quickfix for errors related to error checking in as.peakData

EMSL-Computing · Dec 20, 2024 · a1e0ce1 · a1e0ce1
1 parent d0899b1
commit a1e0ce1
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Showing 3 changed files with 26 additions and 20 deletions.
diff --git a/Observers/upload_observers.R b/Observers/upload_observers.R
@@ -52,7 +52,7 @@ observeEvent(input$upload_click, {
       'Formula column is not a character vector. Please select another.')
 
     ) # End error handling #
-    tryCatch({
+    ftms_obj <- tryCatch({
       revals$warningmessage_upload$makeobject_error <- NULL
       if (input$isotope_yn == 1 & isTRUE(input$iso_info_filter == 1)) { # If there's C13 #
 
@@ -81,10 +81,13 @@ observeEvent(input$upload_click, {
           mf_cname = input$f_column,
           check_rows = TRUE, data_scale = input$data_scale)
       }
+
+      res
     },
     error = function(e) {
       msg = paste0('Error making your peakData: \n System error: ', e)
       revals$warningmessage_upload$makeobject_error <<- sprintf("<p style = 'color:red'>%s</p>", msg)
+      return(NULL)
     })
   }
 
@@ -110,7 +113,7 @@ observeEvent(input$upload_click, {
     for (col in as.character(isolate(extra_elements()))) {
         validate(need(is.numeric(Emeta()[, col]), 'One or more elemental columns are non-numeric.'))
     } # End error handling #
-    tryCatch({
+    ftms_obj <- tryCatch({
       revals$warningmessage_upload$makeobject_error <- NULL
       # Combine Hydrogen and Carbon names with extra element columns
       all_element_cols <- c("C"=input$c_column, "H"=input$h_column, isolate(extra_elements()))
@@ -145,15 +148,18 @@ observeEvent(input$upload_click, {
       if (input$NA_value != "NA") {
         res <- edata_replace(res, input$NA_value, NA)
       }
+
+      res
     },
     error = function(e) {
       msg = paste0('Error making your peakData: \n System error: ', e)
       revals$warningmessage_upload$makeobject_error <<- sprintf("<p style = 'color:red'>%s</p>", msg)
+      return(NULL)
     })
 
   } # End elemental column if statement
 
-  if (exists('res')) {
+  if (!is.null(ftms_obj)) {
     shinyjs::show('upload_success')
 
     # reset 'removed samples' reval
@@ -162,7 +168,7 @@ observeEvent(input$upload_click, {
     updateCollapse(session, 'upload_collapse', close = c('file_upload', 'column_info'))
     shinyjs::show('ok_idcols')
 
-    revals$uploaded_data <- res
+    revals$uploaded_data <- ftms_obj
   }
 
 }) # End peakData creation

diff --git a/renv.lock b/renv.lock
@@ -139,7 +139,7 @@
     },
     "ape": {
       "Package": "ape",
-      "Version": "5.8",
+      "Version": "5.8-1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -154,7 +154,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "16b5ff4dff0ead9ea955f62f794b1535"
+      "Hash": "54e5b03e928da23e75dc5bb633648d27"
     },
     "askpass": {
       "Package": "askpass",
@@ -178,13 +178,13 @@
     },
     "bit": {
       "Package": "bit",
-      "Version": "4.5.0",
+      "Version": "4.5.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "5dc7b2677d65d0e874fc4aaf0e879987"
+      "Hash": "f89f074e0e49bf1dbe3eba0a15a91476"
     },
     "bit64": {
       "Package": "bit64",
@@ -314,13 +314,13 @@
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.5.0",
+      "Version": "0.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "91570bba75d0c9d3f1040c835cee8fba"
+      "Hash": "9df43854f1c84685d095ed6270b52387"
     },
     "crayon": {
       "Package": "crayon",
@@ -359,14 +359,14 @@
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.16.2",
+      "Version": "1.16.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "2e00b378fc3be69c865120d9f313039a"
+      "Hash": "38bbf05fc2503143db4c734a7e5cab66"
     },
     "datadr": {
       "Package": "datadr",
@@ -492,8 +492,8 @@
       "RemoteHost": "api.github.com",
       "RemoteRepo": "ftmsRanalysis",
       "RemoteUsername": "EMSL-Computing",
-      "RemoteRef": "d8338edbe7df167085b60e7c1b660ad018900028",
-      "RemoteSha": "d8338edbe7df167085b60e7c1b660ad018900028",
+      "RemoteRef": "8753cb08900045e0763e9be7aa293e98de62a490",
+      "RemoteSha": "8753cb08900045e0763e9be7aa293e98de62a490",
       "Requirements": [
         "R",
         "RColorBrewer",
@@ -514,7 +514,7 @@
         "tidyr",
         "vegan"
       ],
-      "Hash": "5043412e26f5d551e620aa688e2eb3aa"
+      "Hash": "0f4f9535c3cf1fcda1ad376ca0bcf0b4"
     },
     "generics": {
       "Package": "generics",
@@ -708,7 +708,7 @@
     },
     "igraph": {
       "Package": "igraph",
-      "Version": "2.1.1",
+      "Version": "2.1.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -727,7 +727,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "c03878b48737a0e2da3b772d7b2e22da"
+      "Hash": "9a93b743b2461ba06ba3b5df12011145"
     },
     "isoband": {
       "Package": "isoband",
@@ -970,13 +970,13 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.2.2",
+      "Version": "2.3.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "d413e0fef796c9401a4419485f709ca1"
+      "Hash": "5bfe2927efa9f87766ca9605301ea48f"
     },
     "pander": {
       "Package": "pander",

diff --git a/ui.R b/ui.R
@@ -15,7 +15,7 @@ ui <- tagList(useShinyjs(),
   ),
 
   navbarPage(
-    title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.4")),
+    title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.5")),
     windowTitle = 'FREDA',
     id = "top_page",
     theme = "yeti.css",