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#' List objects in a directory
#'
#' List all objects in a directory, along with their types.
#'
#' @param dir String containing a path to a staging directory.
#' @param include.children Logical scalar indicating whether to include child objects.
#'
#' @return \linkS4class{DataFrame} where each row corresponds to an object and contains;
#' \itemize{
#' \item \code{path}, the relative path to the object's subdirectory inside \code{dir}.
#' \item \code{type}, the type of the object
#' \item \code{child}, whether or not the object is a child of another object.
#' }
#'
#' If \code{include.children=FALSE}, metadata is only returned for non-child objects.
#'
#' @author Aaron Lun
#'
#' @examples
#' tmp <- tempfile()
#' dir.create(tmp)
#'
#' library(S4Vectors)
#' df <- DataFrame(A=1:10, B=LETTERS[1:10])
#' saveObject(df, file.path(tmp, "whee"))
#'
#' ll <- list(A=1, B=LETTERS, C=DataFrame(X=1:5))
#' saveObject(ll, file.path(tmp, "stuff"))
#'
#' listObjects(tmp)
#' listObjects(tmp, include.children=TRUE)
#'
#' @export
#' @aliases listLocalObjects listDirectory
#' @importFrom S4Vectors DataFrame
listObjects <- function(dir, include.children=FALSE) {
DataFrame(.traverse_directory_listing(dir, ".", include.children=include.children))
}
.traverse_directory_listing <- function(root, dir, already.child=FALSE, include.children=FALSE) {
full <- file.path(root, dir)
is.obj <- file.exists(file.path(full, "OBJECT"))
if (is.obj) {
paths <- dir
types <- readObjectFile(full)$type
childs <- already.child
} else {
paths <- character(0)
types <- character(0)
childs <- logical(0)
}
if (include.children || !is.obj) {
more.dirs <- list.dirs(full, recursive=FALSE, full.names=FALSE)
for (k in more.dirs) {
if (dir != ".") {
subdir <- file.path(dir, k)
} else {
subdir <- k
}
sub <- .traverse_directory_listing(root, subdir, already.child=(already.child || is.obj), include.children=include.children)
paths <- c(paths, sub$path)
types <- c(types, sub$type)
childs <- c(childs, sub$child)
}
}
list(path=paths, type=types, child=childs)
}
#######################################
########### OLD STUFF HERE ############
#######################################
#' @export
#' @importFrom jsonlite fromJSON
listDirectory <- function(dir, ignore.children = TRUE) {
all.json <- list.files(dir, pattern="\\.json$", recursive=TRUE)
out <- lapply(file.path(dir, all.json), fromJSON, simplifyVector=FALSE)
names(out) <- vapply(out, function(x) x$path, "")
if (ignore.children) {
child <- vapply(out, function(x) isTRUE(x$is_child), TRUE)
out <- out[!child]
}
out
}
# Soft-deprecated back-compatibility fixes.
#' @export
listLocalObjects <- function(..., ignoreChildren = TRUE) listDirectory(..., ignore.children = ignoreChildren)
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