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#' Read a base list from disk
#'
#' Read a \link{list} from its on-disk representation.
#' This is usually not directly called by users, but is instead called by dispatch in \code{\link{readObject}}.
#'
#' @param path String containing a path to a directory, itself created with the list method for \code{\link{stageObject}}.
#' @param metadata Named list containing metadata for the object, see \code{\link{readObjectFile}} for details.
#' @param simple_list.parallel Whether to perform reading and parsing in parallel for greater speed.
#' Only relevant for lists stored in the JSON format.
#' @param ... Further arguments to be passed to \code{\link{altReadObject}} for complex child objects.
#'
#' @return
#' The list represented by \code{path}.
#'
#' @author Aaron Lun
#'
#' @details
#' The \pkg{uzuki2} specification (see \url{https://github.com/ArtifactDB/uzuki2}) allows length-1 vectors to be stored as-is or as a scalar.
#' If the file stores a length-1 vector as-is, \code{readBaseList} will read the list element as a length-1 vector with the \link{AsIs} class.
#' If the file stores a length-1 vector as a scalar, \code{readBaseList} will read the list element as a length-1 vector without this class.
#' This allows downstream users to distinguish between the storage modes in the rare cases that it is necessary.
#'
#' @seealso
#' \code{"\link{stageObject,list-method}"}, for the staging method.
#'
#' @examples
#' library(S4Vectors)
#' ll <- list(A=1, B=LETTERS, C=DataFrame(X=letters))
#'
#' tmp <- tempfile()
#' saveObject(ll, tmp)
#' readObject(tmp)
#'
#' @export
#' @aliases loadBaseList
readBaseList <- function(path, metadata, simple_list.parallel=TRUE, ...) {
all.children <- list()
child.path <- file.path(path, "other_contents")
if (file.exists(child.path)) {
all.dirs <- list.files(child.path)
all.children <- vector("list", length(all.children))
for (n in all.dirs) {
all.children[[as.integer(n) + 1L]] <- altReadObject(file.path(child.path, n), simple_list.parallel=simple_list.parallel, ...)
}
}
path <- normalizePath(path) # protect C code from ~/.
format <- metadata$simple_list$format
if (is.null(format) || format == "hdf5") {
lpath <- file.path(path, "list_contents.h5")
output <- load_list_hdf5(lpath, "simple_list", all.children)
} else {
lpath <- file.path(path, "list_contents.json.gz")
output <- load_list_json(lpath, all.children, simple_list.parallel)
}
output
}
#######################################
########### OLD STUFF HERE ############
#######################################
#' @export
loadBaseList <- function(info, project, parallel=TRUE) {
children <- info$simple_list$children
for (i in seq_along(children)) {
child.meta <- acquireMetadata(project, children[[i]]$resource$path)
children[[i]] <- altLoadObject(child.meta, project=project)
}
lpath <- acquireFile(project, info$path)
output <- NULL
if ("hdf5_simple_list" %in% names(info)) {
output <- load_list_hdf5(lpath, info$hdf5_simple_list$group, children)
} else {
comp <- info$json_simple_list$compression
if (!is.null(comp) && !(comp %in% c("none", "gzip"))) {
stop("only uncompressed or Gzip-compressed JSON lists are supported")
}
output <- load_list_json(lpath, children, parallel)
}
# Need to replace any Rfc3339's with POSIXct objects for back-compatibility.
# This is done manually because the C++ code already uses Rfc3339 and I don't
# want to have to compile a separate version just to handle the old case.
to_posix <- function(x) {
if (is.list(x) && class(x)[1] == "list") {
lapply(x, to_posix)
} else if (is.Rfc3339(x)) {
as.POSIXct(x)
} else {
x
}
}
to_posix(output)
}
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