Merge branch 'master' into SPARK-18120

Author: salilsurendran

R/pkg/NAMESPACE

@@ -1,3 +1,20 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 # Imports from base R
 # Do not include stats:: "rpois", "runif" - causes error at runtime
 importFrom("methods", "setGeneric", "setMethod", "setOldClass")
@@ -47,7 +64,8 @@ exportMethods("glm",
               "spark.kstest",
               "spark.logit",
               "spark.randomForest",
-              "spark.gbt")
+              "spark.gbt",
+              "spark.bisectingKmeans")
 
 # Job group lifecycle management methods
 export("setJobGroup",
@@ -94,6 +112,7 @@ exportMethods("arrange",
               "freqItems",
               "gapply",
               "gapplyCollect",
+              "getNumPartitions",
               "group_by",
               "groupBy",
               "head",

R/pkg/R/DataFrame.R

@@ -1717,6 +1717,23 @@ getColumn <- function(x, c) {
   column(callJMethod(x@sdf, "col", c))
 }
 
+setColumn <- function(x, c, value) {
+  if (class(value) != "Column" && !is.null(value)) {
+    if (isAtomicLengthOne(value)) {
+      value <- lit(value)
+    } else {
+      stop("value must be a Column, literal value as atomic in length of 1, or NULL")
+    }
+  }
+
+  if (is.null(value)) {
+    nx <- drop(x, c)
+  } else {
+    nx <- withColumn(x, c, value)
+  }
+  nx
+}
+
 #' @param name name of a Column (without being wrapped by \code{""}).
 #' @rdname select
 #' @name $
@@ -1735,19 +1752,7 @@ setMethod("$", signature(x = "SparkDataFrame"),
 #' @note $<- since 1.4.0
 setMethod("$<-", signature(x = "SparkDataFrame"),
           function(x, name, value) {
-            if (class(value) != "Column" && !is.null(value)) {
-              if (isAtomicLengthOne(value)) {
-                value <- lit(value)
-              } else {
-                stop("value must be a Column, literal value as atomic in length of 1, or NULL")
-              }
-            }
-
-            if (is.null(value)) {
-              nx <- drop(x, name)
-            } else {
-              nx <- withColumn(x, name, value)
-            }
+            nx <- setColumn(x, name, value)
             x@sdf <- nx@sdf
             x
           })
@@ -1767,6 +1772,21 @@ setMethod("[[", signature(x = "SparkDataFrame", i = "numericOrcharacter"),
             getColumn(x, i)
           })
 
+#' @rdname subset
+#' @name [[<-
+#' @aliases [[<-,SparkDataFrame,numericOrcharacter-method
+#' @note [[<- since 2.1.1
+setMethod("[[<-", signature(x = "SparkDataFrame", i = "numericOrcharacter"),
+          function(x, i, value) {
+            if (is.numeric(i)) {
+              cols <- columns(x)
+              i <- cols[[i]]
+            }
+            nx <- setColumn(x, i, value)
+            x@sdf <- nx@sdf
+            x
+          })
+
 #' @rdname subset
 #' @name [
 #' @aliases [,SparkDataFrame-method
@@ -1814,6 +1834,8 @@ setMethod("[", signature(x = "SparkDataFrame"),
 #' @param j,select expression for the single Column or a list of columns to select from the SparkDataFrame.
 #' @param drop if TRUE, a Column will be returned if the resulting dataset has only one column.
 #'             Otherwise, a SparkDataFrame will always be returned.
+#' @param value a Column or an atomic vector in the length of 1 as literal value, or \code{NULL}.
+#'              If \code{NULL}, the specified Column is dropped.
 #' @param ... currently not used.
 #' @return A new SparkDataFrame containing only the rows that meet the condition with selected columns.
 #' @export
@@ -3406,3 +3428,26 @@ setMethod("randomSplit",
             }
             sapply(sdfs, dataFrame)
           })
+
+#' getNumPartitions
+#'
+#' Return the number of partitions
+#'
+#' @param x A SparkDataFrame
+#' @family SparkDataFrame functions
+#' @aliases getNumPartitions,SparkDataFrame-method
+#' @rdname getNumPartitions
+#' @name getNumPartitions
+#' @export
+#' @examples
+#'\dontrun{
+#' sparkR.session()
+#' df <- createDataFrame(cars, numPartitions = 2)
+#' getNumPartitions(df)
+#' }
+#' @note getNumPartitions since 2.1.1
+setMethod("getNumPartitions",
+          signature(x = "SparkDataFrame"),
+          function(x) {
+            callJMethod(callJMethod(x@sdf, "rdd"), "getNumPartitions")
+          })

R/pkg/R/RDD.R

@@ -313,7 +313,7 @@ setMethod("checkpoint",
 #' @rdname getNumPartitions
 #' @aliases getNumPartitions,RDD-method
 #' @noRd
-setMethod("getNumPartitions",
+setMethod("getNumPartitionsRDD",
           signature(x = "RDD"),
           function(x) {
             callJMethod(getJRDD(x), "getNumPartitions")
@@ -329,7 +329,7 @@ setMethod("numPartitions",
           signature(x = "RDD"),
           function(x) {
             .Deprecated("getNumPartitions")
-            getNumPartitions(x)
+            getNumPartitionsRDD(x)
           })
 
 #' Collect elements of an RDD
@@ -460,7 +460,7 @@ setMethod("countByValue",
           signature(x = "RDD"),
           function(x) {
             ones <- lapply(x, function(item) { list(item, 1L) })
-            collectRDD(reduceByKey(ones, `+`, getNumPartitions(x)))
+            collectRDD(reduceByKey(ones, `+`, getNumPartitionsRDD(x)))
           })
 
 #' Apply a function to all elements
@@ -780,7 +780,7 @@ setMethod("takeRDD",
             resList <- list()
             index <- -1
             jrdd <- getJRDD(x)
-            numPartitions <- getNumPartitions(x)
+            numPartitions <- getNumPartitionsRDD(x)
             serializedModeRDD <- getSerializedMode(x)
 
             # TODO(shivaram): Collect more than one partition based on size
@@ -846,7 +846,7 @@ setMethod("firstRDD",
 #' @noRd
 setMethod("distinctRDD",
           signature(x = "RDD"),
-          function(x, numPartitions = SparkR:::getNumPartitions(x)) {
+          function(x, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
             identical.mapped <- lapply(x, function(x) { list(x, NULL) })
             reduced <- reduceByKey(identical.mapped,
                                    function(x, y) { x },
@@ -1053,7 +1053,7 @@ setMethod("coalesce",
            signature(x = "RDD", numPartitions = "numeric"),
            function(x, numPartitions, shuffle = FALSE) {
              numPartitions <- numToInt(numPartitions)
-             if (shuffle || numPartitions > SparkR:::getNumPartitions(x)) {
+             if (shuffle || numPartitions > SparkR:::getNumPartitionsRDD(x)) {
                func <- function(partIndex, part) {
                  set.seed(partIndex)  # partIndex as seed
                  start <- as.integer(base::sample(numPartitions, 1) - 1)
@@ -1143,7 +1143,7 @@ setMethod("saveAsTextFile",
 #' @noRd
 setMethod("sortBy",
           signature(x = "RDD", func = "function"),
-          function(x, func, ascending = TRUE, numPartitions = SparkR:::getNumPartitions(x)) {
+          function(x, func, ascending = TRUE, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
             values(sortByKey(keyBy(x, func), ascending, numPartitions))
           })
 
@@ -1175,7 +1175,7 @@ takeOrderedElem <- function(x, num, ascending = TRUE) {
   resList <- list()
   index <- -1
   jrdd <- getJRDD(newRdd)
-  numPartitions <- getNumPartitions(newRdd)
+  numPartitions <- getNumPartitionsRDD(newRdd)
   serializedModeRDD <- getSerializedMode(newRdd)
 
   while (TRUE) {
@@ -1407,7 +1407,7 @@ setMethod("setName",
 setMethod("zipWithUniqueId",
           signature(x = "RDD"),
           function(x) {
-            n <- getNumPartitions(x)
+            n <- getNumPartitionsRDD(x)
 
             partitionFunc <- function(partIndex, part) {
               mapply(
@@ -1450,7 +1450,7 @@ setMethod("zipWithUniqueId",
 setMethod("zipWithIndex",
           signature(x = "RDD"),
           function(x) {
-            n <- getNumPartitions(x)
+            n <- getNumPartitionsRDD(x)
             if (n > 1) {
               nums <- collectRDD(lapplyPartition(x,
                                               function(part) {
@@ -1566,8 +1566,8 @@ setMethod("unionRDD",
 setMethod("zipRDD",
           signature(x = "RDD", other = "RDD"),
           function(x, other) {
-            n1 <- getNumPartitions(x)
-            n2 <- getNumPartitions(other)
+            n1 <- getNumPartitionsRDD(x)
+            n2 <- getNumPartitionsRDD(other)
             if (n1 != n2) {
               stop("Can only zip RDDs which have the same number of partitions.")
             }
@@ -1637,7 +1637,7 @@ setMethod("cartesian",
 #' @noRd
 setMethod("subtract",
           signature(x = "RDD", other = "RDD"),
-          function(x, other, numPartitions = SparkR:::getNumPartitions(x)) {
+          function(x, other, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
             mapFunction <- function(e) { list(e, NA) }
             rdd1 <- map(x, mapFunction)
             rdd2 <- map(other, mapFunction)
@@ -1671,7 +1671,7 @@ setMethod("subtract",
 #' @noRd
 setMethod("intersection",
           signature(x = "RDD", other = "RDD"),
-          function(x, other, numPartitions = SparkR:::getNumPartitions(x)) {
+          function(x, other, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
             rdd1 <- map(x, function(v) { list(v, NA) })
             rdd2 <- map(other, function(v) { list(v, NA) })
 
@@ -1714,7 +1714,7 @@ setMethod("zipPartitions",
             if (length(rrdds) == 1) {
               return(rrdds[[1]])
             }
-            nPart <- sapply(rrdds, getNumPartitions)
+            nPart <- sapply(rrdds, getNumPartitionsRDD)
             if (length(unique(nPart)) != 1) {
               stop("Can only zipPartitions RDDs which have the same number of partitions.")
             }

R/pkg/R/generics.R

@@ -138,9 +138,9 @@ setGeneric("sumRDD", function(x) { standardGeneric("sumRDD") })
 # @export
 setGeneric("name", function(x) { standardGeneric("name") })
 
-# @rdname getNumPartitions
+# @rdname getNumPartitionsRDD
 # @export
-setGeneric("getNumPartitions", function(x) { standardGeneric("getNumPartitions") })
+setGeneric("getNumPartitionsRDD", function(x) { standardGeneric("getNumPartitionsRDD") })
 
 # @rdname getNumPartitions
 # @export
@@ -492,6 +492,10 @@ setGeneric("gapply", function(x, ...) { standardGeneric("gapply") })
 #' @export
 setGeneric("gapplyCollect", function(x, ...) { standardGeneric("gapplyCollect") })
 
+# @rdname getNumPartitions
+# @export
+setGeneric("getNumPartitions", function(x) { standardGeneric("getNumPartitions") })
+
 #' @rdname summary
 #' @export
 setGeneric("describe", function(x, col, ...) { standardGeneric("describe") })
@@ -1338,6 +1342,11 @@ setGeneric("rbind", signature = "...")
 #' @export
 setGeneric("spark.als", function(data, ...) { standardGeneric("spark.als") })
 
+#' @rdname spark.bisectingKmeans
+#' @export
+setGeneric("spark.bisectingKmeans",
+           function(data, formula, ...) { standardGeneric("spark.bisectingKmeans") })
+
 #' @rdname spark.gaussianMixture
 #' @export
 setGeneric("spark.gaussianMixture",