R/findAndMoveInSequence.R

In acidgenomics/r-koopa: Shell Bootloader for Bioinformatics

#' Find and move files in sequence
#'
#' @export
#' @note Updated 2022-09-08.
#'
#' @param sourceDir `character(1)`.
#' Source directory of files to rename.
#'
#' @param targetDir `character(1)`.
#' Target directory of files to rename.
#'
#' @param pattern `character(1)` or `NULL`.
#' File matching pattern. Refer to `list.files()` for details.
#'
#' @return `character`.
#' File paths of renamed files.
#'
#' @examples
#' testDir <- AcidBase::tempdir2()
#' sourceDir <- file.path(testDir, "source")
#' targetDir <- file.path(testDir, "target")
#' paths <- c(sourceDir, targetDir)
#' invisible(lapply(X = paths, FUN = dir.create, recursive = TRUE))
#' invisible(file.create(
#'     file.path(
#'         sourceDir,
#'         paste0(
#'             c("aaa", "bbb", "ccc"),
#'             ".txt"
#'         )
#'     )
#' ))
#' print(sort(list.files(
#'     path = sourceDir,
#'     full.names = FALSE,
#'     recursive = FALSE
#' )))
#' out <- findAndMoveInSequence(
#'     sourceDir = sourceDir,
#'     targetDir = targetDir
#' )
#' print(out)
#' print(sort(list.files(
#'     path = targetDir,
#'     full.names = FALSE,
#'     recursive = FALSE
#' )))
#' AcidBase::unlink2(testDir)
findAndMoveInSequence <-
    function(sourceDir,
             targetDir,
             pattern = NULL) {
        assert(
            requireNamespaces("syntactic"),
            isADir(sourceDir),
            isADir(targetDir),
            !identical(sourceDir, targetDir),
            isString(pattern, nullOk = TRUE)
        )
        sourceFiles <- sort(list.files(
            path = sourceDir,
            pattern = pattern,
            all.files = FALSE,
            full.names = TRUE,
            recursive = TRUE,
            include.dirs = FALSE
        ))
        targetFiles <- file.path(
            targetDir,
            paste0(
                strtrim(
                    syntactic::kebabCase(
                        paste(
                            syntactic::autopadZeros(seq_along(sourceFiles)),
                            basenameSansExt(sourceFiles),
                            sep = "-"
                        ),
                        prefix = FALSE
                    ),
                    width = 100L
                ),
                ".", fileExt(sourceFiles)
            )
        )
        assert(identical(length(sourceFiles), length(targetFiles)))
        invisible(Map(
            from = sourceFiles,
            to = targetFiles,
            f = function(from, to) {
                alert(sprintf("Renaming {.file %s} to {.file %s}.", from, to))
                file.rename(from = from, to = to)
            }
        ))
        alertInfo(sprintf(
            "Successfully renamed %d %s.",
            length(sourceFiles),
            ngettext(
                n = length(sourceFiles),
                msg1 = "file",
                msg2 = "files"
            )
        ))
        invisible(targetFiles)
    }