It's meaningless to display the Streaming tab before `ssc.start()`. So we should attach it in the `ssc.start` method.

Author: zsxwing <zsxwing@gmail.com>

Closes #5898 from zsxwing/SPARK-7350 and squashes the following commits:

e676487 [zsxwing] Attach the Streaming tab when calling ssc.start()

[SPARK-5074] [CORE] [TESTS] Fix the flakey test 'run shuffle with map stage failure' in DAGSchedulerSuite

Test failure: https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/AMPLAB_JENKINS_BUILD_PROFILE=hadoop2.2,label=centos/2240/testReport/junit/org.apache.spark.scheduler/DAGSchedulerSuite/run_shuffle_with_map_stage_failure/

This is because many tests share the same `JobListener`. Because after each test, `scheduler` isn't stopped. So actually it's still running. When running the test `run shuffle with map stage failure`, some previous test may trigger [ResubmitFailedStages](https://github.com/apache/spark/blob/ebc25a4ddfe07a67668217cec59893bc3b8cf730/core/src/main/scala/org/apache/spark/scheduler/DAGScheduler.scala#L1120) logic, and report `jobFailed` and override the global `failure` variable.

This PR uses `after` to call `scheduler.stop()` for each test.

Author: zsxwing <zsxwing@gmail.com>

Closes #5903 from zsxwing/SPARK-5074 and squashes the following commits:

1e6f13e [zsxwing] Fix the flakey test 'run shuffle with map stage failure' in DAGSchedulerSuite

Two minor doc errors in `BytesToBytesMap` and `UnsafeRow`.

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

Closes #5906 from viirya/minor_doc and squashes the following commits:

27f9089 [Liang-Chi Hsieh] Minor update for doc.

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

Author: Jihong MA <linlin200605@gmail.com>

Closes #5904 from JihongMA/SPARK-7357 and squashes the following commits:

7d6153a [Jihong MA] SPARK-7357 Improving HBaseTest example

"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

...aming.InputStreamsSuite.socket input stream

Remove non-deterministic "Thread.sleep" and use deterministic strategies to fix the flaky failure: https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-Maven-pre-YARN/hadoop.version=1.0.4,label=centos/2127/testReport/junit/org.apache.spark.streaming/InputStreamsSuite/socket_input_stream/

Author: zsxwing <zsxwing@gmail.com>

Closes #5891 from zsxwing/SPARK-7341 and squashes the following commits:

611157a [zsxwing] Add wait methods to BatchCounter and use BatchCounter in InputStreamsSuite
014b58f [zsxwing] Use withXXX to clean up the resources
c9bf746 [zsxwing] Move 'waitForStart' into the 'start' method and fix the code style
9d0de6d [zsxwing] [SPARK-7341][Streaming][Tests] Fix the flaky test: org.apache.spark.streaming.InputStreamsSuite.socket input stream

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

Closes #5879 from jerryshao/SPARK-7113 and squashes the following commits:

b0b506c [jerryshao] Address the comments
0babe66 [jerryshao] Support input information reporting for Direct Kafka stream

org.apache.spark.DriverSuite.driver should exit after finishing without cleanup (SPARK-530)
https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/2267/

org.apache.spark.deploy.SparkSubmitSuite.includes jars passed in through --jars
https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/2271/AMPLAB_JENKINS_BUILD_PROFILE=hadoop1.0,label=centos/testReport/

org.apache.spark.streaming.flume.FlumePollingStreamSuite.flume polling test
https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/2269/

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5901 from tdas/ignore-flaky-tests and squashes the following commits:

9cd8667 [Tathagata Das] Ignoring tests.

[SPARK-7139] [STREAMING] Allow received block metadata to be saved to WAL and recovered on driver failure

- Enabled ReceivedBlockTracker WAL by default
- Stored block metadata in the WAL
- Optimized WALBackedBlockRDD by skipping block fetch when the block is known to not exist in Spark

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5732 from tdas/SPARK-7139 and squashes the following commits:

575476e [Tathagata Das] Added more tests to get 100% coverage of the WALBackedBlockRDD
19668ba [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into SPARK-7139
685fab3 [Tathagata Das] Addressed comments in PR
637bc9c [Tathagata Das] Changed segment to handle
466212c [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into SPARK-7139
5f67a59 [Tathagata Das] Fixed HdfsUtils to handle append in local file system
1bc5bc3 [Tathagata Das] Fixed bug on unexpected recovery
d06fa21 [Tathagata Das] Enabled ReceivedBlockTracker by default, stored block metadata and optimized block fetching in WALBackedBlockRDD

Without this, any dependency that pulls ivy transitively may override
the version and potentially cause issue. In my machine, the hive tests
were pulling an old version of ivy, and subsequently failing with a
"NoSuchMethodError".

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5893 from vanzin/ivy-dep-fix and squashes the following commits:

ea2112d [Marcelo Vanzin] [minor] [build] Declare ivy dependency in root pom.

[MINOR] Renamed variables in SparkKMeans.scala, LocalKMeans.scala and kmeans.py to simplify readability

With the previous syntax it could look like that the reduceByKey sums separately abscissas and ordinates of some 2D points. Perhaps in this way should be easier to understand the example, especially for who is starting the functional programming like me now.

Author: Niccolo Becchi <niccolo.becchi@gmail.com>
Author: pippobaudos <niccolo.becchi@gmail.com>

Closes #5875 from pippobaudos/patch-1 and squashes the following commits:

3bb3a47 [pippobaudos] renamed variables in LocalKMeans.scala and kmeans.py to simplify readability
2c2a7a2 [Niccolo Becchi] Update SparkKMeans.scala

This PR upgrades Pyrolite to 4.4, which contains the bug fix for SPARK-3524 and some other performance improvements (e.g., SPARK-6288). The artifact is still under `org.spark-project` on Maven Central since there is no official release published there.

Author: Xiangrui Meng <meng@databricks.com>

Closes #5850 from mengxr/SPARK-7314 and squashes the following commits:

2ed4a95 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7314
da3c2dd [Xiangrui Meng] remove my repo
fe7e29b [Xiangrui Meng] switch to maven central
6ddac0e [Xiangrui Meng] reverse the machine code for float/double
d2d5b5b [Xiangrui Meng] change back to 4.4
7824a9c [Xiangrui Meng] use Pyrolite 3.1
cc3903a [Xiangrui Meng] upgrade Pyrolite to 4.4-0 for testing

Added a check so that if `AkkaUtils.askWithReply` is on the final attempt, it will not sleep for the `retryInterval`.  This should also prevent the thread from sleeping for `Int.Max` when using `askWithReply` with default values for `maxAttempts` and `retryInterval`.

Author: Bryan Cutler <bjcutler@us.ibm.com>

Closes #5896 from BryanCutler/askWithReply-sleep-7236 and squashes the following commits:

653a07b [Bryan Cutler] [SPARK-7236] Fix to prevent AkkaUtils askWithReply from sleeping on final attempt

This should gives us better analysis time error messages (rather than runtime) and automatic type casting.

Author: Reynold Xin <rxin@databricks.com>

Closes #5796 from rxin/expected-input-types and squashes the following commits:

c900760 [Reynold Xin] [SPARK-7266] Add ExpectsInputTypes to expressions when possible.

Computes a pair-wise frequency table of the given columns. Also known as cross-tabulation.
cc mengxr rxin

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5842 from brkyvz/df-cont and squashes the following commits:

a07c01e [Burak Yavuz] addressed comments v4.1
ae9e01d [Burak Yavuz] fix test
9106585 [Burak Yavuz] addressed comments v4.0
bced829 [Burak Yavuz] fix merge conflicts
a63ad00 [Burak Yavuz] addressed comments v3.0
a0cad97 [Burak Yavuz] addressed comments v3.0
6805df8 [Burak Yavuz] addressed comments and fixed test
939b7c4 [Burak Yavuz] lint python
7f098bc [Burak Yavuz] add crosstab pyTest
fd53b00 [Burak Yavuz] added python support for crosstab
27a5a81 [Burak Yavuz] implemented crosstab

This patch adds the functionality to display the RDD DAG on the SparkUI.

This DAG describes the relationships between
- an RDD and its dependencies,
- an RDD and its operation scopes, and
- an RDD's operation scopes and the stage / job hierarchy

An operation scope here refers to the existing public APIs that created the RDDs (e.g. `textFile`, `treeAggregate`). In the future, we can expand this to include higher level operations like SQL queries.

*Note: This blatantly stole a few lines of HTML and JavaScript from #5547 (thanks shroffpradyumn!)*

Here's what the job page looks like:
<img src="https://issues.apache.org/jira/secure/attachment/12730286/job-page.png" width="700px"/>
and the stage page:
<img src="https://issues.apache.org/jira/secure/attachment/12730287/stage-page.png" width="300px"/>

Author: Andrew Or <andrew@databricks.com>

Closes #5729 from andrewor14/viz2 and squashes the following commits:

666c03b [Andrew Or] Round corners of RDD boxes on stage page (minor)
01ba336 [Andrew Or] Change RDD cache color to red (minor)
6f9574a [Andrew Or] Add tests for RDDOperationScope
1c310e4 [Andrew Or] Wrap a few more RDD functions in an operation scope
3ffe566 [Andrew Or] Restore "null" as default for RDD name
5fdd89d [Andrew Or] children -> child (minor)
0d07a84 [Andrew Or] Fix python style
afb98e2 [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz2
0d7aa32 [Andrew Or] Fix python tests
3459ab2 [Andrew Or] Fix tests
832443c [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz2
429e9e1 [Andrew Or] Display cached RDDs on the viz
b1f0fd1 [Andrew Or] Rename OperatorScope -> RDDOperationScope
31aae06 [Andrew Or] Extract visualization logic from listener
83f9c58 [Andrew Or] Implement a programmatic representation of operator scopes
5a7faf4 [Andrew Or] Rename references to viz scopes to viz clusters
ee33d52 [Andrew Or] Separate HTML generating code from listener
f9830a2 [Andrew Or] Refactor + clean up + document JS visualization code
b80cc52 [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz2
0706992 [Andrew Or] Add link from jobs to stages
deb48a0 [Andrew Or] Translate stage boxes taking into account the width
5c7ce16 [Andrew Or] Connect RDDs across stages + update style
ab91416 [Andrew Or] Introduce visualization to the Job Page
5f07e9c [Andrew Or] Remove more return statements from scopes
5e388ea [Andrew Or] Fix line too long
43de96e [Andrew Or] Add parent IDs to StageInfo
6e2cfea [Andrew Or] Remove all return statements in `withScope`
d19c4da [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz2
7ef957c [Andrew Or] Fix scala style
4310271 [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz2
aa868a9 [Andrew Or] Ensure that HadoopRDD is actually serializable
c3bfcae [Andrew Or] Re-implement scopes using closures instead of annotations
52187fc [Andrew Or] Rat excludes
09d361e [Andrew Or] Add ID to node label (minor)
71281fa [Andrew Or] Embed the viz in the UI in a toggleable manner
8dd5af2 [Andrew Or] Fill in documentation + miscellaneous minor changes
fe7816f [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz
205f838 [Andrew Or] Reimplement rendering with dagre-d3 instead of viz.js
5e22946 [Andrew Or] Merge branch 'master' of github.com:apache/spark into viz
6a7cdca [Andrew Or] Move RDD scope util methods and logic to its own file
494d5c2 [Andrew Or] Revert a few unintended style changes
9fac6f3 [Andrew Or] Re-implement scopes through annotations instead
f22f337 [Andrew Or] First working implementation of visualization with vis.js
2184348 [Andrew Or] Translate RDD information to dot file
5143523 [Andrew Or] Expose the necessary information in RDDInfo
a9ed4f9 [Andrew Or] Add a few missing scopes to certain RDD methods
6b3403b [Andrew Or] Scope all RDD methods

Author: 云峤 <chensong.cs@alibaba-inc.com>

Closes #5865 from kaka1992/df.show and squashes the following commits:

c79204b [云峤] Update
a1338f6 [云峤] Update python dataFrame show test and add empty df unit test.
734369c [云峤] Update python dataFrame show test and add empty df unit test.
84aec3e [云峤] Update python dataFrame show test and add empty df unit test.
159b3d5 [云峤] update
03ef434 [云峤] update
7394fd5 [云峤] update test show
ced487a [云峤] update pep8
b6e690b [云峤] Merge remote-tracking branch 'upstream/master' into df.show
30ac311 [云峤] [SPARK-7294] ADD BETWEEN
7d62368 [云峤] [SPARK-7294] ADD BETWEEN
baf839b [云峤] [SPARK-7294] ADD BETWEEN
d11d5b9 [云峤] [SPARK-7294] ADD BETWEEN

This PR added `copy(extra: ParamMap): Params` to `Params`, which makes a copy of the current instance with a randomly generated uid and some extra param values. With this change, we only need to implement `fit` and `transform` without extra param values given the default implementation of `fit(dataset, extra)`:

~~~scala
def fit(dataset: DataFrame, extra: ParamMap): Model = {
  copy(extra).fit(dataset)
}
~~~

Inside `fit` and `transform`, since only the embedded values are used, I added `$` as an alias for `getOrDefault` to make the code easier to read. For example, in `LinearRegression.fit` we have:

~~~scala
val effectiveRegParam = $(regParam) / yStd
val effectiveL1RegParam = $(elasticNetParam) * effectiveRegParam
val effectiveL2RegParam = (1.0 - $(elasticNetParam)) * effectiveRegParam
~~~

Meta-algorithm like `Pipeline` implements its own `copy(extra)`. So the fitted pipeline model stored all copied stages (no matter whether it is a transformer or a model).

Other changes:
* `Params$.inheritValues` is moved to `Params!.copyValues` and returns the target instance.
* `fittingParamMap` was removed because the `parent` carries this information.
* `validate` was renamed to `validateParams` to be more precise.

TODOs:
* [x] add tests for newly added methods
* [ ] update documentation

jkbradley dbtsai

Author: Xiangrui Meng <meng@databricks.com>

Closes #5820 from mengxr/SPARK-5956 and squashes the following commits:

7bef88d [Xiangrui Meng] address comments
05229c3 [Xiangrui Meng] assert -> assertEquals
b2927b1 [Xiangrui Meng] organize imports
f14456b [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5956
93e7924 [Xiangrui Meng] add tests for hasParam & copy
463ecae [Xiangrui Meng] merge master
2b954c3 [Xiangrui Meng] update Binarizer
465dd12 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5956
282a1a8 [Xiangrui Meng] fix test
819dd2d [Xiangrui Meng] merge master
b642872 [Xiangrui Meng] example code runs
5a67779 [Xiangrui Meng] examples compile
c76b4d1 [Xiangrui Meng] fix all unit tests
0f4fd64 [Xiangrui Meng] fix some tests
9286a22 [Xiangrui Meng] copyValues to trained models
53e0973 [Xiangrui Meng] move inheritValues to Params and rename it to copyValues
9ee004e [Xiangrui Meng] merge copy and copyWith; rename validate to validateParams
d882afc [Xiangrui Meng] test compile
f082a31 [Xiangrui Meng] make Params copyable and simply handling of extra params in all spark.ml components

I suspect haven't been using anaconda in tests in a while. I wonder if this change actually does anything but this line as it stands looks strictly less correct.

Author: Andrew Or <andrew@databricks.com>

Closes #5883 from andrewor14/fix-run-tests-typo and squashes the following commits:

a3ad720 [Andrew Or] Fix typo?

This PR is a rebased version of #3946 , and mainly focused on creating an independent tab for the thrift server in spark web UI.

Features:

1. Session related statistics ( username and IP are only supported in hive-0.13.1 )
2. List all the SQL executing or executed on this server
3. Provide links to the job generated by SQL
4. Provide link to show all SQL executing or executed in a specified session

Prototype snapshots:

This is the main page for thrift server

![image](https://cloud.githubusercontent.com/assets/1411869/7361379/df7dcc64-ed89-11e4-9964-4df0b32f475e.png)

Author: tianyi <tianyi.asiainfo@gmail.com>

Closes #5730 from tianyi/SPARK-5100 and squashes the following commits:

cfd14c7 [tianyi] style fix
0efe3d5 [tianyi] revert part of pom change
c0f2fa0 [tianyi] extends HiveThriftJdbcTest to start/stop thriftserver for UI test
aa20408 [tianyi] fix style problem
c9df6f9 [tianyi] add testsuite for thriftserver ui and fix some style issue
9830199 [tianyi] add webui for thriftserver

JIRA: https://issues.apache.org/jira/browse/SPARK-5563
The PR contains the implementation for [Online LDA] (https://www.cs.princeton.edu/~blei/papers/HoffmanBleiBach2010b.pdf) based on the research of  Matt Hoffman and David M. Blei, which provides an efficient option for LDA users. Major advantages for the algorithm are the stream compatibility and economic time/memory consumption due to the corpus split. For more details, please refer to the jira.

Online LDA can act as a fast option for LDA, and will be especially helpful for the users who needs a quick result or with large corpus.

 Correctness test.
I have tested current PR with https://github.com/Blei-Lab/onlineldavb and the results are identical. I've uploaded the result and code to https://github.com/hhbyyh/LDACrossValidation.

Author: Yuhao Yang <hhbyyh@gmail.com>
Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4419 from hhbyyh/ldaonline and squashes the following commits:

1045eec [Yuhao Yang] Merge pull request #2 from jkbradley/hhbyyh-ldaonline2
cf376ff [Joseph K. Bradley] For private vars needed for testing, I made them private and added accessors.  Java doesn’t understand package-private tags, so this minimizes the issues Java users might encounter.
6149ca6 [Yuhao Yang] fix for setOptimizer
cf0007d [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
54cf8da [Yuhao Yang] some style change
68c2318 [Yuhao Yang] add a java ut
4041723 [Yuhao Yang] add ut
138bfed [Yuhao Yang] Merge pull request #1 from jkbradley/hhbyyh-ldaonline-update
9e910d9 [Joseph K. Bradley] small fix
61d60df [Joseph K. Bradley] Minor cleanups: * Update *Concentration parameter documentation * EM Optimizer: createVertices() does not need to be a function * OnlineLDAOptimizer: typos in doc * Clean up the core code for online LDA (Scala style)
a996a82 [Yuhao Yang] respond to comments
b1178cf [Yuhao Yang] fit into the optimizer framework
dbe3cff [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
15be071 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
b29193b [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
d19ef55 [Yuhao Yang] change OnlineLDA to class
97b9e1a [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
e7bf3b0 [Yuhao Yang] move to seperate file
f367cc9 [Yuhao Yang] change to optimization
8cb16a6 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
62405cc [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
02d0373 [Yuhao Yang] fix style in comment
f6d47ca [Yuhao Yang] Merge branch 'ldaonline' of https://github.com/hhbyyh/spark into ldaonline
d86cdec [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
a570c9a [Yuhao Yang] use sample to pick up batch
4a3f27e [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline
e271eb1 [Yuhao Yang] remove non ascii
581c623 [Yuhao Yang] seperate API and adjust batch split
37af91a [Yuhao Yang] iMerge remote-tracking branch 'upstream/master' into ldaonline
20328d1 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline i
aa365d1 [Yuhao Yang] merge upstream master
3a06526 [Yuhao Yang] merge with new example
0dd3947 [Yuhao Yang] kMerge remote-tracking branch 'upstream/master' into ldaonline
0d0f3ee [Yuhao Yang] replace random split with sliding
fa408a8 [Yuhao Yang] ssMerge remote-tracking branch 'upstream/master' into ldaonline
45884ab [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline s
f41c5ca [Yuhao Yang] style fix
26dca1b [Yuhao Yang] style fix and make class private
043e786 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaonline s Conflicts: 	mllib/src/main/scala/org/apache/spark/mllib/clustering/LDA.scala
d640d9c [Yuhao Yang] online lda initial checkin

submitting this PR from a phone, excuse the brevity.
adds Pearson correlation to Dataframes, reusing the covariance calculation code

cc mengxr rxin

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5858 from brkyvz/df-corr and squashes the following commits:

285b838 [Burak Yavuz] addressed comments v2.0
d10babb [Burak Yavuz] addressed comments v0.2
4b74b24 [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into df-corr
4fe693b [Burak Yavuz] addressed comments v0.1
a682d06 [Burak Yavuz] ready for PR

as suggested by justinuang on #5601.

Author: Xiangrui Meng <meng@databricks.com>

Closes #5873 from mengxr/SPARK-7329 and squashes the following commits:

d08f9cf [Xiangrui Meng] simplify tests
b7a7b9b [Xiangrui Meng] simplify grid build

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

This PR adds initial support for loading multiple versions of Hive in a single JVM and provides a common interface for extracting metadata from the `HiveMetastoreClient` for a given version.  This is accomplished by creating an isolated `ClassLoader` that operates according to the following rules:

 - __Shared Classes__: Java, Scala, logging, and Spark classes are delegated to `baseClassLoader`
  allowing the results of calls to the `ClientInterface` to be visible externally.
 - __Hive Classes__: new instances are loaded from `execJars`.  These classes are not
  accessible externally due to their custom loading.
 - __Barrier Classes__: Classes such as `ClientWrapper` are defined in Spark but must link to a specific version of Hive.  As a result, the bytecode is acquired from the Spark `ClassLoader` but a new copy is created for each instance of `IsolatedClientLoader`.
  This new instance is able to see a specific version of hive without using reflection where ever hive is consistent across versions. Since
  this is a unique instance, it is not visible externally other than as a generic
  `ClientInterface`, unless `isolationOn` is set to `false`.

In addition to the unit tests, I have also tested this locally against mysql instances of the Hive Metastore.  I've also successfully ported Spark SQL to run with this client, but due to the size of the changes, that will come in a follow-up PR.

By default, Hive jars are currently downloaded from Maven automatically for a given version to ease packaging and testing.  However, there is also support for specifying their location manually for deployments without internet.

Author: Michael Armbrust <michael@databricks.com>

Closes #5851 from marmbrus/isolatedClient and squashes the following commits:

c72f6ac [Michael Armbrust] rxins comments
1e271fa [Michael Armbrust] [SPARK-6907][SQL] Isolated client for HiveMetastore

Author: Omede Firouz <ofirouz@palantir.com>
Author: Omede <omedefirouz@gmail.com>

Closes #5601 from oefirouz/paramgrid and squashes the following commits:

c9e2481 [Omede Firouz] Make test a doctest
9a8ce22 [Omede] Fix linter issues
8b8a6d2 [Omede Firouz] [SPARK-7022][PySpark][ML] Add ML.Tuning.ParamGridBuilder to PySpark

We should let Thrift Server take these two parameters as it is a daemon. And it is better to read driver-related configs as an app submited by spark-submit.

https://issues.apache.org/jira/browse/SPARK-7031

Author: WangTaoTheTonic <wangtao111@huawei.com>

Closes #5609 from WangTaoTheTonic/SPARK-7031 and squashes the following commits:

8d3fc16 [WangTaoTheTonic] indent
035069b [WangTaoTheTonic] better code style
d3ddfb6 [WangTaoTheTonic] revert the unnecessary changes in suite
624e652 [WangTaoTheTonic] fix break tests
0565831 [WangTaoTheTonic] fix failed tests
4fb25ed [WangTaoTheTonic] let thrift server take SPARK_DAEMON_MEMORY and SPARK_DAEMON_JAVA_OPTS

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

based on #4015, we should not delete `sqlParser` from sqlcontext, that leads to mima failed. Users implement dialect to give a fallback for `sqlParser`  and we should construct `sqlParser` in sqlcontext according to the dialect
`protected[sql] val sqlParser = new SparkSQLParser(getSQLDialect().parse(_))`

Author: Cheng Hao <hao.cheng@intel.com>
Author: scwf <wangfei1@huawei.com>

Closes #5827 from scwf/sqlparser1 and squashes the following commits:

81b9737 [scwf] comment fix
0878bd1 [scwf] remove comments
c19780b [scwf] fix mima tests
c2895cf [scwf] Merge branch 'master' of https://github.com/apache/spark into sqlparser1
493775c [Cheng Hao] update the code as feedback
81a731f [Cheng Hao] remove the unecessary comment
aab0b0b [Cheng Hao] polish the code a little bit
49b9d81 [Cheng Hao] shrink the comment for rebasing

At least in the version of Hive I tested on, the test was deleting
a temp directory generated by Hive instead of one containing partition
data. So fix the filter to only consider partition directories when
deciding what to delete.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5854 from vanzin/hive-test-fix and squashes the following commits:

7594ae9 [Marcelo Vanzin] Fix typo.
729fa80 [Marcelo Vanzin] [minor] [hive] Fix QueryPartitionSuite.

SizeEstimator gives wrong result for Integer on 64bit JVM with UseCompressedOops on, this pr fixes that. For more details, please refer [SPARK-6030](https://issues.apache.org/jira/browse/SPARK-6030)
sryza, I noticed there is a pr to expose SizeEstimator, maybe that should be waited by this pr get merged if we confirm this problem.
And shivaram would you mind to review this pr since you contribute related code. Also cc to srowen and mateiz

Author: Ye Xianjin <advancedxy@gmail.com>

Closes #4783 from advancedxy/SPARK-6030 and squashes the following commits:

c4dcb41 [Ye Xianjin] Add super.beforeEach in the beforeEach method to make the trait stackable.. Remove useless leading whitespace.
3f80640 [Ye Xianjin] The size of Integer class changes from 24 to 16 on a 64-bit JVM with -UseCompressedOops flag on after the fix. I don't how 100000 was originally calculated, It looks like 100000 is the magic number which makes sure spilling. Because of the size change, It fails because there is no spilling at all. Change the number to a slightly larger number fixes that.
e849d2d [Ye Xianjin] Merge two shellSize assignments into one. Add some explanation to alignSizeUp method.
85a0b51 [Ye Xianjin] Fix typos and update wording in comments. Using alignSizeUp to compute alignSize.
d27eb77 [Ye Xianjin] Add some detailed comments in the code. Add some test cases. It's very difficult to design test cases as the final object alignment will hide a lot of filed layout details if we just considering the whole size.
842aed1 [Ye Xianjin] primitiveSize(cls) can just return Int. Use a simplified class field layout method to calculate class instance size. Will add more documents and test cases. Add a new alignSizeUp function which uses bitwise operators to speedup.
62e8ab4 [Ye Xianjin] Don't alignSize for objects' shellSize, alignSize when added to state.size. Add some primitive wrapper objects size tests.

Author: Mridul Muralidharan <mridulm@yahoo-inc.com>

Closes #5862 from mridulm/optimize_aggregator and squashes the following commits:

61cf43a [Mridul Muralidharan] Use insertAll instead of insert - much more expensive to do it per tuple

Author: Dean Chen <deanchen5@gmail.com>

Closes #5866 from deanchen/patch-1 and squashes the following commits:

0028bc4 [Dean Chen] Fix typo in Dataframes.py introduced in [SPARK-3444]

`FileUtils.getTempDirectoryPath()` path may or may not exist. We want to make sure that it does not exist.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5853 from tdas/SPARK-7315 and squashes the following commits:

141afd5 [Tathagata Das] Removed use of FileUtils
b08d4f1 [Tathagata Das] Fix flaky WALBackedBlockRDDSuite

Note: ~600 lines of this is test code, and ~100 lines documentation.

**[SPARK-7121]** ClosureCleaner does not handle nested closures properly. For instance, in SparkContext, I tried to do the following:
```
def scope[T](body: => T): T = body // no-op
def myCoolMethod(path: String): RDD[String] = scope {
  parallelize(1 to 10).map { _ => path }
}
```
and I got an exception complaining that SparkContext is not serializable. The issue here is that the inner closure is getting its path from the outer closure (the scope), but the outer closure references the SparkContext object itself to get the `parallelize` method.

Note, however, that the inner closure doesn't actually need the SparkContext; it just needs a field from the outer closure. If we modify ClosureCleaner to clean the outer closure recursively using only the fields accessed by the inner closure, then we can serialize the inner closure.

**[SPARK-7120]** Also, the other thing is that this file is one of the least understood, partly because it is very low level and is written a long time ago. This patch attempts to change that by adding the missing documentation.

This is blocking my effort on a separate task #5729.

Author: Andrew Or <andrew@databricks.com>

Closes #5685 from andrewor14/closure-cleaner and squashes the following commits:

cd46230 [Andrew Or] Revert a small change that affected streaming
0bbe77f [Andrew Or] Fix style
ea874bc [Andrew Or] Fix tests
26c5072 [Andrew Or] Address comments
16fbcfd [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner
26c7aba [Andrew Or] Revert "In sc.runJob, actually clean the inner closure"
6f75784 [Andrew Or] Revert "Guard against NPE if CC is used outside of an application"
e909a42 [Andrew Or] Guard against NPE if CC is used outside of an application
3998168 [Andrew Or] In sc.runJob, actually clean the inner closure
9187066 [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner
d889950 [Andrew Or] Revert "Bypass SerializationDebugger for now (SPARK-7180)"
9419efe [Andrew Or] Bypass SerializationDebugger for now (SPARK-7180)
6d4d3f1 [Andrew Or] Fix scala style?
4aab379 [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner
e45e904 [Andrew Or] More minor updates (wording, renaming etc.)
8b71cdb [Andrew Or] Update a few comments
eb127e5 [Andrew Or] Use private method tester for a few things
a3aa465 [Andrew Or] Add more tests for individual closure cleaner operations
e672170 [Andrew Or] Guard against potential infinite cycles in method visitor
6d36f38 [Andrew Or] Fix closure cleaner visibility
2106f12 [Andrew Or] Merge branch 'master' of github.com:apache/spark into closure-cleaner
263593d [Andrew Or] Finalize tests
06fd668 [Andrew Or] Make closure cleaning idempotent
a4866e3 [Andrew Or] Add tests (still WIP)
438c68f [Andrew Or] Minor changes
2390a60 [Andrew Or] Feature flag this new behavior
86f7823 [Andrew Or] Implement transitive cleaning + add missing documentation

The python api for DataFrame's plus addressed your comments from previous PR.
rxin

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5859 from brkyvz/df-freq-py2 and squashes the following commits:

f9aa9ce [Burak Yavuz] addressed comments v0.1
4b25056 [Burak Yavuz] added python api for freqItems

Details in JIRA, in a nut-shell, all machinary for custom RDD's to leverage spark shuffle directly (without exposing impl details of shuffle) exists - except for this small piece.

Exposing this will allow for custom dependencies to get a handle to ShuffleHandle - which they can then leverage on reduce side.

Author: Mridul Muralidharan <mridulm@yahoo-inc.com>

Closes #5857 from mridulm/expose_shuffle_handle and squashes the following commits:

d8b6bd4 [Mridul Muralidharan] Expose ShuffleHandle

There are two main parts of this change:

- Extending the bootstrap mechanism in the network library to add a server-side
  bootstrap (which works a little bit differently than the client-side bootstrap), and
  to allow the  bootstraps to modify the underlying channel.

- Use SASL to encrypt data going through the RPC channel.

The second item requires some non-optimal code to be able to work around the
fact that the outbound path in netty is not thread-safe, and ordering is very important
when encryption is in the picture.

A lot of the changes outside the network/common library are just to adjust to the
changed API for initializing the RPC server.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5377 from vanzin/SPARK-6229 and squashes the following commits:

ff01966 [Marcelo Vanzin] Use fancy new size config style.
be53f32 [Marcelo Vanzin] Merge branch 'master' into SPARK-6229
47d4aff [Marcelo Vanzin] Merge branch 'master' into SPARK-6229
7a2a805 [Marcelo Vanzin] Clean up some unneeded changes.
2f92237 [Marcelo Vanzin] Add comment.
67bb0c6 [Marcelo Vanzin] Revert "Avoid exposing ByteArrayWritableChannel outside of test code."
065f684 [Marcelo Vanzin] Add test to verify chunking.
3d1695d [Marcelo Vanzin] Minor cleanups.
73cff0e [Marcelo Vanzin] Skip bytes in decode path too.
318ad23 [Marcelo Vanzin] Avoid exposing ByteArrayWritableChannel outside of test code.
346f829 [Marcelo Vanzin] Avoid trip through channel selector by not reporting 0 bytes written.
a4a5938 [Marcelo Vanzin] Review feedback.
4797519 [Marcelo Vanzin] Remove unused import.
9908ada [Marcelo Vanzin] Fix test, SASL backend disposal.
7fe1489 [Marcelo Vanzin] Add a test that makes sure encryption is actually enabled.
adb6f9d [Marcelo Vanzin] Review feedback.
cf2a605 [Marcelo Vanzin] Clean up some code.
8584323 [Marcelo Vanzin] Fix a comment.
e98bc55 [Marcelo Vanzin] Add option to only allow encrypted connections to the server.
dad42fc [Marcelo Vanzin] Make encryption thread-safe, less memory-intensive.
b00999a [Marcelo Vanzin] Consolidate ByteArrayWritableChannel, fix SASL code to match master changes.
b923cae [Marcelo Vanzin] Make SASL encryption handler thread-safe, handle FileRegion messages.
39539a7 [Marcelo Vanzin] Add config option to enable SASL encryption.
351a86f [Marcelo Vanzin] Add SASL encryption to network library.
fbe6ccb [Marcelo Vanzin] Add TransportServerBootstrap, make SASL code use it.