[SPARK-2852][MLLIB] Separate model from IDF/StandardScaler algorithms

This is part of SPARK-2828:

1. separate IDF model from IDF algorithm (which generates a model)
2. separate StandardScaler model from StandardScaler

CC: dbtsai

Author: Xiangrui Meng <meng@databricks.com>

Closes #1814 from mengxr/feature-api-update and squashes the following commits:

40d863b [Xiangrui Meng] move mean and variance to model
48a0fff [Xiangrui Meng] separate Model from StandardScaler algorithm
89f3486 [Xiangrui Meng] update IDF to separate Model from Algorithm
SPARK-2905 Fixed path sbin => bin

Author: Oleg Danilov <oleg.danilov@wandisco.com>

Closes #1835 from dosoft/SPARK-2905 and squashes the following commits:

4df423c [Oleg Danilov] SPARK-2905 Fixed path sbin => bin
SPARK-2899 Doc generation is back to working in new SBT Build.

The reason for this bug was introduciton of OldDeps project. It had to be excluded to prevent unidocs from trying to put it on "docs compile" classpath.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #1830 from ScrapCodes/doc-fix and squashes the following commits:

e5d52e6 [Prashant Sharma] SPARK-2899 Doc generation is back to working in new SBT Build.
SPARK-2787: Make sort-based shuffle write files directly when there's no sorting/aggregation and # partitions is small

As described in https://issues.apache.org/jira/browse/SPARK-2787, right now sort-based shuffle is more expensive than hash-based for map operations that do no partial aggregation or sorting, such as groupByKey. This is because it has to serialize each data item twice (once when spilling to intermediate files, and then again when merging these files object-by-object). This patch adds a code path to just write separate files directly if the # of output partitions is small, and concatenate them at the end to produce a sorted file.

On the unit test side, I added some tests that force or don't force this bypass path to be used, and checked that our tests for other features (e.g. all the operations) cover both cases.

Author: Matei Zaharia <matei@databricks.com>

Closes #1799 from mateiz/SPARK-2787 and squashes the following commits:

88cf26a [Matei Zaharia] Fix rebase
10233af [Matei Zaharia] Review comments
398cb95 [Matei Zaharia] Fix looking up shuffle manager in conf
ca3efd9 [Matei Zaharia] Add docs for shuffle manager properties, and allow short names for them
d0ae3c5 [Matei Zaharia] Fix some comments
90d084f [Matei Zaharia] Add code path to bypass merge-sort in ExternalSorter, and tests
31e5d7c [Matei Zaharia] Move existing logic for writing partitioned files into ExternalSorter
SPARK-2565. Update ShuffleReadMetrics as blocks are fetched

Author: Sandy Ryza <sandy@cloudera.com>

Closes #1507 from sryza/sandy-spark-2565 and squashes the following commits:

74dad41 [Sandy Ryza] SPARK-2565. Update ShuffleReadMetrics as blocks are fetched
[SPARK-2904] Remove non-used local variable in SparkSubmitArguments

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #1834 from sarutak/SPARK-2904 and squashes the following commits:

38e7d45 [Kousuke Saruta] Removed non-used variable in SparkSubmitArguments
[SPARK-2911]: provide rdd.parent[T](j) to obtain jth parent RDD

Author: Erik Erlandson <eerlands@redhat.com>

Closes #1841 from erikerlandson/spark-2911-pr and squashes the following commits:

4699e2f [Erik Erlandson] [SPARK-2911]: provide rdd.parent[T](j) to obtain jth parent RDD
[SPARK-2888] [SQL] Fix addColumnMetadataToConf in HiveTableScan

JIRA: https://issues.apache.org/jira/browse/SPARK-2888

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

Closes #1817 from yhuai/fixAddColumnMetadataToConf and squashes the following commits:

fba728c [Yin Huai] Fix addColumnMetadataToConf.
[SPARK-2908] [SQL] JsonRDD.nullTypeToStringType does not convert all NullType to StringType

JIRA: https://issues.apache.org/jira/browse/SPARK-2908

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

Closes #1840 from yhuai/SPARK-2908 and squashes the following commits:

86e833e [Yin Huai] Update test.
cb11759 [Yin Huai] nullTypeToStringType should check columns with the type of array of structs.
[SPARK-2877] [SQL] MetastoreRelation should use SparkClassLoader when creating the tableDesc

JIRA: https://issues.apache.org/jira/browse/SPARK-2877

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

Closes #1806 from yhuai/SPARK-2877 and squashes the following commits:

4142bcb [Yin Huai] Use Spark's classloader.
[SPARK-2919] [SQL] Basic support for analyze command in HiveQl

The command we will support is
```
ANALYZE TABLE tablename COMPUTE STATISTICS noscan
```
Other cases shown in https://cwiki.apache.org/confluence/display/Hive/StatsDev#StatsDev-ExistingTables will still be treated as Hive native commands.

JIRA: https://issues.apache.org/jira/browse/SPARK-2919

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

Closes #1848 from yhuai/sqlAnalyze and squashes the following commits:

0b79d36 [Yin Huai] Typo and format.
c59d94b [Yin Huai] Support "ANALYZE TABLE tableName COMPUTE STATISTICS noscan".
[SPARK-2700] [SQL] Hidden files (such as .impala_insert_staging) should be filtered out by sqlContext.parquetFile

Author: chutium <teng.qiu@gmail.com>

Closes #1691 from chutium/SPARK-2700 and squashes the following commits:

b76ae8c [chutium] [SPARK-2700] [SQL] fixed styling issue
d75a8bd [chutium] [SPARK-2700] [SQL] Hidden files (such as .impala_insert_staging) should be filtered out by sqlContext.parquetFile
[SPARK-1997][MLLIB] update breeze to 0.9

0.9 dependences (this version doesn't depend on scalalogging and I excluded commons-math3 from its transitive dependencies):
~~~
+-org.scalanlp:breeze_2.10:0.9 [S]
  +-com.github.fommil.netlib:core:1.1.2
  +-com.github.rwl:jtransforms:2.4.0
  +-net.sf.opencsv:opencsv:2.3
  +-net.sourceforge.f2j:arpack_combined_all:0.1
  +-org.scalanlp:breeze-macros_2.10:0.3.1 [S]
  | +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
  |
  +-org.slf4j:slf4j-api:1.7.5
  +-org.spire-math:spire_2.10:0.7.4 [S]
    +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
    |
    +-org.spire-math:spire-macros_2.10:0.7.4 [S]
      +-org.scalamacros:quasiquotes_2.10:2.0.0 [S]
~~~

Closes #1749

CC: witgo avati

Author: Xiangrui Meng <meng@databricks.com>

Closes #1857 from mengxr/breeze-0.9 and squashes the following commits:

7fc16b6 [Xiangrui Meng] don't know why but exclude a private method for mima
dcc502e [Xiangrui Meng] update breeze to 0.9
[SPARK-2897][SPARK-2920]TorrentBroadcast does use the serializer class specified in the spark option "spark.serializer"

Author: GuoQiang Li <witgo@qq.com>

Closes #1836 from witgo/SPARK-2897 and squashes the following commits:

23cdc5b [GuoQiang Li] review commit
ada4fba [GuoQiang Li] TorrentBroadcast does not support broadcast compression
fb91792 [GuoQiang Li] org.apache.spark.broadcast.TorrentBroadcast does use the serializer class specified in the spark option "spark.serializer"
[Web UI]Make decision order of Worker's WebUI port consistent with Master's

The decision order of Worker's WebUI port is "--webui-port", SPARK_WORKER_WEBUI_POR, 8081(default), spark.worker.ui.port. But in Master, the order is "--webui-port", spark.master.ui.port, SPARK_MASTER_WEBUI_PORT and 8080(default).

So we change the order in Worker's to keep it consistent with Master.

Author: WangTao <barneystinson@aliyun.com>

Closes #1838 from WangTaoTheTonic/reOrder and squashes the following commits:

460f4d4 [WangTao] Make decision order of Worker's WebUI consistent with Master's
[SPARK-2911] apply parent[T](j) to clarify UnionRDD code

References to dependencies(j) for actually obtaining RDD parents are less common than I originally estimated.   It does clarify UnionRDD (also will clarify some of my other PRs)

Use of firstParent[T] is ubiquitous, but not as sure that benefits from being replaced with parent(0)[T].

Author: Erik Erlandson <eerlands@redhat.com>

Closes #1858 from erikerlandson/spark-2911-pr2 and squashes the following commits:

7ffea74 [Erik Erlandson] [SPARK-2911] apply parent[T](j) to clarify UnionRDD code
[SPARK-2635] Fix race condition at SchedulerBackend.isReady in standalone mode

In SPARK-1946(PR #900), configuration <code>spark.scheduler.minRegisteredExecutorsRatio</code> was introduced. However, in standalone mode, there is a race condition where isReady() can return true because totalExpectedExecutors has not been correctly set.

Because expected executors is uncertain in standalone mode, the PR try to use CPU cores(<code>--total-executor-cores</code>) as expected resources to judge whether SchedulerBackend is ready.

Author: li-zhihui <zhihui.li@intel.com>
Author: Li Zhihui <zhihui.li@intel.com>

Closes #1525 from li-zhihui/fixre4s and squashes the following commits:

e9a630b [Li Zhihui] Rename variable totalExecutors and clean codes
abf4860 [Li Zhihui] Push down variable totalExpectedResources to children classes
ca54bd9 [li-zhihui] Format log with String interpolation
88c7dc6 [li-zhihui] Few codes and docs refactor
41cf47e [li-zhihui] Fix race condition at SchedulerBackend.isReady in standalone mode
[SPARK-2861] Fix Doc comment of histogram method

Tested and ready to merge.

Author: Chandan Kumar <chandan.kumar@imaginea.com>

Closes #1786 from nrchandan/spark-2861 and squashes the following commits:

cb0bc1e [Chandan Kumar] [SPARK-2861] Fix a typo in the histogram doc comment
6a2a71b [Chandan Kumar] SPARK-2861. Fix Doc comment of histogram method
[SPARK-1766] sorted functions to meet pedantic requirements

Pedantry is underrated

Author: Chris Cope <ccope@resilientscience.com>

Closes #1859 from copester/master and squashes the following commits:

0fb4499 [Chris Cope] [SPARK-1766] sorted functions to meet pedantic requirements
[SPARK-2894] spark-shell doesn't accept flags

As sryza reported, spark-shell doesn't accept any flags.
The root cause is wrong usage of spark-submit in spark-shell and it come to the surface by #1801

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1715, Closes #1864, and Closes #1861

Closes #1825 from sarutak/SPARK-2894 and squashes the following commits:

47f3510 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-2894
2c899ed [Kousuke Saruta] Removed useless code from java_gateway.py
98287ed [Kousuke Saruta] Removed useless code from java_gateway.py
513ad2e [Kousuke Saruta] Modified util.sh to enable to use option including white spaces
28a374e [Kousuke Saruta] Modified java_gateway.py to recognize arguments
5afc584 [Cheng Lian] Filter out spark-submit options when starting Python gateway
e630d19 [Cheng Lian] Fixing pyspark and spark-shell CLI options