[SPARK-12224][SPARKR] R support for JDBC source

Add R API for `read.jdbc`, `write.jdbc`.

Tested this quite a bit manually with different combinations of parameters. It's not clear if we could have automated tests in R for this - Scala `JDBCSuite` depends on Java H2 in-memory database.

Refactored some code into util so they could be tested.

Core's R SerDe code needs to be updated to allow access to java.util.Properties as `jobj` handle which is required by DataFrameReader/Writer's `jdbc` method. It would be possible, though more code to add a `sql/r/SQLUtils` helper function.

Tested:
```
# with postgresql
../bin/sparkR --driver-class-path /usr/share/java/postgresql-9.4.1207.jre7.jar

# read.jdbc
df <- read.jdbc(sqlContext, "jdbc:postgresql://localhost/db", "films2", user = "user", password = "12345")
df <- read.jdbc(sqlContext, "jdbc:postgresql://localhost/db", "films2", user = "user", password = 12345)

# partitionColumn and numPartitions test
df <- read.jdbc(sqlContext, "jdbc:postgresql://localhost/db", "films2", partitionColumn = "did", lowerBound = 0, upperBound = 200, numPartitions = 4, user = "user", password = 12345)
a <- SparkR:::toRDD(df)
SparkR:::getNumPartitions(a)
[1] 4
SparkR:::collectPartition(a, 2L)

# defaultParallelism test
df <- read.jdbc(sqlContext, "jdbc:postgresql://localhost/db", "films2", partitionColumn = "did", lowerBound = 0, upperBound = 200, user = "user", password = 12345)
SparkR:::getNumPartitions(a)
[1] 2

# predicates test
df <- read.jdbc(sqlContext, "jdbc:postgresql://localhost/db", "films2", predicates = list("did<=105"), user = "user", password = 12345)
count(df) == 1

# write.jdbc, default save mode "error"
irisDf <- as.DataFrame(sqlContext, iris)
write.jdbc(irisDf, "jdbc:postgresql://localhost/db", "films2", user = "user", password = "12345")
"error, already exists"

write.jdbc(irisDf, "jdbc:postgresql://localhost/db", "iris", user = "user", password = "12345")
```

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10480 from felixcheung/rreadjdbc.

R/pkg/NAMESPACE

@@ -101,6 +101,7 @@ exportMethods("arrange",
               "withColumn",
               "withColumnRenamed",
               "write.df",
+              "write.jdbc",
               "write.json",
               "write.parquet",
               "write.text")
@@ -284,6 +285,7 @@ export("as.DataFrame",
        "loadDF",
        "parquetFile",
        "read.df",
+       "read.jdbc",
        "read.json",
        "read.parquet",
        "read.text",

R/pkg/R/DataFrame.R

@@ -2363,7 +2363,7 @@ setMethod("with",
 #' @examples \dontrun{
 #' # Create a DataFrame from the Iris dataset
 #' irisDF <- createDataFrame(sqlContext, iris)
-#' 
+#'
 #' # Show the structure of the DataFrame
 #' str(irisDF)
 #' }
@@ -2468,3 +2468,40 @@ setMethod("drop",
           function(x) {
             base::drop(x)
           })
+
+#' Saves the content of the DataFrame to an external database table via JDBC
+#'
+#' Additional JDBC database connection properties can be set (...)
+#'
+#' Also, mode is used to specify the behavior of the save operation when
+#' data already exists in the data source. There are four modes: \cr
+#'  append: Contents of this DataFrame are expected to be appended to existing data. \cr
+#'  overwrite: Existing data is expected to be overwritten by the contents of this DataFrame. \cr
+#'  error: An exception is expected to be thrown. \cr
+#'  ignore: The save operation is expected to not save the contents of the DataFrame
+#'     and to not change the existing data. \cr
+#'
+#' @param x A SparkSQL DataFrame
+#' @param url JDBC database url of the form `jdbc:subprotocol:subname`
+#' @param tableName The name of the table in the external database
+#' @param mode One of 'append', 'overwrite', 'error', 'ignore' save mode (it is 'error' by default)
+#' @family DataFrame functions
+#' @rdname write.jdbc
+#' @name write.jdbc
+#' @export
+#' @examples
+#'\dontrun{
+#' sc <- sparkR.init()
+#' sqlContext <- sparkRSQL.init(sc)
+#' jdbcUrl <- "jdbc:mysql://localhost:3306/databasename"
+#' write.jdbc(df, jdbcUrl, "table", user = "username", password = "password")
+#' }
+setMethod("write.jdbc",
+          signature(x = "DataFrame", url = "character", tableName = "character"),
+          function(x, url, tableName, mode = "error", ...){
+            jmode <- convertToJSaveMode(mode)
+            jprops <- varargsToJProperties(...)
+            write <- callJMethod(x@sdf, "write")
+            write <- callJMethod(write, "mode", jmode)
+            invisible(callJMethod(write, "jdbc", url, tableName, jprops))
+          })

R/pkg/R/SQLContext.R

@@ -583,3 +583,61 @@ createExternalTable <- function(sqlContext, tableName, path = NULL, source = NUL
   sdf <- callJMethod(sqlContext, "createExternalTable", tableName, source, options)
   dataFrame(sdf)
 }
+
+#' Create a DataFrame representing the database table accessible via JDBC URL
+#'
+#' Additional JDBC database connection properties can be set (...)
+#'
+#' Only one of partitionColumn or predicates should be set. Partitions of the table will be
+#' retrieved in parallel based on the `numPartitions` or by the predicates.
+#'
+#' Don't create too many partitions in parallel on a large cluster; otherwise Spark might crash
+#' your external database systems.
+#'
+#' @param sqlContext SQLContext to use
+#' @param url JDBC database url of the form `jdbc:subprotocol:subname`
+#' @param tableName the name of the table in the external database
+#' @param partitionColumn the name of a column of integral type that will be used for partitioning
+#' @param lowerBound the minimum value of `partitionColumn` used to decide partition stride
+#' @param upperBound the maximum value of `partitionColumn` used to decide partition stride
+#' @param numPartitions the number of partitions, This, along with `lowerBound` (inclusive),
+#'                      `upperBound` (exclusive), form partition strides for generated WHERE
+#'                      clause expressions used to split the column `partitionColumn` evenly.
+#'                      This defaults to SparkContext.defaultParallelism when unset.
+#' @param predicates a list of conditions in the where clause; each one defines one partition
+#' @return DataFrame
+#' @rdname read.jdbc
+#' @name read.jdbc
+#' @export
+#' @examples
+#'\dontrun{
+#' sc <- sparkR.init()
+#' sqlContext <- sparkRSQL.init(sc)
+#' jdbcUrl <- "jdbc:mysql://localhost:3306/databasename"
+#' df <- read.jdbc(sqlContext, jdbcUrl, "table", predicates = list("field<=123"), user = "username")
+#' df2 <- read.jdbc(sqlContext, jdbcUrl, "table2", partitionColumn = "index", lowerBound = 0,
+#'                  upperBound = 10000, user = "username", password = "password")
+#' }
+
+read.jdbc <- function(sqlContext, url, tableName,
+                      partitionColumn = NULL, lowerBound = NULL, upperBound = NULL,
+                      numPartitions = 0L, predicates = list(), ...) {
+  jprops <- varargsToJProperties(...)
+
+  read <- callJMethod(sqlContext, "read")
+  if (!is.null(partitionColumn)) {
+    if (is.null(numPartitions) || numPartitions == 0) {
+      sc <- callJMethod(sqlContext, "sparkContext")
+      numPartitions <- callJMethod(sc, "defaultParallelism")
+    } else {
+      numPartitions <- numToInt(numPartitions)
+    }
+    sdf <- callJMethod(read, "jdbc", url, tableName, as.character(partitionColumn),
+                       numToInt(lowerBound), numToInt(upperBound), numPartitions, jprops)
+  } else if (length(predicates) > 0) {
+    sdf <- callJMethod(read, "jdbc", url, tableName, as.list(as.character(predicates)), jprops)
+  } else {
+    sdf <- callJMethod(read, "jdbc", url, tableName, jprops)
+  }
+  dataFrame(sdf)
+}

R/pkg/R/generics.R

@@ -577,6 +577,12 @@ setGeneric("saveDF", function(df, path, source = NULL, mode = "error", ...) {
   standardGeneric("saveDF")
 })
 
+#' @rdname write.jdbc
+#' @export
+setGeneric("write.jdbc", function(x, url, tableName, mode = "error", ...) {
+  standardGeneric("write.jdbc")
+})
+
 #' @rdname write.json
 #' @export
 setGeneric("write.json", function(x, path) { standardGeneric("write.json") })

R/pkg/R/utils.R

@@ -650,3 +650,14 @@ convertToJSaveMode <- function(mode) {
  jmode <- callJStatic("org.apache.spark.sql.api.r.SQLUtils", "saveMode", mode)
  jmode
 }
+
+varargsToJProperties <- function(...) {
+  pairs <- list(...)
+  props <- newJObject("java.util.Properties")
+  if (length(pairs) > 0) {
+    lapply(ls(pairs), function(k) {
+      callJMethod(props, "setProperty", as.character(k), as.character(pairs[[k]]))
+    })
+  }
+  props
+}

R/pkg/inst/tests/testthat/test_utils.R

@@ -140,3 +140,27 @@ test_that("cleanClosure on R functions", {
   expect_equal(ls(env), "aBroadcast")
   expect_equal(get("aBroadcast", envir = env, inherits = FALSE), aBroadcast)
 })
+
+test_that("varargsToJProperties", {
+  jprops <- newJObject("java.util.Properties")
+  expect_true(class(jprops) == "jobj")
+
+  jprops <- varargsToJProperties(abc = "123")
+  expect_true(class(jprops) == "jobj")
+  expect_equal(callJMethod(jprops, "getProperty", "abc"), "123")
+
+  jprops <- varargsToJProperties(abc = "abc", b = 1)
+  expect_equal(callJMethod(jprops, "getProperty", "abc"), "abc")
+  expect_equal(callJMethod(jprops, "getProperty", "b"), "1")
+
+  jprops <- varargsToJProperties()
+  expect_equal(callJMethod(jprops, "size"), 0L)
+})
+
+test_that("convertToJSaveMode", {
+  s <- convertToJSaveMode("error")
+  expect_true(class(s) == "jobj")
+  expect_match(capture.output(print.jobj(s)), "Java ref type org.apache.spark.sql.SaveMode id ")
+  expect_error(convertToJSaveMode("foo"),
+    'mode should be one of "append", "overwrite", "error", "ignore"') #nolint
+})

core/src/main/scala/org/apache/spark/api/r/SerDe.scala

@@ -356,6 +356,13 @@ private[spark] object SerDe {
           writeInt(dos, v.length)
           v.foreach(elem => writeObject(dos, elem))
 
+        // Handle Properties
+        // This must be above the case java.util.Map below.
+        // (Properties implements Map<Object,Object> and will be serialized as map otherwise)
+        case v: java.util.Properties =>
+          writeType(dos, "jobj")
+          writeJObj(dos, value)
+
         // Handle map
         case v: java.util.Map[_, _] =>
           writeType(dos, "map")