[SPARK-3569][SQL] Add metadata field to StructField

Add `metadata: Metadata` to `StructField` to store extra information of columns. `Metadata` is a simple wrapper over `Map[String, Any]` with value types restricted to Boolean, Long, Double, String, Metadata, and arrays of those types. SerDe is via JSON.

Metadata is preserved through simple operations like `SELECT`.

marmbrus liancheng

Author: Xiangrui Meng <meng@databricks.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #2701 from mengxr/structfield-metadata and squashes the following commits:

dedda56 [Xiangrui Meng] merge remote
5ef930a [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata
c35203f [Xiangrui Meng] Merge pull request #1 from marmbrus/pr/2701
886b85c [Michael Armbrust] Expose Metadata and MetadataBuilder through the public scala and java packages.
589f314 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata
1e2abcf [Xiangrui Meng] change default value of metadata to None in python
611d3c2 [Xiangrui Meng] move metadata from Expr to NamedExpr
ddfcfad [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata
a438440 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata
4266f4d [Xiangrui Meng] add StructField.toString back for backward compatibility
3f49aab [Xiangrui Meng] remove StructField.toString
24a9f80 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata
473a7c5 [Xiangrui Meng] merge master
c9d7301 [Xiangrui Meng] organize imports
1fcbf13 [Xiangrui Meng] change metadata type in StructField for Scala/Java
60cc131 [Xiangrui Meng] add doc and header
60614c7 [Xiangrui Meng] add metadata
e42c452 [Xiangrui Meng] merge master
93518fb [Xiangrui Meng] support metadata in python
905bb89 [Xiangrui Meng] java conversions
618e349 [Xiangrui Meng] make tests work in scala
61b8e0f [Xiangrui Meng] merge master
7e5a322 [Xiangrui Meng] do not output metadata in StructField.toString
c41a664 [Xiangrui Meng] merge master
d8af0ed [Xiangrui Meng] move tests to SQLQuerySuite
67fdebb [Xiangrui Meng] add test on join
d65072e [Xiangrui Meng] remove Map.empty
367d237 [Xiangrui Meng] add test
c194d5e [Xiangrui Meng] add metadata field to StructField and Attribute
[SPARK-3796] Create external service which can serve shuffle files

This patch introduces the tooling necessary to construct an external shuffle service which is independent of Spark executors, and then use this service inside Spark. An example (just for the sake of this PR) of the service creation can be found in Worker, and the service itself is used by plugging in the StandaloneShuffleClient as Spark's ShuffleClient (setup in BlockManager).

This PR continues the work from #2753, which extracted out the transport layer of Spark's block transfer into an independent package within Spark. A new package was created which contains the Spark business logic necessary to retrieve the actual shuffle data, which is completely independent of the transport layer introduced in the previous patch. Similar to the transport layer, this package must not depend on Spark as we anticipate plugging this service as a lightweight process within, say, the YARN NodeManager, and do not wish to include Spark's dependencies (including Scala itself).

There are several outstanding tasks which must be complete before this PR can be merged:
- [x] Complete unit testing of network/shuffle package.
- [x] Performance and correctness testing on a real cluster.
- [x] Remove example service instantiation from Worker.scala.

There are even more shortcomings of this PR which should be addressed in followup patches:
- Don't use Java serializer for RPC layer! It is not cross-version compatible.
- Handle shuffle file cleanup for dead executors once the application terminates or the ContextCleaner triggers.
- Documentation of the feature in the Spark docs.
- Improve behavior if the shuffle service itself goes down (right now we don't blacklist it, and new executors cannot spawn on that machine).
- SSL and SASL integration
- Nice to have: Handle shuffle file consolidation (this would requires changes to Spark's implementation).

Author: Aaron Davidson <aaron@databricks.com>

Closes #3001 from aarondav/shuffle-service and squashes the following commits:

4d1f8c1 [Aaron Davidson] Remove changes to Worker
705748f [Aaron Davidson] Rename Standalone* to External*
fd3928b [Aaron Davidson] Do not unregister executor outputs unduly
9883918 [Aaron Davidson] Make suggested build changes
3d62679 [Aaron Davidson] Add Spark integration test
7fe51d5 [Aaron Davidson] Fix SBT integration
56caa50 [Aaron Davidson] Address comments
c8d1ac3 [Aaron Davidson] Add unit tests
2f70c0c [Aaron Davidson] Fix unit tests
5483e96 [Aaron Davidson] Fix unit tests
46a70bf [Aaron Davidson] Whoops, bracket
5ea4df6 [Aaron Davidson] [SPARK-3796] Create external service which can serve shuffle files
[SPARK-4037][SQL] Removes the SessionState instance created in HiveThriftServer2

`HiveThriftServer2` creates a global singleton `SessionState` instance and overrides `HiveContext` to inject the `SessionState` object. This messes up `SessionState` initialization and causes problems.

This PR replaces the global `SessionState` with `HiveContext.sessionState` to avoid the initialization conflict. Also `HiveContext` reuses existing started `SessionState` if any (this is required by `SparkSQLCLIDriver`, which uses specialized `CliSessionState`).

Author: Cheng Lian <lian@databricks.com>

Closes #2887 from liancheng/spark-4037 and squashes the following commits:

8446675 [Cheng Lian] Removes redundant Driver initialization
a28fef5 [Cheng Lian] Avoid starting HiveContext.sessionState multiple times
49b1c5b [Cheng Lian] Reuses existing started SessionState if any
3cd6fab [Cheng Lian] Fixes SPARK-4037
Revert "[SPARK-4183] Enable NettyBlockTransferService by default"

This reverts commit 59e626c701227634336110e1bc23afd94c535ede.
[SPARK-4121] Set commons-math3 version based on hadoop profiles, instead of shading

In #2928 , we shade commons-math3 to prevent future conflicts with hadoop. It caused problems with our Jenkins master build with maven. Some tests used local-cluster mode, where the assembly jar contains relocated math3 classes, while mllib test code still compiles with core and the untouched math3 classes.

This PR sets commons-math3 version based on hadoop profiles.

pwendell JoshRosen srowen

Author: Xiangrui Meng <meng@databricks.com>

Closes #3023 from mengxr/SPARK-4121-alt and squashes the following commits:

580f6d9 [Xiangrui Meng] replace tab by spaces
7f71f08 [Xiangrui Meng] revert changes to PoissonSampler to avoid conflicts
d3353d9 [Xiangrui Meng] do not shade commons-math3
b4180dc [Xiangrui Meng] temp work
[SPARK-3161][MLLIB] Adding a node Id caching mechanism for training deci...

...sion trees. jkbradley mengxr chouqin Please review this.

Author: Sung Chung <schung@alpinenow.com>

Closes #2868 from codedeft/SPARK-3161 and squashes the following commits:

5f5a156 [Sung Chung] [SPARK-3161][MLLIB] Adding a node Id caching mechanism for training decision trees.
[SPARK-3930] [SPARK-3933] Support fixed-precision decimal in SQL, and some optimizations

- Adds optional precision and scale to Spark SQL's decimal type, which behave similarly to those in Hive 13 (https://cwiki.apache.org/confluence/download/attachments/27362075/Hive_Decimal_Precision_Scale_Support.pdf)
- Replaces our internal representation of decimals with a Decimal class that can store small values in a mutable Long, saving memory in this situation and letting some operations happen directly on Longs

This is still marked WIP because there are a few TODOs, but I'll remove that tag when done.

Author: Matei Zaharia <matei@databricks.com>

Closes #2983 from mateiz/decimal-1 and squashes the following commits:

35e6b02 [Matei Zaharia] Fix issues after merge
227f24a [Matei Zaharia] Review comments
31f915e [Matei Zaharia] Implement Davies's suggestions in Python
eb84820 [Matei Zaharia] Support reading/writing decimals as fixed-length binary in Parquet
4dc6bae [Matei Zaharia] Fix decimal support in PySpark
d1d9d68 [Matei Zaharia] Fix compile error and test issues after rebase
b28933d [Matei Zaharia] Support decimal precision/scale in Hive metastore
2118c0d [Matei Zaharia] Some test and bug fixes
81db9cb [Matei Zaharia] Added mutable Decimal that will be more efficient for small precisions
7af0c3b [Matei Zaharia] Add optional precision and scale to DecimalType, but use Unlimited for now
ec0a947 [Matei Zaharia] Make the result of AVG on Decimals be Decimal, not Double
[SPARK-3466] Limit size of results that a driver collects for each action

Right now, operations like collect() and take() can crash the driver with an OOM if they bring back too many data.

This PR will introduce spark.driver.maxResultSize, after setting it, the driver will abort a job if its result is bigger than it.

By default, it's 1g (for backward compatibility for most the cases).

In local mode, the driver and executor share the same JVM, the default setting can not protect JVM from OOM.

cc mateiz

Author: Davies Liu <davies@databricks.com>

Closes #3003 from davies/collect and squashes the following commits:

248ed5e [Davies Liu] fix compile
272522e [Davies Liu] address comments
2c35773 [Davies Liu] add sizes in message of abort()
5d62303 [Davies Liu] address comments
bc3c077 [Davies Liu] Merge branch 'master' of github.com:apache/spark into collect
11f97c5 [Davies Liu] address comments
47b144f [Davies Liu] check the size of result before send and fetch
3d81af2 [Davies Liu] address comments
ca8267d [Davies Liu] limit the size of data by collect
[SPARK-4166][Core][WebUI] Display the executor ID in the Web UI when ExecutorLostFailure happens

Now when ExecutorLostFailure happens, it only displays `ExecutorLostFailure (executor lost)`. Adding the executor id will help locate the faulted executor.

Author: zsxwing <zsxwing@gmail.com>

Closes #3033 from zsxwing/SPARK-4166 and squashes the following commits:

ff4664c [zsxwing] Backward-compatible support
c5c4cf2 [zsxwing] Display the executor ID in the Web UI when ExecutorLostFailure happens
[HOTFIX][SQL] hive test missing some golden files

cc marmbrus

Author: wangfei <wangfei1@huawei.com>

Closes #3055 from scwf/hotfix and squashes the following commits:

d881bd7 [wangfei] miss golden files
[SPARK-3247][SQL] An API for adding data sources to Spark SQL

This PR introduces a new set of APIs to Spark SQL to allow other developers to add support for reading data from new sources in `org.apache.spark.sql.sources`.

New sources must implement the interface `BaseRelation`, which is responsible for describing the schema of the data.  BaseRelations have three `Scan` subclasses, which are responsible for producing an RDD containing row objects.  The [various Scan interfaces](https://github.com/marmbrus/spark/blob/foreign/sql/core/src/main/scala/org/apache/spark/sql/sources/package.scala#L50) allow for optimizations such as column pruning and filter push down, when the underlying data source can handle these operations.

By implementing a class that inherits from RelationProvider these data sources can be accessed using using pure SQL.  I've used the functionality to update the JSON support so it can now be used in this way as follows:

```sql
CREATE TEMPORARY TABLE jsonTableSQL
USING org.apache.spark.sql.json
OPTIONS (
  path '/home/michael/data.json'
)
```

Further example usage can be found in the test cases: https://github.com/marmbrus/spark/tree/foreign/sql/core/src/test/scala/org/apache/spark/sql/sources

There is also a library that uses this new API to read avro data available here:
https://github.com/marmbrus/sql-avro

Author: Michael Armbrust <michael@databricks.com>

Closes #2475 from marmbrus/foreign and squashes the following commits:

1ed6010 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into foreign
ab2c31f [Michael Armbrust] fix test
1d41bb5 [Michael Armbrust] unify argument names
5b47901 [Michael Armbrust] Remove sealed, more filter types
fab154a [Michael Armbrust] Merge remote-tracking branch 'origin/master' into foreign
e3e690e [Michael Armbrust] Add hook for extraStrategies
a70d602 [Michael Armbrust] Fix style, more tests, FilteredSuite => PrunedFilteredSuite
70da6d9 [Michael Armbrust] Modify API to ease binary compatibility and interop with Java
7d948ae [Michael Armbrust] Fix equality of AttributeReference.
5545491 [Michael Armbrust] Address comments
5031ac3 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into foreign
22963ef [Michael Armbrust] package objects compile wierdly...
b069146 [Michael Armbrust] traits => abstract classes
34f836a [Michael Armbrust] Make @DeveloperApi
0d74bcf [Michael Armbrust] Add documention on object life cycle
3e06776 [Michael Armbrust] remove line wraps
de3b68c [Michael Armbrust] Remove empty file
360cb30 [Michael Armbrust] style and java api
2957875 [Michael Armbrust] add override
0fd3a07 [Michael Armbrust] Draft of data sources API
[SPARK-4182][SQL] Fixes ColumnStats classes for boolean, binary and complex data types

`NoopColumnStats` was once used for binary, boolean and complex data types. This `ColumnStats` doesn't return properly shaped column statistics and causes caching failure if a table contains columns of the aforementioned types.

This PR adds `BooleanColumnStats`, `BinaryColumnStats` and `GenericColumnStats`, used for boolean, binary and all complex data types respectively. In addition, `NoopColumnStats` returns properly shaped column statistics containing null count and row count, but this class is now used for testing purpose only.

Author: Cheng Lian <lian@databricks.com>

Closes #3059 from liancheng/spark-4182 and squashes the following commits:

b398cfd [Cheng Lian] Fixes failed test case
fb3ee85 [Cheng Lian] Fixes SPARK-4182
[SQL] Fixes race condition in CliSuite

`CliSuite` has been flaky for a while, this PR tries to improve this situation by fixing a race condition in `CliSuite`. The `captureOutput` function is used to capture both stdout and stderr output of the forked external process in two background threads and search for expected strings, but wasn't been properly synchronized before.

Author: Cheng Lian <lian@databricks.com>

Closes #3060 from liancheng/fix-cli-suite and squashes the following commits:

a70569c [Cheng Lian] Fixes race condition in CliSuite
[SPARK-3791][SQL] Provides Spark version and Hive version in HiveThriftServer2

This PR overrides the `GetInfo` Hive Thrift API to provide correct version information. Another property `spark.sql.hive.version` is added to reveal the underlying Hive version. These are generally useful for Spark SQL ODBC driver providers. The Spark version information is extracted from the jar manifest. Also took the chance to remove the `SET -v` hack, which was a workaround for Simba ODBC driver connectivity.

TODO

- [x] Find a general way to figure out Hive (or even any dependency) version.

  This [blog post](http://blog.soebes.de/blog/2014/01/02/version-information-into-your-appas-with-maven/) suggests several methods to inspect application version. In the case of Spark, this can be tricky because the chosen method:

  1. must applies to both Maven build and SBT build

    For Maven builds, we can retrieve the version information from the META-INF/maven directory within the assembly jar. But this doesn't work for SBT builds.

  2. must not rely on the original jars of dependencies to extract specific dependency version, because Spark uses assembly jar.

    This implies we can't read Hive version from Hive jar files since standard Spark distribution doesn't include them.

  3. should play well with `SPARK_PREPEND_CLASSES` to ease local testing during development.

     `SPARK_PREPEND_CLASSES` prevents classes to be loaded from the assembly jar, thus we can't locate the jar file and read its manifest.

  Given these, maybe the only reliable method is to generate a source file containing version information at build time. pwendell Do you have any suggestions from the perspective of the build process?

**Update** Hive version is now retrieved from the newly introduced `HiveShim` object.

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

Closes #2843 from liancheng/get-info and squashes the following commits:

a873d0f [Cheng Lian] Updates test case
53f43cd [Cheng Lian] Retrieves underlying Hive verson via HiveShim
1d282b8 [Cheng Lian] Removes the Simba ODBC "SET -v" hack
f857fce [Cheng Lian] Overrides Hive GetInfo Thrift API and adds Hive version property
[SPARK-4191][SQL]move wrapperFor to HiveInspectors to reuse it

Move wrapperFor in InsertIntoHiveTable to HiveInspectors to reuse them, this method can be reused when writing date with ObjectInspector(such as orc support)

Author: wangfei <wangfei1@huawei.com>
Author: scwf <wangfei1@huawei.com>

Closes #3057 from scwf/reuse-wraperfor and squashes the following commits:

7ccf932 [scwf] fix conflicts
d44f4da [wangfei] fix imports
9bf1b50 [wangfei] revert no related change
9a5276a [wangfei] move wrapfor to hiveinspector to reuse them
[SPARK-4185][SQL] JSON schema inference failed when dealing with type conflicts in arrays

JIRA: https://issues.apache.org/jira/browse/SPARK-4185.

This PR also has the fix of #3052.

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

Closes #3056 from yhuai/SPARK-4185 and squashes the following commits:

ed3a5a8 [Yin Huai] Correctly handle type conflicts between structs and primitive types in an array.
[SPARK-2189][SQL] Adds dropTempTable API

This PR adds an API for unregistering temporary tables. If a temporary table has been cached before, it's unpersisted as well.

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

Closes #3039 from liancheng/unregister-temp-table and squashes the following commits:

54ae99f [Cheng Lian] Fixes Scala styling issue
1948c14 [Cheng Lian] Removes the unpersist argument
aca41d3 [Cheng Lian] Ensures thread safety
7d4fb2b [Cheng Lian] Adds unregisterTempTable API
[SPARK-4183] Close transport-related resources between SparkContexts

A leak of event loops may be causing test failures.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3053 from aarondav/leak and squashes the following commits:

e676d18 [Aaron Davidson] Typo!
8f96475 [Aaron Davidson] Keep original ssc semantics
7e49f10 [Aaron Davidson] A leak of event loops may be causing test failures.
[SPARK-3572] [SQL] Internal API for User-Defined Types

This PR adds User-Defined Types (UDTs) to SQL. It is a precursor to using SchemaRDD as a Dataset for the new MLlib API. Currently, the UDT API is private since there is incomplete support (e.g., no Java or Python support yet).

Author: Joseph K. Bradley <joseph@databricks.com>
Author: Michael Armbrust <michael@databricks.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #3063 from marmbrus/udts and squashes the following commits:

7ccfc0d [Michael Armbrust] remove println
46a3aee [Michael Armbrust] Slightly easier to read test output.
6cc434d [Michael Armbrust] Recursively convert rows.
e369b91 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into udts
15c10a6 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into sql-udt2
f3c72fe [Joseph K. Bradley] Fixing merge
e13cd8a [Joseph K. Bradley] Removed Vector UDTs
5817b2b [Joseph K. Bradley] style edits
30ce5b2 [Joseph K. Bradley] updates based on code review
d063380 [Joseph K. Bradley] Cleaned up Java UDT Suite, and added warning about element ordering when creating schema from Java Bean
a571bb6 [Joseph K. Bradley] Removed old UDT code (registry and Java UDTs).  Cleaned up other code.  Extended JavaUserDefinedTypeSuite
6fddc1c [Joseph K. Bradley] Made MyLabeledPoint into a Java Bean
20630bc [Joseph K. Bradley] fixed scalastyle
fa86b20 [Joseph K. Bradley] Removed Java UserDefinedType, and made UDTs private[spark] for now
8de957c [Joseph K. Bradley] Modified UserDefinedType to store Java class of user type so that registerUDT takes only the udt argument.
8b242ea [Joseph K. Bradley] Fixed merge error after last merge.  Note: Last merge commit also removed SQL UDT examples from mllib.
7f29656 [Joseph K. Bradley] Moved udt case to top of all matches.  Small cleanups
b028675 [Xiangrui Meng] allow any type in UDT
4500d8a [Xiangrui Meng] update example code
87264a5 [Xiangrui Meng] remove debug code
3143ac3 [Xiangrui Meng] remove unnecessary changes
cfbc321 [Xiangrui Meng] support UDT in parquet
db16139 [Joseph K. Bradley] Added more doc for UserDefinedType.  Removed unused code in Suite
759af7a [Joseph K. Bradley] Added more doc to UserDefineType
63626a4 [Joseph K. Bradley] Updated ScalaReflectionsSuite per @marmbrus suggestions
51e5282 [Joseph K. Bradley] fixed 1 test
f025035 [Joseph K. Bradley] Cleanups before PR.  Added new tests
85872f6 [Michael Armbrust] Allow schema calculation to be lazy, but ensure its available on executors.
dff99d6 [Joseph K. Bradley] Added UDTs for Vectors in MLlib, plus DatasetExample using the UDTs
cd60cb4 [Joseph K. Bradley] Trying to get other SQL tests to run
34a5831 [Joseph K. Bradley] Added MLlib dependency on SQL.
e1f7b9c [Joseph K. Bradley] blah
2f40c02 [Joseph K. Bradley] renamed UDT types
3579035 [Joseph K. Bradley] udt annotation now working
b226b9e [Joseph K. Bradley] Changing UDT to annotation
fea04af [Joseph K. Bradley] more cleanups
964b32e [Joseph K. Bradley] some cleanups
893ee4c [Joseph K. Bradley] udt finallly working
50f9726 [Joseph K. Bradley] udts
04303c9 [Joseph K. Bradley] udts
39f8707 [Joseph K. Bradley] removed old udt suite
273ac96 [Joseph K. Bradley] basic UDT is working, but deserialization has yet to be done
8bebf24 [Joseph K. Bradley] commented out convertRowToScala for debugging
53de70f [Joseph K. Bradley] more udts...
982c035 [Joseph K. Bradley] still working on UDTs
19b2f60 [Joseph K. Bradley] still working on UDTs
0eaeb81 [Joseph K. Bradley] Still working on UDTs
105c5a3 [Joseph K. Bradley] Adding UserDefinedType to SQL, not done yet.
[SPARK-4183] Enable NettyBlockTransferService by default

Note that we're turning this on for at least the first part of the QA period as a trial. We want to enable this (and deprecate the NioBlockTransferService) as soon as possible in the hopes that NettyBlockTransferService will be more stable and easier to maintain. We will turn it off if we run into major issues.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3049 from aarondav/enable-netty and squashes the following commits:

bb981cc [Aaron Davidson] [SPARK-4183] Enable NettyBlockTransferService by default