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quickfix for errors related to error checking in as.peakData #15

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Merged
clabornd merged 1 commit into from
Dec 20, 2024
Merged

quickfix for errors related to error checking in as.peakData #15

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14 changes: 10 additions & 4 deletions Observers/upload_observers.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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 #

Expand Down Expand Up @@ -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)
})
}

Expand All @@ -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$h_column, isolate(extra_elements()))
Expand Down Expand Up @@ -145,15 +148,18 @@ observeEvent(input$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
Expand All @@ -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
Expand Down
30 changes: 15 additions & 15 deletions renv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,7 @@
},
"ape": {
"Package": "ape",
"Version": "5.8",
"Version": "5.8-1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
Expand All @@ -154,7 +154,7 @@
"stats",
"utils"
],
"Hash": "16b5ff4dff0ead9ea955f62f794b1535"
"Hash": "54e5b03e928da23e75dc5bb633648d27"
},
"askpass": {
"Package": "askpass",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -492,8 +492,8 @@
"RemoteHost": "api.github.com",
"RemoteRepo": "ftmsRanalysis",
"RemoteUsername": "EMSL-Computing",
"RemoteRef": "d8338edbe7df167085b60e7c1b660ad018900028",
"RemoteSha": "d8338edbe7df167085b60e7c1b660ad018900028",
"RemoteRef": "8753cb08900045e0763e9be7aa293e98de62a490",
"RemoteSha": "8753cb08900045e0763e9be7aa293e98de62a490",
"Requirements": [
"R",
"RColorBrewer",
Expand All @@ -514,7 +514,7 @@
"tidyr",
"vegan"
],
"Hash": "5043412e26f5d551e620aa688e2eb3aa"
"Hash": "0f4f9535c3cf1fcda1ad376ca0bcf0b4"
},
"generics": {
"Package": "generics",
Expand Down Expand Up @@ -708,7 +708,7 @@
},
"igraph": {
"Package": "igraph",
"Version": "2.1.1",
"Version": "2.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
Expand All @@ -727,7 +727,7 @@
"utils",
"vctrs"
],
"Hash": "c03878b48737a0e2da3b772d7b2e22da"
"Hash": "9a93b743b2461ba06ba3b5df12011145"
},
"isoband": {
"Package": "isoband",
Expand Down Expand Up @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down