#!/usr/bin/env Rscript
# Author: Jianfeng Li
# Email: lee_jianfeng@sjtu.edu.cn
# Year: 2018
# Homepage: https://github.com/ngsjs/ngsjs
# License: MIT
# Copyrights 2018 Jianfeng All Rights Reserved.
suppressMessages(if(!require('pacman')) install.packages('pacman'))
pkgs <- c("ngstk")
suppressMessages(pacman::p_load(pkgs, character.only = TRUE))

option_list <- list(
  make_option(c("-v", "--verbose"), action = "store_true", default = FALSE, help = "Print extra output [default FALSE]"), 
  make_option(c("-f", "--func"), help = "Index or name of used function [e.g. shiny::runApp (1).", 
              default = "shiny::runApp"),
  make_option(c("-a", "--app_dir"), help = "Bioshiny application dir.", default = system.file('extdata', 'shiny', package = 'bioshiny')), 
  make_option(c("-p", "--port"), help = "Port to start a shiny application.", default = "3333"), 
  make_option(c("--host"), help = "Host to listen.", default = "0.0.0.0"), 
  make_option(c("-r", "--rfunc"), help = "R function (input param 'x') to process the returned colors or length [e.g. function(x){return(x[[2]])} or x[[2]]].", 
  default = NULL),
  make_option(c("-e", "--extra"), help = "Extra parameters [...].", default = ""),
  make_option(c("-d", "--doc"), action = "store_true", default = FALSE, help = "Print functions document")
)

description <- paste(
                     "\trstart_shiny is a R-based tool to start an R bioshiny application.",
                     sep = "\n\t"
                    )
usage <- paste("",
               "%prog [options] [params]",
               "%prog",
               "%prog -p 3434",
               sep = "\n\t")
opt_parser_obj <- opt_parser(option_list = option_list,
                        usage = usage, description = description) 
opt <- parse_args(opt_parser_obj, positional_arguments = TRUE, print_help_and_exit = FALSE) 
opt_args <- opt$args
opt <- opt$option
if (opt[["port"]] == "" && length(opt_args) > 0) opt[["port"]] <- opt_args[1]
if (opt[["app_dir"]] == "" && length(opt_args) > 1) opt[["app_dir"]] <- opt_args[1]
if (!is.null(opt[["rfunc"]]) && length(opt_args) > 2) opt[["rfunc"]] <- opt_args[2]

if ((opt[["port"]] == "" && opt[["app_dir"]] == "" && !opt[["doc"]] ) || opt$help) {
  print_help(opt_parser_obj)
} else {
  port <- as.numeric(opt[["port"]])
  host <- opt[["host"]]
  app_dir <- opt[["app_dir"]]
  if (opt[["extra"]] != "") {
    cmd_text <- sprintf("params <- list(appDir = app_dir, port = port, host = host, %s)", opt[["extra"]])
  } else {
    cmd_text <- sprintf("params <- list(appDir = app_dir, port = port, host = host)")
  }
  eval(parse(text = cmd_text))
  predefined_funcs <- list("1"="shiny::runApp") 
  if (opt[["func"]] %in% names(predefined_funcs)) {
    predefined_func <- predefined_funcs[[ opt[["func"]] ]]
    if (length(grep("::|:::", opt[["func"]])) > 0) {
      dep_pkg <- strsplit(predefined_func, "::|:::")[[1]][1]
      suppressWarnings(suppressMessages(pacman::p_load(dep_pkg, character.only = TRUE)))
    }
    opt[["func"]] <- predefined_func
  }
  if (opt[["doc"]]) {
    eval(parse(text = sprintf("?%s", opt[["func"]])))
  } else {
    eval(parse(text = sprintf("x <- do.call(%s, params)", opt[["func"]])))
    is.function <- length(grep("function", opt[["rfunc"]])) > 0
    if (is.character(opt[["rfunc"]]) && !is.function) {
      opt[["rfunc"]] <- sprintf("function(x) {%s}", opt[["rfunc"]])
    }
    if (is.character(opt[["rfunc"]]))
      x <- do.call(eval(parse(text = opt$rfunc)), list(x=x))
    if (is.character(x) || is.numeric(x)) cat(paste(x, collapse = "\n"), sep = "\n")
    else x
  }
}