[SPARK-1994][SQL] Weird data corruption bug when running Spark SQL on data in HDFS

Basically there is a race condition (possibly a scala bug?) when these values are recomputed on all of the slaves that results in an incorrect projection being generated (possibly because the GUID uniqueness contract is broken?).

In general we should probably enforce that all expression planing occurs on the driver, as is now occurring here.

Author: Michael Armbrust <michael@databricks.com>

Closes #1004 from marmbrus/fixAggBug and squashes the following commits:

e0c116c [Michael Armbrust] Compute aggregate expression during planning instead of lazily on workers.
HOTFIX: Support empty body in merge script

Discovered in #992

Author: Patrick Wendell <pwendell@gmail.com>

Closes #1007 from pwendell/hotfix and squashes the following commits:

af90aa0 [Patrick Wendell] HOTFIX: Support empty body in merge script
SPARK-2056 Set RDD name to input path

Author: Neville Li <neville@spotify.com>

Closes #992 from nevillelyh/master and squashes the following commits:

3011739 [Neville Li] [SPARK-2056] Set RDD name to input path
SPARK-2026: Maven Hadoop Profiles Should Set The Hadoop Version

The Maven Profiles that refer to hadoopX, e.g. `hadoop2.4`, should set the expected
`hadoop.version` and `yarn.version`.

e.g.

```
<profile>
      <id>hadoop-2.4</id>
      <properties>
        <hadoop.version>2.4.0</hadoop.version>
         <yarn.version>${hadoop.version}</yarn.version>
        <protobuf.version>2.5.0</protobuf.version>
        <jets3t.version>0.9.0</jets3t.version>
      </properties>
</profile>
```

Builds can still define the `-Dhadoop.version` option but this will correctly default the
Hadoop Version to the one that is expected according the profile that is selected.

e.g.

```$ mvn -P hadoop-2.4,yarn clean install```
or

```$ mvn -P hadoop-0.23,yarn clean install```

[ticket] : https://issues.apache.org/jira/browse/SPARK-2026

Author      : berngp
Reviewer    : ?

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

Closes #998 from berngp/feature/SPARK-2026 and squashes the following commits:

07ba4f7 [Bernardo Gomez Palacio] SPARK-2026: Maven Hadoop Profiles Should Set The Hadoop Version
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
[SPARK-1508][SQL] Add SQLConf to SQLContext.

This PR (1) introduces a new class SQLConf that stores key-value properties for a SQLContext (2) clean up the semantics of various forms of SET commands.

The SQLConf class unlocks user-controllable optimization opportunities; for example, user can now override the number of partitions used during an Exchange. A SQLConf can be accessed and modified programmatically through its getters and setters. It can also be modified through SET commands executed by `sql()` or `hql()`. Note that users now have the ability to change a particular property for different queries inside the same Spark job, unlike settings configured in SparkConf.

For SET commands: "SET" will return all properties currently set in a SQLConf, "SET key" will return the key-value pair (if set) or an undefined message, and "SET key=value" will call the setter on SQLConf, and if a HiveContext is used, it will be executed in Hive as well.

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

Closes #956 from concretevitamin/sqlconf and squashes the following commits:

4968c11 [Zongheng Yang] Very minor cleanup.
d74dde5 [Zongheng Yang] Remove the redundant mkQueryExecution() method.
c129b86 [Zongheng Yang] Merge remote-tracking branch 'upstream/master' into sqlconf
26c40eb [Zongheng Yang] Make SQLConf a trait and have SQLContext mix it in.
dd19666 [Zongheng Yang] Update a comment.
baa5d29 [Zongheng Yang] Remove default param for shuffle partitions accessor.
5f7e6d8 [Zongheng Yang] Add default num partitions.
22d9ed7 [Zongheng Yang] Fix output() of Set physical. Add SQLConf param accessor method.
e9856c4 [Zongheng Yang] Use java.util.Collections.synchronizedMap on a Java HashMap.
88dd0c8 [Zongheng Yang] Remove redundant SET Keyword.
271f0b1 [Zongheng Yang] Minor change.
f8983d1 [Zongheng Yang] Minor changes per review comments.
1ce8a5e [Zongheng Yang] Invoke runSqlHive() in SQLConf#get for the HiveContext case.
b766af9 [Zongheng Yang] Remove a test.
d52e1bd [Zongheng Yang] De-hardcode number of shuffle partitions for BasicOperators (read from SQLConf).
555599c [Zongheng Yang] Bullet-proof (relatively) parsing SET per review comment.
c2067e8 [Zongheng Yang] Mark SQLContext transient and put it in a second param list.
2ea8cdc [Zongheng Yang] Wrap long line.
41d7f09 [Zongheng Yang] Fix imports.
13279e6 [Zongheng Yang] Refactor the logic of eagerly processing SET commands.
b14b83e [Zongheng Yang] In a HiveContext, make SQLConf a subset of HiveConf.
6983180 [Zongheng Yang] Move a SET test to SQLQuerySuite and make it complete.
5b67985 [Zongheng Yang] New line at EOF.
c651797 [Zongheng Yang] Add commands.scala.
efd82db [Zongheng Yang] Clean up semantics of several cases of SET.
c1017c2 [Zongheng Yang] WIP in changing SetCommand to take two Options (for different semantics of SETs).
0f00d86 [Zongheng Yang] Add a test for singleton set command in SQL.
41acd75 [Zongheng Yang] Add a test for hql() in HiveQuerySuite.
2276929 [Zongheng Yang] Fix default hive result for set commands in HiveComparisonTest.
3b0c71b [Zongheng Yang] Remove Parser for set commands. A few other fixes.
d0c4578 [Zongheng Yang] Tmux typo.
0ecea46 [Zongheng Yang] Changes for HiveQl and HiveContext.
ce22d80 [Zongheng Yang] Fix parsing issues.
cb722c1 [Zongheng Yang] Finish up SQLConf patch.
4ebf362 [Zongheng Yang] First cut at SQLConf inside SQLContext.