Users unknowingly try to set core Spark configs in SQLContext but later realise that it didn't work. eg. sqlContext.sql("SET spark.shuffle.memoryFraction=0.4"). This PR adds a warning message when such operations are done.

Author: Tejas Patil <tejasp@fb.com>

Closes #10849 from tejasapatil/SPARK-12926.

This PR is a follow-up of #10911. It adds specialized update methods for `CountMinSketch` so that we can avoid doing internal/external row format conversion in `DataFrame.countMinSketch()`.

Author: Cheng Lian <lian@databricks.com>

Closes #10968 from liancheng/cms-specialized.

this is stated for --packages and --repositories. Without stating it for --jars, people expect a standard java classpath to work, with expansion and using a different delimiter than a comma. Currently this is only state in the --help for spark-submit "Comma-separated list of local jars to include on the driver and executor classpaths."

Author: James Lohse <jimlohse@users.noreply.github.com>

Closes #10890 from jimlohse/patch-1.

These two classes became identical as the implementation progressed.

Author: Nong Li <nong@databricks.com>

Closes #10952 from nongli/spark-13045.

by explicitly marking annotated parameters as vals (SI-8813).

Caused by #10835.

Author: Andrew Or <andrew@databricks.com>

Closes #10955 from andrewor14/fix-scala211.

This PR moves all the functionality provided by the SparkSQLParser/ExtendedHiveQlParser to the new Parser hierarchy (SparkQl/HiveQl). This also improves the current SET command parsing: the current implementation swallows ```set role ...``` and ```set autocommit ...``` commands, this PR respects these commands (and passes them on to Hive).

This PR and https://github.com/apache/spark/pull/10723 end the use of Parser-Combinator parsers for SQL parsing. As a result we can also remove the ```AbstractSQLParser``` in Catalyst.

The PR is marked WIP as long as it doesn't pass all tests.

cc rxin viirya winningsix (this touches https://github.com/apache/spark/pull/10144)

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #10905 from hvanhovell/SPARK-12866.

This PR integrates Bloom filter from spark-sketch into DataFrame. This version resorts to RDD.aggregate for building the filter. A more performant UDAF version can be built in future follow-up PRs.

This PR also add 2 specify `put` version(`putBinary` and `putLong`) into `BloomFilter`, which makes it easier to build a Bloom filter over a `DataFrame`.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10937 from cloud-fan/bloom-filter.

Spark's `Partition` and `RDD.partitions` APIs have a contract which requires custom implementations of `RDD.partitions` to ensure that for all `x`, `rdd.partitions(x).index == x`; in other words, the `index` reported by a repartition needs to match its position in the partitions array.

If a custom RDD implementation violates this contract, then Spark has the potential to become stuck in an infinite recomputation loop when recomputing a subset of an RDD's partitions, since the tasks that are actually run will not correspond to the missing output partitions that triggered the recomputation. Here's a link to a notebook which demonstrates this problem: https://rawgit.com/JoshRosen/e520fb9a64c1c97ec985/raw/5e8a5aa8d2a18910a1607f0aa4190104adda3424/Violating%2520RDD.partitions%2520contract.html

In order to guard against this infinite loop behavior, this patch modifies Spark so that it fails fast and refuses to compute RDDs' whose `partitions` violate the API contract.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #10932 from JoshRosen/SPARK-13021.

The high level idea is that instead of having the executors send both accumulator updates and TaskMetrics, we should have them send only accumulator updates. This eliminates the need to maintain both code paths since one can be implemented in terms of the other. This effort is split into two parts:

**SPARK-12895: Implement TaskMetrics using accumulators.** TaskMetrics is basically just a bunch of accumulable fields. This patch makes TaskMetrics a syntactic wrapper around a collection of accumulators so we don't need to send TaskMetrics from the executors to the driver.

**SPARK-12896: Send only accumulator updates to the driver.** Now that TaskMetrics are expressed in terms of accumulators, we can capture all TaskMetrics values if we just send accumulator updates from the executors to the driver. This completes the parent issue SPARK-10620.

While an effort has been made to preserve as much of the public API as possible, there were a few known breaking DeveloperApi changes that would be very awkward to maintain. I will gather the full list shortly and post it here.

Note: This was once part of #10717. This patch is split out into its own patch from there to make it easier for others to review. Other smaller pieces of already been merged into master.

Author: Andrew Or <andrew@databricks.com>

Closes #10835 from andrewor14/task-metrics-use-accums.

[SPARK-10847][SQL][PYSPARK] Pyspark - DataFrame - Optional Metadata with `None` triggers cryptic failure

The error message is now changed from "Do not support type class scala.Tuple2." to "Do not support type class org.json4s.JsonAST$JNull$" to be more informative about what is not supported. Also, StructType metadata now handles JNull correctly, i.e., {'a': None}. test_metadata_null is added to tests.py to show the fix works.

Author: Jason Lee <cjlee@us.ibm.com>

Closes #8969 from jasoncl/SPARK-10847.

There's a minor bug in how we handle the `root` module in the `modules_to_test()` function in `dev/run-tests.py`: since `root` now depends on `build` (since every test needs to run on any build test), we now need to check for the presence of root in `modules_to_test` instead of `changed_modules`.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #10933 from JoshRosen/build-module-fix.

JIRA 1680 added a property called spark.yarn.appMasterEnv.  This PR draws users' attention to this special case by adding an explanation in configuration.html#environment-variables

Author: Andrew <weiner.andrew.j@gmail.com>

Closes #10869 from weineran/branch-yarn-docs.

There are some typos or plain unintelligible sentences in the metrics template.

Author: BenFradet <benjamin.fradet@gmail.com>

Closes #10902 from BenFradet/SPARK-12983.

https://issues.apache.org/jira/browse/SPARK-12780

Author: Xusen Yin <yinxusen@gmail.com>

Closes #10724 from yinxusen/SPARK-12780.

If there's an RPC issue while sparkContext is alive but stopped (which would happen only when executing SparkContext.stop), log a warning instead. This is a common occurrence.

vanzin

Author: Nishkam Ravi <nishkamravi@gmail.com>
Author: nishkamravi2 <nishkamravi@gmail.com>

Closes #10881 from nishkamravi2/master_netty.

This PR is a follow-up of PR #10541. It integrates the newly introduced SQL generation feature with native view to make native view canonical.

In this PR, a new SQL option `spark.sql.nativeView.canonical` is added.  When this option and `spark.sql.nativeView` are both `true`, Spark SQL tries to handle `CREATE VIEW` DDL statements using SQL query strings generated from view definition logical plans. If we failed to map the plan to SQL, we fallback to the original native view approach.

One important issue this PR fixes is that, now we can use CTE when defining a view.  Originally, when native view is turned on, we wrap the view definition text with an extra `SELECT`.  However, HiveQL parser doesn't allow CTE appearing as a subquery.  Namely, something like this is disallowed:

```sql
SELECT n
FROM (
  WITH w AS (SELECT 1 AS n)
  SELECT * FROM w
) v
```

This PR fixes this issue because the extra `SELECT` is no longer needed (also, CTE expressions are inlined as subqueries during analysis phase, thus there won't be CTE expressions in the generated SQL query string).

Author: Cheng Lian <lian@databricks.com>
Author: Yin Huai <yhuai@databricks.com>

Closes #10733 from liancheng/spark-12728.integrate-sql-gen-with-native-view.

This PR integrates Count-Min Sketch from spark-sketch into DataFrame. This version resorts to `RDD.aggregate` for building the sketch. A more performant UDAF version can be built in future follow-up PRs.

Author: Cheng Lian <lian@databricks.com>

Closes #10911 from liancheng/cms-df-api.

Add ```covar_samp``` and ```covar_pop``` for SparkR.
Should we also provide ```cov``` alias for ```covar_samp```? There is ```cov``` implementation at stats.R which masks ```stats::cov``` already, but may bring to breaking API change.

cc sun-rui felixcheung shivaram

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10829 from yanboliang/spark-12903.

The intercept in Logistic Regression represents a prior on categories which should not be regularized. In MLlib, the regularization is handled through Updater, and the Updater penalizes all the components without excluding the intercept which resulting poor training accuracy with regularization.
The new implementation in ML framework handles this properly, and we should call the implementation in ML from MLlib since majority of users are still using MLlib api.
Note that both of them are doing feature scalings to improve the convergence, and the only difference is ML version doesn't regularize the intercept. As a result, when lambda is zero, they will converge to the same solution.

Previously partially reviewed at https://github.com/apache/spark/pull/6386#issuecomment-168781424 re-opening for dbtsai to review.

Author: Holden Karau <holden@us.ibm.com>
Author: Holden Karau <holden@pigscanfly.ca>

Closes #10788 from holdenk/SPARK-7780-intercept-in-logisticregressionwithLBFGS-should-not-be-regularized.

This patch adds support for complex types for ColumnarBatch. ColumnarBatch supports structs
and arrays. There is a simple mapping between the richer catalyst types to these two. Strings
are treated as an array of bytes.

ColumnarBatch will contain a column for each node of the schema. Non-complex schemas consists
of just leaf nodes. Structs represent an internal node with one child for each field. Arrays
are internal nodes with one child. Structs just contain nullability. Arrays contain offsets
and lengths into the child array. This structure is able to handle arbitrary nesting. It has
the key property that we maintain columnar throughout and that primitive types are only stored
in the leaf nodes and contiguous across rows. For example, if the schema is
```
array<array<int>>
```
There are three columns in the schema. The internal nodes each have one children. The leaf node contains all the int data stored consecutively.

As part of this, this patch adds append APIs in addition to the Put APIs (e.g. putLong(rowid, v)
vs appendLong(v)). These APIs are necessary when the batch contains variable length elements.
The vectors are not fixed length and will grow as necessary. This should make the usage a lot
simpler for the writer.

Author: Nong Li <nong@databricks.com>

Closes #10820 from nongli/spark-12854.

… Add LibSVMOutputWriter

The behavior of LibSVMRelation is not changed except adding LibSVMOutputWriter
* Partition is still not supported
* Multiple input paths is not supported

Author: Jeff Zhang <zjffdu@apache.org>

Closes #9595 from zjffdu/SPARK-11622.

Right now RpcEndpointRef.ask may throw exception in some corner cases, such as calling ask after stopping RpcEnv. It's better to avoid throwing exception from RpcEndpointRef.ask. We can send the exception to the future for `ask`.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #10568 from zsxwing/send-ask-fail.

The current python ml params require cut-and-pasting the param setup and description between the class & ```__init__``` methods. Remove this possible case of errors & simplify use of custom params by adding a ```_copy_new_parent``` method to param so as to avoid cut and pasting (and cut and pasting at different indentation levels urgh).

Author: Holden Karau <holden@us.ibm.com>

Closes #10216 from holdenk/SPARK-10509-excessive-param-boiler-plate-code.

environment variable ADD_FILES is created for adding python files on spark context to be distributed to executors (SPARK-865), this is deprecated now. User are encouraged to use --py-files for adding python files.

Author: Jeff Zhang <zjffdu@apache.org>

Closes #10913 from zjffdu/SPARK-12993.

Otherwise the `^` character is always marked as error in IntelliJ since it represents an unclosed superscript markup tag.

Author: Cheng Lian <lian@databricks.com>

Closes #10926 from liancheng/agg-doc-fix.

This patch improves our `dev/run-tests` script to test modules in a topologically-sorted order based on modules' dependencies.  This will help to ensure that bugs in upstream projects are not misattributed to downstream projects because those projects' tests were the first ones to exhibit the failure

Topological sorting is also useful for shortening the feedback loop when testing pull requests: if I make a change in SQL then the SQL tests should run before MLlib, not after.

In addition, this patch also updates our test module definitions to split `sql` into `catalyst`, `sql`, and `hive` in order to allow more tests to be skipped when changing only `hive/` files.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #10885 from JoshRosen/SPARK-8725.

https://issues.apache.org/jira/browse/SPARK-12952

Author: Xusen Yin <yinxusen@gmail.com>

Closes #10863 from yinxusen/SPARK-12952.

https://issues.apache.org/jira/browse/SPARK-11923

Author: Xusen Yin <yinxusen@gmail.com>

Closes #10186 from yinxusen/SPARK-11923.

[SPARK-7799][STREAMING][DOCUMENT] Add the linking and deploying instructions for streaming-akka project

Since `actorStream` is an external project, we should add the linking and deploying instructions for it.

A follow up PR of #10744

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #10856 from zsxwing/akka-link-instruction.

This PR adds a new table option (`skip_hive_metadata`) that'd allow the user to skip storing the table metadata in hive metadata format. While this could be useful in general, the specific use-case for this change is that Hive doesn't handle wide schemas well (see https://issues.apache.org/jira/browse/SPARK-12682 and https://issues.apache.org/jira/browse/SPARK-6024) which in turn prevents such tables from being queried in SparkSQL.

Author: Sameer Agarwal <sameer@databricks.com>

Closes #10826 from sameeragarwal/skip-hive-metadata.

Call system.exit explicitly to make sure non-daemon user threads terminate. Without this, user applications might live forever if the cluster manager does not appropriately kill them. E.g., YARN had this bug: HADOOP-12441.

Author: zhuol <zhuol@yahoo-inc.com>

Closes #9946 from zhuoliu/10911.

[SPARK-3369][CORE][STREAMING] Java mapPartitions Iterator->Iterable is inconsistent with Scala's Iterator->Iterator

Fix Java function API methods for flatMap and mapPartitions to require producing only an Iterator, not Iterable. Also fix DStream.flatMap to require a function producing TraversableOnce only, not Traversable.

CC rxin pwendell for API change; tdas since it also touches streaming.

Author: Sean Owen <sowen@cloudera.com>

Closes #10413 from srowen/SPARK-3369.

JIRA: https://issues.apache.org/jira/browse/SPARK-12961

To prevent memory leak in snappy-java, just call the method once and cache the result. After the library releases new version, we can remove this object.

JoshRosen

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

Closes #10875 from viirya/prevent-snappy-memory-leak.

This PR adds serialization support for BloomFilter.

A version number is added to version the serialized binary format.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10920 from cloud-fan/bloom-filter.

This pull request simply fixes a few minor coding style issues in csv, as I was reviewing the change post-hoc.

Author: Reynold Xin <rxin@databricks.com>

Closes #10919 from rxin/csv-minor.

I saw several failures from recent PR builds, e.g., https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/50015/consoleFull. This PR marks the test as ignored and we will fix the flakyness in SPARK-10086.

gliptak Do you know why the test failure didn't show up in the Jenkins "Test Result"?

cc: jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #10909 from mengxr/SPARK-10086.

https://issues.apache.org/jira/browse/SPARK-12834

We use `SerDe.dumps()` to serialize `JavaArray` and `JavaList` in `PythonMLLibAPI`, then deserialize them with `PickleSerializer` in Python side. However, there is no need to transform them in such an inefficient way. Instead of it, we can use type conversion to convert them, e.g. `list(JavaArray)` or `list(JavaList)`. What's more, there is an issue to Ser/De Scala Array as I said in https://issues.apache.org/jira/browse/SPARK-12780

Author: Xusen Yin <yinxusen@gmail.com>

Closes #10772 from yinxusen/SPARK-12834.

Add Python API for ml.feature.QuantileDiscretizer.

One open question: Do we want to do this stuff to re-use the java model, create a new model, or use a different wrapper around the java model.
cc brkyvz & mengxr

Author: Holden Karau <holden@us.ibm.com>

Closes #10085 from holdenk/SPARK-11937-SPARK-11922-Python-API-for-ml.feature.QuantileDiscretizer.

liancheng please take a look

Author: tedyu <yuzhihong@gmail.com>

Closes #10906 from tedyu/master.

This PR adds an initial implementation of bloom filter in the newly added sketch module.  The implementation is based on the [`BloomFilter` class in guava](https://code.google.com/p/guava-libraries/source/browse/guava/src/com/google/common/hash/BloomFilter.java).

Some difference from the design doc:

* expose `bitSize` instead of `sizeInBytes` to user.
* always need the `expectedInsertions` parameter when create bloom filter.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10883 from cloud-fan/bloom-filter.