[SPARK-2060][SQL] Querying JSON Datasets with SQL and DSL in Spark SQL

JIRA: https://issues.apache.org/jira/browse/SPARK-2060

Programming guide: http://yhuai.github.io/site/sql-programming-guide.html

Scala doc of SQLContext: http://yhuai.github.io/site/api/scala/index.html#org.apache.spark.sql.SQLContext

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

Closes #999 from yhuai/newJson and squashes the following commits:

227e89e [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
ce8eedd [Yin Huai] rxin's comments.
bc9ac51 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
94ffdaa [Yin Huai] Remove "get" from method names.
ce31c81 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
e2773a6 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
79ea9ba [Yin Huai] Fix typos.
5428451 [Yin Huai] Newline
1f908ce [Yin Huai] Remove extra line.
d7a005c [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
7ea750e [Yin Huai] marmbrus's comments.
6a5f5ef [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
83013fb [Yin Huai] Update Java Example.
e7a6c19 [Yin Huai] SchemaRDD.javaToPython should convert a field with the StructType to a Map.
6d20b85 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
4fbddf0 [Yin Huai] Programming guide.
9df8c5a [Yin Huai] Python API.
7027634 [Yin Huai] Java API.
cff84cc [Yin Huai] Use a SchemaRDD for a JSON dataset.
d0bd412 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
ab810b0 [Yin Huai] Make JsonRDD private.
6df0891 [Yin Huai] Apache header.
8347f2e [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
66f9e76 [Yin Huai] Update docs and use the entire dataset to infer the schema.
8ffed79 [Yin Huai] Update the example.
a5a4b52 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
4325475 [Yin Huai] If a sampled dataset is used for schema inferring, update the schema of the JsonTable after first execution.
65b87f0 [Yin Huai] Fix sampling...
8846af5 [Yin Huai] API doc.
52a2275 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
0387523 [Yin Huai] Address PR comments.
666b957 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
a2313a6 [Yin Huai] Address PR comments.
f3ce176 [Yin Huai] After type conflict resolution, if a NullType is found, StringType is used.
0576406 [Yin Huai] Add Apache license header.
af91b23 [Yin Huai] Merge remote-tracking branch 'upstream/master' into newJson
f45583b [Yin Huai] Infer the schema of a JSON dataset (a text file with one JSON object per line or a RDD[String] with one JSON object per string) and returns a SchemaRDD.
f31065f [Yin Huai] A query plan or a SchemaRDD can print out its schema.
Revert "SPARK-2038: rename "conf" parameters in the saveAsHadoop functions"

This reverts commit 443f5e1bbcf9ec55e5ce6e4f738a002a47818100.

This commit unfortunately would break source compatibility if users have named
the hadoopConf parameter.
[STREAMING] SPARK-2009 Key not found exception when slow receiver starts

I got "java.util.NoSuchElementException: key not found: 1401756085000 ms" exception when using kafka stream and 1 sec batchPeriod.

Investigation showed that the reason is that ReceiverLauncher.startReceivers is asynchronous (started in a thread).
https://github.com/vchekan/spark/blob/master/streaming/src/main/scala/org/apache/spark/streaming/scheduler/ReceiverTracker.scala#L206

In case of slow starting receiver, such as Kafka, it easily takes more than 2sec to start. In result, no single "compute" will be called on ReceiverInputDStream before first batch job is executed and receivedBlockInfo remains empty (obviously). Batch job will cause ReceiverInputDStream.getReceivedBlockInfo call and "key not found" exception.

The patch makes getReceivedBlockInfo more robust by tolerating missing values.

Author: Vadim Chekan <kot.begemot@gmail.com>

Closes #961 from vchekan/branch-1.0 and squashes the following commits:

e86f82b [Vadim Chekan] Fixed indentation
4609563 [Vadim Chekan] Key not found exception: if receiver is slow to start, it is possible that getReceivedBlockInfo will be called before compute has been called
(cherry picked from commit 26f6b989312a9a48a27a23ecc68702bd14032e55)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-2176][SQL] Extra unnecessary exchange operator in the result of an explain command

```
hql("explain select * from src group by key").collect().foreach(println)

[ExplainCommand [plan#27:0]]
[ Aggregate false, [key#25], [key#25,value#26]]
[  Exchange (HashPartitioning [key#25:0], 200)]
[   Exchange (HashPartitioning [key#25:0], 200)]
[    Aggregate true, [key#25], [key#25]]
[     HiveTableScan [key#25,value#26], (MetastoreRelation default, src, None), None]
```

There are two exchange operators.

However, if we do not use explain...
```
hql("select * from src group by key")

res4: org.apache.spark.sql.SchemaRDD =
SchemaRDD[8] at RDD at SchemaRDD.scala:100
== Query Plan ==
Aggregate false, [key#8], [key#8,value#9]
 Exchange (HashPartitioning [key#8:0], 200)
  Aggregate true, [key#8], [key#8]
   HiveTableScan [key#8,value#9], (MetastoreRelation default, src, None), None
```
The plan is fine.

The cause of this bug is explained below.

When we create an `execution.ExplainCommand`, we use the `executedPlan` as the child of this `ExplainCommand`. But, this `executedPlan` is prepared for execution again when we generate the `executedPlan` for the `ExplainCommand`. Basically, `prepareForExecution` is called twice on a physical plan. Because after `prepareForExecution` we have already bounded those references (in `BoundReference`s), `AddExchange` cannot figure out we are using the same partitioning (we use `AttributeReference`s to create an `ExchangeOperator` and then those references will be changed to `BoundReference`s after `prepareForExecution` is called). So, an extra `ExchangeOperator` is inserted.

I think in `CommandStrategy`, we should just use the `sparkPlan` (`sparkPlan` is the input of `prepareForExecution`) to initialize the `ExplainCommand` instead of using `executedPlan`.

The link to JIRA: https://issues.apache.org/jira/browse/SPARK-2176

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

Closes #1116 from yhuai/SPARK-2176 and squashes the following commits:

197c19c [Yin Huai] Use sparkPlan to initialize a Physical Explain Command instead of using executedPlan.
[SPARK-2162] Double check in doGetLocal to avoid read on removed block.

other wise, it will either read in vain in memory level case, or throw exception in disk level case when it believe the block is there while actually it had been removed.

Author: Raymond Liu <raymond.liu@intel.com>

Closes #1103 from colorant/bm and squashes the following commits:

daac114 [Raymond Liu] Address comments
d1ea287 [Raymond Liu] Double check in doGetLocal to avoid read on removed block.
Updated the comment for SPARK-2162.

A follow up on #1103

@andrewor14

Author: Reynold Xin <rxin@apache.org>

Closes #1117 from rxin/SPARK-2162 and squashes the following commits:

a4231de [Reynold Xin] Updated the comment for SPARK-2162.
[SPARK-1466] Raise exception if pyspark Gateway process doesn't start.

If the gateway process fails to start correctly (e.g., because JAVA_HOME isn't set correctly, there's no Spark jar, etc.), right now pyspark fails because of a very difficult-to-understand error, where we try to parse stdout to get the port where Spark started and there's nothing there. This commit properly catches the error and throws an exception that includes the stderr output for much easier debugging.

Thanks to @shivaram and @stogers for helping to fix this issue!

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #383 from kayousterhout/pyspark and squashes the following commits:

36dd54b [Kay Ousterhout] [SPARK-1466] Raise exception if Gateway process doesn't start.
SPARK-2158 Clean up core/stdout file from FileAppenderSuite

@tdas

Author: Mark Hamstra <markhamstra@gmail.com>

Closes #1100 from markhamstra/SPARK-2158 and squashes the following commits:

ae8e069 [Mark Hamstra] Response to TD's review
2f1e201 [Mark Hamstra] Cleanup 'stdout' file within FileAppenderSuite
Remove unicode operator from RDD.scala

Some IDEs don’t support unicode characters in source code. Check if this breaks binary compatibility.

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1119 from dorx/unicode and squashes the following commits:

05618c3 [Doris Xin] Remove unicode operator from RDD.scala
[SPARK-2184][SQL] AddExchange isn't idempotent

...redPartitioning.

Author: Michael Armbrust <michael@databricks.com>

Closes #1122 from marmbrus/fixAddExchange and squashes the following commits:

3417537 [Michael Armbrust] Don't bind partitioning expressions as that breaks comparison with requiredPartitioning.
Squishing a typo bug before it causes real harm

in updateNumRows method in RowMatrix

Author: Doris Xin <doris.s.xin@gmail.com>

Closes #1125 from dorx/updateNumRows and squashes the following commits:

8564aef [Doris Xin] Squishing a typo bug before it causes real harm
[SPARK-2187] Explain should not run the optimizer twice.

@yhuai @marmbrus @concretevitamin

Author: Reynold Xin <rxin@apache.org>

Closes #1123 from rxin/explain and squashes the following commits:

def83b0 [Reynold Xin] Update unit tests for explain.
a9d3ba8 [Reynold Xin] [SPARK-2187] Explain should not run the optimizer twice.
Minor fix

The value "env" is never used in SparkContext.scala.
Add detailed comment for method setDelaySeconds in MetadataCleaner.scala instead of the unsure one.

Author: WangTao <barneystinson@aliyun.com>

Closes #1105 from WangTaoTheTonic/master and squashes the following commits:

688358e [WangTao] Minor fix
[SPARK-2051]In yarn.ClientBase spark.yarn.dist.* do not work

Author: witgo <witgo@qq.com>

Closes #969 from witgo/yarn_ClientBase and squashes the following commits:

8117765 [witgo] review commit
3bdbc52 [witgo] Merge branch 'master' of https://github.com/apache/spark into yarn_ClientBase
5261b6c [witgo] fix sys.props.get("SPARK_YARN_DIST_FILES")
e3c1107 [witgo] update docs
b6a9aa1 [witgo] merge master
c8b4554 [witgo] review commit
2f48789 [witgo] Merge branch 'master' of https://github.com/apache/spark into yarn_ClientBase
8d7b82f [witgo] Merge branch 'master' of https://github.com/apache/spark into yarn_ClientBase
1048549 [witgo] remove Utils.resolveURIs
871f1db [witgo] add spark.yarn.dist.* documentation
41bce59 [witgo] review commit
35d6fa0 [witgo] move to ClientArguments
55d72fc [witgo] Merge branch 'master' of https://github.com/apache/spark into yarn_ClientBase
9cdff16 [witgo] review commit
8bc2f4b [witgo] review commit
20e667c [witgo] Merge branch 'master' into yarn_ClientBase
0961151 [witgo] merge master
ce609fc [witgo] Merge branch 'master' into yarn_ClientBase
8362489 [witgo] yarn.ClientBase spark.yarn.dist.* do not work
[SPARK-2191][SQL] Make sure InsertIntoHiveTable doesn't execute more than once.

Author: Michael Armbrust <michael@databricks.com>

Closes #1129 from marmbrus/doubleCreateAs and squashes the following commits:

9c6d9e4 [Michael Armbrust] Fix typo.
5128fe2 [Michael Armbrust] Make sure InsertIntoHiveTable doesn't execute each time you ask for its result.
[SPARK-2151] Recognize memory format for spark-submit

int format expected for input memory parameter when spark-submit is invoked in standalone cluster mode. Make it consistent with rest of Spark.

Author: nravi <nravi@c1704.halxg.cloudera.com>

Closes #1095 from nishkamravi2/master and squashes the following commits:

2b630f9 [nravi] Accept memory input as "30g", "512M" instead of an int value, to be consistent with rest of Spark
3bf8fad [nravi] Merge branch 'master' of https://github.com/apache/spark
5423a03 [nravi] Merge branch 'master' of https://github.com/apache/spark
eb663ca [nravi] Merge branch 'master' of https://github.com/apache/spark
df2aeb1 [nravi] Improved fix for ConcurrentModificationIssue (Spark-1097, Hadoop-10456)
6b840f0 [nravi] Undo the fix for SPARK-1758 (the problem is fixed)
5108700 [nravi] Fix in Spark for the Concurrent thread modification issue (SPARK-1097, HADOOP-10456)
681b36f [nravi] Fix for SPARK-1758: failing test org.apache.spark.JavaAPISuite.wholeTextFiles
A few minor Spark SQL Scaladoc fixes.

Author: Reynold Xin <rxin@apache.org>

Closes #1139 from rxin/sparksqldoc and squashes the following commits:

c3049d8 [Reynold Xin] Fixed line length.
66dc72c [Reynold Xin] A few minor Spark SQL Scaladoc fixes.
HOTFIX: SPARK-2208 local metrics tests can fail on fast machines

Author: Patrick Wendell <pwendell@gmail.com>

Closes #1141 from pwendell/hotfix and squashes the following commits:

83e4c79 [Patrick Wendell] HOTFIX: SPARK-2208 local metrics tests can fail on fast machines
More minor scaladoc cleanup for Spark SQL.

Author: Reynold Xin <rxin@apache.org>

Closes #1142 from rxin/sqlclean and squashes the following commits:

67a789e [Reynold Xin] More minor scaladoc cleanup for Spark SQL.
[SQL] Improve Speed of InsertIntoHiveTable

Author: Michael Armbrust <michael@databricks.com>

Closes #1130 from marmbrus/noFunctional and squashes the following commits:

ccdb68c [Michael Armbrust] Remove functional programming and Array allocations from fast path in InsertIntoHiveTable.