This PR is based on #4229, thanks prabeesh.

Closes #4229

Author: Prabeesh K <prabsmails@gmail.com>
Author: zsxwing <zsxwing@gmail.com>
Author: prabs <prabsmails@gmail.com>
Author: Prabeesh K <prabeesh.k@namshi.com>

Closes #7833 from zsxwing/pr4229 and squashes the following commits:

9570bec [zsxwing] Fix the variable name and check null in finally
4a9c79e [zsxwing] Fix pom.xml indentation
abf5f18 [zsxwing] Merge branch 'master' into pr4229
935615c [zsxwing] Fix the flaky MQTT tests
47278c5 [zsxwing] Include the project class files
478f844 [zsxwing] Add unpack
5f8a1d4 [zsxwing] Make the maven build generate the test jar for Python MQTT tests
734db99 [zsxwing] Merge branch 'master' into pr4229
126608a [Prabeesh K] address the comments
b90b709 [Prabeesh K] Merge pull request #1 from zsxwing/pr4229
d07f454 [zsxwing] Register StreamingListerner before starting StreamingContext; Revert unncessary changes; fix the python unit test
a6747cb [Prabeesh K] wait for starting the receiver before publishing data
87fc677 [Prabeesh K] address the comments:
97244ec [zsxwing] Make sbt build the assembly test jar for streaming mqtt
80474d1 [Prabeesh K] fix
1f0cfe9 [Prabeesh K] python style fix
e1ee016 [Prabeesh K] scala style fix
a5a8f9f [Prabeesh K] added Python test
9767d82 [Prabeesh K] implemented Python-friendly class
a11968b [Prabeesh K] fixed python style
795ec27 [Prabeesh K] address comments
ee387ae [Prabeesh K] Fix assembly jar location of mqtt-assembly
3f4df12 [Prabeesh K] updated version
b34c3c1 [prabs] adress comments
3aa7fff [prabs] Added Python streaming mqtt word count example
b7d42ff [prabs] Mqtt streaming support in Python

There are a few changes in this pull request:

1. Moved all data sources to execution.datasources, except the public JDBC APIs.
2. In order to maintain backward compatibility from 1, added a backward compatibility translation map in data source resolution.
3. Moved ui and metric package into execution.
4. Added more documentation on some internal classes.
5. Renamed DataSourceRegister.format -> shortName.
6. Added "override" modifier on shortName.
7. Removed IntSQLMetric.

Author: Reynold Xin <rxin@databricks.com>

Closes #8056 from rxin/SPARK-9763 and squashes the following commits:

9df4801 [Reynold Xin] Removed hardcoded name in test cases.
d9babc6 [Reynold Xin] Shorten.
e484419 [Reynold Xin] Removed VisibleForTesting.
171b812 [Reynold Xin] MimaExcludes.
2041389 [Reynold Xin] Compile ...
79dda42 [Reynold Xin] Compile.
0818ba3 [Reynold Xin] Removed IntSQLMetric.
c46884f [Reynold Xin] Two more fixes.
f9aa88d [Reynold Xin] [SPARK-9763][SQL] Minimize exposure of internal SQL classes.

https://issues.apache.org/jira/browse/SPARK-9602

Although we have hidden Akka behind RPC interface, I found that the Akka/Actor-related comments are still spreading everywhere. To make it consistent, we shall remove "actor"/"akka" words from the comments...

Author: CodingCat <zhunansjtu@gmail.com>

Closes #7936 from CodingCat/SPARK-9602 and squashes the following commits:

e8296a3 [CodingCat] remove actor words from comments

Certain use cases of Spark involve RDDs with long lineages that must be truncated periodically (e.g. GraphX). The existing way of doing it is through `rdd.checkpoint()`, which is expensive because it writes to HDFS. This patch provides an alternative to truncate lineages cheaply *without providing the same level of fault tolerance*.

**Local checkpointing** writes checkpointed data to the local file system through the block manager. It is much faster than replicating to a reliable storage and provides the same semantics as long as executors do not fail. It is accessible through a new operator `rdd.localCheckpoint()` and leaves the old one unchanged. Users may even decide to combine the two and call the reliable one less frequently.

The bulk of this patch involves refactoring the checkpointing interface to accept custom implementations of checkpointing. [Design doc](https://issues.apache.org/jira/secure/attachment/12741708/SPARK-7292-design.pdf).

Author: Andrew Or <andrew@databricks.com>

Closes #7279 from andrewor14/local-checkpoint and squashes the following commits:

729600f [Andrew Or] Oops, fix tests
34bc059 [Andrew Or] Avoid computing all partitions in local checkpoint
e43bbb6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
3be5aea [Andrew Or] Address comments
bf846a6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
ab003a3 [Andrew Or] Fix compile
c2e111b [Andrew Or] Address comments
33f167a [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
e908a42 [Andrew Or] Fix tests
f5be0f3 [Andrew Or] Use MEMORY_AND_DISK as the default local checkpoint level
a92657d [Andrew Or] Update a few comments
e58e3e3 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
4eb6eb1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
1bbe154 [Andrew Or] Simplify LocalCheckpointRDD
48a9996 [Andrew Or] Avoid traversing dependency tree + rewrite tests
62aba3f [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
db70dc2 [Andrew Or] Express local checkpointing through caching the original RDD
87d43c6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
c449b38 [Andrew Or] Fix style
4a182f3 [Andrew Or] Add fine-grained tests for local checkpointing
53b363b [Andrew Or] Rename a few more awkwardly named methods (minor)
e4cf071 [Andrew Or] Simplify LocalCheckpointRDD + docs + clean ups
4880deb [Andrew Or] Fix style
d096c67 [Andrew Or] Fix mima
172cb66 [Andrew Or] Fix mima?
e53d964 [Andrew Or] Fix style
56831c5 [Andrew Or] Add a few warnings and clear exception messages
2e59646 [Andrew Or] Add local checkpoint clean up tests
4dbbab1 [Andrew Or] Refactor CheckpointSuite to test local checkpointing
4514dc9 [Andrew Or] Clean local checkpoint files through RDD cleanups
0477eec [Andrew Or] Rename a few methods with awkward names (minor)
2e902e5 [Andrew Or] First implementation of local checkpointing
8447454 [Andrew Or] Fix tests
4ac1896 [Andrew Or] Refactor checkpoint interface for modularity

Dynamic allocation is a feature that allows a Spark application to scale the number of executors up and down dynamically based on the workload. Support was first introduced in YARN since 1.2, and then extended to Mesos coarse-grained mode recently. Today, it is finally supported in standalone mode as well!

I tested this locally and it works as expected. This is WIP because unit tests are coming.

Author: Andrew Or <andrew@databricks.com>

Closes #7532 from andrewor14/standalone-da and squashes the following commits:

b3c1736 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-da
879e928 [Andrew Or] Add end-to-end tests for standalone dynamic allocation
accc8f6 [Andrew Or] Address comments
ee686a8 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-da
c0a2c02 [Andrew Or] Fix build after merge conflict
24149eb [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-da
2e762d6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-da
6832bd7 [Andrew Or] Add tests for scheduling with executor limit
a82e907 [Andrew Or] Fix comments
0a8be79 [Andrew Or] Simplify logic by removing the worker blacklist
b7742af [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-da
2eb5f3f [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-da
1334e9a [Andrew Or] Fix MiMa
32abe44 [Andrew Or] Fix style
58cb06f [Andrew Or] Privatize worker blacklist for cleanliness
42ac215 [Andrew Or] Clean up comments and rewrite code for readability
49702d1 [Andrew Or] Clean up shuffle files after application exits
80047aa [Andrew Or] First working implementation

This PR adds the Python API for Kinesis, including a Python example and a simple unit test.

Author: zsxwing <zsxwing@gmail.com>

Closes #6955 from zsxwing/kinesis-python and squashes the following commits:

e42e471 [zsxwing] Merge branch 'master' into kinesis-python
455f7ea [zsxwing] Remove streaming_kinesis_asl_assembly module and simply add the source folder to streaming_kinesis_asl module
32e6451 [zsxwing] Merge remote-tracking branch 'origin/master' into kinesis-python
5082d28 [zsxwing] Fix the syntax error for Python 2.6
fca416b [zsxwing] Fix wrong comparison
96670ff [zsxwing] Fix the compilation error after merging master
756a128 [zsxwing] Merge branch 'master' into kinesis-python
6c37395 [zsxwing] Print stack trace for debug
7c5cfb0 [zsxwing] RUN_KINESIS_TESTS -> ENABLE_KINESIS_TESTS
cc9d071 [zsxwing] Fix the python test errors
466b425 [zsxwing] Add python tests for Kinesis
e33d505 [zsxwing] Merge remote-tracking branch 'origin/master' into kinesis-python
3da2601 [zsxwing] Fix the kinesis folder
687446b [zsxwing] Fix the error message and the maven output path
add2beb [zsxwing] Merge branch 'master' into kinesis-python
4957c0b [zsxwing] Add the Python API for Kinesis

This was turned off accidentally in #7591.

Author: Reynold Xin <rxin@databricks.com>

Closes #7637 from rxin/enable-mem-leak-detect and squashes the following commits:

34bc3ef [Reynold Xin] Enable memory leak detection for Tungsten.

Reverts ObjectPool. As it stands, it has a few problems:

1. ObjectPool doesn't work with spilling and memory accounting.
2. I don't think in the long run the idea of an object pool is what we want to support, since it essentially goes back to unmanaged memory, and creates pressure on GC, and is hard to account for the total in memory size.
3. The ObjectPool patch removed the specialized getters for strings and binary, and as a result, actually introduced branches when reading non primitive data types.

If we do want to support arbitrary user defined types in the future, I think we can just add an object array in UnsafeRow, rather than relying on indirect memory addressing through a pool. We also need to pick execution strategies that are optimized for those, rather than keeping a lot of unserialized JVM objects in memory during aggregation.

This is probably the hardest thing I had to revert in Spark, due to recent patches that also change the same part of the code. Would be great to get a careful look.

Author: Reynold Xin <rxin@databricks.com>

Closes #7591 from rxin/revert-object-pool and squashes the following commits:

01db0bc [Reynold Xin] Scala style.
eda89fc [Reynold Xin] Fixed describe.
2967118 [Reynold Xin] Fixed accessor for JoinedRow.
e3294eb [Reynold Xin] Merge branch 'master' into revert-object-pool
657855f [Reynold Xin] Temp commit.
c20f2c8 [Reynold Xin] Style fix.
fe37079 [Reynold Xin] Revert "[SPARK-8579] [SQL] support arbitrary object in UnsafeRow"

I've seen a few cases in the past few weeks that the compiler is throwing warnings that are caused by legitimate bugs. This patch upgrades warnings to errors, except deprecation warnings.

Note that ideally we should be able to mark deprecation warnings as errors as well. However, due to the lack of ability to suppress individual warning messages in the Scala compiler, we cannot do that (since we do need to access deprecated APIs in Hadoop).

Most of the work are done by ericl.

Author: Reynold Xin <rxin@databricks.com>
Author: Eric Liang <ekl@databricks.com>

Closes #7598 from rxin/warnings and squashes the following commits:

beb311b [Reynold Xin] Fixed tests.
542c031 [Reynold Xin] Fixed one more warning.
87c354a [Reynold Xin] Fixed all non-deprecation warnings.
78660ac [Eric Liang] first effort to fix warnings

This way, the sources package contains only public facing interfaces.

Author: Reynold Xin <rxin@databricks.com>

Closes #7565 from rxin/move-ds and squashes the following commits:

7661aff [Reynold Xin] Mima
9d5196a [Reynold Xin] Rearranged imports.
3dd7174 [Reynold Xin] [SPARK-8906][SQL] Move all internal data source classes into execution.datasources.

This PR also remove the duplicated code between registerFunction and UserDefinedFunction.

cc JoshRosen

Author: Davies Liu <davies@databricks.com>

Closes #7450 from davies/fix_return_type and squashes the following commits:

e80bf9f [Davies Liu] remove debugging code
f94b1f6 [Davies Liu] fix mima
8f9c58b [Davies Liu] convert returned object from UDF into internal type

Modifying Vector, DenseVector, and SparseVector to implement argmax functionality. This work is to set the stage for changes to be done in Spark-7423.

Author: George Dittmar <georgedittmar@gmail.com>
Author: George <dittmar@Georges-MacBook-Pro.local>
Author: dittmarg <george.dittmar@webtrends.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #6112 from GeorgeDittmar/SPARK-7422 and squashes the following commits:

3e0a939 [George Dittmar] Merge pull request #1 from mengxr/SPARK-7422
127dec5 [Xiangrui Meng] update argmax impl
2ea6a55 [George Dittmar] Added MimaExcludes for Vectors.argmax
98058f4 [George Dittmar] Merge branch 'master' of github.com:apache/spark into SPARK-7422
5fd9380 [George Dittmar] fixing style check error
42341fb [George Dittmar] refactoring arg max check to better handle zero values
b22af46 [George Dittmar] Fixing spaces between commas in unit test
f2eba2f [George Dittmar] Cleaning up unit tests to be fewer lines
aa330e3 [George Dittmar] Fixing some last if else spacing issues
ac53c55 [George Dittmar] changing dense vector argmax unit test to be one line call vs 2
d5b5423 [George Dittmar] Fixing code style and updating if logic on when to check for zero values
ee1a85a [George Dittmar] Cleaning up unit tests a bit and modifying a few cases
3ee8711 [George Dittmar] Fixing corner case issue with zeros in the active values of the sparse vector. Updated unit tests
b1f059f [George Dittmar] Added comment before we start arg max calculation. Updated unit tests to cover corner cases
f21dcce [George Dittmar] commit
af17981 [dittmarg] Initial work fixing bug that was made clear in pr
eeda560 [George] Fixing SparseVector argmax function to ignore zero values while doing the calculation.
4526acc [George] Merge branch 'master' of github.com:apache/spark into SPARK-7422
df9538a [George] Added argmax to sparse vector and added unit test
3cffed4 [George] Adding unit tests for argmax functions for Dense and Sparse vectors
04677af [George] initial work on adding argmax to Vector and SparseVector

Author: Reynold Xin <rxin@databricks.com>

Closes #7501 from rxin/jsonrdd and squashes the following commits:

767ec55 [Reynold Xin] More Mima
51f456e [Reynold Xin] Mima exclude.
789cb80 [Reynold Xin] Fixed compilation error.
b4cf50d [Reynold Xin] [SPARK-8278] Remove non-streaming JSON reader.

I Implemented the KMeans API for spark.ml Pipelines. But it doesn't include clustering abstractions for spark.ml (SPARK-7610). It would fit for another issues. And I'll try it later, since we are trying to add the hierarchical clustering algorithms in another issue. Thanks.

[SPARK-7879] KMeans API for spark.ml Pipelines - ASF JIRA https://issues.apache.org/jira/browse/SPARK-7879

Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com>

Closes #6756 from yu-iskw/SPARK-7879 and squashes the following commits:

be752de [Yu ISHIKAWA] Add assertions
a14939b [Yu ISHIKAWA] Fix the dashed line's length in pyspark.ml.rst
4c61693 [Yu ISHIKAWA] Remove the test about whether "features" and "prediction" columns exist or not in Python
fb2417c [Yu ISHIKAWA] Use getInt, instead of get
f397be4 [Yu ISHIKAWA] Switch the comparisons.
ca78b7d [Yu ISHIKAWA] Add the Scala docs about the constraints of each parameter.
effc650 [Yu ISHIKAWA] Using expertSetParam and expertGetParam
c8dc6e6 [Yu ISHIKAWA] Remove an unnecessary test
19a9d63 [Yu ISHIKAWA] Include spark.ml.clustering to python tests
1abb19c [Yu ISHIKAWA] Add the statements about spark.ml.clustering into pyspark.ml.rst
f8338bc [Yu ISHIKAWA] Add the placeholders in Python
4a03003 [Yu ISHIKAWA] Test for contains in Python
6566c8b [Yu ISHIKAWA] Use `get`, instead of `apply`
288e8d5 [Yu ISHIKAWA] Using `contains` to check the column names
5a7d574 [Yu ISHIKAWA] Renamce `validateInitializationMode` to `validateInitMode` and remove throwing exception
97cfae3 [Yu ISHIKAWA] Fix the type of return value of `KMeans.copy`
e933723 [Yu ISHIKAWA] Remove the default value of seed from the Model class
978ee2c [Yu ISHIKAWA] Modify the docs of KMeans, according to mllib's KMeans
2ec80bc [Yu ISHIKAWA] Fit on 1 line
e186be1 [Yu ISHIKAWA] Make a few variables, setters and getters be expert ones
b2c205c [Yu ISHIKAWA] Rename the method `getInitializationSteps` to `getInitSteps` and `setInitializationSteps` to `setInitSteps` in Scala and Python
f43f5b4 [Yu ISHIKAWA] Rename the method `getInitializationMode` to `getInitMode` and `setInitializationMode` to `setInitMode` in Scala and Python
3cb5ba4 [Yu ISHIKAWA] Modify the description about epsilon and the validation
4fa409b [Yu ISHIKAWA] Add a comment about the default value of epsilon
2f392e1 [Yu ISHIKAWA] Make some variables `final` and Use `IntParam` and `DoubleParam`
19326f8 [Yu ISHIKAWA] Use `udf`, instead of callUDF
4d2ad1e [Yu ISHIKAWA] Modify the indentations
0ae422f [Yu ISHIKAWA] Add a test for `setParams`
4ff7913 [Yu ISHIKAWA] Add "ml.clustering" to `javacOptions` in SparkBuild.scala
11ffdf1 [Yu ISHIKAWA] Use `===` and the variable
220a176 [Yu ISHIKAWA] Set a random seed in the unit testing
92c3efc [Yu ISHIKAWA] Make the points for a test be fewer
c758692 [Yu ISHIKAWA] Modify the parameters of KMeans in Python
6aca147 [Yu ISHIKAWA] Add some unit testings to validate the setter methods
687cacc [Yu ISHIKAWA] Alias mllib.KMeans as MLlibKMeans in KMeansSuite.scala
a4dfbef [Yu ISHIKAWA] Modify the last brace and indentations
5bedc51 [Yu ISHIKAWA] Remve an extra new line
444c289 [Yu ISHIKAWA] Add the validation for `runs`
e41989c [Yu ISHIKAWA] Modify how to validate `initStep`
7ea133a [Yu ISHIKAWA] Change how to validate `initMode`
7991e15 [Yu ISHIKAWA] Add a validation for `k`
c2df35d [Yu ISHIKAWA] Make `predict` private
93aa2ff [Yu ISHIKAWA] Use `withColumn` in `transform`
d3a79f7 [Yu ISHIKAWA] Remove the inhefited docs
e9532e1 [Yu ISHIKAWA] make `parentModel` of KMeansModel private
8559772 [Yu ISHIKAWA] Remove the `paramMap` parameter of KMeans
6684850 [Yu ISHIKAWA] Rename `initializationSteps` to `initSteps`
99b1b96 [Yu ISHIKAWA] Rename `initializationMode` to `initMode`
79ea82b [Yu ISHIKAWA] Modify the parameters of KMeans docs
6569bcd [Yu ISHIKAWA] Change how to set the default values with `setDefault`
20a795a [Yu ISHIKAWA] Change how to set the default values with `setDefault`
11c2a12 [Yu ISHIKAWA] Limit the imports
badb481 [Yu ISHIKAWA] Alias spark.mllib.{KMeans, KMeansModel}
f80319a [Yu ISHIKAWA] Rebase mater branch and add copy methods
85d92b1 [Yu ISHIKAWA] Add `KMeans.setPredictionCol`
aa9469d [Yu ISHIKAWA] Fix a python test suite error caused by python 3.x
c2d6bcb [Yu ISHIKAWA] ADD Java test suites of the KMeans API for spark.ml Pipeline
598ed2e [Yu ISHIKAWA] Implement the KMeans API for spark.ml Pipelines in Python
63ad785 [Yu ISHIKAWA] Implement the KMeans API for spark.ml Pipelines in Scala

This PR enables SparkR to dynamically ship the SparkR binary package to the AM node in YARN cluster mode, thus it is no longer required that the SparkR package be installed on each worker node.

This PR uses the JDK jar tool to package the SparkR package, because jar is thought to be available on both Linux/Windows platforms where JDK has been installed.

This PR does not address the R worker involved in RDD API. Will address it in a separate JIRA issue.

This PR does not address SBT build. SparkR installation and packaging by SBT will be addressed in a separate JIRA issue.

R/install-dev.bat is not tested. shivaram , Could you help to test it?

Author: Sun Rui <rui.sun@intel.com>

Closes #6743 from sun-rui/SPARK-6797 and squashes the following commits:

ca63c86 [Sun Rui] Adjust MimaExcludes after rebase.
7313374 [Sun Rui] Fix unit test errors.
72695fb [Sun Rui] Fix unit test failures.
193882f [Sun Rui] Fix Mima test error.
fe25a33 [Sun Rui] Fix Mima test error.
35ecfa3 [Sun Rui] Fix comments.
c38a005 [Sun Rui] Unzipped SparkR binary package is still required for standalone and Mesos modes.
b05340c [Sun Rui] Fix scala style.
2ca5048 [Sun Rui] Fix comments.
1acefd1 [Sun Rui] Fix scala style.
0aa1e97 [Sun Rui] Fix scala style.
41d4f17 [Sun Rui] Add support for locating SparkR package for R workers required by RDD APIs.
49ff948 [Sun Rui] Invoke jar.exe with full path in install-dev.bat.
7b916c5 [Sun Rui] Use 'rem' consistently.
3bed438 [Sun Rui] Add a comment.
681afb0 [Sun Rui] Fix a bug that RRunner does not handle client deployment modes.
cedfbe2 [Sun Rui] [SPARK-6797][SPARKR] Add support for YARN cluster mode.

Author: Jonathan Alter <jonalter@users.noreply.github.com>

Closes #7093 from jonalter/SPARK-7977 and squashes the following commits:

ccd44cc [Jonathan Alter] Changed println to log in ThreadingSuite
7fcac3e [Jonathan Alter] Reverting to println in ThreadingSuite
10724b6 [Jonathan Alter] Changing some printlns to logs in tests
eeec1e7 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
0b1dcb4 [Jonathan Alter] More println cleanup
aedaf80 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
925fd98 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
0c16fa3 [Jonathan Alter] Replacing some printlns with logs
45c7e05 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
5c8e283 [Jonathan Alter] Allowing println in audit-release examples
5b50da1 [Jonathan Alter] Allowing printlns in example files
ca4b477 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
83ab635 [Jonathan Alter] Fixing new printlns
54b131f [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
1cd8a81 [Jonathan Alter] Removing some unnecessary comments and printlns
b837c3a [Jonathan Alter] Disallowing println

This PR adds `metadata` to `InputInfo`. `InputDStream` can report its metadata for a batch and it will be shown in the batch page.

For example,

![screen shot](https://cloud.githubusercontent.com/assets/1000778/8403741/d6ffc7e2-1e79-11e5-9888-c78c1575123a.png)

FileInputDStream will display the new files for a batch, and DirectKafkaInputDStream will display its offset ranges.

Author: zsxwing <zsxwing@gmail.com>

Closes #7081 from zsxwing/input-metadata and squashes the following commits:

f7abd9b [zsxwing] Revert the space changes in project/MimaExcludes.scala
d906209 [zsxwing] Merge branch 'master' into input-metadata
74762da [zsxwing] Fix MiMa tests
7903e33 [zsxwing] Merge branch 'master' into input-metadata
450a46c [zsxwing] Address comments
1d94582 [zsxwing] Raname InputInfo to StreamInputInfo and change "metadata" to Map[String, Any]
d496ae9 [zsxwing] Add input metadata in the batch page

This PR fixes the converter for Python DataFrame, especially for DecimalType

Closes #7106

Author: Davies Liu <davies@databricks.com>

Closes #7131 from davies/decimal_python and squashes the following commits:

4d3c234 [Davies Liu] Merge branch 'master' of github.com:apache/spark into decimal_python
20531d6 [Davies Liu] Merge branch 'master' of github.com:apache/spark into decimal_python
7d73168 [Davies Liu] fix conflit
6cdd86a [Davies Liu] Merge branch 'master' of github.com:apache/spark into decimal_python
7104e97 [Davies Liu] improve type infer
9cd5a21 [Davies Liu] run python tests with SPARK_PREPEND_CLASSES
829a05b [Davies Liu] fix UDT in python
c99e8c5 [Davies Liu] fix mima
c46814a [Davies Liu] convert decimal for Python DataFrames

As rxin suggested in #7298 , we should consider to remove `RDDApi`.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #7302 from sarutak/remove-rddapi and squashes the following commits:

e495d35 [Kousuke Saruta] Fixed mima
cb7ebb9 [Kousuke Saruta] Removed overriding RDDApi

[SPARK-6123] [SPARK-6775] [SPARK-6776] [SQL] Refactors Parquet read path for interoperability and backwards-compatibility

This PR is a follow-up of #6617 and is part of [SPARK-6774] [2], which aims to ensure interoperability and backwards-compatibility for Spark SQL Parquet support.  And this one fixes the read path.  Now Spark SQL is expected to be able to read legacy Parquet data files generated by most (if not all) common libraries/tools like parquet-thrift, parquet-avro, and parquet-hive. However, we still need to refactor the write path to write standard Parquet LISTs and MAPs ([SPARK-8848] [4]).

### Major changes

1. `CatalystConverter` class hierarchy refactoring

   - Replaces `CatalystConverter` trait with a much simpler `ParentContainerUpdater`.

     Now instead of extending the original `CatalystConverter` trait, every converter class accepts an updater which is responsible for propagating the converted value to some parent container. For example, appending array elements to a parent array buffer, appending a key-value pairs to a parent mutable map, or setting a converted value to some specific field of a parent row. Root converter doesn't have a parent and thus uses a `NoopUpdater`.

     This simplifies the design since converters don't need to care about details of their parent converters anymore.

   - Unifies `CatalystRootConverter`, `CatalystGroupConverter` and `CatalystPrimitiveRowConverter` into `CatalystRowConverter`

     Specifically, now all row objects are represented by `SpecificMutableRow` during conversion.

   - Refactors `CatalystArrayConverter`, and removes `CatalystArrayContainsNullConverter` and `CatalystNativeArrayConverter`

     `CatalystNativeArrayConverter` was probably designed with the intention of avoiding boxing costs. However, the way it uses Scala generics actually doesn't achieve this goal.

     The new `CatalystArrayConverter` handles both nullable and non-nullable array elements in a consistent way.

   - Implements backwards-compatibility rules in `CatalystArrayConverter`

     When Parquet records are being converted, schema of Parquet files should have already been verified. So we only need to care about the structure rather than field names in the Parquet schema. Since all map objects represented in legacy systems have the same structure as the standard one (see [backwards-compatibility rules for MAP] [1]), we only need to deal with LIST (namely array) in `CatalystArrayConverter`.

2. Requested columns handling

   When specifying requested columns in `RowReadSupport`, we used to use a Parquet `MessageType` converted from a Catalyst `StructType` which contains all requested columns.  This is not preferable when taking compatibility and interoperability into consideration.  Because the actual Parquet file may have different physical structure from the converted schema.

   In this PR, the schema for requested columns is constructed using the following method:

   - For a column that exists in the target Parquet file, we extract the column type by name from the full file schema, and construct a single-field `MessageType` for that column.
   - For a column that doesn't exist in the target Parquet file, we create a single-field `StructType` and convert it to a `MessageType` using `CatalystSchemaConverter`.
   - Unions all single-field `MessageType`s into a full schema containing all requested fields

   With this change, we also fix [SPARK-6123] [3] by validating the global schema against each individual Parquet part-files.

### Testing

This PR also adds compatibility tests for parquet-avro, parquet-thrift, and parquet-hive. Please refer to `README.md` under `sql/core/src/test` for more information about these tests. To avoid build time code generation and adding extra complexity to the build system, Java code generated from testing Thrift schema and Avro IDL is also checked in.

[1]: https://github.com/apache/incubator-parquet-format/blob/master/LogicalTypes.md#backward-compatibility-rules-1
[2]: https://issues.apache.org/jira/browse/SPARK-6774
[3]: https://issues.apache.org/jira/browse/SPARK-6123
[4]: https://issues.apache.org/jira/browse/SPARK-8848

Author: Cheng Lian <lian@databricks.com>

Closes #7231 from liancheng/spark-6776 and squashes the following commits:

360fe18 [Cheng Lian] Adds ParquetHiveCompatibilitySuite
c6fbc06 [Cheng Lian] Removes WIP file committed by mistake
b8c1295 [Cheng Lian] Excludes the whole parquet package from MiMa
598c3e8 [Cheng Lian] Adds extra Maven repo for hadoop-lzo, which is a transitive dependency of parquet-thrift
926af87 [Cheng Lian] Simplifies Parquet compatibility test suites
7946ee1 [Cheng Lian] Fixes Scala styling issues
3d7ab36 [Cheng Lian] Fixes .rat-excludes
a8f13bb [Cheng Lian] Using Parquet writer API to do compatibility tests
f2208cd [Cheng Lian] Adds README.md for Thrift/Avro code generation
1d390aa [Cheng Lian] Adds parquet-thrift compatibility test
440f7b3 [Cheng Lian] Adds generated files to .rat-excludes
13b9121 [Cheng Lian] Adds ParquetAvroCompatibilitySuite
06cfe9d [Cheng Lian] Adds comments about TimestampType handling
a099d3e [Cheng Lian] More comments
0cc1b37 [Cheng Lian] Fixes MiMa checks
884d3e6 [Cheng Lian] Fixes styling issue and reverts unnecessary changes
802cbd7 [Cheng Lian] Fixes bugs related to schema merging and empty requested columns
38fe1e7 [Cheng Lian] Adds explicit return type
7fb21f1 [Cheng Lian] Reverts an unnecessary debugging change
1781dff [Cheng Lian] Adds test case for SPARK-8811
6437d4b [Cheng Lian] Assembles requested schema from Parquet file schema
bcac49f [Cheng Lian] Removes the 16-byte restriction of decimals
a74fb2c [Cheng Lian] More comments
0525346 [Cheng Lian] Removes old Parquet record converters
03c3bd9 [Cheng Lian] Refactors Parquet read path to implement backwards-compatibility rules

All compressed sensing applications, and some of the regression use-cases will have better result by turning the feature scaling off. However, if we implement this naively by training the dataset without doing any standardization, the rate of convergency will not be good. This can be implemented by still standardizing the training dataset but we penalize each component differently to get effectively the same objective function but a better numerical problem. As a result, for those columns with high variances, they will be penalized less, and vice versa. Without this, since all the features are standardized, so they will be penalized the same.

In R, there is an option for this.
`standardize`
Logical flag for x variable standardization, prior to fitting the model sequence. The coefficients are always returned on the original scale. Default is standardize=TRUE. If variables are in the same units already, you might not wish to standardize. See details below for y standardization with family="gaussian".

+cc holdenk mengxr jkbradley

Author: DB Tsai <dbt@netflix.com>

Closes #7080 from dbtsai/lors and squashes the following commits:

877e6c7 [DB Tsai] repahse the doc
7cf45f2 [DB Tsai] address feedback
78d75c9 [DB Tsai] small change
c2c9e60 [DB Tsai] style
6e1a8e0 [DB Tsai] first commit

I am increasing the perm gen size to 256m.

https://issues.apache.org/jira/browse/SPARK-8776

Author: Yin Huai <yhuai@databricks.com>

Closes #7196 from yhuai/SPARK-8776 and squashes the following commits:

60901b4 [Yin Huai] Fix test.
d44b713 [Yin Huai] Make sparkShell and hiveConsole use 256m PermGen size.
30aaf8e [Yin Huai] Increase the default PermGen size to 256m.

Matrices allow zeros to be stored in values. Sometimes a method is handy to check if the numNonZeros are same as number of Active values.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #6904 from MechCoder/nnz_matrix and squashes the following commits:

252c6b7 [MechCoder] Add to MiMa excludes
e2390f5 [MechCoder] Use count instead of foreach
2f62b2f [MechCoder] Add to MiMa excludes
d6e96ef [MechCoder] [SPARK-8479] Add numNonzeros and numActives to linalg.Matrices

Author: jerryshao <saisai.shao@intel.com>

Closes #7120 from jerryshao/SPARK-7820 and squashes the following commits:

6902439 [jerryshao] fix Java8-tests suite compile error under sbt

Author: zsxwing <zsxwing@gmail.com>

Closes #6830 from zsxwing/flume-python and squashes the following commits:

78dfdac [zsxwing] Fix the compile error in the test code
f1bf3c0 [zsxwing] Address TD's comments
0449723 [zsxwing] Add sbt goal streaming-flume-assembly/assembly
e93736b [zsxwing] Fix the test case for determine_modules_to_test
9d5821e [zsxwing] Fix pyspark_core dependencies
f9ee681 [zsxwing] Merge branch 'master' into flume-python
7a55837 [zsxwing] Add streaming_flume_assembly to run-tests.py
b96b0de [zsxwing] Merge branch 'master' into flume-python
ce85e83 [zsxwing] Fix incompatible issues for Python 3
01cbb3d [zsxwing] Add import sys
152364c [zsxwing] Fix the issue that StringIO doesn't work in Python 3
14ba0ff [zsxwing] Add flume-assembly for sbt building
b8d5551 [zsxwing] Merge branch 'master' into flume-python
4762c34 [zsxwing] Fix the doc
0336579 [zsxwing] Refactor Flume unit tests and also add tests for Python API
9f33873 [zsxwing] Add the Python API for Flume

This PR introduces `CatalystSchemaConverter` for converting Parquet schema to Spark SQL schema and vice versa.  Original conversion code in `ParquetTypesConverter` is removed. Benefits of the new version are:

1. When converting Spark SQL schemas, it generates standard Parquet schemas conforming to [the most updated Parquet format spec] [1]. Converting to old style Parquet schemas is also supported via feature flag `spark.sql.parquet.followParquetFormatSpec` (which is set to `false` for now, and should be set to `true` after both read and write paths are fixed).

   Note that although this version of Parquet format spec hasn't been officially release yet, Parquet MR 1.7.0 already sticks to it. So it should be safe to follow.

1. It implements backwards-compatibility rules described in the most updated Parquet format spec. Thus can recognize more schema patterns generated by other/legacy systems/tools.
1. Code organization follows convention used in [parquet-mr] [2], which is easier to follow. (Structure of `CatalystSchemaConverter` is similar to `AvroSchemaConverter`).

To fully implement backwards-compatibility rules in both read and write path, we also need to update `CatalystRowConverter` (which is responsible for converting Parquet records to `Row`s), `RowReadSupport`, and `RowWriteSupport`. These would be done in follow-up PRs.

TODO

- [x] More schema conversion test cases for legacy schema patterns.

[1]: https://github.com/apache/parquet-format/blob/ea095226597fdbecd60c2419d96b54b2fdb4ae6c/LogicalTypes.md
[2]: https://github.com/apache/parquet-mr/

Author: Cheng Lian <lian@databricks.com>

Closes #6617 from liancheng/spark-6777 and squashes the following commits:

2a2062d [Cheng Lian] Don't convert decimals without precision information
b60979b [Cheng Lian] Adds a constructor which accepts a Configuration, and fixes default value of assumeBinaryIsString
743730f [Cheng Lian] Decimal scale shouldn't be larger than precision
a104a9e [Cheng Lian] Fixes Scala style issue
1f71d8d [Cheng Lian] Adds feature flag to allow falling back to old style Parquet schema conversion
ba84f4b [Cheng Lian] Fixes MapType schema conversion bug
13cb8d5 [Cheng Lian] Fixes MiMa failure
81de5b0 [Cheng Lian] Fixes UDT, workaround read path, and add tests
28ef95b [Cheng Lian] More AnalysisExceptions
b10c322 [Cheng Lian] Replaces require() with analysisRequire() which throws AnalysisException
cceaf3f [Cheng Lian] Implements backwards compatibility rules in CatalystSchemaConverter

This commit changes the MiMa tests to test against the released 1.4.0 artifacts rather than 1.4.0-rc4; this change is necessary to fix a Jenkins build break since it seems that the RC4 snapshot is no longer available via Maven.

I also enabled MiMa checks for the `launcher` subproject, which we should have done right after 1.4.0 was released.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6974 from JoshRosen/mima-hotfix and squashes the following commits:

4b4175a [Josh Rosen] [HOTFIX] [BUILD] Fix MiMa checks in master branch; enable MiMa for launcher project

Author: Holden Karau <holden@pigscanfly.ca>

Closes #6927 from holdenk/SPARK-7888-Be-able-to-disable-intercept-in-Linear-Regression-in-ML-package and squashes the following commits:

0ad384c [Holden Karau] Add MiMa excludes
4016fac [Holden Karau] Switch to wild card import, remove extra blank lines
ae5baa8 [Holden Karau] CR feedback, move the fitIntercept down rather than changing ymean and etc above
f34971c [Holden Karau] Fix some more long lines
319bd3f [Holden Karau] Fix long lines
3bb9ee1 [Holden Karau] Update the regression suite tests
7015b9f [Holden Karau] Our code performs the same with R, except we need more than one data point but that seems reasonable
0b0c8c0 [Holden Karau] fix the issue with the sample R code
e2140ba [Holden Karau] Add a test, it fails!
5e84a0b [Holden Karau] Write out thoughts and use the correct trait
91ffc0a [Holden Karau] more murh
006246c [Holden Karau] murp?

This PR change to convert julian day to unix timestamp directly (without Calendar and Timestamp).

cc adrian-wang rxin

Author: Davies Liu <davies@databricks.com>

Closes #6759 from davies/improve_ts and squashes the following commits:

849e301 [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts
b0e4cad [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts
8e2d56f [Davies Liu] address comments
634b9f5 [Davies Liu] fix mima
4891efb [Davies Liu] address comment
bfc437c [Davies Liu] fix build
ae5979c [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts
602b969 [Davies Liu] remove jodd
2f2e48c [Davies Liu] fix test
8ace611 [Davies Liu] fix mima
212143b [Davies Liu] fix mina
c834108 [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts
a3171b8 [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts
5233974 [Davies Liu] fix scala style
361fd62 [Davies Liu] address comments
ea196d4 [Davies Liu] improve timestamp from parquet

…ed KafkaRDD methods.  Possible fix for [SPARK-7122], but probably a worthwhile optimization regardless.

Author: cody koeninger <cody@koeninger.org>

Closes #6632 from koeninger/kafka-rdd-count and squashes the following commits:

321340d [cody koeninger] [SPARK-8127][Streaming][Kafka] additional test of ordering of take()
5a05d0f [cody koeninger] [SPARK-8127][Streaming][Kafka] additional test of isEmpty
f68bd32 [cody koeninger] [Streaming][Kafka][SPARK-8127] code cleanup
9555b73 [cody koeninger] Merge branch 'master' into kafka-rdd-count
253031d [cody koeninger] [Streaming][Kafka][SPARK-8127] mima exclusion for change to private method
8974b9e [cody koeninger] [Streaming][Kafka][SPARK-8127] check offset ranges before constructing KafkaRDD
c3768c5 [cody koeninger] [Streaming][Kafka] Take advantage of offset range info for size-related KafkaRDD methods.  Possible fix for [SPARK-7122], but probably a worthwhile optimization regardless.

to make it easier to start & stop http servers in sbt
https://issues.apache.org/jira/browse/SPARK-6782

Author: Imran Rashid <irashid@cloudera.com>

Closes #5426 from squito/SPARK-6782 and squashes the following commits:

dc4fb19 [Imran Rashid] add sbt-revolved plugin, to make it easier to start & stop http servers in sbt

If you ran "clean" at the top-level sbt project, the temp dir would
go away, so running "test" without restarting sbt would fail. This
fixes that by making sure the temp dir exists before running tests.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #6805 from vanzin/SPARK-8126-fix and squashes the following commits:

12d7768 [Marcelo Vanzin] [SPARK-8126] [build] Make sure temp dir exists when running tests.

Unit test is still in Scala.

Author: Reynold Xin <rxin@databricks.com>

Closes #6738 from rxin/utf8string-java and squashes the following commits:

562dc6e [Reynold Xin] Flag...
98e600b [Reynold Xin] Another try with encoding setting ..
cfa6bdf [Reynold Xin] Merge branch 'master' into utf8string-java
a3b124d [Reynold Xin] Try different UTF-8 encoded characters.
1ff7c82 [Reynold Xin] Enable UTF-8 encoding.
82d58cc [Reynold Xin] Reset run-tests.
2cb3c69 [Reynold Xin] Use utf-8 encoding in set bytes.
53f8ef4 [Reynold Xin] Hack Jenkins to run one test.
9a48e8d [Reynold Xin] Fixed runtime compilation error.
911c450 [Reynold Xin] Moved unit test also to Java.
4eff7bd [Reynold Xin] Improved unit test coverage.
8e89a3c [Reynold Xin] Fixed tests.
77c64bd [Reynold Xin] Fixed string type codegen.
ffedb62 [Reynold Xin] Code review feedback.
0967ce6 [Reynold Xin] Fixed import ordering.
45a123d [Reynold Xin] [SPARK-8286] Rewrite UTF8String in Java and move it into unsafe package.

This change is a simple one and specifies a stack size of 4096k instead of the vendor default for Java tests (the defaults vary between Java vendors). This remedies test failures observed with JavaALSSuite with IBM and Oracle Java owing to a lower default size in comparison to the size with OpenJDK. 4096k is a suitable default where the tests pass with each Java vendor tested. The alternative is to reduce the number of iterations in the test (no observed failures with 5 iterations instead of 15).

-Xss works with Oracle's HotSpot VM, IBM's J9 VM and OpenJDK (IcedTea).

I have ensured this does not have any negative implications for other tests.

Author: Adam Roberts <aroberts@uk.ibm.com>
Author: a-roberts <aroberts@uk.ibm.com>

Closes #6727 from a-roberts/IncJavaStackSize and squashes the following commits:

ab40aea [Adam Roberts] Specify stack size for SBT builds
5032d8d [a-roberts] Update pom.xml

Even with all the efforts to cleanup the temp directories created by
unit tests, Spark leaves a lot of garbage in /tmp after a test run.
This change overrides java.io.tmpdir to place those files under the
build directory instead.

After an sbt full unit test run, I was left with > 400 MB of temp
files. Since they're now under the build dir, it's much easier to
clean them up.

Also make a slight change to a unit test to make it not pollute the
source directory with test data.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #6674 from vanzin/SPARK-8126 and squashes the following commits:

0f8ad41 [Marcelo Vanzin] Make sure tmp dir exists when tests run.
643e916 [Marcelo Vanzin] [MINOR] [BUILD] Use custom temp directory during build.

see if requiring producer acks eliminates the need for waitUntilLeaderOffset calls in tests

Author: cody koeninger <cody@koeninger.org>

Closes #5921 from koeninger/kafka-0.8.2-test-cleanup and squashes the following commits:

1e89dc8 [cody koeninger] Merge branch 'master' into kafka-0.8.2-test-cleanup
4662828 [cody koeninger] [Streaming][Kafka] filter mima issue for removal of method from private test class
af1e083 [cody koeninger] Merge branch 'master' into kafka-0.8.2-test-cleanup
4298ac2 [cody koeninger] [Streaming][Kafka] update comment to trigger jenkins attempt
1274afb [cody koeninger] [Streaming][Kafka] see if requiring producer acks eliminates the need for waitUntilLeaderOffset calls in tests

This reverts commit b16b5434.

Even with all the efforts to cleanup the temp directories created by
unit tests, Spark leaves a lot of garbage in /tmp after a test run.
This change overrides java.io.tmpdir to place those files under the
build directory instead.

After an sbt full unit test run, I was left with > 400 MB of temp
files. Since they're now under the build dir, it's much easier to
clean them up.

Also make a slight change to a unit test to make it not pollute the
source directory with test data.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #6653 from vanzin/unit-test-tmp and squashes the following commits:

31e2dd5 [Marcelo Vanzin] Fix tests that depend on each other.
aa92944 [Marcelo Vanzin] [minor] [build] Use custom temp directory during build.

Derby has a `derby.system.durability` configuration property that can be used to disable I/O synchronization calls for writes. This sacrifices durability but can result in large performance gains, which is appropriate for tests.

We should enable this in our test system properties in order to speed up the Hive compatibility tests. I saw 2-3x speedups locally with this change.

See https://db.apache.org/derby/docs/10.8/ref/rrefproperdurability.html for more documentation of this property.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6651 from JoshRosen/hive-compat-suite-speedup and squashes the following commits:

b7a08a2 [Josh Rosen] Set derby.system.durability=test in our unit tests.

This patch replaces Distinct with Aggregate in the optimizer, so Distinct will become
more efficient over time as we optimize Aggregate (via Tungsten).

Author: Reynold Xin <rxin@databricks.com>

Closes #6637 from rxin/replace-distinct and squashes the following commits:

b3cc50e [Reynold Xin] Mima excludes.
93d6117 [Reynold Xin] Code review feedback.
87e4741 [Reynold Xin] [SPARK-7440][SQL] Remove physical Distinct operator in favor of Aggregate.