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* [SPARK-9360] [SQL] Support BinaryType in PrefixComparators for ↵Takeshi YAMAMURO2015-08-054-0/+78
| | | | | | | | | | | | | | | UnsafeExternalSort The current implementation of UnsafeExternalSort uses NoOpPrefixComparator for binary-typed data. So, we need to add BinaryPrefixComparator in PrefixComparators. Author: Takeshi YAMAMURO <linguin.m.s@gmail.com> Closes #7676 from maropu/BinaryTypePrefixComparator and squashes the following commits: fe6f31b [Takeshi YAMAMURO] Apply comments d943c04 [Takeshi YAMAMURO] Add a codegen'd entry for BinaryType in SortPrefix ecf3ac5 [Takeshi YAMAMURO] Support BinaryType in PrefixComparator
* Closes #7917Reynold Xin2015-08-050-0/+0
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* [SPARK-9581][SQL] Add unit test for JSON UDTEmiliano Leporati2015-08-052-1/+21
| | | | | | | | | | | | | | | | This brings #7416 up-to-date by drubbo. Author: Emiliano Leporati <emiliano.leporati@gmail.com> Author: Reynold Xin <rxin@databricks.com> Closes #7917 from rxin/udt-json-test and squashes the following commits: 93e3954 [Reynold Xin] Fix test. 7035308 [Reynold Xin] Merge pull request #7416 from drubbo/master b5bcd94 [Emiliano Leporati] removed unneded case in MyDenseVector::equals 508a399 [Emiliano Leporati] Merge remote branch 'upstream/master' 7569e42 [Emiliano Leporati] using checkAnswer 62daccd [Emiliano Leporati] added coverage for UDTs in JSON RDDs
* [SPARK-9217] [STREAMING] Make the kinesis receiver reliable by recording ↵Tathagata Das2015-08-0511-197/+605
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | sequence numbers This PR is the second one in the larger issue of making the Kinesis integration reliable and provide WAL-free at-least once guarantee. It is based on the design doc - https://docs.google.com/document/d/1k0dl270EnK7uExrsCE7jYw7PYx0YC935uBcxn3p0f58/edit In this PR, I have updated the Kinesis Receiver to do the following. - Control the block generation, by creating its own BlockGenerator with own callback methods and using it to keep track of the ranges of sequence numbers that go into each block. - More specifically, as the KinesisRecordProcessor provides small batches of records, the records are atomically inserted into the block (that is, either the whole batch is in the block, or not). Accordingly the sequence number range of the batch is recorded. Since there may be many batches added to a block, the receiver tracks all the range of sequence numbers that is added to a block. - When the block is ready to be pushed, the block is pushed and the ranges are reported as metadata of the block. In addition, the ranges are used to find out the latest sequence number for each shard that can be checkpointed through the DynamoDB. - Periodically, each KinesisRecordProcessor checkpoints the latest successfully stored sequence number for it own shard. - The array of ranges in the block metadata is used to create KinesisBackedBlockRDDs. The ReceiverInputDStream has been slightly refactored to allow the creation of KinesisBackedBlockRDDs instead of the WALBackedBlockRDDs. Things to be done - [x] Add new test to verify that the sequence numbers are recovered. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #7825 from tdas/kinesis-receiver and squashes the following commits: 2159be9 [Tathagata Das] Fixed bug 569be83 [Tathagata Das] Fix scala style issue bf31e22 [Tathagata Das] Added more documentation to make the kinesis test endpoint more configurable 3ad8361 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into kinesis-receiver c693a63 [Tathagata Das] Removed unnecessary constructor params from KinesisTestUtils e1f1d0a [Tathagata Das] Addressed PR comments b9fa6bf [Tathagata Das] Fix serialization issues f8b7680 [Tathagata Das] Updated doc 33fe43a [Tathagata Das] Added more tests 7997138 [Tathagata Das] Fix style errors a806710 [Tathagata Das] Fixed unit test and use KinesisInputDStream 40a1709 [Tathagata Das] Fixed KinesisReceiverSuite tests 7e44df6 [Tathagata Das] Added documentation and fixed checkpointing 096383f [Tathagata Das] Added test, and addressed some of the comments. 84a7892 [Tathagata Das] fixed scala style issue e19e37d [Tathagata Das] Added license 1cd7b66 [Tathagata Das] Updated kinesis receiver
* [SPARK-9119] [SPARK-8359] [SQL] match Decimal.precision/scale with DecimalTypeDavies Liu2015-08-0416-50/+122
| | | | | | | | | | | | | | Let Decimal carry the correct precision and scale with DecimalType. cc rxin yhuai Author: Davies Liu <davies@databricks.com> Closes #7925 from davies/decimal_scale and squashes the following commits: e19701a [Davies Liu] some tweaks 57d78d2 [Davies Liu] fix tests 5d5bc69 [Davies Liu] match precision and scale with DecimalType
* [SPARK-8231] [SQL] Add array_containsPedro Rodriguez2015-08-046-5/+163
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR is based on #7580 , thanks to EntilZha PR for work on https://issues.apache.org/jira/browse/SPARK-8231 Currently, I have an initial implementation for contains. Based on discussion on JIRA, it should behave same as Hive: https://github.com/apache/hive/blob/master/ql/src/java/org/apache/hadoop/hive/ql/udf/generic/GenericUDFArrayContains.java#L102-L128 Main points are: 1. If the array is empty, null, or the value is null, return false 2. If there is a type mismatch, throw error 3. If comparison is not supported, throw error Closes #7580 Author: Pedro Rodriguez <prodriguez@trulia.com> Author: Pedro Rodriguez <ski.rodriguez@gmail.com> Author: Davies Liu <davies@databricks.com> Closes #7949 from davies/array_contains and squashes the following commits: d3c08bc [Davies Liu] use foreach() to avoid copy bc3d1fe [Davies Liu] fix array_contains 719e37d [Davies Liu] Merge branch 'master' of github.com:apache/spark into array_contains e352cf9 [Pedro Rodriguez] fixed diff from master 4d5b0ff [Pedro Rodriguez] added docs and another type check ffc0591 [Pedro Rodriguez] fixed unit test 7a22deb [Pedro Rodriguez] Changed test to use strings instead of long/ints which are different between python 2 an 3 b5ffae8 [Pedro Rodriguez] fixed pyspark test 4e7dce3 [Pedro Rodriguez] added more docs 3082399 [Pedro Rodriguez] fixed unit test 46f9789 [Pedro Rodriguez] reverted change d3ca013 [Pedro Rodriguez] Fixed type checking to match hive behavior, then added tests to insure this 8528027 [Pedro Rodriguez] added more tests 686e029 [Pedro Rodriguez] fix scala style d262e9d [Pedro Rodriguez] reworked type checking code and added more tests 2517a58 [Pedro Rodriguez] removed unused import 28b4f71 [Pedro Rodriguez] fixed bug with type conversions and re-added tests 12f8795 [Pedro Rodriguez] fix scala style checks e8a20a9 [Pedro Rodriguez] added python df (broken atm) 65b562c [Pedro Rodriguez] made array_contains nullable false 33b45aa [Pedro Rodriguez] reordered test 9623c64 [Pedro Rodriguez] fixed test 4b4425b [Pedro Rodriguez] changed Arrays in tests to Seqs 72cb4b1 [Pedro Rodriguez] added checkInputTypes and docs 69c46fb [Pedro Rodriguez] added tests and codegen 9e0bfc4 [Pedro Rodriguez] initial attempt at implementation
* [SPARK-9540] [MLLIB] optimize PrefixSpan implementationXiangrui Meng2015-08-043-391/+599
| | | | | | | | | | | | | | | | | | | | | | | | | | | | This is a major refactoring of the PrefixSpan implementation. It contains the following changes: 1. Expand prefix with one item at a time. The existing implementation generates all subsets for each itemset, which might have scalability issue when the itemset is large. 2. Use a new internal format. `<(12)(31)>` is represented by `[0, 1, 2, 0, 1, 3, 0]` internally. We use `0` because negative numbers are used to indicates partial prefix items, e.g., `_2` is represented by `-2`. 3. Remember the start indices of all partial projections in the projected postfix to help next projection. 4. Reuse the original sequence array for projected postfixes. 5. Use `Prefix` IDs in aggregation rather than its content. 6. Use `ArrayBuilder` for building primitive arrays. 7. Expose `maxLocalProjDBSize`. 8. Tests are not changed except using `0` instead of `-1` as the delimiter. `Postfix`'s API doc should be a good place to start. Closes #7594 feynmanliang zhangjiajin Author: Xiangrui Meng <meng@databricks.com> Closes #7937 from mengxr/SPARK-9540 and squashes the following commits: 2d0ec31 [Xiangrui Meng] address more comments 48f450c [Xiangrui Meng] address comments from Feynman; fixed a bug in project and added a test 65f90e8 [Xiangrui Meng] naming and documentation 8afc86a [Xiangrui Meng] refactor impl
* Update docs/README.md to put all prereqs together.Reynold Xin2015-08-041-35/+8
| | | | | | | | | | | | This pull request groups all the prereq requirements into a single section. cc srowen shivaram Author: Reynold Xin <rxin@databricks.com> Closes #7951 from rxin/readme-docs and squashes the following commits: ab7ded0 [Reynold Xin] Updated docs/README.md to put all prereqs together.
* [SPARK-9504] [STREAMING] [TESTS] Fix ↵zsxwing2015-08-041-1/+2
| | | | | | | | | | | | | | o.a.s.streaming.StreamingContextSuite.stop gracefully again The test failure is here: https://amplab.cs.berkeley.edu/jenkins/job/Spark-Master-SBT/3150/AMPLAB_JENKINS_BUILD_PROFILE=hadoop1.0,label=centos/testReport/junit/org.apache.spark.streaming/StreamingContextSuite/stop_gracefully/ There is a race condition in TestReceiver that it may add 1 record and increase `TestReceiver.counter` after stopping `BlockGenerator`. This PR just adds `join` to wait the pushing thread. Author: zsxwing <zsxwing@gmail.com> Closes #7934 from zsxwing/SPARK-9504-2 and squashes the following commits: cfd7973 [zsxwing] Wait for the thread to make sure we won't change TestReceiver.counter after stopping BlockGenerator
* [SPARK-9513] [SQL] [PySpark] Add python API for DataFrame functionsDavies Liu2015-08-042-319/+610
| | | | | | | | | | | | | | | | | This adds Python API for those DataFrame functions that is introduced in 1.5. There is issue with serialize byte_array in Python 3, so some of functions (for BinaryType) does not have tests. cc rxin Author: Davies Liu <davies@databricks.com> Closes #7922 from davies/python_functions and squashes the following commits: 8ad942f [Davies Liu] fix test 5fb6ec3 [Davies Liu] fix bugs 3495ed3 [Davies Liu] fix issues ea5f7bb [Davies Liu] Add python API for DataFrame functions
* [SPARK-7119] [SQL] Give script a default serde with the user specific typeszhichao.li2015-08-043-60/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is to address this issue that there would be not compatible type exception when running this: `from (from src select transform(key, value) using 'cat' as (thing1 int, thing2 string)) t select thing1 + 2;` 15/04/24 00:58:55 ERROR CliDriver: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost): java.lang.ClassCastException: org.apache.spark.sql.types.UTF8String cannot be cast to java.lang.Integer at scala.runtime.BoxesRunTime.unboxToInt(BoxesRunTime.java:106) at scala.math.Numeric$IntIsIntegral$.plus(Numeric.scala:57) at org.apache.spark.sql.catalyst.expressions.Add.eval(arithmetic.scala:127) at org.apache.spark.sql.catalyst.expressions.Alias.eval(namedExpressions.scala:118) at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:68) at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:52) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$class.foreach(Iterator.scala:727) at scala.collection.AbstractIterator.foreach(Iterator.scala:1157) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273) at scala.collection.AbstractIterator.to(Iterator.scala:1157) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252) at scala.collection.AbstractIterator.toArray(Iterator.scala:1157) at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:819) at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:819) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1618) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1618) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63) at org.apache.spark.scheduler.Task.run(Task.scala:64) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:209) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722) chenghao-intel marmbrus Author: zhichao.li <zhichao.li@intel.com> Closes #6638 from zhichao-li/transDataType2 and squashes the following commits: a36cc7c [zhichao.li] style b9252a8 [zhichao.li] delete cacheRow f6968a4 [zhichao.li] give script a default serde
* [SPARK-8313] R Spark packages supportBurak Yavuz2015-08-049-35/+538
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | shivaram cafreeman Could you please help me in testing this out? Exposing and running `rPackageBuilder` from inside the shell works, but for some reason, I can't get it to work during Spark Submit. It just starts relaunching Spark Submit. For testing, you may use the R branch with [sbt-spark-package](https://github.com/databricks/sbt-spark-package). You can call spPackage, and then pass the jar using `--jars`. Author: Burak Yavuz <brkyvz@gmail.com> Closes #7139 from brkyvz/r-submit and squashes the following commits: 0de384f [Burak Yavuz] remove unused imports 2 d253708 [Burak Yavuz] removed unused imports 6603d0d [Burak Yavuz] addressed comments 4258ffe [Burak Yavuz] merged master ddfcc06 [Burak Yavuz] added zipping test 3a1be7d [Burak Yavuz] don't zip 77995df [Burak Yavuz] fix URI ac45527 [Burak Yavuz] added zipping of all libs e6bf7b0 [Burak Yavuz] add println ignores 1bc5554 [Burak Yavuz] add assumes for tests 9778e03 [Burak Yavuz] addressed comments b42b300 [Burak Yavuz] merged master ffd134e [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into r-submit d867756 [Burak Yavuz] add apache header eff5ba1 [Burak Yavuz] ready for review 8838edb [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into r-submit e5b5a06 [Burak Yavuz] added doc bb751ce [Burak Yavuz] fix null bug 0226768 [Burak Yavuz] fixed issues 8810beb [Burak Yavuz] R packages support
* [SPARK-9432][SQL] Audit expression unit tests to make sure we pass the ↵Yijie Shen2015-08-045-4/+164
| | | | | | | | | | | | proper numeric ranges JIRA: https://issues.apache.org/jira/browse/SPARK-9432 Author: Yijie Shen <henry.yijieshen@gmail.com> Closes #7933 from yjshen/numeric_ranges and squashes the following commits: e719f78 [Yijie Shen] proper integral range check
* [SPARK-8601] [ML] Add an option to disable standardization for linear regressionHolden Karau2015-08-043-86/+268
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | All compressed sensing applications, and some of the regression use-cases will have better result by turning the feature scaling off. However, if we implement this naively by training the dataset without doing any standardization, the rate of convergency will not be good. This can be implemented by still standardizing the training dataset but we penalize each component differently to get effectively the same objective function but a better numerical problem. As a result, for those columns with high variances, they will be penalized less, and vice versa. Without this, since all the features are standardized, so they will be penalized the same. In R, there is an option for this. standardize Logical flag for x variable standardization, prior to fitting the model sequence. The coefficients are always returned on the original scale. Default is standardize=TRUE. If variables are in the same units already, you might not wish to standardize. See details below for y standardization with family="gaussian". Note that the primary author for this PR is holdenk Author: Holden Karau <holden@pigscanfly.ca> Author: DB Tsai <dbt@netflix.com> Closes #7875 from dbtsai/SPARK-8522 and squashes the following commits: e856036 [DB Tsai] scala doc 596e96c [DB Tsai] minor bbff347 [DB Tsai] naming baa0805 [DB Tsai] touch up d6234ba [DB Tsai] Merge branch 'master' into SPARK-8522-Disable-Linear_featureScaling-Spark-8601-in-Linear_regression 6b1dc09 [Holden Karau] Merge branch 'master' into SPARK-8522-Disable-Linear_featureScaling-Spark-8601-in-Linear_regression 332f140 [Holden Karau] Merge in master eebe10a [Holden Karau] Use same comparision operator throughout the test 3f92935 [Holden Karau] merge b83a41e [Holden Karau] Expand the tests and make them similar to the other PR also providing an option to disable standardization (but for LoR). 0c334a2 [Holden Karau] Remove extra line 99ce053 [Holden Karau] merge in master e54a8a9 [Holden Karau] Fix long line e47c574 [Holden Karau] Add support for L2 without standardization. 55d3a66 [Holden Karau] Add standardization param for linear regression 00a1dc5 [Holden Karau] Add the param to the linearregression impl
* [SPARK-9609] [MLLIB] Fix spelling of Strategy.defaultStrategyFeynman Liang2015-08-043-4/+8
| | | | | | | | | | | jkbradley Author: Feynman Liang <fliang@databricks.com> Closes #7941 from feynmanliang/SPARK-9609-stategy-spelling and squashes the following commits: d2aafb1 [Feynman Liang] Add deprecated backwards compatibility aa090a8 [Feynman Liang] Fix spelling
* [SPARK-9598][SQL] do not expose generic getter in internal rowWenchen Fan2015-08-0411-108/+80
| | | | | | | | Author: Wenchen Fan <cloud0fan@outlook.com> Closes #7932 from cloud-fan/generic-getter and squashes the following commits: c60de4c [Wenchen Fan] do not expose generic getter in internal row
* [SPARK-9586] [ML] Update BinaryClassificationEvaluator to use ↵Joseph K. Bradley2015-08-041-1/+8
| | | | | | | | | | | | | | | | setRawPredictionCol Update BinaryClassificationEvaluator to use setRawPredictionCol, rather than setScoreCol. Deprecated setScoreCol. I don't think setScoreCol was actually used anywhere (based on search). CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #7921 from jkbradley/binary-eval-rawpred and squashes the following commits: e5d7dfa [Joseph K. Bradley] Update BinaryClassificationEvaluator to use setRawPredictionCol
* [SPARK-6485] [MLLIB] [PYTHON] Add ↵Mike Dusenberry2015-08-046-3/+704
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | CoordinateMatrix/RowMatrix/IndexedRowMatrix to PySpark. This PR adds the RowMatrix, IndexedRowMatrix, and CoordinateMatrix distributed matrices to PySpark. Each distributed matrix class acts as a wrapper around the Scala/Java counterpart by maintaining a reference to the Java object. New distributed matrices can be created using factory methods added to DistributedMatrices, which creates the Java distributed matrix and then wraps it with the corresponding PySpark class. This design allows for simple conversion between the various distributed matrices, and lets us re-use the Scala code. Serialization between Python and Java is implemented using DataFrames as needed for IndexedRowMatrix and CoordinateMatrix for simplicity. Associated documentation and unit-tests have also been added. To facilitate code review, this PR implements access to the rows/entries as RDDs, the number of rows & columns, and conversions between the various distributed matrices (not including BlockMatrix), and does not implement the other linear algebra functions of the matrices, although this will be very simple to add now. Author: Mike Dusenberry <mwdusenb@us.ibm.com> Closes #7554 from dusenberrymw/SPARK-6485_Add_CoordinateMatrix_RowMatrix_IndexedMatrix_to_PySpark and squashes the following commits: bb039cb [Mike Dusenberry] Minor documentation update. b887c18 [Mike Dusenberry] Updating the matrix conversion logic again to make it even cleaner. Now, we allow the 'rows' parameter in the constructors to be either an RDD or the Java matrix object. If 'rows' is an RDD, we create a Java matrix object, wrap it, and then store that. If 'rows' is a Java matrix object of the correct type, we just wrap and store that directly. This is only for internal usage, and publicly, we still require 'rows' to be an RDD. We no longer store the 'rows' RDD, and instead just compute it from the Java object when needed. The point of this is that when we do matrix conversions, we do the conversion on the Scala/Java side, which returns a Java object, so we should use that directly, but exposing 'java_matrix' parameter in the public API is not ideal. This non-public feature of allowing 'rows' to be a Java matrix object is documented in the '__init__' constructor docstrings, which are not part of the generated public API, and doctests are also included. 7f0dcb6 [Mike Dusenberry] Updating module docstring. cfc1be5 [Mike Dusenberry] Use 'new SQLContext(matrix.rows.sparkContext)' rather than 'SQLContext.getOrCreate', as the later doesn't guarantee that the SparkContext will be the same as for the matrix.rows data. 687e345 [Mike Dusenberry] Improving conversion performance. This adds an optional 'java_matrix' parameter to the constructors, and pulls the conversion logic out into a '_create_from_java' function. Now, if the constructors are given a valid Java distributed matrix object as 'java_matrix', they will store those internally, rather than create a new one on the Scala/Java side. 3e50b6e [Mike Dusenberry] Moving the distributed matrices to pyspark.mllib.linalg.distributed. 308f197 [Mike Dusenberry] Using properties for better documentation. 1633f86 [Mike Dusenberry] Minor documentation cleanup. f0c13a7 [Mike Dusenberry] CoordinateMatrix should inherit from DistributedMatrix. ffdd724 [Mike Dusenberry] Updating doctests to make documentation cleaner. 3fd4016 [Mike Dusenberry] Updating docstrings. 27cd5f6 [Mike Dusenberry] Simplifying input conversions in the constructors for each distributed matrix. a409cf5 [Mike Dusenberry] Updating doctests to be less verbose by using lists instead of DenseVectors explicitly. d19b0ba [Mike Dusenberry] Updating code and documentation to note that a vector-like object (numpy array, list, etc.) can be used in place of explicit Vector object, and adding conversions when necessary to RowMatrix construction. 4bd756d [Mike Dusenberry] Adding param documentation to IndexedRow and MatrixEntry. c6bded5 [Mike Dusenberry] Move conversion logic from tuples to IndexedRow or MatrixEntry types from within the IndexedRowMatrix and CoordinateMatrix constructors to separate _convert_to_indexed_row and _convert_to_matrix_entry functions. 329638b [Mike Dusenberry] Moving the Experimental tag to the top of each docstring. 0be6826 [Mike Dusenberry] Simplifying doctests by removing duplicated rows/entries RDDs within the various tests. c0900df [Mike Dusenberry] Adding the colons that were accidentally not inserted. 4ad6819 [Mike Dusenberry] Documenting the and parameters. 3b854b9 [Mike Dusenberry] Minor updates to documentation. 10046e8 [Mike Dusenberry] Updating documentation to use class constructors instead of the removed DistributedMatrices factory methods. 119018d [Mike Dusenberry] Adding static methods to each of the distributed matrix classes to consolidate conversion logic. 4d7af86 [Mike Dusenberry] Adding type checks to the constructors. Although it is slightly verbose, it is better for the user to have a good error message than a cryptic stacktrace. 93b6a3d [Mike Dusenberry] Pulling the DistributedMatrices Python class out of this pull request. f6f3c68 [Mike Dusenberry] Pulling the DistributedMatrices Scala class out of this pull request. 6a3ecb7 [Mike Dusenberry] Updating pattern matching. 08f287b [Mike Dusenberry] Slight reformatting of the documentation. a245dc0 [Mike Dusenberry] Updating Python doctests for compatability between Python 2 & 3. Since Python 3 removed the idea of a separate 'long' type, all values that would have been outputted as a 'long' (ex: '4L') will now be treated as an 'int' and outputed as one (ex: '4'). The doctests now explicitly convert to ints so that both Python 2 and 3 will have the same output. This is fine since the values are all small, and thus can be easily represented as ints. 4d3a37e [Mike Dusenberry] Reformatting a few long Python doctest lines. 7e3ca16 [Mike Dusenberry] Fixing long lines. f721ead [Mike Dusenberry] Updating documentation for each of the distributed matrices. ab0e8b6 [Mike Dusenberry] Updating unit test to be more useful. dda2f89 [Mike Dusenberry] Added wrappers for the conversions between the various distributed matrices. Added logic to be able to access the rows/entries of the distributed matrices, which requires serialization through DataFrames for IndexedRowMatrix and CoordinateMatrix types. Added unit tests. 0cd7166 [Mike Dusenberry] Implemented the CoordinateMatrix API in PySpark, following the idea of the IndexedRowMatrix API, including using DataFrames for serialization. 3c369cb [Mike Dusenberry] Updating the architecture a bit to make conversions between the various distributed matrix types easier. The different distributed matrix classes are now only wrappers around the Java objects, and take the Java object as an argument during construction. This way, we can call for example on an , which returns a reference to a Java RowMatrix object, and then construct a PySpark RowMatrix object wrapped around the Java object. This is analogous to the behavior of PySpark RDDs and DataFrames. We now delegate creation of the various distributed matrices from scratch in PySpark to the factory methods on . 4bdd09b [Mike Dusenberry] Implemented the IndexedRowMatrix API in PySpark, following the idea of the RowMatrix API. Note that for the IndexedRowMatrix, we use DataFrames to serialize the data between Python and Scala/Java, so we accept PySpark RDDs, then convert to a DataFrame, then convert back to RDDs on the Scala/Java side before constructing the IndexedRowMatrix. 23bf1ec [Mike Dusenberry] Updating documentation to add PySpark RowMatrix. Inserting newline above doctest so that it renders properly in API docs. b194623 [Mike Dusenberry] Updating design to have a PySpark RowMatrix simply create and keep a reference to a wrapper over a Java RowMatrix. Updating DistributedMatrices factory methods to accept numRows and numCols with default values. Updating PySpark DistributedMatrices factory method to simply create a PySpark RowMatrix. Adding additional doctests for numRows and numCols parameters. bc2d220 [Mike Dusenberry] Adding unit tests for RowMatrix methods. d7e316f [Mike Dusenberry] Implemented the RowMatrix API in PySpark by doing the following: Added a DistributedMatrices class to contain factory methods for creating the various distributed matrices. Added a factory method for creating a RowMatrix from an RDD of Vectors. Added a createRowMatrix function to the PythonMLlibAPI to interface with the factory method. Added DistributedMatrix, DistributedMatrices, and RowMatrix classes to the pyspark.mllib.linalg api.
* [SPARK-9582] [ML] LDA cleanupsJoseph K. Bradley2015-08-042-43/+58
| | | | | | | | | | | | | | | | Small cleanups to recent LDA additions and docs. CC: feynmanliang Author: Joseph K. Bradley <joseph@databricks.com> Closes #7916 from jkbradley/lda-cleanups and squashes the following commits: f7021d9 [Joseph K. Bradley] broadcasting large matrices for LDA in local model and online learning 97947aa [Joseph K. Bradley] a few more cleanups 5b03f88 [Joseph K. Bradley] reverted split of lda log likelihood c566915 [Joseph K. Bradley] small edit to make review easier 63f6c7d [Joseph K. Bradley] clarified log likelihood for lda models
* [SPARK-9447] [ML] [PYTHON] Added HasRawPredictionCol, HasProbabilityCol to ↵Joseph K. Bradley2015-08-041-1/+12
| | | | | | | | | | | | | | | RandomForestClassifier Added HasRawPredictionCol, HasProbabilityCol to RandomForestClassifier, plus doc tests for those columns. CC: holdenk yanboliang Author: Joseph K. Bradley <joseph@databricks.com> Closes #7903 from jkbradley/rf-prob-python and squashes the following commits: c62a83f [Joseph K. Bradley] made unit test more robust 14eeba2 [Joseph K. Bradley] added HasRawPredictionCol, HasProbabilityCol to RandomForestClassifier in PySpark
* [SPARK-9602] remove "Akka/Actor" words from commentsCodingCat2015-08-0416-31/+27
| | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-9602 Although we have hidden Akka behind RPC interface, I found that the Akka/Actor-related comments are still spreading everywhere. To make it consistent, we shall remove "actor"/"akka" words from the comments... Author: CodingCat <zhunansjtu@gmail.com> Closes #7936 from CodingCat/SPARK-9602 and squashes the following commits: e8296a3 [CodingCat] remove actor words from comments
* [SPARK-9452] [SQL] Support records larger than page size in UnsafeExternalSorterJosh Rosen2015-08-048-167/+372
| | | | | | | | | | | | | | | | | This patch extends UnsafeExternalSorter to support records larger than the page size. The basic strategy is the same as in #7762: store large records in their own overflow pages. Author: Josh Rosen <joshrosen@databricks.com> Closes #7891 from JoshRosen/large-records-in-sql-sorter and squashes the following commits: 967580b [Josh Rosen] Merge remote-tracking branch 'origin/master' into large-records-in-sql-sorter 948c344 [Josh Rosen] Add large records tests for KV sorter. 3c17288 [Josh Rosen] Combine memory and disk cleanup into general cleanupResources() method 380f217 [Josh Rosen] Merge remote-tracking branch 'origin/master' into large-records-in-sql-sorter 27eafa0 [Josh Rosen] Fix page size in PackedRecordPointerSuite a49baef [Josh Rosen] Address initial round of review comments 3edb931 [Josh Rosen] Remove accidentally-committed debug statements. 2b164e2 [Josh Rosen] Support large records in UnsafeExternalSorter.
* [SPARK-9553][SQL] remove the no-longer-necessary createCode and ↵Wenchen Fan2015-08-042-154/+17
| | | | | | | | | | | createStructCode, and replace the usage Author: Wenchen Fan <cloud0fan@outlook.com> Closes #7890 from cloud-fan/minor and squashes the following commits: c3b1be3 [Wenchen Fan] fix style b0cbe2e [Wenchen Fan] remove the createCode and createStructCode, and replace the usage of them by createStructCode
* [SPARK-9606] [SQL] Ignore flaky thrift server testsMichael Armbrust2015-08-041-1/+3
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #7939 from marmbrus/turnOffThriftTests and squashes the following commits: 80d618e [Michael Armbrust] [SPARK-9606][SQL] Ignore flaky thrift server tests
* [SPARK-8069] [ML] Add multiclass thresholds for ProbabilisticClassifierHolden Karau2015-08-0414-40/+265
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR replaces the old "threshold" with a generalized "thresholds" Param. We keep getThreshold,setThreshold for backwards compatibility for binary classification. Note that the primary author of this PR is holdenk Author: Holden Karau <holden@pigscanfly.ca> Author: Joseph K. Bradley <joseph@databricks.com> Closes #7909 from jkbradley/holdenk-SPARK-8069-add-cutoff-aka-threshold-to-random-forest and squashes the following commits: 3952977 [Joseph K. Bradley] fixed pyspark doc test 85febc8 [Joseph K. Bradley] made python unit tests a little more robust 7eb1d86 [Joseph K. Bradley] small cleanups 6cc2ed8 [Joseph K. Bradley] Fixed remaining merge issues. 0255e44 [Joseph K. Bradley] Many cleanups for thresholds, some more tests 7565a60 [Holden Karau] fix pep8 style checks, add a getThreshold method similar to our LogisticRegression.scala one for API compat be87f26 [Holden Karau] Convert threshold to thresholds in the python code, add specialized support for Array[Double] to shared parems codegen, etc. 6747dad [Holden Karau] Override raw2prediction for ProbabilisticClassifier, fix some tests 25df168 [Holden Karau] Fix handling of thresholds in LogisticRegression c02d6c0 [Holden Karau] No default for thresholds 5e43628 [Holden Karau] CR feedback and fixed the renamed test f3fbbd1 [Holden Karau] revert the changes to random forest :( 51f581c [Holden Karau] Add explicit types to public methods, fix long line f7032eb [Holden Karau] Fix a java test bug, remove some unecessary changes adf15b4 [Holden Karau] rename the classifier suite test to ProbabilisticClassifierSuite now that we only have it in Probabilistic 398078a [Holden Karau] move the thresholding around a bunch based on the design doc 4893bdc [Holden Karau] Use numtrees of 3 since previous result was tied (one tree for each) and the switch from different max methods picked a different element (since they were equal I think this is ok) 638854c [Holden Karau] Add a scala RandomForestClassifierSuite test based on corresponding python test e09919c [Holden Karau] Fix return type, I need more coffee.... 8d92cac [Holden Karau] Use ClassifierParams as the head 3456ed3 [Holden Karau] Add explicit return types even though just test a0f3b0c [Holden Karau] scala style fixes 6f14314 [Holden Karau] Since hasthreshold/hasthresholds is in root classifier now ffc8dab [Holden Karau] Update the sharedParams 0420290 [Holden Karau] Allow us to override the get methods selectively 978e77a [Holden Karau] Move HasThreshold into classifier params and start defining the overloaded getThreshold/getThresholds functions 1433e52 [Holden Karau] Revert "try and hide threshold but chainges the API so no dice there" 1f09a2e [Holden Karau] try and hide threshold but chainges the API so no dice there efb9084 [Holden Karau] move setThresholds only to where its used 6b34809 [Holden Karau] Add a test with thresholding for the RFCS 74f54c3 [Holden Karau] Fix creation of vote array 1986fa8 [Holden Karau] Setting the thresholds only makes sense if the underlying class hasn't overridden predict, so lets push it down. 2f44b18 [Holden Karau] Add a global default of null for thresholds param f338cfc [Holden Karau] Wait that wasn't a good idea, Revert "Some progress towards unifying threshold and thresholds" 634b06f [Holden Karau] Some progress towards unifying threshold and thresholds 85c9e01 [Holden Karau] Test passes again... little fnur 099c0f3 [Holden Karau] Move thresholds around some more (set on model not trainer) 0f46836 [Holden Karau] Start adding a classifiersuite f70eb5e [Holden Karau] Fix test compile issues a7d59c8 [Holden Karau] Move thresholding into Classifier trait 5d999d2 [Holden Karau] Some more progress, start adding a test (maybe try and see if we can find a better thing to use for the base of the test) 1fed644 [Holden Karau] Use thresholds to scale scores in random forest classifcation 31d6bf2 [Holden Karau] Start threading the threshold info through 0ef228c [Holden Karau] Add hasthresholds
* [SPARK-9512][SQL] Revert SPARK-9251, Allow evaluation while sortingMichael Armbrust2015-08-043-99/+8
| | | | | | | | | | | The analysis rule has a bug and we ended up making the sorter still capable of doing evaluation, so lets revert this for now. Author: Michael Armbrust <michael@databricks.com> Closes #7906 from marmbrus/revertSortProjection and squashes the following commits: 2da6972 [Michael Armbrust] unrevert unrelated changes 4f2b00c [Michael Armbrust] Revert "[SPARK-9251][SQL] do not order by expressions which still need evaluation"
* [SPARK-9562] Change reference to amplab/spark-ec2 from mesos/Shivaram Venkataraman2015-08-041-1/+1
| | | | | | | | | | cc srowen pwendell nchammas Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #7899 from shivaram/spark-ec2-move and squashes the following commits: 7cc22c9 [Shivaram Venkataraman] Change reference to amplab/spark-ec2 from mesos/
* [SPARK-9541] [SQL] DataTimeUtils cleanupYijie Shen2015-08-041-85/+57
| | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-9541 Author: Yijie Shen <henry.yijieshen@gmail.com> Closes #7870 from yjshen/datetime_cleanup and squashes the following commits: 9203e33 [Yijie Shen] revert getMonth & getDayOfMonth 5cad119 [Yijie Shen] rebase code 7d62a74 [Yijie Shen] remove tmp tuple inside split date e98aaac [Yijie Shen] DataTimeUtils cleanup
* [SPARK-8246] [SQL] Implement get_json_objectDavies Liu2015-08-0417-1/+613
| | | | | | | | | | | | | | | | | | | | | | | | | This is based on #7485 , thanks to NathanHowell Tests were copied from Hive, but do not seem to be super comprehensive. I've generally replicated Hive's unusual behavior rather than following a JSONPath reference, except for one case (as noted in the comments). I don't know if there is a way of fully replicating Hive's behavior without a slower TreeNode implementation, so I've erred on the side of performance instead. Author: Davies Liu <davies@databricks.com> Author: Yin Huai <yhuai@databricks.com> Author: Nathan Howell <nhowell@godaddy.com> Closes #7901 from davies/get_json_object and squashes the following commits: 3ace9b9 [Davies Liu] Merge branch 'get_json_object' of github.com:davies/spark into get_json_object 98766fc [Davies Liu] Merge branch 'master' of github.com:apache/spark into get_json_object a7dc6d0 [Davies Liu] Update JsonExpressionsSuite.scala c818519 [Yin Huai] new results. 18ce26b [Davies Liu] fix tests 6ac29fb [Yin Huai] Golden files. 25eebef [Davies Liu] use HiveQuerySuite e0ac6ec [Yin Huai] Golden answer files. 940c060 [Davies Liu] tweat code style 44084c5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into get_json_object 9192d09 [Nathan Howell] Match Hive’s behavior for unwrapping arrays of one element 8dab647 [Nathan Howell] [SPARK-8246] [SQL] Implement get_json_object
* [SPARK-8244] [SQL] string function: find in setTarek Auel2015-08-046-4/+87
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR is based on #7186 (just fix the conflict), thanks to tarekauel . find_in_set(string str, string strList): int Returns the first occurance of str in strList where strList is a comma-delimited string. Returns null if either argument is null. Returns 0 if the first argument contains any commas. For example, find_in_set('ab', 'abc,b,ab,c,def') returns 3. Only add this to SQL, not DataFrame. Closes #7186 Author: Tarek Auel <tarek.auel@googlemail.com> Author: Davies Liu <davies@databricks.com> Closes #7900 from davies/find_in_set and squashes the following commits: 4334209 [Davies Liu] Merge branch 'master' of github.com:apache/spark into find_in_set 8f00572 [Davies Liu] Merge branch 'master' of github.com:apache/spark into find_in_set 243ede4 [Tarek Auel] [SPARK-8244][SQL] hive compatibility 1aaf64e [Tarek Auel] [SPARK-8244][SQL] unit test fix e4093a4 [Tarek Auel] [SPARK-8244][SQL] final modifier for COMMA_UTF8 0d05df5 [Tarek Auel] Merge branch 'master' into SPARK-8244 208d710 [Tarek Auel] [SPARK-8244] address comments & bug fix 71b2e69 [Tarek Auel] [SPARK-8244] find_in_set 66c7fda [Tarek Auel] Merge branch 'master' into SPARK-8244 61b8ca2 [Tarek Auel] [SPARK-8224] removed loop and split; use unsafe String comparison 4f75a65 [Tarek Auel] Merge branch 'master' into SPARK-8244 e3b20c8 [Tarek Auel] [SPARK-8244] added type check 1c2bbb7 [Tarek Auel] [SPARK-8244] findInSet
* [SPARK-9583] [BUILD] Do not print mvn debug messages to stdout.Marcelo Vanzin2015-08-041-3/+3
| | | | | | | | | | This allows build/mvn to be used by make-distribution.sh. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #7915 from vanzin/SPARK-9583 and squashes the following commits: 6469e60 [Marcelo Vanzin] [SPARK-9583] [build] Do not print mvn debug messages to stdout.
* [SPARK-2016] [WEBUI] RDD partition table pagination for the RDD PageCarson Wang2015-08-043-45/+209
| | | | | | | | | | | | | | | Add pagination for the RDD page to avoid unresponsive UI when the number of the RDD partitions is large. Before: ![rddpagebefore](https://cloud.githubusercontent.com/assets/9278199/8951533/3d9add54-3601-11e5-99d0-5653b473c49b.png) After: ![rddpageafter](https://cloud.githubusercontent.com/assets/9278199/8951536/439d66e0-3601-11e5-9cee-1b380fe6620d.png) Author: Carson Wang <carson.wang@intel.com> Closes #7692 from carsonwang/SPARK-2016 and squashes the following commits: 03c7168 [Carson Wang] Fix style issues 612c18c [Carson Wang] RDD partition table pagination for the RDD Page
* [SPARK-8064] [BUILD] Follow-up. Undo change from SPARK-9507 that was ↵tedyu2015-08-041-3/+0
| | | | | | | | | | | | accidentally reverted This PR removes the dependency reduced POM hack brought back by #7191 Author: tedyu <yuzhihong@gmail.com> Closes #7919 from tedyu/master and squashes the following commits: 1bfbd7b [tedyu] [BUILD] Remove dependency reduced POM hack
* [SPARK-9534] [BUILD] Enable javac lint for scalac parity; fix a lot of build ↵Sean Owen2015-08-0429-107/+167
| | | | | | | | | | | | | | warnings, 1.5.0 edition Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process. I'll explain several of the changes inline in comments. Author: Sean Owen <sowen@cloudera.com> Closes #7862 from srowen/SPARK-9534 and squashes the following commits: ea51618 [Sean Owen] Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process.
* [SPARK-3190] [GRAPHX] Fix VertexRDD.count() overflow regressionAnkur Dave2015-08-031-1/+1
| | | | | | | | | | SPARK-3190 was originally fixed by 96df92906978c5f58e0cc8ff5eebe5b35a08be3b, but a5ef58113667ff73562ce6db381cff96a0b354b0 introduced a regression during refactoring. This commit fixes the regression. Author: Ankur Dave <ankurdave@gmail.com> Closes #7923 from ankurdave/SPARK-3190-reopening and squashes the following commits: a3e1b23 [Ankur Dave] Fix VertexRDD.count() overflow regression
* [SPARK-9521] [DOCS] Addendum. Require Maven 3.3.3+ in the buildSean Owen2015-08-041-1/+2
| | | | | | | | | | Follow on for #7852: Building Spark doc needs to refer to new Maven requirement too Author: Sean Owen <sowen@cloudera.com> Closes #7905 from srowen/SPARK-9521.2 and squashes the following commits: 73285df [Sean Owen] Follow on for #7852: Building Spark doc needs to refer to new Maven requirement too
* [SPARK-9577][SQL] Surface concrete iterator types in various sort classes.Reynold Xin2015-08-034-85/+65
| | | | | | | | | | We often return abstract iterator types in various sort-related classes (e.g. UnsafeKVExternalSorter). It is actually better to return a more concrete type, so the callsite uses that type and JIT can inline the iterator calls. Author: Reynold Xin <rxin@databricks.com> Closes #7911 from rxin/surface-concrete-type and squashes the following commits: 0422add [Reynold Xin] [SPARK-9577][SQL] Surface concrete iterator types in various sort classes.
* [SPARK-8416] highlight and topping the executor threads in thread dumping pageCodingCat2015-08-032-3/+29
| | | | | | | | | | | | | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-8416 To facilitate debugging, I made this patch with three changes: * render the executor-thread and non executor-thread entries with different background colors * put the executor threads on the top of the list * sort the threads alphabetically Author: CodingCat <zhunansjtu@gmail.com> Closes #7808 from CodingCat/SPARK-8416 and squashes the following commits: 34fc708 [CodingCat] fix className d7b79dd [CodingCat] lowercase threadName d032882 [CodingCat] sort alphabetically and change the css class name f0513b1 [CodingCat] change the color & group threads by name 2da6e06 [CodingCat] small fix 3fc9f36 [CodingCat] define classes in webui.css 8ee125e [CodingCat] highlight and put on top the executor threads in thread dumping page
* [SPARK-9263] Added flags to exclude dependencies when using --packagesBurak Yavuz2015-08-034-15/+57
| | | | | | | | | | | | | | | | | | While the functionality is there to exclude packages, there are no flags that allow users to exclude dependencies, in case of dependency conflicts. We should provide users with a flag to add dependency exclusions in case the packages are not resolved properly (or not available due to licensing). The flag I added was --packages-exclude, but I'm open on renaming it. I also added property flags in case people would like to use a conf file to provide dependencies, which is possible if there is a long list of dependencies or exclusions. cc andrewor14 vanzin pwendell Author: Burak Yavuz <brkyvz@gmail.com> Closes #7599 from brkyvz/packages-exclusions and squashes the following commits: 636f410 [Burak Yavuz] addressed nits 6e54ede [Burak Yavuz] is this the culprit b5e508e [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into packages-exclusions 154f5db [Burak Yavuz] addressed initial comments 1536d7a [Burak Yavuz] Added flags to exclude packages using --packages-exclude
* [SPARK-9483] Fix UTF8String.getPrefix for big-endian.Matthew Brandyberry2015-08-031-10/+30
| | | | | | | | | | | Previous code assumed little-endian. Author: Matthew Brandyberry <mbrandy@us.ibm.com> Closes #7902 from mtbrandy/SPARK-9483 and squashes the following commits: ec31df8 [Matthew Brandyberry] [SPARK-9483] Changes from review comments. 17d54c6 [Matthew Brandyberry] [SPARK-9483] Fix UTF8String.getPrefix for big-endian.
* Add a prerequisites section for building docsShivaram Venkataraman2015-08-031-0/+10
| | | | | | | | | | | | This puts all the install commands that need to be run in one section instead of being spread over many paragraphs cc rxin Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu> Closes #7912 from shivaram/docs-setup-readme and squashes the following commits: cf7a204 [Shivaram Venkataraman] Add a prerequisites section for building docs
* [SPARK-8874] [ML] Add missing methods in Word2VecMechCoder2015-08-032-1/+99
| | | | | | | | | | | | | | | | | | Add missing methods 1. getVectors 2. findSynonyms to W2Vec scala and python API mengxr Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #7263 from MechCoder/missing_methods_w2vec and squashes the following commits: 149d5ca [MechCoder] minor doc 69d91b7 [MechCoder] [SPARK-8874] [ML] Add missing methods in Word2Vec
* [SPARK-8064] [SQL] Build against Hive 1.2.1Steve Loughran2015-08-0379-584/+2861
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Cherry picked the parts of the initial SPARK-8064 WiP branch needed to get sql/hive to compile against hive 1.2.1. That's the ASF release packaged under org.apache.hive, not any fork. Tests not run yet: that's what the machines are for Author: Steve Loughran <stevel@hortonworks.com> Author: Cheng Lian <lian@databricks.com> Author: Michael Armbrust <michael@databricks.com> Author: Patrick Wendell <patrick@databricks.com> Closes #7191 from steveloughran/stevel/feature/SPARK-8064-hive-1.2-002 and squashes the following commits: 7556d85 [Cheng Lian] Updates .q files and corresponding golden files ef4af62 [Steve Loughran] Merge commit '6a92bb09f46a04d6cd8c41bdba3ecb727ebb9030' into stevel/feature/SPARK-8064-hive-1.2-002 6a92bb0 [Cheng Lian] Overrides HiveConf time vars dcbb391 [Cheng Lian] Adds com.twitter:parquet-hadoop-bundle:1.6.0 for Hive Parquet SerDe 0bbe475 [Steve Loughran] SPARK-8064 scalastyle rejects the standard Hadoop ASF license header... fdf759b [Steve Loughran] SPARK-8064 classpath dependency suite to be in sync with shading in final (?) hive-exec spark 7a6c727 [Steve Loughran] SPARK-8064 switch to second staging repo of the spark-hive artifacts. This one has the protobuf-shaded hive-exec jar 376c003 [Steve Loughran] SPARK-8064 purge duplicate protobuf declaration 2c74697 [Steve Loughran] SPARK-8064 switch to the protobuf shaded hive-exec jar with tests to chase it down cc44020 [Steve Loughran] SPARK-8064 remove hadoop.version from runtest.py, as profile will fix that automatically. 6901fa9 [Steve Loughran] SPARK-8064 explicit protobuf import da310dc [Michael Armbrust] Fixes for Hive tests. a775a75 [Steve Loughran] SPARK-8064 cherry-pick-incomplete 7404f34 [Patrick Wendell] Add spark-hive staging repo 832c164 [Steve Loughran] SPARK-8064 try to supress compiler warnings on Complex.java pasted-thrift-code 312c0d4 [Steve Loughran] SPARK-8064 maven/ivy dependency purge; calcite declaration needed fa5ae7b [Steve Loughran] HIVE-8064 fix up hive-thriftserver dependencies and cut back on evicted references in the hive- packages; this keeps mvn and ivy resolution compatible, as the reconciliation policy is "by hand" c188048 [Steve Loughran] SPARK-8064 manage the Hive depencencies to that -things that aren't needed are excluded -sql/hive built with ivy is in sync with the maven reconciliation policy, rather than latest-first 4c8be8d [Cheng Lian] WIP: Partial fix for Thrift server and CLI tests 314eb3c [Steve Loughran] SPARK-8064 deprecation warning noise in one of the tests 17b0341 [Steve Loughran] SPARK-8064 IDE-hinted cleanups of Complex.java to reduce compiler warnings. It's all autogenerated code, so still ugly. d029b92 [Steve Loughran] SPARK-8064 rely on unescaping to have already taken place, so go straight to map of serde options 23eca7e [Steve Loughran] HIVE-8064 handle raw and escaped property tokens 54d9b06 [Steve Loughran] SPARK-8064 fix compilation regression surfacing from rebase 0b12d5f [Steve Loughran] HIVE-8064 use subset of hive complex type whose types deserialize fce73b6 [Steve Loughran] SPARK-8064 poms rely implicitly on the version of kryo chill provides fd3aa5d [Steve Loughran] SPARK-8064 version of hive to d/l from ivy is 1.2.1 dc73ece [Steve Loughran] SPARK-8064 revert to master's determinstic pushdown strategy d3c1e4a [Steve Loughran] SPARK-8064 purge UnionType 051cc21 [Steve Loughran] SPARK-8064 switch to an unshaded version of hive-exec-core, which must have been built with Kryo 2.21. This currently looks for a (locally built) version 1.2.1.spark 6684c60 [Steve Loughran] SPARK-8064 ignore RTE raised in blocking process.exitValue() call e6121e5 [Steve Loughran] SPARK-8064 address review comments aa43dc6 [Steve Loughran] SPARK-8064 more robust teardown on JavaMetastoreDatasourcesSuite f2bff01 [Steve Loughran] SPARK-8064 better takeup of asynchronously caught error text 8b1ef38 [Steve Loughran] SPARK-8064: on failures executing spark-submit in HiveSparkSubmitSuite, print command line and all logged output. 5a9ce6b [Steve Loughran] SPARK-8064 add explicit reason for kv split failure, rather than array OOB. *does not address the issue* 642b63a [Steve Loughran] SPARK-8064 reinstate something cut briefly during rebasing 97194dc [Steve Loughran] SPARK-8064 add extra logging to the YarnClusterSuite classpath test. There should be no reason why this is failing on jenkins, but as it is (and presumably its CP-related), improve the logging including any exception raised. 335357f [Steve Loughran] SPARK-8064 fail fast on thrive process spawning tests on exit codes and/or error string patterns seen in log. 3ed872f [Steve Loughran] SPARK-8064 rename field double to dbl bca55e5 [Steve Loughran] SPARK-8064 missed one of the `date` escapes 41d6479 [Steve Loughran] SPARK-8064 wrap tests with withTable() calls to avoid table-exists exceptions 2bc29a4 [Steve Loughran] SPARK-8064 ParquetSuites to escape `date` field name 1ab9bc4 [Steve Loughran] SPARK-8064 TestHive to use sered2.thrift.test.Complex bf3a249 [Steve Loughran] SPARK-8064: more resubmit than fix; tighten startup timeout to 60s. Still no obvious reason why jersey server code in spark-assembly isn't being picked up -it hasn't been shaded c829b8f [Steve Loughran] SPARK-8064: reinstate yarn-rm-server dependencies to hive-exec to ensure that jersey server is on classpath on hadoop versions < 2.6 0b0f738 [Steve Loughran] SPARK-8064: thrift server startup to fail fast on any exception in the main thread 13abaf1 [Steve Loughran] SPARK-8064 Hive compatibilty tests sin sync with explain/show output from Hive 1.2.1 d14d5ea [Steve Loughran] SPARK-8064: DATE is now a predicate; you can't use it as a field in select ops 26eef1c [Steve Loughran] SPARK-8064: HIVE-9039 renamed TOK_UNION => TOK_UNIONALL while adding TOK_UNIONDISTINCT 3d64523 [Steve Loughran] SPARK-8064 improve diagns on uknown token; fix scalastyle failure d0360f6 [Steve Loughran] SPARK-8064: delicate merge in of the branch vanzin/hive-1.1 1126e5a [Steve Loughran] SPARK-8064: name of unrecognized file format wasn't appearing in error text 8cb09c4 [Steve Loughran] SPARK-8064: test resilience/assertion improvements. Independent of the rest of the work; can be backported to earlier versions dec12cb [Steve Loughran] SPARK-8064: when a CLI suite test fails include the full output text in the raised exception; this ensures that the stdout/stderr is included in jenkins reports, so it becomes possible to diagnose the cause. 463a670 [Steve Loughran] SPARK-8064 run-tests.py adds a hadoop-2.6 profile, and changes info messages to say "w/Hive 1.2.1" in console output 2531099 [Steve Loughran] SPARK-8064 successful attempt to get rid of pentaho as a transitive dependency of hive-exec 1d59100 [Steve Loughran] SPARK-8064 (unsuccessful) attempt to get rid of pentaho as a transitive dependency of hive-exec 75733fc [Steve Loughran] SPARK-8064 change thrift binary startup message to "Starting ThriftBinaryCLIService on port" 3ebc279 [Steve Loughran] SPARK-8064 move strings used to check for http/bin thrift services up into constants c80979d [Steve Loughran] SPARK-8064: SparkSQLCLIDriver drops remote mode support. CLISuite Tests pass instead of timing out: undetected regression? 27e8370 [Steve Loughran] SPARK-8064 fix some style & IDE warnings 00e50d6 [Steve Loughran] SPARK-8064 stop excluding hive shims from dependency (commented out , for now) cb4f142 [Steve Loughran] SPARK-8054 cut pentaho dependency from calcite f7aa9cb [Steve Loughran] SPARK-8064 everything compiles with some commenting and moving of classes into a hive package 6c310b4 [Steve Loughran] SPARK-8064 subclass Hive ServerOptionsProcessor to make it public again f61a675 [Steve Loughran] SPARK-8064 thrift server switched to Hive 1.2.1, though it doesn't compile everywhere 4890b9d [Steve Loughran] SPARK-8064, build against Hive 1.2.1
* Revert "[SPARK-9372] [SQL] Filter nulls in join keys"Reynold Xin2015-08-0311-572/+37
| | | | This reverts commit 687c8c37150f4c93f8e57d86bb56321a4891286b.
* [SPARK-8735] [SQL] Expose memory usage for shuffles, joins and aggregationsAndrew Or2015-08-0351-163/+1070
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch exposes the memory used by internal data structures on the SparkUI. This tracks memory used by all spilling operations and SQL operators backed by Tungsten, e.g. `BroadcastHashJoin`, `ExternalSort`, `GeneratedAggregate` etc. The metric exposed is "peak execution memory", which broadly refers to the peak in-memory sizes of each of these data structure. A separate patch will extend this by linking the new information to the SQL operators themselves. <img width="950" alt="screen shot 2015-07-29 at 7 43 17 pm" src="https://cloud.githubusercontent.com/assets/2133137/8974776/b90fc980-362a-11e5-9e2b-842da75b1641.png"> <img width="802" alt="screen shot 2015-07-29 at 7 43 05 pm" src="https://cloud.githubusercontent.com/assets/2133137/8974777/baa76492-362a-11e5-9b77-e364a6a6b64e.png"> <!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/7770) <!-- Reviewable:end --> Author: Andrew Or <andrew@databricks.com> Closes #7770 from andrewor14/expose-memory-metrics and squashes the following commits: 9abecb9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics f5b0d68 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics d7df332 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics 8eefbc5 [Andrew Or] Fix non-failing tests 9de2a12 [Andrew Or] Fix tests due to another logical merge conflict 876bfa4 [Andrew Or] Fix failing test after logical merge conflict 361a359 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics 40b4802 [Andrew Or] Fix style? d0fef87 [Andrew Or] Fix tests? b3b92f6 [Andrew Or] Address comments 0625d73 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics c00a197 [Andrew Or] Fix potential NPEs 10da1cd [Andrew Or] Fix compile 17f4c2d [Andrew Or] Fix compile? a87b4d0 [Andrew Or] Fix compile? d70874d [Andrew Or] Fix test compile + address comments 2840b7d [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics 6aa2f7a [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics b889a68 [Andrew Or] Minor changes: comments, spacing, style 663a303 [Andrew Or] UnsafeShuffleWriter: update peak memory before close d090a94 [Andrew Or] Fix style 2480d84 [Andrew Or] Expand test coverage 5f1235b [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics 1ecf678 [Andrew Or] Minor changes: comments, style, unused imports 0b6926c [Andrew Or] Oops 111a05e [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics a7a39a5 [Andrew Or] Strengthen presence check for accumulator a919eb7 [Andrew Or] Add tests for unsafe shuffle writer 23c845d [Andrew Or] Add tests for SQL operators a757550 [Andrew Or] Address comments b5c51c1 [Andrew Or] Re-enable test in JavaAPISuite 5107691 [Andrew Or] Add tests for internal accumulators 59231e4 [Andrew Or] Fix tests 9528d09 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics 5b5e6f3 [Andrew Or] Add peak execution memory to summary table + tooltip 92b4b6b [Andrew Or] Display peak execution memory on the UI eee5437 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics d9b9015 [Andrew Or] Track execution memory in unsafe shuffles 770ee54 [Andrew Or] Track execution memory in broadcast joins 9c605a4 [Andrew Or] Track execution memory in GeneratedAggregate 9e824f2 [Andrew Or] Add back execution memory tracking for *ExternalSort 4ef4cb1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into expose-memory-metrics e6c3e2f [Andrew Or] Move internal accumulators creation to Stage a417592 [Andrew Or] Expose memory metrics in UnsafeExternalSorter 3c4f042 [Andrew Or] Track memory usage in ExternalAppendOnlyMap / ExternalSorter bd7ab3f [Andrew Or] Add internal accumulators to TaskContext
* [SPARK-9544] [MLLIB] add Python API for RFormulaXiangrui Meng2015-08-032-15/+91
| | | | | | | | | | | | | Add Python API for RFormula. Similar to other feature transformers in Python. This is just a thin wrapper over the Scala implementation. ericl MechCoder Author: Xiangrui Meng <meng@databricks.com> Closes #7879 from mengxr/SPARK-9544 and squashes the following commits: 3d5ff03 [Xiangrui Meng] add an doctest for . and - 5e969a5 [Xiangrui Meng] fix pydoc 1cd41f8 [Xiangrui Meng] organize imports 3c18b10 [Xiangrui Meng] add Python API for RFormula
* [SPARK-9191] [ML] [Doc] Add ml.PCA user guide and code examplesYanbo Liang2015-08-031-0/+86
| | | | | | | | | | | Add ml.PCA user guide document and code examples for Scala/Java/Python. Author: Yanbo Liang <ybliang8@gmail.com> Closes #7522 from yanboliang/ml-pca-md and squashes the following commits: 60dec05 [Yanbo Liang] address comments f992abe [Yanbo Liang] Add ml.PCA doc and examples
* [SPARK-9558][DOCS]Update docs to follow the increase of memory defaults.Kousuke Saruta2015-08-033-2/+3
| | | | | | | | | | Now the memory defaults of master and slave in Standalone mode and History Server is 1g, not 512m. So let's update docs. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #7896 from sarutak/update-doc-for-daemon-memory and squashes the following commits: a77626c [Kousuke Saruta] Fix docs to follow the update of increase of memory defaults
* [SPARK-5133] [ML] Added featureImportance to RandomForestClassifier and ↵Joseph K. Bradley2015-08-0311-16/+351
| | | | | | | | | | | | | | | | | | | | | | | | | | Regressor Added featureImportance to RandomForestClassifier and Regressor. This follows the scikit-learn implementation here: [https://github.com/scikit-learn/scikit-learn/blob/a95203b249c1cf392f86d001ad999e29b2392739/sklearn/tree/_tree.pyx#L3341] CC: yanboliang Would you mind taking a look? Thanks! Author: Joseph K. Bradley <joseph@databricks.com> Author: Feynman Liang <fliang@databricks.com> Closes #7838 from jkbradley/dt-feature-importance and squashes the following commits: 72a167a [Joseph K. Bradley] fixed unit test 86cea5f [Joseph K. Bradley] Modified RF featuresImportances to return Vector instead of Map 5aa74f0 [Joseph K. Bradley] finally fixed unit test for real 33df5db [Joseph K. Bradley] fix unit test 42a2d3b [Joseph K. Bradley] fix unit test fe94e72 [Joseph K. Bradley] modified feature importance unit tests cc693ee [Feynman Liang] Add classifier tests 79a6f87 [Feynman Liang] Compare dense vectors in test 21d01fc [Feynman Liang] Added failing SKLearn test ac0b254 [Joseph K. Bradley] Added featureImportance to RandomForestClassifier/Regressor. Need to add unit tests
* [SPARK-9554] [SQL] Enables in-memory partition pruning by defaultCheng Lian2015-08-031-1/+1
| | | | | | | | Author: Cheng Lian <lian@databricks.com> Closes #7895 from liancheng/spark-9554/enable-in-memory-partition-pruning and squashes the following commits: 67c403e [Cheng Lian] Enables in-memory partition pruning by default
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