[SPARK-2010] Support for nested data in PySpark SQL

JIRA issue https://issues.apache.org/jira/browse/SPARK-2010

This PR adds support for nested collection types in PySpark SQL, including
array, dict, list, set, and tuple. Example,

```
>>> from array import array
>>> from pyspark.sql import SQLContext
>>> sqlCtx = SQLContext(sc)
>>> rdd = sc.parallelize([
...         {"f1" : array('i', [1, 2]), "f2" : {"row1" : 1.0}},
...         {"f1" : array('i', [2, 3]), "f2" : {"row2" : 2.0}}])
>>> srdd = sqlCtx.inferSchema(rdd)
>>> srdd.collect() == [{"f1" : array('i', [1, 2]), "f2" : {"row1" : 1.0}},
...                    {"f1" : array('i', [2, 3]), "f2" : {"row2" : 2.0}}]
True
>>> rdd = sc.parallelize([
...         {"f1" : [[1, 2], [2, 3]], "f2" : set([1, 2]), "f3" : (1, 2)},
...         {"f1" : [[2, 3], [3, 4]], "f2" : set([2, 3]), "f3" : (2, 3)}])
>>> srdd = sqlCtx.inferSchema(rdd)
>>> srdd.collect() == \
... [{"f1" : [[1, 2], [2, 3]], "f2" : set([1, 2]), "f3" : (1, 2)},
...  {"f1" : [[2, 3], [3, 4]], "f2" : set([2, 3]), "f3" : (2, 3)}]
True
```

Author: Kan Zhang <kzhang@apache.org>

Closes #1041 from kanzhang/SPARK-2010 and squashes the following commits:

1b2891d [Kan Zhang] [SPARK-2010] minor doc change and adding a TODO
504f27e [Kan Zhang] [SPARK-2010] Support for nested data in PySpark SQL
[SPARK-1930] The Container is running beyond physical memory limits, so as to be killed

Author: witgo <witgo@qq.com>

Closes #894 from witgo/SPARK-1930 and squashes the following commits:

564307e [witgo] Update the running-on-yarn.md
3747515 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1930
172647b [witgo] add memoryOverhead docs
a0ff545 [witgo] leaving only two configs
a17bda2 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1930
478ca15 [witgo] Merge branch 'master' into SPARK-1930
d1244a1 [witgo] Merge branch 'master' into SPARK-1930
8b967ae [witgo] Merge branch 'master' into SPARK-1930
655a820 [witgo] review commit
71859a7 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1930
e3c531d [witgo] review commit
e16f190 [witgo] different memoryOverhead
ffa7569 [witgo] review commit
5c9581f [witgo] Merge branch 'master' into SPARK-1930
9a6bcf2 [witgo] review commit
8fae45a [witgo] fix NullPointerException
e0dcc16 [witgo] Adding  configuration items
b6a989c [witgo] Fix container memory beyond limit, were killed
[SQL][SPARK-2094] Follow up of PR #1071 for Java API

Updated `JavaSQLContext` and `JavaHiveContext` similar to what we've done to `SQLContext` and `HiveContext` in PR #1071. Added corresponding test case for Spark SQL Java API.

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

Closes #1085 from liancheng/spark-2094-java and squashes the following commits:

29b8a51 [Cheng Lian] Avoided instantiating JavaSparkContext & JavaHiveContext to workaround test failure
92bb4fb [Cheng Lian] Marked test cases in JavaHiveQLSuite with "ignore"
22aec97 [Cheng Lian] Follow up of PR #1071 for Java API
Minor fix: made "EXPLAIN" output to play well with JDBC output format

Fixed the broken JDBC output. Test from Shark `beeline`:

```
beeline> !connect jdbc:hive2://localhost:10000/
scan complete in 2ms
Connecting to jdbc:hive2://localhost:10000/
Enter username for jdbc:hive2://localhost:10000/: lian
Enter password for jdbc:hive2://localhost:10000/:
Connected to: Hive (version 0.12.0)
Driver: Hive (version 0.12.0)
Transaction isolation: TRANSACTION_REPEATABLE_READ
0: jdbc:hive2://localhost:10000/>
0: jdbc:hive2://localhost:10000/> explain select * from src;
+-------------------------------------------------------------------------------+
|                                     plan                                      |
+-------------------------------------------------------------------------------+
| ExplainCommand [plan#2:0]                                                     |
|  HiveTableScan [key#0,value#1], (MetastoreRelation default, src, None), None  |
+-------------------------------------------------------------------------------+
2 rows selected (1.386 seconds)
```

Before this change, the output looked something like this:

```
+-------------------------------------------------------------------------------+
|                                     plan                                      |
+-------------------------------------------------------------------------------+
| ExplainCommand [plan#2:0]
 HiveTableScan [key#0,value#1], (MetastoreRelation default, src, None), None  |
+-------------------------------------------------------------------------------+
```

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

Closes #1097 from liancheng/multiLineExplain and squashes the following commits:

eb37967 [Cheng Lian] Made output of "EXPLAIN" play well with JDBC output format
MLlib documentation fix

Synchronized mllib-optimization.md with Spark Scaladoc: removed reference to GradientDescent.runMiniBatchSGD method

This is a temporary fix to remove  a link from http://spark.apache.org/docs/latest/mllib-optimization.html to GradientDescent.runMiniBatchSGD which is not in the current online GradientDescent Scaladoc.
FIXME: revert this commit after GradientDescent Scaladoc is updated.
See images for details.

![mllib-docs-fix-1](https://cloud.githubusercontent.com/assets/1375501/3294410/ccf19bb8-f5a8-11e3-93f1-f593016209eb.png)
![mllib-docs-fix-2](https://cloud.githubusercontent.com/assets/1375501/3294411/d0b59a7e-f5a8-11e3-8fc8-329c177ef8c8.png)

Author: Anatoli Fomenko <fa@apache.org>

Closes #1098 from afomenko/master and squashes the following commits:

5cb0758 [Anatoli Fomenko] MLlib documentation fix
[SPARK-2130] End-user friendly String repr for StorageLevel in Python

JIRA issue https://issues.apache.org/jira/browse/SPARK-2130

This PR adds an end-user friendly String representation for StorageLevel
in Python, similar to ```StorageLevel.description``` in Scala.
```
>>> rdd = sc.parallelize([1,2])
>>> storage_level = rdd.getStorageLevel()
>>> storage_level
StorageLevel(False, False, False, False, 1)
>>> print(storage_level)
Serialized 1x Replicated
```

Author: Kan Zhang <kzhang@apache.org>

Closes #1096 from kanzhang/SPARK-2130 and squashes the following commits:

7c8b98b [Kan Zhang] [SPARK-2130] Prettier epydoc output
cc5bf45 [Kan Zhang] [SPARK-2130] End-user friendly String representation for StorageLevel in Python
SPARK-1990: added compatibility for python 2.6 for ssh_read command

https://issues.apache.org/jira/browse/SPARK-1990

There were some posts on the lists that spark-ec2 does not work with Python 2.6. In addition, we should check the Python version at the top of the script and exit if it's too old

Author: Anant <anant.asty@gmail.com>

Closes #941 from anantasty/SPARK-1990 and squashes the following commits:

4ca441d [Anant] Implmented check_optput withinthe module to work with python 2.6
c6ed85c [Anant] added compatibility for python 2.6 for ssh_read command
SPARK-2035: Store call stack for stages, display it on the UI.

I'm not sure about the test -- I get a lot of unrelated failures for some reason. I'll try to sort it out. But hopefully the automation will test this for me if I send a pull request :).

I'll attach a demo HTML in [Jira](https://issues.apache.org/jira/browse/SPARK-2035).

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

Closes #981 from darabos/darabos-call-stack and squashes the following commits:

f7c6bfa [Daniel Darabos] Fix bad merge. I undid 83c226d454 by Doris.
3d0a48d [Daniel Darabos] Merge remote-tracking branch 'upstream/master' into darabos-call-stack
b857849 [Daniel Darabos] Style: Break long line.
ecb5690 [Daniel Darabos] Include the last Spark method in the full stack trace. Otherwise it is not visible if the stage name is overridden.
d00a85b [Patrick Wendell] Make call sites for stages non-optional and well defined
b9eba24 [Daniel Darabos] Make StageInfo.details non-optional. Add JSON serialization code for the new field. Verify JSON backward compatibility.
4312828 [Daniel Darabos] Remove Mima excludes for CallSite. They should be unnecessary now, with SPARK-2070 fixed.
0920750 [Daniel Darabos] Merge remote-tracking branch 'upstream/master' into darabos-call-stack
a4b1faf [Daniel Darabos] Add Mima exclusions for the CallSite changes it has picked up. They are private methods/classes, so we ought to be safe.
932f810 [Daniel Darabos] Use empty CallSite instead of null in DAGSchedulerSuite. Outside of testing, this parameter always originates in SparkContext.scala, and will never be null.
ccd89d1 [Daniel Darabos] Fix long lines.
ac173e4 [Daniel Darabos] Hide "show details" if there are no details to show.
6182da6 [Daniel Darabos] Set a configurable limit on maximum call stack depth. It can be useful in memory-constrained situations with large numbers of stages.
8fe2e34 [Daniel Darabos] Store call stack for stages, display it on the UI.
[SPARK-2144] ExecutorsPage reports incorrect # of RDD blocks

This is reproducible whenever we drop a block because of memory pressure.

This is because StorageStatusListener actually never removes anything from the block maps of its StorageStatuses. Instead, when a block is dropped, it sets the block's storage level to `StorageLevel.NONE`, when it should just remove it from the map.

This PR includes this simple fix.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1080 from andrewor14/ui-blocks and squashes the following commits:

fcf9f1a [Andrew Or] Remove BlockStatus if it is no longer cached
[SPARK-2164][SQL] Allow Hive UDF on columns of type struct

Author: Xi Liu <xil@conviva.com>

Closes #796 from xiliu82/sqlbug and squashes the following commits:

328dfc4 [Xi Liu] [Spark SQL] remove a temporary function after test
354386a [Xi Liu] [Spark SQL] add test suite for UDF on struct
8fc6f51 [Xi Liu] [SparkSQL] allow UDF on struct
[SPARK-2053][SQL] Add Catalyst expressions for CASE WHEN.

JIRA ticket: https://issues.apache.org/jira/browse/SPARK-2053

This PR adds support for two types of CASE statements present in Hive. The first type is of the form `CASE WHEN a THEN b [WHEN c THEN d]* [ELSE e] END`, with the semantics like a chain of if statements. The second type is of the form `CASE a WHEN b THEN c [WHEN d THEN e]* [ELSE f] END`, with the semantics like a switch statement on key `a`. Both forms are implemented in `CaseWhen`.

[This link](https://cwiki.apache.org/confluence/display/Hive/LanguageManual+UDF#LanguageManualUDF-ConditionalFunctions) contains more detailed descriptions on their semantics.

Notes / Open issues:

* Please check if any implicit contracts / invariants are broken in the implementations (especially for the operators). I am not very familiar with them and I currently find them tricky to spot.
* We should decide whether or not a non-boolean condition is allowed in a branch of `CaseWhen`. Hive throws a `SemanticException` for this situation and I think it'd be good to mimic it -- the question is where in the whole Spark SQL pipeline should we signal an exception for such a query.

Author: Zongheng Yang <zongheng.y@gmail.com>

Closes #1055 from concretevitamin/caseWhen and squashes the following commits:

4226eb9 [Zongheng Yang] Comment.
79d26fc [Zongheng Yang] Merge branch 'master' into caseWhen
caf9383 [Zongheng Yang] Update a FIXME.
9d26ab8 [Zongheng Yang] Add @transient marker.
788a0d9 [Zongheng Yang] Implement CastNulls, which fixes udf_case and udf_when.
7ef284f [Zongheng Yang] Refactors: remove redundant passes, improve toString, mark transient.
f47ae7b [Zongheng Yang] Modify queries in tests to have shorter golden files.
1c1fbfc [Zongheng Yang] Cleanups per review comments.
7d2b7e2 [Zongheng Yang] Translate CaseKeyWhen to CaseWhen at parsing time.
47d406a [Zongheng Yang] Do toArray once and lazily outside of eval().
bb3d109 [Zongheng Yang] Update scaladoc of a method.
aea3195 [Zongheng Yang] Fix bug that branchesArr is not used; remove unused import.
96870a8 [Zongheng Yang] Turn off scalastyle for some comments.
7392f3a [Zongheng Yang] Minor cleanup.
2cf08bb [Zongheng Yang] Merge branch 'master' into caseWhen
9f84b40 [Zongheng Yang] Add golden outputs from Hive.
db51a85 [Zongheng Yang] Add allCondBooleans check; uncomment tests.
3f9ef0a [Zongheng Yang] Cleanups and bug fixes (mainly in eval() and resolved).
be54bc8 [Zongheng Yang] Rewrite eval() to a low-level implementation. Separate two CASE stmts.
f2bcb9d [Zongheng Yang] WIP
5906f75 [Zongheng Yang] WIP
efd019b [Zongheng Yang] eval() and toString() bug fixes.
7d81e95 [Zongheng Yang] Clean up resolved.
a31d782 [Zongheng Yang] Finish up Case.