Update README to document min R version required for ArvadosR

[arvados.git] / sdk / R / R / util.R

diff --git a/sdk/R/R/util.R b/sdk/R/R/util.R
index 8d4bcc0097fe0e4dcc626c2ad45b989e5ec48dcb..f796cb7b87eca67b3de28d5929221d792554b047 100644 (file)
--- a/sdk/R/R/util.R
+++ b/sdk/R/R/util.R
@@ -1,3 +1,43 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+#' listAll
+#'
+#' List all resources even if the number of items is greater than maximum API limit.
+#'
+#' @param fn Arvados method used to retrieve items from REST service.
+#' @param ... Optional arguments which will be pased to fn .
+#' @examples
+#' \dontrun{
+#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+#' cl <- listAll(arv$collections.list, filters = list(list("name", "like", "test%"))
+#' }
+#' @export 
+listAll <- function(fn, ...)
+{
+    offset <- 0
+    itemsAvailable <- .Machine$integer.max
+    items <- c()
+
+    while(length(items) < itemsAvailable)
+    {
+        serverResponse <- fn(offset = offset, ...)
+
+        if(!is.null(serverResponse$errors))
+            stop(serverResponse$errors)
+
+        items          <- c(items, serverResponse$items)
+        offset         <- length(items)
+        itemsAvailable <- serverResponse$items_available
+    }
+
+    items
+}
+
+
+#NOTE: Package private functions
+
 trimFromStart <- function(sample, trimCharacters)
 {
     if(startsWith(sample, trimCharacters))
@@ -13,3 +53,41 @@ trimFromEnd <- function(sample, trimCharacters)
 
     sample
 }
+
+RListToPythonList <- function(RList, separator = ", ")
+{
+    pythonArrayContent <- sapply(RList, function(elementInList)
+    {
+        if((is.vector(elementInList) || is.list(elementInList)) &&
+            length(elementInList) > 1)
+        {
+            return(RListToPythonList(elementInList, separator))
+        }
+        else
+        {
+            return(paste0("\"", elementInList, "\""))
+        }
+    })
+
+    pythonArray <- paste0("[", paste0(pythonArrayContent, collapse = separator), "]")
+    pythonArray
+}
+
+appendToStartIfNotExist <- function(sample, characters)
+{
+    if(!startsWith(sample, characters))
+        sample <- paste0(characters, sample)
+
+    sample
+}
+
+splitToPathAndName = function(path)
+{
+    path <- appendToStartIfNotExist(path, "/")
+    components <- unlist(stringr::str_split(path, "/"))
+    nameAndPath <- list()
+    nameAndPath$name <- components[length(components)]
+    nameAndPath$path <- trimFromStart(paste0(components[-length(components)], collapse = "/"),
+                                      "/")
+    nameAndPath
+}