Read/write in parallel (#91)

DESCRIPTION

@@ -38,4 +38,8 @@ Suggests:
     rmarkdown,
     crul,
     Rarr,
-    vcr (>= 0.6.0)
+    vcr (>= 0.6.0),
+    pbapply,
+    parallel,
+    future,
+    bench

NAMESPACE

@@ -27,6 +27,7 @@ export(is_key_error)
 export(is_scalar)
 export(is_slice)
 export(obj_list)
+export(pizzarr_option_defaults)
 export(pizzarr_sample)
 export(slice)
 export(zarr_create)
@@ -39,10 +40,3 @@ export(zarr_open_array)
 export(zarr_open_group)
 export(zarr_save_array)
 export(zb_slice)
-importFrom(R6,R6Class)
-importFrom(memoise,memoise)
-importFrom(memoise,timeout)
-importFrom(qs,lz4_compress_raw)
-importFrom(qs,lz4_decompress_raw)
-importFrom(qs,zstd_compress_raw)
-importFrom(qs,zstd_decompress_raw)

R/numcodecs.R

@@ -36,7 +36,6 @@ Codec <- R6::R6Class("Codec",
 #' ZSTD compressor for Zarr
 #' @title ZstdCodec Class
 #' @docType class
-#' @importFrom qs zstd_compress_raw zstd_decompress_raw
 #' @description
 #' Class representing a ZSTD compressor
 
@@ -62,7 +61,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
     #' @return Compressed data.
     encode = function(buf, zarr_arr) {
       # Reference: https://github.com/traversc/qs/blob/84e30f4/R/RcppExports.R#L16
-      result <- zstd_compress_raw(buf, self$level)
+      result <- qs::zstd_compress_raw(buf, self$level)
       return(result)
     },
     #' @description
@@ -71,7 +70,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
     #' @param zarr_arr The ZarrArray instance.
     #' @return Un-compressed data.
     decode = function(buf, zarr_arr) {
-      result <- zstd_decompress_raw(buf)
+      result <- qs::zstd_decompress_raw(buf)
       return(result)
     },
     #' @description
@@ -89,7 +88,6 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
 #' LZ4 compressor for Zarr
 #' @title Lz4Codec Class
 #' @docType class
-#' @importFrom qs lz4_compress_raw lz4_decompress_raw
 #' @description
 #' Class representing a LZ4 compressor
 #'
@@ -115,7 +113,7 @@ Lz4Codec <- R6::R6Class("Lz4Codec",
      #' @return Compressed data.
      encode = function(buf, zarr_arr) {
        # Reference: https://github.com/traversc/qs/blob/84e30f4/R/RcppExports.R#L24
-       body <- lz4_compress_raw(buf, self$acceleration)
+       body <- qs::lz4_compress_raw(buf, self$acceleration)
 
        # The compressed output includes a 4-byte header storing the original size
        # of the decompressed data as a little-endian 32-bit integer.
@@ -135,7 +133,7 @@ Lz4Codec <- R6::R6Class("Lz4Codec",
      decode = function(buf, zarr_arr) {
       body <- buf[5:length(buf)]
 
-      result <- lz4_decompress_raw(body)
+      result <- qs::lz4_decompress_raw(body)
       return(result)
      },
      #' @description

R/onload.R

@@ -0,0 +1,4 @@
+#' @keywords internal
+.onLoad <- function(libname = NULL, pkgname = NULL) {
+    init_options()
+}

R/options.R

@@ -0,0 +1,61 @@
+# Adapted from https://github.com/IRkernel/IRkernel/blob/master/R/options.r
+
+#' pizzarr_option_defaults
+#' @export
+pizzarr_option_defaults <- list(
+    pizzarr.http_store_cache_time_seconds = 3600,
+    pizzarr.parallel_read_enabled = FALSE,
+    pizzarr.parallel_write_enabled = FALSE
+)
+
+#' @keywords internal
+parse_parallel_option <- function(val) {
+  if(val == "future") {
+    return("future")
+  }
+  logical_val <- suppressWarnings(as.logical(val))
+  integer_val <- suppressWarnings(as.integer(val))
+
+  if(is.na(integer_val)) {
+    return(logical_val)
+  }
+  if(integer_val <= 1) {
+    return(as.logical(integer_val))
+  }
+  return(integer_val)
+}
+
+#' @keywords internal
+from_env <- list(
+    PIZZARR_HTTP_STORE_CACHE_TIME_SECONDS = as.integer,
+    PIZZARR_PARALLEL_READ_ENABLED = parse_parallel_option,
+    PIZZARR_PARALLEL_WRITE_ENABLED = parse_parallel_option
+)
+
+# converts e.g. jupyter.log_level to JUPYTER_LOG_LEVEL
+#' @keywords internal
+opt_to_env <- function(nms) {
+    gsub('.', '_', toupper(nms), fixed = TRUE)
+}
+
+# called in .onLoad
+#' @keywords internal
+init_options <- function() {
+    for (opt_name in names(pizzarr_option_defaults)) {
+        # skip option if it is already set, e.g. in the Rprofile
+        if (is.null(getOption(opt_name))) {
+            # prepare `options` call from the default
+            call_arg <- pizzarr_option_defaults[opt_name]  # single [] preserve names
+
+            # if an env var is set, get value from it.
+            env_name <- opt_to_env(opt_name)
+            convert <- from_env[[env_name]]
+            env_val <- Sys.getenv(env_name, unset = NA)
+            if (!is.null(convert) && !is.na(env_val)) {
+                call_arg[[opt_name]] <- convert(env_val)
+            }
+
+            do.call(options, call_arg)
+        }
+    }
+}

R/stores.R

@@ -346,7 +346,6 @@ MemoryStore <- R6::R6Class("MemoryStore",
 #' HttpStore for Zarr
 #' @title HttpStore Class
 #' @docType class
-#' @importFrom memoise memoise timeout
 #' @description
 #' Store class that uses HTTP requests.
 #' Read-only. Depends on the `crul` package.
@@ -363,16 +362,44 @@ HttpStore <- R6::R6Class("HttpStore",
     headers = NULL,
     client = NULL,
     zmetadata = NULL,
-    mem_get = NULL,
-    cache_time_seconds = 3600,
+    make_request_memoized = NULL,
+    cache_enabled = NULL,
+    cache_time_seconds = NULL,
     make_request = function(item) {
       key <- item_to_key(item)
-
-      # mem_get caches in memory on a per-session basis.
-      res <- private$mem_get(private$client, 
-                             paste(private$base_path, key, sep="/"))
-
-      return(res)
+      path <- paste(private$base_path, key, sep="/")
+
+      parallel_option <- getOption("pizzarr.parallel_read_enabled")
+      parallel_option <- parse_parallel_option(parallel_option)
+      is_parallel <- is_truthy_parallel_option(parallel_option)
+
+      if(is_parallel) {
+        # For some reason, the crul::HttpClient fails in parallel settings
+        # This alternative
+        # with HttpRequest and AsyncVaried seems to work.
+        # Reference: https://docs.ropensci.org/crul/articles/async.html
+        req <- crul::HttpRequest$new(
+          url = private$domain,
+          opts = private$options,
+          headers = private$headers
+        )
+        req$get(path = path)
+        res <- crul::AsyncVaried$new(req)
+        res$request()
+        return(unclass(res$responses())[[1]])
+      } else {
+        return(private$client$get(path = path))
+      }
+    },
+    memoize_make_request = function() {
+      if(private$cache_enabled) {
+        private$make_request_memoized <-  memoise::memoise(
+          function(key) private$make_request(key), 
+          ~memoise::timeout(private$cache_time_seconds)
+        )
+      } else {
+        private$make_request_memoized <- private$make_request
+      }
     },
     get_zmetadata = function() {
       res <- private$make_request(".zmetadata")
@@ -405,16 +432,20 @@ HttpStore <- R6::R6Class("HttpStore",
       private$domain <- paste(segments[1:3], collapse="/")
       private$base_path <- paste(segments[4:length(segments)], collapse="/")
 
-      if(!requireNamespace("crul", quietly = TRUE)) stop("HttpStore requires the crul package")
-
+      if(!requireNamespace("crul", quietly = TRUE)) {
+        stop("HttpStore requires the crul package")
+      }
+
       private$client <- crul::HttpClient$new(
         url = private$domain,
         opts = private$options,
         headers = private$headers
       )
-
-      private$mem_get <-  memoise(function(client, path) client$get(path), 
-                                           ~timeout(private$cache_time_seconds))
+
+      private$cache_time_seconds <- getOption("pizzarr.http_store_cache_time_seconds")
+      private$cache_enabled <- private$cache_time_seconds > 0
+
+      private$memoize_make_request()
 
       private$zmetadata <- private$get_zmetadata()
     },
@@ -423,7 +454,7 @@ HttpStore <- R6::R6Class("HttpStore",
     #' @param item The item key.
     #' @return The item data in a vector of type raw.
     get_item = function(item) {
-      res <- private$make_request(item)
+      res <- private$make_request_memoized(item)
       return(res$content)
     },
     #' @description
@@ -438,7 +469,7 @@ HttpStore <- R6::R6Class("HttpStore",
       } else if(!is.null(self$get_consolidated_metadata())) {
         return(FALSE)
       } else {
-        res <- private$make_request(item)
+        res <- private$make_request_memoized(item)
 
         return(res$status_code == 200)        
       }
@@ -475,6 +506,8 @@ HttpStore <- R6::R6Class("HttpStore",
     #' @param seconds number of seconds until cache is invalid -- 0 for no cache
     set_cache_time_seconds = function(seconds) {
       private$cache_time_seconds <- seconds
+      # We need to re-memoize.
+      private$memoize_make_request()
     }
   )
 )

R/utils.R

@@ -349,6 +349,14 @@ item_to_key <- function(item) {
   key
 }
 
+#' @keywords internal
+is_truthy_parallel_option <- function(val) {
+  if(val == "future") {
+    return(TRUE)
+  }
+  return(as.logical(as.integer(val)))
+}
+
 try_from_zmeta <- function(key, store) {
   store$get_consolidated_metadata()$metadata[[key]]
 }