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17317 commits

Author SHA1 Message Date
wm624@hotmail.com 363793f2bf [SPARK-16444][SPARKR] Isotonic Regression wrapper in SparkR
## What changes were proposed in this pull request?

(Please fill in changes proposed in this fix)

Add Isotonic Regression wrapper in SparkR

Wrappers in R and Scala are added.
Unit tests
Documentation

## How was this patch tested?
Manually tested with sudo ./R/run-tests.sh

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

Author: wm624@hotmail.com <wm624@hotmail.com>

Closes #14182 from wangmiao1981/isoR.
2016-08-17 06:15:04 -07:00
jiangxingbo 4d0cc84afc [SPARK-17032][SQL] Add test cases for methods in ParserUtils.
## What changes were proposed in this pull request?

Currently methods in `ParserUtils` are tested indirectly, we should add test cases in `ParserUtilsSuite` to verify their integrity directly.

## How was this patch tested?

New test cases in `ParserUtilsSuite`

Author: jiangxingbo <jiangxb1987@gmail.com>

Closes #14620 from jiangxb1987/parserUtils.
2016-08-17 14:22:36 +02:00
mvervuurt 0f6aa8afaa [MINOR][DOC] Fix the descriptions for properties argument in the documenation for jdbc APIs
## What changes were proposed in this pull request?

This should be credited to mvervuurt. The main purpose of this PR is
 - simply to include the change for the same instance in `DataFrameReader` just to match up.
 - just avoid duplicately verifying the PR (as I already did).

The documentation for both should be the same because both assume the `properties` should be  the same `dict` for the same option.

## How was this patch tested?

Manually building Python documentation.

This will produce the output as below:

- `DataFrameReader`

![2016-08-17 11 12 00](https://cloud.githubusercontent.com/assets/6477701/17722764/b3f6568e-646f-11e6-8b75-4fb672f3f366.png)

- `DataFrameWriter`

![2016-08-17 11 12 10](https://cloud.githubusercontent.com/assets/6477701/17722765/b58cb308-646f-11e6-841a-32f19800d139.png)

Closes #14624

Author: hyukjinkwon <gurwls223@gmail.com>
Author: mvervuurt <m.a.vervuurt@gmail.com>

Closes #14677 from HyukjinKwon/typo-python.
2016-08-16 23:12:59 -07:00
Herman van Hovell f7c9ff57c1 [SPARK-17068][SQL] Make view-usage visible during analysis
## What changes were proposed in this pull request?
This PR adds a field to subquery alias in order to make the usage of views in a resolved `LogicalPlan` more visible (and more understandable).

For example, the following view and query:
```sql
create view constants as select 1 as id union all select 1 union all select 42
select * from constants;
```
...now yields the following analyzed plan:
```
Project [id#39]
+- SubqueryAlias c, `default`.`constants`
   +- Project [gen_attr_0#36 AS id#39]
      +- SubqueryAlias gen_subquery_0
         +- Union
            :- Union
            :  :- Project [1 AS gen_attr_0#36]
            :  :  +- OneRowRelation$
            :  +- Project [1 AS gen_attr_1#37]
            :     +- OneRowRelation$
            +- Project [42 AS gen_attr_2#38]
               +- OneRowRelation$
```
## How was this patch tested?
Added tests for the two code paths in `SessionCatalogSuite` (sql/core) and `HiveMetastoreCatalogSuite` (sql/hive)

Author: Herman van Hovell <hvanhovell@databricks.com>

Closes #14657 from hvanhovell/SPARK-17068.
2016-08-16 23:09:53 -07:00
Herman van Hovell 4a2c375be2 [SPARK-17084][SQL] Rename ParserUtils.assert to validate
## What changes were proposed in this pull request?
This PR renames `ParserUtils.assert` to `ParserUtils.validate`. This is done because this method is used to check requirements, and not to check if the program is in an invalid state.

## How was this patch tested?
Simple rename. Compilation should do.

Author: Herman van Hovell <hvanhovell@databricks.com>

Closes #14665 from hvanhovell/SPARK-17084.
2016-08-16 21:35:39 -07:00
sandy e28a8c5899 [SPARK-17089][DOCS] Remove api doc link for mapReduceTriplets operator
## What changes were proposed in this pull request?

Remove the api doc link for mapReduceTriplets operator because in latest api they are remove so when user link to that api they will not get mapReduceTriplets there so its more good to remove than confuse the user.

## How was this patch tested?
Run all the test cases

![screenshot from 2016-08-16 23-08-25](https://cloud.githubusercontent.com/assets/8075390/17709393/8cfbf75a-6406-11e6-98e6-38f7b319d833.png)

Author: sandy <phalodi@gmail.com>

Closes #14669 from phalodi/SPARK-17089.
2016-08-16 12:50:55 -07:00
Felix Cheung c34b546d67 [SPARK-16519][SPARKR] Handle SparkR RDD generics that create warnings in R CMD check
## What changes were proposed in this pull request?

Rename RDD functions for now to avoid CRAN check warnings.
Some RDD functions are sharing generics with DataFrame functions (hence the problem) so after the renames we need to add new generics, for now.

## How was this patch tested?

unit tests

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #14626 from felixcheung/rrddfunctions.
2016-08-16 11:19:18 -07:00
Yanbo Liang d37ea3c09c [MINOR][SPARKR] spark.glm weightCol should in the signature.
## What changes were proposed in this pull request?
Fix the issue that ```spark.glm``` ```weightCol``` should in the signature.

## How was this patch tested?
Existing tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #14641 from yanboliang/weightCol.
2016-08-16 10:52:35 -07:00
Dongjoon Hyun 12a89e55cb [SPARK-17035] [SQL] [PYSPARK] Improve Timestamp not to lose precision for all cases
## What changes were proposed in this pull request?

`PySpark` loses `microsecond` precision for some corner cases during converting `Timestamp` into `Long`. For example, for the following `datetime.max` value should be converted a value whose last 6 digits are '999999'. This PR improves the logic not to lose precision for all cases.

**Corner case**
```python
>>> datetime.datetime.max
datetime.datetime(9999, 12, 31, 23, 59, 59, 999999)
```

**Before**
```python
>>> from datetime import datetime
>>> from pyspark.sql import Row
>>> from pyspark.sql.types import StructType, StructField, TimestampType
>>> schema = StructType([StructField("dt", TimestampType(), False)])
>>> [schema.toInternal(row) for row in [{"dt": datetime.max}]]
[(253402329600000000,)]
```

**After**
```python
>>> [schema.toInternal(row) for row in [{"dt": datetime.max}]]
[(253402329599999999,)]
```

## How was this patch tested?

Pass the Jenkins test with a new test case.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #14631 from dongjoon-hyun/SPARK-17035.
2016-08-16 10:01:30 -07:00
linbojin 6f0988b129 [MINOR][DOC] Correct code snippet results in quick start documentation
## What changes were proposed in this pull request?

As README.md file is updated over time. Some code snippet outputs are not correct based on new README.md file. For example:
```
scala> textFile.count()
res0: Long = 126
```
should be
```
scala> textFile.count()
res0: Long = 99
```
This pr is to add comments to point out this problem so that new spark learners have a correct reference.
Also, fixed a samll bug, inside current documentation, the outputs of linesWithSpark.count() without and with cache are different (one is 15 and the other is 19)
```
scala> val linesWithSpark = textFile.filter(line => line.contains("Spark"))
linesWithSpark: org.apache.spark.rdd.RDD[String] = MapPartitionsRDD[2] at filter at <console>:27

scala> textFile.filter(line => line.contains("Spark")).count() // How many lines contain "Spark"?
res3: Long = 15

...

scala> linesWithSpark.cache()
res7: linesWithSpark.type = MapPartitionsRDD[2] at filter at <console>:27

scala> linesWithSpark.count()
res8: Long = 19
```

## How was this patch tested?

manual test:  run `$ SKIP_API=1 jekyll serve --watch`

Author: linbojin <linbojin203@gmail.com>

Closes #14645 from linbojin/quick-start-documentation.
2016-08-16 11:37:54 +01:00
Herman van Hovell 8fdc6ce400 [SPARK-16964][SQL] Remove private[hive] from sql.hive.execution package
## What changes were proposed in this pull request?
This PR is a small follow-up to https://github.com/apache/spark/pull/14554. This also widens the visibility of a few (similar) Hive classes.

## How was this patch tested?
No test. Only a visibility change.

Author: Herman van Hovell <hvanhovell@databricks.com>

Closes #14654 from hvanhovell/SPARK-16964-hive.
2016-08-16 01:12:27 -07:00
Sean Zhong 7b65030e7a [SPARK-17034][SQL] adds expression UnresolvedOrdinal to represent the ordinals in GROUP BY or ORDER BY
## What changes were proposed in this pull request?

This PR adds expression `UnresolvedOrdinal` to represent the ordinal in GROUP BY or ORDER BY, and fixes the rules when resolving ordinals.

Ordinals in GROUP BY or ORDER BY like `1` in `order by 1` or `group by 1` should be considered as unresolved before analysis. But in current code, it uses `Literal` expression to store the ordinal. This is inappropriate as `Literal` itself is a resolved expression, it gives the user a wrong message that the ordinals has already been resolved.

### Before this change

Ordinal is stored as `Literal` expression

```
scala> sc.setLogLevel("TRACE")
scala> sql("select a from t group by 1 order by 1")
...
'Sort [1 ASC], true
 +- 'Aggregate [1], ['a]
     +- 'UnresolvedRelation `t
```

For query:

```
scala> Seq(1).toDF("a").createOrReplaceTempView("t")
scala> sql("select count(a), a from t group by 2 having a > 0").show
```

During analysis, the intermediate plan before applying rule `ResolveAggregateFunctions` is:

```
'Filter ('a > 0)
   +- Aggregate [2], [count(1) AS count(1)#83L, a#81]
        +- LocalRelation [value#7 AS a#9]
```

Before this PR, rule `ResolveAggregateFunctions` believes all expressions of `Aggregate` have already been resolved, and tries to resolve the expressions in `Filter` directly. But this is wrong, as ordinal `2` in Aggregate is not really resolved!

### After this change

Ordinals are stored as `UnresolvedOrdinal`.

```
scala> sc.setLogLevel("TRACE")
scala> sql("select a from t group by 1 order by 1")
...
'Sort [unresolvedordinal(1) ASC], true
 +- 'Aggregate [unresolvedordinal(1)], ['a]
      +- 'UnresolvedRelation `t`
```

## How was this patch tested?

Unit tests.

Author: Sean Zhong <seanzhong@databricks.com>

Closes #14616 from clockfly/spark-16955.
2016-08-16 15:51:30 +08:00
Wenchen Fan 7de30d6e9e [SPARK-16916][SQL] serde/storage properties should not have limitations
## What changes were proposed in this pull request?

`CatalogStorageFormat.properties` can be used in 2 ways:

1. for hive tables, it stores the serde properties.
2. for data source tables, it stores the data source options, e.g. `path`, `skipHiveMetadata`, etc.

however, both of them have nothing to do with data source properties, e.g. `spark.sql.sources.provider`, so they should not have limitations about data source properties.

## How was this patch tested?

existing tests

Author: Wenchen Fan <wenchen@databricks.com>

Closes #14506 from cloud-fan/table-prop.
2016-08-15 21:43:41 -07:00
Shixiong Zhu 268b71d0d7 [SPARK-17065][SQL] Improve the error message when encountering an incompatible DataSourceRegister
## What changes were proposed in this pull request?

Add an instruction to ask the user to remove or upgrade the incompatible DataSourceRegister in the error message.

## How was this patch tested?

Test command:
```
build/sbt -Dscala-2.10 package
SPARK_SCALA_VERSION=2.10 bin/spark-shell --packages ai.h2o:sparkling-water-core_2.10:1.6.5

scala> Seq(1).toDS().write.format("parquet").save("foo")
```

Before:
```
java.util.ServiceConfigurationError: org.apache.spark.sql.sources.DataSourceRegister: Provider org.apache.spark.h2o.DefaultSource could not be instantiated
	at java.util.ServiceLoader.fail(ServiceLoader.java:232)
	at java.util.ServiceLoader.access$100(ServiceLoader.java:185)
	at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:384)
	at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404)
	at java.util.ServiceLoader$1.next(ServiceLoader.java:480)
...
Caused by: java.lang.NoClassDefFoundError: org/apache/spark/Logging
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:760)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
	at java.security.AccessController.doPrivileged(Native Method)
...
```

After:

```
java.lang.ClassNotFoundException: Detected an incompatible DataSourceRegister. Please remove the incompatible library from classpath or upgrade it. Error: org.apache.spark.sql.sources.DataSourceRegister: Provider org.apache.spark.h2o.DefaultSource could not be instantiated
	at org.apache.spark.sql.execution.datasources.DataSource.lookupDataSource(DataSource.scala:178)
	at org.apache.spark.sql.execution.datasources.DataSource.providingClass$lzycompute(DataSource.scala:79)
	at org.apache.spark.sql.execution.datasources.DataSource.providingClass(DataSource.scala:79)
	at org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:441)
	at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:213)
	at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:196)
...
```

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #14651 from zsxwing/SPARK-17065.
2016-08-15 15:55:32 -07:00
Davies Liu fffb0c0d19 [SPARK-16700][PYSPARK][SQL] create DataFrame from dict/Row with schema
## What changes were proposed in this pull request?

In 2.0, we verify the data type against schema for every row for safety, but with performance cost, this PR make it optional.

When we verify the data type for StructType, it does not support all the types we support in infer schema (for example, dict), this PR fix that to make them consistent.

For Row object which is created using named arguments, the order of fields are sorted by name, they may be not different than the order in provided schema, this PR fix that by ignore the order of fields in this case.

## How was this patch tested?

Created regression tests for them.

Author: Davies Liu <davies@databricks.com>

Closes #14469 from davies/py_dict.
2016-08-15 12:41:27 -07:00
Marcelo Vanzin 5da6c4b24f [SPARK-16671][CORE][SQL] Consolidate code to do variable substitution.
Both core and sql have slightly different code that does variable substitution
of config values. This change refactors that code and encapsulates the logic
of reading config values and expading variables in a new helper class, which
can be configured so that both core and sql can use it without losing existing
functionality, and allows for easier testing and makes it easier to add more
features in the future.

Tested with existing and new unit tests, and by running spark-shell with
some configs referencing variables and making sure it behaved as expected.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #14468 from vanzin/SPARK-16671.
2016-08-15 11:09:54 -07:00
Junyang Qian 564fe614c1 [SPARK-16508][SPARKR] Split docs for arrange and orderBy methods
## What changes were proposed in this pull request?

This PR splits arrange and orderBy methods according to their functionality (the former for sorting sparkDataFrame and the latter for windowSpec).

## How was this patch tested?

![screen shot 2016-08-06 at 6 39 19 pm](https://cloud.githubusercontent.com/assets/15318264/17459969/51eade28-5c05-11e6-8ca1-8d8a8e344bab.png)
![screen shot 2016-08-06 at 6 39 29 pm](https://cloud.githubusercontent.com/assets/15318264/17459966/51e3c246-5c05-11e6-8d35-3e905ca48676.png)
![screen shot 2016-08-06 at 6 40 02 pm](https://cloud.githubusercontent.com/assets/15318264/17459967/51e650ec-5c05-11e6-8698-0f037f5199ff.png)

Author: Junyang Qian <junyangq@databricks.com>

Closes #14522 from junyangq/SPARK-16508-0.
2016-08-15 11:03:03 -07:00
WeichenXu 3d8bfe7a39 [SPARK-16934][ML][MLLIB] Update LogisticCostAggregator serialization code to make it consistent with LinearRegression
## What changes were proposed in this pull request?

Update LogisticCostAggregator serialization code to make it consistent with #14109

## How was this patch tested?
MLlib 2.0:
![image](https://cloud.githubusercontent.com/assets/19235986/17649601/5e2a79ac-61ee-11e6-833c-3bd8b5250470.png)

After this PR:
![image](https://cloud.githubusercontent.com/assets/19235986/17649599/52b002ae-61ee-11e6-9402-9feb3439880f.png)

Author: WeichenXu <WeichenXu123@outlook.com>

Closes #14520 from WeichenXu123/improve_logistic_regression_costfun.
2016-08-15 06:38:30 -07:00
Yanbo Liang ddf0d1e3fe [TRIVIAL][ML] Fix LogisticRegression typo in error message.
## What changes were proposed in this pull request?
Fix ```LogisticRegression``` typo in error message.

## How was this patch tested?
Docs change, no new tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #14633 from yanboliang/lr-typo.
2016-08-15 10:11:29 +01:00
Stavros Kontopoulos 1a028bdefa [SPARK-11714][MESOS] Make Spark on Mesos honor port restrictions on coarse grain mode
- Make mesos coarse grained scheduler accept port offers and pre-assign ports

Previous attempt was for fine grained: https://github.com/apache/spark/pull/10808

Author: Stavros Kontopoulos <stavros.kontopoulos@lightbend.com>
Author: Stavros Kontopoulos <stavros.kontopoulos@typesafe.com>

Closes #11157 from skonto/honour_ports_coarse.
2016-08-15 09:55:32 +01:00
Zhenglai Zhang 2a3d286f34 [WIP][MINOR][TYPO] Fix several trivival typos
## What changes were proposed in this pull request?

* Fixed one typo `"overriden"` as `"overridden"`, also make sure no other same typo.
* Fixed one typo `"lowcase"` as `"lowercase"`, also make sure no other same typo.

## How was this patch tested?

Since the change is very tiny, so I just make sure compilation is successful.
I am new to the spark community,  please feel free to let me do other necessary steps.

Thanks in advance!

----
Updated: Found another typo `lowcase` later and fixed then in the same patch

Author: Zhenglai Zhang <zhenglaizhang@hotmail.com>

Closes #14622 from zhenglaizhang/fixtypo.
2016-08-14 16:10:34 +01:00
zero323 0ebf7c1bff [SPARK-17027][ML] Avoid integer overflow in PolynomialExpansion.getPolySize
## What changes were proposed in this pull request?

Replaces custom choose function with o.a.commons.math3.CombinatoricsUtils.binomialCoefficient

## How was this patch tested?

Spark unit tests

Author: zero323 <zero323@users.noreply.github.com>

Closes #14614 from zero323/SPARK-17027.
2016-08-14 11:59:24 +01:00
Sean Owen cdaa562c9a [SPARK-16966][SQL][CORE] App Name is a randomUUID even when "spark.app.name" exists
## What changes were proposed in this pull request?

Don't override app name specified in `SparkConf` with a random app name. Only set it if the conf has no app name even after options have been applied.

See also https://github.com/apache/spark/pull/14602
This is similar to Sherry302 's original proposal in https://github.com/apache/spark/pull/14556

## How was this patch tested?

Jenkins test, with new case reproducing the bug

Author: Sean Owen <sowen@cloudera.com>

Closes #14630 from srowen/SPARK-16966.2.
2016-08-13 15:40:43 -07:00
Luciano Resende 67f025d90e [SPARK-17023][BUILD] Upgrade to Kafka 0.10.0.1 release
## What changes were proposed in this pull request?
Update Kafka streaming connector to use Kafka 0.10.0.1 release

## How was this patch tested?
Tested via Spark unit and integration tests

Author: Luciano Resende <lresende@apache.org>

Closes #14606 from lresende/kafka-upgrade.
2016-08-13 11:42:38 +01:00
GraceH 8c8acdec93 [SPARK-16968] Add additional options in jdbc when creating a new table
## What changes were proposed in this pull request?

In the PR, we just allow the user to add additional options when create a new table in JDBC writer.
The options can be table_options or partition_options.
E.g., "CREATE TABLE t (name string) ENGINE=InnoDB DEFAULT CHARSET=utf8"

Here is the usage example:
```
df.write.option("createTableOptions", "ENGINE=InnoDB DEFAULT CHARSET=utf8").jdbc(...)
```
## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
will apply test result soon.

Author: GraceH <93113783@qq.com>

Closes #14559 from GraceH/jdbc_options.
2016-08-13 11:39:58 +01:00
Xin Ren 7f7133bdcc [MINOR][CORE] fix warnings on depreciated methods in MesosClusterSchedulerSuite and DiskBlockObjectWriterSuite
## What changes were proposed in this pull request?

Fixed warnings below after scanning through warnings during build:

```
[warn] /home/jenkins/workspace/SparkPullRequestBuilder/core/src/test/scala/org/apache/spark/scheduler/cluster/mesos/MesosClusterSchedulerSuite.scala:34: imported `Utils' is permanently hidden by definition of object Utils in package mesos
[warn] import org.apache.spark.scheduler.cluster.mesos.Utils
[warn]                                                 ^
```

and
```
[warn] /home/jenkins/workspace/SparkPullRequestBuilder/core/src/test/scala/org/apache/spark/storage/DiskBlockObjectWriterSuite.scala:113: method shuffleBytesWritten in class ShuffleWriteMetrics is deprecated: use bytesWritten instead
[warn]     assert(writeMetrics.shuffleBytesWritten === file.length())
[warn]                         ^
[warn] /home/jenkins/workspace/SparkPullRequestBuilder/core/src/test/scala/org/apache/spark/storage/DiskBlockObjectWriterSuite.scala:119: method shuffleBytesWritten in class ShuffleWriteMetrics is deprecated: use bytesWritten instead
[warn]     assert(writeMetrics.shuffleBytesWritten === file.length())
[warn]                         ^
[warn] /home/jenkins/workspace/SparkPullRequestBuilder/core/src/test/scala/org/apache/spark/storage/DiskBlockObjectWriterSuite.scala:131: method shuffleBytesWritten in class ShuffleWriteMetrics is deprecated: use bytesWritten instead
[warn]     assert(writeMetrics.shuffleBytesWritten === file.length())
[warn]                         ^
[warn] /home/jenkins/workspace/SparkPullRequestBuilder/core/src/test/scala/org/apache/spark/storage/DiskBlockObjectWriterSuite.scala:135: method shuffleBytesWritten in class ShuffleWriteMetrics is deprecated: use bytesWritten instead
[warn]     assert(writeMetrics.shuffleBytesWritten === file.length())
[warn]                         ^
```

## How was this patch tested?

Tested manually on local laptop.

Author: Xin Ren <iamshrek@126.com>

Closes #14609 from keypointt/suiteWarnings.
2016-08-13 11:29:42 +01:00
Jagadeesan e46cb78b3b [SPARK-12370][DOCUMENTATION] Documentation should link to examples …
## What changes were proposed in this pull request?

When documentation is built is should reference examples from the same build. There are times when the docs have links that point to files in the GitHub head which may not be valid on the current release. Changed that in URLs to make them point to the right tag in git using ```SPARK_VERSION_SHORT```

…from its own release version] [Streaming programming guide]

Author: Jagadeesan <as2@us.ibm.com>

Closes #14596 from jagadeesanas2/SPARK-12370.
2016-08-13 11:25:03 +01:00
WeichenXu 91f2735a18 [DOC] add config option spark.ui.enabled into document
## What changes were proposed in this pull request?

The configuration doc lost the config option `spark.ui.enabled` (default value is `true`)
I think this option is important because many cases we would like to turn it off.
so I add it.

## How was this patch tested?

N/A

Author: WeichenXu <WeichenXu123@outlook.com>

Closes #14604 from WeichenXu123/add_doc_param_spark_ui_enabled.
2016-08-12 20:10:09 +01:00
Dongjoon Hyun 2a105134e9 [SPARK-16771][SQL] WITH clause should not fall into infinite loop.
## What changes were proposed in this pull request?

This PR changes the CTE resolving rule to use only **forward-declared** tables in order to prevent infinite loops. More specifically, new logic is like the following.

* Resolve CTEs in `WITH` clauses first before replacing the main SQL body.
* When resolving CTEs, only forward-declared CTEs or base tables are referenced.
  - Self-referencing is not allowed any more.
  - Cross-referencing is not allowed any more.

**Reported Error Scenarios**
```scala
scala> sql("WITH t AS (SELECT 1 FROM t) SELECT * FROM t")
java.lang.StackOverflowError
...
scala> sql("WITH t1 AS (SELECT * FROM t2), t2 AS (SELECT 2 FROM t1) SELECT * FROM t1, t2")
java.lang.StackOverflowError
...
```
Note that `t`, `t1`, and `t2` are not declared in database. Spark falls into infinite loops before resolving table names.

## How was this patch tested?

Pass the Jenkins tests with new two testcases.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #14397 from dongjoon-hyun/SPARK-16771-TREENODE.
2016-08-12 19:07:34 +02:00
Yanbo Liang bbae20ade1 [SPARK-17033][ML][MLLIB] GaussianMixture should use treeAggregate to improve performance
## What changes were proposed in this pull request?
```GaussianMixture``` should use ```treeAggregate``` rather than ```aggregate``` to improve performance and scalability. In my test of dataset with 200 features and 1M instance, I found there is 20% increased performance.
BTW, we should destroy broadcast variable ```compute``` at the end of each iteration.

## How was this patch tested?
Existing tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #14621 from yanboliang/spark-17033.
2016-08-12 10:06:17 -07:00
gatorsmile 79e2caa132 [SPARK-16598][SQL][TEST] Added a test case for verifying the table identifier parsing
#### What changes were proposed in this pull request?
So far, the test cases of `TableIdentifierParserSuite` do not cover the quoted cases. We should add one for avoiding regression.

#### How was this patch tested?
N/A

Author: gatorsmile <gatorsmile@gmail.com>

Closes #14244 from gatorsmile/quotedIdentifiers.
2016-08-12 10:02:00 +01:00
hyukjinkwon f4482225c4 [MINOR][DOC] Fix style in examples across documentation
## What changes were proposed in this pull request?

This PR fixes the documentation as below:

  -  Python has 4 spaces and Java and Scala has 2 spaces (See https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide).

  - Avoid excessive parentheses and curly braces for anonymous functions. (See https://github.com/databricks/scala-style-guide#anonymous)

## How was this patch tested?

N/A

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #14593 from HyukjinKwon/minor-documentation.
2016-08-12 10:00:58 +01:00
hongshen 993923c8f5 [SPARK-16985] Change dataFormat from yyyyMMddHHmm to yyyyMMddHHmmss
## What changes were proposed in this pull request?

In our cluster, sometimes the sql output maybe overrided. When I submit some sql, all insert into the same table, and the sql will cost less one minute, here is the detail,
1 sql1, 11:03 insert into table.
2 sql2, 11:04:11 insert into table.
3 sql3, 11:04:48 insert into table.
4 sql4, 11:05 insert into table.
5 sql5, 11:06 insert into table.
The sql3's output file will override the sql2's output file. here is the log:
```
16/05/04 11:04:11 INFO hive.SparkHiveHadoopWriter: XXfinalPath=hdfs://tl-sng-gdt-nn-tdw.tencent-distribute.com:54310/tmp/assorz/tdw-tdwadmin/20160504/04559505496526517_-1_1204544348/10000/_tmp.p_20160428/attempt_201605041104_0001_m_000000_1

16/05/04 11:04:48 INFO hive.SparkHiveHadoopWriter: XXfinalPath=hdfs://tl-sng-gdt-nn-tdw.tencent-distribute.com:54310/tmp/assorz/tdw-tdwadmin/20160504/04559505496526517_-1_212180468/10000/_tmp.p_20160428/attempt_201605041104_0001_m_000000_1

```

The reason is the output file use SimpleDateFormat("yyyyMMddHHmm"), if two sql insert into the same table in the same minute, the output will be overrite. I think we should change dateFormat to "yyyyMMddHHmmss", in our cluster, we can't finished a sql in one second.

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

Author: hongshen <shenh062326@126.com>

Closes #14574 from shenh062326/SPARK-16985.
2016-08-12 09:58:02 +01:00
petermaxlee 00e103a6ed [SPARK-17013][SQL] Parse negative numeric literals
## What changes were proposed in this pull request?
This patch updates the SQL parser to parse negative numeric literals as numeric literals, instead of unary minus of positive literals.

This allows the parser to parse the minimal value for each data type, e.g. "-32768S".

## How was this patch tested?
Updated test cases.

Author: petermaxlee <petermaxlee@gmail.com>

Closes #14608 from petermaxlee/SPARK-17013.
2016-08-11 23:56:55 -07:00
Dongjoon Hyun abff92bfdc [SPARK-16975][SQL] Column-partition path starting '_' should be handled correctly
## What changes were proposed in this pull request?

Currently, Spark ignores path names starting with underscore `_` and `.`. This causes read-failures for the column-partitioned file data sources whose partition column names starts from '_', e.g. `_col`.

**Before**
```scala
scala> spark.range(10).withColumn("_locality_code", $"id").write.partitionBy("_locality_code").save("/tmp/parquet")
scala> spark.read.parquet("/tmp/parquet")
org.apache.spark.sql.AnalysisException: Unable to infer schema for ParquetFormat at /tmp/parquet20. It must be specified manually;
```

**After**
```scala
scala> spark.range(10).withColumn("_locality_code", $"id").write.partitionBy("_locality_code").save("/tmp/parquet")
scala> spark.read.parquet("/tmp/parquet")
res2: org.apache.spark.sql.DataFrame = [id: bigint, _locality_code: int]
```

## How was this patch tested?

Pass the Jenkins with a new test case.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #14585 from dongjoon-hyun/SPARK-16975-PARQUET.
2016-08-12 14:40:12 +08:00
Yanbo Liang ccc6dc0f4b [MINOR][ML] Rename TreeEnsembleModels to TreeEnsembleModel for PySpark
## What changes were proposed in this pull request?
Fix the typo of ```TreeEnsembleModels``` for PySpark, it should ```TreeEnsembleModel``` which will be consistent with Scala. What's more, it represents a tree ensemble model, so  ```TreeEnsembleModel``` should be more reasonable. This should not be used public, so it will not involve  breaking change.

## How was this patch tested?
No new tests, should pass existing ones.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #14454 from yanboliang/TreeEnsembleModel.
2016-08-11 22:39:19 -07:00
hyukjinkwon ac84fb64dd [SPARK-16434][SQL] Avoid per-record type dispatch in JSON when reading
## What changes were proposed in this pull request?

Currently, `JacksonParser.parse` is doing type-based dispatch for each row to convert the tokens to appropriate values for Spark.
It might not have to be done like this because the schema is already kept.

So, appropriate converters can be created first according to the schema once, and then apply them to each row.

This PR corrects `JacksonParser` so that it creates all converters for the schema once and then applies them to each row rather than type dispatching for every row.

Benchmark was proceeded with the codes below:

#### Parser tests

**Before**

```scala
test("Benchmark for JSON converter") {
  val N = 500 << 8
  val row =
    """{"struct":{"field1": true, "field2": 92233720368547758070},
    "structWithArrayFields":{"field1":[4, 5, 6], "field2":["str1", "str2"]},
    "arrayOfString":["str1", "str2"],
    "arrayOfInteger":[1, 2147483647, -2147483648],
    "arrayOfLong":[21474836470, 9223372036854775807, -9223372036854775808],
    "arrayOfBigInteger":[922337203685477580700, -922337203685477580800],
    "arrayOfDouble":[1.2, 1.7976931348623157E308, 4.9E-324, 2.2250738585072014E-308],
    "arrayOfBoolean":[true, false, true],
    "arrayOfNull":[null, null, null, null],
    "arrayOfStruct":[{"field1": true, "field2": "str1"}, {"field1": false}, {"field3": null}],
    "arrayOfArray1":[[1, 2, 3], ["str1", "str2"]],
    "arrayOfArray2":[[1, 2, 3], [1.1, 2.1, 3.1]]
   }"""
  val data = List.fill(N)(row)
  val dummyOption = new JSONOptions(Map.empty[String, String])
  val schema =
    InferSchema.infer(spark.sparkContext.parallelize(Seq(row)), "", dummyOption)
  val factory = new JsonFactory()

  val benchmark = new Benchmark("JSON converter", N)
  benchmark.addCase("convert JSON file", 10) { _ =>
    data.foreach { input =>
      val parser = factory.createParser(input)
      parser.nextToken()
      JacksonParser.convertRootField(factory, parser, schema)
    }
  }
  benchmark.run()
}
```

```
JSON converter:                          Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
------------------------------------------------------------------------------------------------
convert JSON file                             1697 / 1807          0.1       13256.9       1.0X
```

**After**

```scala
test("Benchmark for JSON converter") {
  val N = 500 << 8
  val row =
    """{"struct":{"field1": true, "field2": 92233720368547758070},
    "structWithArrayFields":{"field1":[4, 5, 6], "field2":["str1", "str2"]},
    "arrayOfString":["str1", "str2"],
    "arrayOfInteger":[1, 2147483647, -2147483648],
    "arrayOfLong":[21474836470, 9223372036854775807, -9223372036854775808],
    "arrayOfBigInteger":[922337203685477580700, -922337203685477580800],
    "arrayOfDouble":[1.2, 1.7976931348623157E308, 4.9E-324, 2.2250738585072014E-308],
    "arrayOfBoolean":[true, false, true],
    "arrayOfNull":[null, null, null, null],
    "arrayOfStruct":[{"field1": true, "field2": "str1"}, {"field1": false}, {"field3": null}],
    "arrayOfArray1":[[1, 2, 3], ["str1", "str2"]],
    "arrayOfArray2":[[1, 2, 3], [1.1, 2.1, 3.1]]
   }"""
  val data = List.fill(N)(row)
  val dummyOption = new JSONOptions(Map.empty[String, String], new SQLConf())
  val schema =
    InferSchema.infer(spark.sparkContext.parallelize(Seq(row)), dummyOption)

  val benchmark = new Benchmark("JSON converter", N)
  benchmark.addCase("convert JSON file", 10) { _ =>
    val parser = new JacksonParser(schema, dummyOption)
    data.foreach { input =>
      parser.parse(input)
    }
  }
  benchmark.run()
}
```

```
JSON converter:                          Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
------------------------------------------------------------------------------------------------
convert JSON file                             1401 / 1461          0.1       10947.4       1.0X
```

It seems parsing time is improved by roughly ~20%

#### End-to-End test

```scala
test("Benchmark for JSON reader") {
  val N = 500 << 8
  val row =
    """{"struct":{"field1": true, "field2": 92233720368547758070},
    "structWithArrayFields":{"field1":[4, 5, 6], "field2":["str1", "str2"]},
    "arrayOfString":["str1", "str2"],
    "arrayOfInteger":[1, 2147483647, -2147483648],
    "arrayOfLong":[21474836470, 9223372036854775807, -9223372036854775808],
    "arrayOfBigInteger":[922337203685477580700, -922337203685477580800],
    "arrayOfDouble":[1.2, 1.7976931348623157E308, 4.9E-324, 2.2250738585072014E-308],
    "arrayOfBoolean":[true, false, true],
    "arrayOfNull":[null, null, null, null],
    "arrayOfStruct":[{"field1": true, "field2": "str1"}, {"field1": false}, {"field3": null}],
    "arrayOfArray1":[[1, 2, 3], ["str1", "str2"]],
    "arrayOfArray2":[[1, 2, 3], [1.1, 2.1, 3.1]]
   }"""
  val df = spark.sqlContext.read.json(spark.sparkContext.parallelize(List.fill(N)(row)))
  withTempPath { path =>
    df.write.format("json").save(path.getCanonicalPath)

    val benchmark = new Benchmark("JSON reader", N)
    benchmark.addCase("reading JSON file", 10) { _ =>
      spark.read.format("json").load(path.getCanonicalPath).collect()
    }
    benchmark.run()
  }
}
```

**Before**

```
JSON reader:                             Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
------------------------------------------------------------------------------------------------
reading JSON file                             6485 / 6924          0.0       50665.0       1.0X
```

**After**

```
JSON reader:                             Best/Avg Time(ms)    Rate(M/s)   Per Row(ns)   Relative
------------------------------------------------------------------------------------------------
reading JSON file                             6350 / 6529          0.0       49609.3       1.0X
```

## How was this patch tested?

Existing test cases should cover this.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #14102 from HyukjinKwon/SPARK-16434.
2016-08-12 11:09:42 +08:00
Jeff Zhang 7a9e25c383 [SPARK-13081][PYSPARK][SPARK_SUBMIT] Allow set pythonExec of driver and executor through conf…
Before this PR, user have to export environment variable to specify the python of driver & executor which is not so convenient for users. This PR is trying to allow user to specify python through configuration "--pyspark-driver-python" & "--pyspark-executor-python"

Manually test in local & yarn mode for pyspark-shell and pyspark batch mode.

Author: Jeff Zhang <zjffdu@apache.org>

Closes #13146 from zjffdu/SPARK-13081.
2016-08-11 20:08:39 -07:00
WangTaoTheTonic ea0bf91b4a [SPARK-17022][YARN] Handle potential deadlock in driver handling messages
## What changes were proposed in this pull request?

We directly send RequestExecutors to AM instead of transfer it to yarnShedulerBackend first, to avoid potential deadlock.

## How was this patch tested?

manual tests

Author: WangTaoTheTonic <wangtao111@huawei.com>

Closes #14605 from WangTaoTheTonic/lock.
2016-08-11 15:09:23 -07:00
huangzhaowei 4ec5c360ce [SPARK-16868][WEB UI] Fix executor be both dead and alive on executor ui.
## What changes were proposed in this pull request?
In a heavy pressure of the spark application, since the executor will register it to driver block manager twice(because of heart beats), the executor will show as picture show:
![image](https://cloud.githubusercontent.com/assets/7404824/17467245/c1359094-5d4e-11e6-843a-f6d6347e1bf6.png)

## How was this patch tested?
NA

Details in: [SPARK-16868](https://issues.apache.org/jira/browse/SPARK-16868)

Author: huangzhaowei <carlmartinmax@gmail.com>

Closes #14530 from SaintBacchus/SPARK-16868.
2016-08-11 14:56:03 -07:00
Bryan Cutler 1c9a386c6b [SPARK-13602][CORE] Add shutdown hook to DriverRunner to prevent driver process leak
## What changes were proposed in this pull request?

Added shutdown hook to DriverRunner to kill the driver process in case the Worker JVM exits suddenly and the `WorkerWatcher` was unable to properly catch this.  Did some cleanup to consolidate driver state management and setting of finalized vars within the running thread.

## How was this patch tested?

Added unit tests to verify that final state and exception variables are set accordingly for successfull, failed, and errors in the driver process.  Retrofitted existing test to verify killing of mocked process ends with the correct state and stops properly

Manually tested (with deploy-mode=cluster) that the shutdown hook is called by forcibly exiting the `Worker` and various points in the code with the `WorkerWatcher` both disabled and enabled.  Also, manually killed the driver through the ui and verified that the `DriverRunner` interrupted, killed the process and exited properly.

Author: Bryan Cutler <cutlerb@gmail.com>

Closes #11746 from BryanCutler/DriverRunner-shutdown-hook-SPARK-13602.
2016-08-11 14:49:11 -07:00
petermaxlee cf9367826c [SPARK-17018][SQL] literals.sql for testing literal parsing
## What changes were proposed in this pull request?
This patch adds literals.sql for testing literal parsing end-to-end in SQL.

## How was this patch tested?
The patch itself is only about adding test cases.

Author: petermaxlee <petermaxlee@gmail.com>

Closes #14598 from petermaxlee/SPARK-17018-2.
2016-08-11 13:55:10 -07:00
Wenchen Fan acaf2a81ad [SPARK-17021][SQL] simplify the constructor parameters of QuantileSummaries
## What changes were proposed in this pull request?

1. `sampled` doesn't need to be `ArrayBuffer`, we never update it, but assign new value
2. `count` doesn't need to be `var`, we never mutate it.
3. `headSampled` doesn't need to be in constructor, we never pass a non-empty `headSampled` to constructor

## How was this patch tested?

existing tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #14603 from cloud-fan/simply.
2016-08-11 11:02:11 -07:00
Davies Liu 0f72e4f04b [SPARK-16958] [SQL] Reuse subqueries within the same query
## What changes were proposed in this pull request?

There could be multiple subqueries that generate same results, we could re-use the result instead of running it multiple times.

This PR also cleanup up how we run subqueries.

For SQL query
```sql
select id,(select avg(id) from t) from t where id > (select avg(id) from t)
```
The explain is
```
== Physical Plan ==
*Project [id#15L, Subquery subquery29 AS scalarsubquery()#35]
:  +- Subquery subquery29
:     +- *HashAggregate(keys=[], functions=[avg(id#15L)])
:        +- Exchange SinglePartition
:           +- *HashAggregate(keys=[], functions=[partial_avg(id#15L)])
:              +- *Range (0, 1000, splits=4)
+- *Filter (cast(id#15L as double) > Subquery subquery29)
   :  +- Subquery subquery29
   :     +- *HashAggregate(keys=[], functions=[avg(id#15L)])
   :        +- Exchange SinglePartition
   :           +- *HashAggregate(keys=[], functions=[partial_avg(id#15L)])
   :              +- *Range (0, 1000, splits=4)
   +- *Range (0, 1000, splits=4)
```
The visualized plan:

![reuse-subquery](https://cloud.githubusercontent.com/assets/40902/17573229/e578d93c-5f0d-11e6-8a3c-0150d81d3aed.png)

## How was this patch tested?

Existing tests.

Author: Davies Liu <davies@databricks.com>

Closes #14548 from davies/subq.
2016-08-11 09:47:19 -07:00
Michael Gummelt 4d496802f5 [SPARK-16952] don't lookup spark home directory when executor uri is set
## What changes were proposed in this pull request?

remove requirement to set spark.mesos.executor.home when spark.executor.uri is used

## How was this patch tested?

unit tests

Author: Michael Gummelt <mgummelt@mesosphere.io>

Closes #14552 from mgummelt/fix-spark-home.
2016-08-11 11:36:20 +01:00
hyukjinkwon 7186e8c318 [SPARK-16886][EXAMPLES][DOC] Fix some examples to be consistent and indentation in documentation
## What changes were proposed in this pull request?

Originally this PR was based on #14491 but I realised that fixing examples are more sensible rather than comments.

This PR fixes three things below:

 - Fix two wrong examples in `structured-streaming-programming-guide.md`. Loading via `read.load(..)` without `as` will be `Dataset<Row>` not `Dataset<String>` in Java.

- Fix indentation across `structured-streaming-programming-guide.md`. Python has 4 spaces and Scala and Java have double spaces. These are inconsistent across the examples.

- Fix `StructuredNetworkWordCountWindowed` and  `StructuredNetworkWordCount` in Java and Scala to initially load `DataFrame` and `Dataset<Row>` to be consistent with the comments and some examples in `structured-streaming-programming-guide.md` and to match Scala and Java to Python one (Python one loads it as `DataFrame` initially).

## How was this patch tested?

N/A

Closes https://github.com/apache/spark/pull/14491

Author: hyukjinkwon <gurwls223@gmail.com>
Author: Ganesh Chand <ganeshchand@Ganeshs-MacBook-Pro-2.local>

Closes #14564 from HyukjinKwon/SPARK-16886.
2016-08-11 11:31:52 +01:00
huangzhaowei a45fefd17e [SPARK-16941] Use concurrentHashMap instead of scala Map in SparkSQLOperationManager.
## What changes were proposed in this pull request?
ThriftServer will have some thread-safe problem in **SparkSQLOperationManager**.
Add a SynchronizedMap trait for the maps in it to avoid this problem.

Details in [SPARK-16941](https://issues.apache.org/jira/browse/SPARK-16941)

## How was this patch tested?
NA

Author: huangzhaowei <carlmartinmax@gmail.com>

Closes #14534 from SaintBacchus/SPARK-16941.
2016-08-11 11:28:28 +01:00
Andrew Ash 8a6b7037bb Correct example value for spark.ssl.YYY.XXX settings
Docs adjustment to:
- link to other relevant section of docs
- correct statement about the only value when actually other values are supported

Author: Andrew Ash <andrew@andrewash.com>

Closes #14581 from ash211/patch-10.
2016-08-11 11:26:57 +01:00
petermaxlee a7b02db457 [SPARK-17015][SQL] group-by/order-by ordinal and arithmetic tests
## What changes were proposed in this pull request?
This patch adds three test files:
1. arithmetic.sql.out
2. order-by-ordinal.sql
3. group-by-ordinal.sql

This includes https://github.com/apache/spark/pull/14594.

## How was this patch tested?
This is a test case change.

Author: petermaxlee <petermaxlee@gmail.com>

Closes #14595 from petermaxlee/SPARK-17015.
2016-08-11 01:43:08 -07:00
petermaxlee 0db373aaf8 [SPARK-17011][SQL] Support testing exceptions in SQLQueryTestSuite
## What changes were proposed in this pull request?
This patch adds exception testing to SQLQueryTestSuite. When there is an exception in query execution, the query result contains the the exception class along with the exception message.

As part of this, I moved some additional test cases for limit from SQLQuerySuite over to SQLQueryTestSuite.

## How was this patch tested?
This is a test harness change.

Author: petermaxlee <petermaxlee@gmail.com>

Closes #14592 from petermaxlee/SPARK-17011.
2016-08-10 23:22:14 -07:00