PACER:

# Get the list of files in a directory
load_directory <- function(dir, filetypes, include_dirs=FALSE){
  return(dir(path = dir,
             recursive = FALSE,
             pattern = filetypes,
             include.dirs = include_dirs,
             full.names = FALSE))
}

# Save the adapters or the genome list
save_info <- function(x, path, delimeter, col_names){
  # If a file already exists, save a backup file
  if(file.exists(path)){
    file.copy(from = path,
              to = paste(path, ".backup", sep = ""),
              overwrite = TRUE, copy.mode = TRUE, copy.date = TRUE)
  }
  write_delim(x = x,
              path = path,
              delim = delimeter,
              col_names = col_names,
              append = FALSE)
  return(file.exists(path))
}

# Combine the numbering and the text to create a list of options for a dropdown
make_choices <- function(choices, numbered=TRUE){
  if(isTRUE(numbered)){
    return(mapply(paste(1:length(choices), choices, sep = " - "), 1:length(choices), FUN = function(x, y){x=y}))
  }else{
    return(mapply(choices, 1:length(choices), FUN = function(x, y){x=y}))
  }
}

# Update the index for the adapter modal
update_adapter_index <- function(session, adapters){
  if(nrow(adapters)>0){
    row.names(adapters) <- 1:nrow(adapters)
    row_choices <- make_choices(adapters$Description)
    toggleState(id = "remove_adapter", condition = TRUE)
  } else{
    row_choices <- c("")
    toggleState(id = "remove_adapter", condition = FALSE)
  }
  updateSelectInput(session = session,
                    inputId = "adapter_index",
                    label = NULL,
                    choices = row_choices,
                    selected = NULL)
}

# Update the index for the genome list on the genome modal
update_genome_index <- function(session, genomes){
  # Toggle buttons based on the number of items in the list
  if(nrow(genomes)>0){
    print("more than 0 genomes")
    row.names(genomes) <- 1:nrow(genomes)
    row_choices <- make_choices(genomes[,2],
                                numbered = TRUE)
    toggleState(id = "load_genome", condition = TRUE)
    toggleState(id = "remove_genome", condition = TRUE)
    toggleState(id = "view_genome", condition = TRUE)
  } else {
    print("0 genomes")
    row_choices <- c(" "=0)
    toggleState(id = "load_genome", condition = FALSE)
    toggleState(id = "remove_genome", condition = FALSE)
    toggleState(id = "view_genome", condition = FALSE)
    toggleElement(id = "genome_details", condition = FALSE)
  }
  # Update the selector
  updateSelectInput(session = session,
                    inputId = "genome_index",
                    label = NULL,
                    choices = row_choices,
                    selected = NULL)
}
# Update the ensembl genome list selector
update_ensembl_genome_index <- function(session, genomes){
  # Toggle buttons based on the number of options
  if(nrow(genomes)>0){
    row.names(genomes) <- 1:nrow(genomes)
    row_choices <- make_choices(genomes[,2],
                                numbered = FALSE)
    toggleState(id = "add_genome", condition = TRUE)
  } else {
    row_choices <- c("")
    toggleState(id = "add_genome", condition = FALSE)
  }
  # Update the dropdown list of ensembl genomes
  updateSelectInput(session = session,
                    inputId = "ensembl_genome_index",
                    label = NULL,
                    choices = row_choices,
                    selected = NULL)
}

# Check if a genome entry is complete
check_for_complete_genome <- function(genome){
  if(nrow(genome)==0) return(genome)
  result <- rep("Incomplete", nrow(genome))
  for(i in 1:nrow(genome)){
    if(genome[i, 5] != "None" &
       genome[i, 6] != "None" &
       genome[i, 7] != "None") result[i] <- "Ready"
  }
  return(result)
}

# Add a genome from the ensembl list to the genome list
add_genome <- function(genomes, new_genome){
  print(names(genomes))
  print(names(new_genome))
  names(new_genome) <- c("Dataset", "Description", "Version")
  if(nrow(genomes)==0){
    print("create new genome list")
    genomes <- data.frame(stringsAsFactors = FALSE, row.names = NULL, new_genome, "Status"="Incomplete", "Interval.Status"="None", "Genome.FASTA"="None", "Bowtie.Index"="None", "Gene Sets"="None")
  } else {
    print("append genome to list")
    genomes <- rbind(genomes, data.frame(stringsAsFactors = FALSE, row.names = NULL, new_genome, "Status"="Incomplete", "Interval.Status"="None", "Genome.FASTA"="None", "Bowtie.Index"="None", "Gene.Sets"="None"))
  }
  return(genomes)
}


create_new_tabset <- function(name){
  newTabset = tabPanel(
    value = paste0("tabset_", name),
    title = name,
    tabsetPanel(id = paste0("tabsetpanel_", name), type = 'tabs',
                tabPanel(title = "5' Distributions",
                         value = paste0("five_prime_", name),
                         wellPanel(id = paste0("five_prime_plot__", name))),
                tabPanel(title = "Scatters",
                         value = paste0("scatters_", name),
                         wellPanel(id = paste0("scatters_", name))),
                tabPanel(title = "Offsets",
                         value = paste0("offsets_", name),
                         wellPanel(id = paste0("offsets_", name))),
                tabPanel(title = "Phasing",
                         value = paste0("phasing_", name),
                         wellPanel(id = paste0("phasing_", name))),
                tabPanel(title = "Heatmaps",
                         value = paste0("heatmaps_", name),
                         wellPanel(id = paste0("heatmaps_", name))),
                tabPanel(title = "Sequence Logos",
                         value = paste0("sequence_logos_", name),
                         wellPanel(id = paste0("sequence_logos_", name)))
    )
  )
  return(newTabset)
}

create_new_output <- function(ID){
  # insertUI(selector = ID,
  #          where = "afterEnd",
  #          immediate = TRUE,
           ui = tagList(
             fluidRow(
               wellPanel(
                 fluidRow(h5(gsub(pattern = "__", replacement = "  -  ", x = ID, fixed = TRUE))),
                 fluidRow(plotOutput(outputId = ID))
               )
             )
           )
           return(ui)
  # )
}

appendTab_new <- function (inputId, tab, select = FALSE, menuName = NULL, session=session()) #session = getDefaultReactiveDomain())
{
  force(select)
  force(menuName)
  inputId <- session$ns(inputId)
  item <- buildTabItem("id", "tsid", TRUE, divTag = tab, textFilter = if (is.character(tab))
    navbarMenuTextFilter
    else NULL)
  # callback <- function() {
    session$sendInsertTab(inputId = inputId, liTag = processDeps(item$liTag,
                                                                 session), divTag = processDeps(item$divTag, session),
                          menuName = menuName, target = NULL, position = "before",
                          select = select)
  # }
  # session$onFlush(callback, once = TRUE)
}

# Update progress
updateProgress <- function(value = NULL, detail = NULL) {
  if (is.null(value)) {
    value <- values$progress$getValue()
    value <- value + (values$progress$getMax() - value) / 5
  }
  values$progress$set(value = value, detail = detail)
}