Logging

DESCRIPTION

@@ -44,6 +44,7 @@ Imports: shiny,
     factoextra,
     heatmaply,
     shinyBS,
-    shinythemes
+    shinythemes,
+    log4r
 RoxygenNote: 6.0.1
 biocViews:

NAMESPACE

@@ -32,6 +32,7 @@ export(pca)
 export(pcaUI)
 export(scatterPlot)
 export(scatterPlotUI)
+export(set_logger)
 export(transformation)
 export(transformationUI)
 import(data.table)

R/and.R

@@ -254,6 +254,8 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
     on.exit(progress$close())
     progress$set(0, message = "Apply Filter")
 
+    log_message(message = "Applying filter...", level = "INFO", token = session$token)
+
     or.modules <- modules()
 
     step <- 0.9 / length(or.modules)
@@ -280,6 +282,8 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
 
     progress$set(1)
 
+    log_message(message = "Done.", level = "INFO", token = session$token)
+
     return(list(bool = and.selection.bool, text = unlist(or.selection.text)))
   })
 

R/featureSelector.R

@@ -143,6 +143,8 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
 
   # reset row_selector
   shiny::observeEvent(input$reset, {
+    log_message(message = "Filter reset", level = "INFO", token = session$token)
+
     value(NULL)
     row_selector <<- shiny::callModule(orNumeric, "row_selector", choices = choices, value = value_wrapper, label = "Select n features from the top and/or bottom of the list", stepsize = 1)
   })
@@ -238,6 +240,8 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
 
   # first filter (and) whole set in table
   select <- shiny::eventReactive(eventExpr = input$select, {
+    log_message(message = "Filtering data", level = "INFO", token = session$token)
+
     data <- data.r()[and_selected()$bool]
   })
 

R/geneView.R

@@ -166,6 +166,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
 
   # reset
   shiny::observeEvent(input$reset, {
+    log_message("GeneView: reset", "INFO", token = session$token)
+
     shinyjs::reset("genes")
     shinyjs::reset("plotType")
     shinyjs::reset("groupby")
@@ -261,6 +263,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
   shinyjs::disable("download")
 
   plot <- shiny::eventReactive(input$plot, {
+    log_message("GeneView: computing plot...", "INFO", token = session$token)
+
     # enable downloadButton
     shinyjs::enable("download")
     clearPlot(FALSE)
@@ -295,6 +299,7 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
       scale = size()$scale
     )
 
+    log_message("GeneView: done.", "INFO", token = session$token)
     progress$set(1, detail = "Return plot")
     return(plot)
   })
@@ -340,6 +345,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
       if(clearPlot()) {
         return()
       } else {
+        log_message("GeneView: render plot interactive", "INFO", token = session$token)
+
         #progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
@@ -359,6 +366,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
         if(clearPlot()) {
           return()
         } else {
+          log_message("GeneView: render plot static", "INFO", token = session$token)
+
           #progress indicator
           progress <- shiny::Progress$new()
           on.exit(progress$close())
@@ -374,6 +383,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
 
   output$download <- shiny::downloadHandler(filename = "geneView.zip",
                                             content = function(file) {
+                                              log_message("GeneView: download", "INFO", token = session$token)
+
                                               download(file = file, filename = "geneView.zip", plot = plot()$plot, width = plot()$width, height = plot()$height, ppi = plot()$ppi, ui = user_input())
                                             })
 

R/global.R

@@ -0,0 +1,37 @@
+
+wilson.globals <- new.env(parent = emptyenv())
+
+#' set a log4r logger used within the package
+#'
+#' @param logger A logger object see \code{\link[log4r]{create.logger}}. NULL to disable logging.
+#' @param token Set a unique identifier for this logger.
+#'
+#' @details This function will save each logger in the wilson.globals environment. Each logger is stored by the name 'logger'[token] (e.g. 'logger6b821824b0b53b1a3e8f531a34d0d6e6').
+#' @details Use onSessionEnded to clean up after logging. See \code{\link[shiny]{onFlush}}.
+#'
+#' @export
+set_logger <- function(logger, token = NULL) {
+  if(is.null(logger) || is(logger, "logger")) {
+    assign(x = paste0("logger", token), value = logger, envir = wilson.globals)
+  }
+}
+
+#' logger message convenience function
+#'
+#' @param message String of message to be written in log. See \code{\link[log4r]{levellog}}.
+#' @param level Set priority level of the message (number or character). See \code{\link[log4r]{levellog}}.
+#' @param token Use token bound to this identifier.
+#'
+log_message <- function(message, level = c("DEBUG", "INFO", "WARN", "ERROR", "FATAL"), token = NULL) {
+  logger <- get(paste0("logger", token), envir = wilson.globals)
+
+  if(!is.null(logger)) {
+    switch(level,
+      DEBUG = log4r::debug(logger, message),
+      INFO = log4r::info(logger, message),
+      WARN = log4r::warn(logger, message),
+      ERROR = log4r::error(logger, message),
+      FATAL = log4r::fatal(logger, message)
+    )
+  }
+}

R/global_cor_heatmap.R

@@ -225,6 +225,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
 
   # reset ui
   shiny::observeEvent(input$reset, {
+    log_message("Global correlation heatmap: reset", "INFO", token = session$token)
+
     shinyjs::reset("calc")
     shinyjs::reset("calc_method")
     shinyjs::reset("distance")
@@ -313,6 +315,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
 
   # build plot object
   plot <- shiny::eventReactive(input$plot, {
+    log_message("Global correlation heatmap: computing plot...", "INFO", token = session$token)
+
     # enable downloadButton
     shinyjs::enable("download")
     # show plot
@@ -362,6 +366,7 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     # update progress indicator
     progress$set(1)
 
+    log_message("Global correlation heatmap: done.", "INFO", token = session$token)
     return(plot)
   })
 
@@ -374,6 +379,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
         if(clearPlot()) {
           return()
         } else {
+          log_message("Global correlation heatmap: render plot static", "INFO", token = session$token)
+
           # progress indicator
           progress <- shiny::Progress$new()
           on.exit(progress$close())
@@ -395,6 +402,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
       if(clearPlot()) {
         return()
       } else {
+        log_message("Global correlation heatmap: render plot interactive", "INFO", token = session$token)
+
         # progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
@@ -412,6 +421,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
 
   output$download <- shiny::downloadHandler(filename = "global_correlation_heatmap.zip",
                                             content = function(file) {
+                                              log_message("Global correlation heatmap: download", "INFO", token = session$token)
+
                                               download(file = file, filename = "global_correlation_heatmap.zip", plot = plot()$plot, width = plot()$width, height = plot()$height, ppi = plot()$ppi, ui = user_input())
                                             })
 

R/heatmap.R

@@ -213,6 +213,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
 
   # reset ui
   shiny::observeEvent(input$reset, {
+    log_message("Heatmap: reset", "INFO", token = session$token)
+
     shinyjs::reset("cluster.distance")
     shinyjs::reset("cluster.method")
     shinyjs::reset("clustering")
@@ -254,6 +256,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
   shinyjs::disable("download")
 
   plot <- shiny::eventReactive(input$plot, {
+    log_message("Heatmap: computing plot...", "INFO", token = session$token)
+
     # enable downloadButton
     shinyjs::enable("download")
     clearPlot(FALSE)
@@ -291,6 +295,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     )
     progress$set(1)
 
+    log_message("Heatmap: done.", "INFO", token = session$token)
     return(plot)
   })
 
@@ -304,6 +309,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
       if(clearPlot()) {
         return()
       } else {
+        log_message("Heatmap: render plot interactive", "INFO", token = session$token)
+
         #new progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
@@ -328,6 +335,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
         if(clearPlot()) {
           return()
         } else {
+          log_message("Heatmap: render plot static", "INFO", token = session$token)
+
           #new progress indicator
           progress <- shiny::Progress$new()
           on.exit(progress$close())
@@ -343,6 +352,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
 
   output$download <- shiny::downloadHandler(filename = "heatmap.zip",
                                             content = function(file) {
+                                              log_message("Heatmap: download", "INFO", token = session$token)
+
                                               download(file = file, filename = "heatmap.zip", plot = plot()$plot, width = plot()$width, height = plot()$height, ppi = plot()$ppi, ui = user_input())
                                             })
 

R/pca.R

@@ -154,6 +154,8 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
 
   #reset ui
   shiny::observeEvent(input$reset, {
+    log_message("PCA: reset", "INFO", token = session$token)
+
     shinyjs::reset("label")
     shinyjs::reset("dimA")
     shinyjs::reset("dimB")
@@ -235,6 +237,8 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
   shinyjs::disable("download")
 
   computed.data <- shiny::eventReactive(input$plot, {
+    log_message("PCA: computing plot...", "INFO", token = session$token)
+
     # enable downloadButton
     shinyjs::enable("download")
     clearPlot(FALSE)
@@ -262,6 +266,8 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
 
     progress$set(1)
 
+    log_message("PCA: done.", "INFO", token = session$token)
+
     # show plot
     shinyjs::show("pca")
 
@@ -287,6 +293,8 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
       if(clearPlot()){
         return()
       } else {
+        log_message("PCA: render plot", "INFO", token = session$token)
+
         computed.data()$plot
       }
     })
@@ -302,6 +310,7 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
 
   output$download <- shiny::downloadHandler(filename = "pca.zip",
                                             content = function(file) {
+                                              log_message("PCA: download", "INFO", token = session$token)
                                               download(file = file, filename = "pca.zip", plot = computed.data()$plot, width = plot_width() / (computed.data()$ppi / 2.54), height = plot_height() / (computed.data()$ppi / 2.54), ppi = computed.data()$ppi, ui = user_input())
                                             })
 

R/scatterPlot.R

@@ -188,6 +188,8 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
 
   #reset ui
   shiny::observeEvent(input$reset, {
+    log_message("Scatterplot: reset", "INFO", token = session$token)
+
     shinyjs::reset("density")
     shinyjs::reset("line")
     shinyjs::reset("pointsize")
@@ -311,6 +313,8 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
   shinyjs::disable("download")
 
   plot <- shiny::eventReactive(input$plot, {
+    log_message("Scatterplot: computing plot...", "INFO", token = session$token)
+
     #enable downloadbutton
     shinyjs::enable("download")
     clearPlot(FALSE)
@@ -358,6 +362,7 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
     )
 
     progress$set(1)
+    log_message("Scatterplot: done.", "INFO", token = session$token)
     return(plot)
   })
 
@@ -382,6 +387,8 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
         if(clearPlot()) {
           return()
         } else {
+          log_message("Scatterplot: render plot static", "INFO", token = session$token)
+
           plot()$plot
         }
       }
@@ -391,6 +398,8 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
       if(clearPlot()) {
         return()
       } else {
+        log_message("Scatterplot: render plot interactive", "INFO", token = session$token)
+
         #new progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
@@ -406,6 +415,7 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
 
   output$download <- shiny::downloadHandler(filename = "scatterPlot.zip",
     content = function(file) {
+      log_message("Scatterplot: download", "INFO", token = session$token)
       download(file = file, filename = "scatterPlot.zip", plot = plot()$plot, width = plot()$width, height = plot()$height, ppi = plot()$ppi, ui = user_input())
     }
   )