…items

Add
1. Class methods squared_dist
3. parse
4. norm
5. numNonzeros
6. copy

I made a few vectorizations wrt squared_dist and dot as well. I have added support for SparseMatrix serialization in a separate PR (apache#5775) and plan to complete support for Matrices in another PR.

Author: MechCoder <[email protected]>

Closes apache#5872 from MechCoder/local_linalg_api and squashes the following commits:

a8ff1e0 [MechCoder] minor
ce3e53e [MechCoder] Add error message for parser
1bd3c04 [MechCoder] Robust parser and removed unnecessary methods
f779561 [MechCoder] [SPARK-7328] Pyspark.mllib.linalg.Vectors: Missing items

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

Author: Octavian Geagla <[email protected]>
Author: Joseph K. Bradley <[email protected]>

Closes apache#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

The compression is based on storage. brkyvz

Author: Xiangrui Meng <[email protected]>

Closes apache#5985 from mengxr/SPARK-6948 and squashes the following commits:

df56a00 [Xiangrui Meng] update python tests
6d90d45 [Xiangrui Meng] compress vectors in VectorAssembler

`Star` and `MultiAlias` just used in `analyzer` and them will be substituted after analyze,  So just like `Alias` they do not need extend `Attribute`

Author: scwf <[email protected]>

Closes apache#5928 from scwf/attribute and squashes the following commits:

73a0560 [scwf] star and multialias do not need extend attribute

…s is set to -1

JIRA: https://issues.apache.org/jira/browse/SPARK-7277

As automatically determining the number of reducers is not supported (`mapred.reduce.tasks` is set to `-1`), we should throw exception to users.

Author: Liang-Chi Hsieh <[email protected]>

Closes apache#5811 from viirya/no_neg_reduce_tasks and squashes the following commits:

e518f96 [Liang-Chi Hsieh] Consider other wrong setting values.
fd9c817 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into no_neg_reduce_tasks
4ede705 [Liang-Chi Hsieh] Throw exception instead of warning message.
68a1c70 [Liang-Chi Hsieh] Show warning message if mapred.reduce.tasks is set to -1.

…entError

Go through the context classloader when reflecting on user types in ScalaReflection.

Replaced calls to `typeOf` with `typeTag[T].in(mirror)`. The convenience method assumes
all types can be found in the classloader that loaded scala-reflect (the primordial
classloader). This assumption is not valid in all contexts (sbt console, Eclipse launchers).

Fixed SPARK-5281

Author: Iulian Dragos <[email protected]>

Closes apache#5981 from dragos/issue/mirrors-missing-requirement-error and squashes the following commits:

d103e70 [Iulian Dragos] Go through the context classloader when reflecting on user types in ScalaReflection

… a WHEN b THEN c * END"

Avoid translating to CaseWhen and evaluate the key expression many times.

Author: Wenchen Fan <[email protected]>

Closes apache#5979 from cloud-fan/condition and squashes the following commits:

3ce54e1 [Wenchen Fan] add CaseKeyWhen

Author: tedyu <[email protected]>

Closes apache#5897 from tedyu/master and squashes the following commits:

473bf9d [tedyu] Address Josh's review comments
1719c5b [tedyu] Correct upper bound in for loop
b51dcaf [tedyu] Add unit test in BitSetSuite for BitSet#anySet()
83f9f87 [tedyu] Merge branch 'master' of github.com:apache/spark
817e3f9 [tedyu] Replace constant 8 with SIZE_OF_LONG
75a467b [tedyu] Correct offset for UNSAFE.getLong()
855374b [tedyu] Remove second loop since bitSetWidthInBytes is WORD aligned
093b7a4 [tedyu] Use UNSAFE.getLong() to speed up BitSetMethods#anySet()
63ee050 [tedyu] Use UNSAFE.getLong() to speed up BitSetMethods#anySet()
4ca0ef6 [tedyu] Use UNSAFE.getLong() to speed up BitSetMethods#anySet()
3e9b691 [tedyu] Use UNSAFE.getLong() to speed up BitSetMethods#anySet()

…tion when jobs are dropped by SparkListener

If jobs are dropped by SparkListener, at least we can show the job ids in BatchPage. Screenshot:

![b1](https://cloud.githubusercontent.com/assets/1000778/7434968/f19aa784-eff3-11e4-8f86-36a073873574.png)

Author: zsxwing <[email protected]>

Closes apache#5840 from zsxwing/SPARK-7305 and squashes the following commits:

aca0ba6 [zsxwing] Fix the code style
718765e [zsxwing] Make generateNormalJobRow private
8073b03 [zsxwing] Merge branch 'master' into SPARK-7305
83dec11 [zsxwing] Make BatchPage show friendly information when jobs are dropped by SparkListener

This PR switches Spark SQL's Hive support to use the isolated hive client interface introduced by apache#5851, instead of directly interacting with the client.  By using this isolated client we can now allow users to dynamically configure the version of Hive that they are connecting to by setting `spark.sql.hive.metastore.version` without the need recompile.  This also greatly reduces the surface area for our interaction with the hive libraries, hopefully making it easier to support other versions in the future.

Jars for the desired hive version can be configured using `spark.sql.hive.metastore.jars`, which accepts the following options:
 - a colon-separated list of jar files or directories for hive and hadoop.
 - `builtin` - attempt to discover the jars that were used to load Spark SQL and use those. This
            option is only valid when using the execution version of Hive.
 - `maven` - download the correct version of hive on demand from maven.

By default, `builtin` is used for Hive 13.

This PR also removes the test step for building against Hive 12, as this will no longer be required to talk to Hive 12 metastores.  However, the full removal of the Shim is deferred until a later PR.

Remaining TODOs:
 - Remove the Hive Shims and inline code for Hive 13.
 - Several HiveCompatibility tests are not yet passing.
  - `nullformatCTAS` - As detailed below, we now are handling CTAS parsing ourselves instead of hacking into the Hive semantic analyzer.  However, we currently only handle the common cases and not things like CTAS where the null format is specified.
  - `combine1` now leaks state about compression somehow, breaking all subsequent tests.  As such we currently add it to the blacklist
  - `part_inherit_tbl_props` and `part_inherit_tbl_props_with_star` do not work anymore.  We are correctly propagating the information
  - "load_dyn_part14.*" - These tests pass when run on their own, but fail when run with all other tests.  It seems our `RESET` mechanism may not be as robust as it used to be?

Other required changes:
 -  `CreateTableAsSelect` no longer carries parts of the HiveQL AST with it through the query execution pipeline.  Instead, we parse CTAS during the HiveQL conversion and construct a `HiveTable`.  The full parsing here is not yet complete as detailed above in the remaining TODOs.  Since the operator is Hive specific, it is moved to the hive package.
 - `Command` is simplified to be a trait that simply acts as a marker for a LogicalPlan that should be eagerly evaluated.

Author: Michael Armbrust <[email protected]>

Closes apache#5876 from marmbrus/useIsolatedClient and squashes the following commits:

258d000 [Michael Armbrust] really really correct path handling
e56fd4a [Michael Armbrust] getAbsolutePath
5a259f5 [Michael Armbrust] fix typos
81bb366 [Michael Armbrust] comments from vanzin
5f3945e [Michael Armbrust] Merge remote-tracking branch 'origin/master' into useIsolatedClient
4b5cd41 [Michael Armbrust] yin's comments
f5de7de [Michael Armbrust] cleanup
11e9c72 [Michael Armbrust] better coverage in versions suite
7e8f010 [Michael Armbrust] better error messages and jar handling
e7b3941 [Michael Armbrust] more permisive checking for function registration
da91ba7 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into useIsolatedClient
5fe5894 [Michael Armbrust] fix serialization suite
81711c4 [Michael Armbrust] Initial support for running without maven
1d8ae44 [Michael Armbrust] fix final tests?
1c50813 [Michael Armbrust] more comments
a3bee70 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into useIsolatedClient
a6f5df1 [Michael Armbrust] style
ab07f7e [Michael Armbrust] WIP
4d8bf02 [Michael Armbrust] Remove hive 12 compilation
8843a25 [Michael Armbrust] [SPARK-6908] [SQL] Use isolated Hive client

the toArray function of the BoundedPriorityQueue does not necessarily preserve order. Add a counter-example as the test, which would fail the original impl.

Author: Shuo Xiang <[email protected]>

Closes apache#5990 from coderxiang/topbykey-test and squashes the following commits:

98804c9 [Shuo Xiang] fix bug in topBykey and update test

With apache@0a2b15c, the serialization stream and deserialization stream has enough information to determine it is handling a key-value pari, a key, or a value. It is safe to use `SparkSqlSerializer2` in more cases.

Author: Yin Huai <[email protected]>

Closes apache#5849 from yhuai/serializer2MoreCases and squashes the following commits:

53a5eaa [Yin Huai] Josh's comments.
487f540 [Yin Huai] Use BufferedOutputStream.
8385f95 [Yin Huai] Always create a new row at the deserialization side to work with sort merge join.
c7e2129 [Yin Huai] Update tests.
4513d13 [Yin Huai] Use Serializer2 in more places.

This only happens if you have `SPARK_PREPEND_CLASSES` set. Then I built it with `build/sbt clean assembly compile` and just ran it with `bin/spark-shell`.
```
...
15/05/07 17:07:30 INFO EventLoggingListener: Logging events to file:/tmp/spark-events/local-1431043649919
15/05/07 17:07:30 INFO SparkILoop: Created spark context..
Spark context available as sc.
java.lang.NoClassDefFoundError: org/apache/hadoop/hive/conf/HiveConf
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2493)
	at java.lang.Class.getConstructor0(Class.java:2803)
...
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.conf.HiveConf
	at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	... 52 more

<console>:10: error: not found: value sqlContext
       import sqlContext.implicits._
              ^
<console>:10: error: not found: value sqlContext
       import sqlContext.sql
              ^
```
yhuai marmbrus

Author: Andrew Or <[email protected]>

Closes apache#5997 from andrewor14/sql-shell-crash and squashes the following commits:

61147e6 [Andrew Or] Also expect NoClassDefFoundError

  Added a new batch named `Substitution` before `Resolution` batch. The motivation for this is there are kind of cases we want to do some substitution on the parsed logical plan before resolve it.
Consider this two cases:
1 CTE, for cte we first build a row logical plan
```
'With Map(q1 -> 'Subquery q1
                   'Project ['key]
                      'UnresolvedRelation [src], None)
 'Project [*]
  'Filter ('key = 5)
   'UnresolvedRelation [q1], None
```
In `With` logicalplan here is a map stored the (`q1-> subquery`), we want first take off the with command and substitute the  `q1` of `UnresolvedRelation` by the `subquery`

2 Another example is Window function, in window function user may define some windows, we also need substitute the window name of child by the concrete window. this should also done in the Substitution batch.

Author: wangfei <[email protected]>

Closes apache#5776 from scwf/addbatch and squashes the following commits:

d4b962f [wangfei] added WindowsSubstitution
70f6932 [wangfei] Merge branch 'master' of https://github.com/apache/spark into addbatch
ecaeafb [wangfei] address yhuai's comments
553005a [wangfei] fix test case
0c54798 [wangfei] address comments
29aaaaf [wangfei] fix compile
1c9a092 [wangfei] added Substitution bastch

Author: Zhang, Liye <[email protected]>

Closes apache#5934 from liyezhang556520/kryoBufSize and squashes the following commits:

5707e04 [Zhang, Liye] fix import order
8693288 [Zhang, Liye] replace multiplier with ByteUnit methods
9bf93e9 [Zhang, Liye] add tests
d91e5ed [Zhang, Liye] change kb to mb

Based on apache#5478 that provide a PYSPARK_ARCHIVES_PATH env. within this PR, we just should export PYSPARK_ARCHIVES_PATH=/user/spark/pyspark.zip,/user/spark/python/lib/py4j-0.8.2.1-src.zip in conf/spark-env.sh when we don't install PySpark on each node of Yarn. i run python application successfully on yarn-client and yarn-cluster with this PR.
andrewor14 sryza Sephiroth-Lin Can you take a look at this?thanks.

Author: Lianhui Wang <[email protected]>

Closes apache#5580 from lianhuiwang/SPARK-6869 and squashes the following commits:

66ffa43 [Lianhui Wang] Update Client.scala
c2ad0f9 [Lianhui Wang] Update Client.scala
1c8f664 [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869
008850a [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869
f0b4ed8 [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869
150907b [Lianhui Wang] Merge remote-tracking branch 'remotes/apache/master' into SPARK-6869
20402cd [Lianhui Wang] use ZipEntry
9d87c3f [Lianhui Wang] update scala style
e7bd971 [Lianhui Wang] address vanzin's comments
4b8a3ed [Lianhui Wang] use pyArchivesEnvOpt
e6b573b [Lianhui Wang] address vanzin's comments
f11f84a [Lianhui Wang] zip pyspark archives
5192cca [Lianhui Wang] update import path
3b1e4c8 [Lianhui Wang] address tgravescs's comments
9396346 [Lianhui Wang] put zip to make-distribution.sh
0d2baf7 [Lianhui Wang] update import paths
e0179be [Lianhui Wang] add zip pyspark archives in build or sparksubmit
31e8e06 [Lianhui Wang] update code style
9f31dac [Lianhui Wang] update code and add comments
f72987c [Lianhui Wang] add archives path to PYTHONPATH

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 <[email protected]>

Closes apache#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

Implemented python wrappers for Scala functions that don't exist in `ml.features`

Author: Burak Yavuz <[email protected]>

Closes apache#5991 from brkyvz/ml-feat-PR and squashes the following commits:

adcca55 [Burak Yavuz] add regex tokenizer to __all__
b91cb44 [Burak Yavuz] addressed comments
bd39fd2 [Burak Yavuz] remove addition
b82bd7c [Burak Yavuz] Parity in PySpark for ml.features

Multiline commands are properly handled in this PR. oefirouz

![screen shot 2015-05-07 at 10 53 25 pm](https://cloud.githubusercontent.com/assets/829644/7531290/02ad2fd4-f50c-11e4-8c04-e58d1a61ad69.png)

Author: Xiangrui Meng <[email protected]>

Closes apache#6001 from mengxr/SPARK-7474 and squashes the following commits:

b94b11d [Xiangrui Meng] update ParamGridBuilder doctest

This patch also removes the RDD docs from being built as a part of roxygen just by the method to delete
" ' '" of " \#' ".

Author: hqzizania <[email protected]>
Author: qhuang <[email protected]>

Closes apache#5969 from hqzizania/R1 and squashes the following commits:

6d27696 [qhuang] fixes in NAMESPACE
eb4b095 [qhuang] remove more docs
6394579 [qhuang] remove RDD docs in generics.R
6813860 [hqzizania] Fill the docs for DataFrame API in SparkR
857220f [hqzizania] remove the pairRDD docs from being built as a part of roxygen
c045d64 [hqzizania] remove the RDD docs from being built as a part of roxygen

…added tests

Author: Jacek Lewandowski <[email protected]>

Closes apache#5977 from jacek-lewandowski/SPARK-7436 and squashes the following commits:

ff0a3c2 [Jacek Lewandowski] SPARK-7436: Fixed instantiation of custom recovery mode factory and added tests

- Colors on the timeline now match the rest of the UI
- The expandable buttons to show timeline view, DAG, etc are now more visible
- Timeline text is smaller
- DAG visualization text and colors are more consistent throughout
- Fix some JavaScript style issues
- Various small fixes throughout (e.g. inconsistent capitalization, some confusing names, HTML escaping, etc)

Author: Matei Zaharia <[email protected]>

Closes apache#5942 from mateiz/ui and squashes the following commits:

def38d0 [Matei Zaharia] Add some tooltips
4c5a364 [Matei Zaharia] Reduce stage and rank separation slightly
43dcbe3 [Matei Zaharia] Some updates to DAG
fac734a [Matei Zaharia] tweaks
6a6705d [Matei Zaharia] More fixes
67629f5 [Matei Zaharia] Various small tweaks

It's the first step: generalize UnresolvedGetField to support all map, struct, and array
TODO: add `apply` in Scala and `__getitem__` in Python, and unify the `getItem` and `getField` methods to one single API(or should we keep them for compatibility?).

Author: Wenchen Fan <[email protected]>

Closes apache#5744 from cloud-fan/generalize and squashes the following commits:

715c589 [Wenchen Fan] address comments
7ea5b31 [Wenchen Fan] fix python test
4f0833a [Wenchen Fan] add python test
f515d69 [Wenchen Fan] add apply method and test cases
8df6199 [Wenchen Fan] fix python test
239730c [Wenchen Fan] fix test compile
2a70526 [Wenchen Fan] use _bin_op in dataframe.py
6bf72bc [Wenchen Fan] address comments
3f880c3 [Wenchen Fan] add java doc
ab35ab5 [Wenchen Fan] fix python test
b5961a9 [Wenchen Fan] fix style
c9d85f5 [Wenchen Fan] generalize UnresolvedGetField to support all map, struct, and array

The previous cleanup-commit for SPARK-6627 renamed ShuffleBlockManager
to ShuffleBlockResolver, but didn't rename the associated subclasses and
variables; this commit does that.

I'm unsure whether it's ok to rename ExternalShuffleBlockManager, since that's technically a public class?

cc pwendell

Author: Kay Ousterhout <[email protected]>

Closes apache#5764 from kayousterhout/SPARK-6627 and squashes the following commits:

43add1e [Kay Ousterhout] Spacing fix
96080bf [Kay Ousterhout] Test fixes
d8a5d36 [Kay Ousterhout] [SPARK-6627] Finished rename to ShuffleBlockResolver

…close input streams

GZIPInputStream allocates native memory that is not freed until close() or
when the finalizer runs. It is best to close() these streams explicitly.

stephenh made the same change for serializeMapStatuses in commit b0d884f. This is the same change for deserialize.

(I ran the unit test suite! it seems to have passed. I did not make a JIRA since this seems "trivial", and the guidelines suggest it is not required for trivial changes)

Author: Evan Jones <[email protected]>

Closes apache#5982 from evanj/master and squashes the following commits:

0d76e85 [Evan Jones] [CORE] MapOutputTracker.deserializeMapStatuses: close input streams

Add `python/lib/pyspark.zip` to `.gitignore`. After merging apache#5580, `python/lib/pyspark.zip` will be generated when building Spark.

Author: zsxwing <[email protected]>

Closes apache#6017 from zsxwing/gitignore and squashes the following commits:

39b10c4 [zsxwing] Ignore python/lib/pyspark.zip

`vis.min.js` refers `vis.map` and this even refers `vis.js` which is used for debug `vis.js` but this debug feature is not needed for Spark itself.

This issue is really minor so I don't file this in JIRA.

/CC andrewor14

Author: Kousuke Saruta <[email protected]>

Closes apache#5994 from sarutak/remove-debug-feature-for-vis and squashes the following commits:

8be038f [Kousuke Saruta] Remove vis.map entry from .rat-exclude
7404945 [Kousuke Saruta] Removed debug feature for vis.js

…la 2.11

Spark shell crashes when compiled with scala 2.11 and  SPARK_PREPEND_CLASSES=true

There is a similar Resolved JIRA issue -SPARK-7470 and a PR apache#5997 , which handled same issue only in scala 2.10

Author: vinodkc <[email protected]>

Closes apache#6013 from vinodkc/fix_sqlcontext_exception_scala_2.11 and squashes the following commits:

119061c [vinodkc] Spark shell crashes when compiled with scala 2.11

The JVM is free to collect references to variables that no longer participate in a computation.  This simple patch adds an operation to the variable 'rdd' to ensure it is not collected early in the test suite's explicit calls to GC.

ref: http://bugs.java.com/view_bug.do?bug_id=6721588

Author: Tim Ellison <[email protected]>

Closes apache#6010 from tellison/master and squashes the following commits:

77d1c8f [Tim Ellison] Defeat early garbage collection of test suite variable by aggressive JVMs

Simple fix. We were comparing an option with `null`.

Before:
<img src="https://issues.apache.org/jira/secure/attachment/12731383/before.png" width="250px"/>
After:
<img src="https://issues.apache.org/jira/secure/attachment/12731384/after.png" width="250px"/>

Author: Andrew Or <[email protected]>

Closes apache#6002 from andrewor14/dag-viz-orphan-nodes and squashes the following commits:

a1468dc [Andrew Or] Fix null check

… file.

Order of initialization code was wrong.

Author: Marcelo Vanzin <[email protected]>

Closes apache#5998 from vanzin/hs-conf-fix and squashes the following commits:

00b6b6b [Marcelo Vanzin] [minor] [core] Allow History Server to read kerberos opts from config file.

The code was treating deep links as if they were attempt IDs, so
for example if you tried to load "/history/app1/jobs" directly,
that would fail because the code would treat "jobs" as an attempt id.

This change modifies the code to try both cases - first without an
attempt id, then with it, so that deep links are handled correctly.
This assumes that the links in the Spark UI do not clash with the
attempt id namespace, though, which is the case for YARN at least,
which is the only backend that currently publishes attempt IDs.

Author: Marcelo Vanzin <[email protected]>

Closes apache#5922 from vanzin/SPARK-7378 and squashes the following commits:

96f648b [Marcelo Vanzin] Fix comparison.
ed3bcd4 [Marcelo Vanzin] Merge branch 'master' into SPARK-7378
23483e4 [Marcelo Vanzin] Fat fingers.
b728f08 [Marcelo Vanzin] [SPARK-7378] [core] Handle deep links to unloaded apps.

…is greater than zero

JIRA: https://issues.apache.org/jira/browse/SPARK-7390

Also fix a minor typo.

Author: Liang-Chi Hsieh <[email protected]>

Closes apache#5931 from viirya/fix_covariancecounter and squashes the following commits:

352eda6 [Liang-Chi Hsieh] Only merge other CovarianceCounter when its count is greater than zero.

based on apache#3558

Author: Jacky Li <[email protected]>
Author: wangfei <[email protected]>
Author: scwf <[email protected]>

Closes apache#5806 from scwf/case and squashes the following commits:

cd51712 [wangfei] fix compile
d4b724f [wangfei] address michael's comment
af512c7 [wangfei] fix conflicts
4ef1be7 [wangfei] fix conflicts
269cf21 [scwf] fix conflicts
b73df6c [scwf] style issue
9e11752 [scwf] improve SimpleCatalystConf
b35529e [scwf] minor style
a3f7659 [scwf] remove unsed imports
2a56515 [scwf] fix conflicts
6db4bf5 [scwf] also fix for HiveContext
7fc4a98 [scwf] fix test case
d5a9933 [wangfei] fix style
eee75ba [wangfei] fix EmptyConf
6ef31cf [wangfei] revert pom changes
5d7c456 [wangfei] set CASE_SENSITIVE false in TestHive
966e719 [wangfei] set CASE_SENSITIVE false in hivecontext
fd30e25 [wangfei] added override
69b3b70 [wangfei] fix AnalysisSuite
5472b08 [wangfei] fix compile issue
56034ca [wangfei] fix conflicts and improve for catalystconf
664d1e9 [Jacky Li] Merge branch 'master' of https://github.com/apache/spark into case
12eca9a [Jacky Li] solve conflict with master
39e369c [Jacky Li] fix confilct after DataFrame PR
dee56e9 [Jacky Li] fix test case failure
05b09a3 [Jacky Li] fix conflict base on the latest master branch
73c16b1 [Jacky Li] fix bug in sql/hive
9bf4cc7 [Jacky Li] fix bug in catalyst
005c56d [Jacky Li] make SQLContext caseSensitivity configurable
6332e0f [Jacky Li] fix bug
fcbf0d9 [Jacky Li] fix scalastyle check
e7bca31 [Jacky Li] make caseSensitive configuration in Analyzer and Catalog
91b1b96 [Jacky Li] make caseSensitive configurable in Analyzer
f57f15c [Jacky Li] add testcase
578d167 [Jacky Li] make caseSensitive configurable

Add a Python API for mllib.feature.ChiSqSelector
https://issues.apache.org/jira/browse/SPARK-5913

Author: Yanbo Liang <[email protected]>

Closes apache#5939 from yanboliang/spark-5913 and squashes the following commits:

cdaac99 [Yanbo Liang] Python API for ChiSqSelector

I needed to run some d2 instances, so I updated the spark_ec2.py accordingly

Author: Brendan Collins <[email protected]>

Closes apache#6014 from brendancol/ec2-instance-types-update and squashes the following commits:

d7b4191 [Brendan Collins] Merge branch 'ec2-instance-types-update' of github.com:brendancol/spark into ec2-instance-types-update
6366c45 [Brendan Collins] added back cc1.4xlarge
fc2931f [Brendan Collins] updated ec2 instance types
80c2aa6 [Brendan Collins] vertically aligned whitespace
85c6236 [Brendan Collins] vertically aligned whitespace
1657c26 [Brendan Collins] updated ec2 instance types

Currently we're doing port retries in the TransportServer level, but this is not specified by the TransportContext API and it has other further-reaching impacts like causing undesirable behavior for the Yarn and Standalone shuffle services.

Author: Aaron Davidson <[email protected]>

Closes apache#5575 from aarondav/port-bind and squashes the following commits:

3c2d6ed [Aaron Davidson] Oops, never do it.
a5d9432 [Aaron Davidson] Remove shouldHostShuffleServiceIfEnabled
e901eb2 [Aaron Davidson] fix local-cluster mode for ExternalShuffleServiceSuite
59e5e38 [Aaron Davidson] [SPARK-6955] Perform port retries at NettyBlockTransferService level

The DAG visualization currently displays only low-level Spark primitives (e.g. `map`, `reduceByKey`, `filter` etc.). For SQL, these aren't particularly useful. Instead, we should display higher level physical operators (e.g. `Filter`, `Exchange`, `ShuffleHashJoin`). cc marmbrus

-----------------
**Before**
<img src="https://issues.apache.org/jira/secure/attachment/12731586/before.png" width="600px"/>
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**After** (Pay attention to the words)
<img src="https://issues.apache.org/jira/secure/attachment/12731587/after.png" width="600px"/>
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Author: Andrew Or <[email protected]>

Closes apache#5999 from andrewor14/dag-viz-sql and squashes the following commits:

0db23a4 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-sql
1e211db [Andrew Or] Update comment
0d49fd6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-sql
ffd237a [Andrew Or] Fix style
202dac1 [Andrew Or] Make ignoreParent false by default
e61b1ab [Andrew Or] Visualize SQL operators, not low-level Spark primitives
569034a [Andrew Or] Add a flag to ignore parent settings and scopes

Author: tedyu <[email protected]>

Closes apache#5959 from ted-yu/master and squashes the following commits:

f83d445 [tedyu] Move cleaning outside of mapPartitionsWithIndex
56d7c92 [tedyu] Consolidate import of Random
f6014c0 [tedyu] Remove cleaning in RDD#filterWith
36feb6c [tedyu] Try to get correct syntax
55d01eb [tedyu] Try to get correct syntax
c2786df [tedyu] Correct syntax
d92bfcf [tedyu] Correct syntax in test
164d3e4 [tedyu] Correct variable name
8b50d93 [tedyu] Address Andrew's review comments
0c8d47e [tedyu] Add test for mapWith()
6846e40 [tedyu] Add test for flatMapWith()
6c124a9 [tedyu] Clean function in several RDD methods

Adds Python Api for `ALS` under `ml.recommendation` in PySpark. Also adds seed as a settable parameter in the Scala Implementation of ALS.

Author: Burak Yavuz <[email protected]>

Closes apache#6015 from brkyvz/ml-rec and squashes the following commits:

be6e931 [Burak Yavuz] addressed comments
eaed879 [Burak Yavuz] readd numFeatures
0bd66b1 [Burak Yavuz] fixed seed
7f6d964 [Burak Yavuz] merged master
52e2bda [Burak Yavuz] added ALS

…sing Spark job to fail

Added a check to handle container exit status for the preemption scenario, log an INFO message in such cases and move on.
andrewor14

Author: Ashwin Shankar <[email protected]>

Closes apache#5993 from ashwinshankar77/SPARK-7451 and squashes the following commits:

90900cf [Ashwin Shankar] Fix log info message
cf8b6cf [Ashwin Shankar] Stop counting preemption of executors as failure

Changes include
1. Rename sortDF to arrange
2. Add new aliases `group_by` and `sample_frac`, `summarize`
3. Add more user friendly column addition (mutate), rename
4. Support mean as an alias for avg in Scala and also support n_distinct, n as in dplyr

Using these changes we can pretty much run the examples as described in http://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html with the same syntax

The only thing missing in SparkR is auto resolving column names when used in an expression i.e. making something like `select(flights, delay)` works in dply but we right now need `select(flights, flights$delay)` or `select(flights, "delay")`. But this is a complicated change and I'll file a new issue for it

cc sun-rui rxin

Author: Shivaram Venkataraman <[email protected]>

Closes apache#6005 from shivaram/sparkr-df-api and squashes the following commits:

5e0716a [Shivaram Venkataraman] Fix some roxygen bugs
1254953 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/apache/spark into sparkr-df-api
0521149 [Shivaram Venkataraman] Changes to make SparkR DataFrame dplyr friendly. Changes include 1. Rename sortDF to arrange 2. Add new aliases `group_by` and `sample_frac`, `summarize` 3. Add more user friendly column addition (mutate), rename 4. Support mean as an alias for avg in Scala and also support n_distinct, n as in dplyr

…apOutputs takes effect

This patch refactors the SQL `Exchange` operator's logic for determining whether map outputs need to be copied before being shuffled. As part of this change, we'll now avoid unnecessary copies in cases where sort-based shuffle operates on serialized map outputs (as in apache#4450 /
SPARK-4550).

This patch also includes a change to copy the input to RangePartitioner partition bounds calculation, which is necessary because this calculation buffers mutable Java objects.

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[<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/5948)
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Author: Josh Rosen <[email protected]>

Closes apache#5948 from JoshRosen/SPARK-7375 and squashes the following commits:

f305ff3 [Josh Rosen] Reduce scope of some variables in Exchange
899e1d7 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-7375
6a6bfce [Josh Rosen] Fix issue related to RangePartitioning:
ad006a4 [Josh Rosen] [SPARK-7375] Avoid defensive copying in exchange operator when sort.serializeMapOutputs takes effect.

…using OWLQN in new ML package

1) Handle scaling and addBias internally.
2) L1/L2 elasticnet using OWLQN optimizer.

Author: DB Tsai <[email protected]>

Closes apache#5967 from dbtsai/lor and squashes the following commits:

fa029bb [DB Tsai] made the bound smaller
0806002 [DB Tsai] better initial intercept and more test
5c31824 [DB Tsai] fix import
c387e25 [DB Tsai] Merge branch 'master' into lor
c84e931 [DB Tsai] Made MultiClassSummarizer private
f98e711 [DB Tsai] address feedback
a784321 [DB Tsai] fix style
8ec65d2 [DB Tsai] remove new line
f3f8c88 [DB Tsai] add more tests and they match R which is good. fix a bug
34705bc [DB Tsai] first commit

In SPARK-7429 and PR apache#5960, I added the varargs annotation to Params.setDefault which takes a variable number of ParamPairs. It worked locally and on Jenkins for me.
However, mengxr reported issues compiling on his machine. So I'm reverting the change introduced in apache#5960 by removing varargs.

Author: Joseph K. Bradley <[email protected]>

Closes apache#6021 from jkbradley/revert-varargs and squashes the following commits:

098ed39 [Joseph K. Bradley] removed varargs annotation from Params.setDefaults taking multiple ParamPairs

…oxDistinct

Author: Vinod K C <[email protected]>

Closes apache#5974 from vinodkc/fix_countApproxDistinct_Validation and squashes the following commits:

3a3d59c [Vinod K C] Reverted removal of validation relativeSD<0.000017
799976e [Vinod K C] Removed testcase to assert IAE when relativeSD>3.7
8ddbfae [Vinod K C] Remove blank line
b1b00a3 [Vinod K C] Removed relativeSD validation from python API,RDD.scala will do validation
122d378 [Vinod K C] Fixed validation of relativeSD in  countApproxDistinct

… case of running on YARN

When we use Spark on YARN and have AllJobPage via ResourceManager's proxy, the link URL in objects which represent each job on timeline view is wrong.

In timeline-view.js, the link is generated as follows.
```
window.location.href = "job/?id=" + getJobId(this);
```

This assumes the URL displayed on the web browser ends with "jobs/" but when we access AllJobPage via the proxy, the url displayed does not end with "jobs/"

The proxy doesn't return status code 301 or 302 so the url displayed still indicates the base url, not "/jobs" even though displaying AllJobPages.

![2015-05-07 3 34 37](https://cloud.githubusercontent.com/assets/4736016/7501079/a8507ad6-f46c-11e4-9bed-62abea170f4c.png)

Author: Kousuke Saruta <[email protected]>

Closes apache#5947 from sarutak/fix-link-in-timeline and squashes the following commits:

aaf40e1 [Kousuke Saruta] Added Copyright for vis.js
01bee7b [Kousuke Saruta] Fixed timeline-view.js in order to get correct href

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

Author: dobashim <[email protected]>

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

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