main.R

#!/usr/bin Rscript
# This script will take a SAG yaml configuration file and generate a ShinyApp
# Accepts two parameters: path to sag yaml configuration file
# Usage: Rscript /path/to/sag.yaml /output/dir/
args = commandArgs(trailingOnly=TRUE)
source("tools.R")
library(yaml)

path_yml <- args[1]
output_dir <- args[2]

APP <<- yaml.load_file(path_yml,handlers = list("float#fix"=function(x){ format(x,scientific=F)}))$App

generate_added_styles <- function () {
  path_css = output_dir + "/www/added_styles.css"

  file.replace(path_css)
}

#============================================================

generate_page_input <- function(res, cnt) {
  
  if(cnt$type == "button") {
    
    if(cnt$icon == "") {
      res <- res + '\t\tactionButton("' + cnt$name + '", "'+ cnt$label +'", class="'+ cnt$class +'")' 
      
    } else {
      res <- res + '\t\tactionButton("' + cnt$name + '", "'+ cnt$label +'",  icon("'+ cnt$icon +'"), class="'+ cnt$class +'")' 
    }
    
  }
  if(cnt$type == "text") {
    
    res <- res + '\t\ttextInput("'+ cnt$name +'", label = "'+ cnt$label +'", value = "'+ format(cnt$value, scientific=F) +'", width = "'+ 'auto' +'")'
    
  }
  if(cnt$type == "textArea") {
    
    res <- res + '\t\ttextAreaInput("'+ cnt$name +'", label = "'+ cnt$label +'", value = "'+ cnt$value +'")'
    
  }
  if(cnt$type == "numeric") {
    
    res <- res + '\t\tnumericInput("'+ cnt$name +'", label = "'+ cnt$label +'", min = '+ cnt$min +', max = '+ cnt$max +', step = '+ cnt$step +', width =  "'+ 'auto' +'", value = '+ format(cnt$value, scientific=F) +')'

  }
  if(cnt$type == "slider") {
    if(length(cnt$value) == 1) {
      res <- res + '\t\tsliderInput("'+ cnt$name +'", label = "'+ cnt$label +'", min = '+ cnt$min +', max = '+ cnt$max +', step = '+ cnt$step +', width =  "'+ 'auto' +'", value = '+ cnt$value +')'
    } else {
      res <- res + '\t\tsliderInput("'+ cnt$name +'", label = "'+ cnt$label +'", min = '+ cnt$min +', max = '+ cnt$max +', step = '+ cnt$step +', width =  "'+ 'auto' +'", value = c('+ cnt$value[1] + ',' + cnt$value[2] + '))'
    }
  }
  if(cnt$type == "help") {
    res <- res + '\t\tp("'+cnt$label+'")'
  }
  if(cnt$type == "link") {
    res <- res + '\t\tp("'+cnt$label+'",a(href="'+cnt$href+'","'+cnt$href+'",target="_blank"))'
  }
  if(cnt$type == "select") {
    
    
    res <- res + '\t\tselectInput("'+ cnt$name +'", label = "'+ cnt$label +'", choices = list('
    
    cpt = 1
    if(length(cnt$choices) > 0) {
      for(ch in cnt$choices){
        
        if(cpt < length(cnt$choices)) {
          res <- res + '"' + names(ch) + '" = "' + ch[names(ch)] + '", '
        } else {
          res <- res + '"' + names(ch) + '" = "' + ch[names(ch)] + '"), '
        }
        cpt = cpt + 1
      }
    }
    
    res <- res + ' selected = "'+cnt$value+'"' + ', width =  "'+ 'auto' +'")'
    
  }
  if(cnt$type == "radio") {
    
    res <- res + '\t\tradioButtons("'+ cnt$name +'", label = "'+ cnt$label +'", choices = list('
    
    cpt = 1
    if(length(cnt$choices) > 0) {
      for(ch in cnt$choices){
        
        if(cpt < length(cnt$choices)) {
          res <- res + '"' + names(ch) + '" = "' + ch[names(ch)] + '", '
        } else {
          res <- res + '"' + names(ch) + '" = "' + ch[names(ch)] + '"), '
        }
        cpt = cpt + 1
      }
    }
    
    res <- res + ' selected = "'+cnt$value+'"' + ', width =  "'+ 'auto' +'")'
    
  }
  if(cnt$type == "checkbox") {
    
    res <- res + '\t\tcheckboxInput("'+ cnt$name +'", label = "'+ cnt$label +'", value = ' + cnt$value + ')'  
    
  }
  if(cnt$type == "chooser") {
    
    vl <- 'c('
    vr <- 'c('
    
    if(length(cnt$value_left) > 0) {
      for(x in 1:length(cnt$value_left)) {
        vl <- vl + '"' + cnt$value_left[[x]] + '"'
        if(x < length(cnt$value_left)) {
          vl <- vl + ', '
        }
      }
    }
    
    vl <- vl + ')'
    
    if(length(cnt$value_right) > 0) {
      vr <- "c("
      for(x in 1:length(cnt$value_right)) {
        vr <- vr + '"' + cnt$value_right[[x]] + '"'
        if(x < length(cnt$value_right)) {
          vr <- vr + ', '
        }
      }
    }
    
    vr <- vr + ')'
  
    res <- res + '\t\tchooserInput("' + cnt$name + '", "Available", "Selected", ' + vl + ', ' + vr + ', size = ' + cnt$size + ', multiple = ' + cnt$multiple + ')'

  }
  if(cnt$type == "checkboxGroupInput") {
    
    res <- res + '\t\tcheckboxGroupInput("'+ cnt$name +'",label = "'+ cnt$label +'", choices = list('
    
    if(length(cnt$choices) > 0) {
      for(ch in 1:length(cnt$choices)){
        
        choices = cnt$choices[[ch]]
        
        value = choices$value
        
        if(is.character(choices$value)) {
          value = '"' + choices$value + '"'
        }
        
        if(ch < length(cnt$choices)) {
          res <- res + '"' + choices$label + '"' + ' = ' + value + ', '
        } else {
          res <- res + '"' + choices$label + '"' + ' = ' + value
        }
      }
    }
    
    res <- res + '), selected = "'+cnt$value+'"' + ', width =  "'+ 'auto' +'")'
    
  }
  if(cnt$type == "input_file_client") {
    
    res <- res + '\t\tfileInput("'+ cnt$name +'", label = "'+ cnt$label + '"'
    
    if(length(cnt$accept) > 0) {
      
      res <- res + ", accept = c("
      
      for(a in 1:length(cnt$accept)){
        form <- cnt$accept[[a]]
        
        res <- res + '"' + form + '"'
        
        
        if(a < length(cnt$accept)) {
          res <- res + ', '
        } else {
          res <- res + ')'
        }
        
      }
      
    }
    
    res <- res + ', multiple = ' + cnt$multiple + ', width =  "'+ 'auto' + '")'
    
  }
  # output_file_server
  if(cnt$type == "input_file_server"){
    res <- res + '\t\ttags$label("' + cnt$label + '"),\n'
    res <- res + '\t\tfluidRow(\n'
    res <- res + '\t\t\tcolumn(4,shinyFilesButton("shinyfiles_' + cnt$name + '",label="Please select a file", title="' + cnt$label + '", multiple=FALSE)),\n'
    res <- res + '\t\t\tcolumn(8,textInput("' + cnt$name + '",label=NULL,value=""))\n'
    res <- res + '\t\t)\n'
  }
  if(cnt$type == "input_dir" || cnt$type == "output_dir"){
    res <- res + '\t\ttags$label("' + cnt$label + '"),\n'
    res <- res + '\t\tfluidRow(\n'
    res <- res + '\t\t\tcolumn(4,shinyDirButton("shinydir_' + cnt$name + '",label="Please select a directory", title="' + cnt$label + '")),\n'
    res <- res + '\t\t\tcolumn(8,textInput("' + cnt$name + '",label=NULL,value=""))\n'
    res <- res + '\t\t)\n'
  }
  if(cnt$type == "input_file"){
    res <- res + '\tbox(title = "' + cnt$label + '", width = 12, status = "success", collapsible = TRUE, solidHeader = TRUE,\n'
    res <- res + '\t\tselectInput("' + cnt$name + '_select",label = "Select where to find the file", selected = "server", choices = c("On server" = "server", "On your machine" = "local")),\n'
    res <- res + '\t\tconditionalPanel(condition = "input.' + cnt$name + '_select == \'server\'",\n'
    res <- res + '\t\t\t\ttags$label("' + cnt$label + '"),\n'
    res <- res + '\t\t\t\tfluidRow(\n'
    res <- res + '\t\t\t\t\tcolumn(4,shinyFilesButton("shinyfiles_' + cnt$name + '",label="Please select a file", title="' + cnt$label + '", multiple=FALSE)),\n'
    res <- res + '\t\t\t\t\tcolumn(8,textInput("' + cnt$name + '_server",label=NULL,value=""))\n'
    res <- res + '\t\t\t\t)\n'
    res <- res + '\t\t\t),\n'
    res <- res + '\t\tconditionalPanel(condition = "input.' + cnt$name + '_select == \'local\'",\n'
    res <- res + '\t\t\tfileInput("' + cnt$name + '_local",label = "' + cnt$label + '")\n'
    res <- res + '\t\t)\n'
    res <- res + '\t)\n'
  }
  
  return(res)
}

generate_page_box <- function(panel, box, res) {
  
  res <- res + 'box(title = "' + box$title + '", width = 12, status = "' + box$status + '", collapsible = TRUE, solidHeader = TRUE'
  
  panel_content = box$content
  
  if(length(panel_content) > 0) {
    
    res <- res + ',\n'
    
    for(z in 1:length(panel_content)) {
      res <- generate_page_input(res, panel_content[[z]])
      
      if(z < length(panel_content)) {
        res <- res + ','
      }
  
      res <- res + '\n\n'
    }
  }
  
  res <- res + '\t)'
  
  return(res)
  
}

#============================================================

generate_pages_server <- function() {
  resG <- ""
  for(x in 1:length(APP$pages)) {
    name <- APP$pages[[x]]$name
    resG <- resG + "\t# \tPage : " + name + "\n"
    path_page = output_dir+"/pages/pages_def_"+tolower(name)+".R"
    file.replace(path_page)
    
    res <- 'tab'+ name + ' = fluidPage(\n\n'
    
    res <- res + 'box(title = "Parameters :", width = 12, status = "primary", collapsible = TRUE, solidHeader = TRUE'
     
    content <- APP$pages[[x]]
    
    if(length(content) > 0) {
      res <- res + ',\n\n'

      boxes = content$boxes
      
      if(length(boxes) > 0) {
        
        if(length(boxes) > 1){
          res <- res + '\tselectInput("select' + content$name + '", label = "Select the tool to use : ", selected = "' + content$default + '", choices = list(' 
          
          for(b in 1:length(boxes)) { # construction list box tools
            res <- res + '"' + boxes[[b]]$name +'" = "' + boxes[[b]]$name + '"'
            
            if(b < length(boxes)) {
              res <- res + ', '
            }
            
          }
          res <- res + ')),\n'
        }
        else{
          res <- res + '\thidden(textInput("select' + content$name + '", label = "", value="'+ boxes[[1]]$name +'")),'
        }
        
        for(b in 1:length(boxes)) { # draw boxes
          
          box <- boxes[[b]]
          
          if(length(boxes) > 1){
            res <- res + "\nconditionalPanel(condition = \"input.select"+content$name+" == '"+box$name+"'\","
          }

          #if(box$defined == TRUE) {
          #  box <- get_predefined_box(box, APP$pages[[x]]$name)
          #} 
          
          res <- generate_page_box(panel, box, res)

          if(length(boxes) > 1){
            res <- res + ")"
          }
          if(b < length(boxes)){
            res <- res + ","
          }
        }
      }
    }
    
    res <- res + '))\n\n'

    write(res, file=path_page)
    
    path_opt = output_dir+"/server/opt_"+tolower(name)+".R"
    #file.replace(path_opt)
    
    res <- ""
    
    content <- APP$pages[[x]]
    
    # if(length(content) > 0) {
      
    #   boxes = content$boxes
      
    #   if(length(boxes) > 0) {
        
        
    #     for(b in 1:length(boxes)) {
          
    #       box <- boxes[[b]]
          
    #       #if(box$defined == TRUE) {
    #       #  box <- get_predefined_box(box, APP$pages[[x]]$name)
    #       #} 
          
          
    #       panel_content = box$content
  
      
    #       if(length(panel_content) > 0) {
      
    #     for(z in 1:length(panel_content)) {
          
    #       cnt <- panel_content[[z]]
          
    #       type <- cnt$type
    #       id <- cnt$name
          
    #       if(type == "button") {
    #           res <- res + '#\' Event when use '+ id +' button\n'
    #           res <- res + 'observeEvent(input$'+id+', {\n\n'
              
    #           res <- res + '})\n\n'
    #       }
    #     }
        
    #   }
      
    #     }
        
    #   }
    # }
    
    run <- APP$run

    if(length(run$options) > 0) {
      
      # res <- res + '#\' Event when use '+ run$shiny_button$name +' button\n'
      # res <- res + 'observeEvent(input$'+ run$shiny_button$name+', {\n\n'
      
      # page_path <- output_dir + '/params/' + 'params_' + APP$pages[[x]]$name + '.yml'
      
      # file.replace(page_path)
      
      
      # res <- res + '# Params \n'
      # res <- res + '\tpath_param <- "' + page_path + '"\n\n'
      # res <- res + '\tres <- ""\n'
      
      # res <- res + '\n\t# Page : ' + APP$pages[[x]]$name+ '\n'
      
      boxes = APP$pages[[x]]$boxes
      
      if(length(boxes) > 0) {

        resG <- resG + '\t\tres = paste0(res , paste("'+APP$pages[[x]]$name + ':", paste0(\'\"\', input$select' + APP$pages[[x]]$name + ', \'\"\'), "\\n", sep = " "))\n'
        for(b in 1:length(boxes)) {  # list boxes
          
          box <- boxes[[b]]
          
          # res <- res + '\n\t# Tool : ' + box$name+ '\n'
          
          # if (length(boxes) > 1){
          #   verif = "input$select" + APP$pages[[x]]$name + ' == "' + box$name + '"'
          # }
          # else{
          #   verif = "TRUE"
          # }

          # res <- res + '\n\tif('+verif+') {\n'
          
          panel_content = box$content
    
          if(length(panel_content) > 0) {

            for(z in 1:length(panel_content)) {
              
              cnt <- panel_content[[z]]
              
              type <- cnt$type
              id <- cnt$name
              
              genR <- ""
            
              if(cnt$type == 'text' || cnt$type == 'textArea' || cnt$type == "input_dir" || cnt$type == "output_dir") {
                genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", format(input$' + id + ', scientific=F), "\\n", sep = " "))\n'
                genR <-  genR + '\t\t} else {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " "))\n'
                genR <-  genR + '\t\t}'
                genR <-  genR + '\t\n\n'
              }
              if(cnt$type == 'numeric') {
                genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", format(input$' + id + ', scientific=F), "\\n", sep = " "))\n'
                genR <-  genR + '\t\t} else {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " "))\n'
                genR <-  genR + '\t\t}'
                genR <-  genR + '\t\n\n'
              }
              if(cnt$type == "slider") {
                if(length(cnt$value) == 1) {
                  genR <-  genR + '\t\tres = paste0(res, paste("' + id + ':", input$' + id + ', "\\n", sep = " "))'
                  genR <-  genR + '\t\n\n'
                } else {
                  genR <-  genR + '\t\tres = paste0(res, paste("' + id + '_min:", input$' + id + '[1], "\\n", sep = " "))\n'
                  genR <-  genR + '\t\tres = paste0(res, paste("' + id + '_max:", input$' + id + '[2], "\\n", sep = " "))\n'
                  genR <-  genR + '\t\tres = paste0(res, paste("' + id + '_step:", "' + cnt$step + '", "\\n", sep = " "))\n'
                  genR <-  genR + '\t\n\n'
                }
              }
              if(cnt$type == "select") {
                genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", input$' + id + ', "\\n", sep = " "))\n'
                genR <-  genR + '\t\t} else {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " "))\n'
                genR <-  genR + '\t\t}'
                genR <-  genR + '\t\n\n'
              }
              if(cnt$type == "file") {
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + '$datapath, \'\"\'), "\\n", sep = " "))'
                genR <-  genR + '\t\n\n'
              }
              if(cnt$type == "checkbox") {
                genR <-  genR + '\t\tif(input$' + id + ') {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", "true", "\\n", sep = " "))\n'
                genR <-  genR + '\t\t} else {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", "false", "\\n", sep = " "))\n'
                genR <-  genR + '\t\t}'
                genR <-  genR + '\t\n\n'
              }
              if(cnt$type == "chooser") {
                genR <-  genR + '\t\tres <- paste0(res, " ' + id + '" + "_left: [")\n'
                genR <-  genR + '\t\tif(length(input$'+ id +'$left) > 0) {\n' 
                genR <-  genR + '\t\tfor(x in 1:length(input$'+ id +'$left)) {\n'
                genR <-  genR + '\t\t\tres <- paste0(res, \'"\', input$'+ id +'$left[[x]], \'"\')\n'
                genR <-  genR + '\t\t\tif(x < length(input$'+ id +'$left)) {\n'
                genR <-  genR + '\t\t\t\tres <- paste0(res, ", ")\n'
                genR <-  genR + '\t\t\t}\n'
                genR <-  genR + '\t\t}\n'
                genR <-  genR + '\t\t}		\n'
                genR <-  genR + '\t\tres <- paste0(res, "]", "\\n")\n\n'
                
                genR <-  genR + '\t\tres <- paste0(res, " ' + id + '" + "_right: [")\n'
                genR <-  genR + '\t\tif(length(input$'+ id +'$right) > 0) {\n' 
                genR <-  genR + '\t\tfor(x in 1:length(input$'+ id +'$right)) {\n'
                genR <-  genR + '\t\t\tres <- paste0(res, \'"\', input$'+ id +'$right[[x]], \'"\')\n'
                genR <-  genR + '\t\t\tif(x < length(input$'+ id +'$right)) {\n'
                genR <-  genR + '\t\t\t\tres <- paste0(res, ", ")\n'
                genR <-  genR + '\t\t\t}\n'
                genR <-  genR + '\t\t}\n'
                genR <-  genR + '\t\t}		\n'
                genR <-  genR + '\t\tres <- paste0(res, "]", "\\n")\n\n'
                
              }
              if(cnt$type == "radio") {
                genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", input$' + id + ', "\\n", sep = " "))\n'
                genR <-  genR + '\t\t} else {\n'
                genR <-  genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " "))\n'
                genR <-  genR + '\t\t}'
                genR <-  genR + '\t\n\n'
              }
              if(cnt$type == "input_file") {
                genR <- genR + '\t\tres = paste0(res, paste("' + id + '_select:", paste0(\'\"\', input$' + id + '_select, \'\"\'), "\\n", sep = " "))\n'
                genR <- genR + '\t\tif(input$' + id + '_select == "server") {\n'
                genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + '_server, \'\"\'), "\\n", sep = " "))\n'
                genR <- genR + '\t\t}\n'
                genR <- genR + '\t\tif(input$' + id + '_select == "local"){\n'
                genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + '_local$datapath, \'\"\'), "\\n", sep = " "))\n'
                genR <- genR + '\t\t}'
                genR <- genR + '\t\n\n'
              }
              
              else {
                #TODO
              }
              
              # res <- res + genR
              resG <- resG + genR
            }
          
          }
      
          # res <- res + '\t}\n'
          
          # res <- res + '\n'
      
        }
        
      }
      
      # res <- res + '\twrite(res, file=path_param)'
      
      # res <- res + '\n\n'
      
      # res <- res + '})\n\n'
      
    }
    #write(res, file=path_opt)
  }
  
  save_params <- "save_params <- function(path_param){\n"
  save_params <- save_params + '\tres = ""'
  save_params <- save_params + resG
  #save_params <- save_params + '\t\tres = paste0(res, paste("final_step:", paste0(\'\"\', input$final_step, \'\"\'), "\\n", sep = " "))\n\n'
  save_params <- save_params + '\ta = yaml.load_file("/workflow/params.total.yml", handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
  save_params <- save_params + '\tp = a[["params"]]\n'
  save_params <- save_params + '\ta["params"] = NULL\n'
  save_params <- save_params + '\tb = yaml.load(res, handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
  save_params <- save_params + '\tpnotb = subset(names(p), !(names(p)%in%names(b)))\n'
  save_params <- save_params + '\td = list()\n'
  save_params <- save_params + '\td$params = c(p[pnotb],b)\n'
  save_params <- save_params + '\tlogical = function(x) {\n'
  save_params <- save_params + '\t\tresult <- ifelse(x, "True", "False")\n'
  save_params <- save_params + '\t\tclass(result) <- "verbatim"\n'
  save_params <- save_params + '\t\treturn(result)\n'
  save_params <- save_params + '\t}\n'
  save_params <- save_params + '\td = c(d,a)\n'
  #save_params <- save_params + '\tget_samples = yaml.load(system(paste0("python3 /workflow/get_samples.py ",input$sample_dir," ",input$SeOrPe),intern = T))\n'
  #save_params <- save_params + '\td$samples = get_samples$samples\n'
  #save_params <- save_params + '\td$params$sample_suffix = get_samples$suffix\n'
  save_params <- save_params + '\twrite_yaml(d,path_param,handlers=list(logical = logical,"float#fix"=function(x){ format(x,scientific=F) }))\n'
  save_params <- save_params + '\t}\n\n'

  res <- save_params

  res <- res + 'force_rule <- function(force_from){\n'
  res <- res + '\tif (input$force_from=="none"){\n'
  res <- res + '\t\treturn("")\n'
  res <- res + '\t}\n'
  res <- res + '\telse if (input$force_from=="all"){ return("--forcerun all") }\n'
  res <- res + '\telse {\n'
  res <- res + '\t\tparams = yaml.load_file(paste0(input$results_dir,"/params.yml"), handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
  res <- res + '\t\toutputs = params[["outputs"]]\n'
  res <- res + '\t\ttool = params[["params"]][[force_from]]\n'
  res <- res + '\t\tsteptool = paste0(force_from,"__",tool)\n'
  res <- res + '\t\tif (length(outputs[[steptool]])==1)\n'
  res <- res + '\t\t\trule = names(outputs[[steptool]])[[1]]\n'
  res <- res + '\t\telse{\n'
  res <- res + '\t\t\trule = names(outputs[[steptool]])[[grep(input$SeOrPe,names(outputs[[steptool]]))]]\n'
  res <- res + '\t\t}\n'
  res <- res + '\t\treturn(paste0("--forcerun ",rule))\n'
  res <- res + '\t}\n'
  res <- res + '}\n'

  # # Compare parameters (give rules that need to be re-runned)
  # res <- res + 'compare_params = function(dossierAnalyse){\n'
  # res <- res + '\tif (!file.exists(paste0(dossierAnalyse,"/lastrun/params.yml"))){\n'
  # res <- res + '\t\treturn(c())\n'
  # res <- res + '\t}\n'
  # res <- res + '\telse{\n'
  # res <- res + '\t\tnew_params = yaml.load_file(paste0(dossierAnalyse,"/params.yml"))\n'
  # res <- res + '\t\told_params = yaml.load_file(paste0(dossierAnalyse,"/workflow/params.yml"))\n'
  # res <- res + '\t\tchanged = new_params[!(new_params %in% old_params)]\n'
  # res <- res + '\t\trules = c()\n'
  # res <- res + '\t\tif (length(changed)>=1){\n'
  # res <- res + '\t\t\tfor (param in names(changed)){\n'
  # res <- res + '\t\t\t\tif (!grepl("_threads$",param)){\n'
  # res <- res + '\t\t\t\t\trules = c(rules, new_params$params_info[[param]]$rule)\n'
  # res <- res + '\t\t\t\t}\n'
  # res <- res + '\t\t\t}\n'
  # res <- res + '\t\t}\n'
  # res <- res + '\t\treturn(unique(rules))\n'
  # res <- res + '\t}\n'
  # res <- res + '}\n'

  file.replace(output_dir+"/server/opt_global.R")
  #res <- ""
  # Event RULEGRAPH
  if ("RULEGRAPH" %in% names(APP)){
    res <- res + '#\' Event when use RULEGRAPH button\n'
    res <- res + 'observeEvent({c(input$sidebarmenu,input$refresh_rg)}, {\n\n'
    res <- res + '\tif (!dir.exists(paste0(input$results_dir,"/logs"))){\n'
    res <- res + '\t\tdir.create(paste0(input$results_dir,"/logs"))\n'
    res <- res + '\t}\n'
    res <- res + '\tif(input$sidebarmenu=="RULEGRAPH"){\n'
    res <- res + '\t\tinput_list <- reactiveValuesToList(input)\n'
    res <- res + '\t\ttoggle_inputs(input_list,F,F)\n'
    res <- res + '\t\tpath_param <- paste0(input$results_dir,"/params.yml")\n\n'
    
    res <- res + '\t\tsave_params(path_param)\n'

	  res <- res + '\t\ti = sample.int(1000,size = 1)\n\n'
	  res <- res + '\t\tsystem(paste0("rm ",input$results_dir,"/rulegraph*"))\n\n'

    res <- res + '\t\toutUI = tryCatch({\n'
    res <- res + '\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile ",input$results_dir,"/params.yml -d ",input$results_dir," all --rulegraph 1> ",input$results_dir,"/rulegraph",i,".dot 2> ",input$results_dir,"/logs/rulegraph.txt"),intern=T)\n'
    res <- res + '\t\t\tsystem(paste0("cat ",input$results_dir,"/rulegraph",i,".dot | dot -Tsvg -Gratio=0.75 > ",input$results_dir,"/rulegraph",i,".svg"),intern=T)\n'
    res <- res + '\t\t\ttagList(img(src = paste0("results/rulegraph",i,".svg") ,alt = "Rulegraph of Snakemake jobs",style="max-width: 100%;height: auto;display: block;margin: auto"))},\n'
    res <- res + '\t\terror = function(e){\n'
    res <- res + '\t\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)\n'
    res <- res + '\t\t\treturn(tags$p(HTML(paste(readLines(paste0(input$results_dir,"/logs/rulegraph.txt"),warn=F), collapse = "<br/>"))))},\n'
    res <- res + '\t\twarning = function(w){\n'
    res <- res + '\t\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)\n'
    res <- res + '\t\t\treturn(tags$p(HTML(paste(readLines(paste0(input$results_dir,"/logs/rulegraph.txt"),warn=F), collapse = "<br/>"))))})\n'

    res <- res + '\t\taddResourcePath("results", input$results_dir)\n'
    res <- res + '\t\toutput$RULEGRAPH_svg = renderUI(outUI)\n'
    res <- res + '\t\ttoggle_inputs(input_list,T,F)\n'
    res <- res + '}})\n'
  }

  # Event dry_run
  res <- res + 'observeEvent({c(input$sidebarmenu,input$dry_run_button)}, {\n'
  res <- res + '\n'
  res <- res + '\tif (!dir.exists(paste0(input$results_dir,"/logs"))){\n'
  res <- res + '\t\tdir.create(paste0(input$results_dir,"/logs"))\n'
  res <- res + '\t}\n'
  res <- res + '\tif(input$sidebarmenu=="RULEGRAPH"){\n'
  res <- res + '\t\tinput_list <- reactiveValuesToList(input)\n'
  res <- res + '\t\ttoggle_inputs(input_list,F,F)\n'
  res <- res + '\t\tpath_param <- paste0(input$results_dir,"/params.yml")\n'
  res <- res + '\n'
  res <- res + '\t\tsave_params(path_param)\n'
  res <- res + '\n'
  res <- res + '\t\tforce = force_rule(input$force_from)\n'
  res <- res + '\t\tdry_out = system(paste0("snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,\t" -d ", input$results_dir ,\t" --cores ", input$cores, " all ", force, " -n -p"),wait = T, intern=T)\n'
  res <- res + '\t\tdryUI = tags$p(HTML(paste(dry_out, collapse = "<br/>")))\n'
  res <- res + '\n'
  res <- res + '\t\toutput$dry_run_div = renderUI(dryUI)\n'
  res <- res + '\t\ttoggle_inputs(input_list,T,F)\n'
  res <- res + '\t}})\n'
  
  # Event Run
  res <- res + '#\' Event when use '+ run$shiny_button$name +' button\n'
  res <- res + 'observeEvent(input$'+run$shiny_button$name+', {\n\n'

  res <- res + '\trv$running = T\n'
  res <- res + '\tinput_list <- reactiveValuesToList(input)\n'
  res <- res + '\ttoggle_inputs(input_list,F,F)\n'
  res <- res + '\tupdateTabsetPanel(session, "sidebarmenu", selected = "run_out")\n'
  
  #panel_path <- output_dir + '/params/' + 'params_' + APP$pages[[x]]$name + '.yml'
  res <- res + '\tpath_param <- paste0(input$results_dir,"/params.yml")\n\n'
  
  res <- res + '\t\tsave_params(path_param)\n'
  res <- res + '\n\n'

  res <- res + '\toutUI = tryCatch({\n'
  res <- res + '\t\tif (!dir.exists(paste0(input$results_dir,"/logs"))){\n'
  res <- res + '\t\t\tdir.create(paste0(input$results_dir,"/logs"))\n'
  res <- res + '\t\t}\n'
  res <- res + '\t\tif (!file.exists(paste0(input$results_dir,"/logs/runlog.txt"))){\n'
  res <- res + '\t\t\tfile.create(paste0(input$results_dir,"/logs/runlog.txt"))\n'
  res <- res + '\t\t}\n'
  res <- res + '\t\tif (file.exists(paste0(input$results_dir,"/logs/workflow_end.ok"))){\n'
  res <- res + '\t\t\tfile.remove(paste0(input$results_dir,"/logs/workflow_end.ok"))\n'
  res <- res + '\t\t}\n'
  res <- res + '\t\tif (file.exists(paste0(input$results_dir,"/logs/workflow_end.error"))){\n'
  res <- res + '\t\t\tfile.remove(paste0(input$results_dir,"/logs/workflow_end.error"))\n'
  res <- res + '\t\t}\n'

  # res <- res + '\t\tforcerun = compare_params(input$results_dir)\n'
  # res <- res + '\t\tif (length(forcerun>1)){\n'
  # res <- res + '\t\t\trules = paste(forcerun, collapse=" ")\n'
  # res <- res + '\t\t\tforcerun = paste(" --forcerun ",rules)\n'
  # res <- res + '\t\t\tshowModal(modalDialog(\n'
  # res <- res + '\t\t\t\ttitle = "Params have changed since the last run",\n'
  # res <- res + '\t\t\t\tforcerun\n'
  # res <- res + '\t\t\t))\n'
  # res <- res + '\t\t}\n'
  # res <- res + '\t\telse{\n'
  # res <- res + '\t\t\tforcerun = ""\n'
  # res <- res + '\t\t}\n'

  res <- res + '\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow.running"),wait = T)\n'

  # RULEGRAPH
  res <- res + '\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile ",input$results_dir,"/params.yml -d ",input$results_dir," all --rulegraph | dot -Tpng -Gratio=0.75 > ",input$results_dir,"/Rule_graph_mqc.png"),wait = T)\n'

  # RUN
  res <- res + '\t\tforce = force_rule(input$force_from)\n'
  res <- res + '\t\trerun = if (input$rerun_incomplete) "--rerun-incomplete" else ""\n'

    ## DRY RUN
    res <- res + '\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ," -d ", input$results_dir ," --cores ", input$cores, " all ", force, " ", rerun, " -n -p > ", input$results_dir, "/Run_Summary_mqc.html"),wait = T)\n'
    res <- res + '\t\t\tsystem(paste0("sed -i \'1 i\\\\<pre> \' ",input$results_dir,"/Run_Summary_mqc.html"))\n'

  res <- res + '\t\tsystem2("python3",paste0("-u -m snakemake -s /workflow/Snakefile --configfile ", paste0(input$results_dir,"/params.yml") ,\t" -d ", input$results_dir ,\t" --cores ", input$cores, " all ", force, " ",rerun),wait = FALSE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"))\n'
  res <- res + '\t\ttags$iframe(src="results/multiqc_report.html",width="100%", height="900px")},\n'
  res <- res + '\t\terror = function(e){\n'
  res <- res + '\t\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)\n'
  res <- res + '\t\t\treturn(tags$p(paste0("error : ",e$message)))},\n'
  res <- res + '\t\twarning = function(w){\n'
  res <- res + '\t\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow_end.error"),wait = T)\n'
  res <- res + '\t\t\treturn(tags$p(paste0("error : ",w$message)))})\n'
  res <- res + '\t\t})\n\n'

  for(page in APP$pages){
    for(box in page$boxes){
      for(cnt in box$content){

        if ("prompt" %in% names(cnt)){
          #res <- res + '\t\t'
          res <- res + '\t\tobserveEvent({input$'+cnt$name+'},{showModal(modalDialog(title = "Info","'+cnt$prompt+'",easyClose = TRUE))},ignoreInit=TRUE)\n'
        }

        if ("volumes" %in% names(cnt)){
          volumes = 'c('
          for (volume in cnt$volumes){
            key = names(volume)
            val = unlist(volume)
            volumes = paste0(volumes,key,'="',val,'",')
          }
          volumes = substr(volumes, 1, nchar(volumes)-1)
          volumes = paste0(volumes,')')
        }
        else{
          volumes = 'c(Data="/Data",Results="/Results")'
        }

        if (cnt$type == "input_file"){
          res <- res + '\t\tshinyFileChoose(input, "shinyfiles_' + cnt$name + '", root=' + volumes + ',session = session)\n'
          res <- res + '\t\tobserveEvent({parseFilePaths(' + volumes + ',input$shinyfiles_' + cnt$name + ')$datapath[1]},{\n'
          res <- res + '\t\t\tif(length(parseFilePaths(' + volumes + ',input$shinyfiles_' + cnt$name + ')$datapath)==1){\n'
          res <- res + '\t\t\t\tupdateTextInput(session,"' + cnt$name + '_server",value = parseFilePaths(' + volumes + ',input$shinyfiles_' + cnt$name + ')$datapath[[1]])\n'
          res <- res + '\t\t\t}\n'
          res <- res + '\t\t})\n\n'
        }
        if (cnt$type == "input_dir" || cnt$type == "output_dir"){
          res <- res + '\t\tshinyDirChoose(input, "shinydir_' + cnt$name + '", root=' + volumes + ',session = session)\n'
          res <- res + '\t\tobserveEvent({parseDirPath(' + volumes + ',input$shinydir_' + cnt$name + ')},{\n'
          res <- res + '\t\t\tupdateTextInput(session,"' + cnt$name + '",value = parseDirPath(' + volumes + ',input$shinydir_' + cnt$name + '))\n'
          res <- res + '\t\t})\n\n'
        }
      }
    }
  }

  write(res, output_dir+"/server/opt_global.R")
}

#============================================================

generate_menu <- function() {
  
  path_file = output_dir + "/R/menugauche.R"
  
  file.replace(path_file)
  
  res <- ""
  
  res <- res + 'MenuGauche = sidebarMenu(id="sidebarmenu",\n\n'
  
  for(x in 1:length(APP$pages)) {
    name <- APP$pages[[x]]$name
    icon <- APP$pages[[x]]$icon
    menu <- APP$pages[[x]]$label
    res <- res + '\tmenuItem("'+menu+'", tabName="'+name+'", icon=icon("'+icon+'", lib="font-awesome"), newtab=FALSE),\n\n'
  }

  if("RULEGRAPH" %in% names(APP)){
    name <- "RULEGRAPH"
    icon <- "gear"
    menu <- "Draw workflow graph"
    res <- res + '\tmenuItem("'+menu+'", tabName="'+name+'", icon=icon("'+icon+'", lib="font-awesome"), newtab=FALSE),\n\n'
  }

  if("download" %in% names(APP)){

    res <- res + '\ttags$br(),\n\n'

    res <- res + '\tdownloadButton("'+ APP$download$shiny_button$name +'", "'+ APP$download$shiny_button$label +'", class="'+ APP$download$shiny_button$class +'", style="color:black;margin: 6px 5px 6px 15px;"),\n\n'

    res <- res + '\ttags$br(),\n\n'
  }

  res <- res + '\ttags$br(),\n\n'

  res <- res + '\tnumericInput("cores", label = "Threads available", min = 1, max = 24, step = 1, width =  "auto", value = 16),\n'
  
  # select where to run again from
  choices = "list('No'='none'"
  for(step in APP$pages[2:length(APP$pages)]){ # all steps but remove global_params page
    choices <- choices + ",'" + step$label + "'='" + step$name + "'"
  }
  res <- res + 'selectInput("force_from", label = "Start again from a step : ", selected = "none", choices = '+choices+')),'
  
  #

  res <- res + '\ttags$br(),\n'
  
  res <- res + '\tactionButton("'+ APP$run$shiny_button$name +'", "'+ APP$run$shiny_button$label +'",  icon("'+ APP$run$shiny_button$icon +'"), class="'+ APP$run$shiny_button$class +'"),\n\n'
  res <- res + '\tactionButton("StopPipeline", "Stop pipeline",  icon("stop"), class="btn btn-secondary"),\n'
  
  res <- res + '\ttags$br(),\n'
  res <- res + '\ttags$br(),\n'

  res <- res + '\tmenuItem("Running Workflow output", tabName="run_out", icon=icon("terminal", lib="font-awesome"), newtab=FALSE),\n'

  if("Report" %in% names(APP)){
    name <- "Report"
    icon <- "file"
    menu <- "Final report"
    res <- res + '\tmenuItem("'+menu+'", tabName="'+name+'", icon=icon("'+icon+'", lib="font-awesome"), newtab=FALSE),\n\n'
  }

  res <- res + '\ttags$br(),\n'
  res <- res + '\tactionButton("close_session", "Close session",  icon("times"), class="btn btn-primary"),\n'
  
  res <- res + '\ttags$br(),tags$br(),\n\n'
  
  res <- res + '\tmenuItem("Powered by mbb", href="http://mbb.univ-montp2.fr/MBB/index.php", newtab=TRUE, icon=icon("book", lib="font-awesome"), selected=NULL)\n\n'
  
  res <- res + ')\n\n'
  
  write(res, file = path_file)
  
}

#============================================================

dir.create.not.exist <- function(path) {
  if(!dir.exists(path)) {
    dir.create(path)
  }
}

#============================================================

generate_rproj <- function(path) {
  file.replace(path)
  res <- ""
  res <- res + "Version: 1.0\n"
  res <- res + " \n"
  res <- res + "RestoreWorkspace: Default\n"
  res <- res + "SaveWorkspace: Default\n"
  res <- res + "AlwaysSaveHistory: Default\n"
  res <- res + " \n"
  res <- res + "EnableCodeIndexing: Yes\n"
  res <- res + "UseSpacesForTab: Yes\n"
  res <- res + "NumSpacesForTab: 2\n"
  res <- res + "Encoding: UTF-8\n"
  res <- res + " \n"
  res <- res + "RnwWeave: Sweave\n"
  res <- res + "LaTeX: pdfLaTeX\n"
  res <- res + " \n"
  write(res, path)
}

#============================================================

generate <- function() {
  
  print("Generate Start")
  
  #YML_TOOLS <<- get_predefined_tool(files_tools)
  
  if(dir.exists(output_dir)) {
    #unlink(output_dir, recursive=TRUE)
  }
  
  dir.create.not.exist(output_dir)
  generate_app()
  
  dir.create.not.exist(output_dir + "/R")
  generate_menu()
  
  dir.create.not.exist(output_dir + "/pages")
  dir.create.not.exist(output_dir + "/server")
  #dir.create.not.exist(output_dir + "/params")
  
  generate_pages_server()