## What changes were proposed in this pull request?

Change the signature of as.data.frame() to be consistent with that in the R base package to meet R user's convention.

## How was this patch tested?
dev/lint-r
SparkR unit tests

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

Closes #11811 from sun-rui/SPARK-13905.

## What changes were proposed in this pull request?
In SPARK-13063, It makes the SPARK YARN STAGING DIR as configurable. But it only support default FileSystem. If there are many clusters, It can be different FileSystem for different cluster in our spark.

## How was this patch tested?
I have tested it successfully with following commands:
MASTER=yarn-client ./bin/spark-shell --conf spark.yarn.stagingDir=hdfs:namenode2/temp
$SPARK_HOME/bin/spark-submit --conf spark.yarn.stagingDir=hdfs:namenode2/temp

cc tgravescs vanzin andrewor14

Author: Lianhui Wang <lianhuiwang09@gmail.com>

Closes #12473 from lianhuiwang/SPARK-14705.

## What changes were proposed in this pull request?

Enable ScalaReflection and User Defined Types for plain Scala classes.

This involves the move of `schemaFor` from `ScalaReflection` trait (which is Runtime and Compile time (macros) reflection) to the `ScalaReflection` object (runtime reflection only) as I believe this code wouldn't work at compile time anyway as it manipulates `Class`'s that are not compiled yet.

## How was this patch tested?

Unit test

Author: Joan <joan@goyeau.com>

Closes #12149 from joan38/SPARK-13929-Scala-reflection.

[SPARK-14407][SQL] Hides HadoopFsRelation related data source API into execution/datasources package #12178

## What changes were proposed in this pull request?

This PR moves `HadoopFsRelation` related data source API into `execution/datasources` package.

Note that to avoid conflicts, this PR is based on #12153. Effective changes for this PR only consist of the last three commits. Will rebase after merging #12153.

## How was this patch tested?

Existing tests.

Author: Yin Huai <yhuai@databricks.com>
Author: Cheng Lian <lian@databricks.com>

Closes #12361 from liancheng/spark-14407-hide-hadoop-fs-relation.

## What changes were proposed in this pull request?

Change unpersist blocking parameter default value to match Scala

## How was this patch tested?

unit tests, manual tests

jkbradley davies

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #12507 from felixcheung/pyunpersist.

This reverts commit ed2de029.

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.

## What changes were proposed in this pull request?

The current benchmark framework runs a code block for several iterations and reports statistics. However there is no way to exclude per-iteration setup time from the overall results. This PR adds a timer control object passed into the closure that can be used for this purpose.

## How was this patch tested?

Existing benchmark code. Also see https://github.com/apache/spark/pull/12490

Author: Eric Liang <ekl@databricks.com>

Closes #12502 from ericl/spark-14733.

### What changes were proposed in this pull request?
This PR adds support for in/exists predicate subqueries to Spark. Predicate sub-queries are used as a filtering condition in a query (this is the only supported use case). A predicate sub-query comes in two forms:

- `[NOT] EXISTS(subquery)`
- `[NOT] IN (subquery)`

This PR is (loosely) based on the work of davies (https://github.com/apache/spark/pull/10706) and chenghao-intel (https://github.com/apache/spark/pull/9055). They should be credited for the work they did.

### How was this patch tested?
Modified parsing unit tests.
Added tests to `org.apache.spark.sql.SQLQuerySuite`

cc rxin, davies & chenghao-intel

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

Closes #12306 from hvanhovell/SPARK-4226.

## What changes were proposed in this pull request?

This PR adds support for specifying an optional custom coalescer to the `coalesce()` method. Currently I have only added this feature to the `RDD` interface, and once we sort out the details we can proceed with adding this feature to the other APIs (`Dataset` etc.)

## How was this patch tested?

Added a unit test for this functionality.

/cc rxin (per our discussion on the mailing list)

Author: Nezih Yigitbasi <nyigitbasi@netflix.com>

Closes #11865 from nezihyigitbasi/custom_coalesce_policy.

## What changes were proposed in this pull request?
This PR returns correct processor name in ```/proc/cpuinfo``` on Linux from  ```Benchmark.getPorcessorName()```. Now, this return ```Unknown processor```.
Since ```Utils.executeAndGetOutput(Seq("which", "grep"))``` return ```/bin/grep\n```, it is failed to execute ```/bin/grep\n```. This PR strips ```\n``` at the end of the line of a result of ```Utils.executeAndGetOutput()```

Before applying this PR
````
Java HotSpot(TM) 64-Bit Server VM 1.8.0_66-b17 on Linux 2.6.32-504.el6.x86_64
Unknown processor
back-to-back filter:                Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
-------------------------------------------------------------------------------------------
Dataset                                   472 /  503         21.2          47.2       1.0X
DataFrame                                  51 /   58        198.0           5.1       9.3X
RDD                                       189 /  211         52.8          18.9       2.5X
````

After applying this PR
```
Java HotSpot(TM) 64-Bit Server VM 1.8.0_66-b17 on Linux 2.6.32-504.el6.x86_64
Intel(R) Xeon(R) CPU E5-2667 v2  3.30GHz
back-to-back filter:                Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
-------------------------------------------------------------------------------------------
Dataset                                   490 /  502         20.4          49.0       1.0X
DataFrame                                  55 /   61        183.4           5.5       9.0X
RDD                                       210 /  237         47.7          21.0       2.3X
```

## How was this patch tested?
Run Benchmark programs on Linux by hand

Author: Kazuaki Ishizaki <ishizaki@jp.ibm.com>

Closes #12411 from kiszk/SPARK-14656.

## What changes were proposed in this pull request?

After https://github.com/apache/spark/pull/12067, we now use expressions to do the aggregation in `TypedAggregateExpression`. To implement buffer merge, we produce a new buffer deserializer expression by replacing `AttributeReference` with right-side buffer attribute, like other `DeclarativeAggregate`s do, and finally combine the left and right buffer deserializer with `Invoke`.

However, after https://github.com/apache/spark/pull/12338, we will add loop variable to class members when codegen `MapObjects`. If the `Aggregator` buffer type is `Seq`, which is implemented by `MapObjects` expression, we will add the same loop variable to class members twice(by left and right buffer deserializer), which cause the `ClassFormatError`.

This PR fixes this issue by calling `distinct` before declare the class menbers.

## How was this patch tested?

new regression test in `DatasetAggregatorSuite`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12468 from cloud-fan/bug.

When `Await.result` throws an exception which originated from a different thread, the resulting stacktrace doesn't include the path leading to the `Await.result` call itself, making it difficult to identify the impact of these exceptions. For example, I've seen cases where broadcast cleaning errors propagate to the main thread and crash it but the resulting stacktrace doesn't include any of the main thread's code, making it difficult to pinpoint which exception crashed that thread.

This patch addresses this issue by explicitly catching, wrapping, and re-throwing exceptions that are thrown by `Await.result`.

I tested this manually using https://github.com/JoshRosen/spark/commit/16b31c825197ee31a50214c6ba3c1df08148f403, a patch which reproduces an issue where an RPC exception which occurs while unpersisting RDDs manages to crash the main thread without any useful stacktrace, and verified that informative, full stacktraces were generated after applying the fix in this PR.

/cc rxin nongli yhuai anabranch

Author: Josh Rosen <joshrosen@databricks.com>

Closes #12433 from JoshRosen/wrap-and-rethrow-await-exceptions.

#### What changes were proposed in this pull request?
https://github.com/apache/spark/pull/12185 contains the original PR I submitted in https://github.com/apache/spark/pull/10418

However, it misses one of the extended example, a wrong description and a few typos for collection functions. This PR is fix all these issues.

#### How was this patch tested?
The existing test cases already cover it.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #12492 from gatorsmile/expressionUpdate.

## What changes were proposed in this pull request?

This PR adds exit code parameter to exitExecutor() so that caller can specify different exit code.

## How was this patch tested?

Existing test

rxin hbhanawat

Author: tedyu <yuzhihong@gmail.com>

Closes #12457 from tedyu/master.

## What changes were proposed in this pull request?

This PR tries to separate the serialization and deserialization logic from object operators, so that it's easier to eliminate unnecessary serializations in optimizer.

Typed aggregate related operators are special, they will deserialize the input row to multiple objects and it's difficult to simply use a deserializer operator to abstract it, so we still mix the deserialization logic there.

## How was this patch tested?

existing tests and new test in `EliminateSerializationSuite`

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12260 from cloud-fan/encoder.

[SPARK-13681][SPARK-14458][SPARK-14566][SQL] Add back once removed CommitFailureTestRelationSuite and SimpleTextHadoopFsRelationSuite

## What changes were proposed in this pull request?

These test suites were removed while refactoring `HadoopFsRelation` related API. This PR brings them back.

This PR also fixes two regressions:

- SPARK-14458, which causes runtime error when saving partitioned tables using `FileFormat` data sources that are not able to infer their own schemata. This bug wasn't detected by any built-in data sources because all of them happen to have schema inference feature.

- SPARK-14566, which happens to be covered by SPARK-14458 and causes wrong query result or runtime error when
  - appending a Dataset `ds` to a persisted partitioned data source relation `t`, and
  - partition columns in `ds` don't all appear after data columns

## How was this patch tested?

`CommitFailureTestRelationSuite` uses a testing relation that always fails when committing write tasks to test write job cleanup.

`SimpleTextHadoopFsRelationSuite` uses a testing relation to test general `HadoopFsRelation` and `FileFormat` interfaces.

The two regressions are both covered by existing test cases.

Author: Cheng Lian <lian@databricks.com>

Closes #12179 from liancheng/spark-13681-commit-failure-test.

## What changes were proposed in this pull request?

We currently disable codegen for `CaseWhen` if the number of branches is greater than 20 (in CaseWhen.MAX_NUM_CASES_FOR_CODEGEN). It would be better if this value is a non-public config defined in SQLConf.

## How was this patch tested?

Pass the Jenkins tests (including a new testcase `Support spark.sql.codegen.maxCaseBranches option`)

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #12353 from dongjoon-hyun/SPARK-14577.

## What changes were proposed in this pull request?

I have compared non-reserved list in Antlr3 and Antlr4 one by one as well as all the existing keywords defined in Antlr4, added the missing keywords to the non-reserved keywords list.  If we need to support more syntax, we can add more keywords by then.

Any recommendation for the above is welcome.

## How was this patch tested?

I manually checked the keywords one by one. Please let me know if there is a better way to test.

Another thought: I suggest to put all the keywords definition and non-reserved list in order, that will be much easier to check in the future.

Author: bomeng <bmeng@us.ibm.com>

Closes #12191 from bomeng/SPARK-14398.

## What changes were proposed in this pull request?

This is roughly based on the input metrics logic in `SqlNewHadoopRDD`

## How was this patch tested?

Not sure how to write a test, I manually verified it in Spark UI.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12352 from cloud-fan/metrics.

## What changes were proposed in this pull request?

Per rxin's suggestions, this patch renames `upstreams()` to `inputRDDs()` in `WholeStageCodegen` for better implied semantics

## How was this patch tested?

N/A

Author: Sameer Agarwal <sameer@databricks.com>

Closes #12486 from sameeragarwal/codegen-cleanup.

## What changes were proposed in this pull request?

The `doGenCode` method currently takes in an `ExprCode`, mutates it and returns the java code to evaluate the given expression. It should instead just return a new `ExprCode` to avoid passing around mutable objects during code generation.

## How was this patch tested?

Existing Tests

Author: Sameer Agarwal <sameer@databricks.com>

Closes #12483 from sameeragarwal/new-exprcode-2.

WriteAheadLogBasedBlockHandler will currently throw exceptions if its BlockManager `put()` calls fail, even though those calls are only performed as a performance optimization. Instead, it should log and ignore exceptions during that `put()`.

This is a longstanding issue that was masked by an incorrect test case. I think that we haven't noticed this in production because

1. most people probably use a `MEMORY_AND_DISK` storage level, and
2. typically, individual blocks may be small enough relative to the total storage memory such that they're able to evict blocks from previous batches, so `put()` failures here may be rare in practice.

This patch fixes the faulty test and fixes the bug.

/cc tdas

Author: Josh Rosen <joshrosen@databricks.com>

Closes #12484 from JoshRosen/received-block-hadndler-fix.

## What changes were proposed in this pull request?
The sort shuffle manager has been the default since Spark 1.2. It is time to remove the old hash shuffle manager.

## How was this patch tested?
Removed some tests related to the old manager.

Author: Reynold Xin <rxin@databricks.com>

Closes #12423 from rxin/SPARK-14667.

https://issues.apache.org/jira/browse/SPARK-13227

It might confuse the future developers when they use OpenHashMap.apply() with a numeric value type.

null.asInstance[Int], null.asInstance[Long], null.asInstace[Float] and null.asInstance[Double] will return 0/0.0/0L, which might confuse the developer if the value set contains 0/0.0/0L with an existing key

The current patch only adds the comments describing the issue, with the respect to apply the minimum changes to the code base

The more direct, yet more aggressive, approach is use Option as the return type

andrewor14  JoshRosen  any thoughts about how to avoid the potential issue?

Author: CodingCat <zhunansjtu@gmail.com>

Closes #11107 from CodingCat/SPARK-13227.

## What changes were proposed in this pull request?

Move the spark-examples.jar from being in examples/target to examples/target/scala-2.11/jars

## How was this patch tested?

Built distribution to make sure examples jar was being included in the tarball.
Ran run-example to make sure examples were run.

Author: Mark Grover <mark@apache.org>

Closes #12476 from markgrover/spark-14711.

## What changes were proposed in this pull request?

PySpark Param constructors need to pass the TypeConverter argument by name, partly to make sure it is not mistaken for the expectedType arg and partly because we will remove the expectedType arg in 2.1. In several places, this is not being done correctly.

This PR changes all usages in pyspark/ml/ to keyword args.

## How was this patch tested?

Existing unit tests.  I will not test type conversion for every Param unless we really think it necessary.

Also, if you start the PySpark shell and import classes (e.g., pyspark.ml.feature.StandardScaler), then you no longer get this warning:
```
/Users/josephkb/spark/python/pyspark/ml/param/__init__.py:58: UserWarning: expectedType is deprecated and will be removed in 2.1. Use typeConverter instead, as a keyword argument.
  "Use typeConverter instead, as a keyword argument.")
```
That warning came from the typeConverter argument being passes as the expectedType arg by mistake.

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #12480 from jkbradley/typeconverter-fix.

## What changes were proposed in this pull request?
Add the missing python example for ChiSqSelector

## How was this patch tested?
manual tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #12283 from zhengruifeng/chi2_pe.

## What changes were proposed in this pull request?

This PR is a follow up for https://github.com/apache/spark/pull/12417, now we always track input/output/shuffle metrics in spark JSON protocol and status API.

Most of the line changes are because of re-generating the gold answer for `HistoryServerSuite`, and we add a lot of 0 values for read/write metrics.

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #12462 from cloud-fan/follow.

## What changes were proposed in this pull request?

When there are multiple tests running, "NettyBlockTransferServiceSuite.can bind to a specific port twice and the second increments" may fail.

E.g., assume there are 2 tests running. Here are the execution order to reproduce the test failure.

| Execution Order | Test 1 | Test 2 |
| ------------- | ------------- | ------------- |
| 1 | service0 binds to 17634 |  |
| 2 |  | service0 binds to 17635 (17634 is occupied) |
| 3 | service1 binds to 17636 |  |
| 4 | pass test |  |
| 5 | service0.close (release 17634) |  |
| 6 |  | service1 binds to 17634 |
| 7 |  | `service1.port should be (service0.port + 1)` fails (17634 != 17635 + 1) |

Here is an example in Jenkins: https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test/job/spark-master-test-maven-hadoop-2.2/786/testReport/junit/org.apache.spark.network.netty/NettyBlockTransferServiceSuite/can_bind_to_a_specific_port_twice_and_the_second_increments/

This PR makes two changes:

- Use a random port between 17634 and 27634 to reduce the possibility of port conflicts.
- Make `service1` use `service0.port` to bind to avoid the above race condition.

## How was this patch tested?

Jenkins unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #12477 from zsxwing/SPARK-14713.

## What changes were proposed in this pull request?

Enable Oracle docker tests

## How was this patch tested?

Existing tests

Author: Luciano Resende <lresende@apache.org>

Closes #12270 from lresende/oracle.

## What changes were proposed in this pull request?

This is just cleanup. This allows us to remove HiveContext later without inflating the diff too much. This PR fixes the conflicts of https://github.com/apache/spark/pull/12431. It also removes the `def hiveConf` from `HiveSqlParser`. So, we will pass the HiveConf associated with a session explicitly instead of relying on Hive's `SessionState` to pass `HiveConf`.

## How was this patch tested?
Existing tests.

Closes #12431

Author: Andrew Or <andrew@databricks.com>
Author: Yin Huai <yhuai@databricks.com>

Closes #12449 from yhuai/hiveconf.

## What changes were proposed in this pull request?

Per rxin's suggestions, this patch renames `s/gen/genCode` and `s/genCode/doGenCode` to better reflect the semantics of these 2 function calls.

## How was this patch tested?

N/A (refactoring only)

Author: Sameer Agarwal <sameer@databricks.com>

Closes #12475 from sameeragarwal/gencode.

## What changes were proposed in this pull request?

This PR reverts some changes in https://github.com/apache/spark/pull/12413. (please see the discussion in that PR).

from
```scala
    words.foreachRDD { (rdd, time) =>
    ...
```

to
```scala
    words.foreachRDD { (rdd: RDD[String], time: Time) =>
    ...
```

Also, this was discussed in dev-mailing list, [here](http://apache-spark-developers-list.1001551.n3.nabble.com/Question-about-Scala-style-explicit-typing-within-transformation-functions-and-anonymous-val-td17173.html)

## How was this patch tested?

This was tested with `sbt scalastyle`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #12452 from HyukjinKwon/revert-explicit-typing.

## What changes were proposed in this pull request?

https://issues.apache.org/jira/browse/SPARK-14299

Delete duplications in scala/examples/ml.

TrainValidationSplitExample.scala --> ModelSelectionViaTrainValidationSplitExample
CrossValidatorExample.scala --> ModelSelectionViaCrossValidationExample

## How was this patch tested?

Existing tests passed.

(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

Author: Xusen Yin <yinxusen@gmail.com>

Closes #12366 from yinxusen/SPARK-14299-2.

## What changes were proposed in this pull request?

https://issues.apache.org/jira/browse/SPARK-14440

Remove

* PipelineMLWriter
* PipelineMLReader
* PipelineModelMLWriter
* PipelineModelMLReader

and modify comments.

## How was this patch tested?

test with unit test.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #12216 from yinxusen/SPARK-14440.

## What changes were proposed in this pull request?

This patch adds a SharedState that groups state shared across multiple SQLContexts. This is analogous to the SessionState added in SPARK-13526 that groups session-specific state. This cleanup makes the constructors of the contexts simpler and ultimately allows us to remove HiveContext in the near future.

## How was this patch tested?
Existing tests.

Author: Yin Huai <yhuai@databricks.com>

Closes #12463 from yhuai/sharedState.

## What changes were proposed in this pull request?
Added windowSize getter/setter to ML/MLlib

## How was this patch tested?
Added test cases in tests.py under both ML and MLlib

Author: Jason Lee <cjlee@us.ibm.com>

Closes #12428 from jasoncl/SPARK-14564.

## What changes were proposed in this pull request?

Currently, `HiveTypeCoercion.IfCoercion` removes all predicates whose return-type are null. However, some UDFs need evaluations because they are designed to throw exceptions. This PR fixes that to preserve the predicates. Also, `assert_true` is implemented as Spark SQL function.

**Before**
```
scala> sql("select if(assert_true(false),2,3)").head
res2: org.apache.spark.sql.Row = [3]
```

**After**
```
scala> sql("select if(assert_true(false),2,3)").head
... ASSERT_TRUE ...
```

**Hive**
```
hive> select if(assert_true(false),2,3);
OK
Failed with exception java.io.IOException:org.apache.hadoop.hive.ql.metadata.HiveException: ASSERT_TRUE(): assertion failed.
```

## How was this patch tested?

Pass the Jenkins tests (including a new testcase in `HivePlanTest`)

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #12340 from dongjoon-hyun/SPARK-14580.