bypass upload_module_outliers (crashing) in order to test computation…

…; clean up
bigomics · Mar 12, 2024 · 1ba9b06 · 1ba9b06
1 parent ee12084
commit 1ba9b06
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Showing 3 changed files with 13 additions and 13 deletions.
diff --git a/components/board.upload/R/upload_module_computepgx.R b/components/board.upload/R/upload_module_computepgx.R
@@ -406,6 +406,7 @@ upload_module_computepgx_server <- function(
         if (!is.null(upload_wizard()) && upload_wizard() != "wizard_finished") {
           return(NULL)
         }
+        browser()
 
         # TODO MOVE THIS TO THE WIZARD MODULE OR in selected_upload listener
         # if (!is.null(input$selected_name) && !isValidFileName(input$selected_name)) {
@@ -429,17 +430,17 @@ upload_module_computepgx_server <- function(
           return(NULL)
         }
 
-        ## check for name and description
-        has.name <- input$selected_name != ""
-        has.description <- input$selected_description != ""
-        if (!has.name || !has.description) {
-          shinyalert::shinyalert(
-            title = "ERROR",
-            text = "You must give a dataset name and description",
-            type = "error"
-          )
-          return(NULL)
-        }
+        # #TODO check for name and description.. remove this code as its not necessary anymore
+        # has.name <- input$selected_name != ""
+        # has.description <- input$selected_description != ""
+        # if (!has.name || !has.description) {
+        #   shinyalert::shinyalert(
+        #     title = "ERROR",
+        #     text = "You must give a dataset name and description",
+        #     type = "error"
+        #   )
+        #   return(NULL)
+        # }
 
         ## -----------------------------------------------------------
         ## Retrieve the most recent matrices from reactive values

diff --git a/components/board.upload/R/upload_module_outliers.R b/components/board.upload/R/upload_module_outliers.R
@@ -195,7 +195,6 @@ upload_module_outliers_server <- function(id, r_X, r_samples, r_contrasts,
 
       ## IMPUTE FIRST OR NORMALIZE????
       imputedX <- reactive({
-
         shiny::req(r_X())
         counts <- r_X()
         X <- log2(1 + counts)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
@@ -574,7 +574,7 @@ UploadBoard <- function(id,
 
     computed_pgx <- upload_module_computepgx_server(
       id = "compute",
-      countsRT = corrected1$correctedCounts,
+      countsRT = shiny::reactive(checked_counts()$matrix), #TODO add return from new-bc module: corrected1$correctedCounts,
       samplesRT = shiny::reactive(checked_samples()$matrix),
       contrastsRT = modified_ct,
       raw_dir = raw_dir,