[SPARK-11949][SQL] Set field nullable property for GroupingSets to get correct results for null values

JIRA: https://issues.apache.org/jira/browse/SPARK-11949

The result of cube plan uses incorrect schema. The schema of cube result should set nullable property to true because the grouping expressions will have null values.

Author: Liang-Chi Hsieh <viirya@appier.com>

Closes #10038 from viirya/fix-cube.

jira: https://issues.apache.org/jira/browse/SPARK-11898
syn0Global and sync1Global in word2vec are quite large objects with size (vocab * vectorSize * 8), yet they are passed to worker using basic task serialization.

Use broadcast can greatly improve the performance. My benchmark shows that, for 1M vocabulary and default vectorSize 100, changing to broadcast can help,

1. decrease the worker memory consumption by 45%.
2. decrease running time by 40%.

This will also help extend the upper limit for Word2Vec.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #9878 from hhbyyh/w2vBC.

JIRA: https://issues.apache.org/jira/browse/SPARK-12018

The code of common subexpression elimination can be factored and simplified. Some unnecessary variables can be removed.

Author: Liang-Chi Hsieh <viirya@appier.com>

Closes #10009 from viirya/refactor-subexpr-eliminate.

I accidentally omitted these as part of #10049.

Avoid potential deadlock with a user app's shutdown hook thread by more narrowly synchronizing access to 'hooks'

Author: Sean Owen <sowen@cloudera.com>

Closes #10042 from srowen/SPARK-12049.

This change seems large, but most of it is just replacing `byte[]`
with `ByteBuffer` and `new byte[]` with `ByteBuffer.allocate()`,
since it changes the network library's API.

The following are parts of the code that actually have meaningful
changes:

- The Message implementations were changed to inherit from a new
  AbstractMessage that can optionally hold a reference to a body
  (in the form of a ManagedBuffer); this is similar to how
  ResponseWithBody worked before, except now it's not restricted
  to just responses.

- The TransportFrameDecoder was pretty much rewritten to avoid
  copies as much as possible; it doesn't rely on CompositeByteBuf
  to accumulate incoming data anymore, since CompositeByteBuf
  has issues when slices are retained. The code now is able to
  create frames without having to resort to copying bytes except
  for a few bytes (containing the frame length) in very rare cases.

- Some minor changes in the SASL layer to convert things back to
  `byte[]` since the JDK SASL API operates on those.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #9987 from vanzin/SPARK-12007.

https://issues.apache.org/jira/browse/SPARK-12037

a simple fix by changing the order of the statements

Author: CodingCat <zhunansjtu@gmail.com>

Closes #10032 from CodingCat/SPARK-12037.

https://issues.apache.org/jira/browse/SPARK-12035

When we debuging lots of example code files, like in https://github.com/apache/spark/pull/10002, it's hard to know which file causes errors due to limited information in `include_example.rb`. With their filenames, we can locate bugs easily.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #10026 from yinxusen/SPARK-12035.

This pull request fixes multiple issues with API doc generation.

- Modify the Jekyll plugin so that the entire doc build fails if API docs cannot be generated. This will make it easy to detect when the doc build breaks, since this will now trigger Jenkins failures.
- Change how we handle the `-target` compiler option flag in order to fix `javadoc` generation.
- Incorporate doc changes from thunterdb (in #10048).

Closes #10048.

Author: Josh Rosen <joshrosen@databricks.com>
Author: Timothy Hunter <timhunter@databricks.com>

Closes #10049 from JoshRosen/fix-doc-build.

KinesisStreamTests in test.py is broken because of #9403. See https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/46896/testReport/(root)/KinesisStreamTests/test_kinesis_stream/

Because Streaming Python didn’t work when merging https://github.com/apache/spark/pull/9403, the PR build didn’t report the Python test failure actually.

This PR just disabled the test to unblock #10039

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #10047 from zsxwing/disable-python-kinesis-test.

CC jkbradley mengxr josepablocam

Author: Feynman Liang <feynman.liang@gmail.com>

Closes #10005 from feynmanliang/streaming-test-user-guide.

Remove duplicate mllib example (DT/RF/GBT in Java/Python).
Since we have tutorial code for DT/RF/GBT classification/regression in Scala/Java/Python and example applications for DT/RF/GBT in Scala, so we mark these as duplicated and remove them.
mengxr

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9954 from yanboliang/SPARK-11975.

jira: https://issues.apache.org/jira/browse/SPARK-11689

Add simple user guide for LDA under spark.ml and example code under examples/. Use include_example to include example code in the user guide markdown. Check SPARK-11606 for instructions.

Original PR is reverted due to document build error. https://github.com/apache/spark/pull/9722

mengxr feynmanliang yinxusen  Sorry for the troubling.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #9974 from hhbyyh/ldaMLExample.

```EventLoggingListener.getLogPath``` needs 4 input arguments:
https://github.com/apache/spark/blob/v1.6.0-preview2/core/src/main/scala/org/apache/spark/scheduler/EventLoggingListener.scala#L276-L280

the 3rd parameter should be appAttemptId, 4th parameter is codec...

Author: Teng Qiu <teng.qiu@gmail.com>

Closes #10044 from chutium/SPARK-12053.

This reverts commit cc243a07 / PR #9297

I'm reverting this because it broke SQLListenerMemoryLeakSuite in the master Maven builds.

See #9991 for a discussion of why this broke the tests.

The list in ml-ensembles.md wasn't properly formatted and, as a result, was looking like this:
![old](http://i.imgur.com/2ZhELLR.png)

This PR aims to make it look like this:
![new](http://i.imgur.com/0Xriwd2.png)

Author: BenFradet <benjamin.fradet@gmail.com>

Closes #10025 from BenFradet/ml-ensembles-doc.

This PR improve the performance of CartesianProduct by caching the result of right plan.

After this patch, the query time of TPC-DS Q65 go down to 4 seconds from 28 minutes (420X faster).

cc nongli

Author: Davies Liu <davies@databricks.com>

Closes #9969 from davies/improve_cartesian.

In 1.6, we introduce a public API to have a SQLContext for current thread, SparkPlan should use that.

Author: Davies Liu <davies@databricks.com>

Closes #9990 from davies/leak_context.

[SPARK-11989][SQL] Only use commit in JDBC data source if the underlying database supports transactions

Fixes [SPARK-11989](https://issues.apache.org/jira/browse/SPARK-11989

)

Author: CK50 <christian.kurz@oracle.com>
Author: Christian Kurz <christian.kurz@oracle.com>

Closes #9973 from CK50/branch-1.6_non-transactional.

(cherry picked from commit a589736a)
Signed-off-by: Reynold Xin <rxin@databricks.com>

this is a trivial fix, discussed [here](http://stackoverflow.com/questions/28500401/maven-assembly-plugin-warning-the-assembly-descriptor-contains-a-filesystem-roo/).

Author: Prashant Sharma <scrapcodes@gmail.com>

Closes #10014 from ScrapCodes/assembly-warning.

Top is implemented in terms of takeOrdered, which already maintains the
order, so top should, too.

Author: Wieland Hoffmann <themineo@gmail.com>

Closes #10013 from mineo/top-order.

[MINOR][BUILD] Changed the comment to reflect the plugin project is there to support SBT pom reader only.

Author: Prashant Sharma <scrapcodes@gmail.com>

Closes #10012 from ScrapCodes/minor-build-comment.

[SPARK-11859][MESOS] SparkContext accepts invalid Master URLs in the form zk://host:port for a multi-master Mesos cluster using ZooKeeper

* According to below doc and validation logic in [SparkSubmit.scala](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala#L231), master URL for a mesos cluster should always start with `mesos://`

http://spark.apache.org/docs/latest/running-on-mesos.html
`The Master URLs for Mesos are in the form mesos://host:5050 for a single-master Mesos cluster, or mesos://zk://host:2181 for a multi-master Mesos cluster using ZooKeeper.`

* However, [SparkContext.scala](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/SparkContext.scala#L2749) fails the validation and can receive master URL in the form `zk://host:port`

* For the master URLs in the form `zk:host:port`, the valid form should be `mesos://zk://host:port`

* This PR restrict the validation in `SparkContext.scala`, and now only mesos master URLs prefixed with `mesos://` can be accepted.

* This PR also updated corresponding unit test.

Author: toddwan <tawan0109@outlook.com>

Closes #9886 from toddwan/S11859.

[SPARK-12039] [SQL] Ignore HiveSparkSubmitSuite's "SPARK-9757 Persist Parquet relation with decimal column".

https://issues.apache.org/jira/browse/SPARK-12039

Since it is pretty flaky in hadoop 1 tests, we can disable it while we are investigating the cause.

Author: Yin Huai <yhuai@databricks.com>

Closes #10035 from yhuai/SPARK-12039-ignore.

In https://github.com/apache/spark/pull/9409 we enabled multi-column counting. The approach taken in that PR introduces a bit of overhead by first creating a row only to check if all of the columns are non-null.

This PR fixes that technical debt. Count now takes multiple columns as its input. In order to make this work I have also added support for multiple columns in the single distinct code path.

cc yhuai

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #10015 from hvanhovell/SPARK-12024.

Author: Sun Rui <rui.sun@intel.com>

Closes #9769 from sun-rui/SPARK-11781.

Add support for for colnames, colnames<-, coltypes<-
Also added tests for names, names<- which have no test previously.

I merged with PR 8984 (coltypes). Clicked the wrong thing, crewed up the PR. Recreated it here. Was #9218

shivaram sun-rui

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #9654 from felixcheung/colnamescoltypes.

[SPARK-12029][SPARKR] Improve column functions signature, param check, tests, fix doc and add examples

shivaram sun-rui

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10019 from felixcheung/rfunctionsdoc.

When calling `get_json_object` for the following two cases, both results are `"null"`:

```scala
    val tuple: Seq[(String, String)] = ("5", """{"f1": null}""") :: Nil
    val df: DataFrame = tuple.toDF("key", "jstring")
    val res = df.select(functions.get_json_object($"jstring", "$.f1")).collect()
```
```scala
    val tuple2: Seq[(String, String)] = ("5", """{"f1": "null"}""") :: Nil
    val df2: DataFrame = tuple2.toDF("key", "jstring")
    val res3 = df2.select(functions.get_json_object($"jstring", "$.f1")).collect()
```

Fixed the problem and also added a test case.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #10018 from gatorsmile/get_json_object.

https://issues.apache.org/jira/browse/SPARK-12020

Author: Yin Huai <yhuai@databricks.com>

Closes #10010 from yhuai/SPARK-12020.

In StreamingListenerSuite."don't call ssc.stop in listener", after the main thread calls `ssc.stop()`,  `StreamingContextStoppingCollector` may call  `ssc.stop()` in the listener bus thread, which is a dead-lock. This PR updated `StreamingContextStoppingCollector` to only call `ssc.stop()` in the first batch to avoid the dead-lock.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #10011 from zsxwing/fix-test-deadlock.

Change ```cumeDist -> cume_dist, denseRank -> dense_rank, percentRank -> percent_rank, rowNumber -> row_number``` at SparkR side.
There are two reasons that we should make this change:
* We should follow the [naming convention rule of R](http://www.inside-r.org/node/230645)
* Spark DataFrame has deprecated the old convention (such as ```cumeDist```) and will remove it in Spark 2.0.

It's better to fix this issue before 1.6 release, otherwise we will make breaking API change.
cc shivaram sun-rui

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10016 from yanboliang/SPARK-12025.

Check for partition column null-ability while building the partition spec.

Author: Dilip Biswal <dbiswal@us.ibm.com>

Closes #10001 from dilipbiswal/spark-11997.

If `--private-ips` is required but not provided, spark_ec2.py may behave inappropriately, including attempting to ssh to localhost in attempts to verify ssh connectivity to the cluster.

This fixes that behavior by raising a `UsageError` exception if `get_dns_name` is unable to determine a hostname as a result.

Author: Jeremy Derr <jcderr@radius.com>

Closes #9975 from jcderr/SPARK-11991/ec_spark.py_hostname_check.

Fix regression test for SPARK-11778.
 marmbrus
Could you please take a look?
Thank you very much!!

Author: Huaxin Gao <huaxing@oc0558782468.ibm.com>

Closes #9890 from huaxingao/spark-11778-regression-test.

Author: Jeff Zhang <zjffdu@apache.org>

Closes #9903 from zjffdu/SPARK-11917.

Reference: https://jdbc.postgresql.org/documentation/head/query.html#query-with-cursor
In order for PostgreSQL to honor the fetchSize non-zero setting, its Connection.autoCommit needs to be set to false. Otherwise, it will just quietly ignore the fetchSize setting.

This adds a new side-effecting dialect specific beforeFetch method that will fire before a select query is ran.

Author: mariusvniekerk <marius.v.niekerk@gmail.com>

Closes #9861 from mariusvniekerk/SPARK-11881.

Spark SQL aggregate function:
```Java
stddev
stddev_pop
stddev_samp
variance
var_pop
var_samp
skewness
kurtosis
collect_list
collect_set
```
should support ```columnName``` as arguments like other aggregate function(max/min/count/sum).

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9994 from yanboliang/SPARK-12011.