@@ -21,7 +21,7 @@ geneSetsServer <- function(id){

   moduleServer( id, function(input, output, session){

     geneSets <- reactive({

       if(input$genesetSourceType == "fileGeneset"){

-        if(is.null(input$genesetFile)) return(NULL)

+        if(is.null(input$genesetFile)) return(NULL) #this is in order to disable "run" btn

         genesets <- getGmt(input$genesetFile$datapath)

       } else {

         if(is.null(input$genesetVar)) return(NULL)

deleted file mode 100644

@@ -1,13 +0,0 @@

-name: shinyApp

-title: shinyApp

-username:

-account: prodriguez-bio2

-server: shinyapps.io

-hostUrl: https://api.shinyapps.io/v1

-appId: 3971711

-bundleId: 4476074

-url: https://prodriguez-bio2.shinyapps.io/shinyapp/

-when: 1618503477.40691

-lastSyncTime: 1618503477.40694

-asMultiple: FALSE

-asStatic: FALSE

@@ -30,26 +30,46 @@ function(input, output, session) {

   # ARGUMENTS

   argInp <- argumentsDataServer("argumentsInput")

+  

   #### GSVA RESULTS ####

+  ## REACTIVE VALUES

   rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

-                       errors.gsva = NULL)

+                       p2=NULL, p3=NULL, errors.gsva = NULL, sample.c = NULL)

   gsva.cancel <- reactiveVal(FALSE)

+  ## GSVA RESULT

   observeEvent( input$button, {

+    

+    ## This js is in order to reset the event_data from the plotlys,

+    ## so every time the .user hits the 'run' button, plotlys get back to null

     runjs("Shiny.setInputValue('plotly_click-click1', null);")

     runjs("Shiny.setInputValue('plotly_click-click2', null);")

+    

+    ## here we reset all the reactiveValues to NULL

     rv$gs <- NULL

     rv$dat.t <- NULL

     rv$p <- NULL

     rv$p2 <- NULL

     rv$p3 <- NULL

-    rv$errors.gsva = NULL

+    rv$sample.c <- NULL

+    rv$errors.gsva <- NULL

+    

+    ## this is a flag for the future. Futures cannot be canceled or

+    ## terminated in a strict way, so when they get interrupted they

+    ## throw an error that is not related to gsva(). When future is 

+    ## interrupted, the flag goes TRUE in order to make the errors

+    ## message print NULL

     gsva.cancel(FALSE)

+    

     modalGSVAUI("modal.text")

-    # future() cannot take reactive values, so we must isolate() them

+    

+    ## future() cannot take reactive values, so we must isolate() them

     future({

+      ## sink() will redirect all console cats and prints to a

+      ## text file that the main session will be reading in order

+      ## to print the progress bar from bplaply()

       sink(rout)

       result <- gsva(isolate(matrix()),

                      isolate(genesets()), 

@@ -64,20 +84,35 @@ function(input, output, session) {

                      ssgsea.norm=isolate(argInp$ssgseaNorm()),

                      verbose=TRUE)

       sink()

+      ## when gsva() ends, we reset the console text file to empty

       write("", file=rout)

       return(result)

     }, seed = TRUE) %...>%

       (function(result){

+        ## the future's result will be the gsva() result, and we save it

+        ## and transform it in reactiveValues(). In order to make the future

+        ## not block the app at an inner-session level, we save the results in

+        ## reactiveValues() and then at the end of the observeEvent() we return NULL

+        ## in order to make the plots.

+        ## https://github.com/rstudio/promises/issues/23#issuecomment-386687705

         rv$gs <- result

         rv$dat.t <- melt(as.data.table(rv$gs, keep.rownames = "gene.sets"),

                          variable.name = "Sample", id.vars="gene.sets")

         rv$n <- length(levels(rv$dat.t$Sample))

         rv$dd.col <- hcl(h = seq(15, 375, length=rv$n), l = 65, c = 100)[1:rv$n]

         names(rv$dd.col)  <- levels(rv$dat.t$Sample)

+        

+        ## finally, we leave the console.text file empty again and

+        ## remove the modal

         write("", file=rout)

         removeModal()

       }) %...!%

       (function(error){

+        ## there can be two ways to get an error here: 

+        ## 1. gsva() fails, which is an ok error and should be returnet to user

+        ## 2. User interrupts the future, which shouldn't be printed, that's

+        ## why I use a flag to identify if error comes from pressing "Cancel" btn

+        ## on the modal

         removeModal()

         write("", file=rout)

         if(gsva.cancel()){