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#' Validate a directory of objects
#'
#' Check whether each object in a directory is valid by calling \code{\link{validateObject}} on each non-nested object.
#'
#' @param dir String containing the path to a directory with subdirectories populated by \code{\link{saveObject}}.
#' @param legacy Logical scalar indicating whether to validate a directory with legacy objects (created by the old \code{stageObject}).
#' If \code{NULL}, this is auto-detected from the contents of \code{dir}.
#' @param ... Further arguments to use when \code{legacy=TRUE}, for back-compatibility only.
#'
#' @return Character vector of the paths inside \code{dir} that were validated, invisibly.
#' If any validation failed, an error is raised.
#'
#' @details
#' We assume that the process of validating an object will call \code{\link{validateObject}} on any nested objects.
#' This allows us to skip explicit calls to \code{\link{validateObject}} on each component of a complex object.
#'
#' @author Aaron Lun
#' @examples
#' # Mocking up an object:
#' library(S4Vectors)
#' ncols <- 123
#' df <- DataFrame(
#' X = rep(LETTERS[1:3], length.out=ncols),
#' Y = runif(ncols)
#' )
#' df$Z <- DataFrame(AA = sample(ncols))
#'
#' # Mocking up the directory:
#' tmp <- tempfile()
#' dir.create(tmp, recursive=TRUE)
#' saveObject(df, file.path(tmp, "foo"))
#'
#' # Checking that it's valid:
#' validateDirectory(tmp)
#'
#' # Adding an invalid object:
#' dir.create(file.path(tmp, "bar"))
#' write(file=file.path(tmp, "bar", "OBJECT"), '[ "WHEEE" ]')
#' try(validateDirectory(tmp))
#'
#' @aliases checkValidDirectory
#' @export
validateDirectory <- function(dir, legacy=NULL, ...) {
if (is.null(legacy)) {
legacy <- length(list.files(dir, recursive=TRUE, pattern="^OBJECT$")) == 0L
}
if (!legacy) {
objects <- listObjects(dir)
for (x in objects$path) {
tryCatch(validateObject(file.path(dir, x)), error=function(e) stop("failed to validate '", x, "'; ", e$message))
}
invisible(objects$path)
} else {
legacy.validateDirectory(dir, ...)
}
}
legacy.validateDirectory <- function(dir, validate.metadata = TRUE, schema.locations = NULL, attempt.load = FALSE) {
all.files <- list.files(dir, recursive=TRUE)
is.json <- endsWith(all.files, ".json")
meta.files <- all.files[is.json]
other.files <- all.files[!is.json]
schema.paths <- list()
if (is.null(schema.locations)) {
schema.locations <- .default_schema_locations()
}
# Opening all the metadata files.
am.child <- character(0)
not.child <- character(0)
expected.child <- character(0)
redirects <- character(0)
for (metapath in meta.files) {
jpath <- file.path(dir, metapath)
meta <- fromJSON(jpath, simplifyVector=TRUE, simplifyMatrix=FALSE, simplifyDataFrame=FALSE)
schema.id <- meta[["$schema"]]
if (validate.metadata) {
if (!(schema.id %in% schema.paths)) {
schema.path <- .hunt_for_schemas(meta[["$schema"]], schema.locations)
schema.paths[[schema.id]] <- schema.path
}
schema.path <- schema.paths[[schema.id]]
}
# Special case for redirections
if (startsWith(schema.id, "redirection/")) {
if (paste0(meta$path, ".json") != metapath) {
stop("metadata in '", metapath, "' references an unexpected path '", meta$path, "'")
}
if (meta$path %in% all.files) {
stop("metadata in '", metapath, "' contains a redirection from existing path '", meta$path, "'")
}
for (target in meta[["redirection"]][["targets"]]) {
if (target$type == "local") {
redirects <- c(redirects, target$location)
}
}
next
}
# Checking the path.
if (!(meta$path %in% all.files)) {
stop("metadata in '", metapath, "' references a non-existent path '", meta$path, "'")
}
if (meta$path != metapath && paste0(meta$path, ".json") != metapath) {
stop("metadata in '", metapath, "' references an unexpected path '", meta$path, "'")
}
if (!isTRUE(meta$is_child)) {
not.child <- c(not.child, meta$path)
if (attempt.load) {
tryCatch(
altLoadObject(meta, dir),
error=function(e) {
stop("failed to load non-child object at '", meta$path, "'\n - ", e$message)
}
)
}
} else {
am.child <- c(am.child, meta$path)
}
# Checking that all children live in subdirectories of metapath's directory, not at the top level.
children <- .fetch_resource_paths(meta)
subdir.prefix <- paste0(dirname(metapath), "/")
if (any(nonnest <- !startsWith(dirname(children), subdir.prefix))) {
stop("metadata in '", metapath, "' references non-nested child '", children[nonnest][1], "'")
}
expected.child <- c(expected.child, children)
}
# Checking that all children are not marked as non-children.
conflicts <- intersect(expected.child, not.child)
if (length(conflicts)) {
stop("non-child object in '", conflicts[1], "' is referenced by another object")
}
if (dup <- anyDuplicated(expected.child)) {
stop("multiple references to child at '", expected.child[dup], "'")
}
missing.child <- setdiff(expected.child, am.child)
if (length(missing.child)) {
stop("missing child object '", missing.child[1], "'")
}
extra.child <- setdiff(am.child, expected.child)
if (length(extra.child)) {
stop("non-referenced child object in '", extra.child[1], "'")
}
extra.other <- setdiff(other.files, c(am.child, not.child))
if (length(extra.other)) {
stop("unknown file at '", extra.other[1], "'")
}
# Checking that non-children are not nested within each other.
safe.set <- "."
offenders <- sort(dirname(not.child))
for (i in seq_along(offenders)) {
if (i > 1 && startsWith(offenders[i], paste0(offenders[i-1], "/"))) {
stop("non-child object at '", offenders[i], "' is nested inside the directory of '", offenders[i-1], "'")
}
}
# Checking that redirects are valid.
dangling.direct <- !(redirects %in% am.child) & !(redirects %in% not.child)
if (any(dangling.direct)) {
stop("invalid redirection to '", dangling.direct[1], "'")
}
}
.fetch_resource_paths <- function(x) {
if (!is.list(x)) {
return(NULL)
}
if (!is.null(names(x))) {
is.res <- which(names(x) == "resource")
if (length(is.res)) {
return(x[[is.res[1]]]$path)
}
}
collected <- character(0)
for (i in seq_along(x)) {
collected <- c(collected, .fetch_resource_paths(x[[i]]))
}
collected
}
# Soft-deprecated back-compatibility fixes.
#' @export
checkValidDirectory <- function(...) validateDirectory(...)
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