[SQL] SPARK-1424 Generalize insertIntoTable functions on SchemaRDDs

This makes it possible to create tables and insert into them using the DSL and SQL for the scala and java apis.

Author: Michael Armbrust <michael@databricks.com>

Closes #354 from marmbrus/insertIntoTable and squashes the following commits:

6c6f227 [Michael Armbrust] Create random temporary files in python parquet unit tests.
f5e6d5c [Michael Armbrust] Merge remote-tracking branch 'origin/master' into insertIntoTable
765c506 [Michael Armbrust] Add to JavaAPI.
77b512c [Michael Armbrust] typos.
5c3ef95 [Michael Armbrust] use names for boolean args.
882afdf [Michael Armbrust] Change createTableAs to saveAsTable.  Clean up api annotations.
d07d94b [Michael Armbrust] Add tests, support for creating parquet files and hive tables.
fa3fe81 [Michael Armbrust] Make insertInto available on JavaSchemaRDD as well.  Add createTableAs function.
[SPARK-959] Updated SBT from 0.13.1 to 0.13.2

JIRA issue: [SPARK-959](https://spark-project.atlassian.net/browse/SPARK-959)

SBT 0.13.2 has been officially released. This version updated Ivy 2.0 to Ivy 2.3, which fixes [IVY-899](https://issues.apache.org/jira/browse/IVY-899). This PR also removed previous workaround.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #426 from liancheng/updateSbt and squashes the following commits:

95e3dc8 [Cheng Lian] Updated SBT from 0.13.1 to 0.13.2 to fix SPARK-959
Make "spark logo" link refer to "/".

This is not an issue with the driver UI, but when you fire
up the history server, there's currently no way to go back to
the app listing page without editing the browser's location
field (since the logo's link points to the root of the
application's own UI - i.e. the "stages" tab).

The change just points the logo link to "/", which is the app
listing for the history server, and the stages tab for the
driver's UI.

Tested with both history server and live driver.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #408 from vanzin/web-ui-root and squashes the following commits:

1b60cb6 [Marcelo Vanzin] Make "spark logo" link refer to "/".
Loads test tables when running "sbt hive/console" without HIVE_DEV_HOME

When running Hive tests, the working directory is `$SPARK_HOME/sql/hive`, while when running `sbt hive/console`, it becomes `$SPARK_HOME`, and test tables are not loaded if `HIVE_DEV_HOME` is not defined.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #417 from liancheng/loadTestTables and squashes the following commits:

7cea8d6 [Cheng Lian] Loads test tables when running "sbt hive/console" without HIVE_DEV_HOME
update spark.default.parallelism

actually, the value 8 is only valid in mesos fine-grained mode :
<code>
  override def defaultParallelism() = sc.conf.getInt("spark.default.parallelism", 8)
</code>

while in coarse-grained model including mesos coares-grained, the value of the property depending on core numbers!
<code>
override def defaultParallelism(): Int = {
   conf.getInt("spark.default.parallelism", math.max(totalCoreCount.get(), 2))
  }
</code>

Author: Chen Chao <crazyjvm@gmail.com>

Closes #389 from CrazyJvm/patch-2 and squashes the following commits:

84a7fe4 [Chen Chao] miss </li> at the end of every single line
04a9796 [Chen Chao] change format
ee0fae0 [Chen Chao] update spark.default.parallelism
SPARK-1310: Start adding k-fold cross validation to MLLib [adds kFold to MLUtils & fixes bug in BernoulliSampler]

Author: Holden Karau <holden@pigscanfly.ca>

Closes #18 from holdenk/addkfoldcrossvalidation and squashes the following commits:

208db9b [Holden Karau] Fix a bad space
e84f2fc [Holden Karau] Fix the test, we should be looking at the second element instead
6ddbf05 [Holden Karau] swap training and validation order
7157ae9 [Holden Karau] CR feedback
90896c7 [Holden Karau] New line
150889c [Holden Karau] Fix up error messages in the MLUtilsSuite
2cb90b3 [Holden Karau] Fix the names in kFold
c702a96 [Holden Karau] Fix imports in MLUtils
e187e35 [Holden Karau] Move { up to same line as whenExecuting(random) in RandomSamplerSuite.scala
c5b723f [Holden Karau] clean up
7ebe4d5 [Holden Karau] CR feedback, remove unecessary learners (came back during merge mistake) and insert an empty line
bb5fa56 [Holden Karau] extra line sadness
163c5b1 [Holden Karau] code review feedback 1.to -> 1 to and folds -> numFolds
5a33f1d [Holden Karau] Code review follow up.
e8741a7 [Holden Karau] CR feedback
b78804e [Holden Karau] Remove cross validation [TODO in another pull request]
91eae64 [Holden Karau] Consolidate things in mlutils
264502a [Holden Karau] Add a test for the bug that was found with BernoulliSampler not copying the complement param
dd0b737 [Holden Karau] Wrap long lines (oops)
c0b7fa4 [Holden Karau] Switch FoldedRDD to use BernoulliSampler and PartitionwiseSampledRDD
08f8e4d [Holden Karau] Fix BernoulliSampler to respect complement
a751ec6 [Holden Karau] Add k-fold cross validation to MLLib
SPARK-1497. Fix scalastyle warnings in YARN, Hive code

(I wasn't sure how to automatically set `SPARK_YARN=true` and `SPARK_HIVE=true` when running scalastyle, but these are the errors that turn up.)

Author: Sean Owen <sowen@cloudera.com>

Closes #413 from srowen/SPARK-1497 and squashes the following commits:

f0c9318 [Sean Owen] Fix more scalastyle warnings in yarn
80bf4c3 [Sean Owen] Add YARN alpha / YARN profile to scalastyle check
026319c [Sean Owen] Fix scalastyle warnings in YARN, Hive code
Minor addition to SPARK-1497
SPARK-1469: Scheduler mode should accept lower-case definitions and have...

... nicer error messages

There are  two improvements to Scheduler Mode:
1. Made the built in ones case insensitive (fair/FAIR, fifo/FIFO).
2. If an invalid mode is given we should print a better error message.

Author: Sandeep <sandeep@techaddict.me>

Closes #388 from techaddict/1469 and squashes the following commits:

a31bbd5 [Sandeep] SPARK-1469: Scheduler mode should accept lower-case definitions and have nicer error messages There are  two improvements to Scheduler Mode: 1. Made the built in ones case insensitive (fair/FAIR, fifo/FIFO). 2. If an invalid mode is given we should print a better error message.
SPARK-1465: Spark compilation is broken with the latest hadoop-2.4.0 release

YARN-1824 changes the APIs (addToEnvironment, setEnvFromInputString) in Apps, which causes the spark build to break if built against a version 2.4.0. To fix this, create the spark own function to do that functionality which will not break compiling against 2.3 and other 2.x versions.

Author: xuan <xuan@MacBook-Pro.local>
Author: xuan <xuan@macbook-pro.home>

Closes #396 from xgong/master and squashes the following commits:

42b5984 [xuan] Remove two extra imports
bc0926f [xuan] Remove usage of org.apache.hadoop.util.Shell
be89fa7 [xuan] fix Spark compilation is broken with the latest hadoop-2.4.0 release
[SPARK-1511] use Files.move instead of renameTo in TestUtils.scala

JIRA issue:[SPARK-1511](https://issues.apache.org/jira/browse/SPARK-1511)

TestUtils.createCompiledClass method use renameTo() to move files which fails when the src and dest files are in different disks or partitions. This pr uses Files.move() instead. The move method will try to use renameTo() and then fall back to copy() and delete(). I think this should handle this issue.

I didn't found a test suite for this file, so I add file existence detection after file moving.

Author: Ye Xianjin <advancedxy@gmail.com>

Closes #427 from advancedxy/SPARK-1511 and squashes the following commits:

a2b97c7 [Ye Xianjin] Based on @srowen's comment, assert file existence.
6f95550 [Ye Xianjin] use Files.move instead of renameTo to handle the src and dest files are in different disks or partitions.
Add clean to build
Rebuild routing table after Graph.reverse

GraphImpl.reverse used to reverse edges in each partition of the edge RDD but preserve the routing table and replicated vertex view, since reversing should not affect partitioning.

However, the old routing table would then have incorrect information for srcAttrOnly and dstAttrOnly. These RDDs should be switched.

A simple fix is for Graph.reverse to rebuild the routing table and replicated vertex view.

Thanks to Bogdan Ghidireac for reporting this issue on the [mailing list](http://apache-spark-user-list.1001560.n3.nabble.com/graph-reverse-amp-Pregel-API-td4338.html).

Author: Ankur Dave <ankurdave@gmail.com>

Closes #431 from ankurdave/fix-reverse-bug and squashes the following commits:

75d63cb [Ankur Dave] Rebuild routing table after Graph.reverse
SPARK-1329: Create pid2vid with correct number of partitions

Each vertex partition is co-located with a pid2vid array created in RoutingTable.scala. This array maps edge partition IDs to the list of vertices in the current vertex partition that are mentioned by edges in that partition. Therefore the pid2vid array should have one entry per edge partition.

GraphX currently creates one entry per *vertex* partition, which is a bug that leads to an ArrayIndexOutOfBoundsException when there are more edge partitions than vertex partitions. This commit fixes the bug and adds a test for this case.

Resolves SPARK-1329. Thanks to Daniel Darabos for reporting this bug.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #368 from ankurdave/fix-pid2vid-size and squashes the following commits:

5a5c52a [Ankur Dave] SPARK-1329: Create pid2vid with correct number of partitions
remove unnecessary brace and semicolon in 'putBlockInfo.synchronize'  block

delete semicolon

Author: Chen Chao <crazyjvm@gmail.com>

Closes #411 from CrazyJvm/patch-5 and squashes the following commits:

72333a3 [Chen Chao] remove unnecessary brace
de5d9a7 [Chen Chao] style fix
Fixing a race condition in event listener unit test

Author: Kan Zhang <kzhang@apache.org>

Closes #401 from kanzhang/fix-1475 and squashes the following commits:

c6058bd [Kan Zhang] Fixing a race condition in event listener unit test
misleading task number of groupByKey

"By default, this uses only 8 parallel tasks to do the grouping." is a big misleading. Please refer to https://github.com/apache/spark/pull/389

detail is as following code :

  def defaultPartitioner(rdd: RDD[_], others: RDD[_]*): Partitioner = {
    val bySize = (Seq(rdd) ++ others).sortBy(_.partitions.size).reverse
    for (r <- bySize if r.partitioner.isDefined) {
      return r.partitioner.get
    }
    if (rdd.context.conf.contains("spark.default.parallelism")) {
      new HashPartitioner(rdd.context.defaultParallelism)
    } else {
      new HashPartitioner(bySize.head.partitions.size)
    }
  }

Author: Chen Chao <crazyjvm@gmail.com>

Closes #403 from CrazyJvm/patch-4 and squashes the following commits:

42f6c9e [Chen Chao] fix format
829a995 [Chen Chao] fix format
1568336 [Chen Chao] misleading task number of groupByKey
Update ReducedWindowedDStream.scala

change  _slideDuration  to   _windowDuration

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #425 from baishuo/master and squashes the following commits:

6f09ea1 [baishuo(白硕)] Update ReducedWindowedDStream.scala
Include stack trace for exceptions thrown by user code.

It is very confusing when your code throws an exception, but the only stack trace show is in the DAGScheduler.  This is a simple patch to include the stack trace for the actual failure in the error message.  Suggestions on formatting welcome.

Before:
```
scala> sc.parallelize(1 :: Nil).map(_ => sys.error("Ahh!")).collect()
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0.0:3 failed 1 times (most recent failure: Exception failure in TID 3 on host localhost: java.lang.RuntimeException: Ahh!)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1055)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1039)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1037)
...
```

After:
```
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0.0:3 failed 1 times, most recent failure: Exception failure in TID 3 on host localhost: java.lang.RuntimeException: Ahh!
        scala.sys.package$.error(package.scala:27)
        $iwC$$iwC$$iwC$$iwC$$anonfun$1.apply(<console>:13)
        $iwC$$iwC$$iwC$$iwC$$anonfun$1.apply(<console>:13)
        scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        scala.collection.Iterator$class.foreach(Iterator.scala:727)
        scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
        scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
        scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
        scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
        scala.collection.AbstractIterator.to(Iterator.scala:1157)
        scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
        scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
        scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
        scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
        org.apache.spark.rdd.RDD$$anonfun$6.apply(RDD.scala:676)
        org.apache.spark.rdd.RDD$$anonfun$6.apply(RDD.scala:676)
        org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1048)
        org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1048)
        org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:110)
        org.apache.spark.scheduler.Task.run(Task.scala:50)
        org.apache.spark.executor.Executor$TaskRunner$$anonfun$run$1.apply$mcV$sp(Executor.scala:211)
        org.apache.spark.deploy.SparkHadoopUtil.runAsUser(SparkHadoopUtil.scala:46)
        org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:176)
        java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        java.lang.Thread.run(Thread.java:744)
Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1055)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1039)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1037)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$abortStage(DAGScheduler.scala:1037)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$processEvent$10.apply(DAGScheduler.scala:614)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$processEvent$10.apply(DAGScheduler.scala:614)
	at scala.Option.foreach(Option.scala:236)
	at org.apache.spark.scheduler.DAGScheduler.processEvent(DAGScheduler.scala:614)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$start$1$$anon$2$$anonfun$receive$1.applyOrElse(DAGScheduler.scala:143)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
	at akka.actor.ActorCell.invoke(ActorCell.scala:456)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
	at akka.dispatch.Mailbox.run(Mailbox.scala:219)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
	at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
```

Author: Michael Armbrust <michael@databricks.com>

Closes #409 from marmbrus/stacktraces and squashes the following commits:

3e4eb65 [Michael Armbrust] indent. include header for driver stack trace.
018b06b [Michael Armbrust] Include stack trace for exceptions in user code.
SPARK-1462: Examples of ML algorithms are using deprecated APIs

This will also fix SPARK-1464: Update MLLib Examples to Use Breeze.

Author: Sandeep <sandeep@techaddict.me>

Closes #416 from techaddict/1462 and squashes the following commits:

a43638e [Sandeep] Some Style Changes
3ce69c3 [Sandeep] Fix Ordering and Naming of Imports in Examples
6c7e543 [Sandeep] SPARK-1462: Examples of ML algorithms are using deprecated APIs