[SPARK-2478] [mllib] DecisionTree Python API

Added experimental Python API for Decision Trees.

API:
* class DecisionTreeModel
** predict() for single examples and RDDs, taking both feature vectors and LabeledPoints
** numNodes()
** depth()
** __str__()
* class DecisionTree
** trainClassifier()
** trainRegressor()
** train()

Examples and testing:
* Added example testing classification and regression with batch prediction: examples/src/main/python/mllib/tree.py
* Have also tested example usage in doc of python/pyspark/mllib/tree.py which tests single-example prediction with dense and sparse vectors

Also: Small bug fix in python/pyspark/mllib/_common.py: In _linear_predictor_typecheck, changed check for RDD to use isinstance() instead of type() in order to catch RDD subclasses.

CC mengxr manishamde

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

Closes #1727 from jkbradley/decisiontree-python-new and squashes the following commits:

3744488 [Joseph K. Bradley] Renamed test tree.py to decision_tree_runner.py Small updates based on github review.
6b86a9d [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
affceb9 [Joseph K. Bradley] * Fixed bug in doc tests in pyspark/mllib/util.py caused by change in loadLibSVMFile behavior.  (It used to threshold labels at 0 to make them 0/1, but it now leaves them as they are.) * Fixed small bug in loadLibSVMFile: If a data file had no features, then loadLibSVMFile would create a single all-zero feature.
67a29bc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
cf46ad7 [Joseph K. Bradley] Python DecisionTreeModel * predict(empty RDD) returns an empty RDD instead of an error. * Removed support for calling predict() on LabeledPoint and RDD[LabeledPoint] * predict() does not cache serialized RDD any more.
aa29873 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
bf21be4 [Joseph K. Bradley] removed old run() func from DecisionTree
fa10ea7 [Joseph K. Bradley] Small style update
7968692 [Joseph K. Bradley] small braces typo fix
e34c263 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
4801b40 [Joseph K. Bradley] Small style update to DecisionTreeSuite
db0eab2 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix2' into decisiontree-python-new
6873fa9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
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.
93953f1 [Joseph K. Bradley] Likely done with Python API.
6df89a9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
4562c08 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
665ba78 [Joseph K. Bradley] Small updates towards Python DecisionTree API
188cb0d [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
6622247 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
b8fac57 [Joseph K. Bradley] Finished Python DecisionTree API and example but need to test a bit more.
2b20c61 [Joseph K. Bradley] Small doc and style updates
1b29c13 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
584449a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
dab0b67 [Joseph K. Bradley] Added documentation for DecisionTree internals
8bb8aa0 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
978cfcf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
6eed482 [Joseph K. Bradley] In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type.
376dca2 [Joseph K. Bradley] Updated meaning of maxDepth by 1 to fit scikit-learn and rpart. * In code, replaced usages of maxDepth <-- maxDepth + 1 * In params, replace settings of maxDepth <-- maxDepth - 1
e06e423 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
bab3f19 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
59750f8 [Joseph K. Bradley] * Updated Strategy to check numClassesForClassification only if algo=Classification. * Updates based on comments: ** DecisionTreeRunner *** Made dataFormat arg default to libsvm ** Small cleanups ** tree.Node: Made recursive helper methods private, and renamed them.
52e17c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
f5a036c [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
da50db7 [Joseph K. Bradley] Added one more test to DecisionTreeSuite: stump with 2 continuous variables for binary classification.  Caused problems in past, but fixed now.
8e227ea [Joseph K. Bradley] Changed Strategy so it only requires numClassesForClassification >= 2 for classification
cd1d933 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
8ea8750 [Joseph K. Bradley] Bug fix: Off-by-1 when finding thresholds for splits for continuous features.
8a758db [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
5fe44ed [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
2283df8 [Joseph K. Bradley] 2 bug fixes.
73fbea2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
5f920a1 [Joseph K. Bradley] Demonstration of bug before submitting fix: Updated DecisionTreeSuite so that 3 tests fail.  Will describe bug in next commit.
f825352 [Joseph K. Bradley] Wrote Python API and example for DecisionTree.  Also added toString, depth, and numNodes methods to DecisionTreeModel.
[SQL] Set outputPartitioning of BroadcastHashJoin correctly.

I think we will not generate the plan triggering this bug at this moment. But, let me explain it...

Right now, we are using `left.outputPartitioning` as the `outputPartitioning` of a `BroadcastHashJoin`. We may have a wrong physical plan for cases like...
```sql
SELECT l.key, count(*)
FROM (SELECT key, count(*) as cnt
      FROM src
      GROUP BY key) l // This is buildPlan
JOIN r // This is the streamedPlan
ON (l.cnt = r.value)
GROUP BY l.key
```
Let's say we have a `BroadcastHashJoin` on `l` and `r`. For this case, we will pick `l`'s `outputPartitioning` for the `outputPartitioning`of the `BroadcastHashJoin` on `l` and `r`. Also, because the last `GROUP BY` is using `l.key` as the key, we will not introduce an `Exchange` for this aggregation. However, `r`'s outputPartitioning may not match the required distribution of the last `GROUP BY` and we fail to group data correctly.

JIRA is being reindexed. I will create a JIRA ticket once it is back online.

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

Closes #1735 from yhuai/BroadcastHashJoin and squashes the following commits:

96d9cb3 [Yin Huai] Set outputPartitioning correctly.
[SPARK-1981] Add AWS Kinesis streaming support

Author: Chris Fregly <chris@fregly.com>

Closes #1434 from cfregly/master and squashes the following commits:

4774581 [Chris Fregly] updated docs, renamed retry to retryRandom to be more clear, removed retries around store() method
0393795 [Chris Fregly] moved Kinesis examples out of examples/ and back into extras/kinesis-asl
691a6be [Chris Fregly] fixed tests and formatting, fixed a bug with JavaKinesisWordCount during union of streams
0e1c67b [Chris Fregly] Merge remote-tracking branch 'upstream/master'
74e5c7c [Chris Fregly] updated per TD's feedback.  simplified examples, updated docs
e33cbeb [Chris Fregly] Merge remote-tracking branch 'upstream/master'
bf614e9 [Chris Fregly] per matei's feedback:  moved the kinesis examples into the examples/ dir
d17ca6d [Chris Fregly] per TD's feedback:  updated docs, simplified the KinesisUtils api
912640c [Chris Fregly] changed the foundKinesis class to be a publically-avail class
db3eefd [Chris Fregly] Merge remote-tracking branch 'upstream/master'
21de67f [Chris Fregly] Merge remote-tracking branch 'upstream/master'
6c39561 [Chris Fregly] parameterized the versions of the aws java sdk and kinesis client
338997e [Chris Fregly] improve build docs for kinesis
828f8ae [Chris Fregly] more cleanup
e7c8978 [Chris Fregly] Merge remote-tracking branch 'upstream/master'
cd68c0d [Chris Fregly] fixed typos and backward compatibility
d18e680 [Chris Fregly] Merge remote-tracking branch 'upstream/master'
b3b0ff1 [Chris Fregly] [SPARK-1981] Add AWS Kinesis streaming support
SPARK-2804: Remove scalalogging-slf4j dependency

This also Closes #1701.

Author: GuoQiang Li <witgo@qq.com>

Closes #1208 from witgo/SPARK-1470 and squashes the following commits:

422646b [GuoQiang Li] Remove scalalogging-slf4j dependency
[SPARK-2097][SQL] UDF Support

This patch adds the ability to register lambda functions written in Python, Java or Scala as UDFs for use in SQL or HiveQL.

Scala:
```scala
registerFunction("strLenScala", (_: String).length)
sql("SELECT strLenScala('test')")
```
Python:
```python
sqlCtx.registerFunction("strLenPython", lambda x: len(x), IntegerType())
sqlCtx.sql("SELECT strLenPython('test')")
```
Java:
```java
sqlContext.registerFunction("stringLengthJava", new UDF1<String, Integer>() {
  Override
  public Integer call(String str) throws Exception {
    return str.length();
  }
}, DataType.IntegerType);

sqlContext.sql("SELECT stringLengthJava('test')");
```

Author: Michael Armbrust <michael@databricks.com>

Closes #1063 from marmbrus/udfs and squashes the following commits:

9eda0fe [Michael Armbrust] newline
747c05e [Michael Armbrust] Add some scala UDF tests.
d92727d [Michael Armbrust] Merge remote-tracking branch 'apache/master' into udfs
005d684 [Michael Armbrust] Fix naming and formatting.
d14dac8 [Michael Armbrust] Fix last line of autogened java files.
8135c48 [Michael Armbrust] Move UDF unit tests to pyspark.
40b0ffd [Michael Armbrust] Merge remote-tracking branch 'apache/master' into udfs
6a36890 [Michael Armbrust] Switch logging so that SQLContext can be serializable.
7a83101 [Michael Armbrust] Drop toString
795fd15 [Michael Armbrust] Try to avoid capturing SQLContext.
e54fb45 [Michael Armbrust] Docs and tests.
437cbe3 [Michael Armbrust] Update use of dataTypes, fix some python tests, address review comments.
01517d6 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into udfs
8e6c932 [Michael Armbrust] WIP
3f96a52 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into udfs
6237c8d [Michael Armbrust] WIP
2766f0b [Michael Armbrust] Move udfs support to SQL from hive. Add support for Java UDFs.
0f7d50c [Michael Armbrust] Draft of native Spark SQL UDFs for Scala and Python.
[SPARK-2785][SQL] Remove assertions that throw when users try unsupported Hive commands.

Author: Michael Armbrust <michael@databricks.com>

Closes #1742 from marmbrus/asserts and squashes the following commits:

5182d54 [Michael Armbrust] Remove assertions that throw when users try unsupported Hive commands.
[SPARK-2729][SQL] Added test case for SPARK-2729

This is a follow up of #1636.

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

Closes #1738 from liancheng/test-for-spark-2729 and squashes the following commits:

b13692a [Cheng Lian] Added test case for SPARK-2729
[SPARK-2797] [SQL] SchemaRDDs don't support unpersist()

The cause is explained in https://issues.apache.org/jira/browse/SPARK-2797.

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

Closes #1745 from yhuai/SPARK-2797 and squashes the following commits:

7b1627d [Yin Huai] The unpersist method of the Scala RDD cannot be called without the input parameter (blocking) from PySpark.
[SPARK-2739][SQL] Rename registerAsTable to registerTempTable

There have been user complaints that the difference between `registerAsTable` and `saveAsTable` is too subtle.  This PR addresses this by renaming `registerAsTable` to `registerTempTable`, which more clearly reflects what is happening.  `registerAsTable` remains, but will cause a deprecation warning.

Author: Michael Armbrust <michael@databricks.com>

Closes #1743 from marmbrus/registerTempTable and squashes the following commits:

d031348 [Michael Armbrust] Merge remote-tracking branch 'apache/master' into registerTempTable
4dff086 [Michael Armbrust] Fix .java files too
89a2f12 [Michael Armbrust] Merge remote-tracking branch 'apache/master' into registerTempTable
0b7b71e [Michael Armbrust] Rename registerAsTable to registerTempTable
SPARK-2602 [BUILD] Tests steal focus under Java 6

As per https://issues.apache.org/jira/browse/SPARK-2602 , this may be resolved for Java 6 with the java.awt.headless system property, which never hurt anyone running a command line app. I tested it and seemed to get rid of focus stealing.

Author: Sean Owen <srowen@gmail.com>

Closes #1747 from srowen/SPARK-2602 and squashes the following commits:

b141018 [Sean Owen] Set java.awt.headless during tests
SPARK-2414 [BUILD] Add LICENSE entry for jquery

The JIRA concerned removing jquery, and this does not remove jquery. While it is distributed by Spark it should have an accompanying line in LICENSE, very technically, as per http://www.apache.org/dev/licensing-howto.html

Author: Sean Owen <srowen@gmail.com>

Closes #1748 from srowen/SPARK-2414 and squashes the following commits:

2fdb03c [Sean Owen] Add LICENSE entry for jquery
[Minor] Fixes on top of #1679

Minor fixes on top of #1679.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1736 from andrewor14/amend-#1679 and squashes the following commits:

3b46f5e [Andrew Or] Minor fixes