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* [SPARK-18541][PYTHON] Add metadata parameter to pyspark.sql.Column.alias()Sheamus K. Parkes2017-02-142-3/+33
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Add a `metadata` keyword parameter to `pyspark.sql.Column.alias()` to allow users to mix-in metadata while manipulating `DataFrame`s in `pyspark`. Without this, I believe it was necessary to pass back through `SparkSession.createDataFrame` each time a user wanted to manipulate `StructField.metadata` in `pyspark`. This pull request also improves consistency between the Scala and Python APIs (i.e. I did not add any functionality that was not already in the Scala API). Discussed ahead of time on JIRA with marmbrus ## How was this patch tested? Added unit tests (and doc tests). Ran the pertinent tests manually. Author: Sheamus K. Parkes <shea.parkes@milliman.com> Closes #16094 from shea-parkes/pyspark-column-alias-metadata.
* [SPARK-19162][PYTHON][SQL] UserDefinedFunction should validate that func is ↵zero3232017-02-142-0/+12
| | | | | | | | | | | | | | | | callable ## What changes were proposed in this pull request? UDF constructor checks if `func` argument is callable and if it is not, fails fast instead of waiting for an action. ## How was this patch tested? Unit tests. Author: zero323 <zero323@users.noreply.github.com> Closes #16535 from zero323/SPARK-19162.
* [SPARK-19453][PYTHON][SQL][DOC] Correct and extend DataFrame.replace docstringzero3232017-02-141-6/+12
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? - Provides correct description of the semantics of a `dict` argument passed as `to_replace`. - Describes type requirements for collection arguments. - Describes behavior with `to_replace: List[T]` and `value: T` ## How was this patch tested? Manual testing, documentation build. Author: zero323 <zero323@users.noreply.github.com> Closes #16792 from zero323/SPARK-19453.
* [SPARK-19589][SQL] Removal of SQLGEN filesXiao Li2017-02-14126-654/+0
| | | | | | | | | | | | ### What changes were proposed in this pull request? SQLGen is removed. Thus, the generated files should be removed too. ### How was this patch tested? N/A Author: Xiao Li <gatorsmile@gmail.com> Closes #16921 from gatorsmile/removeSQLGenFiles.
* [SPARK-19585][DOC][SQL] Fix the cacheTable and uncacheTable api call in the docSunitha Kambhampati2017-02-131-2/+2
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? https://spark.apache.org/docs/latest/sql-programming-guide.html#caching-data-in-memory In the doc, the call spark.cacheTable(“tableName”) and spark.uncacheTable(“tableName”) actually needs to be spark.catalog.cacheTable and spark.catalog.uncacheTable ## How was this patch tested? Built the docs and verified the change shows up fine. Author: Sunitha Kambhampati <skambha@us.ibm.com> Closes #16919 from skambha/docChange.
* [SPARK-19539][SQL] Block duplicate temp table during creationXin Wu2017-02-1310-137/+160
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Current `CREATE TEMPORARY TABLE ... ` is deprecated and recommend users to use `CREATE TEMPORARY VIEW ...` And it does not support `IF NOT EXISTS `clause. However, if there is an existing temporary view defined, it is possible to unintentionally replace this existing view by issuing `CREATE TEMPORARY TABLE ...` with the same table/view name. This PR is to disallow `CREATE TEMPORARY TABLE ...` with an existing view name. Under the cover, `CREATE TEMPORARY TABLE ...` will be changed to create temporary view, however, passing in a flag `replace=false`, instead of currently `true`. So when creating temporary view under the cover, if there is existing view with the same name, the operation will be blocked. ## How was this patch tested? New unit test case is added and updated some existing test cases to adapt the new behavior Author: Xin Wu <xinwu@us.ibm.com> Closes #16878 from xwu0226/block_duplicate_temp_table.
* [SPARK-19115][SQL] Supporting Create Table Like Locationouyangxiaochen2017-02-135-37/+159
| | | | | | | | | | | | | | | | | | What changes were proposed in this pull request? Support CREATE [EXTERNAL] TABLE LIKE LOCATION... syntax for Hive serde and datasource tables. In this PR,we follow SparkSQL design rules : supporting create table like view or physical table or temporary view with location. creating a table with location,this table will be an external table other than managed table. How was this patch tested? Add new test cases and update existing test cases Author: ouyangxiaochen <ou.yangxiaochen@zte.com.cn> Closes #16868 from ouyangxiaochen/spark19115.
* [SPARK-19429][PYTHON][SQL] Support slice arguments in Column.__getitem__zero3232017-02-132-3/+16
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? - Add support for `slice` arguments in `Column.__getitem__`. - Remove obsolete `__getslice__` bindings. ## How was this patch tested? Existing unit tests, additional tests covering `[]` with `slice`. Author: zero323 <zero323@users.noreply.github.com> Closes #16771 from zero323/SPARK-19429.
* [SPARK-19520][STREAMING] Do not encrypt data written to the WAL.Marcelo Vanzin2017-02-138-30/+120
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Spark's I/O encryption uses an ephemeral key for each driver instance. So driver B cannot decrypt data written by driver A since it doesn't have the correct key. The write ahead log is used for recovery, thus needs to be readable by a different driver. So it cannot be encrypted by Spark's I/O encryption code. The BlockManager APIs used by the WAL code to write the data automatically encrypt data, so changes are needed so that callers can to opt out of encryption. Aside from that, the "putBytes" API in the BlockManager does not do encryption, so a separate situation arised where the WAL would write unencrypted data to the BM and, when those blocks were read, decryption would fail. So the WAL code needs to ask the BM to encrypt that data when encryption is enabled; this code is not optimal since it results in a (temporary) second copy of the data block in memory, but should be OK for now until a more performant solution is added. The non-encryption case should not be affected. Tested with new unit tests, and by running streaming apps that do recovery using the WAL data with I/O encryption turned on. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #16862 from vanzin/SPARK-19520.
* [SPARK-19435][SQL] Type coercion between ArrayTypeshyukjinkwon2017-02-132-43/+120
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR proposes to support type coercion between `ArrayType`s where the element types are compatible. **Before** ``` Seq(Array(1)).toDF("a").selectExpr("greatest(a, array(1D))") org.apache.spark.sql.AnalysisException: cannot resolve 'greatest(`a`, array(1.0D))' due to data type mismatch: The expressions should all have the same type, got GREATEST(array<int>, array<double>).; line 1 pos 0; Seq(Array(1)).toDF("a").selectExpr("least(a, array(1D))") org.apache.spark.sql.AnalysisException: cannot resolve 'least(`a`, array(1.0D))' due to data type mismatch: The expressions should all have the same type, got LEAST(array<int>, array<double>).; line 1 pos 0; sql("SELECT * FROM values (array(0)), (array(1D)) as data(a)") org.apache.spark.sql.AnalysisException: incompatible types found in column a for inline table; line 1 pos 14 Seq(Array(1)).toDF("a").union(Seq(Array(1D)).toDF("b")) org.apache.spark.sql.AnalysisException: Union can only be performed on tables with the compatible column types. ArrayType(DoubleType,false) <> ArrayType(IntegerType,false) at the first column of the second table;; sql("SELECT IF(1=1, array(1), array(1D))") org.apache.spark.sql.AnalysisException: cannot resolve '(IF((1 = 1), array(1), array(1.0D)))' due to data type mismatch: differing types in '(IF((1 = 1), array(1), array(1.0D)))' (array<int> and array<double>).; line 1 pos 7; ``` **After** ```scala Seq(Array(1)).toDF("a").selectExpr("greatest(a, array(1D))") res5: org.apache.spark.sql.DataFrame = [greatest(a, array(1.0)): array<double>] Seq(Array(1)).toDF("a").selectExpr("least(a, array(1D))") res6: org.apache.spark.sql.DataFrame = [least(a, array(1.0)): array<double>] sql("SELECT * FROM values (array(0)), (array(1D)) as data(a)") res8: org.apache.spark.sql.DataFrame = [a: array<double>] Seq(Array(1)).toDF("a").union(Seq(Array(1D)).toDF("b")) res10: org.apache.spark.sql.Dataset[org.apache.spark.sql.Row] = [a: array<double>] sql("SELECT IF(1=1, array(1), array(1D))") res15: org.apache.spark.sql.DataFrame = [(IF((1 = 1), array(1), array(1.0))): array<double>] ``` ## How was this patch tested? Unit tests in `TypeCoercion` and Jenkins tests and building with scala 2.10 ```scala ./dev/change-scala-version.sh 2.10 ./build/mvn -Pyarn -Phadoop-2.4 -Dscala-2.10 -DskipTests clean package ``` Author: hyukjinkwon <gurwls223@gmail.com> Closes #16777 from HyukjinKwon/SPARK-19435.
* [SPARK-17714][CORE][TEST-MAVEN][TEST-HADOOP2.6] Avoid using ↵Shixiong Zhu2017-02-136-27/+38
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ExecutorClassLoader to load Netty generated classes ## What changes were proposed in this pull request? Netty's `MessageToMessageEncoder` uses [Javassist](https://github.com/netty/netty/blob/91a0bdc17a8298437d6de08a8958d753799bd4a6/common/src/main/java/io/netty/util/internal/JavassistTypeParameterMatcherGenerator.java#L62) to generate a matcher class and the implementation calls `Class.forName` to check if this class is already generated. If `MessageEncoder` or `MessageDecoder` is created in `ExecutorClassLoader.findClass`, it will cause `ClassCircularityError`. This is because loading this Netty generated class will call `ExecutorClassLoader.findClass` to search this class, and `ExecutorClassLoader` will try to use RPC to load it and cause to load the non-exist matcher class again. JVM will report `ClassCircularityError` to prevent such infinite recursion. ##### Why it only happens in Maven builds It's because Maven and SBT have different class loader tree. The Maven build will set a URLClassLoader as the current context class loader to run the tests and expose this issue. The class loader tree is as following: ``` bootstrap class loader ------ ... ----- REPL class loader ---- ExecutorClassLoader | | URLClasssLoader ``` The SBT build uses the bootstrap class loader directly and `ReplSuite.test("propagation of local properties")` is the first test in ReplSuite, which happens to load `io/netty/util/internal/__matchers__/org/apache/spark/network/protocol/MessageMatcher` into the bootstrap class loader (Note: in maven build, it's loaded into URLClasssLoader so it cannot be found in ExecutorClassLoader). This issue can be reproduced in SBT as well. Here are the produce steps: - Enable `hadoop.caller.context.enabled`. - Replace `Class.forName` with `Utils.classForName` in `object CallerContext`. - Ignore `ReplSuite.test("propagation of local properties")`. - Run `ReplSuite` using SBT. This PR just creates a singleton MessageEncoder and MessageDecoder and makes sure they are created before switching to ExecutorClassLoader. TransportContext will be created when creating RpcEnv and that happens before creating ExecutorClassLoader. ## How was this patch tested? Jenkins Author: Shixiong Zhu <shixiong@databricks.com> Closes #16859 from zsxwing/SPARK-17714.
* [SPARK-19542][SS] Delete the temp checkpoint if a query is stopped without ↵Shixiong Zhu2017-02-133-3/+53
| | | | | | | | | | | | | | | | errors ## What changes were proposed in this pull request? When a query uses a temp checkpoint dir, it's better to delete it if it's stopped without errors. ## How was this patch tested? New unit tests. Author: Shixiong Zhu <shixiong@databricks.com> Closes #16880 from zsxwing/delete-temp-checkpoint.
* [SPARK-19514] Enhancing the test for Range interruption.Ala Luszczak2017-02-131-11/+10
| | | | | | | | Improve the test for SPARK-19514, so that it's clear which stage is being cancelled. Author: Ala Luszczak <ala@databricks.com> Closes #16914 from ala/fix-range-test.
* [SPARK-19529] TransportClientFactory.createClient() shouldn't call ↵Josh Rosen2017-02-139-24/+30
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | awaitUninterruptibly() ## What changes were proposed in this pull request? This patch replaces a single `awaitUninterruptibly()` call with a plain `await()` call in Spark's `network-common` library in order to fix a bug which may cause tasks to be uncancellable. In Spark's Netty RPC layer, `TransportClientFactory.createClient()` calls `awaitUninterruptibly()` on a Netty future while waiting for a connection to be established. This creates problem when a Spark task is interrupted while blocking in this call (which can happen in the event of a slow connection which will eventually time out). This has bad impacts on task cancellation when `interruptOnCancel = true`. As an example of the impact of this problem, I experienced significant numbers of uncancellable "zombie tasks" on a production cluster where several tasks were blocked trying to connect to a dead shuffle server and then continued running as zombies after I cancelled the associated Spark stage. The zombie tasks ran for several minutes with the following stack: ``` java.lang.Object.wait(Native Method) java.lang.Object.wait(Object.java:460) io.netty.util.concurrent.DefaultPromise.await0(DefaultPromise.java:607) io.netty.util.concurrent.DefaultPromise.awaitUninterruptibly(DefaultPromise.java:301) org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:224) org.apache.spark.network.client.TransportClientFactory.createClient(TransportClientFactory.java:179) => holding Monitor(java.lang.Object1849476028}) org.apache.spark.network.shuffle.ExternalShuffleClient$1.createAndStart(ExternalShuffleClient.java:105) org.apache.spark.network.shuffle.RetryingBlockFetcher.fetchAllOutstanding(RetryingBlockFetcher.java:140) org.apache.spark.network.shuffle.RetryingBlockFetcher.start(RetryingBlockFetcher.java:120) org.apache.spark.network.shuffle.ExternalShuffleClient.fetchBlocks(ExternalShuffleClient.java:114) org.apache.spark.storage.ShuffleBlockFetcherIterator.sendRequest(ShuffleBlockFetcherIterator.scala:169) org.apache.spark.storage.ShuffleBlockFetcherIterator.fetchUpToMaxBytes(ShuffleBlockFetcherIterator.scala: 350) org.apache.spark.storage.ShuffleBlockFetcherIterator.initialize(ShuffleBlockFetcherIterator.scala:286) org.apache.spark.storage.ShuffleBlockFetcherIterator.<init>(ShuffleBlockFetcherIterator.scala:120) org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:45) org.apache.spark.sql.execution.ShuffledRowRDD.compute(ShuffledRowRDD.scala:169) org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323) org.apache.spark.rdd.RDD.iterator(RDD.scala:287) [...] ``` As far as I can tell, `awaitUninterruptibly()` might have been used in order to avoid having to declare that methods throw `InterruptedException` (this code is written in Java, hence the need to use checked exceptions). This patch simply replaces this with a regular, interruptible `await()` call,. This required several interface changes to declare a new checked exception (these are internal interfaces, though, and this change doesn't significantly impact binary compatibility). An alternative approach would be to wrap `InterruptedException` into `IOException` in order to avoid having to change interfaces. The problem with this approach is that the `network-shuffle` project's `RetryingBlockFetcher` code treats `IOExceptions` as transitive failures when deciding whether to retry fetches, so throwing a wrapped `IOException` might cause an interrupted shuffle fetch to be retried, further prolonging the lifetime of a cancelled zombie task. Note that there are three other `awaitUninterruptibly()` in the codebase, but those calls have a hard 10 second timeout and are waiting on a `close()` operation which is expected to complete near instantaneously, so the impact of uninterruptibility there is much smaller. ## How was this patch tested? Manually. Author: Josh Rosen <joshrosen@databricks.com> Closes #16866 from JoshRosen/SPARK-19529.
* [SPARK-19427][PYTHON][SQL] Support data type string as a returnType argument ↵zero3232017-02-132-3/+20
| | | | | | | | | | | | | | | | | | | | | | | of UDF ## What changes were proposed in this pull request? Add support for data type string as a return type argument of `UserDefinedFunction`: ```python f = udf(lambda x: x, "integer") f.returnType ## IntegerType ``` ## How was this patch tested? Existing unit tests, additional unit tests covering new feature. Author: zero323 <zero323@users.noreply.github.com> Closes #16769 from zero323/SPARK-19427.
* [SPARK-19506][ML][PYTHON] Import warnings in pyspark.ml.utilzero3232017-02-131-0/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Add missing `warnings` import. ## How was this patch tested? Manual tests. Author: zero323 <zero323@users.noreply.github.com> Closes #16846 from zero323/SPARK-19506.
* [SPARK-19544][SQL] Improve error message when some column types are ↵hyukjinkwon2017-02-134-14/+38
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | compatible and others are not in set operations ## What changes were proposed in this pull request? This PR proposes to fix the error message when some data types are compatible and others are not in set/union operation. Currently, the code below: ```scala Seq((1,("a", 1))).toDF.union(Seq((1L,("a", "b"))).toDF) ``` throws an exception saying `LongType` and `IntegerType` are incompatible types. It should say something about `StructType`s with more readable format as below: **Before** ``` Union can only be performed on tables with the compatible column types. LongType <> IntegerType at the first column of the second table;; ``` **After** ``` Union can only be performed on tables with the compatible column types. struct<_1:string,_2:string> <> struct<_1:string,_2:int> at the second column of the second table;; ``` *I manually inserted a newline in the messages above for readability only in this PR description. ## How was this patch tested? Unit tests in `AnalysisErrorSuite`, manual tests and build wth Scala 2.10. Author: hyukjinkwon <gurwls223@gmail.com> Closes #16882 from HyukjinKwon/SPARK-19544.
* [SPARK-19496][SQL] to_date udf to return null when input date is invalidwindpiger2017-02-132-4/+75
| | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Currently the udf `to_date` has different return value with an invalid date input. ``` SELECT to_date('2015-07-22', 'yyyy-dd-MM') -> return `2016-10-07` SELECT to_date('2014-31-12') -> return null ``` As discussed in JIRA [SPARK-19496](https://issues.apache.org/jira/browse/SPARK-19496), we should return null in both situations when the input date is invalid ## How was this patch tested? unit test added Author: windpiger <songjun@outlook.com> Closes #16870 from windpiger/to_date.
* [SPARK-19562][BUILD] Added exclude for dev/pr-deps to gitignoreArmin Braun2017-02-131-0/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Just adding a missing .gitignore entry. ## How was this patch tested? Entry added, now repo is not dirty anymore after running the build. Author: Armin Braun <me@obrown.io> Closes #16904 from original-brownbear/SPARK-19562.
* [SPARK-19574][ML][DOCUMENTATION] Fix Liquid Exception: Start indices amount ↵Xiao Li2017-02-131-1/+1
| | | | | | | | | | | | | | | | | | | | is not equal to end indices amount ### What changes were proposed in this pull request? ``` Liquid Exception: Start indices amount is not equal to end indices amount, see /Users/xiao/IdeaProjects/sparkDelivery/docs/../examples/src/main/java/org/apache/spark/examples/ml/JavaTokenizerExample.java. in ml-features.md ``` So far, the build is broken after merging https://github.com/apache/spark/pull/16789 This PR is to fix it. ## How was this patch tested? Manual Author: Xiao Li <gatorsmile@gmail.com> Closes #16908 from gatorsmile/docMLFix.
* [SPARK-19564][SPARK-19559][SS][KAFKA] KafkaOffsetReader's consumers should ↵Liwei Lin2017-02-121-4/+7
| | | | | | | | | | | | | | | | | | | | not be in the same group ## What changes were proposed in this pull request? In `KafkaOffsetReader`, when error occurs, we abort the existing consumer and create a new consumer. In our current implementation, the first consumer and the second consumer would be in the same group (which leads to SPARK-19559), **_violating our intention of the two consumers not being in the same group._** The cause is that, in our current implementation, the first consumer is created before `groupId` and `nextId` are initialized in the constructor. Then even if `groupId` and `nextId` are increased during the creation of that first consumer, `groupId` and `nextId` would still be initialized to default values in the constructor for the second consumer. We should make sure that `groupId` and `nextId` are initialized before any consumer is created. ## How was this patch tested? Ran 100 times of `KafkaSourceSuite`; all passed Author: Liwei Lin <lwlin7@gmail.com> Closes #16902 from lw-lin/SPARK-19564-.
* [SPARK-19342][SPARKR] bug fixed in collect method for collecting timestamp ↵titicaca2017-02-123-4/+43
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | column ## What changes were proposed in this pull request? Fix a bug in collect method for collecting timestamp column, the bug can be reproduced as shown in the following codes and outputs: ``` library(SparkR) sparkR.session(master = "local") df <- data.frame(col1 = c(0, 1, 2), col2 = c(as.POSIXct("2017-01-01 00:00:01"), NA, as.POSIXct("2017-01-01 12:00:01"))) sdf1 <- createDataFrame(df) print(dtypes(sdf1)) df1 <- collect(sdf1) print(lapply(df1, class)) sdf2 <- filter(sdf1, "col1 > 0") print(dtypes(sdf2)) df2 <- collect(sdf2) print(lapply(df2, class)) ``` As we can see from the printed output, the column type of col2 in df2 is converted to numeric unexpectedly, when NA exists at the top of the column. This is caused by method `do.call(c, list)`, if we convert a list, i.e. `do.call(c, list(NA, as.POSIXct("2017-01-01 12:00:01"))`, the class of the result is numeric instead of POSIXct. Therefore, we need to cast the data type of the vector explicitly. ## How was this patch tested? The patch can be tested manually with the same code above. Author: titicaca <fangzhou.yang@hotmail.com> Closes #16689 from titicaca/sparkr-dev.
* [SPARK-19448][SQL] optimize some duplication functions between ↵windpiger2017-02-117-157/+88
| | | | | | | | | | | | | | | | | | HiveClientImpl and HiveUtils ## What changes were proposed in this pull request? There are some duplicate functions between `HiveClientImpl` and `HiveUtils`, we can merge them to one place. such as: `toHiveTable` 、`toHivePartition`、`fromHivePartition`. And additional modify is change `MetastoreRelation.attributes` to `MetastoreRelation.dataColKeys` https://github.com/apache/spark/blob/master/sql/hive/src/main/scala/org/apache/spark/sql/hive/MetastoreRelation.scala#L234 ## How was this patch tested? N/A Author: windpiger <songjun@outlook.com> Closes #16787 from windpiger/todoInMetaStoreRelation.
* [SPARK-19537] Move pendingPartitions to ShuffleMapStage.Kay Ousterhout2017-02-103-9/+26
| | | | | | | | | | | | | | The pendingPartitions instance variable should be moved to ShuffleMapStage, because it is only used by ShuffleMapStages. This change is purely refactoring and does not change functionality. I fixed this in an attempt to clarify some of the discussion around #16620, which I was having trouble reasoning about. I stole the helpful comment Imran wrote for pendingPartitions and used it here. cc squito markhamstra jinxing64 Author: Kay Ousterhout <kayousterhout@gmail.com> Closes #16876 from kayousterhout/SPARK-19537.
* [SPARK-19548][SQL] Support Hive UDFs which return typed Lists/MapsHerman van Hovell2017-02-1011-57/+250
| | | | | | | | | | | | ## What changes were proposed in this pull request? This PR adds support for Hive UDFs that return fully typed java Lists or Maps, for example `List<String>` or `Map<String, Integer>`. It is also allowed to nest these structures, for example `Map<String, List<Integer>>`. Raw collections or collections using wildcards are still not supported, and cannot be supported due to the lack of type information. ## How was this patch tested? Modified existing tests in `HiveUDFSuite`, and I have added test cases for raw collection and collection using wildcards. Author: Herman van Hovell <hvanhovell@databricks.com> Closes #16886 from hvanhovell/SPARK-19548.
* [SPARK-19549] Allow providing reason for stage/job cancellingAla Luszczak2017-02-107-29/+138
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? This change add an optional argument to `SparkContext.cancelStage()` and `SparkContext.cancelJob()` functions, which allows the caller to provide exact reason for the cancellation. ## How was this patch tested? Adds unit test. Author: Ala Luszczak <ala@databricks.com> Closes #16887 from ala/cancel.
* [SPARK-18613][ML] make spark.mllib LDA dependencies in spark.ml LDA privatesueann2017-02-101-6/+6
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? spark.ml.*LDAModel classes were exposing spark.mllib LDA models via protected methods. Made them package (clustering) private. ## How was this patch tested? ``` build/sbt doc # "millib.clustering" no longer appears in the docs for *LDA* classes build/sbt compile # compiles build/sbt > mllib/testOnly # tests pass ``` Author: sueann <sueann@databricks.com> Closes #16860 from sueann/SPARK-18613.
* [SPARK-19459][SQL] Add Hive datatype (char/varchar) to StructField metadataHerman van Hovell2017-02-106-25/+76
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Reading from an existing ORC table which contains `char` or `varchar` columns can fail with a `ClassCastException` if the table metadata has been created using Spark. This is caused by the fact that spark internally replaces `char` and `varchar` columns with a `string` column. This PR fixes this by adding the hive type to the `StructField's` metadata under the `HIVE_TYPE_STRING` key. This is picked up by the `HiveClient` and the ORC reader, see https://github.com/apache/spark/pull/16060 for more details on how the metadata is used. ## How was this patch tested? Added a regression test to `OrcSourceSuite`. Author: Herman van Hovell <hvanhovell@databricks.com> Closes #16804 from hvanhovell/SPARK-19459.
* [SPARK-19466][CORE][SCHEDULER] Improve Fair Scheduler LoggingEren Avsarogullari2017-02-101-21/+46
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fair Scheduler Logging for the following cases can be useful for the user. 1. If **valid** `spark.scheduler.allocation.file` property is set, user can be informed and aware which scheduler file is processed when `SparkContext` initializes. 2. If **invalid** `spark.scheduler.allocation.file` property is set, currently, the following stacktrace is shown to user. In addition to this, more meaningful message can be shown to user by emphasizing the problem at building level of fair scheduler. Also other potential issues can be covered at this level as **Fair Scheduler can not be built. + exception stacktrace** ``` Exception in thread "main" java.io.FileNotFoundException: INVALID_FILE (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at java.io.FileInputStream.<init>(FileInputStream.java:93) at org.apache.spark.scheduler.FairSchedulableBuilder$$anonfun$buildPools$1.apply(SchedulableBuilder.scala:76) at org.apache.spark.scheduler.FairSchedulableBuilder$$anonfun$buildPools$1.apply(SchedulableBuilder.scala:75) ``` 3. If `spark.scheduler.allocation.file` property is not set and **default** fair scheduler file (**fairscheduler.xml**) is found in classpath, it will be loaded but currently, user is not informed for using default file so logging can be useful as **Fair Scheduler file: fairscheduler.xml is found successfully and will be parsed.** 4. If **spark.scheduler.allocation.file** property is not set and **default** fair scheduler file does not exist in classpath, currently, user is not informed so logging can be useful as **No Fair Scheduler file found.** Also this PR is related with https://github.com/apache/spark/pull/15237 to emphasize fileName in warning logs when fair scheduler file has invalid minShare, weight or schedulingMode values. ## How was this patch tested? Added new Unit Tests. Author: erenavsarogullari <erenavsarogullari@gmail.com> Closes #16813 from erenavsarogullari/SPARK-19466.
* Encryption of shuffle filesHervé2017-02-101-5/+1
| | | | | | | | | | | | | | | | Hello According to my understanding of commits 4b4e329e49f8af28fa6301bd06c48d7097eaf9e6 & 8b325b17ecdf013b7a6edcb7ee3773546bd914df, one may now encrypt shuffle files regardless of the cluster manager in use. However I have limited understanding of the code, I'm not able to find out whether theses changes also comprise all "temporary local storage, such as shuffle files, cached data, and other application files". Please feel free to amend or reject my PR if I'm wrong. dud Author: Hervé <dud225@users.noreply.github.com> Closes #16885 from dud225/patch-1.
* [SPARK-10748][MESOS] Log error instead of crashing Spark Mesos dispatcher ↵Devaraj K2017-02-101-9/+19
| | | | | | | | | | | | | | | when a job is misconfigured ## What changes were proposed in this pull request? Now handling the spark exception which gets thrown for invalid job configuration, marking that job as failed and continuing to launch the other drivers instead of throwing the exception. ## How was this patch tested? I verified manually, now the misconfigured jobs move to Finished Drivers section in UI and continue to launch the other jobs. Author: Devaraj K <devaraj@apache.org> Closes #13077 from devaraj-kavali/SPARK-10748.
* [SPARK-19545][YARN] Fix compile issue for Spark on Yarn when building ↵jerryshao2017-02-102-8/+23
| | | | | | | | | | | | | | | | against Hadoop 2.6.0~2.6.3 ## What changes were proposed in this pull request? Due to the newly added API in Hadoop 2.6.4+, Spark builds against Hadoop 2.6.0~2.6.3 will meet compile error. So here still reverting back to use reflection to handle this issue. ## How was this patch tested? Manual verification. Author: jerryshao <sshao@hortonworks.com> Closes #16884 from jerryshao/SPARK-19545.
* [SPARK-19543] from_json fails when the input row is emptyBurak Yavuz2017-02-102-1/+9
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Using from_json on a column with an empty string results in: java.util.NoSuchElementException: head of empty list. This is because `parser.parse(input)` may return `Nil` when `input.trim.isEmpty` ## How was this patch tested? Regression test in `JsonExpressionsSuite` Author: Burak Yavuz <brkyvz@gmail.com> Closes #16881 from brkyvz/json-fix.
* [SPARK-19263] Fix race in SchedulerIntegrationSuite.jinxing2017-02-091-7/+7
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? All the process of offering resource and generating `TaskDescription` should be guarded by taskScheduler.synchronized in `reviveOffers`, otherwise there is race condition. ## How was this patch tested? Existing unit tests. Author: jinxing <jinxing@meituan.com> Closes #16831 from jinxing64/SPARK-19263-FixRaceInTest.
* [SPARK-19481] [REPL] [MAVEN] Avoid to leak SparkContext in ↵Shixiong Zhu2017-02-095-11/+20
| | | | | | | | | | | | | | | | | | Signaling.cancelOnInterrupt ## What changes were proposed in this pull request? `Signaling.cancelOnInterrupt` leaks a SparkContext per call and it makes ReplSuite unstable. This PR adds `SparkContext.getActive` to allow `Signaling.cancelOnInterrupt` to get the active `SparkContext` to avoid the leak. ## How was this patch tested? Jenkins Author: Shixiong Zhu <shixiong@databricks.com> Closes #16825 from zsxwing/SPARK-19481.
* [SPARK-16554][CORE] Automatically Kill Executors and Nodes when they are ↵José Hiram Soltren2017-02-0911-26/+248
| | | | | | | | | | | | | | | | | | | | | | | Blacklisted ## What changes were proposed in this pull request? In SPARK-8425, we introduced a mechanism for blacklisting executors and nodes (hosts). After a certain number of failures, these resources would be "blacklisted" and no further work would be assigned to them for some period of time. In some scenarios, it is better to fail fast, and to simply kill these unreliable resources. This changes proposes to do so by having the BlacklistTracker kill unreliable resources when they would otherwise be "blacklisted". In order to be thread safe, this code depends on the CoarseGrainedSchedulerBackend sending a message to the driver backend in order to do the actual killing. This also helps to prevent a race which would permit work to begin on a resource (executor or node), between the time the resource is marked for killing and the time at which it is finally killed. ## How was this patch tested? ./dev/run-tests Ran https://github.com/jsoltren/jose-utils/blob/master/blacklist/test-blacklist.sh, and checked logs to see executors and nodes being killed. Testing can likely be improved here; suggestions welcome. Author: José Hiram Soltren <jose@cloudera.com> Closes #16650 from jsoltren/SPARK-16554-submit.
* [SPARK-19025][SQL] Remove SQL builder for operatorsjiangxingbo2017-02-096-2196/+3
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? With the new approach of view resolution, we can get rid of SQL generation on view creation, so let's remove SQL builder for operators. Note that, since all sql generation for operators is defined in one file (org.apache.spark.sql.catalyst.SQLBuilder), it’d be trivial to recover it in the future. ## How was this patch tested? N/A Author: jiangxingbo <jiangxb1987@gmail.com> Closes #16869 from jiangxb1987/SQLBuilder.
* [SPARK-19512][SQL] codegen for compare structs failsBogdan Raducanu2017-02-093-4/+24
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Set currentVars to null in GenerateOrdering.genComparisons before genCode is called. genCode ignores INPUT_ROW if currentVars is not null and in genComparisons we want it to use INPUT_ROW. ## How was this patch tested? Added test with 2 queries in WholeStageCodegenSuite Author: Bogdan Raducanu <bogdan.rdc@gmail.com> Closes #16852 from bogdanrdc/SPARK-19512.
* [SPARK-19514] Making range interruptible.Ala Luszczak2017-02-093-6/+52
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Previously range operator could not be interrupted. For example, using DAGScheduler.cancelStage(...) on a query with range might have been ineffective. This change adds periodic checks of TaskContext.isInterrupted to codegen version, and InterruptibleOperator to non-codegen version. I benchmarked the performance of codegen version on a sample query `spark.range(1000L * 1000 * 1000 * 10).count()` and there is no measurable difference. ## How was this patch tested? Adds a unit test. Author: Ala Luszczak <ala@databricks.com> Closes #16872 from ala/SPARK-19514b.
* [SPARK-17874][CORE] Add SSL port configuration.Marcelo Vanzin2017-02-097-89/+164
| | | | | | | | | | | | | | | | | | | | | | Make the SSL port configuration explicit, instead of deriving it from the non-SSL port, but retain the existing functionality in case anyone depends on it. The change starts the HTTPS and HTTP connectors separately, so that it's possible to use independent ports for each. For that to work, the initialization of the server needs to be shuffled around a bit. The change also makes it so the initialization of both connectors is similar, and end up using the same Scheduler - previously only the HTTP connector would use the correct one. Also fixed some outdated documentation about a couple of services that were removed long ago. Tested with unit tests and by running spark-shell with SSL configs. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #16625 from vanzin/SPARK-17874.
* [MINOR][CORE] Fix incorrect documentation of WritableConverterLee Dongjin2017-02-091-8/+10
| | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? `WritableConverter` and `WritableFactory` work in opposite directions. But both of them are documented with same description: > A class encapsulating how to convert some type T to Writable. It stores both the Writable class corresponding to T (e.g. IntWritable for Int) and a function for doing the conversion. This error is a result of commit 2604939. As a note, `WritableFactory` was added from commit d37978d, which resolves [SPARK-4795](https://issues.apache.org/jira/browse/SPARK-4795) with the correct description. This PR fix the documentation of `WritableConverter`, along with some improvements on type description. ## How was this patch tested? `build/mvn clean checkstyle:checkstyle` Author: Lee Dongjin <dongjin@apache.org> Closes #16830 from dongjinleekr/feature/fix-writableconverter-doc.
* [SPARK-19265][SQL][FOLLOW-UP] Configurable `tableRelationCache` maximum sizeLiwei Lin2017-02-096-3/+63
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? SPARK-19265 had made table relation cache general; this follow-up aims to make `tableRelationCache`'s maximum size configurable. In order to do sanity-check, this patch also adds a `checkValue()` method to `TypedConfigBuilder`. ## How was this patch tested? new test case: `test("conf entry: checkValue()")` Author: Liwei Lin <lwlin7@gmail.com> Closes #16736 from lw-lin/conf.
* [SPARK-19359][SQL] renaming partition should not leave useless directoriesWenchen Fan2017-02-093-15/+84
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Hive metastore is not case-preserving and keep partition columns with lower case names. If Spark SQL creates a table with upper-case partition column names using `HiveExternalCatalog`, when we rename partition, it first calls the HiveClient to renamePartition, which will create a new lower case partition path, then Spark SQL renames the lower case path to upper-case. However, when we rename a nested path, different file systems have different behaviors. e.g. in jenkins, renaming `a=1/b=2` to `A=2/B=2` will success, but leave an empty directory `a=1`. in mac os, the renaming doesn't work as expected and result to `a=1/B=2`. This PR renames the partition directory recursively from the first partition column in `HiveExternalCatalog`, to be most compatible with different file systems. ## How was this patch tested? new regression test Author: Wenchen Fan <wenchen@databricks.com> Closes #16837 from cloud-fan/partition.
* [SPARK-18872][SQL][TESTS] New test cases for EXISTS subquery (Aggregate, ↵Dilip Biswal2017-02-096-0/+885
| | | | | | | | | | | | | | | | | | | | | | | | | | Having, Orderby, Limit) ## What changes were proposed in this pull request? This PR adds the second set of tests for EXISTS subquery. File name | Brief description ------------------------| ----------------- exists-aggregate.sql |Tests aggregate expressions in outer query and EXISTS subquery. exists-having.sql|Tests HAVING clause in subquery. exists-orderby-limit.sql|Tests EXISTS subquery support with ORDER BY and LIMIT clauses. DB2 results are attached here as reference : [exists-aggregate-db2.txt](https://github.com/apache/spark/files/743287/exists-aggregate-db2.txt) [exists-having-db2.txt](https://github.com/apache/spark/files/743286/exists-having-db2.txt) [exists-orderby-limit-db2.txt](https://github.com/apache/spark/files/743288/exists-orderby-limit-db2.txt) ## How the patch was tested. The test result is compared with the result run from another SQL engine (in this case is IBM DB2). If the result are equivalent, we assume the result is correct. Author: Dilip Biswal <dbiswal@us.ibm.com> Closes #16760 from dilipbiswal/exists-pr2.
* [SPARK-19464][BUILD][HOTFIX] run-tests should use hadoop2.6Dongjoon Hyun2017-02-083-11/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? After SPARK-19464, **SparkPullRequestBuilder** fails because it still tries to use hadoop2.3. **BEFORE** https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/72595/console ``` ======================================================================== Building Spark ======================================================================== [error] Could not find hadoop2.3 in the list. Valid options are ['hadoop2.6', 'hadoop2.7'] Attempting to post to Github... > Post successful. ``` **AFTER** https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/72595/console ``` ======================================================================== Building Spark ======================================================================== [info] Building Spark (w/Hive 1.2.1) using SBT with these arguments: -Phadoop-2.6 -Pmesos -Pkinesis-asl -Pyarn -Phive-thriftserver -Phive test:package streaming-kafka-0-8-assembly/assembly streaming-flume-assembly/assembly streaming-kinesis-asl-assembly/assembly Using /usr/java/jdk1.8.0_60 as default JAVA_HOME. Note, this will be overridden by -java-home if it is set. ``` ## How was this patch tested? Pass the existing test. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #16858 from dongjoon-hyun/hotfix_run-tests.
* [SPARK-19400][ML] Allow GLM to handle intercept only modelactuaryzhang2017-02-083-1/+60
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Intercept-only GLM is failing for non-Gaussian family because of reducing an empty array in IWLS. The following code `val maxTolOfCoefficients = oldCoefficients.toArray.reduce { (x, y) => math.max(math.abs(x), math.abs(y))` fails in the intercept-only model because `oldCoefficients` is empty. This PR fixes this issue. yanboliang srowen imatiach-msft zhengruifeng ## How was this patch tested? New test for intercept only model. Author: actuaryzhang <actuaryzhang10@gmail.com> Closes #16740 from actuaryzhang/interceptOnly.
* [SPARK-19464][BUILD][HOTFIX][TEST-HADOOP2.6] Add back mockito test dep in ↵Sean Owen2017-02-081-0/+6
| | | | | | | | | | | | | | YARN module, as it ends up being required in a Maven build Add back mockito test dep in YARN module, as it ends up being required in a Maven build ## How was this patch tested? PR builder again, but also a local `mvn` run using the command that the broken Jenkins job uses Author: Sean Owen <sowen@cloudera.com> Closes #16853 from srowen/SPARK-19464.2.
* [SPARK-19279][SQL][FOLLOW-UP] Infer Schema for Hive Serde Tablesgatorsmile2017-02-083-1/+53
| | | | | | | | | | | | ### What changes were proposed in this pull request? `table.schema` is always not empty for partitioned tables, because `table.schema` also contains the partitioned columns, even if the original table does not have any column. This PR is to fix the issue. ### How was this patch tested? Added a test case Author: gatorsmile <gatorsmile@gmail.com> Closes #16848 from gatorsmile/inferHiveSerdeSchema.
* [SPARK-19409][BUILD][TEST-MAVEN] Fix ParquetAvroCompatibilitySuite failure ↵Dongjoon Hyun2017-02-082-0/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | due to test dependency on avro ## What changes were proposed in this pull request? After using Apache Parquet 1.8.2, `ParquetAvroCompatibilitySuite` fails on **Maven** test. It is because `org.apache.parquet.avro.AvroParquetWriter` in the test code used new `avro 1.8.0` specific class, `LogicalType`. This PR aims to fix the test dependency of `sql/core` module to use avro 1.8.0. https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/spark-master-test-maven-hadoop-2.7/2530/consoleFull ``` ParquetAvroCompatibilitySuite: *** RUN ABORTED *** java.lang.NoClassDefFoundError: org/apache/avro/LogicalType at org.apache.parquet.avro.AvroParquetWriter.writeSupport(AvroParquetWriter.java:144) ``` ## How was this patch tested? Pass the existing test with **Maven**. ``` $ build/mvn -Pyarn -Phadoop-2.7 -Pkinesis-asl -Phive -Phive-thriftserver test ... [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:07 h [INFO] Finished at: 2017-02-04T05:41:43+00:00 [INFO] Final Memory: 77M/987M [INFO] ------------------------------------------------------------------------ ``` Author: Dongjoon Hyun <dongjoon@apache.org> Closes #16795 from dongjoon-hyun/SPARK-19409-2.
* [SPARK-19464][CORE][YARN][TEST-HADOOP2.6] Remove support for Hadoop 2.5 and ↵Sean Owen2017-02-0834-1201/+202
| | | | | | | | | | | | | | | | | | | earlier ## What changes were proposed in this pull request? - Remove support for Hadoop 2.5 and earlier - Remove reflection and code constructs only needed to support multiple versions at once - Update docs to reflect newer versions - Remove older versions' builds and profiles. ## How was this patch tested? Existing tests Author: Sean Owen <sowen@cloudera.com> Closes #16810 from srowen/SPARK-19464.
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