Added user guide sections with code examples.
Also added small Java unit tests to test Java example in guide.

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #6127 from jkbradley/feature-guide-2 and squashes the following commits:

cd47f4b [Joseph K. Bradley] Updated based on code review
f16bcec [Joseph K. Bradley] Fixed merge issues and update Python examples print calls for Python 3
0a862f9 [Joseph K. Bradley] Added Normalizer, StandardScaler to ml-features doc, plus small Java unit tests
a21c2d6 [Joseph K. Bradley] Updated ml-features.md with IDF

Just a small change: fixed a broken link in the MLlib Linear Methods documentation by removing a newline character between the link title and link address.

Author: Mike Dusenberry <dusenberrymw@gmail.com>

Closes #6340 from dusenberrymw/Fix_MLlib_Linear_Methods_link and squashes the following commits:

0a57818 [Mike Dusenberry] Fixing broken link in MLlib Linear Methods documentation.

Added VectorIndexer section to ML user guide.  Also added javaCategoryMaps() method and Java unit test for it.

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #6255 from jkbradley/vector-indexer-guide and squashes the following commits:

dbb8c4c [Joseph K. Bradley] simplified VectorIndexerModel.javaCategoryMaps
f692084 [Joseph K. Bradley] Added VectorIndexer section to ML user guide.  Also added javaCategoryMaps() method and Java unit test for it.

to be consistent with other string names in MLlib. This PR also updates the implementation to use vals instead of hardcoded strings. jkbradley leahmcguire

Author: Xiangrui Meng <meng@databricks.com>

Closes #6277 from mengxr/SPARK-7752 and squashes the following commits:

f38b662 [Xiangrui Meng] add another case _ back in test
ae5c66a [Xiangrui Meng] model type -> modelType
711d1c6 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7752
40ae53e [Xiangrui Meng] fix Java test suite
264a814 [Xiangrui Meng] add case _ back
3c456a8 [Xiangrui Meng] update NB user guide
17bba53 [Xiangrui Meng] update naive Bayes to use lowercase model type strings

…rther extension to non-json outputs too.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #6273 from harishreedharan/json-to-api and squashes the following commits:

e14b73b [Hari Shreedharan] Rename `getJsonServlet` to `getServletHandler` i
42f8acb [Hari Shreedharan] Import order fixes.
2ef852f [Hari Shreedharan] [SPARK-7750][WebUI] Rename endpoints from `json` to `api` to allow further extension to non-json outputs too.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #6126 from sryza/sandy-spark-7579 and squashes the following commits:

5af803d [Sandy Ryza] SPARK-7579 [MLLIB] User guide update for OneHotEncoder

Added faster RM-heartbeats on pending container allocations with multiplicative back-off.
Also updated related documentations.

Author: ehnalis <zoltan.zvara@gmail.com>

Closes #6082 from ehnalis/yarn and squashes the following commits:

a1d2101 [ehnalis] MIss-spell fixed.
90f8ba4 [ehnalis] Changed default HB values.
6120295 [ehnalis] Removed the bug, when allocation heartbeat would not start from initial value.
08bac63 [ehnalis] Refined style, grammar, removed duplicated code.
073d283 [ehnalis] [SPARK-7533] [YARN] Decrease spacing between AM-RM heartbeats.
d4408c9 [ehnalis] [SPARK-7533] [YARN] Decrease spacing between AM-RM heartbeats.

[SPARK-7744] [DOCS] [MLLIB] Distributed matrix" section in MLlib "Data Types" documentation should be reordered.

The documentation for BlockMatrix should come after RowMatrix, IndexedRowMatrix, and CoordinateMatrix, as BlockMatrix references the later three types, and RowMatrix is considered the "basic" distributed matrix.  This will improve comprehensibility of the "Distributed matrix" section, especially for the new reader.

Author: Mike Dusenberry <dusenberrymw@gmail.com>

Closes #6270 from dusenberrymw/Reorder_MLlib_Data_Types_Distributed_matrix_docs and squashes the following commits:

6313bab [Mike Dusenberry] The documentation for BlockMatrix should come after RowMatrix, IndexedRowMatrix, and CoordinateMatrix, as BlockMatrix references the later three types, and RowMatrix is considered the "basic" distributed matrix.  This will improve comprehensibility of the "Distributed matrix" section, especially for the new reader.

CC jkbradley.

JIRA [issue](https://issues.apache.org/jira/browse/SPARK-7586).

Author: Xusen Yin <yinxusen@gmail.com>

Closes #6181 from yinxusen/SPARK-7586 and squashes the following commits:

77014c5 [Xusen Yin] comment fix
57a4c07 [Xusen Yin] small fix for docs
1178c8f [Xusen Yin] remove the correctness check in java suite
1c3f389 [Xusen Yin] delete sbt commit
1af152b [Xusen Yin] check python example code
1b5369e [Xusen Yin] add docs of word2vec

The change per SPARK-4397 makes implicit objects in SparkContext to be found by the compiler automatically. So that we don't need to import the o.a.s.SparkContext._ explicitly any more and can remove some statements around the "implicit conversions" from the latest Programming Guides (1.3.0 and higher)

Author: Dice <poleon.kd@gmail.com>

Closes #6234 from daisukebe/patch-1 and squashes the following commits:

b77ecd9 [Dice] fix a typo
45dfcd3 [Dice] rewording per Sean's advice
a094bcf [Dice] Adding a note for users on any previous releases
a29be5f [Dice] Updating Programming Guides per SPARK-4397

https://issues.apache.org/jira/browse/SPARK-7723

Author: Saleem Ansari <tuxdna@gmail.com>

Closes #6258 from tuxdna/master and squashes the following commits:

2bb5a42 [Saleem Ansari] Merge branch 'master' into mllib-pipeline
e39db9c [Saleem Ansari] Fix string interpolation in pipeline examples

Just a few minor fixes in the guide, so a new JIRA issue was not created per the guidelines.

Author: Mike Dusenberry <dusenberrymw@gmail.com>

Closes #6240 from dusenberrymw/Fix_Programming_Guide_Typos and squashes the following commits:

ffa76eb [Mike Dusenberry] Fixing a few basic typos in the Programming Guide.

JIRA [here](https://issues.apache.org/jira/browse/SPARK-7581).

CC jkbradley

Author: Xusen Yin <yinxusen@gmail.com>

Closes #6113 from yinxusen/SPARK-7581 and squashes the following commits:

1a7d80d [Xusen Yin] merge with master
892a8e9 [Xusen Yin] fix python 3 compatibility
ec935bf [Xusen Yin] small fix
3e9fa1d [Xusen Yin] delete note
69fcf85 [Xusen Yin] simplify and add python example
81d21dc [Xusen Yin] add programming guide for Polynomial Expansion
40babfb [Xusen Yin] add java test suite for PolynomialExpansion

https://issues.apache.org/jira/browse/SPARK-7272

Author: Vincenzo Selvaggio <vselvaggio@hotmail.it>

Closes #6219 from selvinsource/mllib_pmml_model_export_SPARK-7272 and squashes the following commits:

c866fb8 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
1beda98 [Vincenzo Selvaggio] [SPARK-7272] Initial user guide for pmml export
d670662 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
2731375 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
680dc33 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
2e298b5 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
a932f51 [Vincenzo Selvaggio] Create mllib-pmml-model-export.md

Add note on building a runnable distribution with make-distribution.sh

Author: Sean Owen <sowen@cloudera.com>

Closes #6186 from srowen/SPARK-4556 and squashes the following commits:

4002966 [Sean Owen] Add pointer to --help flag
9fa7883 [Sean Owen] Add note on building a runnable distribution with make-distribution.sh

There is a mistake in the URL of Matrices in the MLlib Data Types documentation (Local matrix scala section), the URL points to https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Matrices which is a mistake, since Matrices is an object that implements factory methods for Matrix that does not have a companion class. The correct link should point to https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Matrices$

There is another mistake, in the Local Vector section in Scala, Java and Python

In the Scala section the URL of Vectors points to the trait Vector (https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Vector) and not to the factory methods implemented in Vectors.

The correct link should be: https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Vectors$

In the Java section the URL of Vectors points to the Interface Vector (https://spark.apache.org/docs/latest/api/java/org/apache/spark/mllib/linalg/Vector.html) and not to the Class Vectors

The correct link should be:
https://spark.apache.org/docs/latest/api/java/org/apache/spark/mllib/linalg/Vectors.html

In the Python section the URL of Vectors points to the class Vector (https://spark.apache.org/docs/latest/api/python/pyspark.mllib.html#pyspark.mllib.linalg.Vector) and not the Class Vectors

The correct link should be:
https://spark.apache.org/docs/latest/api/python/pyspark.mllib.html#pyspark.mllib.linalg.Vectors

Author: FavioVazquez <favio.vazquezp@gmail.com>

Closes #6196 from FavioVazquez/fix-typo-matrices-mllib-datatypes and squashes the following commits:

3e9efd5 [FavioVazquez] - Fixed wrong URLs in the MLlib Data Types Documentation
9af7074 [FavioVazquez] Merge remote-tracking branch 'upstream/master'
edab1ef [FavioVazquez] Merge remote-tracking branch 'upstream/master'
b2e2f8c [FavioVazquez] Merge remote-tracking branch 'upstream/master'

[SPARK-7556] [ML] [DOC] Add user guide for spark.ml Binarizer, including Scala, Java and Python examples

JIRA: https://issues.apache.org/jira/browse/SPARK-7556

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #6116 from viirya/binarizer_doc and squashes the following commits:

40cb677 [Liang-Chi Hsieh] Better print out.
5b7ef1d [Liang-Chi Hsieh] Make examples more clear.
1bf9c09 [Liang-Chi Hsieh] For comments.
6cf8cba [Liang-Chi Hsieh] Add user guide for Binarizer.

Updated Hadoop dependencies due to inconsistency in the versions. Now the global properties are the ones used by the hadoop-2.2 profile, and the profile was set to empty but kept for backwards compatibility reasons.

Changes proposed by vanzin resulting from previous pull-request https://github.com/apache/spark/pull/5783 that did not fixed the problem correctly.

Please let me know if this is the correct way of doing this, the comments of vanzin are in the pull-request mentioned.

Author: FavioVazquez <favio.vazquezp@gmail.com>

Closes #5786 from FavioVazquez/update-hadoop-dependencies and squashes the following commits:

11670e5 [FavioVazquez] - Added missing instance of -Phadoop-2.2 in create-release.sh
379f50d [FavioVazquez] - Added instances of -Phadoop-2.2 in create-release.sh, run-tests, scalastyle and building-spark.md - Reconstructed docs to not ask users to rely on default behavior
3f9249d [FavioVazquez] Merge branch 'master' of https://github.com/apache/spark into update-hadoop-dependencies
31bdafa [FavioVazquez] - Added missing instances in -Phadoop-1 in create-release.sh, run-tests and in the building-spark documentation
cbb93e8 [FavioVazquez] - Added comment related to SPARK-3710 about  hadoop-yarn-server-tests in Hadoop 2.2 that fails to pull some needed dependencies
83dc332 [FavioVazquez] - Cleaned up the main POM concerning the yarn profile - Erased hadoop-2.2 profile from yarn/pom.xml and its content was integrated into yarn/pom.xml
93f7624 [FavioVazquez] - Deleted unnecessary comments and <activation> tag on the YARN profile in the main POM
668d126 [FavioVazquez] - Moved <dependencies> <activation> and <properties> sections of the hadoop-2.2 profile in the YARN POM to the YARN profile in the root POM - Erased unnecessary hadoop-2.2 profile from the YARN POM
fda6a51 [FavioVazquez] - Updated hadoop1 releases in create-release.sh  due to changes in the default hadoop version set - Erased unnecessary instance of -Dyarn.version=2.2.0 in create-release.sh - Prettify comment in yarn/pom.xml
0470587 [FavioVazquez] - Erased unnecessary instance of -Phadoop-2.2 -Dhadoop.version=2.2.0 in create-release.sh - Updated how the releases are made in the create-release.sh no that the default hadoop version is the 2.2.0 - Erased unnecessary instance of -Phadoop-2.2 -Dhadoop.version=2.2.0 in scalastyle - Erased unnecessary instance of -Phadoop-2.2 -Dhadoop.version=2.2.0 in run-tests - Better example given in the hadoop-third-party-distributions.md now that the default hadoop version is 2.2.0
a650779 [FavioVazquez] - Default value of avro.mapred.classifier has been set to hadoop2 in pom.xml - Cleaned up hadoop-2.3 and 2.4 profiles due to change in the default set in avro.mapred.classifier in pom.xml
199f40b [FavioVazquez] - Erased unnecessary CDH5-specific note in docs/building-spark.md - Remove example of instance -Phadoop-2.2 -Dhadoop.version=2.2.0 in docs/building-spark.md - Enabled hadoop-2.2 profile when the Hadoop version is 2.2.0, which is now the default .Added comment in the yarn/pom.xml to specify that.
88a8b88 [FavioVazquez] - Simplified Hadoop profiles due to new setting of global properties in the pom.xml file - Added comment to specify that the hadoop-2.2 profile is now the default hadoop profile in the pom.xml file - Erased hadoop-2.2 from related hadoop profiles now that is a no-op in the make-distribution.sh file
70b8344 [FavioVazquez] - Fixed typo in the make-distribution.sh file and added hadoop-1 in the Related profiles
287fa2f [FavioVazquez] - Updated documentation about specifying the hadoop version in building-spark. Now is clear that Spark will build against Hadoop 2.2.0 by default. - Added Cloudera CDH 5.3.3 without MapReduce example in the building-spark doc.
1354292 [FavioVazquez] - Fixed hadoop-1 version to match jenkins build profile in hadoop1.0 tests and documentation
6b4bfaf [FavioVazquez] - Cleanup in hadoop-2.x profiles since they contained mostly redundant stuff.
7e9955d [FavioVazquez] - Updated Hadoop dependencies due to inconsistency in the versions. Now the global properties are the ones used by the hadoop-2.2 profile, and the profile was set to empty but kept for backwards compatibility reasons
660decc [FavioVazquez] - Updated Hadoop dependencies due to inconsistency in the versions. Now the global properties are the ones used by the hadoop-2.2 profile, and the profile was set to empty but kept for backwards compatibility reasons
ec91ce3 [FavioVazquez] - Updated protobuf-java version of com.google.protobuf dependancy to fix blocking error when connecting to HDFS via the Hadoop Cloudera HDFS CDH5 (fix for 2.5.0-cdh5.3.3 version)

Added feature transformer subsection to spark.ml guide, with HashingTF and Tokenizer.  Added JavaHashingTFSuite to test Java examples in new guide.

I've run Scala, Python examples in the Spark/PySpark shells.  I ran the Java examples via the test suite (with small modifications for printing).

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #6093 from jkbradley/hashingtf-guide and squashes the following commits:

d5d213f [Joseph K. Bradley] small fix
dd6e91a [Joseph K. Bradley] fixes from code review of user guide
33c3ff9 [Joseph K. Bradley] small fix
bc6058c [Joseph K. Bradley] fix link
361a174 [Joseph K. Bradley] Added subsection for feature transformers to spark.ml guide, with HashingTF and Tokenizer.  Added JavaHashingTFSuite to test Java examples in new guide

jira: https://issues.apache.org/jira/browse/SPARK-7496

Update LDA subsection of clustering section of MLlib programming guide to include OnlineLDA.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #6046 from hhbyyh/ldaDocument and squashes the following commits:

4b6fbfa [Yuhao Yang] add online paper and some comparison
fd4c983 [Yuhao Yang] update lda document for optimizers

add docs for https://issues.apache.org/jira/browse/SPARK-6994

Author: vidmantas zemleris <vidmantas@vinted.com>

Closes #6030 from vidma/docs/row-with-named-fields and squashes the following commits:

241b401 [vidmantas zemleris] [SPARK-6994][SQL] Update docs for fetching Row fields by name

Author: Reynold Xin <rxin@databricks.com>

Closes #6062 from rxin/agg-retain-doc and squashes the following commits:

43e511e [Reynold Xin] [SPARK-7462][SQL] Update documentation for retaining grouping columns in DataFrames.

JIRA: https://issues.apache.org/jira/browse/SPARK-7516

In sql-programming-guide, deprecated python data frame api inferSchema() should be replaced by createDataFrame():

schemaPeople = sqlContext.inferSchema(people) ->
schemaPeople = sqlContext.createDataFrame(people)

Author: gchen <chenguancheng@gmail.com>

Closes #6041 from gchen/python-docs and squashes the following commits:

c27eb7c [gchen] replace inferSchema() with createDataFrame()

Now PySpark on YARN with cluster mode is supported so let's update doc.

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

Closes #6040 from sarutak/update-doc-for-pyspark-on-yarn and squashes the following commits:

ad9f88c [Kousuke Saruta] Brushed up sentences
469fd2e [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into update-doc-for-pyspark-on-yarn
fcfdb92 [Kousuke Saruta] Updated doc for PySpark on YARN with cluster mode

This is difficult to write a test for because it relies on the latest version of YARN, but I verified manually that the patch does pass along the label expression on this version and containers are successfully launched.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #5242 from sryza/sandy-spark-6470 and squashes the following commits:

6af87b9 [Sandy Ryza] Change info to warning
6e22d99 [Sandy Ryza] [YARN] SPARK-6470.  Add support for YARN node labels.

I implement a simple PCA wrapper for easy transform of vectors by PCA for example LabeledPoint or another complicated structure.

Example of usage:
```
  import org.apache.spark.mllib.regression.LinearRegressionWithSGD
  import org.apache.spark.mllib.regression.LabeledPoint
  import org.apache.spark.mllib.linalg.Vectors
  import org.apache.spark.mllib.feature.PCA

  val data = sc.textFile("data/mllib/ridge-data/lpsa.data").map { line =>
    val parts = line.split(',')
    LabeledPoint(parts(0).toDouble, Vectors.dense(parts(1).split(' ').map(_.toDouble)))
  }.cache()

  val splits = data.randomSplit(Array(0.6, 0.4), seed = 11L)
  val training = splits(0).cache()
  val test = splits(1)

  val pca = PCA.create(training.first().features.size/2, data.map(_.features))
  val training_pca = training.map(p => p.copy(features = pca.transform(p.features)))
  val test_pca = test.map(p => p.copy(features = pca.transform(p.features)))

  val numIterations = 100
  val model = LinearRegressionWithSGD.train(training, numIterations)
  val model_pca = LinearRegressionWithSGD.train(training_pca, numIterations)

  val valuesAndPreds = test.map { point =>
    val score = model.predict(point.features)
    (score, point.label)
  }

  val valuesAndPreds_pca = test_pca.map { point =>
    val score = model_pca.predict(point.features)
    (score, point.label)
  }

  val MSE = valuesAndPreds.map{case(v, p) => math.pow((v - p), 2)}.mean()
  val MSE_pca = valuesAndPreds_pca.map{case(v, p) => math.pow((v - p), 2)}.mean()

  println("Mean Squared Error = " + MSE)
  println("PCA Mean Squared Error = " + MSE_pca)
```

Author: Kirill A. Korinskiy <catap@catap.ru>
Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4304 from catap/pca and squashes the following commits:

501bcd9 [Joseph K. Bradley] Small updates: removed k from Java-friendly PCA fit().  In PCASuite, converted results to set for comparison. Added an error message for bad k in PCA.
9dcc02b [Kirill A. Korinskiy] [SPARK-5521] fix scala style
1892a06 [Kirill A. Korinskiy] [SPARK-5521] PCA wrapper for easy transform vectors

A little fix about wrong url of the API document. (org.apache.spark.streaming.scheduler.StreamingListener)

Author: dobashim <dobashim@oss.nttdata.co.jp>

Closes #6024 from dobashim/master and squashes the following commits:

ac9a955 [dobashim] [STREAMING][DOCS] Fix wrong url about API docs of StreamingListener

Exposes data available in the UI as json over http.  Key points:

* new endpoints, handled independently of existing XyzPage classes.  Root entrypoint is `JsonRootResource`
* Uses jersey + jackson for routing & converting POJOs into json
* tests against known results in `HistoryServerSuite`
* also fixes some minor issues w/ the UI -- synchronizing on access to `StorageListener` & `StorageStatusListener`, and fixing some inconsistencies w/ the way we handle retained jobs & stages.

Author: Imran Rashid <irashid@cloudera.com>

Closes #5940 from squito/SPARK-3454_better_test_files and squashes the following commits:

1a72ed6 [Imran Rashid] rats
85fdb3e [Imran Rashid] Merge branch 'no_php' into SPARK-3454
1fc65b0 [Imran Rashid] Revert "Revert "[SPARK-3454] separate json endpoints for data in the UI""
1276900 [Imran Rashid] get rid of giant event file, replace w/ smaller one; check both shuffle read & shuffle write
4e12013 [Imran Rashid] just use test case name for expectation file name
863ef64 [Imran Rashid] rename json files to avoid strange file names and not look like php

See https://issues.apache.org/jira/browse/SPARK-5726

Author: Octavian Geagla <ogeagla@gmail.com>
Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4580 from ogeagla/spark-mllib-weighting and squashes the following commits:

fac12ad [Octavian Geagla] [SPARK-5726] [MLLIB] Use new createTransformFunc.
90f7e39 [Joseph K. Bradley] small cleanups
4595165 [Octavian Geagla] [SPARK-5726] [MLLIB] Remove erroneous test case.
ded3ac6 [Octavian Geagla] [SPARK-5726] [MLLIB] Pass style checks.
37d4705 [Octavian Geagla] [SPARK-5726] [MLLIB] Incorporated feedback.
1dffeee [Octavian Geagla] [SPARK-5726] [MLLIB] Pass style checks.
e436896 [Octavian Geagla] [SPARK-5726] [MLLIB] Remove 'TF' from 'ElementwiseProductTF'
cb520e6 [Octavian Geagla] [SPARK-5726] [MLLIB] Rename HadamardProduct to ElementwiseProduct
4922722 [Octavian Geagla] [SPARK-5726] [MLLIB] Hadamard Vector Product Transformer

Author: ksonj <kson@siberie.de>

Closes #5971 from ksonj/doc and squashes the following commits:

dadfebb [ksonj] __getitem__ is cleaner than __getattr__

This reverts commit d4973580.

The commit broke Spark on Windows.

The default value will be changed to `1000` in #5533. So here I just used `1000`.

Author: zsxwing <zsxwing@gmail.com>

Closes #5899 from zsxwing/SPARK-7351 and squashes the following commits:

e1ec515 [zsxwing] [SPARK-7351][Streaming][Docs] Add spark.streaming.ui.retainedBatches to docs

Exposes data available in the UI as json over http.  Key points:

* new endpoints, handled independently of existing XyzPage classes.  Root entrypoint is `JsonRootResource`
* Uses jersey + jackson for routing & converting POJOs into json
* tests against known results in `HistoryServerSuite`
* also fixes some minor issues w/ the UI -- synchronizing on access to `StorageListener` & `StorageStatusListener`, and fixing some inconsistencies w/ the way we handle retained jobs & stages.

Author: Imran Rashid <irashid@cloudera.com>

Closes #4435 from squito/SPARK-3454 and squashes the following commits:

da1e35f [Imran Rashid] typos etc.
5e78b4f [Imran Rashid] fix rendering problems
5ae02ad [Imran Rashid] Merge branch 'master' into SPARK-3454
f016182 [Imran Rashid] change all constructors json-pojo class constructors to be private[spark] to protect us from mima-false-positives if we add fields
3347b72 [Imran Rashid] mark EnumUtil as @Private
ec140a2 [Imran Rashid] create @Private
cc1febf [Imran Rashid] add docs on the metrics-as-json api
cbaf287 [Imran Rashid] Merge branch 'master' into SPARK-3454
56db31e [Imran Rashid] update tests for mulit-attempt
7f3bc4e [Imran Rashid] Revert "add sbt-revolved plugin, to make it easier to start & stop http servers in sbt"
67008b4 [Imran Rashid] rats
9e51400 [Imran Rashid] style
c9bae1c [Imran Rashid] handle multiple attempts per app
b87cd63 [Imran Rashid] add sbt-revolved plugin, to make it easier to start & stop http servers in sbt
188762c [Imran Rashid] multi-attempt
2af11e5 [Imran Rashid] Merge branch 'master' into SPARK-3454
befff0c [Imran Rashid] review feedback
14ac3ed [Imran Rashid] jersey-core needs to be explicit; move version & scope to parent pom.xml
f90680e [Imran Rashid] Merge branch 'master' into SPARK-3454
dc8a7fe [Imran Rashid] style, fix errant comments
acb7ef6 [Imran Rashid] fix indentation
7bf1811 [Imran Rashid] move MetricHelper so mima doesnt think its exposed; comments
9d889d6 [Imran Rashid] undo some unnecessary changes
f48a7b0 [Imran Rashid] docs
52bbae8 [Imran Rashid] StorageListener & StorageStatusListener needs to synchronize internally to be thread-safe
31c79ce [Imran Rashid] asm no longer needed for SPARK_PREPEND_CLASSES
b2f8b91 [Imran Rashid] @DeveloperApi
2e19be2 [Imran Rashid] lazily convert ApplicationInfo to avoid memory overhead
ba3d9d2 [Imran Rashid] upper case enums
39ac29c [Imran Rashid] move EnumUtil
d2bde77 [Imran Rashid] update error handling & scoping
4a234d3 [Imran Rashid] avoid jersey-media-json-jackson b/c of potential version conflicts
a157a2f [Imran Rashid] style
7bd4d15 [Imran Rashid] delete security test, since it doesnt do anything
a325563 [Imran Rashid] style
a9c5cf1 [Imran Rashid] undo changes superceeded by master
0c6f968 [Imran Rashid] update deps
1ed0d07 [Imran Rashid] Merge branch 'master' into SPARK-3454
4c92af6 [Imran Rashid] style
f2e63ad [Imran Rashid] Merge branch 'master' into SPARK-3454
c22b11f [Imran Rashid] fix compile error
9ea682c [Imran Rashid] go back to good ol' java enums
cf86175 [Imran Rashid] style
d493b38 [Imran Rashid] Merge branch 'master' into SPARK-3454
f05ae89 [Imran Rashid] add in ExecutorSummaryInfo for MiMa :(
101a698 [Imran Rashid] style
d2ef58d [Imran Rashid] revert changes that had HistoryServer refresh the application listing more often
b136e39b [Imran Rashid] Revert "add sbt-revolved plugin, to make it easier to start & stop http servers in sbt"
e031719 [Imran Rashid] fixes from review
1f53a66 [Imran Rashid] style
b4a7863 [Imran Rashid] fix compile error
2c8b7ee [Imran Rashid] rats
1578a4a [Imran Rashid] doc
674f8dc [Imran Rashid] more explicit about total numbers of jobs & stages vs. number retained
9922be0 [Imran Rashid] Merge branch 'master' into stage_distributions
f5a5196 [Imran Rashid] undo removal of renderJson from MasterPage, since there is no substitute yet
db61211 [Imran Rashid] get JobProgressListener directly from UI
fdfc181 [Imran Rashid] stage/taskList
63eb4a6 [Imran Rashid] tests for taskSummary
ad27de8 [Imran Rashid] error handling on quantile values
b2efcaf [Imran Rashid] cleanup, combine stage-related paths into one resource
aaba896 [Imran Rashid] wire up task summary
a4b1397 [Imran Rashid] stage metric distributions
e48ba32 [Imran Rashid] rename
eaf3bbb [Imran Rashid] style
25cd894 [Imran Rashid] if only given day, assume GMT
51eaedb [Imran Rashid] more visibility fixes
9f28b7e [Imran Rashid] ack, more cleanup
99764e1 [Imran Rashid] Merge branch 'SPARK-3454_w_jersey' into SPARK-3454
a61a43c [Imran Rashid] oops, remove accidental checkin
a066055 [Imran Rashid] set visibility on a lot of classes
1f361c8 [Imran Rashid] update rat-excludes
0be5120 [Imran Rashid] Merge branch 'master' into SPARK-3454_w_jersey
2382bef [Imran Rashid] switch to using new "enum"
fef6605 [Imran Rashid] some utils for working w/ new "enum" format
dbfc7bf [Imran Rashid] style
b86bcb0 [Imran Rashid] update test to look at one stage attempt
5f9df24 [Imran Rashid] style
7fd156a [Imran Rashid] refactor jsonDiff to avoid code duplication
73f1378 [Imran Rashid] test json; also add test cases for cleaned stages & jobs
97d411f [Imran Rashid] json endpoint for one job
0c96147 [Imran Rashid] better error msgs for bad stageId vs bad attemptId
dddbd29 [Imran Rashid] stages have attempt; jobs are sorted; resource for all attempts for one stage
190c17a [Imran Rashid] StagePage should distinguish no task data, from unknown stage
84cd497 [Imran Rashid] AllJobsPage should still report correct completed & failed job count, even if some have been cleaned, to make it consistent w/ AllStagesPage
36e4062 [Imran Rashid] SparkUI needs to know about startTime, so it can list its own applicationInfo
b4c75ed [Imran Rashid] fix merge conflicts; need to widen visibility in a few cases
e91750a [Imran Rashid] Merge branch 'master' into SPARK-3454_w_jersey
56d2fc7 [Imran Rashid] jersey needs asm for SPARK_PREPEND_CLASSES to work
f7df095 [Imran Rashid] add test for accumulables, and discover that I need update after all
9c0c125 [Imran Rashid] add accumulableInfo
00e9cc5 [Imran Rashid] more style
3377e61 [Imran Rashid] scaladoc
d05f7a9 [Imran Rashid] dont use case classes for status api POJOs, since they have binary compatibility issues
654cecf [Imran Rashid] move all the status api POJOs to one file
b86e2b0 [Imran Rashid] style
18a8c45 [Imran Rashid] Merge branch 'master' into SPARK-3454_w_jersey
5598f19 [Imran Rashid] delete some unnecessary code, more to go
56edce0 [Imran Rashid] style
017c755 [Imran Rashid] add in metrics now available
1b78cb7 [Imran Rashid] fix some import ordering
0dc3ea7 [Imran Rashid] if app isnt found, reload apps from FS before giving up
c7d884f [Imran Rashid] fix merge conflicts
0c12b50 [Imran Rashid] Merge branch 'master' into SPARK-3454_w_jersey
b6a96a8 [Imran Rashid] compare json by AST, not string
cd37845 [Imran Rashid] switch to using java.util.Dates for times
a4ab5aa [Imran Rashid] add in explicit dependency on jersey 1.9 -- maven wasn't happy before this
4fdc39f [Imran Rashid] refactor case insensitive enum parsing
cba1ef6 [Imran Rashid] add security (maybe?) for metrics json
f0264a7 [Imran Rashid] switch to using jersey for metrics json
bceb3a9 [Imran Rashid] set http response code on error, some testing
e0356b6 [Imran Rashid] put new test expectation files in rat excludes (is this OK?)
b252e7a [Imran Rashid] small cleanup of accidental changes
d1a8c92 [Imran Rashid] add sbt-revolved plugin, to make it easier to start & stop http servers in sbt
4b398d0 [Imran Rashid] expose UI data as json in new endpoints

"The best way to size the amount of memory consumption your dataset will require is to create an RDD, put it into cache, and look at the SparkContext logs on your driver program. The logs will tell you how much memory each partition is consuming, which you can aggregate to get the total size of the RDD."
-the Tuning Spark page

This is a pain. It would be much nicer to expose simply functionality for understanding the memory footprint of a Java object.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3913 from sryza/sandy-spark-5112 and squashes the following commits:

8d9e082 [Sandy Ryza] Add SizeEstimator in org.apache.spark
2e1a906 [Sandy Ryza] Revert "Move SizeEstimator out of util"
93f4cd0 [Sandy Ryza] Move SizeEstimator out of util
e21c1f4 [Sandy Ryza] Remove unused import
798ab88 [Sandy Ryza] Update documentation and add to SparkContext
34c523c [Sandy Ryza] SPARK-5112. Expose SizeEstimator as a developer api

Author: shekhar.bansal <shekhar.bansal@guavus.com>

Closes #5719 from zuxqoj/master and squashes the following commits:

5574ff7 [shekhar.bansal] [SPARK-6653][yarn] New config to specify port for sparkYarnAM actor system
5117258 [shekhar.bansal] [SPARK-6653][yarn] New config to specify port for sparkYarnAM actor system
9de5330 [shekhar.bansal] [SPARK-6653][yarn] New config to specify port for sparkYarnAM actor system
456a592 [shekhar.bansal] [SPARK-6653][yarn] New configuration property to specify port for sparkYarnAM actor system
803e93e [shekhar.bansal] [SPARK-6653][yarn] New configuration property to specify port for sparkYarnAM actor system

Remove references to Hadoop 0.23

CC tgravescs Is this what you had in mind? basically all refs to 0.23?
We don't support YARN 0.23, but also don't support Hadoop 0.23 anymore AFAICT. There are no builds or releases for it.

In fact, on a related note, refs to CDH3 (Hadoop 0.20.2) should be removed as this certainly isn't supported either.

Author: Sean Owen <sowen@cloudera.com>

Closes #5863 from srowen/SPARK-7302 and squashes the following commits:

42f5d1e [Sean Owen] Remove CDH3 (Hadoop 0.20.2) refs too
dad02e3 [Sean Owen] Remove references to Hadoop 0.23

Added documentation for spark.streaming.kafka.maxRetries

Author: BenFradet <benjamin.fradet@gmail.com>

Closes #5808 from BenFradet/master and squashes the following commits:

cc72e7a [BenFradet] updated doc for spark.streaming.kafka.maxRetries to explain the default value
18f823e [BenFradet] Added "consecutive" to the spark.streaming.kafka.maxRetries doc
597fdeb [BenFradet] Mention that spark.streaming.kafka.maxRetries only applies to the direct kafka api
0efad39 [BenFradet] Added documentation for spark.streaming.kafka.maxRetries

This patch adds partial support for running spark on mesos inside of a docker container. Only fine-grained mode is presently supported, and there is no checking done to ensure that the version of libmesos is recent enough to have a DockerInfo structure in the protobuf (other than pinning a mesos version in the pom.xml).

Author: Chris Heller <hellertime@gmail.com>

Closes #3074 from hellertime/SPARK-2691 and squashes the following commits:

d504af6 [Chris Heller] Assist type inference
f64885d [Chris Heller] Fix errant line length
17c41c0 [Chris Heller] Base Dockerfile on mesosphere/mesos image
8aebda4 [Chris Heller] Simplfy Docker image docs
1ae7f4f [Chris Heller] Style points
974bd56 [Chris Heller] Convert map to flatMap
5d8bdf7 [Chris Heller] Factor out the DockerInfo construction.
7b75a3d [Chris Heller] Align to styleguide
80108e7 [Chris Heller] Bend to the will of RAT
ba77056 [Chris Heller] Explicit RAT exclude
abda5e5 [Chris Heller] Wildcard .rat-excludes
2f2873c [Chris Heller] Exclude spark-mesos from RAT
a589a5b [Chris Heller] Add example Dockerfile
b6825ce [Chris Heller] Remove use of EasyMock
eae1b86 [Chris Heller] Move properties under 'spark.mesos.'
c184d00 [Chris Heller] Use map on Option to be consistent with non-coarse code
fb9501a [Chris Heller] Bumped mesos version to current release
fa11879 [Chris Heller] Add listenerBus to EasyMock
882151e [Chris Heller] Changes to scala style
b22d42d [Chris Heller] Exclude template from RAT
db536cf [Chris Heller] Remove unneeded mocks
dea1bd5 [Chris Heller] Force default protocol
7dac042 [Chris Heller] Add test for DockerInfo
5456c0c [Chris Heller] Adjust syntax style
521c194 [Chris Heller] Adjust version info
6e38f70 [Chris Heller] Document Mesos Docker properties
29572ab [Chris Heller] Support all DockerInfo fields
b8c0dea [Chris Heller] Support for mesos DockerInfo in coarse-mode.
482a9fd [Chris Heller] Support for mesos DockerInfo in fine-grained mode.

Take 2. Does the same thing as #4688, but fixes Hadoop-1 build.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #5823 from harishreedharan/kerberos-longrunning and squashes the following commits:

3c86bba [Hari Shreedharan] Import fixes. Import postfixOps explicitly.
4d04301 [Hari Shreedharan] Minor formatting fixes.
b5e7a72 [Hari Shreedharan] Remove reflection, use a method in SparkHadoopUtil to update the token renewer.
7bff6e9 [Hari Shreedharan] Make sure all required classes are present in the jar. Fix import order.
e851f70 [Hari Shreedharan] Move the ExecutorDelegationTokenRenewer to yarn module. Use reflection to use it.
36eb8a9 [Hari Shreedharan] Change the renewal interval config param. Fix a bunch of comments.
611923a [Hari Shreedharan] Make sure the namenodes are listed correctly for creating tokens.
09fe224 [Hari Shreedharan] Use token.renew to get token's renewal interval rather than using hdfs-site.xml
6963bbc [Hari Shreedharan] Schedule renewal in AM before starting user class. Else, a restarted AM cannot access HDFS if the user class tries to.
072659e [Hari Shreedharan] Fix build failure caused by thread factory getting moved to ThreadUtils.
f041dd3 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning
42eead4 [Hari Shreedharan] Remove RPC part. Refactor and move methods around, use renewal interval rather than max lifetime to create new tokens.
ebb36f5 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning
bc083e3 [Hari Shreedharan] Overload RegisteredExecutor to send tokens. Minor doc updates.
7b19643 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning
8a4f268 [Hari Shreedharan] Added docs in the security guide. Changed some code to ensure that the renewer objects are created only if required.
e800c8b [Hari Shreedharan] Restore original RegisteredExecutor message, and send new tokens via NewTokens message.
0e9507e [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning
7f1bc58 [Hari Shreedharan] Minor fixes, cleanup.
bcd11f9 [Hari Shreedharan] Refactor AM and Executor token update code into separate classes, also send tokens via akka on executor startup.
f74303c [Hari Shreedharan] Move the new logic into specialized classes. Add cleanup for old credentials files.
2f9975c [Hari Shreedharan] Ensure new tokens are written out immediately on AM restart. Also, pikc up the latest suffix from HDFS if the AM is restarted.
61b2b27 [Hari Shreedharan] Account for AM restarts by making sure lastSuffix is read from the files on HDFS.
62c45ce [Hari Shreedharan] Relogin from keytab periodically.
fa233bd [Hari Shreedharan] Adding logging, fixing minor formatting and ordering issues.
42813b4 [Hari Shreedharan] Remove utils.sh, which was re-added due to merge with master.
0de27ee [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning
55522e3 [Hari Shreedharan] Fix failure caused by Preconditions ambiguity.
9ef5f1b [Hari Shreedharan] Added explanation of how the credentials refresh works, some other minor fixes.
f4fd711 [Hari Shreedharan] Fix SparkConf usage.
2debcea [Hari Shreedharan] Change the file structure for credentials files. I will push a followup patch which adds a cleanup mechanism for old credentials files. The credentials files are small and few enough for it to cause issues on HDFS.
af6d5f0 [Hari Shreedharan] Cleaning up files where changes weren't required.
f0f54cb [Hari Shreedharan] Be more defensive when updating the credentials file.
f6954da [Hari Shreedharan] Got rid of Akka communication to renew, instead the executors check a known file's modification time to read the credentials.
5c11c3e [Hari Shreedharan] Move tests to YarnSparkHadoopUtil to fix compile issues.
b4cb917 [Hari Shreedharan] Send keytab to AM via DistributedCache rather than directly via HDFS
0985b4e [Hari Shreedharan] Write tokens to HDFS and read them back when required, rather than sending them over the wire.
d79b2b9 [Hari Shreedharan] Make sure correct credentials are passed to FileSystem#addDelegationTokens()
8c6928a [Hari Shreedharan] Fix issue caused by direct creation of Actor object.
fb27f46 [Hari Shreedharan] Make sure principal and keytab are set before CoarseGrainedSchedulerBackend is started. Also schedule re-logins in CoarseGrainedSchedulerBackend#start()
41efde0 [Hari Shreedharan] Merge branch 'master' into kerberos-longrunning
d282d7a [Hari Shreedharan] Fix ClientSuite to set YARN mode, so that the correct class is used in tests.
bcfc374 [Hari Shreedharan] Fix Hadoop-1 build by adding no-op methods in SparkHadoopUtil, with impl in YarnSparkHadoopUtil.
f8fe694 [Hari Shreedharan] Handle None if keytab-login is not scheduled.
2b0d745 [Hari Shreedharan] [SPARK-5342][YARN] Allow long running Spark apps to run on secure YARN/HDFS.
ccba5bc [Hari Shreedharan] WIP: More changes wrt kerberos
77914dd [Hari Shreedharan] WIP: Add kerberos principal and keytab to YARN client.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5813 from vanzin/SPARK-7281 and squashes the following commits:

1cb6f42 [Marcelo Vanzin] [SPARK-7281] [yarn] Add option to set AM's lib path in client mode.