inst/ubinc/templates/ubiquity_server_custom.R

In ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

rm(list=ls())


require(shiny)
require(shinydashboard)
require(deSolve)
require(ggplot2)
require(foreach)
require(doParallel)
require(rhandsontable)

#
# If we're operating out of a "stand alone" directory we load the files from
# there. Otherwise we try to load the ubiquity package
#

if("ubiquity" %in% (.packages())){
  ubiquity_distribution = "package"
} else if(file.exists(file.path('library', 'r_general', 'ubiquity.R'))){
  source(file.path('library', 'r_general', 'ubiquity.R'))
  ubiquity_distribution = "stand alone"
} else { 
  library(ubiquity) 
  ubiquity_distribution = "package"
}

source(file.path("transient", "app_base", "auto_rcomponents.R"))
#-----------------------------------------
# Updates the diagnostics log file
user_log_update <- function(input, output, session) {
  state = fetch_state(input, session)
  cfg=state[["cfg"]]
  fileReaderData <- reactiveFileReader(500, session, cfg$gui$user_log_file, readLines)
  output$text_user_log <- renderText({
    # Read the text, and make it a consistent number of lines so
    # that the output box doesn't grow in height.
    text <- fileReaderData()
    length(text) <- cfg$gui$user_log_length
    text[is.na(text)] <- ""
    paste(text, collapse = '\n')
  })
}

#-----------------------------------------
# Puling up the app state
#
app_fetch_cfg  <-function(){
  cfg = NULL
  # This should load the default app state:
  load(file= file.path(getwd(), "transient", "app_base", "rgui", "gui_state.RData"))
  return(cfg)}


#-----------------------------------------
# Getting the current state
fetch_state <- function(input, session) {

  #-------------------------
  # Sets the current app state
  if(is.null(session[["userData"]][["state"]])){
    # The first time this funciton is called the state element should be null
    # so we initialize it here:
    #-------------------------
    # Loading the default ubiquity system object
    cfg = app_fetch_cfg()

    #-------------------------
    # Defining/creating the user directory
    user_dir = find_user_dir(session)
    if(!dir.exists(user_dir)){
      dir.create(user_dir, recursive=TRUE)}

    #-------------------------
    # Initializing the user log file
    user_log_file = file.path(user_dir, "ubiquity_log.txt")
    # This creates an empty file for logging
    if(file.exists(user_log_file)){
      file.remove(user_log_file) }
    file.create(user_log_file) 
    cfg[["gui"]][["user_log_file"]] = user_log_file

    user_log_entry(cfg, "App initialization...")
    user_log_entry(cfg, paste("  user directory:", user_dir))

    #-------------------------
    # Defining/creating the output directory
    output_dir = file.path(user_dir, "output")
    if(!dir.exists(output_dir)){
      dir.create(output_dir) }

    cfg = system_set_option(cfg, 
      group        = "general",
      option       = "output_directory",
      output_dir)
    user_log_entry(cfg, paste("  output directory:", output_dir))


    #-------------------------
    # Default to integrating with r scripts
    cfg[["options"]][["simulation_options"]][["integrate_with"]]  = "r-file"
    # If the dynamic library exists we try to load it
    if(file.exists(file.path("transient", "app_base", paste("ubiquity_app_base", .Platform$dynlib.ext, sep = "")))){
      user_log_entry(cfg, "Found dynamic library attempting to load")
      dyn.load(file.path("transient", "app_base", paste("ubiquity_app_base", .Platform$dynlib.ext, sep = ""))) }
   
    # If the library has been loaded we switch to C
    if(is.null(getLoadedDLLs()$ubiquity_app_base) == FALSE){
      if(getLoadedDLLs()$ubiquity_app_base[["dynamicLookup"]] == TRUE){
        user_log_entry(cfg, "Dynamic library seems to be loaded, setting")
        user_log_entry(cfg, "integration method to c-file")
        cfg[["options"]][["simulation_options"]][["integrate_with"]]  = "c-file"
      }
    }

    # all done.
    user_log_entry(cfg, "App initialized!")

    # Saving the ubiquity system object
    state = list()
    state[["cfg"]] = cfg
  }else{
    # After the first time this function is called the 
    # app state should be set, so we pull that state here:
    state = session[["userData"]][["state"]]
  }
       
  #-------------------------
  # Add any code here to check input elements or
  # append them to the app state:

  #-------------------------
  # Saving the state with any changes:
  session[["userData"]][["state"]] = state

state}
#-----------------------------------------
# This function finds a place to store the user information for the current
# session. If the user variable is set, we use that to store the user session,
# otherwise we use the session token. If for some reason those fail we store
# them in 'default'
#
# If full is FALSE then we just get the name of the user specific directory.
# If full is TRUE we return the full path to that directory.
#
# To do this we need to figure out if the app is deployed. This is triggered
# by the looking at the file "DEPLOYING" in transient/app_base. If that file
# has the word TRUE, then we store everything in the session temporary
# directory. If the app isn't deployed then we store everything in the working
# directory to allow for debugging later.
find_user_dir <- function(session, full=TRUE) {

  # Trying to determine where to store the user information
  # First we see if the session$user exists, if not we look for the
  # session token, then we look for 
  if(!is.null(session$user)){
    user = session$user 
  } else if (!is.null(session$token)) {
    user = session$token 
  } else {
    user = 'default'  
  }

  if(full){
    # First we set deploying to false
    DEPLOYING = FALSE
    # Next we try to open the file that contains the deploying switch. It's
    # created at the end of the ubiquity_app.R file:
    DEPINFO_file = file.path(getwd(), "transient", "app_base" ,"DEPLOYING")
    if(file.exists(DEPINFO_file)){
      # This file should contain a single line with either TRUE if the app is
      # being deployed and false if it's not
      DEPLOYINGConn<-file(file.path(getwd(), "transient", "app_base" ,"DEPLOYING"))
      if(readLines(DEPINFO_file)[1] == "TRUE"){
        DEPLOYING = TRUE
      }
      close(DEPLOYINGConn)
    } 
    
    if(DEPLOYING){
        # If we're deploying we store the user files in the temporary
        # directory:
        user = file.path(tempdir(),"transient", "app_base", "rgui", user) 
      } else {
        # otherwise we store them locally 
        user = file.path(getwd(),"transient", "app_base", "rgui") 
      }
  }

  return(user)
}
#-----------------------------------------
user_log_entry = function(cfg, text){
  logfile = cfg$gui$user_log_file

  # First we add it to the GUI log entry
  GUI_log_entry(cfg, text)

    # now we read in the contents of the gui log file
    current_file = file(logfile, open="r")
    lines = readLines(current_file)
    close(current_file)
    
    # appending the text to the log file
    lines = c(lines, text)
    
    # only pulling the last n lines
    lines = tail(lines, cfg$gui$user_log_length)
    
    # writing those back to the log file
    # Now we dump it to the log file:
    write(lines, file=logfile, append=FALSE)

}

#-----------------------------------------
server <- function(input, output, session) {

  #state = fetch_state(input, session)
  user_log_update(input, output, session)

}