If classes implementing Serializable or Externalizable interfaces throw
exceptions other than IOException or ClassNotFoundException from their
(de)serialization methods, then this results in an unhelpful
"IOException: unexpected exception type" rather than the actual exception that
produced the (de)serialization error.

This patch fixes this by adding a utility method that re-wraps any uncaught
exceptions in IOException (unless they are already instances of IOException).

Author: Josh Rosen <joshrosen@databricks.com>

Closes #2932 from JoshRosen/SPARK-4080 and squashes the following commits:

cd3a9be [Josh Rosen] [SPARK-4080] Only throw IOException from [write|read][Object|External].

@harishreedharan @pwendell
See JIRA for diagnosis of the problem
https://issues.apache.org/jira/browse/SPARK-3912

The solution was to reimplement it.
1. Find a free port (by binding and releasing a server-scoket), and then use that port
2. Remove thread.sleep()s, instead repeatedly try to create a sender and send data and check whether data was sent. Use eventually() to minimize waiting time.
3. Check whether all the data was received, without caring about batches.

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

Closes #2773 from tdas/flume-test-fix and squashes the following commits:

93cd7f6 [Tathagata Das] Reimplimented FlumeStreamSuite to be more robust.

Thread names are useful for correlating failures.

Author: Reynold Xin <rxin@apache.org>

Closes #2600 from rxin/log4j and squashes the following commits:

83ffe88 [Reynold Xin] [SPARK-3748] Log thread name in unit test logs

Since it looked quite easy, I took the liberty of making a quick PR that just uses `Utils.startServiceOnPort` to fix this. It works locally for me.

Author: Sean Owen <sowen@cloudera.com>

Closes #2601 from srowen/SPARK-3744 and squashes the following commits:

ddc9319 [Sean Owen] Avoid port contention in tests by retrying several ports for Flume stream

...ing for the channel size.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #2531 from harishreedharan/sparksinksuite-fix and squashes the following commits:

30393c1 [Hari Shreedharan] Use more deterministic method to figure out when batches come in.
6ce9d8b [Hari Shreedharan] [SPARK-3686][STREAMING] Wait for sink to commit the channel before checking for the channel size.

Details can be seen in [SPARK-3615](https://issues.apache.org/jira/browse/SPARK-3615).

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

Closes #2483 from jerryshao/SPARK_3615 and squashes the following commits:

8555563 [jerryshao] Fix Kafka unit test hard coded Zookeeper port issue

Author: GuoQiang Li <witgo@qq.com>

Closes #2268 from witgo/SPARK-3397 and squashes the following commits:

eaf913f [GuoQiang Li] Bump pom.xml version number of master branch to 1.2.0-SNAPSHOT

Author: GuoQiang Li <witgo@qq.com>

Closes #2265 from witgo/FlumeStreamSuite and squashes the following commits:

6c99e6e [GuoQiang Li] Remove extra semicolon in FlumeStreamSuite.scala

Currently lot of errors get thrown from Avro IPC layer when the dstream
or sink is shutdown. This PR cleans it up. Some refactoring is done in the
receiver code to put all of the RPC code into a single Try and just recover
from that. The sink code has also been cleaned up.

Author: Hari Shreedharan <hshreedharan@apache.org>

Closes #2065 from harishreedharan/clean-flume-shutdown and squashes the following commits:

f93a07c [Hari Shreedharan] Formatting fixes.
d7427cc [Hari Shreedharan] More fixes!
a0a8852 [Hari Shreedharan] Fix race condition, hopefully! Minor other changes.
4c9ed02 [Hari Shreedharan] Remove unneeded list in Callback handler. Other misc changes.
8fee36f [Hari Shreedharan] Scala-library is required, else maven build fails. Also catch InterruptedException in TxnProcessor.
445e700 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into clean-flume-shutdown
87232e0 [Hari Shreedharan] Refactor Flume Input Stream. Clean up code, better error handling.
9001d26 [Hari Shreedharan] Change log level to debug in TransactionProcessor#shutdown method
e7b8d82 [Hari Shreedharan] Incorporate review feedback
598efa7 [Hari Shreedharan] Clean up some exception handling code
e1027c6 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into clean-flume-shutdown
ed608c8 [Hari Shreedharan] [SPARK-3154][STREAMING] Make FlumePollingInputDStream shutdown cleaner.

(EDIT) Since the scalatest issue was since resolved, this is now about a few small problems in the Flume Sink `pom.xml`

- `scalatest` is not declared as a test-scope dependency
- Its Avro version doesn't match the rest of the build
- Its Flume version is not synced with the other Flume module
- The other Flume module declares its dependency on Flume Sink slightly incorrectly, hard-coding the Scala 2.10 version
- It depends on Scala Lang directly, which it shouldn't

Author: Sean Owen <sowen@cloudera.com>

Closes #1726 from srowen/SPARK-2798 and squashes the following commits:

a46e2c6 [Sean Owen] scalatest to test scope, harmonize Avro and Flume versions, remove direct Scala dependency, fix '2.10' in Flume dependency

Due to maven bug https://jira.codehaus.org/browse/MNG-1378, maven could not resolve spark streaming classes required by the spark-streaming test-jar dependency of external/flume-sink. There is no particular reason that the external/flume-sink has to depend on Spark Streaming at all, so I am eliminating this dependency. Also I have removed the exclusions present in the Flume dependencies, as there is no reason to exclude them (they were excluded in the external/flume module to prevent dependency collisions with Spark).

Since Jenkins will test the sbt build and the unit test, I only tested maven compilation locally.

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

Closes #2101 from tdas/spark-sink-pom-fix and squashes the following commits:

8f42621 [Tathagata Das] Added Flume sink exclusions back, and added netty to test dependencies
93b559f [Tathagata Das] Removed dependency on spark streaming test from spark flume sink

This patch adds unit tests for Spark Sink.

It also removes the private[flume] for Spark Sink,
since the sink is instantiated from Flume configuration (looks like this is ignored by reflection which is used by
Flume, but we should still remove it anyway).

Author: Hari Shreedharan <hshreedharan@apache.org>
Author: Hari Shreedharan <hshreedharan@cloudera.com>

Closes #1958 from harishreedharan/spark-sink-test and squashes the following commits:

e3110b9 [Hari Shreedharan] Add a sleep to allow sink to commit the transactions
120b81e [Hari Shreedharan] Fix complexity in threading model in test
4df5be6 [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into spark-sink-test
c9190d1 [Hari Shreedharan] Indentation and spaces changes
7fedc5a [Hari Shreedharan] Merge remote-tracking branch 'asf/master' into spark-sink-test
abc20cb [Hari Shreedharan] Minor test changes
7b9b649 [Hari Shreedharan] Merge branch 'master' into spark-sink-test
f2c56c9 [Hari Shreedharan] Update SparkSinkSuite.scala
a24aac8 [Hari Shreedharan] Remove unused var
c86d615 [Hari Shreedharan] [SPARK-3054][STREAMING] Add unit tests for Spark Sink.

Author: Hari Shreedharan <harishreedharan@gmail.com>

Closes #1820 from harishreedharan/use-free-ports and squashes the following commits:

b939067 [Hari Shreedharan] Remove unused import.
67856a8 [Hari Shreedharan] Remove findFreePort.
0ea51d1 [Hari Shreedharan] Make some changes to getPort to use map on the serverOpt.
1fb0283 [Hari Shreedharan] Merge branch 'master' of https://github.com/apache/spark into use-free-ports
b351651 [Hari Shreedharan] Allow Netty to choose port, and query it to decide the port to bind to. Leaving findFreePort as is, if other tests want to use it at some point.
e6c9620 [Hari Shreedharan] Making sure the second sink uses the correct port.
11c340d [Hari Shreedharan] Add info about race condition to scaladoc.
e89d135 [Hari Shreedharan] Adding Scaladoc.
6013bb0 [Hari Shreedharan] [STREAMING] Find free ports to use before attempting to create Flume Sink in Flume Polling Suite

This is failing my tests in #1777. @tdas

Author: Andrew Or <andrewor14@gmail.com>

Closes #1803 from andrewor14/fix-flaky-streaming-test and squashes the following commits:

ea11a03 [Andrew Or] Catch all exceptions caused by BindExceptions
54a0ca0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into fix-flaky-streaming-test
664095c [Andrew Or] Tone down bind exception message
af3ddc9 [Andrew Or] Handle port collisions in flume polling test

https://github.com/apache/spark/pull/1751 caused maven builds to fail.

```
~/Apache/spark(branch-1.1|) ➤ mvn -U -DskipTests clean install
.
.
.
[error] Apache/spark/external/kafka/src/test/scala/org/apache/spark/streaming/kafka/KafkaStreamSuite.scala:36: object NIOServerCnxnFactory is not a member of package org.apache.zookeeper.server
[error] import org.apache.zookeeper.server.NIOServerCnxnFactory
[error]        ^
[error] Apache/spark/external/kafka/src/test/scala/org/apache/spark/streaming/kafka/KafkaStreamSuite.scala:199: not found: type NIOServerCnxnFactory
[error]     val factory = new NIOServerCnxnFactory()
[error]                       ^
[error] two errors found
[error] Compile failed at Aug 5, 2014 1:42:36 PM [0.503s]
```

The problem is how SBT and Maven resolves multiple versions of the same library, which in this case, is Zookeeper. Observing and comparing the dependency trees from Maven and SBT showed this. Spark depends on ZK 3.4.5 whereas Apache Kafka transitively depends on upon ZK 3.3.4. SBT decides to evict 3.3.4 and use the higher version 3.4.5. But Maven decides to stick to the closest (in the tree) dependent version of 3.3.4. And 3.3.4 does not have NIOServerCnxnFactory.

The solution in this patch excludes zookeeper from the apache-kafka dependency in streaming-kafka module so that it just inherits zookeeper from Spark core.

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

Closes #1797 from tdas/kafka-zk-fix and squashes the following commits:

94b3931 [Tathagata Das] Fixed zookeeper dependency of Kafka

This PR is a updated version of (https://github.com/apache/spark/pull/557) to actually test sending and receiving data through Kafka, and fix previous flaky issues.

@tdas, would you mind reviewing this PR? Thanks a lot.

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

Closes #1751 from jerryshao/kafka-unit-test and squashes the following commits:

b6a505f [jerryshao] code refactor according to comments
5222330 [jerryshao] Change JavaKafkaStreamSuite to better test it
5525f10 [jerryshao] Fix flaky issue of Kafka real unit test
4559310 [jerryshao] Minor changes for Kafka unit test
860f649 [jerryshao] Minor style changes, and tests ignored due to flakiness
796d4ca [jerryshao] Add real Kafka streaming test

This has been failing on master. One possible cause is that the port
gets contended if multiple test runs happen concurrently and they
hit this test at the same time. Since this test takes a long time
(60 seconds) that's very plausible. This patch randomizes the port
used in this test to avoid contention.

We needed to add an explicit dependency on scalatest since this
module will not get it from spark core like others do.

This PR updates previous Manifest for KafkaInputDStream's Decoder to ClassTag, also fix the problem addressed in [SPARK-2103](https://issues.apache.org/jira/browse/SPARK-2103).

Previous Java interface cannot actually get the type of Decoder, so when using this Manifest to reconstruct the decode object will meet reflection exception.

Also for other two Java interfaces, ClassTag[String] is useless because calling Scala API will get the right implicit ClassTag.

Current Kafka unit test cannot actually verify the interface. I've tested these interfaces in my local and distribute settings.

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

Closes #1508 from jerryshao/SPARK-2103 and squashes the following commits:

e90c37b [jerryshao] Add Mima excludes
7529810 [jerryshao] Change Manifest to ClassTag for KafkaInputDStream's Decoder and fix Decoder construct issue when using Java API

SPARK-2749 [BUILD]. Spark SQL Java tests aren't compiling in Jenkins' Maven builds; missing junit:junit dep

The Maven-based builds in the build matrix have been failing for a few days:

https://amplab.cs.berkeley.edu/jenkins/view/Spark/

On inspection, it looks like the Spark SQL Java tests don't compile:

https://amplab.cs.berkeley.edu/jenkins/view/Spark/job/Spark-Master-Maven-pre-YARN/hadoop.version=1.0.4,label=centos/244/consoleFull

I confirmed it by repeating the command vs master:

`mvn -Dhadoop.version=1.0.4 -Dlabel=centos -DskipTests clean package`

The problem is that this module doesn't depend on JUnit. In fact, none of the modules do, but `com.novocode:junit-interface` (the SBT-JUnit bridge) pulls it in, in most places. However this module doesn't depend on `com.novocode:junit-interface`

Adding the `junit:junit` dependency fixes the compile problem. In fact, the other modules with Java tests should probably depend on it explicitly instead of happening to get it via `com.novocode:junit-interface`, since that is a bit SBT/Scala-specific (and I am not even sure it's needed).

Author: Sean Owen <srowen@gmail.com>

Closes #1660 from srowen/SPARK-2749 and squashes the following commits:

858ff7c [Sean Owen] Add explicit junit dep to other modules with Java tests for robustness
9636794 [Sean Owen] Add junit dep so that Spark SQL Java tests compile

...sh model

Currently Spark uses Flume's internal Avro Protocol to ingest data from Flume. If the executor running the
receiver fails, it currently has to be restarted on the same node to be able to receive data.

This commit adds a new Sink which can be deployed to a Flume agent. This sink can be polled by a new
DStream that is also included in this commit. This model ensures that data can be pulled into Spark from
Flume even if the receiver is restarted on a new node. This also allows the receiver to receive data on
multiple threads for better performance.

Author: Hari Shreedharan <harishreedharan@gmail.com>
Author: Hari Shreedharan <hshreedharan@apache.org>
Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: harishreedharan <hshreedharan@cloudera.com>

Closes #807 from harishreedharan/master and squashes the following commits:

e7f70a3 [Hari Shreedharan] Merge remote-tracking branch 'asf-git/master'
96cfb6f [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
e48d785 [Hari Shreedharan] Documenting flume-sink being ignored for Mima checks.
5f212ce [Hari Shreedharan] Ignore Spark Sink from mima.
981bf62 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
7a1bc6e [Hari Shreedharan] Fix SparkBuild.scala
a082eb3 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
1f47364 [Hari Shreedharan] Minor fixes.
73d6f6d [Hari Shreedharan] Cleaned up tests a bit. Added some docs in multiple places.
65b76b4 [Hari Shreedharan] Fixing the unit test.
e59cc20 [Hari Shreedharan] Use SparkFlumeEvent instead of the new type. Also, Flume Polling Receiver now uses the store(ArrayBuffer) method.
f3c99d1 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
3572180 [Hari Shreedharan] Adding a license header, making Jenkins happy.
799509f [Hari Shreedharan] Fix a compile issue.
3c5194c [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
d248d22 [harishreedharan] Merge pull request #1 from tdas/flume-polling
10b6214 [Tathagata Das] Changed public API, changed sink package, and added java unit test to make sure Java API is callable from Java.
1edc806 [Hari Shreedharan] SPARK-1729. Update logging in Spark Sink.
8c00289 [Hari Shreedharan] More debug messages
393bd94 [Hari Shreedharan] SPARK-1729. Use LinkedBlockingQueue instead of ArrayBuffer to keep track of connections.
120e2a1 [Hari Shreedharan] SPARK-1729. Some test changes and changes to utils classes.
9fd0da7 [Hari Shreedharan] SPARK-1729. Use foreach instead of map for all Options.
8136aa6 [Hari Shreedharan] Adding TransactionProcessor to map on returning batch of data
86aa274 [Hari Shreedharan] Merge remote-tracking branch 'asf/master'
205034d [Hari Shreedharan] Merging master in
4b0c7fc [Hari Shreedharan] FLUME-1729. New Flume-Spark integration.
bda01fc [Hari Shreedharan] FLUME-1729. Flume-Spark integration.
0d69604 [Hari Shreedharan] FLUME-1729. Better Flume-Spark integration.
3c23c18 [Hari Shreedharan] SPARK-1729. New Spark-Flume integration.
70bcc2a [Hari Shreedharan] SPARK-1729. New Flume-Spark integration.
d6fa3aa [Hari Shreedharan] SPARK-1729. New Flume-Spark integration.
e7da512 [Hari Shreedharan] SPARK-1729. Fixing import order
9741683 [Hari Shreedharan] SPARK-1729. Fixes based on review.
c604a3c [Hari Shreedharan] SPARK-1729. Optimize imports.
0f10788 [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
87775aa [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
8df37e4 [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
03d6c1c [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
08176ad [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
d24d9d4 [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model
6d6776a [Hari Shreedharan] SPARK-1729. Make Flume pull data from source, rather than the current push model

JIRA issue: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)

Another try for #1399 & #1600. Those two PR breaks Jenkins builds because we made a separate profile `hive-thriftserver` in sub-project `assembly`, but the `hive-thriftserver` module is defined outside the `hive-thriftserver` profile. Thus every time a pull request that doesn't touch SQL code will also execute test suites defined in `hive-thriftserver`, but tests fail because related .class files are not included in the assembly jar.

In the most recent commit, module `hive-thriftserver` is moved into its own profile to fix this problem. All previous commits are squashed for clarity.

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

Closes #1620 from liancheng/jdbc-with-maven-fix and squashes the following commits:

629988e [Cheng Lian] Moved hive-thriftserver module definition into its own profile
ec3c7a7 [Cheng Lian] Cherry picked the Hive Thrift server

This reverts commit f6ff2a61.

(This is a replacement of #1399, trying to fix potential `HiveThriftServer2` port collision between parallel builds. Please refer to [these comments](https://github.com/apache/spark/pull/1399#issuecomment-50212572) for details.)

JIRA issue: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)

Merging the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.

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

Closes #1600 from liancheng/jdbc and squashes the following commits:

ac4618b [Cheng Lian] Uses random port for HiveThriftServer2 to avoid collision with parallel builds
090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server

This reverts commit 06dc0d2c.

#1399 is making Jenkins fail.  We should investigate and put this back after its passing tests.

Author: Michael Armbrust <michael@databricks.com>

Closes #1594 from marmbrus/revertJDBC and squashes the following commits:

59748da [Michael Armbrust] Revert "[SPARK-2410][SQL] Merging Hive Thrift/JDBC server"

JIRA issue:

- Main: [SPARK-2410](https://issues.apache.org/jira/browse/SPARK-2410)
- Related: [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678)

Cherry picked the Hive Thrift/JDBC server from [branch-1.0-jdbc](https://github.com/apache/spark/tree/branch-1.0-jdbc).

(Thanks chenghao-intel for his initial contribution of the Spark SQL CLI.)

TODO

- [x] Use `spark-submit` to launch the server, the CLI and beeline
- [x] Migration guideline draft for Shark users

----

Hit by a bug in `SparkSubmitArguments` while working on this PR: all application options that are recognized by `SparkSubmitArguments` are stolen as `SparkSubmit` options. For example:

```bash
$ spark-submit --class org.apache.hive.beeline.BeeLine spark-internal --help
```

This actually shows usage information of `SparkSubmit` rather than `BeeLine`.

~~Fixed this bug here since the `spark-internal` related stuff also touches `SparkSubmitArguments` and I'd like to avoid conflict.~~

**UPDATE** The bug mentioned above is now tracked by [SPARK-2678](https://issues.apache.org/jira/browse/SPARK-2678). Decided to revert changes to this bug since it involves more subtle considerations and worth a separate PR.

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

Closes #1399 from liancheng/thriftserver and squashes the following commits:

090beea [Cheng Lian] Revert changes related to SPARK-2678, decided to move them to another PR
21c6cf4 [Cheng Lian] Updated Spark SQL programming guide docs
fe0af31 [Cheng Lian] Reordered spark-submit options in spark-shell[.cmd]
199e3fb [Cheng Lian] Disabled MIMA for hive-thriftserver
1083e9d [Cheng Lian] Fixed failed test suites
7db82a1 [Cheng Lian] Fixed spark-submit application options handling logic
9cc0f06 [Cheng Lian] Starts beeline with spark-submit
cfcf461 [Cheng Lian] Updated documents and build scripts for the newly added hive-thriftserver profile
061880f [Cheng Lian] Addressed all comments by @pwendell
7755062 [Cheng Lian] Adapts test suites to spark-submit settings
40bafef [Cheng Lian] Fixed more license header issues
e214aab [Cheng Lian] Added missing license headers
b8905ba [Cheng Lian] Fixed minor issues in spark-sql and start-thriftserver.sh
f975d22 [Cheng Lian] Updated docs for Hive compatibility and Shark migration guide draft
3ad4e75 [Cheng Lian] Starts spark-sql shell with spark-submit
a5310d1 [Cheng Lian] Make HiveThriftServer2 play well with spark-submit
61f39f4 [Cheng Lian] Starts Hive Thrift server via spark-submit
2c4c539 [Cheng Lian] Cherry picked the Hive Thrift server

Stopping the Twitter Receiver would call twitter4j's TwitterStream.shutdown, which in turn causes an Exception to be thrown to the listener. This exception caused the Receiver to be restarted. This patch check whether the receiver was stopped or not, and accordingly restarts on exception.

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

Closes #1577 from tdas/twitter-stop and squashes the following commits:

011b525 [Tathagata Das] Fixed Twitter stream stopping bug.

The line break inadvertently means this was interpreted as a call to the no-arg constructor. This doesn't exist in older Netty even. (Also fixed a val name typo.)

Author: Sean Owen <srowen@gmail.com>

Closes #1466 from srowen/SPARK-1478.2 and squashes the following commits:

59c3501 [Sean Owen] Line break caused Scala to interpret NioServerSocketChannelFactory constructor as the no-arg version, which is not even present in some versions of Netty

This is a modified version of this PR https://github.com/apache/spark/pull/1168 done by @tmalaska
Adds MIMA binary check exclusions.

Author: tmalaska <ted.malaska@cloudera.com>
Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #1347 from tdas/FLUME-1915 and squashes the following commits:

96065df [Tathagata Das] Added Mima exclusion for FlumeReceiver.
41d5338 [tmalaska] Address line 57 that was too long
12617e5 [tmalaska] SPARK-1478: Upgrade FlumeInputDStream's Flume...

Patch introduces the new way of working also retaining the existing ways of doing things.

For example build instruction for yarn in maven is
`mvn -Pyarn -PHadoop2.2 clean package -DskipTests`
in sbt it can become
`MAVEN_PROFILES="yarn, hadoop-2.2" sbt/sbt clean assembly`
Also supports
`sbt/sbt -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0 clean assembly`

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #772 from ScrapCodes/sbt-maven and squashes the following commits:

a8ac951 [Prashant Sharma] Updated sbt version.
62b09bb [Prashant Sharma] Improvements.
fa6221d [Prashant Sharma] Excluding sql from mima
4b8875e [Prashant Sharma] Sbt assembly no longer builds tools by default.
72651ca [Prashant Sharma] Addresses code reivew comments.
acab73d [Prashant Sharma] Revert "Small fix to run-examples script."
ac4312c [Prashant Sharma] Revert "minor fix"
6af91ac [Prashant Sharma] Ported oldDeps back. + fixes issues with prev commit.
65cf06c [Prashant Sharma] Servelet API jars mess up with the other servlet jars on the class path.
446768e [Prashant Sharma] minor fix
89b9777 [Prashant Sharma] Merge conflicts
d0a02f2 [Prashant Sharma] Bumped up pom versions, Since the build now depends on pom it is better updated there. + general cleanups.
dccc8ac [Prashant Sharma] updated mima to check against 1.0
a49c61b [Prashant Sharma] Fix for tools jar
a2f5ae1 [Prashant Sharma] Fixes a bug in dependencies.
cf88758 [Prashant Sharma] cleanup
9439ea3 [Prashant Sharma] Small fix to run-examples script.
96cea1f [Prashant Sharma] SPARK-1776 Have Spark's SBT build read dependencies from Maven.
36efa62 [Patrick Wendell] Set project name in pom files and added eclipse/intellij plugins.
4973dbd [Patrick Wendell] Example build using pom reader.

Tobias noted today on the mailing list:

========

I am trying to use Spark Streaming with Kafka, which works like a
charm – except for shutdown. When I run my program with "sbt
run-main", sbt will never exit, because there are two non-daemon
threads left that don't die.
I created a minimal example at
<https://gist.github.com/tgpfeiffer/b1e765064e983449c6b6#file-kafkadoesntshutdown-scala>.
It starts a StreamingContext and does nothing more than connecting to
a Kafka server and printing what it receives. Using the `future
Unknown macro: { ... }
` construct, I shut down the StreamingContext after some seconds and
then print the difference between the threads at start time and at end
time. The output can be found at
<https://gist.github.com/tgpfeiffer/b1e765064e983449c6b6#file-output1>.
There are a number of threads remaining that will prevent sbt from
exiting.
When I replace `KafkaUtils.createStream(...)` with a call that does
exactly the same, except that it calls `consumerConnector.shutdown()`
in `KafkaReceiver.onStop()` (which it should, IMO), the output is as
shown at <https://gist.github.com/tgpfeiffer/b1e765064e983449c6b6#file-output2>.
Does anyone have any idea what is going on here and why the program
doesn't shut down properly? The behavior is the same with both kafka
0.8.0 and 0.8.1.1, by the way.

========

Something similar was noted last year:

http://mail-archives.apache.org/mod_mbox/spark-dev/201309.mbox/%3C1380220041.2428.YahooMailNeo@web160804.mail.bf1.yahoo.com%3E

KafkaInputDStream doesn't close `ConsumerConnector` in `onStop()`, and does not close the `Executor` it creates. The latter leaves non-daemon threads and can prevent the JVM from shutting down even if streaming is closed properly.

Author: Sean Owen <sowen@cloudera.com>

Closes #980 from srowen/SPARK-2034 and squashes the following commits:

9f31a8d [Sean Owen] Restore ClassTag to private class because MIMA flags it; is the shadowing intended?
2d579a8 [Sean Owen] Close ConsumerConnector in onStop; shutdown() the local Executor that is created so that its threads stop when done; close the Zookeeper client even on exception; fix a few typos; log exceptions that otherwise vanish

flume event sent to Spark will fail if the body is too large and numHeaders is greater than zero

Author: joyyoj <sunshch@gmail.com>

Closes #951 from joyyoj/master and squashes the following commits:

f4660c5 [joyyoj] [SPARK-1998] SparkFlumeEvent with body bigger than 1020 bytes are not read properly

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #974 from ueshin/issues/SPARK-2029 and squashes the following commits:

e19e8f4 [Takuya UESHIN] Bump version number to 1.1.0-SNAPSHOT.

The changes could be ported back to 0.9 as well.
Changing in.read to in.readFully to read the whole input stream rather than the first 1020 bytes.
This should ok considering that Flume caps the body size to 32K by default.

Author: David Lemieux <david.lemieux@radialpoint.com>

Closes #865 from lemieud/SPARK-1916 and squashes the following commits:

a265673 [David Lemieux] Updated SparkFlumeEvent to read the whole stream rather than the first X bytes.
(cherry picked from commit 0b769b73)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>

This is a few changes based on the original patch by @scrapcodes.

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #785 from pwendell/package-docs and squashes the following commits:

c32b731 [Patrick Wendell] Changes based on Prashant's patch
c0463d3 [Prashant Sharma] added eof new line
ce8bf73 [Prashant Sharma] Added eof new line to all files.
4c35f2e [Prashant Sharma] SPARK-1563 Add package-info.java and package.scala files for all packages that appear in docs

Pretty self-explanatory

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

Closes #722 from tdas/example-fix and squashes the following commits:

7839979 [Tathagata Das] Minor changes.
0673441 [Tathagata Das] Fixed java docs of java streaming example
e687123 [Tathagata Das] Fixed scala style errors.
9b8d112 [Tathagata Das] Fixed streaming examples docs to use run-example instead of spark-submit.

Three issues related to temp files that tests generate – these should be touched up for hygiene but are not urgent.

Modules have a log4j.properties which directs the unit-test.log output file to a directory like `[module]/target/unit-test.log`. But this ends up creating `[module]/[module]/target/unit-test.log` instead of former.

The `work/` directory is not deleted by "mvn clean", in the parent and in modules. Neither is the `checkpoint/` directory created under the various external modules.

Many tests create a temp directory, which is not usually deleted. This can be largely resolved by calling `deleteOnExit()` at creation and trying to call `Utils.deleteRecursively` consistently to clean up, sometimes in an `@After` method.

_If anyone seconds the motion, I can create a more significant change that introduces a new test trait along the lines of `LocalSparkContext`, which provides management of temp directories for subclasses to take advantage of._

Author: Sean Owen <sowen@cloudera.com>

Closes #732 from srowen/SPARK-1798 and squashes the following commits:

5af578e [Sean Owen] Try to consistently delete test temp dirs and files, and set deleteOnExit() for each
b21b356 [Sean Owen] Remove work/ and checkpoint/ dirs with mvn clean
bdd0f41 [Sean Owen] Remove duplicate module dir in log4j.properties output path for tests

TL;DR is there is a bit of JAR hell trouble with Netty, that can be mostly resolved and will resolve a test failure.

I hit the error described at http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-startup-time-out-td1753.html while running FlumeStreamingSuite, and have for a short while (is it just me?)

velvia notes:
"I have found a workaround.  If you add akka 2.2.4 to your dependencies, then everything works, probably because akka 2.2.4 brings in newer version of Jetty."

There are at least 3 versions of Netty in play in the build:

- the new Flume 1.4.0 dependency brings in io.netty:netty:3.4.0.Final, and that is the immediate problem
- the custom version of akka 2.2.3 depends on io.netty:netty:3.6.6.
- but, Spark Core directly uses io.netty:netty-all:4.0.17.Final

The POMs try to exclude other versions of netty, but are excluding org.jboss.netty:netty, when in fact older versions of io.netty:netty (not netty-all) are also an issue.

The org.jboss.netty:netty excludes are largely unnecessary. I replaced many of them with io.netty:netty exclusions until everything agreed on io.netty:netty-all:4.0.17.Final.

But this didn't work, since Akka 2.2.3 doesn't work with Netty 4.x. Down-grading to 3.6.6.Final across the board made some Spark code not compile.

If the build *keeps* io.netty:netty:3.6.6.Final as well, everything seems to work. Part of the reason seems to be that Netty 3.x used the old `org.jboss.netty` packages. This is less than ideal, but is no worse than the current situation.

So this PR resolves the issue and improves the JAR hell, even if it leaves the existing theoretical Netty 3-vs-4 conflict:

- Remove org.jboss.netty excludes where possible, for clarity; they're not needed except with Hadoop artifacts
- Add io.netty:netty excludes where needed -- except, let akka keep its io.netty:netty
- Change a bit of test code that actually depended on Netty 3.x, to use 4.x equivalent
- Update SBT build accordingly

A better change would be to update Akka far enough such that it agrees on Netty 4.x, but I don't know if that's feasible.

Author: Sean Owen <sowen@cloudera.com>

Closes #723 from srowen/SPARK-1789 and squashes the following commits:

43661b7 [Sean Owen] Update and add Netty excludes to prevent some JAR conflicts that cause test issues

1, Fix SPARK-1441: compile spark core error with hadoop 0.23.x
2, Fix SPARK-1491: maven hadoop-provided profile fails to build
3, Fix org.scala-lang: * ,org.apache.avro:* inconsistent versions dependency
4, A modified on the sql/catalyst/pom.xml,sql/hive/pom.xml,sql/core/pom.xml (Four spaces formatted into two spaces)

Author: witgo <witgo@qq.com>

Closes #480 from witgo/format_pom and squashes the following commits:

03f652f [witgo] review commit
b452680 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
bee920d [witgo] revert fix SPARK-1629: Spark Core missing commons-lang dependence
7382a07 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
6902c91 [witgo] fix SPARK-1629: Spark Core missing commons-lang dependence
0da4bc3 [witgo] merge master
d1718ed [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
e345919 [witgo] add avro dependency to yarn-alpha
77fad08 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
62d0862 [witgo] Fix org.scala-lang: * inconsistent versions dependency
1a162d7 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
934f24d [witgo] review commit
cf46edc [witgo] exclude jruby
06e7328 [witgo] Merge branch 'SparkBuild' into format_pom
99464d2 [witgo] fix maven hadoop-provided profile fails to build
0c6c1fc [witgo] Fix compile spark core error with hadoop 0.23.x
6851bec [witgo] Maintain consistent SparkBuild.scala, pom.xml

Unfortunately, this is not exhaustive - particularly hive tests still fail due to path issues.

Author: Mridul Muralidharan <mridulm80@apache.org>

This patch had conflicts when merged, resolved by
Committer: Matei Zaharia <matei@databricks.com>

Closes #505 from mridulm/windows_fixes and squashes the following commits:

ef12283 [Mridul Muralidharan] Move to org.apache.commons.lang3 for StringEscapeUtils. Earlier version was buggy appparently
cdae406 [Mridul Muralidharan] Remove leaked changes from > 2G fix branch
3267f4b [Mridul Muralidharan] Fix build failures
35b277a [Mridul Muralidharan] Fix Scalastyle failures
bc69d14 [Mridul Muralidharan] Change from hardcoded path separator
10c4d78 [Mridul Muralidharan] Use explicit encoding while using getBytes
1337abd [Mridul Muralidharan] fix classpath while running in windows