Merge pull request #1305 from bigomics/upload-fail-catch

Catch upload data error

components/board.upload/R/upload_module_preview_contrasts.R

@@ -332,21 +332,27 @@ upload_table_preview_contrasts_server <- function(
         return()
       }
 
-      ct <- playbase::read.as_matrix(input$contrasts_csv$datapath)
-
-      ## IK: should we do contrasts.convertToLabelMatrix here
-      ## already?  to allow for short/old formats?
-      ## samples <- checked_samples()$SAMPLES
-      samples <- uploaded$samples.csv
-      new.ct <- try(playbase::contrasts.convertToLabelMatrix(
-        contrasts = ct, samples = samples
-      ))
-      if (!"try-error" %in% class(new.ct)) {
-        ct <- new.ct
+      ct <- tryCatch({
+        playbase::read.as_matrix(input$contrasts_csv$datapath)
+      }, error = function(w) {NULL})
+      if (is.null(ct)) {
+        data_error_modal(
+          path = input$contrasts_csv$datapath,
+          data_type = "contrasts"
+        )
+      } else {
+        ## IK: should we do contrasts.convertToLabelMatrix here
+        ## already?  to allow for short/old formats?
+        ## samples <- checked_samples()$SAMPLES
+        samples <- uploaded$samples.csv
+        new.ct <- try(playbase::contrasts.convertToLabelMatrix(
+          contrasts = ct, samples = samples
+        ))
+        if (!"try-error" %in% class(new.ct)) {
+          ct <- new.ct
+        }
+        uploaded$contrasts.csv <- ct
       }
-
-
-      uploaded$contrasts.csv <- ct
     })
 
     observeEvent(input$remove_contrasts, {

components/board.upload/R/upload_module_preview_counts.R

@@ -271,24 +271,51 @@ upload_table_preview_counts_server <- function(
 
       sel <- grep("count|expression|abundance", tolower(input$counts_csv$name))
       if (length(sel)) {
-        df <- playbase::read_counts(input$counts_csv$datapath[sel[1]])
-        uploaded$counts.csv <- df
+        df <- tryCatch({
+          playbase::read_counts(input$counts_csv$datapath[sel[1]])
+        }, error = function(w) {NULL})
+        if (is.null(df)) {
+          data_error_modal(
+            path = input$counts_csv$datapath[sel[1]],
+            data_type = "counts"
+          )
+        } else {
+          uploaded$counts.csv <- df
 
-        ## if counts file contains annotation
-        af <- playbase::read_annot(input$counts_csv$datapath[sel[1]])
-        uploaded$annot.csv <- af
+          # if counts file contains annotation
+          af <- playbase::read_annot(input$counts_csv$datapath[sel[1]])
+          uploaded$annot.csv <- af
+        }
       }
 
       sel <- grep("samples", tolower(input$counts_csv$name))
       if (length(sel)) {
-        df <- playbase::read_samples(input$counts_csv$datapath[sel[1]])
-        uploaded$samples.csv <- df
+        df <- tryCatch({
+          playbase::read_samples(input$counts_csv$datapath[sel[1]])
+        }, error = function(w) {NULL})
+        if (is.null(df)) {
+          data_error_modal(
+            path = input$counts_csv$datapath[sel[1]],
+            data_type = "samples"
+          )
+        } else {
+          uploaded$samples.csv <- df
+        }
       }
 
       sel <- grep("contrast|comparison", tolower(input$counts_csv$name))
       if (length(sel)) {
-        df <- playbase::read_contrasts(input$counts_csv$datapath[sel[1]])
-        uploaded$contrasts.csv <- df
+        df <- tryCatch({
+          playbase::read_contrasts(input$counts_csv$datapath[sel[1]])
+        }, error = function(w) {NULL})
+        if (is.null(df)) {
+          data_error_modal(
+            path = input$counts_csv$datapath[sel[1]],
+            data_type = "contrasts"
+          )
+        } else {
+          uploaded$contrasts.csv <- df
+        }
       }
 
       sel <- grep("params.RData", input$counts_csv$name)

components/board.upload/R/upload_module_preview_samples.R

@@ -287,7 +287,17 @@ upload_table_preview_samples_server <- function(
         overwrite = TRUE
       )
 
-      uploaded$samples.csv <- playbase::read.as_matrix(input$samples_csv$datapath)
+      df <- tryCatch({
+        playbase::read.as_matrix(input$samples_csv$datapath)
+      }, error = function(w) {NULL})
+      if (is.null(df)) {
+        data_error_modal(
+          path = input$samples_csv$datapath,
+          data_type = "samples"
+        )
+      } else {
+        uploaded$samples.csv <- df
+      }
     })
 
     observeEvent(input$remove_samples, {

components/board.upload/R/upload_module_utils.R

@@ -0,0 +1,37 @@
+data_error_modal <- function(path, data_type) {
+  con <- file(path, "rb")
+  text_raw <- readBin(con, "raw", n = 1000)
+  close(con)
+  is_bin <- tryCatch({
+    paste(rawToChar(text_raw), collapse = "")
+  }, error = function(w) {NULL})
+  if (!is.null(is_bin)) {
+    shinyalert::shinyalert(
+      title = "Upload error",
+      text = shiny::tagList(
+        shiny::HTML(glue::glue("There seems to be an issue with your data file. It could be the data has been wrongly exported, <u><b><a href='https://omicsplayground.readthedocs.io/en/latest/dataprep/{data_type}/' target='_blank'>here</a></b></u> you can find the file specification documentation, and <u><b><a href='https://raw.githubusercontent.com/bigomics/playbase/refs/heads/main/inst/extdata/{data_type}.csv' target='_blank'>here</a></b></u> you can find a correct data file. <br><br> The 10 first lines of the input file are the following:")),
+        shiny::HTML("<br><br>"),
+        shiny::tags$pre(
+          paste(readLines(path, n = 10), collapse = "\n")
+        ),
+        shiny::HTML("We suggest visualizing on your computer the data using a plain text editor (rather than Excel) to check on your end the file is correct.")
+      ),
+      html = TRUE,
+      size = "l",
+      type = "error",
+      className = "left-align"
+    )
+  } else {
+    shinyalert::shinyalert(
+      title = "Upload error",
+      text = shiny::tagList(
+        shiny::HTML(glue::glue("There seems to be an issue with your data file. We detected it is a binary file rather than a plain text csv file. It could be the data has been wrongly exported. You can find the file specification documentation <u><b><a href='https://omicsplayground.readthedocs.io/en/latest/dataprep/{data_type}/' target='_blank'>here</a></b></u>.<br><br>")),
+        shiny::HTML("We suggest visualizing on your computer the data using a plain text editor (rather than Excel) to check on your end the file is correct.")
+      ),
+      html = TRUE,
+      size = "l",
+      type = "error",
+      className = "left-align"
+    )
+  }
+}

scss/components/_shinyalert.scss

@@ -0,0 +1,3 @@
+.left-align {
+  text-align: left !important;
+}

scss/main.scss

@@ -19,3 +19,4 @@
 @import "components/carousel.scss";
 @import "components/tick.scss";
 @import "components/navbar.scss";
+@import "components/shinyalert.scss";