shiny progress bar appearing prematurely - shiny

Question

I am trying to use progress bars (via the command 'withProgress') to monitor the completion of a pipeline that I am running in shiny.
There are 6 progress bars. The pipeline is initiated by the uploading of a file and subsequent clicking of an "actionButton" (inputId=action). However, 3 of the progress bars appear temporarily before I have even uploaded the file. And then when I run the pipeline they appear in the wrong order i.e. the one that should be first comes second etc.
Can anyone tell me why this might be happening and how I can rectify it?
Below is a sample of what the pipeline looks like:
#ui.R
shinyUI(fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file1', 'Choose CSV File',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
tags$hr(),
checkboxInput('header', 'Header', TRUE),
radioButtons('sep', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
'"')
),
mainPanel(
plotOutput('plot')
)
)
))
#server.R
server <- function(input, output, session) {
read <- reactive({
dataInput <- eventReactive(input$action{
inFile <- input$file1
if (is.null(inFile))
return(NULL)
isolate(file<-read.csv(inFile$datapath, header = input$header,
sep = input$sep))
file
})
file_data_manipulated<-reactive({
withProgress(message = 'Please Wait',
detail = 'This may take a while...', value = 0, {
for (i in 1:15) {
incProgress(1/15)
Sys.sleep(0.25)
}
as.numeric(dataInput())
})
})
output$plot<-renderPlot({
withProgress(message = 'Please Wait',
detail = 'This may take a while...', value = 0, {
for (i in 1:15) {
incProgress(1/15)
Sys.sleep(0.25)
}
plot(file_data_manipulated(), main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5, cex.axis = 1.5, cex.main = 2)
abline(h = input$cutoff_filter, col = "red")
#legend("bottomleft", scc$csize>1, pt.bg=unique(node_colors), pch=21)
})
})

Answer 1

I think that your code is incomplete. The progress bars appear before because as soon as the server function is called, all the code inside the reactive function will be executed, you need to provide mechanism to control when to show the progress bars. In this case just checking that the file was correctly uploaded with a if would be enough.
I modified your code to show how to control the reactive functions. Since I don't know how your input file is, I just plot some basic data. Also, I don't know how are you using the read <- reactive({, so just removed it.
library(shiny)
ui <- shinyUI(fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput('file1', 'Choose CSV File',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
tags$hr(),
checkboxInput('header', 'Header', TRUE),
radioButtons('sep', 'Separator',
c(Comma=',',
Semicolon=';',
Tab='\t'),
','),
radioButtons('quote', 'Quote',
c(None='',
'Double Quote'='"',
'Single Quote'="'"),
'"'),
br(),
actionButton('action', 'action')
),
mainPanel(
plotOutput('plot')
)
)
))
server <- function(input, output, session) {
dataInput <- eventReactive(input$action, {
inFile <- input$file1
if (is.null(inFile))
return(NULL)
isolate({
file <- read.csv(inFile$datapath, header = input$header,
sep = input$sep)
})
file
})
file_data_manipulated <- reactive({
input$action
if (is.null(dataInput()))
return(NULL)
withProgress(message = 'Please Wait 1',
detail = 'This may take a while...', value = 0, {
for (i in 1:15) {
incProgress(1/15)
Sys.sleep(0.25)
}
as.numeric(dataInput())
})
})
output$plot <- renderPlot({
input$action
if (is.null(dataInput()))
return(NULL)
withProgress(message = 'Please Wait 2',
detail = 'This may take a while...', value = 0, {
for (i in 1:15) {
incProgress(1/15)
Sys.sleep(0.25)
}
# plot(file_data_manipulated(), main = "Sample clustering to detect outliers",
# sub="", xlab="", cex.lab = 1.5, cex.axis = 1.5, cex.main = 2)
# abline(h = input$cutoff_filter, col = "red")
#legend("bottomleft", scc$csize>1, pt.bg=unique(node_colors), pch=21)
plot(sin, -pi, 2*pi)
})
})
}
runApp(list(ui = ui, server = server))