feat: handle deletion of samples when contrasts are already uploaded

bigomics · Mar 1, 2024 · c83cf2c · c83cf2c
1 parent bd0e001
commit c83cf2c
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Showing 3 changed files with 26 additions and 16 deletions.
diff --git a/components/00SourceAll.R b/components/00SourceAll.R
@@ -173,10 +173,7 @@ if(!file.exists('00SourceAll.R')) {
   source('board.upload/R/upload_module_makecontrast.R',encoding='UTF-8')
   source('board.upload/R/upload_module_outliers.R',encoding='UTF-8')
   source('board.upload/R/upload_module_preview.R',encoding='UTF-8')
-  source('board.upload/R/upload_plot_contraststats.R',encoding='UTF-8')
-  source('board.upload/R/upload_plot_countstats.R',encoding='UTF-8')
   source('board.upload/R/upload_plot_pcaplot.R',encoding='UTF-8')
-  source('board.upload/R/upload_plot_phenostats.R',encoding='UTF-8')
   source('board.upload/R/upload_server.R',encoding='UTF-8')
   source('board.upload/R/upload_ui.R',encoding='UTF-8')
   source('board.upload/R/upload_utils.R',encoding='UTF-8')

diff --git a/components/board.upload/R/upload_module_preview.R b/components/board.upload/R/upload_module_preview.R
@@ -192,8 +192,8 @@ upload_table_preview_counts_server <- function(
           showCancelButton = TRUE,
           closeOnEsc = FALSE,
           callbackR = delete_all_files_counts,
-          confirmButtonText = "Yes, remove counts",
-          cancelButtonText = "No, cancel"
+          confirmButtonText = "Yes, remove all files.",
+          cancelButtonText = "No, cancel deletion."
         )} else {
           uploaded$counts.csv <- NULL
         }
@@ -360,7 +360,30 @@ upload_table_preview_samples_server <- function(
     })
 
     observeEvent(input$remove_samples, {
-      uploaded$samples.csv <- NULL
+
+      delete_all_files_samples <- function(value) {
+        if(input$alert_delete_samples){
+          uploaded$samples.csv <- NULL
+          uploaded$contrasts.csv <- NULL
+        }
+      }
+
+      # if samples is not null, warn user that it will be deleted
+      if(!is.null(uploaded$contrasts.csv)){
+        # make a pop up and give user option to delete all files or just counts
+        shinyalert::shinyalert(
+          inputId = "alert_delete_samples",
+          title = "Warning",
+          text = "Removing samples will also remove contrasts. Do you want to proceed?",
+          type = "warning",
+          showCancelButton = TRUE,
+          closeOnEsc = FALSE,
+          callbackR = delete_all_files_samples,
+          confirmButtonText = "Yes, remove samples and contrasts.",
+          cancelButtonText = "No, cancel deletion."
+        )} else {
+          uploaded$counts.csv <- NULL
+        }
     })
 
     observeEvent(input$load_example, {

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
@@ -481,16 +481,6 @@ UploadBoard <- function(id,
 
         ## Check if samples.csv exists before uploading contrast.csv
         cc <- checked_samples()
-        if (!is.null(checked) && is.null(cc$matrix)) {
-          status <- "ERROR: please upload samples file first."
-          checked <- NULL
-          # pop up telling the user to upload samples.csv first
-          shinyalert::shinyalert(
-            title = "Samples.csv file missing",
-            text = "Please upload the samples.csv file first.",
-            type = "error"
-          )
-        }
 
         ## -------------- max contrast check ------------------
         MAXCONTRASTS <- as.integer(auth$options$MAX_COMPARISONS)