SPARK-2712 - Add a small note to maven doc that mvn package must happen ...

Per request by Reynold adding small note about proper sequencing of build then test.

Author: Stephen Boesch <javadba@gmail.com>

Closes #1615 from javadba/docs and squashes the following commits:

6c3183e [Stephen Boesch] Moved updated testing blurb per PWendell
5764757 [Stephen Boesch] SPARK-2712 - Add a small note to maven doc that mvn package must happen before test
(cherry picked from commit f8cd143b6b1b4d8aac87c229e5af263b0319b3ea)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
SPARK-2246: Add user-data option to EC2 scripts

Author: Allan Douglas R. de Oliveira <allan@chaordicsystems.com>

Closes #1186 from douglaz/spark_ec2_user_data and squashes the following commits:

94a36f9 [Allan Douglas R. de Oliveira] Added user data option to EC2 script
(cherry picked from commit a0bcbc159e89be868ccc96175dbf1439461557e1)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-2197] [mllib] Java DecisionTree bug fix and easy-of-use

Bug fix: Before, when an RDD was created in Java and passed to DecisionTree.train(), the fake class tag caused problems.
* Fix: DecisionTree: Used new RDD.retag() method to allow passing RDDs from Java.

Other improvements to Decision Trees for easy-of-use with Java:
* impurity classes: Added instance() methods to help with Java interface.
* Strategy: Added Java-friendly constructor
--> Note: I removed quantileCalculationStrategy from the Java-friendly constructor since (a) it is a special class and (b) there is only 1 option currently.  I suspect we will redo the API before the other options are included.

CC: mengxr

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #1740 from jkbradley/dt-java-new and squashes the following commits:

0805dc6 [Joseph K. Bradley] Changed Strategy to use JavaConverters instead of JavaConversions
519b1b7 [Joseph K. Bradley] * Organized imports in JavaDecisionTreeSuite.java * Using JavaConverters instead of JavaConversions in DecisionTreeSuite.scala
f7b5ca1 [Joseph K. Bradley] Improvements to make it easier to run DecisionTree from Java. * DecisionTree: Used new RDD.retag() method to allow passing RDDs from Java. * impurity classes: Added instance() methods to help with Java interface. * Strategy: Added Java-friendly constructor ** Note: I removed quantileCalculationStrategy from the Java-friendly constructor since (a) it is a special class and (b) there is only 1 option currently.  I suspect we will redo the API before the other options are included.
d78ada6 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-java
320853f [Joseph K. Bradley] Added JavaDecisionTreeSuite, partly written
13a585e [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-java
f1a8283 [Joseph K. Bradley] Added old JavaDecisionTreeSuite, to be updated later
225822f [Joseph K. Bradley] Bug: In DecisionTree, the method sequentialBinSearchForOrderedCategoricalFeatureInClassification() indexed bins from 0 to (math.pow(2, featureCategories.toInt - 1) - 1). This upper bound is the bound for unordered categorical features, not ordered ones. The upper bound should be the arity (i.e., max value) of the feature.

(cherry picked from commit 2998e38a942351974da36cb619e863c6f0316e7a)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[SPARK-2784][SQL] Deprecate hql() method in favor of a config option, 'spark.sql.dialect'

Many users have reported being confused by the distinction between the `sql` and `hql` methods.  Specifically, many users think that `sql(...)` cannot be used to read hive tables.  In this PR I introduce a new configuration option `spark.sql.dialect` that picks which dialect with be used for parsing.  For SQLContext this must be set to `sql`.  In `HiveContext` it defaults to `hiveql` but can also be set to `sql`.

The `hql` and `hiveql` methods continue to act the same but are now marked as deprecated.

**This is a possibly breaking change for some users unless they set the dialect manually, though this is unlikely.**

For example: `hiveContex.sql("SELECT 1")` will now throw a parsing exception by default.

Author: Michael Armbrust <michael@databricks.com>

Closes #1746 from marmbrus/sqlLanguageConf and squashes the following commits:

ad375cc [Michael Armbrust] Merge remote-tracking branch 'apache/master' into sqlLanguageConf
20c43f8 [Michael Armbrust] override function instead of just setting the value
7e4ae93 [Michael Armbrust] Deprecate hql() method in favor of a config option, 'spark.sql.dialect'

(cherry picked from commit 236dfac6769016e433b2f6517cda2d308dea74bc)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2814][SQL] HiveThriftServer2 throws NPE when executing native commands

JIRA issue: [SPARK-2814](https://issues.apache.org/jira/browse/SPARK-2814)

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

Closes #1753 from liancheng/spark-2814 and squashes the following commits:

c74a3b2 [Cheng Lian] Fixed SPARK-2814

(cherry picked from commit ac33cbbf33bd1ab29bc8165c9be02fb8934b1fdf)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-2783][SQL] Basic support for analyze in HiveContext

JIRA: https://issues.apache.org/jira/browse/SPARK-2783

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1741 from yhuai/analyzeTable and squashes the following commits:

7bb5f02 [Yin Huai] Use sql instead of hql.
4d09325 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
e3ebcd4 [Yin Huai] Renaming.
c170f4e [Yin Huai] Do not use getContentSummary.
62393b6 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
db233a6 [Yin Huai] Trying to debug jenkins...
fee84f0 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
f0501f3 [Yin Huai] Fix compilation error.
24ad391 [Yin Huai] Merge remote-tracking branch 'upstream/master' into analyzeTable
8918140 [Yin Huai] Wording.
23df227 [Yin Huai] Add a simple analyze method to get the size of a table and update the "totalSize" property of this table in the Hive metastore.

(cherry picked from commit e139e2be60ef23281327744e1b3e74904dfdf63f)
Signed-off-by: Michael Armbrust <michael@databricks.com>
[SPARK-1740] [PySpark] kill the python worker

Kill only the python worker related to cancelled tasks.

The daemon will start a background thread to monitor all the opened sockets for all workers. If the socket is closed by JVM, this thread will kill the worker.

When an task is cancelled, the socket to worker will be closed, then the worker will be killed by deamon.

Author: Davies Liu <davies.liu@gmail.com>

Closes #1643 from davies/kill and squashes the following commits:

8ffe9f3 [Davies Liu] kill worker by deamon, because runtime.exec() is too heavy
46ca150 [Davies Liu] address comment
acd751c [Davies Liu] kill the worker when task is canceled

(cherry picked from commit 55349f9fe81ba5af5e4a5e4908ebf174e63c6cc9)
Signed-off-by: Josh Rosen <joshrosen@apache.org>
[SPARK-2810] upgrade to scala-maven-plugin 3.2.0

Needed for Scala 2.11 compiler-interface

Signed-off-by: Anand Avati <avatiredhat.com>

Author: Anand Avati <avati@redhat.com>

Closes #1711 from avati/SPARK-1812-scala-maven-plugin and squashes the following commits:

9a22fc8 [Anand Avati] SPARK-1812: upgrade to scala-maven-plugin 3.2.0
Fix some bugs with spaces in directory name.

Any time you use the directory name (`FWDIR`) it needs to be surrounded
in quotes. If you're also using wildcards, you can safely put the quotes
around just `$FWDIR`.

Author: Sarah Gerweck <sarah.a180@gmail.com>

Closes #1756 from sarahgerweck/folderSpaces and squashes the following commits:

732629d [Sarah Gerweck] Fix some bugs with spaces in directory name.
(cherry picked from commit 5507dd8e18fbb52d5e0c64a767103b2418cb09c6)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
SPARK-2272 [MLlib] Feature scaling which standardizes the range of independent variables or features of data

Feature scaling is a method used to standardize the range of independent variables or features of data. In data processing, it is generally performed during the data preprocessing step.

In this work, a trait called `VectorTransformer` is defined for generic transformation on a vector. It contains one method to be implemented, `transform` which applies transformation on a vector.

There are two implementations of `VectorTransformer` now, and they all can be easily extended with PMML transformation support.

1) `StandardScaler` - Standardizes features by removing the mean and scaling to unit variance using column summary statistics on the samples in the training set.

2) `Normalizer` - Normalizes samples individually to unit L^n norm

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #1207 from dbtsai/dbtsai-feature-scaling and squashes the following commits:

78c15d3 [DB Tsai] Alpine Data Labs

(cherry picked from commit ae58aea2d1435b5bb011e68127e1bcddc2edf5b2)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
[MLlib] [SPARK-2510]Word2Vec: Distributed Representation of Words

This is a pull request regarding SPARK-2510 at https://issues.apache.org/jira/browse/SPARK-2510. Word2Vec creates vector representation of words in a text corpus. The algorithm first constructs a vocabulary from the corpus and then learns vector representation of words in the vocabulary. The vector representation can be used as features in natural language processing and machine learning algorithms.

To make our implementation more scalable, we train each partition separately and merge the model of each partition after each iteration. To make the model more accurate, multiple iterations may be needed.

To investigate the vector representations is to find the closest words for a query word. For example, the top 20 closest words to "china" are for 1 partition and 1 iteration :

taiwan 0.8077646146334014
korea 0.740913304563621
japan 0.7240667798885471
republic 0.7107151279078352
thailand 0.6953217332072862
tibet 0.6916782118129544
mongolia 0.6800858715972612
macau 0.6794925677480378
singapore 0.6594048695593799
manchuria 0.658989931844148
laos 0.6512978726001666
nepal 0.6380792327845325
mainland 0.6365469459587788
myanmar 0.6358614338840394
macedonia 0.6322366180313249
xinjiang 0.6285291551708028
russia 0.6279951236068411
india 0.6272874944023487
shanghai 0.6234544135576999
macao 0.6220588462925876

The result with 10 partitions and 5 iterations is:
taiwan 0.8310495079388313
india 0.7737171315919039
japan 0.756777901233668
korea 0.7429767187102452
indonesia 0.7407557427278356
pakistan 0.712883426985585
mainland 0.7053379963140822
thailand 0.696298191073948
mongolia 0.693690656871415
laos 0.6913069680735292
macau 0.6903427690029617
republic 0.6766381604813666
malaysia 0.676460699141784
singapore 0.6728790997360923
malaya 0.672345232966194
manchuria 0.6703732292753156
macedonia 0.6637955686322028
myanmar 0.6589462882439646
kazakhstan 0.657017801081494
cambodia 0.6542383836451932

Author: Liquan Pei <lpei@gopivotal.com>
Author: Xiangrui Meng <meng@databricks.com>
Author: Liquan Pei <liquanpei@gmail.com>

Closes #1719 from Ishiihara/master and squashes the following commits:

2ba9483 [Liquan Pei] minor fix for Word2Vec test
e248441 [Liquan Pei] minor style change
26a948d [Liquan Pei] Merge pull request #1 from mengxr/Ishiihara-master
c14da41 [Xiangrui Meng] fix styles
384c771 [Xiangrui Meng] remove minCount and window from constructor change model to use float instead of double
e93e726 [Liquan Pei] use treeAggregate instead of aggregate
1a8fb41 [Liquan Pei] use weighted sum in combOp
7efbb6f [Liquan Pei] use broadcast version of vocab in aggregate
6bcc8be [Liquan Pei] add multiple iteration support
720b5a3 [Liquan Pei] Add test for Word2Vec algorithm, minor fixes
2e92b59 [Liquan Pei] modify according to feedback
57dc50d [Liquan Pei] code formatting
e4a04d3 [Liquan Pei] minor fix
0aafb1b [Liquan Pei] Add comments, minor fixes
8d6befe [Liquan Pei] initial commit

(cherry picked from commit e053c55819363fab7068bb9165e3379f0c2f570c)
Signed-off-by: Xiangrui Meng <meng@databricks.com>