[SQL] Support transforming TreeNodes with Option children.

Thanks goes to @marmbrus for his implementation.

Author: Michael Armbrust <michael@databricks.com>
Author: Zongheng Yang <zongheng.y@gmail.com>

Closes #1074 from concretevitamin/option-treenode and squashes the following commits:

ef27b85 [Zongheng Yang] Merge pull request #1 from marmbrus/pr/1074
73133c2 [Michael Armbrust] TreeNodes can't be inner classes.
ab78420 [Zongheng Yang] Add a test.
2ccb721 [Michael Armbrust] Add support for transformation of optional children.
[SPARK-937] adding EXITED executor state and not relaunching cleanly exited executors

There seems to be 2 issues.

1. When job is done, driver asks executor to shutdown. However, this clean exit was assigned FAILED executor state by Worker. I introduced EXITED executor state for executors who voluntarily exit (both normal and abnormal exit depending on the exit code).

2. When Master gets notified an executor has exited, it launches another one to replace it, regardless of reason why the executor had exited. When the reason was job has finished, the unnecessary replacement got subsequently killed when App disassociates. This launching and killing of unnecessary executors shows up in the log and is confusing to users. I added check for executor exit status and avoid launching (and subsequent killing) of unnecessary replacements when executors exit cleanly.

One could ask the scheduler to tell Master job is done so that Master wouldn't launch the replacement executor. However, there is a race condition between App telling Master job is done and Worker telling Master an executor had exited. There is no guarantee the former will happen before the later. Instead, I chose to check the exit code when executor exits. If the exit code is 0, I assume executor has been asked to shutdown by driver and Master will not launch replacements.

Due to race condition, it could also happen that (although didn't happen on my local cluster), Master detects App disassociation event before the executor exits by itself. In such cases, the executor will be rightfully killed and labeled as KILLED, while the App state will show FINISHED.

Author: Kan Zhang <kzhang@apache.org>

Closes #306 from kanzhang/SPARK-1118 and squashes the following commits:

cb0cc86 [Kan Zhang] [SPARK-937] adding EXITED executor state and not relaunching cleanly exited executors
SPARK-1999: StorageLevel in storage tab and RDD Storage Info never changes

StorageLevel in 'storage tab' and 'RDD Storage Info' never changes even if you call rdd.unpersist() and then you give the rdd another different storage level.

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #968 from CrazyJvm/ui-storagelevel and squashes the following commits:

62555fa [CrazyJvm] change RDDInfo constructor param 'storageLevel' to var, so there's need to add another variable _storageLevel。
9f1571e [CrazyJvm] JIRA https://issues.apache.org/jira/browse/SPARK-1999 UI : StorageLevel in storage tab and RDD Storage Info never changes
SPARK-2148 Add link to requirements for custom equals() and hashcode() methods

https://issues.apache.org/jira/browse/SPARK-2148

Author: Andrew Ash <andrew@andrewash.com>

Closes #1092 from ash211/SPARK-2148 and squashes the following commits:

93513df [Andrew Ash] SPARK-2148 Add link to requirements for custom equals() and hashcode() methods
Updating docs to include missing information about reducers and clarify ...

...how the OFFHEAP storage level works (there has been confusion around this).

Author: Ali Ghodsi <alig@cs.berkeley.edu>

Closes #1089 from alig/master and squashes the following commits:

ca8114d [Ali Ghodsi] Updating docs to include missing information about reducers and clarify how the OFFHEAP storage level works (there has been confusion around this).
SPARK-2039: apply output dir existence checking for all output formats

https://issues.apache.org/jira/browse/SPARK-2039

apply output dir existence checking for all output formats

Author: CodingCat <zhunansjtu@gmail.com>

Closes #1088 from CodingCat/SPARK-2039 and squashes the following commits:

c52747a [CodingCat] apply output dir existence checking for all output formats
[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.
SPARK-1063 Add .sortBy(f) method on RDD

This never got merged from the apache/incubator-spark repo (which is now deleted) but there had been several rounds of code review on this PR there.

I think this is ready for merging.

Author: Andrew Ash <andrew@andrewash.com>

This patch had conflicts when merged, resolved by
Committer: Reynold Xin <rxin@apache.org>

Closes #369 from ash211/sortby and squashes the following commits:

d09147a [Andrew Ash] Fix Ordering import
43d0a53 [Andrew Ash] Fix missing .collect()
29a54ed [Andrew Ash] Re-enable test by converting to a closure
5a95348 [Andrew Ash] Add license for RDDSuiteUtils
64ed6e3 [Andrew Ash] Remove leaked diff
d4de69a [Andrew Ash] Remove scar tissue
63638b5 [Andrew Ash] Add Python version of .sortBy()
45e0fde [Andrew Ash] Add Java version of .sortBy()
adf84c5 [Andrew Ash] Re-indent to keep line lengths under 100 chars
9d9b9d8 [Andrew Ash] Use parentheses on .collect() calls
0457b69 [Andrew Ash] Ignore failing test
99f0baf [Andrew Ash] Merge branch 'master' into sortby
222ae97 [Andrew Ash] Try moving Ordering objects out to a different class
3fd0dd3 [Andrew Ash] Add (failing) test for sortByKey with explicit Ordering
b8b5bbc [Andrew Ash] Align remove extra spaces that were used to align ='s in test code
8c53298 [Andrew Ash] Actually use ascending and numPartitions parameters
381eef2 [Andrew Ash] Correct silly typo
7db3e84 [Andrew Ash] Support ascending and numPartitions params in sortBy()
0f685fd [Andrew Ash] Merge remote-tracking branch 'origin/master' into sortby
ca4490d [Andrew Ash] Add .sortBy(f) method on RDD
SPARK-2146.  Fix takeOrdered doc

Removes Python syntax in Scaladoc, corrects result in Scaladoc, and removes irrelevant cache() call in Python doc.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1086 from sryza/sandy-spark-2146 and squashes the following commits:

185ff18 [Sandy Ryza] Use Seq instead of Array
c996120 [Sandy Ryza] SPARK-2146.  Fix takeOrdered doc
SPARK-2038: rename "conf" parameters in the saveAsHadoop functions

to distinguish with SparkConf object

https://issues.apache.org/jira/browse/SPARK-2038

Author: CodingCat <zhunansjtu@gmail.com>

Closes #1087 from CodingCat/SPARK-2038 and squashes the following commits:

763975f [CodingCat] style fix
d91288d [CodingCat] rename "conf" parameters in the saveAsHadoop functions