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* [SPARK-8661][ML] for LinearRegressionSuite.scala, changed javadoc-style ↵Rosstin2015-06-291-96/+96
| | | | | | | | | | | | | | | | | comments to regular multiline comments, to make copy-pasting R code more simple for mllib/src/test/scala/org/apache/spark/ml/regression/LinearRegressionSuite.scala, changed javadoc-style comments to regular multiline comments, to make copy-pasting R code more simple Author: Rosstin <asterazul@gmail.com> Closes #7098 from Rosstin/SPARK-8661 and squashes the following commits: 5a05dee [Rosstin] SPARK-8661 for LinearRegressionSuite.scala, changed javadoc-style comments to regular multiline comments to make it easier to copy-paste the R code. bb9a4b1 [Rosstin] Merge branch 'master' of github.com:apache/spark into SPARK-8660 242aedd [Rosstin] SPARK-8660, changed comment style from JavaDoc style to normal multiline comment in order to make copypaste into R easier, in file classification/LogisticRegressionSuite.scala 2cd2985 [Rosstin] Merge branch 'master' of github.com:apache/spark into SPARK-8639 21ac1e5 [Rosstin] Merge branch 'master' of github.com:apache/spark into SPARK-8639 6c18058 [Rosstin] fixed minor typos in docs/README.md and docs/api.md
* [SPARK-8660][ML] Convert JavaDoc style comments ↵Rosstin2015-06-291-171/+171
| | | | | | | | | | | | | | | inLogisticRegressionSuite.scala to regular multiline comments, to make copy-pasting R commands easier Converted JavaDoc style comments in mllib/src/test/scala/org/apache/spark/ml/classification/LogisticRegressionSuite.scala to regular multiline comments, to make copy-pasting R commands easier. Author: Rosstin <asterazul@gmail.com> Closes #7096 from Rosstin/SPARK-8660 and squashes the following commits: 242aedd [Rosstin] SPARK-8660, changed comment style from JavaDoc style to normal multiline comment in order to make copypaste into R easier, in file classification/LogisticRegressionSuite.scala 2cd2985 [Rosstin] Merge branch 'master' of github.com:apache/spark into SPARK-8639 21ac1e5 [Rosstin] Merge branch 'master' of github.com:apache/spark into SPARK-8639 6c18058 [Rosstin] fixed minor typos in docs/README.md and docs/api.md
* [SPARK-8575] [SQL] Deprecate callUDF in favor of udfBenFradet2015-06-285-32/+44
| | | | | | | | | | | | | | | | | | | | | | | | | | | Follow up of [SPARK-8356](https://issues.apache.org/jira/browse/SPARK-8356) and #6902. Removes the unit test for the now deprecated ```callUdf``` Unit test in SQLQuerySuite now uses ```udf``` instead of ```callUDF``` Replaced ```callUDF``` by ```udf``` where possible in mllib Author: BenFradet <benjamin.fradet@gmail.com> Closes #6993 from BenFradet/SPARK-8575 and squashes the following commits: 26f5a7a [BenFradet] 2 spaces instead of 1 1ddb452 [BenFradet] renamed initUDF in order to be consistent in OneVsRest 48ca15e [BenFradet] used vector type tag for udf call in VectorIndexer 0ebd0da [BenFradet] replace the now deprecated callUDF by udf in VectorIndexer 8013409 [BenFradet] replaced the now deprecated callUDF by udf in Predictor 94345b5 [BenFradet] unifomized udf calls in ProbabilisticClassifier 1305492 [BenFradet] uniformized udf calls in Classifier a672228 [BenFradet] uniformized udf calls in OneVsRest 49e4904 [BenFradet] Revert "removal of the unit test for the now deprecated callUdf" bbdeaf3 [BenFradet] fixed syntax for init udf in OneVsRest fe2a10b [BenFradet] callUDF => udf in ProbabilisticClassifier 0ea30b3 [BenFradet] callUDF => udf in Classifier where possible 197ec82 [BenFradet] callUDF => udf in OneVsRest 84d6780 [BenFradet] modified unit test in SQLQuerySuite to use udf instead of callUDF 477709f [BenFradet] removal of the unit test for the now deprecated callUdf
* [SPARK-5962] [MLLIB] Python support for Power Iteration ClusteringYanbo Liang2015-06-282-0/+59
| | | | | | | | | | | | Python support for Power Iteration Clustering https://issues.apache.org/jira/browse/SPARK-5962 Author: Yanbo Liang <ybliang8@gmail.com> Closes #6992 from yanboliang/pyspark-pic and squashes the following commits: 6b03d82 [Yanbo Liang] address comments 4be4423 [Yanbo Liang] Python support for Power Iteration Clustering
* [SPARK-7212] [MLLIB] Add sequence learning flagFeynman Liang2015-06-282-10/+80
| | | | | | | | | | | | | | | | Support mining of ordered frequent item sequences. Author: Feynman Liang <fliang@databricks.com> Closes #6997 from feynmanliang/fp-sequence and squashes the following commits: 7c14e15 [Feynman Liang] Improve scalatests with R code and Seq 0d3e4b6 [Feynman Liang] Fix python test ce987cb [Feynman Liang] Backwards compatibility aux constructor 34ef8f2 [Feynman Liang] Fix failing test due to reverse orderering f04bd50 [Feynman Liang] Naming, add ordered to FreqItemsets, test ordering using Seq 648d4d4 [Feynman Liang] Test case for frequent item sequences 252a36a [Feynman Liang] Add sequence learning flag
* [SPARK-8683] [BUILD] Depend on mockito-core instead of mockito-allJosh Rosen2015-06-271-1/+1
| | | | | | | | | | | | Spark's tests currently depend on `mockito-all`, which bundles Hamcrest and Objenesis classes. Instead, it should depend on `mockito-core`, which declares those libraries as Maven dependencies. This is necessary in order to fix a dependency conflict that leads to a NoSuchMethodError when using certain Hamcrest matchers. See https://github.com/mockito/mockito/wiki/Declaring-mockito-dependency for more details. Author: Josh Rosen <joshrosen@databricks.com> Closes #7061 from JoshRosen/mockito-core-instead-of-all and squashes the following commits: 70eccbe [Josh Rosen] Depend on mockito-core instead of mockito-all.
* [SPARK-8613] [ML] [TRIVIAL] add param to disable linear feature scalingHolden Karau2015-06-262-0/+20
| | | | | | | | | | | | | Add a param to disable linear feature scaling (to be implemented later in linear & logistic regression). Done as a seperate PR so we can use same param & not conflict while working on the sub-tasks. Author: Holden Karau <holden@pigscanfly.ca> Closes #7024 from holdenk/SPARK-8522-Disable-Linear_featureScaling-Spark-8613-Add-param and squashes the following commits: ce8931a [Holden Karau] Regenerate the sharedParams code fa6427e [Holden Karau] update text for standardization param. 7b24a2b [Holden Karau] generate the new standardization param 3c190af [Holden Karau] Add the standardization param to sharedparamscodegen
* [MINOR] [MLLIB] rename some functions of PythonMLLibAPIYanbo Liang2015-06-251-3/+3
| | | | | | | | | | | | | | | | | | | | | | | Keep the same naming conventions for PythonMLLibAPI. Only the following three functions is different from others ```scala trainNaiveBayes trainGaussianMixture trainWord2Vec ``` So change them to ```scala trainNaiveBayesModel trainGaussianMixtureModel trainWord2VecModel ``` It does not affect any users and public APIs, only to make better understand for developer and code hacker. Author: Yanbo Liang <ybliang8@gmail.com> Closes #7011 from yanboliang/py-mllib-api-rename and squashes the following commits: 771ffec [Yanbo Liang] rename some functions of PythonMLLibAPI
* [SPARK-8525] [MLLIB] fix LabeledPoint parser when there is a whitespace ↵Oleksiy Dyagilev2015-06-233-0/+14
| | | | | | | | | | | | | | between label and features vector fix LabeledPoint parser when there is a whitespace between label and features vector, e.g. (y, [x1, x2, x3]) Author: Oleksiy Dyagilev <oleksiy_dyagilev@epam.com> Closes #6954 from fe2s/SPARK-8525 and squashes the following commits: 0755b9d [Oleksiy Dyagilev] [SPARK-8525][MLLIB] addressing comment, removing dep on commons-lang c1abc2b [Oleksiy Dyagilev] [SPARK-8525][MLLIB] fix LabeledPoint parser when there is a whitespace on specific position
* [SPARK-8265] [MLLIB] [PYSPARK] Add LinearDataGenerator to pyspark.mllib.utilsMechCoder2015-06-231-1/+31
| | | | | | | | | | | | It is useful to generate linear data for easy testing of linear models and in general. Scala already has it. This is just a wrapper around the Scala code. Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6715 from MechCoder/generate_linear_input and squashes the following commits: 6182884 [MechCoder] Minor changes 8bda047 [MechCoder] Minor style fixes 0f1053c [MechCoder] [SPARK-8265] Add LinearDataGenerator to pyspark.mllib.utils
* [SPARK-7888] Be able to disable intercept in linear regression in ml packageHolden Karau2015-06-232-12/+167
| | | | | | | | | | | | | | | | | | | Author: Holden Karau <holden@pigscanfly.ca> Closes #6927 from holdenk/SPARK-7888-Be-able-to-disable-intercept-in-Linear-Regression-in-ML-package and squashes the following commits: 0ad384c [Holden Karau] Add MiMa excludes 4016fac [Holden Karau] Switch to wild card import, remove extra blank lines ae5baa8 [Holden Karau] CR feedback, move the fitIntercept down rather than changing ymean and etc above f34971c [Holden Karau] Fix some more long lines 319bd3f [Holden Karau] Fix long lines 3bb9ee1 [Holden Karau] Update the regression suite tests 7015b9f [Holden Karau] Our code performs the same with R, except we need more than one data point but that seems reasonable 0b0c8c0 [Holden Karau] fix the issue with the sample R code e2140ba [Holden Karau] Add a test, it fails! 5e84a0b [Holden Karau] Write out thoughts and use the correct trait 91ffc0a [Holden Karau] more murh 006246c [Holden Karau] murp?
* [SPARK-7781] [MLLIB] gradient boosted trees.train regressor missing max binsHolden Karau2015-06-221-1/+3
| | | | | | | | | | | 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-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-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-7604] [MLLIB] Python API for PCA and PCAModelYanbo Liang2015-06-211-0/+10
| | | | | | | | | | | 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-8468] [ML] Take the negative of some metrics in RegressionEvaluator ↵Liang-Chi Hsieh2015-06-204-8/+43
| | | | | | | | | | | | | | | | 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-4118] [MLLIB] [PYSPARK] Python bindings for StreamingKMeansMechCoder2015-06-191-0/+15
| | | | | | | | | | | | | | | | | | | | | | 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-8151] [MLLIB] pipeline components should correctly implement copyXiangrui Meng2015-06-1960-55/+343
| | | | | | | | | | | | | | | | | | Otherwise, extra params get ignored in `PipelineModel.transform`. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6622 from mengxr/SPARK-8087 and squashes the following commits: 0e4c8c4 [Xiangrui Meng] fix merge issues 26fc1f0 [Xiangrui Meng] address comments e607a04 [Xiangrui Meng] merge master b85b57e [Xiangrui Meng] fix examples/compile d6f7891 [Xiangrui Meng] rename defaultCopyWithParams to defaultCopy 84ec278 [Xiangrui Meng] remove setter checks due to generics 2cf2ed0 [Xiangrui Meng] snapshot 291814f [Xiangrui Meng] OneVsRest.copy 1dfe3bd [Xiangrui Meng] PipelineModel.copy should copy stages
* [SPARK-7605] [MLLIB] [PYSPARK] Python API for ElementwiseProductMechCoder2015-06-171-0/+8
| | | | | | | | | | | Python API for org.apache.spark.mllib.feature.ElementwiseProduct Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6346 from MechCoder/spark-7605 and squashes the following commits: 79d1ef5 [MechCoder] Consistent and support list / array types 5f81d81 [MechCoder] [SPARK-7605] [MLlib] Python API for ElementwiseProduct
* [SPARK-6390] [SQL] [MLlib] Port MatrixUDT to PySparkMechCoder2015-06-171-0/+2
| | | | | | | | | | | | | MatrixUDT was recently coded in scala. This has been ported to PySpark Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6354 from MechCoder/spark-6390 and squashes the following commits: fc4dc1e [MechCoder] Better error message c940a44 [MechCoder] Added test aa9c391 [MechCoder] Add pyUDT to MatrixUDT 62a2a7d [MechCoder] [SPARK-6390] Port MatrixUDT to PySpark
* [SPARK-7916] [MLLIB] MLlib Python doc parity check for classification and ↵Yanbo Liang2015-06-161-1/+1
| | | | | | | | | | | | | | | regression Check then make the MLlib Python classification and regression doc to be as complete as the Scala doc. Author: Yanbo Liang <ybliang8@gmail.com> Closes #6460 from yanboliang/spark-7916 and squashes the following commits: f8deda4 [Yanbo Liang] trigger jenkins 6dc4d99 [Yanbo Liang] address comments ce2a43e [Yanbo Liang] truncate too long line and remove extra sparse 3eaf6ad [Yanbo Liang] MLlib Python doc parity check for classification and regression
* [SPARK-8314][MLlib] improvement in performance of MLUtils.appendBiasRoger Menezes2015-06-122-7/+23
| | | | | | | | | | | | | | | | | | | | | MLUtils.appendBias method is heavily used in creating intercepts for linear models. This method uses Breeze's vector concatenation which is very slow compared to the plain System.arrayCopy. This improvement is to change the implementation to use System.arrayCopy. I saw the following performance improvements after the change: Benchmark with mnist dataset for 50 times: MLUtils.appendBias (SparseVector Before): 47320 ms MLUtils.appendBias (SparseVector After): 1935 ms MLUtils.appendBias (DenseVector Before): 5340 ms MLUtils.appendBias (DenseVector After): 4080 ms This is almost a 24 times performance boost for SparseVectors. Author: Roger Menezes <rmenezes@netflix.com> Closes #6768 from rogermenezes/improve-append-bias and squashes the following commits: 4e42f75 [Roger Menezes] address feedback e999d79 [Roger Menezes] first commit
* [SPARK-8200] [MLLIB] Check for empty RDDs in StreamingLinearAlgorithmPaavo2015-06-103-6/+43
| | | | | | | | | | | | | | | | | Test cases for both StreamingLinearRegression and StreamingLogisticRegression, and code fix. Edit: This contribution is my original work and I license the work to the project under the project's open source license. Author: Paavo <pparkkin@gmail.com> Closes #6713 from pparkkin/streamingmodel-empty-rdd and squashes the following commits: ff5cd78 [Paavo] Update strings to use interpolation. db234cf [Paavo] Use !rdd.isEmpty. 54ad89e [Paavo] Test case for empty stream. 393e36f [Paavo] Ignore empty RDDs. 0bfc365 [Paavo] Test case for empty stream.
* [SPARK-8140] [MLLIB] Remove construct to get weights in StreamingLinearAlgorithmMechCoder2015-06-091-6/+1
| | | | | | | | Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6720 from MechCoder/empty_model_check and squashes the following commits: 3a07de5 [MechCoder] Remove construct to get weights in StreamingLinearAlgorithm
* [SPARK-8168] [MLLIB] Add Python friendly constructor to PipelineModelXiangrui Meng2015-06-082-0/+25
| | | | | | | | | | This makes the constructor callable in Python. dbtsai Author: Xiangrui Meng <meng@databricks.com> Closes #6709 from mengxr/SPARK-8168 and squashes the following commits: f871de4 [Xiangrui Meng] Add Python friendly constructor to PipelineModel
* [SPARK-8140] [MLLIB] Remove empty model check in StreamingLinearAlgorithmMechCoder2015-06-084-8/+5
| | | | | | | | | | | 1. Prevent creating a map of data to find numFeatures 2. If model is empty, then initialize with a zero vector of numFeature Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6684 from MechCoder/spark-8140 and squashes the following commits: 7fbf5f9 [MechCoder] [SPARK-8140] Remove empty model check in StreamingLinearAlgorithm And other minor cosmits
* [SPARK-7639] [PYSPARK] [MLLIB] Python API for KernelDensityMechCoder2015-06-061-1/+11
| | | | | | | | | | | | | Python API for KernelDensity Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6387 from MechCoder/spark-7639 and squashes the following commits: 17abc62 [MechCoder] add tests 2de6540 [MechCoder] style tests bf4acc0 [MechCoder] Added doctests 84359d5 [MechCoder] [SPARK-7639] Python API for KernelDensity
* [SPARK-6164] [ML] CrossValidatorModel should keep stats from fittingleahmcguire2015-06-032-3/+8
| | | | | | | | | | | | | | | | | Added stats from cross validation as a val in the cross validation model to save them for user access. Author: leahmcguire <lmcguire@salesforce.com> Closes #5915 from leahmcguire/saveCVmetrics and squashes the following commits: 49b507b [leahmcguire] fixed tyle error 67537b1 [leahmcguire] rebased 85907f0 [leahmcguire] fixed name 59987cc [leahmcguire] changed param name and test according to comments 36e71e3 [leahmcguire] rebasing 4b8223e [leahmcguire] fixed name 4ddffc6 [leahmcguire] changed param name and test according to comments 3a995da [leahmcguire] Added stats from cross validation as a val in the cross validation model to save them for user access
* [SPARK-8051] [MLLIB] make StringIndexerModel silent if input column does not ↵Xiangrui Meng2015-06-032-1/+23
| | | | | | | | | | | | | | | exist This is just a workaround to a bigger problem. Some pipeline stages may not be effective during prediction, and they should not complain about missing required columns, e.g. `StringIndexerModel`. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6595 from mengxr/SPARK-8051 and squashes the following commits: b6a36b9 [Xiangrui Meng] add doc f143fd4 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-8051 8ee7c7e [Xiangrui Meng] use SparkFunSuite e112394 [Xiangrui Meng] make StringIndexerModel silent if input column does not exist
* [SPARK-8054] [MLLIB] Added several Java-friendly APIs + unit testsJoseph K. Bradley2015-06-0313-19/+284
| | | | | | | | | | | | | | | | | | | | | | | | | | Java-friendly APIs added: * GaussianMixture.run() * GaussianMixtureModel.predict() * DistributedLDAModel.javaTopicDistributions() * StreamingKMeans: trainOn, predictOn, predictOnValues * Statistics.corr * params * added doc to w() since Java docs do not inherit doc * removed non-Java-friendly w() from StringArrayParam and DoubleArrayParam * made DoubleArrayParam Java-friendly w() actually Java-friendly I generated the doc and verified all changes. CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6562 from jkbradley/java-api-1.4 and squashes the following commits: c16821b [Joseph K. Bradley] Small fixes based on code review. d955581 [Joseph K. Bradley] unit test fixes 29b6b0d [Joseph K. Bradley] small fixes fe6dcfe [Joseph K. Bradley] Added several Java-friendly APIs + unit tests: NaiveBayes, GaussianMixture, LDA, StreamingKMeans, Statistics.corr, params
* [SPARK-7801] [BUILD] Updating versions to SPARK 1.5.0Patrick Wendell2015-06-031-1/+1
| | | | | | | | | | | | | Author: Patrick Wendell <patrick@databricks.com> Closes #6328 from pwendell/spark-1.5-update and squashes the following commits: 2f42d02 [Patrick Wendell] A few more excludes 4bebcf0 [Patrick Wendell] Update to RC4 61aaf46 [Patrick Wendell] Using new release candidate 55f1610 [Patrick Wendell] Another exclude 04b4f04 [Patrick Wendell] More issues with transient 1.4 changes 36f549b [Patrick Wendell] [SPARK-7801] [BUILD] Updating versions to SPARK 1.5.0
* [SPARK-7983] [MLLIB] Add require for one-based indices in loadLibSVMFileYuhao Yang2015-06-032-0/+47
| | | | | | | | | | | | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-7983 Customers frequently use zero-based indices in their LIBSVM files. No warnings or errors from Spark will be reported during their computation afterwards, and usually it will lead to wired result for many algorithms (like GBDT). add a quick check. Author: Yuhao Yang <hhbyyh@gmail.com> Closes #6538 from hhbyyh/loadSVM and squashes the following commits: 79d9c11 [Yuhao Yang] optimization as respond to comments 4310710 [Yuhao Yang] merge conflict 96460f1 [Yuhao Yang] merge conflict 20a2811 [Yuhao Yang] use require 6e4f8ca [Yuhao Yang] add check for ascending order 9956365 [Yuhao Yang] add ut for 0-based loadlibsvm exception 5bd1f9a [Yuhao Yang] add require for one-based in loadLIBSVM
* [SPARK-8053] [MLLIB] renamed scalingVector to scalingVecJoseph K. Bradley2015-06-022-8/+8
| | | | | | | | | | | | I searched the Spark codebase for all occurrences of "scalingVector" CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #6596 from jkbradley/scalingVec-rename and squashes the following commits: d3812f8 [Joseph K. Bradley] renamed scalingVector to scalingVec
* [SPARK-7691] [SQL] Refactor CatalystTypeConverter to use type-specific row ↵Josh Rosen2015-06-021-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | accessors This patch significantly refactors CatalystTypeConverters to both clean up the code and enable these conversions to work with future Project Tungsten features. At a high level, I've reorganized the code so that all functions dealing with the same type are grouped together into type-specific subclasses of `CatalystTypeConveter`. In addition, I've added new methods that allow the Catalyst Row -> Scala Row conversions to access the Catalyst row's fields through type-specific `getTYPE()` methods rather than the generic `get()` / `Row.apply` methods. This refactoring is a blocker to being able to unit test new operators that I'm developing as part of Project Tungsten, since those operators may output `UnsafeRow` instances which don't support the generic `get()`. The stricter type usage of types here has uncovered some bugs in other parts of Spark SQL: - #6217: DescribeCommand is assigned wrong output attributes in SparkStrategies - #6218: DataFrame.describe() should cast all aggregates to String - #6400: Use output schema, not relation schema, for data source input conversion Spark SQL current has undefined behavior for what happens when you try to create a DataFrame from user-specified rows whose values don't match the declared schema. According to the `createDataFrame()` Scaladoc: > It is important to make sure that the structure of every [[Row]] of the provided RDD matches the provided schema. Otherwise, there will be runtime exception. Given this, it sounds like it's technically not a break of our API contract to fail-fast when the data types don't match. However, there appear to be many cases where we don't fail even though the types don't match. For example, `JavaHashingTFSuite.hasingTF` passes a column of integers values for a "label" column which is supposed to contain floats. This column isn't actually read or modified as part of query processing, so its actual concrete type doesn't seem to matter. In other cases, there could be situations where we have generic numeric aggregates that tolerate being called with different numeric types than the schema specified, but this can be okay due to numeric conversions. In the long run, we will probably want to come up with precise semantics for implicit type conversions / widening when converting Java / Scala rows to Catalyst rows. Until then, though, I think that failing fast with a ClassCastException is a reasonable behavior; this is the approach taken in this patch. Note that certain optimizations in the inbound conversion functions for primitive types mean that we'll probably preserve the old undefined behavior in a majority of cases. Author: Josh Rosen <joshrosen@databricks.com> Closes #6222 from JoshRosen/catalyst-converters-refactoring and squashes the following commits: 740341b [Josh Rosen] Optimize method dispatch for primitive type conversions befc613 [Josh Rosen] Add tests to document Option-handling behavior. 5989593 [Josh Rosen] Use new SparkFunSuite base in CatalystTypeConvertersSuite 6edf7f8 [Josh Rosen] Re-add convertToScala(), since a Hive test still needs it 3f7b2d8 [Josh Rosen] Initialize converters lazily so that the attributes are resolved first 6ad0ebb [Josh Rosen] Fix JavaHashingTFSuite ClassCastException 677ff27 [Josh Rosen] Fix null handling bug; add tests. 8033d4c [Josh Rosen] Fix serialization error in UserDefinedGenerator. 85bba9d [Josh Rosen] Fix wrong input data in InMemoryColumnarQuerySuite 9c0e4e1 [Josh Rosen] Remove last use of convertToScala(). ae3278d [Josh Rosen] Throw ClassCastException errors during inbound conversions. 7ca7fcb [Josh Rosen] Comments and cleanup 1e87a45 [Josh Rosen] WIP refactoring of CatalystTypeConverters
* [SPARK-7547] [ML] Scala Example code for ElasticNetDB Tsai2015-06-025-9/+13
| | | | | | | | | | | | | | This is scala example code for both linear and logistic regression. Python and Java versions are to be added. Author: DB Tsai <dbt@netflix.com> Closes #6576 from dbtsai/elasticNetExample and squashes the following commits: e7ca406 [DB Tsai] fix test 6bb6d77 [DB Tsai] fix suite and remove duplicated setMaxIter 136e0dd [DB Tsai] address feedback 1ec29d4 [DB Tsai] fix style 9462f5f [DB Tsai] add example
* [SPARK-8049] [MLLIB] drop tmp col from OneVsRest outputXiangrui Meng2015-06-022-0/+10
| | | | | | | | | | | The temporary column should be dropped after we get the prediction column. harsha2010 Author: Xiangrui Meng <meng@databricks.com> Closes #6592 from mengxr/SPARK-8049 and squashes the following commits: 1d89107 [Xiangrui Meng] use SparkFunSuite 6ee70de [Xiangrui Meng] drop tmp col from OneVsRest output
* [SPARK-7985] [ML] [MLlib] [Docs] Remove "fittingParamMap" references. ↵Mike Dusenberry2015-06-0210-10/+10
| | | | | | | | | | | | | | | | | Updating ML Doc "Estimator, Transformer, and Param" examples. Updating ML Doc's *"Estimator, Transformer, and Param"* example to use `model.extractParamMap` instead of `model.fittingParamMap`, which no longer exists. mengxr, I believe this addresses (part of) the *update documentation* TODO list item from [PR 5820](https://github.com/apache/spark/pull/5820). Author: Mike Dusenberry <dusenberrymw@gmail.com> Closes #6514 from dusenberrymw/Fix_ML_Doc_Estimator_Transformer_Param_Example and squashes the following commits: 6366e1f [Mike Dusenberry] Updating instances of model.extractParamMap to model.parent.extractParamMap, since the Params of the parent Estimator could possibly differ from thos of the Model. d850e0e [Mike Dusenberry] Removing all references to "fittingParamMap" throughout Spark, since it has been removed. 0480304 [Mike Dusenberry] Updating the ML Doc "Estimator, Transformer, and Param" Java example to use model.extractParamMap() instead of model.fittingParamMap(), which no longer exists. 7d34939 [Mike Dusenberry] Updating ML Doc "Estimator, Transformer, and Param" example to use model.extractParamMap instead of model.fittingParamMap, which no longer exists.
* [SPARK-7582] [MLLIB] user guide for StringIndexerXiangrui Meng2015-06-011-0/+77
| | | | | | | | | | | | | This PR adds a Java unit test and user guide for `StringIndexer`. I put it before `OneHotEncoder` because they are closely related. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6561 from mengxr/SPARK-7582 and squashes the following commits: 4bba4f1 [Xiangrui Meng] fix example ba1cd1b [Xiangrui Meng] fix style 7fa18d1 [Xiangrui Meng] add user guide for StringIndexer 136cb93 [Xiangrui Meng] add a Java unit test for StringIndexer
* [SPARK-7584] [MLLIB] User guide for VectorAssemblerXiangrui Meng2015-06-011-0/+78
| | | | | | | | | | | | | | | | This PR adds a section in the user guide for `VectorAssembler` with code examples in Python/Java/Scala. It also adds a unit test in Java. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #6556 from mengxr/SPARK-7584 and squashes the following commits: 11313f6 [Xiangrui Meng] simplify Java example 0cd47f3 [Xiangrui Meng] update user guide fd36292 [Xiangrui Meng] update Java unit test ce61ca0 [Xiangrui Meng] add Java unit test for VectorAssembler e399942 [Xiangrui Meng] scala/python example code
* [SPARK-3850] Trim trailing spaces for MLlib.Reynold Xin2015-05-3130-189/+189
| | | | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #6534 from rxin/whitespace-mllib and squashes the following commits: 38926e3 [Reynold Xin] [SPARK-3850] Trim trailing spaces for MLlib.
* [SPARK-7979] Enforce structural type checker.Reynold Xin2015-05-311-0/+2
| | | | | | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #6536 from rxin/structural-type-checker and squashes the following commits: f833151 [Reynold Xin] Fixed compilation. 633f9a1 [Reynold Xin] Fixed typo. d1fa804 [Reynold Xin] [SPARK-7979] Enforce structural type checker.
* [SPARK-7920] [MLLIB] Make MLlib ChiSqSelector Serializable (& Fix Related ↵Mike Dusenberry2015-05-301-1/+1
| | | | | | | | | | | | | | | Documentation Example). The MLlib ChiSqSelector class is not serializable, and so the example in the ChiSqSelector documentation fails. Also, that example is missing the import of ChiSqSelector. This PR makes ChiSqSelector extend Serializable in MLlib, and adds the ChiSqSelector import statement to the associated example in the documentation. Author: Mike Dusenberry <dusenberrymw@gmail.com> Closes #6462 from dusenberrymw/Make_ChiSqSelector_Serializable_and_Fix_Related_Docs_Example and squashes the following commits: 9cb2f94 [Mike Dusenberry] Make MLlib ChiSqSelector Serializable. d9003bf [Mike Dusenberry] Add missing import in MLlib ChiSqSelector Docs Scala example.
* [HOT FIX] [BUILD] Fix maven build failuresAndrew Or2015-05-291-0/+7
| | | | | | | | | | | | | | | | | | | This patch fixes a build break in maven caused by #6441. Note that this patch reverts the changes in flume-sink because this module does not currently depend on Spark core, but the tests require it. There is not an easy way to make this work because mvn test dependencies are not transitive (MNG-1378). For now, we will leave the one test suite in flume-sink out until we figure out a better solution. This patch is mainly intended to unbreak the maven build. Author: Andrew Or <andrew@databricks.com> Closes #6511 from andrewor14/fix-build-mvn and squashes the following commits: 3d53643 [Andrew Or] [HOT FIX #6441] Fix maven build failures
* [SPARK-7558] Demarcate tests in unit-tests.logAndrew Or2015-05-29100-307/+224
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Right now `unit-tests.log` are not of much value because we can't tell where the test boundaries are easily. This patch adds log statements before and after each test to outline the test boundaries, e.g.: ``` ===== TEST OUTPUT FOR o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' ===== 15/05/27 12:36:39.596 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO SparkContext: Starting job: count at KryoSerializerSuite.scala:230 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Got job 3 (count at KryoSerializerSuite.scala:230) with 4 output partitions (allowLocal=false) 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Final stage: ResultStage 3(count at KryoSerializerSuite.scala:230) 15/05/27 12:36:39.596 dag-scheduler-event-loop INFO DAGScheduler: Parents of final stage: List() 15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Missing parents: List() 15/05/27 12:36:39.597 dag-scheduler-event-loop INFO DAGScheduler: Submitting ResultStage 3 (ParallelCollectionRDD[5] at parallelize at KryoSerializerSuite.scala:230), which has no missing parents ... 15/05/27 12:36:39.624 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO DAGScheduler: Job 3 finished: count at KryoSerializerSuite.scala:230, took 0.028563 s 15/05/27 12:36:39.625 pool-1-thread-1-ScalaTest-running-KryoSerializerSuite INFO KryoSerializerSuite: ***** FINISHED o.a.s.serializer.KryoSerializerSuite: 'kryo with parallelize for primitive arrays' ***** ... ``` Author: Andrew Or <andrew@databricks.com> Closes #6441 from andrewor14/demarcate-tests and squashes the following commits: 879b060 [Andrew Or] Fix compile after rebase d622af7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 017c8ba [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 7790b6c [Andrew Or] Fix tests after logical merge conflict c7460c0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests c43ffc4 [Andrew Or] Fix tests? 8882581 [Andrew Or] Fix tests ee22cda [Andrew Or] Fix log message fa9450e [Andrew Or] Merge branch 'master' of github.com:apache/spark into demarcate-tests 12d1e1b [Andrew Or] Various whitespace changes (minor) 69cbb24 [Andrew Or] Make all test suites extend SparkFunSuite instead of FunSuite bbce12e [Andrew Or] Fix manual things that cannot be covered through automation da0b12f [Andrew Or] Add core tests as dependencies in all modules f7d29ce [Andrew Or] Introduce base abstract class for all test suites
* [SPARK-7940] Enforce whitespace checking for DO, TRY, CATCH, FINALLY, MATCH, ↵Reynold Xin2015-05-292-3/+3
| | | | | | | | | | | | LARROW, RARROW in style checker. … Author: Reynold Xin <rxin@databricks.com> Closes #6491 from rxin/more-whitespace and squashes the following commits: f6e63dc [Reynold Xin] [SPARK-7940] Enforce whitespace checking for DO, TRY, CATCH, FINALLY, MATCH, LARROW, RARROW in style checker.
* [SPARK-7946] [MLLIB] DecayFactor wrongly set in StreamingKMeansMechCoder2015-05-292-1/+8
| | | | | | | | | Author: MechCoder <manojkumarsivaraj334@gmail.com> Closes #6497 from MechCoder/spark-7946 and squashes the following commits: 2fdd0a3 [MechCoder] Add non-regression test 8c988c6 [MechCoder] [SPARK-7946] DecayFactor wrongly set in StreamingKMeans
* [SPARK-7912] [SPARK-7921] [MLLIB] Update OneHotEncoder to handle ML ↵Xiangrui Meng2015-05-292-59/+143
| | | | | | | | | | | | | | | | | | | | | | | | | | | attributes and change includeFirst to dropLast This PR contains two major changes to `OneHotEncoder`: 1. more robust handling of ML attributes. If the input attribute is unknown, we look at the values to get the max category index 2. change `includeFirst` to `dropLast` and leave the default to `true`. There are couple benefits: a. consistent with other tutorials of one-hot encoding (or dummy coding) (e.g., http://www.ats.ucla.edu/stat/mult_pkg/faq/general/dummy.htm) b. keep the indices unmodified in the output vector. If we drop the first, all indices will be shifted by 1. c. If users use `StringIndex`, the last element is the least frequent one. Sorry for including two changes in one PR! I'll update the user guide in another PR. jkbradley sryza Author: Xiangrui Meng <meng@databricks.com> Closes #6466 from mengxr/SPARK-7912 and squashes the following commits: a280dca [Xiangrui Meng] fix tests d8f234d [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7912 171b276 [Xiangrui Meng] mention the difference between our impl vs sklearn's 00dfd96 [Xiangrui Meng] update OneHotEncoder in Python 208ddad [Xiangrui Meng] update OneHotEncoder to handle ML attributes and change includeFirst to dropLast
* [SPARK-7922] [MLLIB] use DataFrames for user/item factors in ALSModelXiangrui Meng2015-05-281-44/+57
| | | | | | | | | | | | | Expose user/item factors in DataFrames. This is to be more consistent with the pipeline API. It also helps maintain consistent APIs across languages. This PR also removed fitting params from `ALSModel`. coderxiang Author: Xiangrui Meng <meng@databricks.com> Closes #6468 from mengxr/SPARK-7922 and squashes the following commits: 7bfb1d5 [Xiangrui Meng] update ALSModel in PySpark 1ba5607 [Xiangrui Meng] use DataFrames for user/item factors in ALS
* [SPARK-7927] [MLLIB] Enforce whitespace for more tokens in style checkerXiangrui Meng2015-05-2833-71/+88
| | | | | | | | | | | | rxin Author: Xiangrui Meng <meng@databricks.com> Closes #6481 from mengxr/mllib-scalastyle and squashes the following commits: 3ca4d61 [Xiangrui Meng] revert scalastyle config 30961ba [Xiangrui Meng] adjust spaces in mllib/test 571b5c5 [Xiangrui Meng] fix spaces in mllib
* [SPARK-7577] [ML] [DOC] add bucketizer docXusen Yin2015-05-281-0/+80
| | | | | | | | | | | | | CC jkbradley Author: Xusen Yin <yinxusen@gmail.com> Closes #6451 from yinxusen/SPARK-7577 and squashes the following commits: e2dc32e [Xusen Yin] rename colums e350e49 [Xusen Yin] add all demos 006ddf1 [Xusen Yin] add java test 3238481 [Xusen Yin] add bucketizer
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