app.R

message("* Loading libraries *")

suppressMessages(library(magrittr))
suppressMessages(library(tidyverse))
suppressMessages(library(shiny))
suppressMessages(library(shinythemes))
suppressMessages(library(foreach))
suppressMessages(library(openxlsx))
suppressMessages(library(gplots))
suppressMessages(library(enviPat))
suppressMessages(library(RColorBrewer))
suppressMessages(library(DT))

options(shiny.maxRequestSize=100*1024^2) 

dir1 <- "Scripts"

message("* Loading scripts *")

for (f in list.files(dir1, pattern = "\\.R$")) {
  source(file.path(dir1, f))

}

if (Sys.info()["user"] == "cedlich") {
  assign("DEBUG", TRUE, env = .GlobalEnv)
} else {
  assign("DEBUG", FALSE, env = .GlobalEnv)
}

message("* Assigning global variables *")

assign("MY_SHINY_PREFERENCES",
       if(file.exists("shiny_preferences.RDS")) my_read_shiny_prefs() else list(),
       envir = .GlobalEnv
)

# data("isotopes")


assign("colours1", colours() %>% keep(!grepl("^gr[ea]y", .) & !grepl("[0-9]$", .)) %>% sort(), envir = .GlobalEnv)


message("* Starting shiny *")


#### ui ####
ui <- 
  
  fluidPage(
    navbarPage(
      title = "Shiny Filter",
      tabPanel("Infile", source(file.path("ui_code", "0100_ui_infile.R"),  local = TRUE)$value),
      tabPanel("Filter", source(file.path("ui_code", "0200_ui_filter.R"),  local = TRUE)$value),
      tabPanel("Outfile", source(file.path("ui_code", "0300_ui_outfile.R"),  local = TRUE)$value)
    )
  )


server <- function(input, output, session) {
  
  my_raw_data <- reactiveValues()
  
  my_pca <- reactiveValues()

  my_plot <- reactiveValues()
  
  my_filter <- reactiveValues()
  
  source(file.path("server_code", "0100_server_infile.R"),  local = TRUE)$value
  source(file.path("server_code", "0200_server_filter.R"),  local = TRUE)$value
  source(file.path("server_code", "0300_server_outfile.R"),  local = TRUE)$value
  
  onStop(function() {
    
    env = parent.env(environment())
    
    ls(envir = env) %>%
      ## .. excluding e.g. session" and "output"
      setdiff(c("session", "output", "my_pref_update")) %>%
      ## object in a list
      mget(envir = env) %>% 
      ## keep only reactive values
      subset(., subset = sapply(., is.reactivevalues)) %>% 
      ## convert reactive values
      sapply(function(z) isolate(reactiveValuesToList(z)), simplify=F) %>% 
      ## assign to global environment
      list2env(envir = .GlobalEnv)
    cat("Session stopped\n")
    cat("Type `save(list=ls(), file='tmp.RData')` to save state variables in your current working directory\n")
    cat("Find out what current working directory by typing `getwd()`\n")
  })
}


shinyApp(ui, server)