liftr/R/utils.R

# convert string vectors to single quote-marked
# string separated by comma
quote_str = function(x) {
  paste0("\'", paste(x, collapse = "','"), "\'")
}

# get directory of the file
file_dir = function(x) {
  dirname(normalizePath(x))
}

# get file name with extension
file_name = function(x) {
  basename(normalizePath(x))
}

# get file name without extension
sans_ext = tools::file_path_sans_ext
file_name_sans = function(x) {
  basename(sans_ext(normalizePath(x)))
}

# generate UUID for Docker container names
# derived from https://stackoverflow.com/questions/10492817/
uuid = function() {
  id = paste(sample(c(letters[1:6], 0:9), 30, replace = TRUE), collapse = '')
  paste(
    substr(id, 1, 8), '_', substr(id, 9, 12), '_', '4',
    substr(id, 13, 15), '_', sample(c('8', '9', 'a', 'b'), 1),
    substr(id, 16, 18), '_', substr(id, 19, 30), sep = '',
    collapse = '')
}

#' check if from Bioconductor base images
#' @importFrom stringr str_trim
#' @noRd
is_from_bioc = function(x) {
  substr(str_trim(x), 1L, 13L) == 'bioconductor/'
}

#' check if from the rocker/rstudio base image
#' @importFrom stringr str_trim
#' @noRd
is_from_rstudio = function(x) {
  substr(str_trim(x), 1L, 14L) == 'rocker/rstudio'
}

# remove consecutive blank lines and only keep one
sanitize_blank = function(txt) {
  blank = which(txt == "")
  # if no blank lines at all
  if (length(blank) == 0L) return(txt)
  idx = which(diff(blank) == 1L) + 1L
  # if no consecutive blank lines
  if (length(idx) == 0L) return(txt)
  txt = txt[-blank[idx]]
  txt
}

# determine os type
check_os = function() {
  if (Sys.info()[['sysname']] == 'Darwin') 'mac' else if
  (.Platform$OS.type == 'windows') 'win' else 'lnx'
}