[SPARK-3527] [SQL] Strip the string message

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

Closes #2392 from chenghao-intel/trim and squashes the following commits:

e52024f [Cheng Hao] trim the string message
[SPARK-3519] add distinct(n) to PySpark

Added missing rdd.distinct(numPartitions) and associated tests

Author: Matthew Farrellee <matt@redhat.com>

Closes #2383 from mattf/SPARK-3519 and squashes the following commits:

30b837a [Matthew Farrellee] Combine test cases to save on JVM startups
6bc4a2c [Matthew Farrellee] [SPARK-3519] add distinct(n) to SchemaRDD in PySpark
7a17f2b [Matthew Farrellee] [SPARK-3519] add distinct(n) to PySpark
[SPARK-3308][SQL] Ability to read JSON Arrays as tables

This PR aims to support reading top level JSON arrays and take every element in such an array as a row (an empty array will not generate a row).

JIRA: https://issues.apache.org/jira/browse/SPARK-3308

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #2400 from yhuai/SPARK-3308 and squashes the following commits:

990077a [Yin Huai] Handle top level JSON arrays.
[SPARK-2890][SQL] Allow reading of data when case insensitive resolution could cause possible ambiguity.

Throwing an error in the constructor makes it possible to run queries, even when there is no actual ambiguity.  Remove this check in favor of throwing an error in analysis when they query is actually is ambiguous.

Also took the opportunity to add test cases that would have caught a subtle bug in my first attempt at fixing this and refactor some other test code.

Author: Michael Armbrust <michael@databricks.com>

Closes #2209 from marmbrus/sameNameStruct and squashes the following commits:

729cca4 [Michael Armbrust] Better tests.
a003aeb [Michael Armbrust] Remove error (it'll be caught in analysis).
[SPARK-2314][SQL] Override collect and take in python library, and count in java library, with optimized versions.

SchemaRDD overrides RDD functions, including collect, count, and take, with optimized versions making use of the query optimizer.  The java and python interface classes wrapping SchemaRDD need to ensure the optimized versions are called as well.  This patch overrides relevant calls in the python and java interfaces with optimized versions.

Adds a new Row serialization pathway between python and java, based on JList[Array[Byte]] versus the existing RDD[Array[Byte]]. I wasn’t overjoyed about doing this, but I noticed that some QueryPlans implement optimizations in executeCollect(), which outputs an Array[Row] rather than the typical RDD[Row] that can be shipped to python using the existing serialization code. To me it made sense to ship the Array[Row] over to python directly instead of converting it back to an RDD[Row] just for the purpose of sending the Rows to python using the existing serialization code.

Author: Aaron Staple <aaron.staple@gmail.com>

Closes #1592 from staple/SPARK-2314 and squashes the following commits:

89ff550 [Aaron Staple] Merge with master.
6bb7b6c [Aaron Staple] Fix typo.
b56d0ac [Aaron Staple] [SPARK-2314][SQL] Override count in JavaSchemaRDD, forwarding to SchemaRDD's count.
0fc9d40 [Aaron Staple] Fix comment typos.
f03cdfa [Aaron Staple] [SPARK-2314][SQL] Override collect and take in sql.py, forwarding to SchemaRDD's collect.
[Docs] minor punctuation fix

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2414 from nchammas/patch-1 and squashes the following commits:

14664bf [Nicholas Chammas] [Docs] minor punctuation fix
[SQL][DOCS] Improve section on thrift-server

Taken from liancheng's updates. Merged conflicts with #2316.

Author: Michael Armbrust <michael@databricks.com>

Closes #2384 from marmbrus/sqlDocUpdate and squashes the following commits:

2db6319 [Michael Armbrust] @liancheng's updates
[SPARK-3546] InputStream of ManagedBuffer is not closed and causes running out of file descriptor

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

Closes #2408 from sarutak/resolve-resource-leak-issue and squashes the following commits:

074781d [Kousuke Saruta] Modified SuffleBlockFetcherIterator
5f63f67 [Kousuke Saruta] Move metrics increment logic and debug logging outside try block
b37231a [Kousuke Saruta] Modified FileSegmentManagedBuffer#nioByteBuffer to check null or not before invoking channel.close
bf29d4a [Kousuke Saruta] Modified FileSegment to close channel
[SPARK-3430] [PySpark] [Doc] generate PySpark API docs using Sphinx

Using Sphinx to generate API docs for PySpark.

requirement: Sphinx

```
$ cd python/docs/
$ make html
```

The generated API docs will be located at python/docs/_build/html/index.html

It can co-exists with those generated by Epydoc.

This is the first working version, after merging in, then we can continue to improve it and replace the epydoc finally.

Author: Davies Liu <davies.liu@gmail.com>

Closes #2292 from davies/sphinx and squashes the following commits:

425a3b1 [Davies Liu] cleanup
1573298 [Davies Liu] move docs to python/docs/
5fe3903 [Davies Liu] Merge branch 'master' into sphinx
9468ab0 [Davies Liu] fix makefile
b408f38 [Davies Liu] address all comments
e2ccb1b [Davies Liu] update name and version
9081ead [Davies Liu] generate PySpark API docs using Sphinx
[SPARK-787] Add S3 configuration parameters to the EC2 deploy scripts

When deploying to AWS, there is additional configuration that is required to read S3 files. EMR creates it automatically, there is no reason that the Spark EC2 script shouldn't.

This PR requires a corresponding PR to the mesos/spark-ec2 to be merged, as it gets cloned in the process of setting up machines: https://github.com/mesos/spark-ec2/pull/58

Author: Dan Osipov <daniil.osipov@shazam.com>

Closes #1120 from danosipov/s3_credentials and squashes the following commits:

758da8b [Dan Osipov] Modify documentation to include the new parameter
71fab14 [Dan Osipov] Use a parameter --copy-aws-credentials to enable S3 credential deployment
7e0da26 [Dan Osipov] Get AWS credentials out of boto connection instance
39bdf30 [Dan Osipov] Add S3 configuration parameters to the EC2 deploy scripts
Add a Community Projects page

This adds a new page to the docs listing community projects -- those created outside of Apache Spark that are of interest to the community of Spark users.   Anybody can add to it just by submitting a PR.

There was a discussion thread about alternatives:
* Creating a Github organization for Spark projects -  we could not find any sponsors for this, and it would be difficult to organize since many folks just create repos in their company organization or personal accounts
* Apache has some place for storing community projects, but it was deemed difficult to work with, and again would be some permissions issues -- not everyone could update it.

Author: Evan Chan <velvia@gmail.com>

Closes #2219 from velvia/community-projects-page and squashes the following commits:

7316822 [Evan Chan] Point to Spark wiki: supplemental projects page
613b021 [Evan Chan] Add a few more projects
a85eaaf [Evan Chan] Add a Community Projects page
[SPARK-3555] Fix UISuite race condition

The test "jetty selects different port under contention" is flaky.

If another process binds to 4040 before the test starts, then the first server we start there will fail, and the subsequent servers we start thereafter may successfully bind to 4040 if it was released between the servers starting. Instead, we should just let Java find a random free port for us and hold onto it for the duration of the test.

Author: Andrew Or <andrewor14@gmail.com>

Closes #2418 from andrewor14/fix-port-contention and squashes the following commits:

0cd4974 [Andrew Or] Stop them servers
a7071fe [Andrew Or] Pick random port instead of 4040
[Minor]ignore all config files in conf

Some config files in ```conf``` should ignore, such as
        conf/fairscheduler.xml
        conf/hive-log4j.properties
        conf/metrics.properties
...
So ignore all ```sh```/```properties```/```conf```/```xml``` files

Author: wangfei <wangfei1@huawei.com>

Closes #2395 from scwf/patch-2 and squashes the following commits:

3dc53f2 [wangfei] duplicate ```conf/*.conf```
3c2986f [wangfei] ignore all config files
[Docs] Correct spark.files.fetchTimeout default value

change the value of spark.files.fetchTimeout

Author: viper-kun <xukun.xu@huawei.com>

Closes #2406 from viper-kun/master and squashes the following commits:

ecb0d46 [viper-kun] [Docs] Correct spark.files.fetchTimeout default value
7cf4c7a [viper-kun] Update configuration.md
SPARK-3177 (on Master Branch)

The JIRA and PR was original created for branch-1.1, and move to master branch now.
Chester

The Issue is due to that yarn-alpha and yarn have different APIs for certain class fields. In this particular case,  the ClientBase using reflection to to address this issue, and we need to different way to test the ClientBase's method.  Original ClientBaseSuite using getFieldValue() method to do this. But it doesn't work for yarn-alpha as the API returns an array of String instead of just String (which is the case for Yarn-stable API).

 To fix the test, I add a new method

  def getFieldValue2[A: ClassTag, A1: ClassTag, B](clazz: Class[_], field: String,
                                                      defaults: => B)
                              (mapTo:  A => B)(mapTo1: A1 => B) : B =
    Try(clazz.getField(field)).map(_.get(null)).map {
      case v: A => mapTo(v)
      case v1: A1 => mapTo1(v1)
      case _ => defaults
    }.toOption.getOrElse(defaults)

to handle the cases where the field type can be either type A or A1. In this new method the type A or A1 is pattern matched and corresponding mapTo function (mapTo or mapTo1) is used.

Author: chesterxgchen <chester@alpinenow.com>

Closes #2204 from chesterxgchen/SPARK-3177-master and squashes the following commits:

e72a6ea [chesterxgchen]  The Issue is due to that yarn-alpha and yarn have different APIs for certain class fields. In this particular case,  the ClientBase using reflection to to address this issue, and we need to different way to test the ClientBase's method.  Original ClientBaseSuite using getFieldValue() method to do this. But it doesn't work for yarn-alpha as the API returns an array of String instead of just String (which is the case for Yarn-stable API).
Added sql/hbase module for 0.96.1.1-hadoop2
Fixed assembly for hbase
Skeleton HBaseSQLContext working
incremental HBaseStrategies updates
Removed spurious manual merge error in pom.xml