R/get.adapr.options.R

In gelfondjal/adapr: Implementation of an Accountable Data Analysis Process

#' Returns the primary hub file with project location and id information
#' @param setoptions Logical specifying Execute Options
#' @return adaproptions
#' @export
#' @examples 
#'\dontrun{
#' opt <- getAdaprOptions()
#' print(opt)
#'} 
#' 
getAdaprOptions <- function(setoptions=FALSE){
    # 
  option.file <- "adapr_options.csv"
  
  options.site <- file.path(path.expand.2("~"),"ProjectPaths", option.file)  
  
  if(!file.exists(options.site)){
    
    dir.create(dirname(options.site),recursive=TRUE)
    
    options.site0 <- system.file(option.file,package='adapr')
    file.copy(options.site0,options.site)    
 
  }
  
  suppressWarnings(option.data <- utils::read.csv(options.site,as.is=TRUE))
  
  adapr_options <- list()
  
  if(nrow(option.data)){  for(i in 1:nrow(option.data)){adapr_options[[option.data$option[i]]] <- option.data$value[i]}  }
                            
  if(setoptions){
    
    if(!(is.null(adapr_options[["PATH"]]))){Sys.setenv(PATH=adapr_options[["PATH"]])}
    
  }
  
  return(adapr_options)
}


#' Returns Modifies the primary adapr option file
#' @param optionname is name of option to modify
#' @param optionvalue is new value to give optionname
#' @return adaproptions
#' @export
#' @examples 
#'\dontrun{
#' opt <- getAdaprOptions()
#' setAdaprOptions("project.path",opt$project.path)
#' opt2 <- getAdaprOptions()
#' identical(opt,opt2)
#'} 
#' 
setAdaprOptions <- function(optionname="",optionvalue=""){
  # 
  optionvalue <- as.character(optionvalue)
  optionname <- as.character(optionname)
  
  options <- getAdaprOptions(FALSE)
  
  if(!(optionname %in% names(options))){
    print("Current adapr options:")
    print(names(options))
    warning(paste("Setting up new adapr option:",optionname))
    }
  
  if((as.numeric(version$major) +as.numeric(version$minor)/10)>=3.2){
  
  if(optionname=="project.path"){
    
    if(!dir.exists(optionvalue)){
      
      stop("Option project.path directory does not exist")
    }
    
  }
  
  if(optionname=="publish.path"){
    
    if(!dir.exists(optionvalue)){
      
      stop("Option publish.path directory does not exist")
    }
    
  }
  
  }#check dir exists if r version gt or = 3.2
  
  if(optionname=="git"){
    
    
    if(!(optionvalue %in% c("TRUE","FALSE"))){
      
      stop("Option git needs to be \"TRUE\" or \"FALSE\"")
    }
    
    # Check git configuration when turning on git 
    
    testActive <- length(getAdaprOptions()$git)==0
    
    if(!testActive){testActive <- getAdaprOptions()$git=="FALSE"}
 
    if(testActive&(optionvalue=="TRUE")){
      
      print("Use gitCongifure to set git user information")
      print(gitConfigureTest())
      
      email <- ""
      
      try({
        email <-  paste(git2r::config()[["global"]]$user.email,git2r::config()[["local"]]$user.email)
      })
      
      
      if (!grepl("@",email)) {print("Git is not configured. Run: gitConfigure(user.name, user.email)")}
      
      
    } #END: Check git configuration when turning on git  
  } # check git options are TRUE or FALSE
  

  options[[optionname]] <- optionvalue
  
  dfout <- NULL
  
  for(i in 1:length(options)){
    dfout <- rbind(dfout,data.frame(option=names(options[i]),value=options[[i]]))
  }
  
  option.file <- "adapr_options.csv"
  
  options.site <- file.path(path.expand.2("~"),"ProjectPaths", option.file)  
  
  utils::write.csv(dfout,options.site,row.names=FALSE)
  
  return(options)
}