R/load_lipds_helpers.R

In chrismheiser/lipdR: LiPD utilities for R

###############################################
## Load LiPD - Helpers
## Misc functions that aid the loading of LiPD
## files
###############################################

#' #' Import each of the required modules for the package
#' #' @export
#' #' @keywords internal
#' #' @return none
#' setModules <- function(){
#'   suppressPackageStartupMessages(library(tools, quietly=TRUE, verbose=FALSE))
#'   suppressPackageStartupMessages(library(Kmisc, quietly=TRUE, verbose=FALSE))
#'   suppressPackageStartupMessages(library(RJSONIO, quietly=TRUE, verbose=FALSE))
#'   suppressPackageStartupMessages(library(jsonlite, quietly=TRUE, verbose=FALSE))
#'   suppressPackageStartupMessages(library(BBmisc, quietly=TRUE, verbose=FALSE))
#' }

#' Get list of all LiPD files in current directory
#' @export
#' @keywords internal
#' @param path.and.file Target directory and 1+ files
#' @return f List of LiPD files w. ext
getListLpdExt <- function(path.and.file){
  file <- path.and.file[["file"]]
  # Multiple file grab. No single filename given.
  if (is.null(file)){
    f <- list.files(path=getwd(), pattern='\\.lpd$')
  }
  # Single file given. Create list of one filename.
  else {
    f <- list()
    f[[1]] <- file
  }
  return(f)
}


#' Unzip LiPD file to the temporary directory
#' @export
#' @keywords internal
#' @param file One LiPD file to unzip
#' @param tmp Temporary directory
#' @return none
unzipper <- function(file, tmp){
  if(length(file)>0){
    # sapply(files, function(f){
    #   unzip(f, exdir = tmp)
    # })
    unzip(file, exdir = tmp)
  }
}

#' Remove the file extension from string name
#' @export
#' @keywords internal
#' @param filename One LiPD filename
#' @return x LiPD filename w/o extension
stripExtension <- function(filename){
  filename <- Kmisc::strip_extension(filename)
  return(filename)
}

#' Get list of csv files in current directory and below
#' @export
#' @keywords internal
#' @return f List of csv files
listFiles <- function(x){
  # create the file type filter string
  ft <- paste0("\\.", x, "$")
  # get the list of filenames from the current directory and below
  f <- list.files(path=getwd(), pattern=ft, recursive=TRUE)
  return(f)
}

#' Remove CSV and metadata layer from LiPD file. Also, remove empties
#' @export
#' @keywords internal
#' @param d LiPD file
#' @return d Modified LiPD file
removeLayers <- function(d){
  d <- removeEmptyRec(d[["metadata"]])
  return(d)
}

#' Ask if user wants to load one file or a directory with multiple files.
#' @export
#' @keywords internal
#' @return ans Answer to prompt (s/m)
askHowMany <- function(){
  ans <- readline(prompt="Are you loading one file or multiple? (s/m): ")
  # Test if input matches what we expect. Keep prompting until valid input.
  if(!grepl("\\<s\\>",ans) & !grepl("\\<m\\>", ans))
  { return(askHowMany()) }
  # Return a valid answer
  return(as.character(ans))
}


#' Convert column type: data frame to list
#' Function may be unused right now
#' @export
#' @keywords internal
#' @param table Data table
#' @return table Converted data table
colsToList <- function(table){
  meta.list <- list()

  # columns are at index 1
  cols <- table[[1]][["columns"]][[1]]

  # loop over dim
  for (i in 1:dim(cols)){
    #make it a list
    meta.list[[i]]=as.list(cols[i,])
  }
  # insert new columns
  table[[1]][["columns"]] <- meta.list

  return(meta.list)
}

#' Convert table type: data frame to list
#' @export
#' @keywords internal
#' @param table Data table
#' @return table Converted data table
tableToList <- function(table){

  # convert table index
  if (is.dataframe(table[[1]])){
    table <- as.list(table[[1]])
  }
  # convert table
  if (is.dataframe(table)){
    table <- as.list(table)
  }
  return(table)
}