This is a WIP patch for SPARK-8844  for collecting reviews.

This bug is about reading an empty DataFrame. in readCol(),
      lapply(1:numRows, function(x) {
does not take into consideration the case where numRows = 0.

Will add unit test case.

Author: Sun Rui <rui.sun@intel.com>

Closes #7419 from sun-rui/SPARK-8844.

The `initialSize` argument of `ColumnBuilder.initialize()` should be the
number of rows rather than bytes.  However `InMemoryColumnarTableScan`
passes in a byte size, which makes Spark SQL allocate more memory than
necessary when building in-memory columnar buffers.

Author: Kun Xu <viper_kun@163.com>

Closes #8189 from viper-kun/errorSize.

Recently, PySpark ML streaming tests have been flaky, most likely because of the batches not being processed in time.  Proposal: Replace the use of _ssc_wait (which waits for a fixed amount of time) with a method which waits for a fixed amount of time but can terminate early based on a termination condition method.  With this, we can extend the waiting period (to make tests less flaky) but also stop early when possible (making tests faster on average, which I verified locally).

CC: mengxr tdas freeman-lab

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #8087 from jkbradley/streaming-ml-tests.

We should skip unresolved `LogicalPlan`s for `PullOutNondeterministic`, as calling `output` on unresolved `LogicalPlan` will produce confusing error message.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #8203 from cloud-fan/error-msg and squashes the following commits:

1c67ca7 [Wenchen Fan] move test
7593080 [Wenchen Fan] correct error message for aggregate

Tiny modification to a few comments ```sbt publishLocal``` work again.

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

Closes #8209 from hvanhovell/SPARK-9980.

The BYTE_ARRAY_OFFSET could be different in JVM with different configurations (for example, different heap size, 24 if heap > 32G, otherwise 16), so offset of UTF8String is not portable, we should handler that during serialization.

Author: Davies Liu <davies@databricks.com>

Closes #8210 from davies/serialize_utf8string.

Author: zc he <farseer90718@gmail.com>

Closes #8188 from farseer90718/farseer-patch-1.

This pull request creates a new operator interface that is more similar to traditional database query iterators (with open/close/next/get).

These local operators are not currently used anywhere, but will become the basis for SPARK-9983 (local physical operators for query execution).

cc zsxwing

Author: Reynold Xin <rxin@databricks.com>

Closes #8212 from rxin/SPARK-9984.

This PR enforce dynamic partition column data type requirements by adding analysis rules.

JIRA: https://issues.apache.org/jira/browse/SPARK-8887

Author: Yijie Shen <henry.yijieshen@gmail.com>

Closes #8201 from yjshen/dynamic_partition_columns.

Also alias the ExtractValue instead of wrapping it with UnresolvedAlias when resolve attribute in LogicalPlan, as this alias will be trimmed if it's unnecessary.

Based on #7957 without the changes to mllib, but instead maintaining earlier behavior when using `withColumn` on expressions that already have metadata.

Author: Wenchen Fan <cloud0fan@outlook.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #8215 from marmbrus/pr/7957.

Author: Davies Liu <davies@databricks.com>

Closes #8219 from davies/fix_typo.

Deprecate NIO ConnectionManager in Spark 1.5.0, before removing it in Spark 1.6.0.

Author: Reynold Xin <rxin@databricks.com>

Closes #8162 from rxin/SPARK-9934.

https://issues.apache.org/jira/browse/SPARK-9949

Author: Yin Huai <yhuai@databricks.com>

Closes #8179 from yhuai/SPARK-9949.

When the rate limiter is actually limiting the rate at which data is inserted into the buffer, the synchronized block of BlockGenerator.addData stays blocked for long time. This causes the thread switching the buffer and generating blocks (synchronized with addData) to starve and not generate blocks for seconds. The correct solution is to not block on the rate limiter within the synchronized block for adding data to the buffer.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #8204 from tdas/SPARK-9968 and squashes the following commits:

8cbcc1b [Tathagata Das] Removed unused val
a73b645 [Tathagata Das] Reduced time spent within synchronized block

1. The rate estimator should not estimate any rate when there are no records in the batch, as there is no data to estimate the rate. In the current state, it estimates and set the rate to zero. That is incorrect.

2. The rate estimator should not never set the rate to zero under any circumstances. Otherwise the system will stop receiving data, and stop generating useful estimates (see reason 1). So the fix is to define a parameters that sets a lower bound on the estimated rate, so that the system always receives some data.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #8199 from tdas/SPARK-9966 and squashes the following commits:

829f793 [Tathagata Das] Fixed unit test and added comments
3a994db [Tathagata Das] Added min rate and updated tests in PIDRateEstimator

This bug is caused by a wrong column-exist-check in `__getitem__` of pyspark dataframe. `DataFrame.apply` accepts not only top level column names, but also nested column name like `a.b`, so we should remove that check from `__getitem__`.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #8202 from cloud-fan/nested.

Also added unit test for integration between StringIndexerModel and IndexToString

CC: holdenk We realized we should have left in your unit test (to catch the issue with removing the inverse() method), so this adds it back.  mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #8211 from jkbradley/stridx-labels.

Author: Davies Liu <davies@databricks.com>

Closes #8213 from davies/fix_window.

Detailed exception log can be seen in [SPARK-9877](https://issues.apache.org/jira/browse/SPARK-9877), the problem is when creating `StandaloneRestServer`, `self` (`masterEndpoint`) is null.  So this fix is creating `StandaloneRestServer` when `self` is available.

Author: jerryshao <sshao@hortonworks.com>

Closes #8127 from jerryshao/SPARK-9877.

In these tests, we use a custom listener and we assert on fields in the stage / task completion events. However, these events are posted in a separate thread so they're not guaranteed to be posted in time. This commit fixes this flakiness through a job end registration callback.

Author: Andrew Or <andrew@databricks.com>

Closes #8176 from andrewor14/fix-accumulator-suite.

When a stage failed and another stage was resubmitted with only part of partitions to compute, all the tasks failed with error message: java.util.NoSuchElementException: key not found: peakExecutionMemory.
This is because the internal accumulators are not properly initialized for this stage while other codes assume the internal accumulators always exist.

Author: Carson Wang <carson.wang@intel.com>

Closes #8090 from carsonwang/SPARK-9809.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #8110 from MechCoder/spark-9828.

We can do this now that SPARK-9580 is resolved.

Author: Andrew Or <andrew@databricks.com>

Closes #8208 from andrewor14/reenable-sql-tests.

Currently, we access the `page.pageNumer` after it's freed, that could be modified by other thread, cause NPE.

The same TaskMemoryManager could be used by multiple threads (for example, Python UDF and TransportScript), so it should be thread safe to allocate/free memory/page. The underlying Bitset and HashSet are not thread safe, we should put them inside a synchronized block.

cc JoshRosen

Author: Davies Liu <davies@databricks.com>

Closes #8177 from davies/memory_manager.

Modified type of ShuffleMapStage.numAvailableOutputs from Long to Int

Author: Neelesh Srinivas Salian <nsalian@cloudera.com>

Closes #8183 from nssalian/SPARK-9923.

in MLlib sometimes we need to set metadata for the new column, thus we will alias the new column with metadata before call `withColumn` and in `withColumn` we alias this clolumn again. Here I overloaded `withColumn` to allow user set metadata, just like what we did  for `Column.as`.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #8159 from cloud-fan/withColumn.

It would be helpful to allow users to pass a pre-computed index to create an indexer, rather than always going through StringIndexer to create the model.

Author: Holden Karau <holden@pigscanfly.ca>

Closes #7267 from holdenk/SPARK-8744-StringIndexerModel-should-have-public-constructor.

This modifies DecisionTreeMetadata construction to treat 1-category features as continuous, so that trees do not fail with such features.  It is important for the pipelines API, where VectorIndexer can automatically categorize certain features as categorical.

As stated in the JIRA, this is a temp fix which we can improve upon later by automatically filtering out those features. That will take longer, though, since it will require careful indexing.

Targeted for 1.5 and master

CC: manishamde  mengxr yanboliang

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #8187 from jkbradley/tree-1cat.

Some minor clean-ups after SPARK-9661. See my inline comments. MechCoder jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #8190 from mengxr/SPARK-9661-fix.

[SPARK-9958] [SQL] Make HiveThriftServer2Listener thread-safe and update the tab name to "JDBC/ODBC Server"

This PR fixed the thread-safe issue of HiveThriftServer2Listener, and also changed the tab name to "JDBC/ODBC Server" since it's conflict with the new SQL tab.

<img width="1377" alt="thriftserver" src="https://cloud.githubusercontent.com/assets/1000778/9265707/c46f3f2c-4269-11e5-8d7e-888c9113ab4f.png">

Author: zsxwing <zsxwing@gmail.com>

Closes #8185 from zsxwing/SPARK-9958.

As `InternalRow` does not extend `Row` now, I think we can remove it.

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

Closes #8170 from viirya/remove_canequal.

Currently, pageSize of TungstenSort is calculated from driver.memory, it should use executor.memory instead.

Also, in the worst case, the safeFactor could be 4 (because of rounding), increase it to 16.

cc rxin

Author: Davies Liu <davies@databricks.com>

Closes #8175 from davies/page_size.

A fundamental limitation of the existing SQL tests is that *there is simply no way to create your own `SparkContext`*. This is a serious limitation because the user may wish to use a different master or config. As a case in point, `BroadcastJoinSuite` is entirely commented out because there is no way to make it pass with the existing infrastructure.

This patch removes the singletons `TestSQLContext` and `TestData`, and instead introduces a `SharedSQLContext` that starts a context per suite. Unfortunately the singletons were so ingrained in the SQL tests that this patch necessarily needed to touch *all* the SQL test files.

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Author: Andrew Or <andrew@databricks.com>

Closes #8111 from andrewor14/sql-tests-refactor.

When the free memory in executor goes low, the cached broadcast objects need to serialized into disk, but currently the deserialized UnsafeHashedRelation can't be serialized , fail with NPE. This PR fixes that.

cc rxin

Author: Davies Liu <davies@databricks.com>

Closes #8174 from davies/serialize_hashed.

This bug only happen on Python 3 and Windows.

I tested this manually with python 3 and disable python daemon, no unit test yet.

Author: Davies Liu <davies@databricks.com>

Closes #8181 from davies/open_mode.

What `StringIndexerInverse` does is not strictly associated with `StringIndexer`, and the name is not clearly describing the transformation. Renaming to `IndexToString` might be better.

~~I also changed `invert` to `inverse` without arguments. `inputCol` and `outputCol` could be set after.~~
I also removed `invert`.

jkbradley holdenk

Author: Xiangrui Meng <meng@databricks.com>

Closes #8152 from mengxr/SPARK-9922.

https://issues.apache.org/jira/browse/SPARK-9935

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #8163 from HyukjinKwon/master.

If pandas is broken (can't be imported, raise other exceptions other than ImportError), pyspark can't be imported, we should ignore all the exceptions.

Author: Davies Liu <davies@databricks.com>

Closes #8173 from davies/fix_pandas.

I skimmed through the docs for various instance of Object and replaced them with Java compaible versions of the same.

1. Some methods in LDAModel.
2. runMiniBatchSGD
3. kolmogorovSmirnovTest

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #8126 from MechCoder/java_incop.

This particular test did not load the default configurations so
it continued to start the REST server, which causes port bind
exceptions.