R/dbpf_FG2toGP5W.R

In geocryology/PermafrostDB: PermafrostDB

# =============================================================================
#'
#' @title Convert FG2 to GP5W
#'
#' @description Returns connection to permafrost database
#'
#' @param inPath character, path to FG2 directory or specific FG2 file
#'
#' @return Creates directory with new files.
#'
#' @return Log of which files were converted
#'
#' @details Function takes a file path, scans for FG2 files to be converted.
#' @export
#' @author Hannah Macdonell <hannah.macdonell@@carleton.ca>
# =============================================================================
dbpf_FG2toGP5W <- function(inPath){
  direc <- FALSE
  file <- FALSE
  # test for existence
  if (file_test("-f", inPath) == 1) file <- TRUE
  else if (dir.exists(inPath) == 1) direc <- TRUE
  else {
    print(paste0("Location '", inPath, "' does not exist."))
    return(0)
  }

  newDir <- paste(dirname(inPath),"/convertedFG2",sep='')

  ############ DIRECTORY #################

  if (direc == TRUE){
    inPath <- rewritedir(inPath)
    inFiles <- list.files(inPath)
    print(paste0("Files successfully converted and moved to '", newDir, "' include:",sep=''))
    for (file in inFiles){
      file <- paste(inPath,file,sep='')
      if (fileType(file) == "FG2"){
        convertFG2(file)
       }
    }
  }

  ############# FILE ###################

  else if (file == TRUE){
    if (fileType(inPath) == "FG2"){
      convertFG2(inPath)
      # Log
      print(paste(basename(inPath),"converted and moved to",newDir))
    }
  }

}


convertFG2 <- function(filePath){
  # Takes FG2 file path and converts to GP5W
  con <- file(filePath, open='r')
  lines <- readLines(con)

  direc <- paste(dirname(filePath),"convertedFG2", sep='/')

  # Checking to see if /convertedFG2 exists in cur dir
  if (dir.exists(direc) == 0) dir.create(direc)

  # Creating new file
  newFile <- (basename(filePath))
  newDir <- paste0(dirname(filePath), "_GP5WFormatted")
  print(newFile)
  print(newDir)
  sink(paste(direc, newFile, sep='/'))

  headerCount <- TRUE # To avoid multiple headers

  for(line in lines){
    # If info line: translate
    if (grepl("<LOGGER", line) == 1) {
      logger <- substr(stringr::str_extract(line, "\\$......\\>"), 2, 7) # Pulls out 6-Digit logger ID
      newLine <- sprintf("Logger: #%s 'PT1000TEMP' - USP_EXP2 - (CGI) Expander for GP5W - (V2.7, Jan 12 2016)\n", logger)
      cat(newLine)
      next
    }

    # If any other header line: skip
    if (grepl("<",line) == 1) next

    # If first col names: translate
    if (grepl("NO,TIME,", line)){
      if (headerCount) {
        headerCount <- FALSE
        line <- gsub("NO", "No", line)
        line <- gsub("TIME", "Time", line)
        line <- gsub("HK-BAT", "#HK-Bat:V", line)
        line <- gsub("HK-TEMP....", "#HK-Temp:oC", line)
        line <- gsub("\\(\\(unk\\.\\)\\)", ":oC", line) # Replace ((unk.))
        cat(line,  sep="\n")
        next
      }
      else next
    }

    # Regular time stamp info, nothing to change.
    else cat(line, sep="\n")

  } # End of for loop
  sink()
  close(con)
  closeAllConnections()

}

# Function returns whether file is FG2, GP5W, or unidentifiable(FALSE)
fileType <- function(inPath){
  # Is it a file?
  if (file_test("-f", inPath) == 1) {
    # Is file a csv?
    if (file_ext(inPath) == "csv"){
      chars <- readLines(file(inPath,"r"),n=1)
      # Is file a fg2?
      if (grepl("FG2", chars) == 1){
        return("FG2")
      }
    }
  }
  # File is not FG2
  return("Not an FG2")
}

# Ensures directory feature a trailing '/'
rewritedir <- function(inPath){
  char <- substr(inPath, nchar(inPath), nchar(inPath))
  if (char != '/') inPath <- paste(inPath, '/', sep='')
  return(inPath)
}