[SPARK-9803] [SPARKR] Add subset and transform + tests

Add subset and transform
Also reorganize `[` & `[[` to subset instead of select

Note: for transform, transform is very similar to mutate. Spark doesn't seem to replace existing column with the name in mutate (ie. `mutate(df, age = df$age + 2)` - returned DataFrame has 2 columns with the same name 'age'), so therefore not doing that for now in transform.
Though it is clearly stated it should replace column with matching name (should I open a JIRA for mutate/transform?)

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #8503 from felixcheung/rsubset_transform.

(cherry picked from commit 2a4e00ca4d4e7a148b4ff8ce0ad1c6d517cee55f)
Signed-off-by: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

4 files changed, 85 insertions, 17 deletions

diff --git a/R/pkg/NAMESPACE b/R/pkg/NAMESPACE
index 5286c01986..9d39630706 100644
--- a/R/pkg/NAMESPACE
+++ b/R/pkg/NAMESPACE
@@ -69,9 +69,11 @@ exportMethods("arrange",
               "selectExpr",
               "show",
               "showDF",
+              "subset",
               "summarize",
               "summary",
               "take",
+              "transform",
               "unionAll",
               "unique",
               "unpersist",
diff --git a/R/pkg/R/DataFrame.R b/R/pkg/R/DataFrame.R
index 19cf1a9e07..f833e70a0f 100644
--- a/R/pkg/R/DataFrame.R
+++ b/R/pkg/R/DataFrame.R
@@ -956,7 +956,7 @@ setMethod("$<-", signature(x = "DataFrame"),
 
 setClassUnion("numericOrcharacter", c("numeric", "character"))
 
-#' @rdname select
+#' @rdname subset
 #' @name [[
 setMethod("[[", signature(x = "DataFrame", i = "numericOrcharacter"),
           function(x, i) {
@@ -967,7 +967,7 @@ setMethod("[[", signature(x = "DataFrame", i = "numericOrcharacter"),
             getColumn(x, i)
           })
 
-#' @rdname select
+#' @rdname subset
 #' @name [
 setMethod("[", signature(x = "DataFrame", i = "missing"),
           function(x, i, j, ...) {
@@ -981,7 +981,7 @@ setMethod("[", signature(x = "DataFrame", i = "missing"),
             select(x, j)
           })
 
-#' @rdname select
+#' @rdname subset
 #' @name [
 setMethod("[", signature(x = "DataFrame", i = "Column"),
           function(x, i, j, ...) {
@@ -989,12 +989,43 @@ setMethod("[", signature(x = "DataFrame", i = "Column"),
             # https://stat.ethz.ch/R-manual/R-devel/library/base/html/Extract.data.frame.html
             filtered <- filter(x, i)
             if (!missing(j)) {
-              filtered[, j]
+              filtered[, j, ...]
             } else {
               filtered
             }
           })
 
+#' Subset
+#'
+#' Return subsets of DataFrame according to given conditions
+#' @param x A DataFrame
+#' @param subset A logical expression to filter on rows
+#' @param select expression for the single Column or a list of columns to select from the DataFrame
+#' @return A new DataFrame containing only the rows that meet the condition with selected columns
+#' @export
+#' @rdname subset
+#' @name subset
+#' @aliases [
+#' @family subsetting functions
+#' @examples
+#' \dontrun{
+#'   # Columns can be selected using `[[` and `[`
+#'   df[[2]] == df[["age"]]
+#'   df[,2] == df[,"age"]
+#'   df[,c("name", "age")]
+#'   # Or to filter rows
+#'   df[df$age > 20,]
+#'   # DataFrame can be subset on both rows and Columns
+#'   df[df$name == "Smith", c(1,2)]
+#'   df[df$age %in% c(19, 30), 1:2]
+#'   subset(df, df$age %in% c(19, 30), 1:2)
+#'   subset(df, df$age %in% c(19), select = c(1,2))
+#' }
+setMethod("subset", signature(x = "DataFrame"),
+          function(x, subset, select, ...) {
+            x[subset, select, ...]
+          })
+
 #' Select
 #'
 #' Selects a set of columns with names or Column expressions.
@@ -1003,6 +1034,8 @@ setMethod("[", signature(x = "DataFrame", i = "Column"),
 #' @return A new DataFrame with selected columns
 #' @export
 #' @rdname select
+#' @name select
+#' @family subsetting functions
 #' @examples
 #' \dontrun{
 #'   select(df, "*")
@@ -1010,15 +1043,8 @@ setMethod("[", signature(x = "DataFrame", i = "Column"),
 #'   select(df, df$name, df$age + 1)
 #'   select(df, c("col1", "col2"))
 #'   select(df, list(df$name, df$age + 1))
-#'   # Columns can also be selected using `[[` and `[`
-#'   df[[2]] == df[["age"]]
-#'   df[,2] == df[,"age"]
-#'   df[,c("name", "age")]
 #'   # Similar to R data frames columns can also be selected using `$`
 #'   df$age
-#'   # It can also be subset on rows and Columns
-#'   df[df$name == "Smith", c(1,2)]
-#'   df[df$age %in% c(19, 30), 1:2]
 #' }
 setMethod("select", signature(x = "DataFrame", col = "character"),
           function(x, col, ...) {
@@ -1090,7 +1116,7 @@ setMethod("selectExpr",
 #' @return A DataFrame with the new column added.
 #' @rdname withColumn
 #' @name withColumn
-#' @aliases mutate
+#' @aliases mutate transform
 #' @export
 #' @examples
 #'\dontrun{
@@ -1110,11 +1136,12 @@ setMethod("withColumn",
 #'
 #' Return a new DataFrame with the specified columns added.
 #'
-#' @param x A DataFrame
+#' @param .data A DataFrame
 #' @param col a named argument of the form name = col
 #' @return A new DataFrame with the new columns added.
 #' @rdname withColumn
 #' @name mutate
+#' @aliases withColumn transform
 #' @export
 #' @examples
 #'\dontrun{
@@ -1124,10 +1151,12 @@ setMethod("withColumn",
 #' df <- jsonFile(sqlContext, path)
 #' newDF <- mutate(df, newCol = df$col1 * 5, newCol2 = df$col1 * 2)
 #' names(newDF) # Will contain newCol, newCol2
+#' newDF2 <- transform(df, newCol = df$col1 / 5, newCol2 = df$col1 * 2)
 #' }
 setMethod("mutate",
-          signature(x = "DataFrame"),
-          function(x, ...) {
+          signature(.data = "DataFrame"),
+          function(.data, ...) {
+            x <- .data
             cols <- list(...)
             stopifnot(length(cols) > 0)
             stopifnot(class(cols[[1]]) == "Column")
@@ -1142,6 +1171,16 @@ setMethod("mutate",
             do.call(select, c(x, x$"*", cols))
           })
 
+#' @export
+#' @rdname withColumn
+#' @name transform
+#' @aliases withColumn mutate
+setMethod("transform",
+          signature(`_data` = "DataFrame"),
+          function(`_data`, ...) {
+            mutate(`_data`, ...)
+          })
+
 #' WithColumnRenamed
 #'
 #' Rename an existing column in a DataFrame.
@@ -1269,6 +1308,7 @@ setMethod("orderBy",
 #' @return A DataFrame containing only the rows that meet the condition.
 #' @rdname filter
 #' @name filter
+#' @family subsetting functions
 #' @export
 #' @examples
 #'\dontrun{
diff --git a/R/pkg/R/generics.R b/R/pkg/R/generics.R
index b578b8789d..43dd8d283a 100644
--- a/R/pkg/R/generics.R
+++ b/R/pkg/R/generics.R
@@ -467,7 +467,7 @@ setGeneric("merge")
 
 #' @rdname withColumn
 #' @export
-setGeneric("mutate", function(x, ...) {standardGeneric("mutate") })
+setGeneric("mutate", function(.data, ...) {standardGeneric("mutate") })
 
 #' @rdname arrange
 #' @export
@@ -507,6 +507,10 @@ setGeneric("saveAsTable", function(df, tableName, source, mode, ...) {
   standardGeneric("saveAsTable")
 })
 
+#' @rdname withColumn
+#' @export
+setGeneric("transform", function(`_data`, ...) {standardGeneric("transform") })
+
 #' @rdname write.df
 #' @export
 setGeneric("write.df", function(df, path, ...) { standardGeneric("write.df") })
@@ -531,6 +535,10 @@ setGeneric("selectExpr", function(x, expr, ...) { standardGeneric("selectExpr")
 #' @export
 setGeneric("showDF", function(x,...) { standardGeneric("showDF") })
 
+# @rdname subset
+# @export
+setGeneric("subset", function(x, subset, select, ...) { standardGeneric("subset") })
+
 #' @rdname agg
 #' @export
 setGeneric("summarize", function(x,...) { standardGeneric("summarize") })
diff --git a/R/pkg/inst/tests/test_sparkSQL.R b/R/pkg/inst/tests/test_sparkSQL.R
index 8ebd78ed61..2062bc72b1 100644
--- a/R/pkg/inst/tests/test_sparkSQL.R
+++ b/R/pkg/inst/tests/test_sparkSQL.R
@@ -612,6 +612,10 @@ test_that("subsetting", {
   df5 <- df[df$age %in% c(19), c(1,2)]
   expect_equal(count(df5), 1)
   expect_equal(columns(df5), c("name", "age"))
+
+  df6 <- subset(df, df$age %in% c(30), c(1,2))
+  expect_equal(count(df6), 1)
+  expect_equal(columns(df6), c("name", "age"))
 })
 
 test_that("selectExpr() on a DataFrame", {
@@ -1028,7 +1032,7 @@ test_that("withColumn() and withColumnRenamed()", {
   expect_equal(columns(newDF2)[1], "newerAge")
 })
 
-test_that("mutate(), rename() and names()", {
+test_that("mutate(), transform(), rename() and names()", {
   df <- jsonFile(sqlContext, jsonPath)
   newDF <- mutate(df, newAge = df$age + 2)
   expect_equal(length(columns(newDF)), 3)
@@ -1042,6 +1046,20 @@ test_that("mutate(), rename() and names()", {
   names(newDF2) <- c("newerName", "evenNewerAge")
   expect_equal(length(names(newDF2)), 2)
   expect_equal(names(newDF2)[1], "newerName")
+
+  transformedDF <- transform(df, newAge = -df$age, newAge2 = df$age / 2)
+  expect_equal(length(columns(transformedDF)), 4)
+  expect_equal(columns(transformedDF)[3], "newAge")
+  expect_equal(columns(transformedDF)[4], "newAge2")
+  expect_equal(first(filter(transformedDF, transformedDF$name == "Andy"))$newAge, -30)
+
+  # test if transform on local data frames works
+  # ensure the proper signature is used - otherwise this will fail to run
+  attach(airquality)
+  result <- transform(Ozone, logOzone = log(Ozone))
+  expect_equal(nrow(result), 153)
+  expect_equal(ncol(result), 2)
+  detach(airquality)
 })
 
 test_that("write.df() on DataFrame and works with parquetFile", {