attempt to rewrite ref$df from counts_log_correction namespace

components/board.upload/R/upload_server.R

@@ -228,6 +228,7 @@ UploadBoard <- function(id,
       },
       {
         ## get uploaded counts
+        check <- NULL
         df0 <- uploaded$counts.csv
         if (is.null(df0)) {
           return(list(status = "Missing counts.csv", matrix = NULL))
@@ -240,11 +241,14 @@ UploadBoard <- function(id,
         write_check_output(res$checks, "COUNTS", raw_dir())
 
         # check if error 29 exists (log2 transform detected), give action to user revert to intensities or skip correction
-        counts_log_correction <- function() {
+        counts_log_correction <- function(res) {
           if (input$logCorrectCounts) {
-            res$df <- 2**res$df
-            if(min(res$df,na.rm=TRUE) > 0) res$df <- res$df - 1
+            res$df <<- 2**res$df
+            if(min(res$df,na.rm=TRUE) > 0) res$df <<- res$df - 1
           }
+          # store check and data regardless of it errors (after counts log correction if user accepts it)
+          write.csv(res$df, file.path(OPG, "user_counts_log_corrected.csv"), row.names = TRUE)
+          checked <<- res$df
         }
 
         if ("e29" %in% names(res$checks)) {
@@ -259,10 +263,13 @@ UploadBoard <- function(id,
             immediate = TRUE,
             callbackR = counts_log_correction
           )
+        } else {
+          checked <- res$df
         }
 
-        # store check and data regardless of it errors (after counts log correction if user accepts it)
-        checked <- res$df
+        # R continues execution after shinyalert, so we need to check if checked is defined.
+        browser()
+        req(exists("check"), check)
 
         checklist[["counts.csv"]]$checks <- res$checks
         if (res$PASS) {