[SPARK-4372][MLLIB] Make LR and SVM's default parameters consistent in Scala and Python

The current default regParam is 1.0 and regType is claimed to be none in Python (but actually it is l2), while regParam = 0.0 and regType is L2 in Scala. We should make the default values consistent. This PR sets the default regType to L2 and regParam to 0.01. Note that the default regParam value in LIBLINEAR (and hence scikit-learn) is 1.0. However, we use average loss instead of total loss in our formulation. Hence regParam=1.0 is definitely too heavy.

In LinearRegression, we set regParam=0.0 and regType=None, because we have separate classes for Lasso and Ridge, both of which use regParam=0.01 as the default.

davies atalwalkar

Author: Xiangrui Meng <meng@databricks.com>

Closes #3232 from mengxr/SPARK-4372 and squashes the following commits:

9979837 [Xiangrui Meng] update Ridge/Lasso to use default regParam 0.01 cast input arguments
d3ba096 [Xiangrui Meng] change 'none' back to None
1909a6e [Xiangrui Meng] change default regParam to 0.01 and regType to L2 in LR and SVM
[SPARK-4310][WebUI] Sort 'Submitted' column in Stage page by time

Author: zsxwing <zsxwing@gmail.com>

Closes #3179 from zsxwing/SPARK-4310 and squashes the following commits:

b0d29f5 [zsxwing] Sort 'Submitted' column in Stage page by time
[SPARK-3722][Docs]minor improvement and fix in docs

https://issues.apache.org/jira/browse/SPARK-3722

Author: WangTao <barneystinson@aliyun.com>

Closes #2579 from WangTaoTheTonic/docsWork and squashes the following commits:

6f91cec [WangTao] use more wording express
29d22fa [WangTao] delete the specified version link
34cb4ea [WangTao] Update running-on-yarn.md
4ee1a26 [WangTao] minor improvement and fix in docs
[SPARK-4394][SQL] Data Sources API Improvements

This PR adds two features to the data sources API:
 - Support for pushing down `IN` filters
 - The ability for relations to optionally provide information about their `sizeInBytes`.

Author: Michael Armbrust <michael@databricks.com>

Closes #3260 from marmbrus/sourcesImprovements and squashes the following commits:

9a5e171 [Michael Armbrust] Use method instead of configuration directly
99c0e6b [Michael Armbrust] Add support for sizeInBytes.
416f167 [Michael Armbrust] Support for IN in data sources API.
2a04ab3 [Michael Armbrust] Simplify implementation of InSet.
[SPARK-4398][PySpark] specialize sc.parallelize(xrange)

`sc.parallelize(range(1 << 20), 1).count()` may take 15 seconds to finish and the rdd object stores the entire list, making task size very large. This PR adds a specialized version for xrange.

JoshRosen davies

Author: Xiangrui Meng <meng@databricks.com>

Closes #3264 from mengxr/SPARK-4398 and squashes the following commits:

8953c41 [Xiangrui Meng] follow davies' suggestion
cbd58e3 [Xiangrui Meng] specialize sc.parallelize(xrange)
[Spark Core] SPARK-4380 Edit spilling log from MB to B

https://issues.apache.org/jira/browse/SPARK-4380

Author: Hong Shen <hongshen@tencent.com>

Closes #3243 from shenh062326/spark_change and squashes the following commits:

4653378 [Hong Shen] Edit spilling log from MB to B
21ee960 [Hong Shen] Edit spilling log from MB to B
e9145e8 [Hong Shen] Edit spilling log from MB to B
da761c2 [Hong Shen] Edit spilling log from MB to B
946351c [Hong Shen] Edit spilling log from MB to B
SPARK-3663 Document SPARK_LOG_DIR and SPARK_PID_DIR

These descriptions are from the header of spark-daemon.sh

Author: Andrew Ash <andrew@andrewash.com>

Closes #2518 from ash211/SPARK-3663 and squashes the following commits:

058b257 [Andrew Ash] Complete hanging clause in SPARK_PID_DIR description
a17cb4b [Andrew Ash] Update docs for default locations per SPARK-4110
af89096 [Andrew Ash] SPARK-3663 Document SPARK_LOG_DIR and SPARK_PID_DIR
[SPARK-4313][WebUI][Yarn] Fix link issue of the executor thread dump page in yarn-cluster mode

In yarn-cluster mode, the Web UI is running behind a yarn proxy server. Some features(or bugs?) of yarn proxy server will break the links for thread dump.

1. Yarn proxy server will do http redirect internally, so if opening `http://example.com:8088/cluster/app/application_1415344371838_0012/executors`, it will fetch `http://example.com:8088/cluster/app/application_1415344371838_0012/executors/` and return the content but won't change the link in the browser. Then when a user clicks `Thread Dump`, it will jump to `http://example.com:8088/proxy/application_1415344371838_0012/threadDump/?executorId=2`. This is a wrong link. The correct link should be `http://example.com:8088/proxy/application_1415344371838_0012/executors/threadDump/?executorId=2`.

Adding "/" to the tab links will fix it.

2. Yarn proxy server has a bug about the URL encode/decode. When a user accesses `http://example.com:8088/proxy/application_1415344371838_0006/executors/threadDump/?executorId=%3Cdriver%3E`, the yarn proxy server will require `http://example.com:36429/executors/threadDump/?executorId=%25253Cdriver%25253E`. But Spark web server expects `http://example.com:36429/executors/threadDump/?executorId=%3Cdriver%3E`. Related to [YARN-2844](https://issues.apache.org/jira/browse/YARN-2844).

For now, it's a tricky approach to bypass the yarn bug.

![threaddump](https://cloud.githubusercontent.com/assets/1000778/4972567/d1ccba64-68ad-11e4-983e-257530cef35a.png)

Author: zsxwing <zsxwing@gmail.com>

Closes #3183 from zsxwing/SPARK-4313 and squashes the following commits:

3379ca8 [zsxwing] Encode the executor id in the thread dump link and update the comment
abfa063 [zsxwing] Fix link issue of the executor thread dump page in yarn-cluster mode
Update failed assert text to match code in SizeEstimatorSuite

Author: Jeff Hammerbacher <jeff.hammerbacher@gmail.com>

Closes #3242 from hammer/patch-1 and squashes the following commits:

f88d635 [Jeff Hammerbacher] Update failed assert text to match code in SizeEstimatorSuite
[SPARK-4239] [SQL] support view in HiveQl

Currently still not support view like

CREATE VIEW view3(valoo)
TBLPROPERTIES ("fear" = "factor")
AS SELECT upper(value) FROM src WHERE key=86;

because the text in metastore for this view is like

select \`_c0\` as \`valoo\` from (select upper(\`src\`.\`value\`) from \`default\`.\`src\` where ...) \`view3\`

while catalyst cannot resolve \`_c0\` for this query.
For view without colname definition in parentheses, it works fine.

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #3131 from adrian-wang/view and squashes the following commits:

8a56fd6 [Daoyuan Wang] michael's comments
e46c056 [Daoyuan Wang] add some golden file
079290a [Daoyuan Wang] remove useless import
88afcad [Daoyuan Wang] support view in HiveQl
[SPARK-4245][SQL] Fix containsNull of the result ArrayType of CreateArray expression.

The `containsNull` of the result `ArrayType` of `CreateArray` should be `true` only if the children is empty or there exists nullable child.

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

Closes #3110 from ueshin/issues/SPARK-4245 and squashes the following commits:

6f64746 [Takuya UESHIN] Move equalsIgnoreNullability method into DataType.
5a90e02 [Takuya UESHIN] Refine InsertIntoHiveType and add some comments.
cbecba8 [Takuya UESHIN] Fix a test title.
884ec37 [Takuya UESHIN] Merge branch 'master' into issues/SPARK-4245
3c5274b [Takuya UESHIN] Add tests to insert data of types ArrayType / MapType / StructType with nullability is false into Hive table.
41a94a9 [Takuya UESHIN] Replace InsertIntoTable with InsertIntoHiveTable if data types ignoring nullability are same.
43e6ef5 [Takuya UESHIN] Fix containsNull for empty array.
778e997 [Takuya UESHIN] Fix containsNull of the result ArrayType of CreateArray expression.
SPARK-4375. no longer require -Pscala-2.10

It seems like the winds might have moved away from this approach, but wanted to post the PR anyway because I got it working and to show what it would look like.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3239 from sryza/sandy-spark-4375 and squashes the following commits:

0ffbe95 [Sandy Ryza] Enable -Dscala-2.11 in sbt
cd42d94 [Sandy Ryza] Update doc
f6644c3 [Sandy Ryza] SPARK-4375 take 2
[SPARK-4333][SQL]  Correctly log number of iterations in RuleExecutor

When iterator of RuleExecutor breaks, the num of iterator should be (iteration - 1) not (iteration ).Because log looks like "Fixed point reached for batch ${batch.name} after 3 iterations.", but it did 2 iterations really!

Author: DoingDone9 <799203320@qq.com>

Closes #3180 from DoingDone9/issue_01 and squashes the following commits:

571e2ed [DoingDone9] Update RuleExecutor.scala
46514b6 [DoingDone9] When iterator of RuleExecutor breaks, the num of iterator should be iteration - 1 not iteration.
[SPARK-4062][Streaming]Add ReliableKafkaReceiver in Spark Streaming Kafka connector

Add ReliableKafkaReceiver in Kafka connector to prevent data loss if WAL in Spark Streaming is enabled. Details and design doc can be seen in [SPARK-4062](https://issues.apache.org/jira/browse/SPARK-4062).

Author: jerryshao <saisai.shao@intel.com>
Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: Saisai Shao <saisai.shao@intel.com>

Closes #2991 from jerryshao/kafka-refactor and squashes the following commits:

5461f1c [Saisai Shao] Merge pull request #8 from tdas/kafka-refactor3
eae4ad6 [Tathagata Das] Refectored KafkaStreamSuiteBased to eliminate KafkaTestUtils and made Java more robust.
fab14c7 [Tathagata Das] minor update.
149948b [Tathagata Das] Fixed mistake
14630aa [Tathagata Das] Minor updates.
d9a452c [Tathagata Das] Minor updates.
ec2e95e [Tathagata Das] Removed the receiver's locks and essentially reverted to Saisai's original design.
2a20a01 [jerryshao] Address some comments
9f636b3 [Saisai Shao] Merge pull request #5 from tdas/kafka-refactor
b2b2f84 [Tathagata Das] Refactored Kafka receiver logic and Kafka testsuites
e501b3c [jerryshao] Add Mima excludes
b798535 [jerryshao] Fix the missed issue
e5e21c1 [jerryshao] Change to while loop
ea873e4 [jerryshao] Further address the comments
98f3d07 [jerryshao] Fix comment style
4854ee9 [jerryshao] Address all the comments
96c7a1d [jerryshao] Update the ReliableKafkaReceiver unit test
8135d31 [jerryshao] Fix flaky test
a949741 [jerryshao] Address the comments
16bfe78 [jerryshao] Change the ordering of imports
0894aef [jerryshao] Add some comments
77c3e50 [jerryshao] Code refactor and add some unit tests
dd9aeeb [jerryshao] Initial commit for reliable Kafka receiver
[SPARK-4390][SQL] Handle NaN cast to decimal correctly

Author: Michael Armbrust <michael@databricks.com>

Closes #3256 from marmbrus/NanDecimal and squashes the following commits:

4c3ba46 [Michael Armbrust] fix style
d360f83 [Michael Armbrust] Handle NaN cast to decimal
[SPARK-4391][SQL] Configure parquet filters using SQLConf

This is more uniform with the rest of SQL configuration and allows it to be turned on and off without restarting the SparkContext.  In this PR I also turn off filter pushdown by default due to a number of outstanding issues (in particular SPARK-4258).  When those are fixed we should turn it back on by default.

Author: Michael Armbrust <michael@databricks.com>

Closes #3258 from marmbrus/parquetFilters and squashes the following commits:

5655bfe [Michael Armbrust] Remove extra line.
15e9a98 [Michael Armbrust] Enable filters for tests
75afd39 [Michael Armbrust] Fix comments
78fa02d [Michael Armbrust] off by default
e7f9e16 [Michael Armbrust] First draft of correctly configuring parquet filter pushdown
[SQL] Minor cleanup of comments, errors and override.

Author: Michael Armbrust <michael@databricks.com>

Closes #3257 from marmbrus/minorCleanup and squashes the following commits:

d8b5abc [Michael Armbrust] Use interpolation.
2fdf903 [Michael Armbrust] Better error message when coalesce can't be resolved.
f9fa6cf [Michael Armbrust] Methods in a final class do not also need to be final, use override.
199fd98 [Michael Armbrust] Fix typo
[SQL] Don't shuffle code generated rows

When sort based shuffle and code gen are on we were trying to ship the code generated rows during a shuffle.  This doesn't work because the classes don't exist on the other side.  Instead we now copy into a generic row before shipping.

Author: Michael Armbrust <michael@databricks.com>

Closes #3263 from marmbrus/aggCodeGen and squashes the following commits:

f6ba8cf [Michael Armbrust] fix and test
[SPARK-4322][SQL] Enables struct fields as sub expressions of grouping fields

While resolving struct fields, the resulted `GetField` expression is wrapped with an `Alias` to make it a named expression. Assume `a` is a struct instance with a field `b`, then `"a.b"` will be resolved as `Alias(GetField(a, "b"), "b")`. Thus, for this following SQL query:

```sql
SELECT a.b + 1 FROM t GROUP BY a.b + 1
```

the grouping expression is

```scala
Add(GetField(a, "b"), Literal(1, IntegerType))
```

while the aggregation expression is

```scala
Add(Alias(GetField(a, "b"), "b"), Literal(1, IntegerType))
```

This mismatch makes the above SQL query fail during the both analysis and execution phases. This PR fixes this issue by removing the alias when substituting aggregation expressions.

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Author: Cheng Lian <lian@databricks.com>

Closes #3248 from liancheng/spark-4322 and squashes the following commits:

23a46ea [Cheng Lian] Code simplification
dd20a79 [Cheng Lian] Should only trim aliases around `GetField`s
7f46532 [Cheng Lian] Enables struct fields as sub expressions of grouping fields
[SPARK-4386] Improve performance when writing Parquet files.

If you profile the writing of a Parquet file, the single worst time consuming call inside of org.apache.spark.sql.parquet.MutableRowWriteSupport.write is actually in the scala.collection.AbstractSequence.size call. This is because the size call actually ends up COUNTING the elements in a scala.collection.LinearSeqOptimized.length ("optimized?").

This doesn't need to be done. "size" is called repeatedly where needed rather than called once at the top of the method and stored in a 'val'.

Author: Jim Carroll <jim@dontcallme.com>

Closes #3254 from jimfcarroll/parquet-perf and squashes the following commits:

30cc0b5 [Jim Carroll] Improve performance when writing Parquet files.