SPARK-1898: In deploy.yarn.Client, use YarnClient not YarnClientImpl

https://issues.apache.org/jira/browse/SPARK-1898

Author: Colin Patrick McCabe <cmccabe@cloudera.com>

Closes #850 from cmccabe/master and squashes the following commits:

d66eddc [Colin Patrick McCabe] SPARK-1898: In deploy.yarn.Client, use YarnClient rather than YarnClientImpl
SPARK-1628: Add missing hashCode methods in Partitioner subclasses

JIRA: https://issues.apache.org/jira/browse/SPARK-1628

Added `hashCode` in HashPartitioner, RangePartitioner, PythonPartitioner and PageRankUtils.CustomPartitioner.

Author: zsxwing <zsxwing@gmail.com>

Closes #549 from zsxwing/SPARK-1628 and squashes the following commits:

2620936 [zsxwing] SPARK-1628: Add missing hashCode methods in Partitioner subclasses
Update run-example

Old code can only be ran under spark_home and use "bin/run-example".
 Error "./run-example: line 55: ./bin/spark-submit: No such file or directory" appears when running in other place. So change this

Author: maji2014 <maji3@asiainfo-linkage.com>

Closes #1011 from maji2014/master and squashes the following commits:

2cc1af6 [maji2014] Update run-example

Closes #988.
SPARK-1628 follow up: Improve RangePartitioner's documentation.

Adding a paragraph clarifying a weird behavior in RangePartitioner.

See also #549.

Author: Reynold Xin <rxin@apache.org>

Closes #1012 from rxin/partitioner-doc and squashes the following commits:

6f0109e [Reynold Xin] SPARK-1628 follow up: Improve RangePartitioner's documentation.
[SPARK-2067] use relative path for Spark logo in UI

Author: Neville Li <neville@spotify.com>

Closes #1006 from nevillelyh/gh/SPARK-2067 and squashes the following commits:

9ee64cf [Neville Li] [SPARK-2067] use relative path for Spark logo in UI
Grammar: read -> reads

Author: Andrew Ash <andrew@andrewash.com>

Closes #1016 from ash211/patch-6 and squashes the following commits:

e3865c8 [Andrew Ash] Grammar: read -> reads
[SPARK-1308] Add getNumPartitions to pyspark RDD

Add getNumPartitions to pyspark RDD to provide an intuitive way to get number of partitions in RDD like we can do in scala today.

Author: Syed Hashmi <shashmi@cloudera.com>

Closes #995 from syedhashmi/master and squashes the following commits:

de0ed5e [Syed Hashmi] [SPARK-1308] Add getNumPartitions to pyspark RDD
SPARK-1944 Document --verbose in spark-shell -h

https://issues.apache.org/jira/browse/SPARK-1944

Author: Andrew Ash <andrew@andrewash.com>

Closes #1020 from ash211/SPARK-1944 and squashes the following commits:

a831c4d [Andrew Ash] SPARK-1944 Document --verbose in spark-shell -h
[SPARK-1495][SQL]add support for left semi join

Just submit another solution for #395

Author: Daoyuan <daoyuan.wang@intel.com>
Author: Michael Armbrust <michael@databricks.com>
Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #837 from adrian-wang/left-semi-join-support and squashes the following commits:

d39cd12 [Daoyuan Wang] Merge pull request #1 from marmbrus/pr/837
6713c09 [Michael Armbrust] Better debugging for failed query tests.
035b73e [Michael Armbrust] Add test for left semi that can't be done with a hash join.
5ec6fa4 [Michael Armbrust] Add left semi to SQL Parser.
4c726e5 [Daoyuan] improvement according to Michael
8d4a121 [Daoyuan] add golden files for leftsemijoin
83a3c8a [Daoyuan] scala style fix
14cff80 [Daoyuan] add support for left semi join
Added a TaskSetManager unit test.

This test ensures that when there are no
alive executors that satisfy a particular locality level,
the TaskSetManager doesn't ever use that as the maximum
allowed locality level (this optimization ensures that a
job doesn't wait extra time in an attempt to satisfy
a scheduling locality level that is impossible).

@mateiz and @lirui-intel this unit test illustrates an issue
with #892 (it fails with that patch).

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #1024 from kayousterhout/scheduler_unit_test and squashes the following commits:

de6a08f [Kay Ousterhout] Added a TaskSetManager unit test.
[SPARK-1522] : YARN ClientBase throws a NPE if there is no YARN Application CP

The current implementation of ClientBase.getDefaultYarnApplicationClasspath inspects
the MRJobConfig class for the field DEFAULT_YARN_APPLICATION_CLASSPATH when it should
be really looking into YarnConfiguration. If the Application Configuration has no
yarn.application.classpath defined a NPE exception will be thrown.

Additional Changes include:
* Test Suite for ClientBase added

[ticket: SPARK-1522] : https://issues.apache.org/jira/browse/SPARK-1522

Author      : bernardo.gomezpalacio@gmail.com
Testing     : SPARK_HADOOP_VERSION=2.3.0 SPARK_YARN=true ./sbt/sbt test

Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>

Closes #433 from berngp/feature/SPARK-1522 and squashes the following commits:

2c2e118 [Bernardo Gomez Palacio] [SPARK-1522]: YARN ClientBase throws a NPE if there is no YARN Application specific CP
[SQL] Simple framework for debugging query execution

Only records number of tuples and unique dataTypes output right now...

Example:
```scala
scala> import org.apache.spark.sql.execution.debug._
scala> hql("SELECT value FROM src WHERE key > 10").debug(sparkContext)

Results returned: 489
== Project [value#1:0] ==
Tuples output: 489
 value StringType: {java.lang.String}
== Filter (key#0:1 > 10) ==
Tuples output: 489
 value StringType: {java.lang.String}
 key IntegerType: {java.lang.Integer}
== HiveTableScan [value#1,key#0], (MetastoreRelation default, src, None), None ==
Tuples output: 500
 value StringType: {java.lang.String}
 key IntegerType: {java.lang.Integer}
```

Author: Michael Armbrust <michael@databricks.com>

Closes #1005 from marmbrus/debug and squashes the following commits:

dcc3ca6 [Michael Armbrust] Add comments.
c9dded2 [Michael Armbrust] Simple framework for debugging query execution
[SPARK-1704][SQL] Fully support EXPLAIN commands as SchemaRDD.

This PR attempts to resolve [SPARK-1704](https://issues.apache.org/jira/browse/SPARK-1704) by introducing a physical plan for EXPLAIN commands, which just prints out the debug string (containing various SparkSQL's plans) of the corresponding QueryExecution for the actual query.

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

Closes #1003 from concretevitamin/explain-cmd and squashes the following commits:

5b7911f [Zongheng Yang] Add a regression test.
1bfa379 [Zongheng Yang] Modify output().
719ada9 [Zongheng Yang] Override otherCopyArgs for ExplainCommandPhysical.
4318fd7 [Zongheng Yang] Make all output one Row.
439c6ab [Zongheng Yang] Minor cleanups.
408f574 [Zongheng Yang] SPARK-1704: Add CommandStrategy and ExplainCommandPhysical.
Make sure that empty string is filtered out when we get the secondary jars from conf

Author: DB Tsai <dbtsai@dbtsai.com>

Closes #1027 from dbtsai/dbtsai-classloader and squashes the following commits:

9ac6be3 [DB Tsai] Fixed line too long
c9c7ad7 [DB Tsai] Make sure that empty string is filtered out when we get the secondary jars from conf.
SPARK-1416: PySpark support for SequenceFile and Hadoop InputFormats

So I finally resurrected this PR. It seems the old one against the incubator mirror is no longer available, so I cannot reference it.

This adds initial support for reading Hadoop ```SequenceFile```s, as well as arbitrary Hadoop ```InputFormat```s, in PySpark.

# Overview
The basics are as follows:
1. ```PythonRDD``` object contains the relevant methods, that are in turn invoked by ```SparkContext``` in PySpark
2. The SequenceFile or InputFormat is read on the Scala side and converted from ```Writable``` instances to the relevant Scala classes (in the case of primitives)
3. Pyrolite is used to serialize Java objects. If this fails, the fallback is ```toString```
4. ```PickleSerializer``` on the Python side deserializes.

This works "out the box" for simple ```Writable```s:
* ```Text```
* ```IntWritable```, ```DoubleWritable```, ```FloatWritable```
* ```NullWritable```
* ```BooleanWritable```
* ```BytesWritable```
* ```MapWritable```

It also works for simple, "struct-like" classes. Due to the way Pyrolite works, this requires that the classes satisfy the JavaBeans convenstions (i.e. with fields and a no-arg constructor and getters/setters). (Perhaps in future some sugar for case classes and reflection could be added).

I've tested it out with ```ESInputFormat```  as an example and it works very nicely:
```python
conf = {"es.resource" : "index/type" }
rdd = sc.newAPIHadoopRDD("org.elasticsearch.hadoop.mr.EsInputFormat", "org.apache.hadoop.io.NullWritable", "org.elasticsearch.hadoop.mr.LinkedMapWritable", conf=conf)
rdd.first()
```

I suspect for things like HBase/Cassandra it will be a bit trickier to get it to work out the box.

# Some things still outstanding:
1. ~~Requires ```msgpack-python``` and will fail without it. As originally discussed with Josh, add a ```as_strings``` argument that defaults to ```False```, that can be used if ```msgpack-python``` is not available~~
2. ~~I see from https://github.com/apache/spark/pull/363 that Pyrolite is being used there for SerDe between Scala and Python. @ahirreddy @mateiz what is the plan behind this - is Pyrolite preferred? It seems from a cursory glance that adapting the ```msgpack```-based SerDe here to use Pyrolite wouldn't be too hard~~
3. ~~Support the key and value "wrapper" that would allow a Scala/Java function to be plugged in that would transform whatever the key/value Writable class is into something that can be serialized (e.g. convert some custom Writable to a JavaBean or ```java.util.Map``` that can be easily serialized)~~
4. Support ```saveAsSequenceFile``` and ```saveAsHadoopFile``` etc. This would require SerDe in the reverse direction, that can be handled by Pyrolite. Will work on this as a separate PR

Author: Nick Pentreath <nick.pentreath@gmail.com>

Closes #455 from MLnick/pyspark-inputformats and squashes the following commits:

268df7e [Nick Pentreath] Documentation changes mer @pwendell comments
761269b [Nick Pentreath] Address @pwendell comments, simplify default writable conversions and remove registry.
4c972d8 [Nick Pentreath] Add license headers
d150431 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
cde6af9 [Nick Pentreath] Parameterize converter trait
5ebacfa [Nick Pentreath] Update docs for PySpark input formats
a985492 [Nick Pentreath] Move Converter examples to own package
365d0be [Nick Pentreath] Make classes private[python]. Add docs and @Experimental annotation to Converter interface.
eeb8205 [Nick Pentreath] Fix path relative to SPARK_HOME in tests
1eaa08b [Nick Pentreath] HBase -> Cassandra app name oversight
3f90c3e [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
2c18513 [Nick Pentreath] Add examples for reading HBase and Cassandra InputFormats from Python
b65606f [Nick Pentreath] Add converter interface
5757f6e [Nick Pentreath] Default key/value classes for sequenceFile asre None
085b55f [Nick Pentreath] Move input format tests to tests.py and clean up docs
43eb728 [Nick Pentreath] PySpark InputFormats docs into programming guide
94beedc [Nick Pentreath] Clean up args in PythonRDD. Set key/value converter defaults to None for PySpark context.py methods
1a4a1d6 [Nick Pentreath] Address @mateiz style comments
01e0813 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
15a7d07 [Nick Pentreath] Remove default args for key/value classes. Arg names to camelCase
9fe6bd5 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
84fe8e3 [Nick Pentreath] Python programming guide space formatting
d0f52b6 [Nick Pentreath] Python programming guide
7caa73a [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
93ef995 [Nick Pentreath] Add back context.py changes
9ef1896 [Nick Pentreath] Recover earlier changes lost in previous merge for serializers.py
077ecb2 [Nick Pentreath] Recover earlier changes lost in previous merge for context.py
5af4770 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
35b8e3a [Nick Pentreath] Another fix for test ordering
bef3afb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
e001b94 [Nick Pentreath] Fix test failures due to ordering
78978d9 [Nick Pentreath] Add doc for SequenceFile and InputFormat support to Python programming guide
64eb051 [Nick Pentreath] Scalastyle fix
e7552fa [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
44f2857 [Nick Pentreath] Remove msgpack dependency and switch serialization to Pyrolite, plus some clean up and refactoring
c0ebfb6 [Nick Pentreath] Change sequencefile test data generator to easily be called from PySpark tests
1d7c17c [Nick Pentreath] Amend tests to auto-generate sequencefile data in temp dir
17a656b [Nick Pentreath] remove binary sequencefile for tests
f60959e [Nick Pentreath] Remove msgpack dependency and serializer from PySpark
450e0a2 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
31a2fff [Nick Pentreath] Scalastyle fixes
fc5099e [Nick Pentreath] Add Apache license headers
4e08983 [Nick Pentreath] Clean up docs for PySpark context methods
b20ec7e [Nick Pentreath] Clean up merge duplicate dependencies
951c117 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
f6aac55 [Nick Pentreath] Bring back msgpack
9d2256e [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
1bbbfb0 [Nick Pentreath] Clean up SparkBuild from merge
a67dfad [Nick Pentreath] Clean up Msgpack serialization and registering
7237263 [Nick Pentreath] Add back msgpack serializer and hadoop file code lost during merging
25da1ca [Nick Pentreath] Add generator for nulls, bools, bytes and maps
65360d5 [Nick Pentreath] Adding test SequenceFiles
0c612e5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
d72bf18 [Nick Pentreath] msgpack
dd57922 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
e67212a [Nick Pentreath] Add back msgpack dependency
f2d76a0 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
41856a5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
97ef708 [Nick Pentreath] Remove old writeToStream
2beeedb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
795a763 [Nick Pentreath] Change name to WriteInputFormatTestDataGenerator. Cleanup some var names. Use SPARK_HOME in path for writing test sequencefile data.
174f520 [Nick Pentreath] Add back graphx settings
703ee65 [Nick Pentreath] Add back msgpack
619c0fa [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
1c8efbc [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
eb40036 [Nick Pentreath] Remove unused comment lines
4d7ef2e [Nick Pentreath] Fix indentation
f1d73e3 [Nick Pentreath] mergeConfs returns a copy rather than mutating one of the input arguments
0f5cd84 [Nick Pentreath] Remove unused pair UTF8 class. Add comments to msgpack deserializer
4294cbb [Nick Pentreath] Add old Hadoop api methods. Clean up and expand comments. Clean up argument names
818a1e6 [Nick Pentreath] Add seqencefile and Hadoop InputFormat support to PythonRDD
4e7c9e3 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
c304cc8 [Nick Pentreath] Adding supporting sequncefiles for tests. Cleaning up
4b0a43f [Nick Pentreath] Refactoring utils into own objects. Cleaning up old commented-out code
d86325f [Nick Pentreath] Initial WIP of PySpark support for SequenceFile and arbitrary Hadoop InputFormat
Merge remote-tracking branch 'apache/master' into SPARK-1672
Merge remote-tracking branch 'apache/master' into SPARK-1672
set exclusion rules for ALS