input_mode = session$userData$input_mode %||% "adnca"
   )
 
+  # Store SDTM-specific settings
+  if (identical(payload$input_mode, "sdtm")) {
+    payload$sdtm_metabolites <- session$userData$sdtm_metabolites
+  }
+
   dataset_name <- session$userData$dataset_filename %||% ""
 
   active_tab <- tryCatch(
@@ -631,9 +649,14 @@ prepare_export_files <- function(target_dir,
 #' @keywords internal
 #' @noRd
 .export_script <- function(target_dir, session) {
-  template_path <- "www/templates/script_template.R"
+  mode <- session$userData$input_mode %||% "adnca"
+  template_file <- if (mode == "sdtm") {
+    "www/templates/script_template_sdtm.R"
+  } else {
+    "www/templates/script_template.R"
+  }
   get_session_code(
-    template_path = system.file(template_path, package = "aNCA"),
+    template_path = system.file(template_file, package = "aNCA"),
     session,
     file.path(target_dir, "session_code.R")
   )

inst/shiny/modules/tab_data.R

@@ -350,7 +350,9 @@ tab_data_server <- function(id) {
       id = "column_mapping",
       adnca_data = uploaded_data$adnca_raw,
       imported_mapping = imported_mapping,
-      trigger = trigger_mapping_submit
+      trigger = trigger_mapping_submit,
+      input_mode = uploaded_data$input_mode,
+      sdtm_raw = uploaded_data$sdtm_raw
     )
     #' Reactive value for the processed dataset
     adnca_mapped <- column_mapping$processed_data
@@ -419,12 +421,29 @@ tab_data_server <- function(id) {
       log_trace("Creating PKNCA::data object.")
 
       tryCatch({
-        pknca_object <- PKNCA_create_data_object(
-          adnca_data = uploaded_data$adnca_raw(),
-          mapping = column_mapping$mapping(),
-          applied_filters = filtering_result$applied_filters(),
-          time_duplicate_rows = column_mapping$time_duplicate_rows()
-        )
+        mode <- uploaded_data$input_mode()
+
+        if (mode == "sdtm") {
+          # SDTM: PKNCAdata was already created in the mapping step;
+          # update concentration data with filtered rows
+          log_trace("SDTM mode: retrieving PKNCAdata from mapping step...")
+          pknca_object <- column_mapping$sdtm_pknca_data()
+          req(pknca_object)
+          pknca_object$conc$data <- processed_data()
+          log_trace(
+            "SDTM: PKNCAdata updated with filtered data (",
+            nrow(processed_data()), " rows)."
+          )
+        } else {
+          # ADNCA: create PKNCAdata from mapped data
+          pknca_object <- PKNCA_create_data_object(
+            adnca_data = uploaded_data$adnca_raw(),
+            mapping = column_mapping$mapping(),
+            applied_filters = filtering_result$applied_filters(),
+            time_duplicate_rows = column_mapping$time_duplicate_rows()
+          )
+        }
+
         pknca_object$units <- .simplify_volume_units(pknca_object$units)
         log_success("PKNCA data object created.")
 
@@ -453,7 +472,8 @@ tab_data_server <- function(id) {
       adnca_raw = uploaded_data$adnca_raw,
       extra_group_vars = extra_group_vars,
       settings_override = uploaded_data$settings_override,
-      auto_replay_ready = auto_replay_ready
+      auto_replay_ready = auto_replay_ready,
+      input_mode = uploaded_data$input_mode
     )
   })
 }