Spark parquet improvements

A few improvements to the Parquet support for SQL queries:
- Instead of files a ParquetRelation is now backed by a directory, which simplifies importing data from other
  sources
- InsertIntoParquetTable operation now supports switching between overwriting or appending (at least in
  HiveQL)
- tests now use the new API
- Parquet logging can be set to WARNING level (Default)
- Default compression for Parquet files (GZIP, as in parquet-mr)

Author: Andre Schumacher <andre.schumacher@iki.fi>

Closes #195 from AndreSchumacher/spark_parquet_improvements and squashes the following commits:

54df314 [Andre Schumacher] SPARK-1383 [SQL] Improvements to ParquetRelation
[SPARK-1360] Add Timestamp Support for SQL

This PR includes:
1) Add new data type Timestamp
2) Add more data type casting base on Hive's Rule
3) Fix bug missing data type in both parsers (HiveQl & SQLParser).

Author: Cheng Hao <hao.cheng@intel.com>

Closes #275 from chenghao-intel/timestamp and squashes the following commits:

df709e5 [Cheng Hao] Move orc_ends_with_nulls to blacklist
24b04b0 [Cheng Hao] Put 3 cases into the black lists(describe_pretty,describe_syntax,lateral_view_outer)
fc512c2 [Cheng Hao] remove the unnecessary data type equality check in data casting
d0d1919 [Cheng Hao] Add more data type for scala reflection
3259808 [Cheng Hao] Add the new Golden files
3823b97 [Cheng Hao] Update the UnitTest cases & add timestamp type for HiveQL
54a0489 [Cheng Hao] fix bug mapping to 0 (which is supposed to be null) when NumberFormatException occurs
9cb505c [Cheng Hao] Fix issues according to PR comments
e529168 [Cheng Hao] Fix bug of converting from String
6fc8100 [Cheng Hao] Update Unit Test & CodeStyle
8a1d4d6 [Cheng Hao] Add DataType for SqlParser
ce4385e [Cheng Hao] Add TimestampType Support
Spark 1162 Implemented takeOrdered in pyspark.

Since python does not have a library for max heap and usual tricks like inverting values etc.. does not work for all cases.

We have our own implementation of max heap.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #97 from ScrapCodes/SPARK-1162/pyspark-top-takeOrdered2 and squashes the following commits:

35f86ba [Prashant Sharma] code review
2b1124d [Prashant Sharma] fixed tests
e8a08e2 [Prashant Sharma] Code review comments.
49e6ba7 [Prashant Sharma] SPARK-1162 added takeOrdered to pyspark
[SQL] SPARK-1333 First draft of java API

WIP: Some work remains...
 * [x] Hive support
 * [x] Tests
 * [x] Update docs

Feedback welcome!

Author: Michael Armbrust <michael@databricks.com>

Closes #248 from marmbrus/javaSchemaRDD and squashes the following commits:

b393913 [Michael Armbrust] @srowen 's java style suggestions.
f531eb1 [Michael Armbrust] Address matei's comments.
33a1b1a [Michael Armbrust] Ignore JavaHiveSuite.
822f626 [Michael Armbrust] improve docs.
ab91750 [Michael Armbrust] Improve Java SQL API: * Change JavaRow => Row * Add support for querying RDDs of JavaBeans * Docs * Tests * Hive support
0b859c8 [Michael Armbrust] First draft of java API.
[SPARK-1134] Fix and document passing of arguments to IPython

This is based on @dianacarroll's previous pull request https://github.com/apache/spark/pull/227, and @joshrosen's comments on https://github.com/apache/spark/pull/38. Since we do want to allow passing arguments to IPython, this does the following:
* It documents that IPython can't be used with standalone jobs for now. (Later versions of IPython will deal with PYTHONSTARTUP properly and enable this, see https://github.com/ipython/ipython/pull/5226, but no released version has that fix.)
* If you run `pyspark` with `IPYTHON=1`, it passes your command-line arguments to it. This way you can do stuff like `IPYTHON=1 bin/pyspark notebook`.
* The old `IPYTHON_OPTS` remains, but I've removed it from the documentation. This is in case people read an old tutorial that uses it.

This is not a perfect solution and I'd also be okay with keeping things as they are today (ignoring `$@` for IPython and using IPYTHON_OPTS), and only doing the doc change. With this change though, when IPython fixes https://github.com/ipython/ipython/pull/5226, people will immediately be able to do `IPYTHON=1 bin/pyspark myscript.py` to run a standalone script and get all the benefits of running scripts in IPython (presumably better debugging and such). Without it, there will be no way to run scripts in IPython.

@joshrosen you should probably take the final call on this.

Author: Diana Carroll <dcarroll@cloudera.com>

Closes #294 from mateiz/spark-1134 and squashes the following commits:

747bb13 [Diana Carroll] SPARK-1134 bug with ipython prevents non-interactive use with spark; only call ipython if no command line arguments were supplied
[BUILD FIX] Fix compilation of Spark SQL Java API.

The JavaAPI and the Parquet improvements PRs didn't conflict, but broke the build.

Author: Michael Armbrust <michael@databricks.com>

Closes #316 from marmbrus/hotFixJavaApi and squashes the following commits:

0b84c2d [Michael Armbrust] Fix compilation of Spark SQL Java API.
Fix jenkins from giving the green light to builds that don't compile.

 Adding `| grep` swallows the non-zero return code from sbt failures. See [here](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/13735/consoleFull) for a Jenkins run that fails to compile, but still gets a green light.

Note the [BUILD FIX] commit isn't actually part of this PR, but github is out of date.

Author: Michael Armbrust <michael@databricks.com>

Closes #317 from marmbrus/fixJenkins and squashes the following commits:

7c77ff9 [Michael Armbrust] Remove output filter that was swallowing non-zero exit codes for test failures.
Revert "[SPARK-1398] Removed findbugs jsr305 dependency"

This reverts commit 92a86b285f8a4af1bdf577dd4c4ea0fd5ca8d682.
SPARK-1337: Application web UI garbage collects newest stages

Simple fix...

Author: Patrick Wendell <pwendell@gmail.com>

Closes #320 from pwendell/stage-clean-up and squashes the following commits:

29be62e [Patrick Wendell] SPARK-1337: Application web UI garbage collects newest stages instead old ones
SPARK-1350. Always use JAVA_HOME to run executor container JVMs.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #313 from sryza/sandy-spark-1350 and squashes the following commits:

bb6d187 [Sandy Ryza] SPARK-1350. Always use JAVA_HOME to run executor container JVMs.
SPARK-1404: Always upgrade spark-env.sh vars to environment vars

This was broken when spark-env.sh was made idempotent, as the idempotence check is an environment variable, but the spark-env.sh variables may not have been.

Tested in zsh, bash, and sh.

Author: Aaron Davidson <aaron@databricks.com>

Closes #310 from aarondav/SPARK-1404 and squashes the following commits:

c3406a5 [Aaron Davidson] Add extra export in spark-shell
6a0e340 [Aaron Davidson] SPARK-1404: Always upgrade spark-env.sh vars to environment vars
[SPARK-1133] Add whole text files reader in MLlib

Here is a pointer to the former [PR164](https://github.com/apache/spark/pull/164).

I add the pull request for the JIRA issue [SPARK-1133](https://spark-project.atlassian.net/browse/SPARK-1133), which brings a new files reader API in MLlib.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #252 from yinxusen/whole-files-input and squashes the following commits:

7191be6 [Xusen Yin] refine comments
0af3faf [Xusen Yin] add JavaAPI test
01745ee [Xusen Yin] fix deletion error
cc97dca [Xusen Yin] move whole text file API to Spark core
d792cee [Xusen Yin] remove the typo character "+"
6bdf2c2 [Xusen Yin] test for small local file system block size
a1f1e7e [Xusen Yin] add two extra spaces
28cb0fe [Xusen Yin] add whole text files reader
SPARK-1375. Additional spark-submit cleanup

Author: Sandy Ryza <sandy@cloudera.com>

Closes #278 from sryza/sandy-spark-1375 and squashes the following commits:

5fbf1e9 [Sandy Ryza] SPARK-1375. Additional spark-submit cleanup
Don't create SparkContext in JobProgressListenerSuite.

This reduces the time of the test from 11 seconds to 20 milliseconds.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #324 from pwendell/job-test and squashes the following commits:

868d9eb [Patrick Wendell] Don't create SparkContext in JobProgressListenerSuite.
[SPARK-1198] Allow pipes tasks to run in different sub-directories

This works as is on Linux/Mac/etc but doesn't cover working on Windows.  In here I use ln -sf for symlinks. Putting this up for comments on that. Do we want to create perhaps some classes for doing shell commands - Linux vs Windows.  Is there some other way we want to do this?   I assume we are still supporting jdk1.6?

Also should I update the Java API for pipes to allow this parameter?

Author: Thomas Graves <tgraves@apache.org>

Closes #128 from tgravescs/SPARK1198 and squashes the following commits:

abc1289 [Thomas Graves] remove extra tag in pom file
ba23fc0 [Thomas Graves] Add support for symlink on windows, remove commons-io usage
da4b221 [Thomas Graves] Merge branch 'master' of https://github.com/tgravescs/spark into SPARK1198
61be271 [Thomas Graves] Fix file name filter
6b783bd [Thomas Graves] style fixes
1ab49ca [Thomas Graves] Add support for running pipe tasks is separate directories
[SQL] Minor fixes.

Author: Michael Armbrust <michael@databricks.com>

Closes #315 from marmbrus/minorFixes and squashes the following commits:

b23a15d [Michael Armbrust] fix scaladoc
11062ac [Michael Armbrust] Fix registering "SELECT *" queries as tables and caching them.  As some tests for this and self-joins.
3997dc9 [Michael Armbrust] Move Row extractor to catalyst.
208bf5e [Michael Armbrust] More idiomatic naming of DSL functions. * subquery => as * for join condition => on, i.e., `r.join(s, condition = 'a == 'b)` =>`r.join(s, on = 'a == 'b)`
87211ce [Michael Armbrust] Correctly handle self joins of in-memory cached tables.
69e195e [Michael Armbrust] Change != to !== in the DSL since != will always translate to != on Any.
01f2dd5 [Michael Armbrust] Correctly assign aliases to tables in SqlParser.
SPARK-1414. Python API for SparkContext.wholeTextFiles

Also clarified comment on each file having to fit in memory

Author: Matei Zaharia <matei@databricks.com>

Closes #327 from mateiz/py-whole-files and squashes the following commits:

9ad64a5 [Matei Zaharia] SPARK-1414. Python API for SparkContext.wholeTextFiles
Add test utility for generating Jar files with compiled classes.

This was requested by a few different people and may be generally
useful, so I'd like to contribute this and not block on a different
PR for it to get in.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #326 from pwendell/class-loader-test-utils and squashes the following commits:

ff3e88e [Patrick Wendell] Add test utility for generating Jar files with compiled classes.
[SPARK-1419] Bumped parent POM to apache 14

Keeping up-to-date with the parent, which includes some bugfixes.

Author: Mark Hamstra <markhamstra@gmail.com>

Closes #328 from markhamstra/Apache14 and squashes the following commits:

3f19975 [Mark Hamstra] Bumped parent POM to apache 14
SPARK-1305: Support persisting RDD's directly to Tachyon

Move the PR#468 of apache-incubator-spark to the apache-spark
"Adding an option to persist Spark RDD blocks into Tachyon."

Author: Haoyuan Li <haoyuan@cs.berkeley.edu>
Author: RongGu <gurongwalker@gmail.com>

Closes #158 from RongGu/master and squashes the following commits:

72b7768 [Haoyuan Li] merge master
9f7fa1b [Haoyuan Li] fix code style
ae7834b [Haoyuan Li] minor cleanup
a8b3ec6 [Haoyuan Li] merge master branch
e0f4891 [Haoyuan Li] better check offheap.
55b5918 [RongGu] address matei's comment on the replication of offHeap storagelevel
7cd4600 [RongGu] remove some logic code for tachyonstore's replication
51149e7 [RongGu] address aaron's comment on returning value of the remove() function in tachyonstore
8adfcfa [RongGu] address arron's comment on inTachyonSize
120e48a [RongGu] changed the root-level dir name in Tachyon
5cc041c [Haoyuan Li] address aaron's comments
9b97935 [Haoyuan Li] address aaron's comments
d9a6438 [Haoyuan Li] fix for pspark
77d2703 [Haoyuan Li] change python api.git status
3dcace4 [Haoyuan Li] address matei's comments
91fa09d [Haoyuan Li] address patrick's comments
589eafe [Haoyuan Li] use TRY_CACHE instead of MUST_CACHE
64348b2 [Haoyuan Li] update conf docs.
ed73e19 [Haoyuan Li] Merge branch 'master' of github.com:RongGu/spark-1
619a9a8 [RongGu] set number of directories in TachyonStore back to 64; added a TODO tag for duplicated code from the DiskStore
be79d77 [RongGu] find a way to clean up some unnecessay metods and classed to make the code simpler
49cc724 [Haoyuan Li] update docs with off_headp option
4572f9f [RongGu] reserving the old apply function API of StorageLevel
04301d3 [RongGu] rename StorageLevel.TACHYON to Storage.OFF_HEAP
c9aeabf [RongGu] rename the StorgeLevel.TACHYON as StorageLevel.OFF_HEAP
76805aa [RongGu] unifies the config properties name prefix; add the configs into docs/configuration.md
e700d9c [RongGu] add the SparkTachyonHdfsLR example and some comments
fd84156 [RongGu] use randomUUID to generate sparkapp directory name on tachyon;minor code style fix
939e467 [Haoyuan Li] 0.4.1-thrift from maven central
86a2eab [Haoyuan Li] tachyon 0.4.1-thrift is in the staging repo. but jenkins failed to download it. temporarily revert it back to 0.4.1
16c5798 [RongGu] make the dependency on tachyon as tachyon-0.4.1-thrift
eacb2e8 [RongGu] Merge branch 'master' of https://github.com/RongGu/spark-1
bbeb4de [RongGu] fix the JsonProtocolSuite test failure problem
6adb58f [RongGu] Merge branch 'master' of https://github.com/RongGu/spark-1
d827250 [RongGu] fix JsonProtocolSuie test failure
716e93b [Haoyuan Li] revert the version
ca14469 [Haoyuan Li] bump tachyon version to 0.4.1-thrift
2825a13 [RongGu] up-merging to the current master branch of the apache spark
6a22c1a [Haoyuan Li] fix scalastyle
8968b67 [Haoyuan Li] exclude more libraries from tachyon dependency to be the same as referencing tachyon-client.
77be7e8 [RongGu] address mateiz's comment about the temp folder name problem. The implementation followed mateiz's advice.
1dcadf9 [Haoyuan Li] typo
bf278fa [Haoyuan Li] fix python tests
e82909c [Haoyuan Li] minor cleanup
776a56c [Haoyuan Li] address patrick's and ali's comments from the previous PR
8859371 [Haoyuan Li] various minor fixes and clean up
e3ddbba [Haoyuan Li] add doc to use Tachyon cache mode.
fcaeab2 [Haoyuan Li] address Aaron's comment
e554b1e [Haoyuan Li] add python code
47304b3 [Haoyuan Li] make tachyonStore in BlockMananger lazy val; add more comments StorageLevels.
dc8ef24 [Haoyuan Li] add old storelevel constructor
e01a271 [Haoyuan Li] update tachyon 0.4.1
8011a96 [RongGu] fix a brought-in mistake in StorageLevel
70ca182 [RongGu] a bit change in comment
556978b [RongGu] fix the scalastyle errors
791189b [RongGu] "Adding an option to persist Spark RDD blocks into Tachyon." move the PR#468 of apache-incubator-spark to the apache-spark