include grouping columns in agg()

add docs for groupBy() and agg()

pkg/R/DataFrame.R

@@ -697,8 +697,23 @@ setMethod("toRDD",
 #'
 #' Groups the DataFrame using the specified columns, so we can run aggregation on them.
 #'
+#' @param x a DataFrame
+#' @return a GroupedData
+#' @seealso GroupedData
+#' @rdname DataFrame
+#' @export
+#' @examples
+#' \dontrun {
+#'   # Compute the average for all numeric columns grouped by department.
+#'   avg(groupBy(df, "department"))
+#'
+#'   // Compute the max age and average salary, grouped by department and gender.
+#'   agg(groupBy(df, "department", "gender"), salary="avg", "age" -> "max")
+#' }
 setGeneric("groupBy", function(x, ...) { standardGeneric("groupBy") })
 
+#' @rdname DataFrame
+#' @export
 setMethod("groupBy",
            signature(x = "DataFrame"),
            function(x, ...) {
@@ -712,7 +727,12 @@ setMethod("groupBy",
              groupedData(sgd)
            })
 
-
+#' Agg
+#'
+#' Compute aggregates by specifying a list of columns
+#'
+#' @rdname DataFrame
+#' @export
 setMethod("agg",
           signature(x = "DataFrame"),
           function(x, ...) {

pkg/R/group.R

@@ -1,19 +1,39 @@
-############################## GroupedData ########################################
+# group.R - GroupedData class and methods implemented in S4 OO classes
 
+setOldClass("jobj")
+
+#' @title S4 class that represents a GroupedData
+#' @description GroupedDatas can be created using groupBy() on a DataFrame
+#' @rdname GroupedData
+#' @seealso groupBy
+#'
+#' @param sgd A Java object reference to the backing Scala GroupedData
+#' @export
 setClass("GroupedData",
-         slots = list(env = "environment",
-                      sgd = "jobj"))
+         slots = list(sgd = "jobj"))
 
 setMethod("initialize", "GroupedData", function(.Object, sgd) {
-  .Object@env <- new.env()
   .Object@sgd <- sgd
   .Object
 })
 
+#' @rdname DataFrame
 groupedData <- function(sgd) {
   new("GroupedData", sgd)
 }
 
+
+#' Count
+#'
+#' Count the number of rows for each group.
+#' The resulting DataFrame will also contain the grouping columns.
+#'
+#' @param x a GroupedData
+#' @return a DataFrame
+#' @export
+#' @examples
+#' \dontrun {
+#' }
 setMethod("count",
           signature(x = "GroupedData"),
           function(x) {
@@ -23,9 +43,13 @@ setMethod("count",
 #' Agg
 #'
 #' Aggregates on the entire DataFrame without groups.
+#' The resulting DataFrame will also contain the grouping columns.
 #'
 #' df2 <- agg(df, <column> = <aggFunction>)
 #' df2 <- agg(df, newColName = aggFunction(column))
+#'
+#' @param x a GroupedData
+#' @return a DataFrame
 #' @examples
 #' \dontrun{
 #'  df2 <- agg(df, age = "sum")  # new column name will be created as 'SUM(age#0)'
@@ -51,15 +75,17 @@ setMethod("agg",
                 }
               }
               jcols <- lapply(cols, function(c) { c@jc })
-              sdf <- callJMethod(x@sgd, "agg", jcols[[1]], listToSeq(jcols[-1]))
+              # the GroupedData.agg(col, cols*) API does not contain grouping Column
+              sdf <- callJStatic("edu.berkeley.cs.amplab.sparkr.SQLUtils", "aggWithGrouping",
+                                 x@sgd, listToSeq(jcols))
             } else {
               stop("agg can only support Column or character")
             }
             dataFrame(sdf)
           })
 
-#' sum/mean/avg/min/max
 
+# sum/mean/avg/min/max
 methods <- c("sum", "mean", "avg", "min", "max")
 
 createMethod <- function(name) {

pkg/inst/tests/test_sparkSQL.R

@@ -368,7 +368,7 @@ test_that("group by", {
   expect_true(1 == count(df1))
   df1 <- agg(df, age2 = max(df$age))
   expect_true(1 == count(df1))
-  expect_true(columns(df1) == c("age2"))
+  expect_equal(columns(df1), c("age2"))
 
   gd <- groupBy(df, "name")
   expect_true(inherits(gd, "GroupedData"))
@@ -380,6 +380,11 @@ test_that("group by", {
   expect_true(inherits(df3, "DataFrame"))
   expect_true(3 == count(df3))
 
+  df3 <- agg(gd, age = sum(df$age))
+  expect_true(inherits(df3, "DataFrame"))
+  expect_true(3 == count(df3))
+  expect_equal(columns(df3), c("name", "age"))
+
   df4 <- sum(gd, "age")
   expect_true(inherits(df4, "DataFrame"))
   expect_true(3 == count(df4))

pkg/src/src/main/scala/edu/berkeley/cs/amplab/sparkr/SQLUtils.scala

@@ -1,13 +1,10 @@
 package edu.berkeley.cs.amplab.sparkr
 
-import java.io.ByteArrayOutputStream
-import java.io.DataOutputStream
+import java.io.{ByteArrayOutputStream, DataOutputStream}
 
-import org.apache.spark.rdd.RDD
 import org.apache.spark.api.java.{JavaRDD, JavaSparkContext}
-import org.apache.spark.sql.{SQLContext, DataFrame, Row, SaveMode}
-
-import edu.berkeley.cs.amplab.sparkr.SerDe._
+import org.apache.spark.sql.catalyst.expressions.{Alias, Expression, NamedExpression}
+import org.apache.spark.sql.{Column, DataFrame, GroupedData, Row, SQLContext, SaveMode}
 
 object SQLUtils {
   def createSQLContext(jsc: JavaSparkContext): SQLContext = {
@@ -18,6 +15,22 @@ object SQLUtils {
     arr.toSeq
   }
 
+  // A helper to include grouping columns in Agg()
+  def aggWithGrouping(gd: GroupedData, exprs: Column*): DataFrame = {
+    val aggExprs = exprs.map{ col =>
+      val f = col.getClass.getDeclaredField("expr")
+      f.setAccessible(true)
+      val expr = f.get(col).asInstanceOf[Expression]
+      expr match {
+        case expr: NamedExpression => expr
+        case expr: Expression => Alias(expr, expr.simpleString)()
+      }
+    }
+    val toDF = gd.getClass.getDeclaredMethods.filter(f => f.getName == "toDF").head
+    toDF.setAccessible(true)
+    toDF.invoke(gd, aggExprs).asInstanceOf[DataFrame]
+  }
+
   def dfToRowRDD(df: DataFrame): JavaRDD[Array[Byte]] = {
     df.map(r => rowToRBytes(r))
   }

pkg/src/src/main/scala/edu/berkeley/cs/amplab/sparkr/SparkRBackendHandler.scala

@@ -80,29 +80,28 @@ class SparkRBackendHandler(server: SparkRBackend)
       dis: DataInputStream,
       dos: DataOutputStream) {
     var obj: Object = null
-    var cls: Option[Class[_]] = None
     try {
-      if (isStatic) {
-        cls = Some(Class.forName(objId))
+      val cls = if (isStatic) {
+        Class.forName(objId)
       } else {
         JVMObjectTracker.get(objId) match {
           case None => throw new IllegalArgumentException("Object not found " + objId)
           case Some(o) =>
-            cls = Some(o.getClass)
             obj = o
+            o.getClass
         }
       }
 
       val args = readArgs(numArgs, dis)
 
-      val methods = cls.get.getMethods
+      val methods = cls.getMethods
       val selectedMethods = methods.filter(m => m.getName == methodName)
       if (selectedMethods.length > 0) {
         val methods = selectedMethods.filter { x =>
           matchMethod(numArgs, args, x.getParameterTypes)
         }
         if (methods.isEmpty) {
-          System.err.println(s"cannot find matching method ${cls.get}.$methodName. "
+          System.err.println(s"cannot find matching method ${cls}.$methodName. "
             + s"Candidates are:")
           selectedMethods.foreach { method =>
             System.err.println(s"$methodName(${method.getParameterTypes.mkString(",")})")
@@ -116,7 +115,7 @@ class SparkRBackendHandler(server: SparkRBackend)
         writeObject(dos, ret.asInstanceOf[AnyRef])
       } else if (methodName == "<init>") {
         // methodName should be "<init>" for constructor
-        val ctor = cls.get.getConstructors.filter { x =>
+        val ctor = cls.getConstructors.filter { x =>
           matchMethod(numArgs, args, x.getParameterTypes)
         }.head