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* [SPARK-8432] [SQL] fix hashCode() and equals() of BinaryType in RowDavies Liu2015-06-2310-135/+139
| | | | | | | | | | | | | | | | | | | | Also added more tests in LiteralExpressionSuite Author: Davies Liu <davies@databricks.com> Closes #6876 from davies/fix_hashcode and squashes the following commits: 429c2c0 [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_hashcode 32d9811 [Davies Liu] fix test a0626ed [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_hashcode 89c2432 [Davies Liu] fix style bd20780 [Davies Liu] check with catalyst types 41caec6 [Davies Liu] change for to while d96929b [Davies Liu] address comment 6ad2a90 [Davies Liu] fix style 5819d33 [Davies Liu] unify equals() and hashCode() 0fff25d [Davies Liu] fix style 53c38b1 [Davies Liu] fix hashCode() and equals() of BinaryType in Row
* [SPARK-7235] [SQL] Refactor the grouping setsCheng Hao2015-06-235-71/+78
| | | | | | | | | | | The logical plan `Expand` takes the `output` as constructor argument, which break the references chain. We need to refactor the code, as well as the column pruning. Author: Cheng Hao <hao.cheng@intel.com> Closes #5780 from chenghao-intel/expand and squashes the following commits: 76e4aa4 [Cheng Hao] revert the change for case insenstive 7c10a83 [Cheng Hao] refactor the grouping sets
* [SQL] [DOCS] updated the documentation for explodelockwobr2015-06-241-1/+1
| | | | | | | | | | the syntax was incorrect in the example in explode Author: lockwobr <lockwobr@gmail.com> Closes #6943 from lockwobr/master and squashes the following commits: 3d864d1 [lockwobr] updated the documentation for explode
* [SPARK-8498] [TUNGSTEN] fix npe in errorhandling path in unsafeshuffle writerHolden Karau2015-06-232-2/+33
| | | | | | | | | | | | | | Author: Holden Karau <holden@pigscanfly.ca> Closes #6918 from holdenk/SPARK-8498-fix-npe-in-errorhandling-path-in-unsafeshuffle-writer and squashes the following commits: f807832 [Holden Karau] Log error if we can't throw it 855f9aa [Holden Karau] Spelling - not my strongest suite. Fix Propegates to Propagates. 039d620 [Holden Karau] Add missing closeandwriteoutput 30e558d [Holden Karau] go back to try/finally e503b8c [Holden Karau] Improve the test to ensure we aren't masking the underlying exception ae0b7a7 [Holden Karau] Fix the test 2e6abf7 [Holden Karau] Be more cautious when cleaning up during failed write and re-throw user exceptions
* [SPARK-8300] DataFrame hint for broadcast join.Reynold Xin2015-06-234-8/+59
| | | | | | | | | | | | | | | | Users can now do ```scala left.join(broadcast(right), "joinKey") ``` to give the query planner a hint that "right" DataFrame is small and should be broadcasted. Author: Reynold Xin <rxin@databricks.com> Closes #6751 from rxin/broadcastjoin-hint and squashes the following commits: 953eec2 [Reynold Xin] Code review feedback. 88752d8 [Reynold Xin] Fixed import. 8187b88 [Reynold Xin] [SPARK-8300] DataFrame hint for broadcast join.
* [SPARK-8541] [PYSPARK] test the absolute error in approx doctestsScott Taylor2015-06-221-2/+2
| | | | | | | | | | A minor change but one which is (presumably) visible on the public api docs webpage. Author: Scott Taylor <github@megatron.me.uk> Closes #6942 from megatron-me-uk/patch-3 and squashes the following commits: fbed000 [Scott Taylor] test the absolute error in approx doctests
* [SPARK-8483] [STREAMING] Remove commons-lang3 dependency from Flume Si…Hari Shreedharan2015-06-222-6/+2
| | | | | | | | | | | …nk. Also bump Flume version to 1.6.0 Author: Hari Shreedharan <hshreedharan@apache.org> Closes #6910 from harishreedharan/remove-commons-lang3 and squashes the following commits: 9875f7d [Hari Shreedharan] Revert back to Flume 1.4.0 ca35eb0 [Hari Shreedharan] [SPARK-8483][Streaming] Remove commons-lang3 dependency from Flume Sink. Also bump Flume version to 1.6.0
* [SPARK-8359] [SQL] Fix incorrect decimal precision after multiplicationLiang-Chi Hsieh2015-06-222-2/+9
| | | | | | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-8359 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #6814 from viirya/fix_decimal2 and squashes the following commits: 071a757 [Liang-Chi Hsieh] Remove maximum precision and use MathContext.UNLIMITED. df217d4 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into fix_decimal2 a43bfc3 [Liang-Chi Hsieh] Add MathContext with maximum supported precision. 72eeb3f [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into fix_decimal2 44c9348 [Liang-Chi Hsieh] Fix incorrect decimal precision after multiplication.
* [SPARK-8431] [SPARKR] Add in operator to DataFrame Column in SparkRYu ISHIKAWA2015-06-222-0/+26
| | | | | | | | | | | | | [[SPARK-8431] Add in operator to DataFrame Column in SparkR - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8431) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6941 from yu-iskw/SPARK-8431 and squashes the following commits: 1f64423 [Yu ISHIKAWA] Modify the comment f4309a7 [Yu ISHIKAWA] Make a `setMethod` for `%in%` be independent 6e37936 [Yu ISHIKAWA] Modify a variable name c196173 [Yu ISHIKAWA] [SPARK-8431][SparkR] Add in operator to DataFrame Column in SparkR
* [SPARK-7781] [MLLIB] gradient boosted trees.train regressor missing max binsHolden Karau2015-06-223-9/+24
| | | | | | | | | | | Author: Holden Karau <holden@pigscanfly.ca> Closes #6331 from holdenk/SPARK-7781-GradientBoostedTrees.trainRegressor-missing-max-bins and squashes the following commits: 2894695 [Holden Karau] remove extra blank line 2573e8d [Holden Karau] Update the scala side of the pythonmllibapi and make the test a bit nicer too 3a09170 [Holden Karau] add maxBins to to the train method as well af7f274 [Holden Karau] Add maxBins to GradientBoostedTrees.trainRegressor and correctly mention the default of 32 in other places where it mentioned 100
* [SPARK-8548] [SPARKR] Remove the trailing whitespaces from the SparkR filesYu ISHIKAWA2015-06-2222-188/+182
| | | | | | | | | | | | | [[SPARK-8548] Remove the trailing whitespaces from the SparkR files - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8548) - This is the result of `lint-r` https://gist.github.com/yu-iskw/0019b37a2c1167f33986 Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6945 from yu-iskw/SPARK-8548 and squashes the following commits: 0bd567a [Yu ISHIKAWA] [SPARK-8548][SparkR] Remove the trailing whitespaces from the SparkR files
* MAINTENANCE: Automated closing of pull requests.Patrick Wendell2015-06-220-0/+0
| | | | | | | | | | | | | This commit exists to close the following pull requests on Github: Closes #2849 (close requested by 'srowen') Closes #2786 (close requested by 'andrewor14') Closes #4678 (close requested by 'JoshRosen') Closes #5457 (close requested by 'andrewor14') Closes #3346 (close requested by 'andrewor14') Closes #6518 (close requested by 'andrewor14') Closes #5403 (close requested by 'pwendell') Closes #2110 (close requested by 'srowen')
* [SPARK-7859] [SQL] Collect_set() behavior differences which fails the unit ↵Cheng Hao2015-06-223-26/+105
| | | | | | | | | | | | | | | | | | | test under jdk8 To reproduce that: ``` JAVA_HOME=/home/hcheng/Java/jdk1.8.0_45 | build/sbt -Phadoop-2.3 -Phive 'test-only org.apache.spark.sql.hive.execution.HiveWindowFunctionQueryWithoutCodeGenSuite' ``` A simple workaround to fix that is update the original query, for getting the output size instead of the exact elements of the array (output by collect_set()) Author: Cheng Hao <hao.cheng@intel.com> Closes #6402 from chenghao-intel/windowing and squashes the following commits: 99312ad [Cheng Hao] add order by for the select clause edf8ce3 [Cheng Hao] update the code as suggested 7062da7 [Cheng Hao] fix the collect_set() behaviour differences under different versions of JDK
* [SPARK-8307] [SQL] improve timestamp from parquetDavies Liu2015-06-2224-252/+175
| | | | | | | | | | | | | | | | | | | | | | | | | | | This PR change to convert julian day to unix timestamp directly (without Calendar and Timestamp). cc adrian-wang rxin Author: Davies Liu <davies@databricks.com> Closes #6759 from davies/improve_ts and squashes the following commits: 849e301 [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts b0e4cad [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts 8e2d56f [Davies Liu] address comments 634b9f5 [Davies Liu] fix mima 4891efb [Davies Liu] address comment bfc437c [Davies Liu] fix build ae5979c [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts 602b969 [Davies Liu] remove jodd 2f2e48c [Davies Liu] fix test 8ace611 [Davies Liu] fix mima 212143b [Davies Liu] fix mina c834108 [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts a3171b8 [Davies Liu] Merge branch 'master' of github.com:apache/spark into improve_ts 5233974 [Davies Liu] fix scala style 361fd62 [Davies Liu] address comments ea196d4 [Davies Liu] improve timestamp from parquet
* [SPARK-7153] [SQL] support all integral type ordinal in GetArrayItemWenchen Fan2015-06-223-2/+21
| | | | | | | | | | first convert `ordinal` to `Number`, then convert to int type. Author: Wenchen Fan <cloud0fan@outlook.com> Closes #5706 from cloud-fan/7153 and squashes the following commits: 915db79 [Wenchen Fan] fix 7153
* [HOTFIX] [TESTS] Typo mqqt -> mqttAndrew Or2015-06-221-4/+4
| | | | This was introduced in #6866.
* [SPARK-8492] [SQL] support binaryType in UnsafeRowDavies Liu2015-06-224-46/+72
| | | | | | | | | | | | | | | | | | Support BinaryType in UnsafeRow, just like StringType. Also change the layout of StringType and BinaryType in UnsafeRow, by combining offset and size together as Long, which will limit the size of Row to under 2G (given that fact that any single buffer can not be bigger than 2G in JVM). Author: Davies Liu <davies@databricks.com> Closes #6911 from davies/unsafe_bin and squashes the following commits: d68706f [Davies Liu] update comment 519f698 [Davies Liu] address comment 98a964b [Davies Liu] Merge branch 'master' of github.com:apache/spark into unsafe_bin 180b49d [Davies Liu] fix zero-out 22e4c0a [Davies Liu] zero-out padding bytes 6abfe93 [Davies Liu] fix style 447dea0 [Davies Liu] support binaryType in UnsafeRow
* [SPARK-8356] [SQL] Reconcile callUDF and callUdfBenFradet2015-06-222-1/+55
| | | | | | | | | | | | Deprecates ```callUdf``` in favor of ```callUDF```. Author: BenFradet <benjamin.fradet@gmail.com> Closes #6902 from BenFradet/SPARK-8356 and squashes the following commits: ef4e9d8 [BenFradet] deprecated callUDF, use udf instead 9b1de4d [BenFradet] reinstated unit test for the deprecated callUdf cbd80a5 [BenFradet] deprecated callUdf in favor of callUDF
* [SPARK-8537] [SPARKR] Add a validation rule about the curly braces in SparkR ↵Yu ISHIKAWA2015-06-221-1/+1
| | | | | | | | | | | | to `.lintr` [[SPARK-8537] Add a validation rule about the curly braces in SparkR to `.lintr` - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8537) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6940 from yu-iskw/SPARK-8537 and squashes the following commits: 7eec1a0 [Yu ISHIKAWA] [SPARK-8537][SparkR] Add a validation rule about the curly braces in SparkR to `.lintr`
* [SPARK-8455] [ML] Implement n-gram feature transformerFeynman Liang2015-06-222-0/+163
| | | | | | | | | | | | Implementation of n-gram feature transformer for ML. Author: Feynman Liang <fliang@databricks.com> Closes #6887 from feynmanliang/ngram-featurizer and squashes the following commits: d2c839f [Feynman Liang] Make n > input length yield empty output 9fadd36 [Feynman Liang] Add empty and corner test cases, fix names and spaces fe93873 [Feynman Liang] Implement n-gram feature transformer
* [SPARK-8532] [SQL] In Python's DataFrameWriter, ↵Yin Huai2015-06-222-11/+51
| | | | | | | | | | | | | | | | | | | | | save/saveAsTable/json/parquet/jdbc always override mode https://issues.apache.org/jira/browse/SPARK-8532 This PR has two changes. First, it fixes the bug that save actions (i.e. `save/saveAsTable/json/parquet/jdbc`) always override mode. Second, it adds input argument `partitionBy` to `save/saveAsTable/parquet`. Author: Yin Huai <yhuai@databricks.com> Closes #6937 from yhuai/SPARK-8532 and squashes the following commits: f972d5d [Yin Huai] davies's comment. d37abd2 [Yin Huai] style. d21290a [Yin Huai] Python doc. 889eb25 [Yin Huai] Minor refactoring and add partitionBy to save, saveAsTable, and parquet. 7fbc24b [Yin Huai] Use None instead of "error" as the default value of mode since JVM-side already uses "error" as the default value. d696dff [Yin Huai] Python style. 88eb6c4 [Yin Huai] If mode is "error", do not call mode method. c40c461 [Yin Huai] Regression test.
* [SPARK-8104] [SQL] auto alias expressions in analyzerWenchen Fan2015-06-2216-117/+150
| | | | | | | | | | | | | | | | | Currently we auto alias expression in parser. However, during parser phase we don't have enough information to do the right alias. For example, Generator that has more than 1 kind of element need MultiAlias, ExtractValue don't need Alias if it's in middle of a ExtractValue chain. Author: Wenchen Fan <cloud0fan@outlook.com> Closes #6647 from cloud-fan/alias and squashes the following commits: 552eba4 [Wenchen Fan] fix python 5b5786d [Wenchen Fan] fix agg 73a90cb [Wenchen Fan] fix case-preserve of ExtractValue 4cfd23c [Wenchen Fan] fix order by d18f401 [Wenchen Fan] refine 9f07359 [Wenchen Fan] address comments 39c1aef [Wenchen Fan] small fix 33640ec [Wenchen Fan] auto alias expressions in analyzer
* [SPARK-8511] [PYSPARK] Modify a test to remove a saved model in `regression.py`Yu ISHIKAWA2015-06-225-11/+21
| | | | | | | | | | | [[SPARK-8511] Modify a test to remove a saved model in `regression.py` - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8511) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6926 from yu-iskw/SPARK-8511 and squashes the following commits: 7cd0948 [Yu ISHIKAWA] Use `shutil.rmtree()` to temporary directories for saving model testings, instead of `os.removedirs()` 4a01c9e [Yu ISHIKAWA] [SPARK-8511][pyspark] Modify a test to remove a saved model in `regression.py`
* [SPARK-8482] Added M4 instances to the list.Pradeep Chhetri2015-06-221-2/+14
| | | | | | | | | | | AWS recently added M4 instances (https://aws.amazon.com/blogs/aws/the-new-m4-instance-type-bonus-price-reduction-on-m3-c4/). Author: Pradeep Chhetri <pradeep.chhetri89@gmail.com> Closes #6899 from pradeepchhetri/master and squashes the following commits: 4f4ea79 [Pradeep Chhetri] Added t2.large instance 3d2bb6c [Pradeep Chhetri] Added M4 instances to the list
* [SPARK-8429] [EC2] Add ability to set additional tagsStefano Parmesan2015-06-221-8/+20
| | | | | | | | | | | | | | | Add the `--additional-tags` parameter that allows to set additional tags to all the created instances (masters and slaves). The user can specify multiple tags by separating them with a comma (`,`), while each tag name and value should be separated by a colon (`:`); for example, `Task:MySparkProject,Env:production` would add two tags, `Task` and `Env`, with the given values. Author: Stefano Parmesan <s.parmesan@gmail.com> Closes #6857 from armisael/patch-1 and squashes the following commits: c5ac92c [Stefano Parmesan] python style (pep8) 8e614f1 [Stefano Parmesan] Set multiple tags in a single request bfc56af [Stefano Parmesan] Address SPARK-7900 by inceasing sleep time daf8615 [Stefano Parmesan] Add ability to set additional tags
* [SPARK-8406] [SQL] Adding UUID to output file name to avoid accidental ↵Cheng Lian2015-06-228-72/+120
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | overwriting This PR fixes a Parquet output file name collision bug which may cause data loss. Changes made: 1. Identify each write job issued by `InsertIntoHadoopFsRelation` with a UUID All concrete data sources which extend `HadoopFsRelation` (Parquet and ORC for now) must use this UUID to generate task output file path to avoid name collision. 2. Make `TestHive` use a local mode `SparkContext` with 32 threads to increase parallelism The major reason for this is that, the original parallelism of 2 is too low to reproduce the data loss issue. Also, higher concurrency may potentially caught more concurrency bugs during testing phase. (It did help us spotted SPARK-8501.) 3. `OrcSourceSuite` was updated to workaround SPARK-8501, which we detected along the way. NOTE: This PR is made a little bit more complicated than expected because we hit two other bugs on the way and have to work them around. See [SPARK-8501] [1] and [SPARK-8513] [2]. [1]: https://github.com/liancheng/spark/tree/spark-8501 [2]: https://github.com/liancheng/spark/tree/spark-8513 ---- Some background and a summary of offline discussion with yhuai about this issue for better understanding: In 1.4.0, we added `HadoopFsRelation` to abstract partition support of all data sources that are based on Hadoop `FileSystem` interface. Specifically, this makes partition discovery, partition pruning, and writing dynamic partitions for data sources much easier. To support appending, the Parquet data source tries to find out the max part number of part-files in the destination directory (i.e., `<id>` in output file name `part-r-<id>.gz.parquet`) at the beginning of the write job. In 1.3.0, this step happens on driver side before any files are written. However, in 1.4.0, this is moved to task side. Unfortunately, for tasks scheduled later, they may see wrong max part number generated of files newly written by other finished tasks within the same job. This actually causes a race condition. In most cases, this only causes nonconsecutive part numbers in output file names. But when the DataFrame contains thousands of RDD partitions, it's likely that two tasks may choose the same part number, then one of them gets overwritten by the other. Before `HadoopFsRelation`, Spark SQL already supports appending data to Hive tables. From a user's perspective, these two look similar. However, they differ a lot internally. When data are inserted into Hive tables via Spark SQL, `InsertIntoHiveTable` simulates Hive's behaviors: 1. Write data to a temporary location 2. Move data in the temporary location to the final destination location using - `Hive.loadTable()` for non-partitioned table - `Hive.loadPartition()` for static partitions - `Hive.loadDynamicPartitions()` for dynamic partitions The important part is that, `Hive.copyFiles()` is invoked in step 2 to move the data to the destination directory (I found the name is kinda confusing since no "copying" occurs here, we are just moving and renaming stuff). If a file in the source directory and another file in the destination directory happen to have the same name, say `part-r-00001.parquet`, the former is moved to the destination directory and renamed with a `_copy_N` postfix (`part-r-00001_copy_1.parquet`). That's how Hive handles appending and avoids name collision between different write jobs. Some alternatives fixes considered for this issue: 1. Use a similar approach as Hive This approach is not preferred in Spark 1.4.0 mainly because file metadata operations in S3 tend to be slow, especially for tables with lots of file and/or partitions. That's why `InsertIntoHadoopFsRelation` just inserts to destination directory directly, and is often used together with `DirectParquetOutputCommitter` to reduce latency when working with S3. This means, we don't have the chance to do renaming, and must avoid name collision from the very beginning. 2. Same as 1.3, just move max part number detection back to driver side This isn't doable because unlike 1.3, 1.4 also takes dynamic partitioning into account. When inserting into dynamic partitions, we don't know which partition directories will be touched on driver side before issuing the write job. Checking all partition directories is simply too expensive for tables with thousands of partitions. 3. Add extra component to output file names to avoid name collision This seems to be the only reasonable solution for now. To be more specific, we need a JOB level unique identifier to identify all write jobs issued by `InsertIntoHadoopFile`. Notice that TASK level unique identifiers can NOT be used. Because in this way a speculative task will write to a different output file from the original task. If both tasks succeed, duplicate output will be left behind. Currently, the ORC data source adds `System.currentTimeMillis` to the output file name for uniqueness. This doesn't work because of exactly the same reason. That's why this PR adds a job level random UUID in `BaseWriterContainer` (which is used by `InsertIntoHadoopFsRelation` to issue write jobs). The drawback is that record order is not preserved any more (output files of a later job may be listed before those of a earlier job). However, we never promise to preserve record order when writing data, and Hive doesn't promise this either because the `_copy_N` trick breaks the order. Author: Cheng Lian <lian@databricks.com> Closes #6864 from liancheng/spark-8406 and squashes the following commits: db7a46a [Cheng Lian] More comments f5c1133 [Cheng Lian] Addresses comments 85c478e [Cheng Lian] Workarounds SPARK-8513 088c76c [Cheng Lian] Adds comment about SPARK-8501 99a5e7e [Cheng Lian] Uses job level UUID in SimpleTextRelation and avoids double task abortion 4088226 [Cheng Lian] Works around SPARK-8501 1d7d206 [Cheng Lian] Adds more logs 8966bbb [Cheng Lian] Fixes Scala style issue 18b7003 [Cheng Lian] Uses job level UUID to take speculative tasks into account 3806190 [Cheng Lian] Lets TestHive use all cores by default 748dbd7 [Cheng Lian] Adding UUID to output file name to avoid accidental overwriting
* [SPARK-7426] [MLLIB] [ML] Updated Attribute.fromStructField to allow any ↵Mike Dusenberry2015-06-212-2/+7
| | | | | | | | | | | | NumericType. Updated `Attribute.fromStructField` to allow any `NumericType`, rather than just `DoubleType`, and added unit tests for a few of the other NumericTypes. Author: Mike Dusenberry <dusenberrymw@gmail.com> Closes #6540 from dusenberrymw/SPARK-7426_AttributeFactory.fromStructField_Should_Allow_NumericTypes and squashes the following commits: 87fecb3 [Mike Dusenberry] Updated Attribute.fromStructField to allow any NumericType, rather than just DoubleType, and added unit tests for a few of the other NumericTypes.
* [SPARK-7715] [MLLIB] [ML] [DOC] Updated MLlib programming guide for release 1.4Joseph K. Bradley2015-06-214-33/+65
| | | | | | | | | | | | | | | | Reorganized docs a bit. Added migration guides. **Q**: Do we want to say more for the 1.3 -> 1.4 migration guide for ```spark.ml```? It would be a lot. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6897 from jkbradley/ml-guide-1.4 and squashes the following commits: 4bf26d6 [Joseph K. Bradley] tiny fix 8085067 [Joseph K. Bradley] fixed spacing/layout issues in ml guide from previous commit in this PR 6cd5c78 [Joseph K. Bradley] Updated MLlib programming guide for release 1.4
* [SPARK-8508] [SQL] Ignores a test case to cleanup unnecessary testing output ↵Cheng Lian2015-06-211-1/+1
| | | | | | | | | | | | | | until #6882 is merged Currently [the test case for SPARK-7862] [1] writes 100,000 lines of integer triples to stderr and makes Jenkins build output unnecessarily large and it's hard to debug other build errors. A proper fix is on the way in #6882. This PR ignores this test case temporarily until #6882 is merged. [1]: https://github.com/apache/spark/pull/6404/files#diff-1ea02a6fab84e938582f7f87cc4d9ea1R641 Author: Cheng Lian <lian@databricks.com> Closes #6925 from liancheng/spark-8508 and squashes the following commits: 41e5b47 [Cheng Lian] Ignores the test case until #6882 is merged
* [SPARK-7604] [MLLIB] Python API for PCA and PCAModelYanbo Liang2015-06-212-0/+45
| | | | | | | | | | | Python API for PCA and PCAModel Author: Yanbo Liang <ybliang8@gmail.com> Closes #6315 from yanboliang/spark-7604 and squashes the following commits: 1d58734 [Yanbo Liang] remove transform() in PCAModel, use default behavior 4d9d121 [Yanbo Liang] Python API for PCA and PCAModel
* [SPARK-8379] [SQL] avoid speculative tasks write to the same filejeanlyn2015-06-212-7/+5
| | | | | | | | | | | | | | | | | | | | The issue link [SPARK-8379](https://issues.apache.org/jira/browse/SPARK-8379) Currently,when we insert data to the dynamic partition with speculative tasks we will get the Exception ``` org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.LeaseExpiredException): Lease mismatch on /tmp/hive-jeanlyn/hive_2015-06-15_15-20-44_734_8801220787219172413-1/-ext-10000/ds=2015-06-15/type=2/part-00301.lzo owned by DFSClient_attempt_201506031520_0011_m_000189_0_-1513487243_53 but is accessed by DFSClient_attempt_201506031520_0011_m_000042_0_-1275047721_57 ``` This pr try to write the data to temporary dir when using dynamic parition avoid the speculative tasks writing the same file Author: jeanlyn <jeanlyn92@gmail.com> Closes #6833 from jeanlyn/speculation and squashes the following commits: 64bbfab [jeanlyn] use FileOutputFormat.getTaskOutputPath to get the path 8860af0 [jeanlyn] remove the never using code e19a3bd [jeanlyn] avoid speculative tasks write same file
* [SPARK-8301] [SQL] Improve UTF8String substring/startsWith/endsWith/contains ↵Tarek Auel2015-06-203-18/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | performance Jira: https://issues.apache.org/jira/browse/SPARK-8301 Added the private method startsWith(prefix, offset) to implement startsWith, endsWith and contains without copying the array I hope that the component SQL is still correct. I copied it from the Jira ticket. Author: Tarek Auel <tarek.auel@googlemail.com> Author: Tarek Auel <tarek.auel@gmail.com> Closes #6804 from tarekauel/SPARK-8301 and squashes the following commits: f5d6b9a [Tarek Auel] fixed parentheses and annotation 6d7b068 [Tarek Auel] [SPARK-8301] removed null checks 9ca0473 [Tarek Auel] [SPARK-8301] removed null checks 1c327eb [Tarek Auel] [SPARK-8301] removed new 9f17cc8 [Tarek Auel] [SPARK-8301] fixed conversion byte to string in codegen 3a0040f [Tarek Auel] [SPARK-8301] changed call of UTF8String.set to UTF8String.from e4530d2 [Tarek Auel] [SPARK-8301] changed call of UTF8String.set to UTF8String.from a5f853a [Tarek Auel] [SPARK-8301] changed visibility of set to protected. Changed annotation of bytes from Nullable to Nonnull d2fb05f [Tarek Auel] [SPARK-8301] added additional null checks 79cb55b [Tarek Auel] [SPARK-8301] null check. Added test cases for null check. b17909e [Tarek Auel] [SPARK-8301] removed unnecessary copying of UTF8String. Added a private function startsWith(prefix, offset) to implement the check for startsWith, endsWith and contains.
* [SPARK-8495] [SPARKR] Add a `.lintr` file to validate the SparkR files and ↵Yu ISHIKAWA2015-06-205-0/+63
| | | | | | | | | | | | | | the `lint-r` script Thank Shivaram Venkataraman for your support. This is a prototype script to validate the R files. Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #6922 from yu-iskw/SPARK-6813 and squashes the following commits: c1ffe6b [Yu ISHIKAWA] Modify to save result to a log file and add a rule to validate 5520806 [Yu ISHIKAWA] Exclude the .lintr file not to check Apache lincence 8f94680 [Yu ISHIKAWA] [SPARK-8495][SparkR] Add a `.lintr` file to validate the SparkR files and the `lint-r` script
* [SPARK-8422] [BUILD] [PROJECT INFRA] Add a module abstraction to dev/run-testsJosh Rosen2015-06-201-156/+411
| | | | | | | | | | | | | | | | | | | | | | | | | | | This patch builds upon #5694 to add a 'module' abstraction to the `dev/run-tests` script which groups together the per-module test logic, including the mapping from file paths to modules, the mapping from modules to test goals and build profiles, and the dependencies / relationships between modules. This refactoring makes it much easier to increase the granularity of test modules, which will let us skip even more tests. It's also a prerequisite for other changes that will reduce test time, such as running subsets of the Python tests based on which files / modules have changed. This patch also adds doctests for the new graph traversal / change mapping code. Author: Josh Rosen <joshrosen@databricks.com> Closes #6866 from JoshRosen/more-dev-run-tests-refactoring and squashes the following commits: 75de450 [Josh Rosen] Use module system to determine which build profiles to enable. 4224da5 [Josh Rosen] Add documentation to Module. a86a953 [Josh Rosen] Clean up modules; add new modules for streaming external projects e46539f [Josh Rosen] Fix camel-cased endswith() 35a3052 [Josh Rosen] Enable Hive tests when running all tests df10e23 [Josh Rosen] update to reflect fact that no module depends on root 3670d50 [Josh Rosen] mllib should depend on streaming dc6f1c6 [Josh Rosen] Use changed files' extensions to decide whether to run style checks 7092d3e [Josh Rosen] Skip SBT tests if no test goals are specified 43a0ced [Josh Rosen] Minor fixes 3371441 [Josh Rosen] Test everything if nothing has changed (needed for non-PRB builds) 37f3fb3 [Josh Rosen] Remove doc profiles option, since it's not actually needed (see #6865) f53864b [Josh Rosen] Finish integrating module changes f0249bd [Josh Rosen] WIP
* [SPARK-8468] [ML] Take the negative of some metrics in RegressionEvaluator ↵Liang-Chi Hsieh2015-06-205-11/+48
| | | | | | | | | | | | | | | | to get correct cross validation JIRA: https://issues.apache.org/jira/browse/SPARK-8468 Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #6905 from viirya/cv_min and squashes the following commits: 930d3db [Liang-Chi Hsieh] Fix python unit test and add document. d632135 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into cv_min 16e3b2c [Liang-Chi Hsieh] Take the negative instead of reciprocal. c3dd8d9 [Liang-Chi Hsieh] For comments. b5f52c1 [Liang-Chi Hsieh] Add param to CrossValidator for choosing whether to maximize evaulation value.
* [SPARK-8127] [STREAMING] [KAFKA] KafkaRDD optimize count() take() isEmpty()cody koeninger2015-06-198-24/+122
| | | | | | | | | | | | | | | | …ed KafkaRDD methods. Possible fix for [SPARK-7122], but probably a worthwhile optimization regardless. Author: cody koeninger <cody@koeninger.org> Closes #6632 from koeninger/kafka-rdd-count and squashes the following commits: 321340d [cody koeninger] [SPARK-8127][Streaming][Kafka] additional test of ordering of take() 5a05d0f [cody koeninger] [SPARK-8127][Streaming][Kafka] additional test of isEmpty f68bd32 [cody koeninger] [Streaming][Kafka][SPARK-8127] code cleanup 9555b73 [cody koeninger] Merge branch 'master' into kafka-rdd-count 253031d [cody koeninger] [Streaming][Kafka][SPARK-8127] mima exclusion for change to private method 8974b9e [cody koeninger] [Streaming][Kafka][SPARK-8127] check offset ranges before constructing KafkaRDD c3768c5 [cody koeninger] [Streaming][Kafka] Take advantage of offset range info for size-related KafkaRDD methods. Possible fix for [SPARK-7122], but probably a worthwhile optimization regardless.
* [HOTFIX] [SPARK-8489] Correct JIRA number in previous commitAndrew Or2015-06-194-8/+8
| | | | It should be SPARK-8489, not SPARK-8498.
* [SPARK-8498] [SQL] Add regression test for SPARK-8470Andrew Or2015-06-194-0/+76
| | | | | | | | | | | | | | **Summary of the problem in SPARK-8470.** When using `HiveContext` to create a data frame of a user case class, Spark throws `scala.reflect.internal.MissingRequirementError` when it tries to infer the schema using reflection. This is caused by `HiveContext` silently overwriting the context class loader containing the user classes. **What this issue is about.** This issue adds regression tests for SPARK-8470, which is already fixed in #6891. We closed SPARK-8470 as a duplicate because it is a different manifestation of the same problem in SPARK-8368. Due to the complexity of the reproduction, this requires us to pre-package a special test jar and include it in the Spark project itself. I tested this with and without the fix in #6891 and verified that it passes only if the fix is present. Author: Andrew Or <andrew@databricks.com> Closes #6909 from andrewor14/SPARK-8498 and squashes the following commits: 5e9d688 [Andrew Or] Add regression test for SPARK-8470
* [SPARK-8390] [STREAMING] [KAFKA] fix docs related to HasOffsetRangescody koeninger2015-06-193-26/+71
| | | | | | | | | | | | Author: cody koeninger <cody@koeninger.org> Closes #6863 from koeninger/SPARK-8390 and squashes the following commits: 26a06bd [cody koeninger] Merge branch 'master' into SPARK-8390 3744492 [cody koeninger] [Streaming][Kafka][SPARK-8390] doc changes per TD, test to make sure approach shown in docs actually compiles + runs b108c9d [cody koeninger] [Streaming][Kafka][SPARK-8390] further doc fixes, clean up spacing bb4336b [cody koeninger] [Streaming][Kafka][SPARK-8390] fix docs related to HasOffsetRanges, cleanup 3f3c57a [cody koeninger] [Streaming][Kafka][SPARK-8389] Example of getting offset ranges out of the existing java direct stream api
* [SPARK-8420] [SQL] Fix comparision of timestamps/dates with stringsMichael Armbrust2015-06-196-11/+88
| | | | | | | | | | | | | | | | | | | | | In earlier versions of Spark SQL we casted `TimestampType` and `DataType` to `StringType` when it was involved in a binary comparison with a `StringType`. This allowed comparing a timestamp with a partial date as a user would expect. - `time > "2014-06-10"` - `time > "2014"` In 1.4.0 we tried to cast the String instead into a Timestamp. However, since partial dates are not a valid complete timestamp this results in `null` which results in the tuple being filtered. This PR restores the earlier behavior. Note that we still special case equality so that these comparisons are not affected by not printing zeros for subsecond precision. Author: Michael Armbrust <michael@databricks.com> Closes #6888 from marmbrus/timeCompareString and squashes the following commits: bdef29c [Michael Armbrust] test partial date 1f09adf [Michael Armbrust] special handling of equality 1172c60 [Michael Armbrust] more test fixing 4dfc412 [Michael Armbrust] fix tests aaa9508 [Michael Armbrust] newline 04d908f [Michael Armbrust] [SPARK-8420][SQL] Fix comparision of timestamps/dates with strings
* [SPARK-8093] [SQL] Remove empty structs inferred from JSON documentsNathan Howell2015-06-193-17/+48
| | | | | | | | Author: Nathan Howell <nhowell@godaddy.com> Closes #6799 from NathanHowell/spark-8093 and squashes the following commits: 76ac3e8 [Nathan Howell] [SPARK-8093] [SQL] Remove empty structs inferred from JSON documents
* [SPARK-8452] [SPARKR] expose jobGroup API in SparkRHossein2015-06-193-0/+56
| | | | | | | | | | | | | | | | | | | | | | This pull request adds following methods to SparkR: ```R setJobGroup() cancelJobGroup() clearJobGroup() ``` For each method, the spark context is passed as the first argument. There does not seem to be a good way to test these in R. cc shivaram and davies Author: Hossein <hossein@databricks.com> Closes #6889 from falaki/SPARK-8452 and squashes the following commits: 9ce9f1e [Hossein] Added basic tests to verify methods can be called and won't throw errors c706af9 [Hossein] Added examples a2c19af [Hossein] taking spark context as first argument 343ca77 [Hossein] Added setJobGroup, cancelJobGroup and clearJobGroup to SparkR
* [SPARK-4118] [MLLIB] [PYSPARK] Python bindings for StreamingKMeansMechCoder2015-06-194-9/+411
| | | | | | | | | | | | | | | | | | | | | | Python bindings for StreamingKMeans Will change status to MRG once docs, tests and examples are updated. Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6499 from MechCoder/spark-4118 and squashes the following commits: 7722d16 [MechCoder] minor style fixes 51052d3 [MechCoder] Doc fixes 2061a76 [MechCoder] Add tests for simultaneous training and prediction Minor style fixes 81482fd [MechCoder] minor 5d9fe61 [MechCoder] predictOn should take into account the latest model 8ab9e89 [MechCoder] Fix Python3 error a9817df [MechCoder] Better tests and minor fixes c80e451 [MechCoder] Add ignore_unicode_prefix ee8ce16 [MechCoder] Update tests, doc and examples 4b1481f [MechCoder] Some changes and tests d8b066a [MechCoder] [SPARK-4118] [MLlib] [PySpark] Python bindings for StreamingKMeans
* [SPARK-8461] [SQL] fix codegen with REPL class loaderDavies Liu2015-06-196-34/+29
| | | | | | | | | | | | | | The ExecutorClassLoader for REPL will cause Janino failed to find class for those in java.lang, so switch to use default class loader for Janino, which will also help performance. cc liancheng yhuai Author: Davies Liu <davies@databricks.com> Closes #6898 from davies/fix_class_loader and squashes the following commits: 24276d4 [Davies Liu] add regression test 4ff0457 [Davies Liu] address comment, refactor 7f5ffbe [Davies Liu] fix REPL class loader with codegen
* [HOTFIX] Fix scala style in DFSReadWriteTest that causes tests failedLiang-Chi Hsieh2015-06-191-2/+2
| | | | | | | | | | This scala style problem causes tested failed. Author: Liang-Chi Hsieh <viirya@gmail.com> Closes #6907 from viirya/hotfix_style and squashes the following commits: c53f188 [Liang-Chi Hsieh] Fix scala style.
* [SPARK-8368] [SPARK-8058] [SQL] HiveContext may override the context class ↵Yin Huai2015-06-195-15/+219
| | | | | | | | | | | | | | | | | loader of the current thread https://issues.apache.org/jira/browse/SPARK-8368 Also, I add tests according https://issues.apache.org/jira/browse/SPARK-8058. Author: Yin Huai <yhuai@databricks.com> Closes #6891 from yhuai/SPARK-8368 and squashes the following commits: 37bb3db [Yin Huai] Update test timeout and comment. 8762eec [Yin Huai] Style. 695cd2d [Yin Huai] Correctly set the class loader in the conf of the state in client wrapper. b3378fe [Yin Huai] Failed tests.
* [SPARK-5836] [DOCS] [STREAMING] Clarify what may cause long-running Spark ↵Sean Owen2015-06-191-3/+5
| | | | | | | | | | | | apps to preserve shuffle files Clarify what may cause long-running Spark apps to preserve shuffle files Author: Sean Owen <sowen@cloudera.com> Closes #6901 from srowen/SPARK-5836 and squashes the following commits: a9faef0 [Sean Owen] Clarify what may cause long-running Spark apps to preserve shuffle files
* [SPARK-8451] [SPARK-7287] SparkSubmitSuite should check exit codeAndrew Or2015-06-191-5/+12
| | | | | | | | | | | | | | This patch also reenables the tests. Now that we have access to the log4j logs it should be easier to debug the flakiness. yhuai brkyvz Author: Andrew Or <andrew@databricks.com> Closes #6886 from andrewor14/spark-submit-suite-fix and squashes the following commits: 3f99ff1 [Andrew Or] Move destroy to finally block 9a62188 [Andrew Or] Re-enable ignored tests 2382672 [Andrew Or] Check for exit code
* [SPARK-7180] [SPARK-8090] [SPARK-8091] Fix a number of SerializationDebugger ↵Tathagata Das2015-06-193-12/+223
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugs and limitations This PR solves three SerializationDebugger issues. * SPARK-7180 - SerializationDebugger fails with ArrayOutOfBoundsException * SPARK-8090 - SerializationDebugger does not handle classes with writeReplace correctly * SPARK-8091 - SerializationDebugger does not handle classes with writeObject method The solutions for each are explained as follows * SPARK-7180 - The wrong slot desc was used for getting the value of the fields in the object being tested. * SPARK-8090 - Test the type of the replaced object. * SPARK-8091 - Use a dummy ObjectOutputStream to collect all the objects written by the writeObject() method, and then test those objects as usual. I also added more tests in the testsuite to increase code coverage. For example, added tests for cases where there are not serializability issues. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #6625 from tdas/SPARK-7180 and squashes the following commits: c7cb046 [Tathagata Das] Addressed comments on docs ae212c8 [Tathagata Das] Improved docs 304c97b [Tathagata Das] Fixed build error 26b5179 [Tathagata Das] more tests.....92% line coverage 7e2fdcf [Tathagata Das] Added more tests d1967fb [Tathagata Das] Added comments. da75d34 [Tathagata Das] Removed unnecessary lines. 50a608d [Tathagata Das] Fixed bugs and added support for writeObject
* Add example that reads a local file, writes to a DFS path provided by th...RJ Nowling2015-06-191-0/+138
| | | | | | | | | | | | | | | | | | | | | ...e user, reads the file back from the DFS, and compares word counts on the local and DFS versions. Useful for verifying DFS correctness. Author: RJ Nowling <rnowling@gmail.com> Closes #3347 from rnowling/dfs_read_write_test and squashes the following commits: af8ccb7 [RJ Nowling] Don't use java.io.File since DFS may not be POSIX-compatible b0ef9ea [RJ Nowling] Fix string style 07c6132 [RJ Nowling] Fix string style 7d9a8df [RJ Nowling] Fix string style f74c160 [RJ Nowling] Fix else statement style b9edf12 [RJ Nowling] Fix spark wc style 44415b9 [RJ Nowling] Fix local wc style 94a4691 [RJ Nowling] Fix space df59b65 [RJ Nowling] Fix if statements 1b314f0 [RJ Nowling] Add scaladoc a931d70 [RJ Nowling] Fix import order 0c89558 [RJ Nowling] Add example that reads a local file, writes to a DFS path provided by the user, reads the file back from the DFS, and compares word counts on the local and DFS versions. Useful for verifying DFS correctness.
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