feat: replace logger with lightweight console logging + ZIP export

DESCRIPTION

@@ -33,7 +33,6 @@ Imports:
     glue,
     htmltools,
     htmlwidgets,
-    logger,
     magrittr,
     PKNCA (>= 0.12.1),
     plotly (>= 4.11.0),

NAMESPACE

@@ -140,7 +140,7 @@ importFrom(glue,glue)
 importFrom(grid,convertUnit)
 importFrom(htmltools,tags)
 importFrom(htmlwidgets,onRender)
-importFrom(logger,log_info)
+
 importFrom(magrittr,`%>%`)
 importFrom(plotly,add_lines)
 importFrom(plotly,add_trace)

R/imports-shiny.R

@@ -7,7 +7,6 @@
 #' @importFrom bslib page_sidebar
 #' @importFrom htmltools tags
 #' @importFrom htmlwidgets onRender
-#' @importFrom logger log_info
 #' @importFrom reactable reactable
 #' @importFrom reactable.extras reactable_extras_dependency
 #' @importFrom shiny runApp

inst/shiny/app.R

@@ -3,7 +3,6 @@ require(aNCA)
 require(bslib)
 require(dplyr)
 require(htmlwidgets)
-require(logger)
 require(formatters)
 require(magrittr)
 require(plotly)

inst/shiny/functions/logging.R

@@ -0,0 +1,84 @@
+# Lightweight logging system for the aNCA Shiny app.
+#
+# Replaces the `logger` package with console-only output and in-memory
+# log capture for ZIP export. Supports glue-style interpolation and
+# paste-style multi-argument calls.
+#
+# Log levels: TRACE < DEBUG < INFO < SUCCESS < WARN < ERROR
+# Default threshold: INFO (configurable via aNCA_LOG_LEVEL env var).
+#
+# The log captures application-level events only — not raw R console
+# output. Warnings and errors from third-party packages appear only
+# when explicitly caught by tryCatch blocks with log_warn/log_error.
+#
+# The in-memory buffer is exported as session_log.txt in the ZIP
+# download. For a full reference of logged events, see:
+# https://pharmaverse.github.io/aNCA/articles/session_log.html
+
+.log_env <- new.env(parent = emptyenv())
+.log_env$threshold <- "INFO"
+.log_env$buffer <- character(0)
+
+.LOG_LEVELS <- c(TRACE = 1L, DEBUG = 2L, INFO = 3L, SUCCESS = 4L, WARN = 5L, ERROR = 6L)
+
+#' Initialise the logging system.
+#'
+#' Reads the threshold from the `aNCA_LOG_LEVEL` environment variable
+#' (default `"INFO"`) and clears the in-memory log buffer.
+setup_logger <- function() {
+  level <- toupper(Sys.getenv("aNCA_LOG_LEVEL", "INFO"))
+  if (!level %in% names(.LOG_LEVELS)) level <- "INFO"
+  .log_env$threshold <- level
+  .log_env$buffer <- character(0)
+}
+
+#' Core logging function.
+#' @param level Character: one of the log level names.
+#' @param ... Message parts. If the first argument contains `{`, it is
+#'   evaluated as a glue string in the caller's environment. Otherwise
+#'   all arguments are pasted together.
+#' @noRd
+.log_msg <- function(level, ...) {
+  if (.LOG_LEVELS[[level]] < .LOG_LEVELS[[.log_env$threshold]]) return(invisible(NULL))
+
+  args <- list(...)
+  if (length(args) == 0L) {
+    msg <- ""
+  } else if (length(args) == 1L && grepl("\\{", args[[1]])) {
+    msg <- tryCatch(
+      glue::glue(args[[1]], .envir = parent.frame(2)),
+      error = function(e) paste0(args, collapse = "")
+    )
+  } else {
+    msg <- paste0(args, collapse = "")
+  }
+
+  timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
+  line <- paste0("[", timestamp, "] ", level, ": ", msg)
+
+  .log_env$buffer <- c(.log_env$buffer, line)
+  message(line)
+  invisible(NULL)
+}
+
+# Public log functions matching the logger API
+log_trace   <- function(...) .log_msg("TRACE", ...)
+log_debug   <- function(...) .log_msg("DEBUG", ...)
+log_info    <- function(...) .log_msg("INFO", ...)
+log_success <- function(...) .log_msg("SUCCESS", ...)
+log_warn    <- function(...) .log_msg("WARN", ...)
+log_error   <- function(...) .log_msg("ERROR", ...)
+
+#' Logs a list or data frame at DEBUG level.
+#'
+#' @param title Title for the log entry.
+#' @param l     List or data.frame to log.
+log_debug_list <- function(title, l) {
+  log_debug(aNCA:::.concatenate_list(title, l))
+}
+
+#' Return the in-memory log buffer as a character vector.
+#' @noRd
+get_log_buffer <- function() {
+  .log_env$buffer
+}

inst/shiny/functions/utils-exclusions.R

@@ -91,6 +91,12 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
     exclusion_list(append(current, list_new_reason))
     updateTextInput(session, "exclusion_reason", value = "")
     updateReactable(table_id, selected = NA)
+
+    type_label <- .exclusion_type_label(nca_checked, tlg_checked)
+    log_info(
+      "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+      ", reason='", reason, "'"
+    )
   }
 }
 
@@ -211,7 +217,8 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
 #' @param registered_ids reactiveVal holding character vector of registered IDs.
 #' @param input Shiny input object.
 #' @noRd
-.register_remove_observers <- function(exclusion_list, registered_ids, input) {
+.register_remove_observers <- function(exclusion_list, registered_ids, input,
+                                       on_remove = NULL) {
   lst <- exclusion_list()
   already <- registered_ids()
   new_ids <- setdiff(
@@ -223,6 +230,10 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
       local_id <- xbtn_id
       observeEvent(input[[local_id]], {
         current <- exclusion_list()
+        removed <- Filter(function(x) x$xbtn_id == local_id, current)
+        if (is.function(on_remove) && length(removed) > 0) {
+          on_remove(removed[[1]])
+        }
         exclusion_list(Filter(function(x) x$xbtn_id != local_id, current))
       }, ignoreInit = TRUE, once = TRUE)
     })

inst/shiny/functions/utils.R

@@ -1,45 +1,3 @@
-#' Sets up the logger package for the application.
-#'
-#' @details
-#' The application logs everything to a log file located in `/log` directory. If such folder
-#' does not exist, it will be created. Logfile for each session will be separate. The application
-#' will keep 5 log files at any given time - if this number is exceeded, the oldest log file
-#' will be deleted.
-#'
-#' In addition, information of the level specified by the user will be logged to console.
-#' As a default, this level is INFO - this is so that the user has good information on what is
-#' happening inside the app, but is not overwhelmed with tracing and debugging information. This
-#' level can be changed using `aNCA_LOG_LEVEL` environmental variable, set for example in
-#' `.Renviron` file.
-setup_logger <- function() {
-  log_layout(layout_glue_colors)
-  log_formatter(formatter_glue)
-  log_threshold(TRACE)
-  log_threshold(Sys.getenv("aNCA_LOG_LEVEL", "INFO"), index = 2)
-
-  log_dir <- "./log"
-  if (!dir.exists(log_dir)) dir.create(log_dir)
-  existing_logs <- list.files(log_dir, full.names = TRUE)
-  if (length(existing_logs) >= 5) file.remove(sort(existing_logs)[1]) # keep only five log files
-  logfile_name <- paste0(log_dir, "/aNCA_app_", format(Sys.time(), "%y%m%d-%H%M%S-"), ".log")
-
-  log_appender(appender_file(logfile_name))
-  log_appender(appender_console, index = 2)
-}
-
-#' Logs a list and data frame objects.
-#'
-#' @details
-#' Utilitary function for logging a list object (like mapping list or used settings) in
-#' a nice format. Parses a list into nice string and logs at DEBUG level. Can also process
-#' data frames, which will be converted into a list of rows.
-#'
-#' @param title Title for the logs.
-#' @param l     List object to be parsed into log. Can also be a data.frame.
-log_debug_list <- function(title, l) {
-  log_debug(aNCA:::.concatenate_list(title, l))
-}
-
 #' Needed to properly reset reactable.extras widgets
 #'
 #' @details

inst/shiny/functions/zip-utils.R

@@ -454,6 +454,12 @@ prepare_export_files <- function(target_dir,
                  detail = "Saving session info...")
     .export_session_info(target_dir)
   }
+
+  if ("session_log" %in% input$res_tree) {
+    progress$set(message = "Creating exports...",
+                 detail = "Saving session log...")
+    .export_session_log(target_dir)
+  }
   progress$inc(0.8)
 
   .clean_export_dir(target_dir, input, custom_names)
@@ -685,6 +691,45 @@ prepare_export_files <- function(target_dir,
   writeLines(lines, file.path(target_dir, "session_info.txt"))
 }
 
+#' Export the in-memory session log to a text file.
+#' @param target_dir Target directory for the export.
+#' @keywords internal
+.export_session_log <- function(target_dir) {
+  log_buffer <- get_log_buffer()
+
+  threshold <- .log_env$threshold
+  header <- c(
+    "# aNCA Session Log",
+    "#",
+    "# This file contains application events captured during your session.",
+    "# It records data upload, mapping, NCA settings, parameter selection,",
+    "# slope adjustments, exclusions, calculation results, and exports.",
+    "#",
+    "# Warnings and errors from these operations are included when caught",
+    "# by the application. Unexpected R errors or warnings from third-party",
+    "# packages that are not explicitly handled will NOT appear here.",
+    "#",
+    paste0("# Log level: ", threshold,
+           " (configurable via aNCA_LOG_LEVEL env var)"),
+    paste0("# Levels shown at current threshold: ",
+           paste(names(.LOG_LEVELS)[.LOG_LEVELS >= .LOG_LEVELS[[threshold]]],
+                 collapse = ", ")),
+    "#",
+    "# For a full reference of logged events, see:",
+    "# https://pharmaverse.github.io/aNCA/articles/session_log.html",
+    "#",
+    paste0("# Generated: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z")),
+    "# -------------------------------------------------------------------",
+    ""
+  )
+
+  if (length(log_buffer) == 0L) {
+    log_buffer <- "(No log entries captured during this session.)"
+  }
+
+  writeLines(c(header, log_buffer), file.path(target_dir, "session_log.txt"))
+}
+
 #' Clean Export Directory
 #' @param target_dir Target directory to clean
 #' @param input Shiny input object
@@ -722,6 +767,10 @@ prepare_export_files <- function(target_dir,
     files_req <- c(files_req, grep("session_info\\.txt$", all_files,
                                    value = TRUE))
   }
+  if ("session_log" %in% fnames) {
+    files_req <- c(files_req, grep("session_log\\.txt$", all_files,
+                                   value = TRUE))
+  }
   file.remove(all_files[!all_files %in% files_req])
 
   # Recursive directory cleanup — remove dirs that contain no files at any depth

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

@@ -196,6 +196,15 @@ data_imputation_server <- function(id, settings_override) {
       }
     })
 
+    observeEvent(input$select_blq_strategy, {
+      log_info("BLQ imputation strategy changed: ", input$select_blq_strategy)
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$should_impute_c0, {
+      state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
+      log_info("Start concentration imputation ", state)
+    }, ignoreInit = TRUE)
+
     blq_imputation_rule <- reactive({
       req(input$select_blq_strategy)
       rule_list <- switch(input$select_blq_strategy,

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

@@ -131,6 +131,7 @@ general_exclusions_server <- function(
 
         xbtn_counter(max(new_ids))
         exclusion_list(rehydrated_list)
+        log_info("Exclusions restored from settings: ", length(overrides), " rules loaded")
       }
     })
 
@@ -166,7 +167,12 @@ general_exclusions_server <- function(
 
     # Register observers for new remove buttons (shared helper)
     observe({
-      .register_remove_observers(exclusion_list, registered_xbtns, input)
+      .register_remove_observers(
+        exclusion_list, registered_xbtns, input,
+        on_remove = function(item) {
+          log_info("Exclusion removed: reason='", item$reason, "'")
+        }
+      )
     })
 
     # Render the exclusions table (not shown if empty)

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

@@ -84,7 +84,7 @@ manual_slopes_table_server <- function(
 
     # Add a new row to the table when the user clicks the add button
     observeEvent(input$add_rule, {
-      log_trace("{id}: adding manual slopes row")
+      log_trace("Slope selector: adding manual slope rule")
       first_group <- slopes_pknca_groups()[1, ]
       time_col <- pknca_data()$conc$columns$time
       new_row <- cbind(
@@ -121,7 +121,7 @@ manual_slopes_table_server <- function(
 
     # Remove selected rows from the table when the user clicks the remove button
     observeEvent(input$remove_rule, {
-      log_trace("{id}: removing manual slopes row")
+      log_trace("Slope selector: removing manual slope rule")
       req(manual_slopes())
       selected <- getReactableState("manual_slopes", "selected")
       req(selected)
@@ -135,7 +135,7 @@ manual_slopes_table_server <- function(
     # Render the manual slopes table (reactable)
     output$manual_slopes <- renderReactable({
       req(manual_slopes())
-      log_trace("{id}: rendering slope edit data table")
+      log_trace(id, ": rendering slope edit data table")
       isolate({
         data <- manual_slopes()
       })

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

@@ -318,6 +318,18 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       )
     })
 
+    # Log parameter selection changes (debounced to avoid noise from rapid clicks)
+    selections_debounced <- debounce(selections_state, 2000)
+    observeEvent(selections_debounced(), {
+      state <- selections_debounced()
+      req(state)
+      study_types <- study_types_list()
+      for (st in study_types) {
+        n_params <- sum(state[[st]], na.rm = TRUE)
+        log_info("Parameter selection for '", st, "': ", n_params, " parameters selected.")
+      }
+    }, ignoreInit = TRUE)
+
     observeEvent(input$clear_all, {
       state <- selections_state()
       req(state)