mirror of
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652 lines
21 KiB
R
652 lines
21 KiB
R
# A context object for tracking a cache that needs to be dirtied when a set of
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# files changes on disk. Each time the cache is dirtied, the set of files is
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# cleared. Therefore, the set of files needs to be re-built each time the cached
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# code executes. This approach allows for dynamic dependency graphs.
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CacheContext <- R6Class(
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'CacheContext',
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portable = FALSE,
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class = FALSE,
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public = list(
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.dirty = TRUE,
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# List of functions that return TRUE if dirty
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.tests = list(),
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addDependencyFile = function(file) {
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if (.dirty)
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return()
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file <- normalizePath(file)
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mtime <- file.info(file)$mtime
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.tests <<- c(.tests, function() {
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newMtime <- try(file.info(file)$mtime, silent=TRUE)
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if (inherits(newMtime, 'try-error'))
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return(TRUE)
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return(!identical(mtime, newMtime))
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})
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invisible()
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},
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forceDirty = function() {
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.dirty <<- TRUE
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.tests <<- list()
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invisible()
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},
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isDirty = function() {
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if (.dirty)
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return(TRUE)
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for (test in .tests) {
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if (test()) {
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forceDirty()
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return(TRUE)
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}
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}
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return(FALSE)
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},
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reset = function() {
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.dirty <<- FALSE
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.tests <<- list()
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},
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with = function(func) {
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oldCC <- .currentCacheContext$cc
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.currentCacheContext$cc <- self
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on.exit(.currentCacheContext$cc <- oldCC)
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return(func())
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}
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)
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)
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.currentCacheContext <- new.env()
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# Indicates to Shiny that the given file path is part of the dependency graph
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# for whatever is currently executing (so far, only ui.R). By default, ui.R only
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# gets re-executed when it is detected to have changed; this function allows the
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# caller to indicate that it should also re-execute if the given file changes.
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#
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# If NULL or NA is given as the argument, then ui.R will re-execute next time.
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dependsOnFile <- function(filepath) {
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if (is.null(.currentCacheContext$cc))
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return()
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if (is.null(filepath) || is.na(filepath))
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.currentCacheContext$cc$forceDirty()
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else
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.currentCacheContext$cc$addDependencyFile(filepath)
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}
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#' Create a disk cache object
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#'
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#' A disk cache object is a key-value store that saves the values as files in a
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#' directory on disk. Objects can be stored and retrieved using the \code{get()}
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#' and \code{set()} methods. Objects are automatically pruned from the cache
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#' according to the parameters \code{max_size}, \code{max_age}, \code{max_n},
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#' and \code{evict}.
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#'
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#'
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#' @section Cache pruning:
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#'
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#' Cache pruning occurs each time \code{get()} and \code{set()} are called, or
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#' it can be invoked manually by calling \code{prune()}.
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#'
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#' If there are any objects that are older than \code{max_age}, they will be
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#' removed when a pruning occurs.
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#'
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#' The \code{max_size} and \code{max_n} parameters are applied to the cache as
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#' a whole, in contrast to \code{max_age}, which is applied to each object
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#' individually.
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#'
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#' If the number of objects in the cache exceeds \code{max_n}, then objects
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#' will be removed from the cache according to the eviction policy, which is
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#' set with the \code{evict} parameter. Objects will be removed so that the
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#' number of items is \code{max_n}.
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#'
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#' If the size of the objects in the cache exceeds \code{max_size}, then
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#' objects will be removed from the cache. Objects will be removed from
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#' the cache so that the total size remains under \code{max_size}. Note that
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#' the size is calculated using the size of the files, not the size of disk
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#' space used by the files -- these two values can differ because of files
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#' are stored in blocks on disk. For example, if the block size is 4096 bytes,
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#' then a file that is one byte in size will take 4096 bytes on disk.
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#'
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#'
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#' @section Eviction policies:
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#'
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#' If \code{max_n} or \code{max_size} are used, then objects will be removed
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#' from the cache according to an eviction policy. The available eviction
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#' policies are:
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#'
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#' \describe{
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#' \item{\code{"lru"}}{
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#' Least Recently Used. The least recently used objects will be removed.
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#' This uses the filesystem's atime property. Some filesystems do not
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#' support atime, or have a very low atime resolution. The DiskCache will
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#' check for atime support, and if the filesystem does not support atime,
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#' a warning will be issued and the "fifo" policy will be used instead.
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#' }
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#' \item{\code{"fifo"}}{
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#' First-in-first-out. The oldest objects will be removed.
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#' }
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#' }
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#'
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#' @section Methods:
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#'
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#' A disk cache object has the following methods:
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#'
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#' \describe{
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#' \item{\code{get(key)}}{
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#' Returns the value associated with \code{key}. If the key is not in the
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#' cache, this throws an error.
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#' }
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#' \item{\code{set(key, value)}}{
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#' Stores the \code{key}-\code{value} pair in the cache.
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#' }
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#' \item{\code{has(key)}}{
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#' Returns \code{TRUE} if the cache contains the key, otherwise
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#' \code{FALSE}.
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#' }
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#' \item{\code{size()}}{
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#' Returns the number of items currently in the cache.
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#' }
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#' \item{\code{keys()}}{
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#' Returns a character vector of all keys currently in the cache.
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#' }
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#' \item{\code{reset()}}{
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#' Clears all objects from the cache.
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#' }
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#' \item{\code{destroy()}}{
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#' Clears all objects in the cache, and removes the cache directory from
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#' disk.
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#' }
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#' \item{\code{prune()}}{
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#' Prunes the cache, using the parameters specified by \code{max_size},
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#' \code{max_age}, \code{max_n}, and \code{evict}.
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#' }
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#' }
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#'
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#' @param dir Directory to store files for the cache. By default, it will use
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#' a temporary directory.
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#' @param max_age Maximum age of files in cache before they are evicted, in
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#' seconds.
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#' @param max_size Maximum size of the cache, in bytes. If the cache exceeds
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#' this size, cached objects will be removed according to the value of the
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#' \code{evict}.
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#' @param max_n Maximum number of objects in the cache. If the number of objects
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#' exceeds this value, then cached objects will be removed according to the
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#' value of \code{evict}.
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#' @param evict The eviction policy to use to decide which objects are removed
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#' when a cache pruning occurs. Currently, \code{"lru"} and \code{"fifo"} are
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#' supported.
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#' @param destroy_on_finalize If \code{TRUE}, then when the DiskCache object is
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#' garbage collected, the cache directory and all objects inside of it will be
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#' deleted from disk.
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#' @export
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diskCache <- function(dir = tempfile("DiskCache-"),
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max_size = 5 * 1024 ^ 2,
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max_age = Inf,
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max_n = Inf,
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evict = "fifo",
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destroy_on_finalize = TRUE)
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{
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DiskCache$new(dir, max_size, max_age, max_n, evict, destroy_on_finalize)
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}
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DiskCache <- R6Class("DiskCache",
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public = list(
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initialize = function(dir = tempfile("DiskCache-"),
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max_size = 5 * 1024 ^ 2,
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max_age = Inf,
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max_n = Inf,
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evict = c("lru", "fifo"),
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destroy_on_finalize = TRUE)
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{
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if (!dirExists(dir)) {
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message("Creating ", dir)
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dir.create(dir, recursive = TRUE, mode = "0700")
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private$dir_was_created <- TRUE
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}
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private$dir <- absolutePath(dir)
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private$max_size <- max_size
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private$max_age <- max_age
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private$max_n <- max_n
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private$evict <- match.arg(evict)
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if (private$evict == "lru" && !check_atime_support(private$dir)) {
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# Another possibility for handling lack of atime support would be to
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# create a file on disk that contains atimes. However, this would not
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# be safe when multiple processes are sharing a cache.
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warning("DiskCache: can't use eviction policy \"lru\" because filesystem for ",
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private$dir, " does not support atime, or has low atime resolution. Using \"fifo\" instead."
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)
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private$evict <- "fifo"
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}
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private$destroy_on_finalize <- destroy_on_finalize
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},
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# TODO:
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# Should call has() and return some sentinal object if not present?
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# Should be atomic to avoid race conditions with other processes.
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# Reduce pruning for mset/mget
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get = function(key) {
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validate_key(key)
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if (!self$has(key)) {
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stop("Key not available: ", key)
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}
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value <- readRDS(private$key_to_filename(key))
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self$prune()
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value
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},
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set = function(key, value) {
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validate_key(key)
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self$prune()
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saveRDS(value, file = private$key_to_filename(key))
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invisible(self)
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},
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has = function(key) {
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validate_key(key)
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file.exists(private$key_to_filename(key))
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},
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# Return all keys in the cache
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keys = function() {
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files <- dir(private$dir, "*.rds")
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sub("\\.rds$", "", files)
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},
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remove = function(key) {
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validate_key(key)
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file.remove(private$key_to_filename(key))
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invisible(self)
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},
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reset = function() {
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file.remove(dir(private$dir, "*.rds", full.names = TRUE))
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invisible(self)
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},
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prune = function() {
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files <- file.info(dir(private$dir, "*.rds", full.names = TRUE))
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files <- files[files$isdir == FALSE, ]
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files$name <- rownames(files)
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rownames(files) <- NULL
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# 1. Remove any files where the age exceeds max age.
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timediff <- as.numeric(Sys.time() - files[["mtime"]], units = "secs")
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rm_idx <- timediff > private$max_age
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if (any(rm_idx)) {
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message("max_age: Removing ", paste(files$name[rm_idx], collapse = ", "))
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}
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file.remove(files$name[rm_idx])
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# Remove rows of files that were deleted.
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files <- files[!rm_idx, ]
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# Sort files by priority, according to eviction policy.
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if (private$evict == "lru") {
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files <- files[order(files[["atime"]], decreasing = TRUE), ]
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} else if (private$evict == "fifo") {
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files <- files[order(files[["mtime"]], decreasing = TRUE), ]
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} else {
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stop('Unknown eviction policy "', private$evict, '"')
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}
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# 2. Remove files if there are too many.
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if (nrow(files) > private$max_n) {
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rm_idx <- seq_len(nrow(files)) > private$max_n
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if (any(rm_idx)) {
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message("max_n: Removing ", paste(files$name[rm_idx], collapse = ", "))
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}
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file.remove(files$name[rm_idx])
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}
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# 3. Remove files if cache is too large.
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if (sum(files$size) > private$max_size) {
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cum_size <- cumsum(files$size)
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rm_idx <- cum_size > private$max_size
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if (any(rm_idx)) {
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message("max_size: Removing ", paste(files$name[rm_idx], collapse = ", "))
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}
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file.remove(files$name[rm_idx])
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}
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invisible(self)
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},
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size = function() {
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length(dir(private$dir, "*.rds"))
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},
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destroy = function() {
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if (private$destroyed) {
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return(invisible)
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}
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private$destroyed <- TRUE
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self$reset()
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if (private$dir_was_created) {
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message("Removing ", private$dir)
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dirRemove(private$dir)
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}
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},
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is_destroyed = function() {
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private$destroyed
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},
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finalize = function() {
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if (private$destroy_on_finalize) {
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self$destroy()
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}
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}
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),
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private = list(
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dir = NULL,
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max_age = NULL,
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max_size = NULL,
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max_n = NULL,
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evict = NULL,
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dir_was_created = FALSE,
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destroy_on_finalize = NULL,
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destroyed = FALSE,
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key_to_filename = function(key) {
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if (! (is.character(key) && length(key)==1) ) {
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stop("Key must be a character vector of length 1.")
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}
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file.path(private$dir, paste0(key, ".rds"))
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}
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)
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)
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#' Create a memory cache object
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#'
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#' A memory cache object is a key-value store that saves the values in an
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#' environment. Objects can be stored and retrieved using the \code{get()} and
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#' \code{set()} methods. Objects are automatically pruned from the cache
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#' according to the parameters \code{max_size}, \code{max_age}, \code{max_n},
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#' and \code{evict}.
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#'
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#'
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#' @section Cache pruning:
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#'
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#' Cache pruning occurs each time \code{get()} and \code{set()} are called, or
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#' it can be invoked manually by calling \code{prune()}.
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#'
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#' If there are any objects that are older than \code{max_age}, they will be
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#' removed when a pruning occurs.
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#'
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#' The \code{max_size} and \code{max_n} parameters are applied to the cache as
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#' a whole, in contrast to \code{max_age}, which is applied to each object
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#' individually.
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#'
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#' If the number of objects in the cache exceeds \code{max_n}, then objects
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#' will be removed from the cache according to the eviction policy, which is
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#' set with the \code{evict} parameter. Objects will be removed so that the
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#' number of items is \code{max_n}.
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#'
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#' If the size of the objects in the cache exceeds \code{max_size}, then
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#' objects will be removed from the cache. Objects will be removed from the
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#' cache so that the total size remains under \code{max_size}. The size is
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#' calculated by calling \code{\link{object.size}} on an object. Note that if
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#' two keys are associated with the same object, the size calculation will
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#' count the object's size twice, even though there is only one copy in
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#' memory.
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#'
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#' @section Eviction policies:
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#'
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#' If \code{max_n} or \code{max_size} are used, then objects will be removed
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#' from the cache according to an eviction policy. The available eviction
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#' policies are:
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#'
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#' \describe{
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#' \item{\code{"lru"}}{
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#' Least Recently Used. The least recently used objects will be removed.
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#' This uses the filesystem's atime property. Some filesystems do not
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#' support atime, or have a very low atime resolution. The DiskCache will
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#' check for atime support, and if the filesystem does not support atime,
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#' a warning will be issued and the "fifo" policy will be used instead.
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#' }
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#' \item{\code{"fifo"}}{
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#' First-in-first-out. The oldest objects will be removed.
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#' }
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#' }
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#'
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#' @section Methods:
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#'
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#' A disk cache object has the following methods:
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#'
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#' \describe{
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#' \item{\code{get(key)}}{
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#' Returns the value associated with \code{key}. If the key is not in the
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#' cache, this throws an error.
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#' }
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#' \item{\code{set(key, value)}}{
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#' Stores the \code{key}-\code{value} pair in the cache.
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#' }
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#' \item{\code{has(key)}}{
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#' Returns \code{TRUE} if the cache contains the key, otherwise
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#' \code{FALSE}.
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#' }
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#' \item{\code{size()}}{
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#' Returns the number of items currently in the cache.
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#' }
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#' \item{\code{keys()}}{
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#' Returns a character vector of all keys currently in the cache.
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#' }
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#' \item{\code{reset()}}{
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#' Clears all objects from the cache.
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#' }
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#' \item{\code{destroy()}}{
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#' Clears all objects in the cache, and removes the cache directory from
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#' disk.
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#' }
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#' \item{\code{prune()}}{
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#' Prunes the cache, using the parameters specified by \code{max_size},
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#' \code{max_age}, \code{max_n}, and \code{evict}.
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#' }
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#' }
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#'
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#' @param max_age Maximum age of files in cache before they are evicted, in
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#' seconds.
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#' @param max_size Maximum size of the cache, in bytes. If the cache exceeds
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#' this size, cached objects will be removed according to the value of the
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#' \code{evict}.
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#' @param max_n Maximum number of objects in the cache. If the number of objects
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#' exceeds this value, then cached objects will be removed according to the
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#' value of \code{evict}.
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#' @param evict The eviction policy to use to decide which objects are removed
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#' when a cache pruning occurs. Currently, \code{"lru"} and \code{"fifo"} are
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#' supported.
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#' @export
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memoryCache <- function(
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max_size = 10 * 1024 ^ 2,
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max_age = Inf,
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max_n = Inf,
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evict = c("lru", "fifo"))
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{
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MemoryCache$new(max_size, max_age, max_n, evict)
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}
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MemoryCache <- R6Class("MemoryCache",
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public = list(
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initialize = function(max_size = 10 * 1024 ^ 2,
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max_age = Inf,
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max_n = Inf,
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evict = c("lru", "fifo"))
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{
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private$cache <- new.env(parent = emptyenv())
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private$max_size <- max_size
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private$max_age <- max_age
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private$max_n <- max_n
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private$evict <- match.arg(evict)
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},
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get = function(key) {
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validate_key(key)
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if (!self$has(key)) {
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stop("Key not available: ", key)
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}
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value <- private$cache[[key]]$value
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self$prune()
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value
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},
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set = function(key, value) {
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validate_key(key)
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self$prune()
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time <- as.numeric(Sys.time())
|
|
private$cache[[key]] <- list(
|
|
key = key,
|
|
value = value,
|
|
size = as.numeric(object.size(value)), # Reported size is rough! See ?object.size.
|
|
mtime = time,
|
|
atime = time
|
|
)
|
|
invisible(self)
|
|
},
|
|
|
|
has = function(key) {
|
|
validate_key(key)
|
|
exists(key, envir = private$cache, inherits = FALSE)
|
|
},
|
|
|
|
keys = function() {
|
|
ls(private$cache, sorted = FALSE) # Faster with sorted=FALSE
|
|
},
|
|
|
|
remove = function(key) {
|
|
validate_key(key)
|
|
rm(list = key, envir = private$cache)
|
|
invisible(self)
|
|
},
|
|
|
|
reset = function() {
|
|
rm(list = self$keys(), envir = private$cache)
|
|
invisible(self)
|
|
},
|
|
|
|
prune = function() {
|
|
info <- private$object_info()
|
|
|
|
# 1. Remove any objects where the age exceeds max age.
|
|
time <- as.numeric(Sys.time())
|
|
timediff <- time - info$mtime
|
|
rm_idx <- timediff > private$max_age
|
|
if (any(rm_idx)) {
|
|
message("max_age: Removing ", paste(info$key[rm_idx], collapse = ", "))
|
|
}
|
|
|
|
# Remove items from cache
|
|
rm(list = info$key[rm_idx], envir = private$cache)
|
|
info <- info[!rm_idx, ]
|
|
|
|
# Sort files by priority, according to eviction policy.
|
|
if (private$evict == "lru") {
|
|
files <- files[order(files[["atime"]], decreasing = TRUE), ]
|
|
} else if (private$evict == "fifo") {
|
|
files <- files[order(files[["mtime"]], decreasing = TRUE), ]
|
|
} else {
|
|
stop('Unknown eviction policy "', private$evict, '"')
|
|
}
|
|
|
|
# 2. Remove objects if there are too many.
|
|
if (nrow(info) > private$max_n) {
|
|
rm_idx <- seq_len(nrow(info)) > private$max_n
|
|
if (any(rm_idx)) {
|
|
message("max_n: Removing ", paste(info$key[rm_idx], collapse = ", "))
|
|
}
|
|
rm(list = info$key[rm_idx], envir = private$cache)
|
|
info <- info[!rm_idx, ]
|
|
}
|
|
|
|
# 3. Remove objects if cache is too large.
|
|
if (sum(info$size) > private$max_size) {
|
|
cum_size <- cumsum(info$size)
|
|
rm_idx <- cum_size > private$max_size
|
|
if (any(rm_idx)) {
|
|
message("max_size: Removing ", paste(info$key[rm_idx], collapse = ", "))
|
|
}
|
|
rm(list = info$key[rm_idx], envir = private$cache)
|
|
info <- info[!rm_idx, ]
|
|
}
|
|
invisible(self)
|
|
},
|
|
|
|
size = function() {
|
|
# TODO: Validate this against metadata?
|
|
length(self$key())
|
|
},
|
|
|
|
destroy = function() {
|
|
if (is.null(private$cache)) {
|
|
return(invisible)
|
|
}
|
|
|
|
private$cache <- NULL
|
|
},
|
|
|
|
is_destroyed = function() {
|
|
is.null(private$cache)
|
|
}
|
|
),
|
|
|
|
private = list(
|
|
cache = NULL,
|
|
meta = NULL, # Metadata used for pruning
|
|
max_age = NULL,
|
|
max_size = NULL,
|
|
max_n = NULL,
|
|
evict = NULL,
|
|
|
|
object_info = function() {
|
|
keys <- ls(private$cache, sorted = FALSE)
|
|
data.frame(
|
|
key = keys,
|
|
size = vapply(keys, function(key) private$cache[[key]]$size, 0),
|
|
mtime = vapply(keys, function(key) private$cache[[key]]$mtime, 0),
|
|
atime = vapply(keys, function(key) private$cache[[key]]$atime, 0),
|
|
stringsAsFactors = FALSE
|
|
)
|
|
}
|
|
)
|
|
)
|
|
|
|
validate_key <- function(key) {
|
|
if (grepl("[^a-z0-9]", key)) {
|
|
stop("Invalid key: ", key, ". Only lowercase letters and numbers are allowed.")
|
|
}
|
|
}
|
|
|
|
# Checks if a filesystem has atime support, by creating a file in a specified
|
|
# directory, waiting 0.1 seconds, then reading the file. If the timestamp does
|
|
# not change, then the filesystem does not support atime, or has very low atime
|
|
# resolution. For example, FAT has an atime resolution of 1 day. If the
|
|
# timestamp does change, then the filesystem supports atime. (Although it is
|
|
# possible in very rare cases that the filesystem has a low atime resolution and
|
|
# the pause just happend to cross a boundary.)
|
|
check_atime_support <- function(dir) {
|
|
dir <- "."
|
|
temp_file <- tempfile("check-atime-support-", dir)
|
|
|
|
file.create(temp_file)
|
|
on.exit(unlink(temp_file), add = TRUE)
|
|
atime1 <- as.numeric(file.info(temp_file)[["atime"]])
|
|
|
|
Sys.sleep(0.1)
|
|
readBin(temp_file, "raw", 1L)
|
|
atime2 <- as.numeric(file.info(temp_file)[["atime"]])
|
|
|
|
if (atime1 == atime2) {
|
|
return(FALSE)
|
|
}
|
|
|
|
TRUE
|
|
}
|