[SPARK-1977][MLLIB] register mutable BitSet in MovieLenseALS

Author: Neville Li <neville@spotify.com>

Closes #1319 from nevillelyh/gh/SPARK-1977 and squashes the following commits:

1f0a355 [Neville Li] [SPARK-1977][MLLIB] register mutable BitSet in MovieLenseALS
[SPARK-2339][SQL] SQL parser in sql-core is case sensitive, but a table alias is converted to lower case when we create Subquery

Reported by http://apache-spark-user-list.1001560.n3.nabble.com/Spark-SQL-Join-throws-exception-td8599.html
After we get the table from the catalog, because the table has an alias, we will temporarily insert a Subquery. Then, we convert the table alias to lower case no matter if the parser is case sensitive or not.
To see the issue ...
```
val sqlContext = new org.apache.spark.sql.SQLContext(sc)
import sqlContext.createSchemaRDD

case class Person(name: String, age: Int)

val people = sc.textFile("examples/src/main/resources/people.txt").map(_.split(",")).map(p => Person(p(0), p(1).trim.toInt))
people.registerAsTable("people")

sqlContext.sql("select PEOPLE.name from people PEOPLE")
```
The plan is ...
```
== Query Plan ==
Project ['PEOPLE.name]
 ExistingRdd [name#0,age#1], MapPartitionsRDD[4] at mapPartitions at basicOperators.scala:176
```
You can find that `PEOPLE.name` is not resolved.

This PR introduces three changes.
1.  If a table has an alias, the catalog will not lowercase the alias. If a lowercase alias is needed, the analyzer will do the work.
2.  A catalog has a new val caseSensitive that indicates if this catalog is case sensitive or not. For example, a SimpleCatalog is case sensitive, but
3.  Corresponding unit tests.
With this PR, case sensitivity of database names and table names is handled by the catalog. Case sensitivity of other identifiers are handled by the analyzer.

JIRA: https://issues.apache.org/jira/browse/SPARK-2339

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1317 from yhuai/SPARK-2339 and squashes the following commits:

12d8006 [Yin Huai] Handling case sensitivity correctly. This patch introduces three changes. 1. If a table has an alias, the catalog will not lowercase the alias. If a lowercase alias is needed, the analyzer will do the work. 2. A catalog has a new val caseSensitive that indicates if this catalog is case sensitive or not. For example, a SimpleCatalog is case sensitive, but 3. Corresponding unit tests. With this patch, case sensitivity of database names and table names is handled by the catalog. Case sensitivity of other identifiers is handled by the analyzer.
[SPARK-2386] [SQL] RowWriteSupport should use the exact types to cast.

When execute `saveAsParquetFile` with non-primitive type, `RowWriteSupport` uses wrong type `Int` for `ByteType` and `ShortType`.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #1315 from ueshin/issues/SPARK-2386 and squashes the following commits:

20d89ec [Takuya UESHIN] Use None instead of null.
bd88741 [Takuya UESHIN] Add a test.
323d1d2 [Takuya UESHIN] Modify RowWriteSupport to use the exact types to cast.
[SPARK-2375][SQL] JSON schema inference may not resolve type conflicts correctly for a field inside an array of structs

For example, for
```
{"array": [{"field":214748364700}, {"field":1}]}
```
the type of field is resolved as IntType. While, for
```
{"array": [{"field":1}, {"field":214748364700}]}
```
the type of field is resolved as LongType.

JIRA: https://issues.apache.org/jira/browse/SPARK-2375

Author: Yin Huai <huaiyin.thu@gmail.com>

Closes #1308 from yhuai/SPARK-2375 and squashes the following commits:

3e2e312 [Yin Huai] Update unit test.
1b2ff9f [Yin Huai] Merge remote-tracking branch 'upstream/master' into SPARK-2375
10794eb [Yin Huai] Correctly resolve the type of a field inside an array of structs.
[SPARK-2376][SQL] Selecting list values inside nested JSON objects raises java.lang.IllegalArgumentException

JIRA: https://issues.apache.org/jira/browse/SPARK-2376

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1320 from yhuai/SPARK-2376 and squashes the following commits:

0107417 [Yin Huai] Merge remote-tracking branch 'upstream/master' into SPARK-2376
480803d [Yin Huai] Correctly handling JSON arrays in PySpark.
[SPARK-2235][SQL]Spark SQL basicOperator add Intersect operator

Hi all,
I want to submit a basic operator Intersect
For example , in sql case
select * from table1
intersect
select * from table2
So ,i want use this operator support this function in Spark SQL
This operator will return the  the intersection of SparkPlan child table RDD .
JIRA:https://issues.apache.org/jira/browse/SPARK-2235

Author: Yanjie Gao <gaoyanjie55@163.com>
Author: YanjieGao <396154235@qq.com>

Closes #1150 from YanjieGao/patch-5 and squashes the following commits:

4629afe [YanjieGao] reformat the code
bdc2ac0 [YanjieGao] reformat the code as Michael's suggestion
3b29ad6 [YanjieGao] Merge remote branch 'upstream/master' into patch-5
1cfbfe6 [YanjieGao] refomat some files
ea78f33 [YanjieGao] resolve conflict and add annotation on basicOperator and remove HiveQl
0c7cca5 [YanjieGao] modify format problem
a802ca8 [YanjieGao] Merge remote branch 'upstream/master' into patch-5
5e374c7 [YanjieGao] resolve conflict in SparkStrategies and basicOperator
f7961f6 [Yanjie Gao] update the line less than
bdc4a05 [Yanjie Gao] Update basicOperators.scala
0b49837 [Yanjie Gao] delete the annotation
f1288b4 [Yanjie Gao] delete annotation
e2b64be [Yanjie Gao] Update basicOperators.scala
4dd453e [Yanjie Gao] Update SQLQuerySuite.scala
790765d [Yanjie Gao] Update SparkStrategies.scala
ac73e60 [Yanjie Gao] Update basicOperators.scala
d4ac5e5 [Yanjie Gao] Update HiveQl.scala
61e88e7 [Yanjie Gao] Update SqlParser.scala
469f099 [Yanjie Gao] Update basicOperators.scala
e5bff61 [Yanjie Gao] Spark SQL basicOperator add Intersect operator
Updated programming-guide.md

Made sure that readers know the random number generator seed argument, within the 'takeSample' method, is optional.

Author: Rishi Verma <riverma@apache.org>

Closes #1324 from riverma/patch-1 and squashes the following commits:

4699676 [Rishi Verma] Updated programming-guide.md
Resolve sbt warnings during build Ⅱ

Author: witgo <witgo@qq.com>

Closes #1153 from witgo/expectResult and squashes the following commits:

97541d8 [witgo] merge master
ead26e7 [witgo] Resolve sbt warnings during build
[SPARK-2391][SQL] Custom take() for LIMIT queries.

Using Spark's take can result in an entire in-memory partition to be shipped in order to retrieve a single row.

Author: Michael Armbrust <michael@databricks.com>

Closes #1318 from marmbrus/takeLimit and squashes the following commits:

77289a5 [Michael Armbrust] Update scala doc
32f0674 [Michael Armbrust] Custom take implementation for LIMIT queries.
[EC2] Add default history server port to ec2 script

Right now I have to open it manually

Author: Andrew Or <andrewor14@gmail.com>

Closes #1296 from andrewor14/hist-serv-port and squashes the following commits:

8895a1f [Andrew Or] Add default history server port to ec2 script
[SPARK-2395][SQL] Optimize common LIKE patterns.

Author: Michael Armbrust <michael@databricks.com>

Closes #1325 from marmbrus/slowLike and squashes the following commits:

023c3eb [Michael Armbrust] add comment.
8b421c2 [Michael Armbrust] Handle the case where the final % is actually escaped.
d34d37e [Michael Armbrust] add periods.
3bbf35f [Michael Armbrust] Roll back changes to SparkBuild
53894b1 [Michael Armbrust] Fix grammar.
4094462 [Michael Armbrust] Fix grammar.
6d3d0a0 [Michael Armbrust] Optimize common LIKE patterns.
[SPARK-2403] Catch all errors during serialization in DAGScheduler

https://issues.apache.org/jira/browse/SPARK-2403

Spark hangs for us whenever we forget to register a class with Kryo. This should be a simple fix for that. But let me know if you have a better suggestion.

I did not write a new test for this. It would be pretty complicated and I'm not sure it's worthwhile for such a simple change. Let me know if you disagree.

Author: Daniel Darabos <darabos.daniel@gmail.com>

Closes #1329 from darabos/spark-2403 and squashes the following commits:

3aceaad [Daniel Darabos] Print full stack trace for miscellaneous exceptions during serialization.
52c22ba [Daniel Darabos] Only catch NonFatal exceptions.
361e962 [Daniel Darabos] Catch all errors during serialization in DAGScheduler.
SPARK-2400 : fix spark.yarn.max.executor.failures explaination

According to
```scala
  private val maxNumExecutorFailures = sparkConf.getInt("spark.yarn.max.executor.failures",
    sparkConf.getInt("spark.yarn.max.worker.failures", math.max(args.numExecutors * 2, 3)))
```
default value should be numExecutors * 2, with minimum of 3,  and it's same to the config
`spark.yarn.max.worker.failures`

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #1282 from CrazyJvm/yarn-doc and squashes the following commits:

1a5f25b [CrazyJvm] remove deprecated config
c438aec [CrazyJvm] fix style
86effa6 [CrazyJvm] change expression
211f130 [CrazyJvm] fix html tag
2900d23 [CrazyJvm] fix style
a4b2e27 [CrazyJvm] fix configuration spark.yarn.max.executor.failures
[SPARK-2409] Make SQLConf thread safe.

Author: Reynold Xin <rxin@apache.org>

Closes #1334 from rxin/sqlConfThreadSafetuy and squashes the following commits:

c1e0a5a [Reynold Xin] Fixed the duplicate comment.
7614372 [Reynold Xin] [SPARK-2409] Make SQLConf thread safe.
[SPARK-2362] Fix for newFilesOnly logic in file DStream

The newFilesOnly logic should be inverted: the logic should be that if the flag newFilesOnly==true then only start reading files older than current time. As the code is now if newFilesOnly==true then it will start to read files that are older than 0L (that is: every file in the directory).

Author: Gabriele Nizzoli <mail@nizzoli.net>

Closes #1077 from gabrielenizzoli/master and squashes the following commits:

4f1d261 [Gabriele Nizzoli] Fix for newFilesOnly logic in file DStream
[SPARK-2392] Executors should not start their own HTTP servers

Executors currently start their own unused HTTP file servers. This is because we use the same SparkEnv class for both executors and drivers, and we do not distinguish this case.

In the longer term, we should separate out SparkEnv for the driver and SparkEnv for the executors.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1335 from andrewor14/executor-http-server and squashes the following commits:

46ef263 [Andrew Or] Start HTTP server only on the driver
[SPARK-2413] Upgrade junit_xml_listener to 0.5.1

which fixes the following issues

1) fix the class name to be fully qualified classpath
2) make sure the the reporting time is in second not in miliseond, which causing JUnit HTML to report incorrect number
3) make sure the duration of the tests are accumulative.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #1333 from dbtsai/dbtsai-junit and squashes the following commits:

bbeac4b [DB Tsai] Upgrade junit_xml_listener to 0.5.1 which fixes the following issues
[SPARK-2152][MLlib] fix bin offset in DecisionTree node aggregations (also resolves SPARK-2160)

Hi, this pull fixes (what I believe to be) a bug in DecisionTree.scala.

In the extractLeftRightNodeAggregates function, the first set of rightNodeAgg values for Regression are set in line 792 as follows:

rightNodeAgg(featureIndex)(2 * (numBins - 2))
  = binData(shift + (2 * numBins - 1)))

Then there is a loop that sets the rest of the values, as in line 809:

rightNodeAgg(featureIndex)(2 * (numBins - 2 - splitIndex)) =
  binData(shift + (2 *(numBins - 2 - splitIndex))) +
  rightNodeAgg(featureIndex)(2 * (numBins - 1 - splitIndex))

But since splitIndex starts at 1, this ends up skipping a set of binData values.

The changes here address this issue, for both the Regression and Classification cases.

Author: johnnywalleye <jsondag@gmail.com>

Closes #1316 from johnnywalleye/master and squashes the following commits:

73809da [johnnywalleye] fix bin offset in DecisionTree node aggregations
[SPARK-2384] Add tooltips to UI.

This patch adds tooltips to clarify some points of confusion in the UI.  When users mouse over some of the table headers (shuffle read, write, and input size) as well as over the "scheduler delay" metric shown for each stage, a black tool tip (see image below) pops up describing the metric in more detail.  After the tooltip mechanism is added by this commit, I imagine others may want to add more tooltips for other things in the UI, but I think this is a good starting point.

![tooltip](https://cloud.githubusercontent.com/assets/1108612/3491905/994e179e-059f-11e4-92f2-c6c12d248d81.jpg)

This looks scary-big but much of it is adding the bootstrap tool tip JavaScript.

Also I have no idea what to put for the license in tooltip (I left it the same -- the Twitter apache header) or for JQuery (left it as nothing) -- @mateiz what's the right thing here?

cc @pwendell @andrewor14 @rxin

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1314 from kayousterhout/tooltips and squashes the following commits:

19981b5 [Kay Ousterhout] Exclude non-licensed javascript files from style check
d9ab5a9 [Kay Ousterhout] Response to Andrew's review
7752449 [Kay Ousterhout] [SPARK-2384] Add tooltips to UI.
[STREAMING] SPARK-2343: Fix QueueInputDStream with oneAtATime false

Fix QueueInputDStream which was not removing dequeued items when used with the oneAtATime flag disabled.

Author: Manuel Laflamme <manuel.laflamme@gmail.com>

Closes #1285 from mlaflamm/spark-2343 and squashes the following commits:

61c9e38 [Manuel Laflamme] Unit tests for queue input stream
c51d029 [Manuel Laflamme] Fix QueueInputDStream with oneAtATime false