How to Implement a Cleanup Routine in R Shiny

How to implement a cleanup routine in R Shiny?

The correct way to do this is to assign a function that performs your clean-up with session$onSessionEnded. For example, in server.R:

cancel.onSessionEnded <- session$onSessionEnded(function() {
    dbDisconnect(db)
})

You can then call cancel.onSessionEnded to undo the assignment.

How to clean up the shiny sidebar UI

Will this do?

library(shiny)
library(leaflet)

ui <- fluidPage(
    titlePanel("ShinyApp"),
    sidebarLayout(
        sidebarPanel(
            div(style='border: 1px solid grey; margin:1px;',
                h3("Separate1")
            ),
            div(style='border: 1px solid grey; margin:1px;',
                h3("Separate2")
            ),
            div(style='border: 1px solid grey; margin:1px;',
                h3("Separate3")
            ),
            div(style='border: 1px solid grey; margin:1px;',
                h3("Separate4")
            ),
            div(style='border: 1px solid grey; margin:1px;',
                h3("Separate5")
            )
            
        ),
        mainPanel(
            leafletOutput('maps')
        )
    )
)

server <- function(input, output, session) {
    
    output$maps <- renderLeaflet({
        leaflet() %>%
            addTiles()
    })
    
}
shinyApp(ui, server)

Sample Image

Cleaning a data frame inputed with fileInput and plotting it - R Shiny

I used the data that you had provided above and I managed to debug your code.

First of all I changed the last value of the variable dept to 10 and similarly the choices in selectInput because the merging of a and Dept_Names had resulted in an empty data frame and the app had crashed. To prevent crashing I added a function validate that requires that the data set a after merging is non empty.
I changed C to c within selectInput
data had no return value and I set it to the list where total_complete is a cleaned data frame and ofn is the name of the downloaded data frame:
```
return(list(total_complete = total_complete, ofn = ofn))
```
within two render* functions I added req(data()) which prevents errors if the data() is not available (when it is NULL)
added data()$ within render* functions to total_complete and changed Departments to Dept

To get nonempty plot and a nonempty table, after uploading the data which you included in your question, set the value of the selectInput to 10

I've made comments in the code to indicate all above changes.

Full code:

library(shiny)
library(shinydashboard)
library(ggplot2)
library(dplyr)

rm(ui)
rm(server)

Dept <- c(1,2,10) # changed 3 to 10 to avoid an empty data set a after merging.
DepartmentName <-c("abc","def","ghi")
Dept_Names <- cbind.data.frame(Dept,DepartmentName)

ui <- dashboardPage(   
  dashboardHeader(title="ABC"),
  dashboardSidebar(width = 150,
                   sidebarMenu(  
                     menuItem("DataInput",tabName = "DataInput"),      
                     menuItem("Dashboard", tabName = "Dashboard")
                   )),
  dashboardBody(
    tabItems(
      tabItem(tabName = "DataInput", 
              box(fileInput('file1', 'Choose CSV File',
                            accept=c('.csv')),
                  tags$hr(),
                  checkboxInput('header', 'Header', TRUE),
                  radioButtons('sep', 'Separator',
                               c(Comma=',',
                                 Semicolon=';',
                                 Tab='\t',
                                 Whitespace = " "),
                               ','),
                  actionButton("Load", "Load the File"))
      ),
      tabItem( tabName = "Dashboard",
               fluidRow(column(9,box(status = "primary", plotOutput("plot1"))
               ),
               column(3,
                      box(title="Controls",
                          selectInput(inputId = "Dept", 
                                      label = "Select", 
                                      choices = c(1,2,10)), # changed C to c and 3 to 10 
                          numericInput(inputId = "ClassNum", 
                                       label = "Enter the Class Number", value = 1, min=0, max=100000),
                          status = "warning", solidHeader = TRUE, width="100%"),

                      downloadButton('downloadData', 'Download')

               )
               ), 
               box(DT::dataTableOutput("table"), width = "100%,",status = "primary")
      )
    )
  )
)

server <- function(input,output) { 

  data <- reactive({
    if(input$Load == 0) {
      return(NULL)
    }
    inFile <- input$file1
    if (is.null(inFile)) {
      return(NULL)
    }
      a <- read.csv(inFile$datapath, header = input$header,sep = input$sep,stringsAsFactors =FALSE)

      options(stringsAsFactors = FALSE) 
      a <- a[,1:5] 
      names(a) <- c("Dept","Description","Price","ClassNum","Quantity") 

      a <- a %>%
        filter(Quantity > 0) %>%
        filter(!(Price==""))  

      for (i in 1:length(a)) {  
        for (j in 1:nrow(a)) {
          if (i==2) {next}
          a[j,i] <- gsub(",", "", a[j,i])
        }  
      }  
      rm(i,j)  

      # You have to be careful here because it can be an empty data frame!
      a <- merge(a, Dept_Names, by="Dept")

      validate(
        need(nrow(a) != 0, 'Merge was not successful')
      )


      for (j in 1:nrow(a)) { 
        if (a$ClassNum[j]=="") {
          a[j,4] <-0
        } else {
          a[j,4] <- a$ClassNum[j]
        }
      } 
      rm(j)

      a$Dept <- as.numeric(as.character(a$Dept))
      a$ClassNum <- as.numeric(as.character(a$ClassNum))
      a$Price <- as.numeric(as.character(a$Price))
      a$Quantity <- as.numeric(as.character(a$Quantity))

      a <- a %>%
        mutate(Revenue=Price*Quantity,Key1=paste(Dept, "_", ClassNum, sep="")) 

      total_complete <- a %>%
        group_by(Dept, ClassNum) %>%
        summarise(Revenue=sum(Revenue)) %>%
        arrange(Dept, desc(Revenue)) %>%
        mutate(Key1=paste(Dept, "_", ClassNum, sep="")) 

      ofn <- paste0("ABC",Sys.time(),".csv")
      ofn <- gsub(":","_",ofn)


      # It looks like that you want to return a list
      # total_complete is a processed data frame and ofn is a name of the file
      # that is going to be downloaded
      return(list(total_complete = total_complete, ofn = ofn))

    })


  output$downloadData <- downloadHandler( 
    filename = function() { # added a function as in an example from ?downloadHandler
      data()$ofn
    },
    content = function(file) {
      write.csv(data()$total_complete, file, row.names = FALSE)
    }
  )


  output$table <- DT::renderDataTable({ 
    req(data()) # require that data() is available
    DT::datatable(data()$total_complete[data()$total_complete[,1]==input$Dept ,])
  })

  output$plot1 <- renderPlot({
    req(data()) # require that data() is available

    # there is no such variable as "Department" hence changed to $Dept
    # added data()$
    ggplot(data()$total_complete[data()$total_complete$Dept==input$Dept,], 
           aes(reorder(x=Key1,desc(Revenue)), y=Revenue, fill=Key1)) +
      geom_bar(stat="identity") +
      theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5)) 
  })
} 

shinyApp(ui, server)

How to embed cleaning code in an R Shiny app?

I think you are really close on this. I asked a question in the comment, but I'm guessing you want the data cleaned before it displays on the table. Essentially all you need to do is pop in your "cleaning code" into the reactive. I put the read.csv into a new variable named "data" to fit your cleaning functions, then placed a final output "citationdata" after. Hopefully this is what you are looking for:

library(tidyverse)
library(shiny)

ui <- fluidPage(
  fluidPage(
    titlePanel("Uploading Files"),
    sidebarLayout(
      sidebarPanel(
        fileInput('data', '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'="'"),
                     '"'),
        downloadButton('downloadData', 'Download')
      ),
      mainPanel(
        tableOutput('contents')
      )
    )
  )
)
server <- function(input, output) {
  
  getData <- reactive({
    
    inFile <- input$data
    
    if (is.null(input$data))
      return(NULL)
    
    data<-read.csv(inFile$datapath, header=input$header, sep=input$sep, 
             quote=input$quote)

    # #data is the name of the csv after I load it
    datasubset= subset(data, select = c(Author.Full.Names,Article.Title,Source.Title,Volume,Issue,Article.Number,DOI,Publication.Date,Publication.Year,Open.Access.Designations))
    datasubset$Full.Date <- paste(datasubset$Publication.Date, datasubset$Publication.Year)
    datasubset$Citation <- paste("Author(s): ",datasubset$Author.Full.Names,". Title:",datasubset$Article.Title,". Volume:",datasubset$Volume,". Issue:",datasubset$Issue,". Article Number:",datasubset$Article.Number,". DOI:",datasubset$DOI,". Published:",datasubset$Full.Date)
    citationdata = subset(datasubset, select=c(Citation,Open.Access.Designations))
    citationdata
    
  })
  output$contents <- renderTable(
    
    getData()
    
  )
  
  
  output$downloadData <- downloadHandler(
    
    filename = function() { 
      paste("data-", Sys.Date(), ".csv", sep="")
    },
    
    content = function(file) {
      
      write.csv(getData(), file)
      
    })
  
}
shinyApp(ui, server)

How to Implement a Cleanup Routine in R Shiny