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#' Convert spectral data files to csv files
#'
#' @param overwrite logical. Should the function overwrite existing files with
#' the same name? (defaults to `FALSE`).
#' @param metadata logical (defaults to `TRUE`). Should metadata be exported as
#' well? They will be exported in csv files will the `_metadata.csv` suffix.
#'
#' @inheritParams lr_get_spec
#'
#' @inherit lr_get_spec details
#'
#' @return Convert input files to csv and invisibly return the list of created
#' file paths
#'
#' @section Warning:
#'
#' When `metadata = TRUE`, if **either** the data **or** metadata export fails,
#' nothing will be returned for this file.
#'
#' @importFrom tools file_path_sans_ext
#' @importFrom utils write.csv
#' @importFrom future.apply future_lapply
#' @importFrom progressr with_progress progressor
#'
#' @export
lr_convert_tocsv <- function(where = NULL, ext = "txt", decimal = ".",
sep = NULL, subdir = FALSE,
ignore.case = TRUE, overwrite = FALSE,
metadata = TRUE) {
if (is.null(where)) {
warning("Please provide a valid location to read and write the files.",
call. = FALSE)
return(NULL)
}
extension <- paste0("\\.", ext, "$", collapse = "|")
file_names <- list.files(
where,
pattern = extension, ignore.case = ignore.case,
recursive = subdir, include.dirs = subdir
)
nb_files <- length(file_names)
if (nb_files == 0) {
warning('No files found. Try a different value for argument "ext".',
call. = FALSE)
return(NULL)
}
files <- file.path(where, file_names)
message(nb_files, " files found")
with_progress({
p <- progressor(along = files)
tmp <- future_lapply(files, function(x) {
p()
tryCatch(
spec2csv_single(
x, decimal = decimal, sep = sep,
overwrite = overwrite, metadata = metadata
),
error = function(e) {
warning(conditionMessage(e))
return(NULL)
})
})
})
whichfailed <- which(vapply(tmp, is.null, logical(1)))
if (length(whichfailed) == nb_files) {
warning("File import failed.\n",
"Check input files and function arguments.", call. = FALSE)
return(NULL)
}
if (length(whichfailed) > 0) {
warning(
"Could not import one or more files:\n",
paste0(files[whichfailed], collapse = "\n"),
call. = FALSE
)
}
invisible(unlist(tmp))
}
#' @noRd
spec2csv_single <- function(filename, decimal, sep, overwrite, metadata) {
exported <- dispatch_parser(filename, decimal = decimal, sep = sep)
csv_name_data <- paste0(file_path_sans_ext(filename), ".csv")
csv_name_metadata <- paste0(file_path_sans_ext(filename), "_metadata.csv")
if (file.exists(csv_name_data) && !overwrite) {
stop(
csv_name_data, " already exists. Select `overwrite = TRUE` to overwrite.",
call. = FALSE
)
}
if (metadata && file.exists(csv_name_metadata) && !overwrite) {
stop(
csv_name_metadata,
" already exists. Select `overwrite = TRUE` to overwrite.",
call. = FALSE
)
}
write.csv(exported[[1]], csv_name_data, row.names = FALSE)
write.csv(exported[[2]], csv_name_metadata, row.names = FALSE)
invisible(csv_name_data)
}
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