[SPARK-2062][GraphX] VertexRDD.apply does not use the mergeFunc

VertexRDD.apply had a bug where it ignored the merge function for
duplicate vertices and instead used whichever vertex attribute occurred
first. This commit fixes the bug by passing the merge function through
to ShippableVertexPartition.apply, which merges any duplicates using the
merge function and then fills in missing vertices using the specified
default vertex attribute. This commit also adds a unit test for
VertexRDD.apply.

Author: Larry Xiao <xiaodi@sjtu.edu.cn>
Author: Blie Arkansol <xiaodi@sjtu.edu.cn>
Author: Ankur Dave <ankurdave@gmail.com>

Closes #1903 from larryxiao/2062 and squashes the following commits:

625aa9d [Blie Arkansol] Merge pull request #1 from ankurdave/SPARK-2062
476770b [Ankur Dave] ShippableVertexPartition.initFrom: Don't run mergeFunc on default values
614059f [Larry Xiao] doc update: note about the default null value vertices construction
dfdb3c9 [Larry Xiao] minor fix
1c70366 [Larry Xiao] scalastyle check: wrap line, parameter list indent 4 spaces
e4ca697 [Larry Xiao] [TEST] VertexRDD.apply mergeFunc
6a35ea8 [Larry Xiao] [TEST] VertexRDD.apply mergeFunc
4fbc29c [Blie Arkansol] undo unnecessary change
efae765 [Larry Xiao] fix mistakes: should be able to call with or without mergeFunc
b2422f9 [Larry Xiao] Merge branch '2062' of github.com:larryxiao/spark into 2062
52dc7f7 [Larry Xiao] pass mergeFunc to VertexPartitionBase, where merge is handled
581e9ee [Larry Xiao] TODO: VertexRDDSuite
20d80a3 [Larry Xiao] [SPARK-2062][GraphX] VertexRDD.apply does not use the mergeFunc
MAINTENANCE: Automated closing of pull requests.

This commit exists to close the following pull requests on Github:

Closes #726 (close requested by 'pwendell')
Closes #151 (close requested by 'pwendell')
[SPARK-1701] Clarify slice vs partition in the programming guide

This is a partial solution to SPARK-1701, only addressing the
documentation confusion.

Additional work can be to actually change the numSlices parameter name
across languages, with care required for scala & python to maintain
backward compatibility for named parameters.

Author: Matthew Farrellee <matt@redhat.com>

Closes #2305 from mattf/SPARK-1701 and squashes the following commits:

c0af05d [Matthew Farrellee] Further tweak
06f80fc [Matthew Farrellee] Wording tweak from Josh Rosen's review
7b045e0 [Matthew Farrellee] [SPARK-1701] Clarify slice vs partition in the programming guide
[SPARK-1701] [PySpark] remove slice terminology from python examples

Author: Matthew Farrellee <matt@redhat.com>

Closes #2304 from mattf/SPARK-1701-partition-over-slice-for-python-examples and squashes the following commits:

928a581 [Matthew Farrellee] [SPARK-1701] [PySpark] remove slice terminology from python examples
[SPARK-3491] [MLlib] [PySpark] use pickle to serialize data in MLlib

Currently, we serialize the data between JVM and Python case by case manually, this cannot scale to support so many APIs in MLlib.

This patch will try to address this problem by serialize the data using pickle protocol, using Pyrolite library to serialize/deserialize in JVM. Pickle protocol can be easily extended to support customized class.

All the modules are refactored to use this protocol.

Known issues: There will be some performance regression (both CPU and memory, the serialized data increased)

Author: Davies Liu <davies.liu@gmail.com>

Closes #2378 from davies/pickle_mllib and squashes the following commits:

dffbba2 [Davies Liu] Merge branch 'master' of github.com:apache/spark into pickle_mllib
810f97f [Davies Liu] fix equal of matrix
032cd62 [Davies Liu] add more type check and conversion for user_product
bd738ab [Davies Liu] address comments
e431377 [Davies Liu] fix cache of rdd, refactor
19d0967 [Davies Liu] refactor Picklers
2511e76 [Davies Liu] cleanup
1fccf1a [Davies Liu] address comments
a2cc855 [Davies Liu] fix tests
9ceff73 [Davies Liu] test size of serialized Rating
44e0551 [Davies Liu] fix cache
a379a81 [Davies Liu] fix pickle array in python2.7
df625c7 [Davies Liu] Merge commit '154d141' into pickle_mllib
154d141 [Davies Liu] fix autobatchedpickler
44736d7 [Davies Liu] speed up pickling array in Python 2.7
e1d1bfc [Davies Liu] refactor
708dc02 [Davies Liu] fix tests
9dcfb63 [Davies Liu] fix style
88034f0 [Davies Liu] rafactor, address comments
46a501e [Davies Liu] choose batch size automatically
df19464 [Davies Liu] memorize the module and class name during pickleing
f3506c5 [Davies Liu] Merge branch 'master' into pickle_mllib
722dd96 [Davies Liu] cleanup _common.py
0ee1525 [Davies Liu] remove outdated tests
b02e34f [Davies Liu] remove _common.py
84c721d [Davies Liu] Merge branch 'master' into pickle_mllib
4d7963e [Davies Liu] remove muanlly serialization
6d26b03 [Davies Liu] fix tests
c383544 [Davies Liu] classification
f2a0856 [Davies Liu] mllib/regression
d9f691f [Davies Liu] mllib/util
cccb8b1 [Davies Liu] mllib/tree
8fe166a [Davies Liu] Merge branch 'pickle' into pickle_mllib
aa2287e [Davies Liu] random
f1544c4 [Davies Liu] refactor clustering
52d1350 [Davies Liu] use new protocol in mllib/stat
b30ef35 [Davies Liu] use pickle to serialize data for mllib/recommendation
f44f771 [Davies Liu] enable tests about array
3908f5c [Davies Liu] Merge branch 'master' into pickle
c77c87b [Davies Liu] cleanup debugging code
60e4e2f [Davies Liu] support unpickle array.array for Python 2.6
[SPARK-3501] [SQL] Fix the bug of Hive SimpleUDF creates unnecessary type cast

When do the query like:
```
select datediff(cast(value as timestamp), cast('2002-03-21 00:00:00' as timestamp)) from src;
```
SparkSQL will raise exception:
```
[info] scala.MatchError: TimestampType (of class org.apache.spark.sql.catalyst.types.TimestampType$)
[info] at org.apache.spark.sql.catalyst.expressions.Cast.castToTimestamp(Cast.scala:77)
[info] at org.apache.spark.sql.catalyst.expressions.Cast.cast$lzycompute(Cast.scala:251)
[info] at org.apache.spark.sql.catalyst.expressions.Cast.cast(Cast.scala:247)
[info] at org.apache.spark.sql.catalyst.expressions.Cast.eval(Cast.scala:263)
[info] at org.apache.spark.sql.catalyst.optimizer.ConstantFolding$$anonfun$apply$5$$anonfun$applyOrElse$2.applyOrElse(Optimizer.scala:217)
[info] at org.apache.spark.sql.catalyst.optimizer.ConstantFolding$$anonfun$apply$5$$anonfun$applyOrElse$2.applyOrElse(Optimizer.scala:210)
[info] at org.apache.spark.sql.catalyst.trees.TreeNode.transformDown(TreeNode.scala:144)
[info] at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4$$anonfun$apply$2.apply(TreeNode.scala:180)
[info] at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
[info] at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
```

Author: Cheng Hao <hao.cheng@intel.com>

Closes #2368 from chenghao-intel/cast_exception and squashes the following commits:

5c9c3a5 [Cheng Hao] make more clear code
49dfc50 [Cheng Hao] Add no-op for Cast and revert the position of SimplifyCasts
b804abd [Cheng Hao] Add unit test to show the failure in identical data type casting
330a5c8 [Cheng Hao] Update Code based on comments
b834ed4 [Cheng Hao] Fix bug of HiveSimpleUDF with unnecessary type cast which cause exception in constant folding
[SPARK-2594][SQL] Support CACHE TABLE <name> AS SELECT ...

This feature allows user to add cache table from the select query.
Example : ```CACHE TABLE testCacheTable AS SELECT * FROM TEST_TABLE```
Spark takes this type of SQL as command and it does lazy caching just like ```SQLContext.cacheTable```, ```CACHE TABLE <name>``` does.
It can be executed from both SQLContext and HiveContext.

Recreated the pull request after rebasing with master.And fixed all the comments raised in previous pull requests.
https://github.com/apache/spark/pull/2381
https://github.com/apache/spark/pull/2390

Author : ravipesala ravindra.pesalahuawei.com

Author: ravipesala <ravindra.pesala@huawei.com>

Closes #2397 from ravipesala/SPARK-2594 and squashes the following commits:

a5f0beb [ravipesala] Simplified the code as per Admin comment.
8059cd2 [ravipesala] Changed the behaviour from eager caching to lazy caching.
d6e469d [ravipesala] Code review comments by Admin are handled.
c18aa38 [ravipesala] Merge remote-tracking branch 'remotes/ravipesala/Add-Cache-table-as' into SPARK-2594
394d5ca [ravipesala] Changed style
fb1759b [ravipesala] Updated as per Admin comments
8c9993c [ravipesala] Changed the style
d8b37b2 [ravipesala] Updated as per the comments by Admin
bc0bffc [ravipesala] Merge remote-tracking branch 'ravipesala/Add-Cache-table-as' into Add-Cache-table-as
e3265d0 [ravipesala] Updated the code as per the comments by Admin in pull request.
724b9db [ravipesala] Changed style
aaf5b59 [ravipesala] Added comment
dc33895 [ravipesala] Updated parser to support add cache table command
b5276b2 [ravipesala] Updated parser to support add cache table command
eebc0c1 [ravipesala] Add CACHE TABLE <name> AS SELECT ...
6758f80 [ravipesala] Changed style
7459ce3 [ravipesala] Added comment
13c8e27 [ravipesala] Updated parser to support add cache table command
4e858d8 [ravipesala] Updated parser to support add cache table command
b803fc8 [ravipesala] Add CACHE TABLE <name> AS SELECT ...
[SPARK-3592] [SQL] [PySpark] support applySchema to RDD of Row

Fix the issue when applySchema() to an RDD of Row.

Also add type mapping for BinaryType.

Author: Davies Liu <davies.liu@gmail.com>

Closes #2448 from davies/row and squashes the following commits:

dd220cf [Davies Liu] fix test
3f3f188 [Davies Liu] add more test
f559746 [Davies Liu] add tests, fix serialization
9688fd2 [Davies Liu] support applySchema to RDD of Row
SPARK-3605. Fix typo in SchemaRDD.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #2460 from sryza/sandy-spark-3605 and squashes the following commits:

09d940b [Sandy Ryza] SPARK-3605. Fix typo in SchemaRDD.
[SPARK-3485][SQL] Use GenericUDFUtils.ConversionHelper for Simple UDF type conversions

This is just another solution to SPARK-3485, in addition to PR #2355
In this patch, we will use ConventionHelper and FunctionRegistry to invoke a simple udf evaluation, which rely more on hive, but much cleaner and safer.
We can discuss which one is better.

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #2407 from adrian-wang/simpleudf and squashes the following commits:

15762d2 [Daoyuan Wang] add posmod test which would fail the test but now ok
0d69eb4 [Daoyuan Wang] another way to pass to hive simple udf
[Build] Fix passing of args to sbt

Simple mistake, simple fix:
```shell
args="arg1 arg2 arg3"

sbt $args    # sbt sees 3 arguments
sbt "$args"  # sbt sees 1 argument
```

Should fix the problems we are seeing [here](https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/694/AMPLAB_JENKINS_BUILD_PROFILE=hadoop1.0,label=centos/console), for example.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2462 from nchammas/fix-sbt-master-build and squashes the following commits:

4500c86 [Nicholas Chammas] warn about quoting
10018a6 [Nicholas Chammas] Revert "test hadoop1 build"
7d5356c [Nicholas Chammas] Revert "re-add bad quoting for testing"
061600c [Nicholas Chammas] re-add bad quoting for testing
b2de56c [Nicholas Chammas] test hadoop1 build
43fb854 [Nicholas Chammas] unquote profile args
[Docs] Fix outdated docs for standalone cluster

This is now supported!

Author: andrewor14 <andrewor14@gmail.com>
Author: Andrew Or <andrewor14@gmail.com>

Closes #2461 from andrewor14/document-standalone-cluster and squashes the following commits:

85c8b9e [andrewor14] Wording change per Patrick
35e30ee [Andrew Or] Fix outdated docs for standalone cluster
SPARK-3608 Break if the instance tag naming succeeds

Author: Vida Ha <vida@databricks.com>

Closes #2466 from vidaha/vida/spark-3608 and squashes the following commits:

9509776 [Vida Ha] Break if the instance tag naming succeeds
Fix Java example in Streaming Programming Guide

"val conf" was used instead of "SparkConf conf" in Java snippet.

Author: Santiago M. Mola <santi@mola.io>

Closes #2472 from smola/patch-1 and squashes the following commits:

5bfeb9b [Santiago M. Mola] Fix Java example in Streaming Programming Guide
[PySpark] remove unnecessary use of numSlices from pyspark tests

Author: Matthew Farrellee <matt@redhat.com>

Closes #2467 from mattf/master-pyspark-remove-numslices-from-tests and squashes the following commits:

c49a87b [Matthew Farrellee] [PySpark] remove unnecessary use of numSlices from pyspark tests
SPARK-3574. Shuffle finish time always reported as -1

The included test waits 100 ms after job completion for task completion events to come in so it can verify they have reasonable finish times.  Does anyone know a better way to wait on listener events that are expected to come in?

Author: Sandy Ryza <sandy@cloudera.com>

Closes #2440 from sryza/sandy-spark-3574 and squashes the following commits:

c81439b [Sandy Ryza] Fix test failure
b340956 [Sandy Ryza] SPARK-3574. Remove shuffleFinishTime metric
[SPARK-3609][SQL] Adds sizeInBytes statistics for Limit operator when all output attributes are of native data types

This helps to replace shuffled hash joins with broadcast hash joins in some cases.

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

Closes #2468 from liancheng/more-stats and squashes the following commits:

32687dc [Cheng Lian] Moved the test case to PlannerSuite
5595a91 [Cheng Lian] Removes debugging code
73faf69 [Cheng Lian] Test case for auto choosing broadcast hash join
f30fe1d [Cheng Lian] Adds sizeInBytes estimation for Limit when all output types are native types
[SPARK-3414][SQL] Replace LowerCaseSchema with Resolver

**This PR introduces a subtle change in semantics for HiveContext when using the results in Python or Scala.  Specifically, while resolution remains case insensitive, it is now case preserving.**

_This PR is a follow up to #2293 (and to a lesser extent #2262 #2334)._

In #2293 the catalog was changed to store analyzed logical plans instead of unresolved ones.  While this change fixed the reported bug (which was caused by yet another instance of us forgetting to put in a `LowerCaseSchema` operator) it had the consequence of breaking assumptions made by `MultiInstanceRelation`.  Specifically, we can't replace swap out leaf operators in a tree without rewriting changed expression ids (which happens when you self join the same RDD that has been registered as a temp table).

In this PR, I instead remove the need to insert `LowerCaseSchema` operators at all, by moving the concern of matching up identifiers completely into analysis.  Doing so allows the test cases from both #2293 and #2262 to pass at the same time (and likely fixes a slew of other "unknown unknown" bugs).

While it is rolled back in this PR, storing the analyzed plan might actually be a good idea.  For instance, it is kind of confusing if you register a temporary table, change the case sensitivity of resolution and now you can't query that table anymore.  This can be addressed in a follow up PR.

Follow-ups:
 - Configurable case sensitivity
 - Consider storing analyzed plans for temp tables

Author: Michael Armbrust <michael@databricks.com>

Closes #2382 from marmbrus/lowercase and squashes the following commits:

c21171e [Michael Armbrust] Ensure the resolver is used for field lookups and ensure that case insensitive resolution is still case preserving.
d4320f1 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into lowercase
2de881e [Michael Armbrust] Address comments.
219805a [Michael Armbrust] style
5b93711 [Michael Armbrust] Replace LowerCaseSchema with Resolver.
[SPARK-3599]Avoid loading properties file frequently

https://issues.apache.org/jira/browse/SPARK-3599

Author: WangTao <barneystinson@aliyun.com>
Author: WangTaoTheTonic <barneystinson@aliyun.com>

Closes #2454 from WangTaoTheTonic/avoidLoadingFrequently and squashes the following commits:

3681182 [WangTao] do not use clone
7dca036 [WangTao] use lazy val instead
2a79f26 [WangTaoTheTonic] Avoid loaing properties file frequently
Merge branch 'master' of git://git.apache.org/spark into metrics-structure-improvement2