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* [SPARK-13629][ML] Add binary toggle Param to CountVectorizerYuhao Yang2016-03-181-14/+9
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This is a continued work for https://github.com/apache/spark/pull/11536#issuecomment-198511013, containing some comment update and style adjustment. jkbradley ## How was this patch tested? unit tests. Author: Yuhao Yang <hhbyyh@gmail.com> Closes #11830 from hhbyyh/cvToggle.
* [MINOR][ML] When trainingSummary is None, it should throw RuntimeException.Yanbo Liang2016-03-184-20/+8
| | | | | | | | | | | | ## What changes were proposed in this pull request? When trainingSummary is None, it should throw ```RuntimeException```. cc mengxr ## How was this patch tested? Existing tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11784 from yanboliang/fix-summary.
* [SPARK-10788][MLLIB][ML] Remove duplicate bins for decision treessethah2016-03-179-49/+54
| | | | | | | | | | | | | | | | | | Decision trees in spark.ml (RandomForest.scala) communicate twice as much data as needed for unordered categorical features. Here's an example. Say there are 3 categories A, B, C. We consider 3 splits: * A vs. B, C * A, B vs. C * A, C vs. B Currently, we collect statistics for each of the 6 subsets of categories (3 * 2 = 6). However, we could instead collect statistics for the 3 subsets on the left-hand side of the 3 possible splits: A and A,B and A,C. If we also have stats for the entire node, then we can compute the stats for the 3 subsets on the right-hand side of the splits. In pseudomath: stats(B,C) = stats(A,B,C) - stats(A). This patch adds a parent stats array to the `DTStatsAggregator` so that the right child stats do not need to be stored. The right child stats are computed by subtracting left child stats from the parent stats for unordered categorical features. Author: sethah <seth.hendrickson16@gmail.com> Closes #9474 from sethah/SPARK-10788.
* [SPARK-13761][ML] Remove remaining uses of validateParamsJoseph K. Bradley2016-03-177-61/+27
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Cleanups from [https://github.com/apache/spark/pull/11620]: remove remaining uses of validateParams, and put functionality into transformSchema ## How was this patch tested? Existing unit tests, modified to check using transformSchema instead of validateParams Author: Joseph K. Bradley <joseph@databricks.com> Closes #11790 from jkbradley/SPARK-13761-cleanup.
* [SPARK-11891] Model export/import for RFormula and RFormulaModelXusen Yin2016-03-173-17/+207
| | | | | | | | https://issues.apache.org/jira/browse/SPARK-11891 Author: Xusen Yin <yinxusen@gmail.com> Closes #9884 from yinxusen/SPARK-11891.
* [SPARK-13928] Move org.apache.spark.Logging into ↵Wenchen Fan2016-03-1766-69/+90
| | | | | | | | | | | | | | | | org.apache.spark.internal.Logging ## What changes were proposed in this pull request? Logging was made private in Spark 2.0. If we move it, then users would be able to create a Logging trait themselves to avoid changing their own code. ## How was this patch tested? existing tests. Author: Wenchen Fan <wenchen@databricks.com> Closes #11764 from cloud-fan/logger.
* [SPARK-13629][ML] Add binary toggle Param to CountVectorizerYuhao Yang2016-03-172-2/+46
| | | | | | | | | | | | | | | ## What changes were proposed in this pull request? It would be handy to add a binary toggle Param to CountVectorizer, as in the scikit-learn one: http://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.CountVectorizer.html If set, then all non-zero counts will be set to 1. ## How was this patch tested? unit tests Author: Yuhao Yang <hhbyyh@gmail.com> Closes #11536 from hhbyyh/cvToggle.
* [SPARK-13761][ML] Deprecate validateParamsYuhao Yang2016-03-1633-89/+36
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Deprecate validateParams() method here: https://github.com/apache/spark/blob/035d3acdf3c1be5b309a861d5c5beb803b946b5e/mllib/src/main/scala/org/apache/spark/ml/param/params.scala#L553 Move all functionality in overridden methods to transformSchema(). Check docs to make sure they indicate complex Param interaction checks should be done in transformSchema. ## How was this patch tested? unit tests Author: Yuhao Yang <hhbyyh@gmail.com> Closes #11620 from hhbyyh/depreValid.
* [SPARK-11011][SQL] Narrow type of UDT serializationJakob Odersky2016-03-162-2/+2
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Narrow down the parameter type of `UserDefinedType#serialize()`. Currently, the parameter type is `Any`, however it would logically make more sense to narrow it down to the type of the actual user defined type. ## How was this patch tested? Existing tests were successfully run on local machine. Author: Jakob Odersky <jakob@odersky.com> Closes #11379 from jodersky/SPARK-11011-udt-types.
* [SPARK-13927][MLLIB] add row/column iterator to local matricesXiangrui Meng2016-03-162-1/+76
| | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Add row/column iterator to local matrices to simplify tasks like BlockMatrix => RowMatrix conversion. It handles dense and sparse matrices properly. ## How was this patch tested? Unit tests on sparse and dense matrix. cc: dbtsai Author: Xiangrui Meng <meng@databricks.com> Closes #11757 from mengxr/SPARK-13927.
* [SPARK-11888][ML] Decision tree persistence in spark.mlJoseph K. Bradley2016-03-1623-71/+428
| | | | | | | | | | | | | | | | | | | | ### What changes were proposed in this pull request? Made these MLReadable and MLWritable: DecisionTreeClassifier, DecisionTreeClassificationModel, DecisionTreeRegressor, DecisionTreeRegressionModel * The shared implementation is in treeModels.scala * I use case classes to create a DataFrame to save, and I use the Dataset API to parse loaded files. Other changes: * Made CategoricalSplit.numCategories public (to use in persistence) * Fixed a bug in DefaultReadWriteTest.testEstimatorAndModelReadWrite, where it did not call the checkModelData function passed as an argument. This caused an error in LDASuite, which I fixed. ### How was this patch tested? Persistence is tested via unit tests. For each algorithm, there are 2 non-trivial trees (depth 2). One is built with continuous features, and one with categorical; this ensures that both types of splits are tested. Author: Joseph K. Bradley <joseph@databricks.com> Closes #11581 from jkbradley/dt-io.
* [SPARK-13613][ML] Provide ignored tests to export test dataset into CSV formatYanbo Liang2016-03-164-33/+97
| | | | | | | | | | | | ## What changes were proposed in this pull request? Provide ignored test cases to export the test dataset into CSV format in ```LinearRegressionSuite```, ```LogisticRegressionSuite```, ```AFTSurvivalRegressionSuite``` and ```GeneralizedLinearRegressionSuite```, so users can validate the training accuracy compared with R's glm, glmnet and survival package. cc mengxr ## How was this patch tested? The test suite is ignored, but I have enabled all these cases offline and it works as expected. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11463 from yanboliang/spark-13613.
* [SPARK-13894][SQL] SqlContext.range return type from DataFrame to DataSetCheng Hao2016-03-161-1/+1
| | | | | | | | | | | | | ## What changes were proposed in this pull request? https://issues.apache.org/jira/browse/SPARK-13894 Change the return type of the `SQLContext.range` API from `DataFrame` to `Dataset`. ## How was this patch tested? No additional unit test required. Author: Cheng Hao <hao.cheng@intel.com> Closes #11730 from chenghao-intel/range.
* [SPARK-13823][SPARK-13397][SPARK-13395][CORE] More warnings, StandardCharset ↵Sean Owen2016-03-161-2/+2
| | | | | | | | | | | | | | | | | | | | follow up ## What changes were proposed in this pull request? Follow up to https://github.com/apache/spark/pull/11657 - Also update `String.getBytes("UTF-8")` to use `StandardCharsets.UTF_8` - And fix one last new Coverity warning that turned up (use of unguarded `wait()` replaced by simpler/more robust `java.util.concurrent` classes in tests) - And while we're here cleaning up Coverity warnings, just fix about 15 more build warnings ## How was this patch tested? Jenkins tests Author: Sean Owen <sowen@cloudera.com> Closes #11725 from srowen/SPARK-13823.2.
* [SPARK-9837][ML] R-like summary statistics for GLMs via iteratively ↵Yanbo Liang2016-03-153-11/+796
| | | | | | | | | | | | | reweighted least squares ## What changes were proposed in this pull request? Provide R-like summary statistics for GLMs via iteratively reweighted least squares. ## How was this patch tested? unit tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11694 from yanboliang/spark-9837.
* [SPARK-12379][ML][MLLIB] Copy GBT implementation to spark.mlsethah2016-03-1512-15/+306
| | | | | | | | | | | Currently, GBTs in spark.ml wrap the implementation in spark.mllib. This is preventing several improvements to GBTs in spark.ml, so we need to move the implementation to ml and use spark.ml decision trees in the implementation. At first, we should make minimal changes to the implementation. Performance testing should be done to ensure there were no regressions. Performance testing results are [here](https://docs.google.com/document/d/1dYd2mnfGdUKkQ3vZe2BpzsTnI5IrpSLQ-NNKDZhUkgw/edit?usp=sharing) Author: sethah <seth.hendrickson16@gmail.com> Closes #10607 from sethah/SPARK-12379.
* [SPARK-13664][SQL] Add a strategy for planning partitioned and bucketed ↵Michael Armbrust2016-03-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | scans of files This PR adds a new strategy, `FileSourceStrategy`, that can be used for planning scans of collections of files that might be partitioned or bucketed. Compared with the existing planning logic in `DataSourceStrategy` this version has the following desirable properties: - It removes the need to have `RDD`, `broadcastedHadoopConf` and other distributed concerns in the public API of `org.apache.spark.sql.sources.FileFormat` - Partition column appending is delegated to the format to avoid an extra copy / devectorization when appending partition columns - It minimizes the amount of data that is shipped to each executor (i.e. it does not send the whole list of files to every worker in the form of a hadoop conf) - it natively supports bucketing files into partitions, and thus does not require coalescing / creating a `UnionRDD` with the correct partitioning. - Small files are automatically coalesced into fewer tasks using an approximate bin-packing algorithm. Currently only a testing source is planned / tested using this strategy. In follow-up PRs we will port the existing formats to this API. A stub for `FileScanRDD` is also added, but most methods remain unimplemented. Other minor cleanups: - partition pruning is pushed into `FileCatalog` so both the new and old code paths can use this logic. This will also allow future implementations to use indexes or other tricks (i.e. a MySQL metastore) - The partitions from the `FileCatalog` now propagate information about file sizes all the way up to the planner so we can intelligently spread files out. - `Array` -> `Seq` in some internal APIs to avoid unnecessary `toArray` calls - Rename `Partition` to `PartitionDirectory` to differentiate partitions used earlier in pruning from those where we have already enumerated the files and their sizes. Author: Michael Armbrust <michael@databricks.com> Closes #11646 from marmbrus/fileStrategy.
* [SPARK-11826][MLLIB] Refactor add() and subtract() methodsEhsan M.Kermani2016-03-142-13/+88
| | | | | | | | srowen Could you please check this when you have time? Author: Ehsan M.Kermani <ehsanmo1367@gmail.com> Closes #9916 from ehsanmok/JIRA-11826.
* [SPARK-13686][MLLIB][STREAMING] Add a constructor parameter `reqParam` to ↵Dongjoon Hyun2016-03-142-6/+18
| | | | | | | | | | | | | | | | | (Streaming)LinearRegressionWithSGD ## What changes were proposed in this pull request? `LinearRegressionWithSGD` and `StreamingLinearRegressionWithSGD` does not have `regParam` as their constructor arguments. They just depends on GradientDescent's default reqParam values. To be consistent with other algorithms, we had better add them. The same default value is used. ## How was this patch tested? Pass the existing unit test. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11527 from dongjoon-hyun/SPARK-13686.
* [MINOR][DOCS] Fix more typos in comments/strings.Dongjoon Hyun2016-03-149-9/+9
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR fixes 135 typos over 107 files: * 121 typos in comments * 11 typos in testcase name * 3 typos in log messages ## How was this patch tested? Manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11689 from dongjoon-hyun/fix_more_typos.
* [SPARK-13823][CORE][STREAMING][SQL] Always specify Charset in String <-> ↵Sean Owen2016-03-134-10/+11
| | | | | | | | | | | | | | | | | | | | byte[] conversions (and remaining Coverity items) ## What changes were proposed in this pull request? - Fixes calls to `new String(byte[])` or `String.getBytes()` that rely on platform default encoding, to use UTF-8 - Same for `InputStreamReader` and `OutputStreamWriter` constructors - Standardizes on UTF-8 everywhere - Standardizes specifying the encoding with `StandardCharsets.UTF-8`, not the Guava constant or "UTF-8" (which means handling `UnuspportedEncodingException`) - (also addresses the other remaining Coverity scan issues, which are pretty trivial; these are separated into commit https://github.com/srowen/spark/commit/1deecd8d9ca986d8adb1a42d315890ce5349d29c ) ## How was this patch tested? Jenkins tests Author: Sean Owen <sowen@cloudera.com> Closes #11657 from srowen/SPARK-13823.
* [MINOR][DOCS] Replace `DataFrame` with `Dataset` in Javadoc.Dongjoon Hyun2016-03-132-7/+7
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? SPARK-13817 (PR #11656) replaces `DataFrame` with `Dataset` from Java. This PR fixes the remaining broken links and sample Java code in `package-info.java`. As a result, it will update the following Javadoc. * http://spark.apache.org/docs/latest/api/java/org/apache/spark/ml/attribute/package-summary.html * http://spark.apache.org/docs/latest/api/java/org/apache/spark/ml/feature/package-summary.html ## How was this patch tested? Manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11675 from dongjoon-hyun/replace_dataframe_with_dataset_in_javadoc.
* [SPARK-13841][SQL] Removes Dataset.collectRows()/takeRows()Cheng Lian2016-03-131-1/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR removes two methods, `collectRows()` and `takeRows()`, from `Dataset[T]`. These methods were added in PR #11443, and were later considered not useful. ## How was this patch tested? Existing tests should do the work. Author: Cheng Lian <lian@databricks.com> Closes #11678 from liancheng/remove-collect-rows-and-take-rows.
* [SPARK-13244][SQL] Migrates DataFrame to DatasetCheng Lian2016-03-1029-99/+118
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR unifies DataFrame and Dataset by migrating existing DataFrame operations to Dataset and make `DataFrame` a type alias of `Dataset[Row]`. Most Scala code changes are source compatible, but Java API is broken as Java knows nothing about Scala type alias (mostly replacing `DataFrame` with `Dataset<Row>`). There are several noticeable API changes related to those returning arrays: 1. `collect`/`take` - Old APIs in class `DataFrame`: ```scala def collect(): Array[Row] def take(n: Int): Array[Row] ``` - New APIs in class `Dataset[T]`: ```scala def collect(): Array[T] def take(n: Int): Array[T] def collectRows(): Array[Row] def takeRows(n: Int): Array[Row] ``` Two specialized methods `collectRows` and `takeRows` are added because Java doesn't support returning generic arrays. Thus, for example, `DataFrame.collect(): Array[T]` actually returns `Object` instead of `Array<T>` from Java side. Normally, Java users may fall back to `collectAsList` and `takeAsList`. The two new specialized versions are added to avoid performance regression in ML related code (but maybe I'm wrong and they are not necessary here). 1. `randomSplit` - Old APIs in class `DataFrame`: ```scala def randomSplit(weights: Array[Double], seed: Long): Array[DataFrame] def randomSplit(weights: Array[Double]): Array[DataFrame] ``` - New APIs in class `Dataset[T]`: ```scala def randomSplit(weights: Array[Double], seed: Long): Array[Dataset[T]] def randomSplit(weights: Array[Double]): Array[Dataset[T]] ``` Similar problem as above, but hasn't been addressed for Java API yet. We can probably add `randomSplitAsList` to fix this one. 1. `groupBy` Some original `DataFrame.groupBy` methods have conflicting signature with original `Dataset.groupBy` methods. To distinguish these two, typed `Dataset.groupBy` methods are renamed to `groupByKey`. Other noticeable changes: 1. Dataset always do eager analysis now We used to support disabling DataFrame eager analysis to help reporting partially analyzed malformed logical plan on analysis failure. However, Dataset encoders requires eager analysi during Dataset construction. To preserve the error reporting feature, `AnalysisException` now takes an extra `Option[LogicalPlan]` argument to hold the partially analyzed plan, so that we can check the plan tree when reporting test failures. This plan is passed by `QueryExecution.assertAnalyzed`. ## How was this patch tested? Existing tests do the work. ## TODO - [ ] Fix all tests - [ ] Re-enable MiMA check - [ ] Update ScalaDoc (`since`, `group`, and example code) Author: Cheng Lian <lian@databricks.com> Author: Yin Huai <yhuai@databricks.com> Author: Wenchen Fan <wenchen@databricks.com> Author: Cheng Lian <liancheng@users.noreply.github.com> Closes #11443 from liancheng/ds-to-df.
* [SPARK-3854][BUILD] Scala style: require spaces before `{`.Dongjoon Hyun2016-03-1011-15/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Since the opening curly brace, '{', has many usages as discussed in [SPARK-3854](https://issues.apache.org/jira/browse/SPARK-3854), this PR adds a ScalaStyle rule to prevent '){' pattern for the following majority pattern and fixes the code accordingly. If we enforce this in ScalaStyle from now, it will improve the Scala code quality and reduce review time. ``` // Correct: if (true) { println("Wow!") } // Incorrect: if (true){ println("Wow!") } ``` IntelliJ also shows new warnings based on this. ## How was this patch tested? Pass the Jenkins ScalaStyle test. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11637 from dongjoon-hyun/SPARK-3854.
* [SPARK-11108][ML] OneHotEncoder should support other numeric typessethah2016-03-102-3/+35
| | | | | | | | | | | | | | Adding support for other numeric types: * Integer * Short * Long * Float * Decimal Author: sethah <seth.hendrickson16@gmail.com> Closes #9777 from sethah/SPARK-11108.
* [SPARK-11861][ML] Add feature importances for decision treessethah2016-03-0910-27/+126
| | | | | | | | This patch adds an API entry point for single decision tree feature importances. Author: sethah <seth.hendrickson16@gmail.com> Closes #9912 from sethah/SPARK-11861.
* [SPARK-13615][ML] GeneralizedLinearRegression supports save/loadYanbo Liang2016-03-092-10/+96
| | | | | | | | | | | | ## What changes were proposed in this pull request? ```GeneralizedLinearRegression``` supports ```save/load```. cc mengxr ## How was this patch tested? unit test. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11465 from yanboliang/spark-13615.
* [SPARK-13702][CORE][SQL][MLLIB] Use diamond operator for generic instance ↵Dongjoon Hyun2016-03-098-12/+12
| | | | | | | | | | | | | | | | | | | | | | | | | creation in Java code. ## What changes were proposed in this pull request? In order to make `docs/examples` (and other related code) more simple/readable/user-friendly, this PR replaces existing codes like the followings by using `diamond` operator. ``` - final ArrayList<Product2<Object, Object>> dataToWrite = - new ArrayList<Product2<Object, Object>>(); + final ArrayList<Product2<Object, Object>> dataToWrite = new ArrayList<>(); ``` Java 7 or higher supports **diamond** operator which replaces the type arguments required to invoke the constructor of a generic class with an empty set of type parameters (<>). Currently, Spark Java code use mixed usage of this. ## How was this patch tested? Manual. Pass the existing tests. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11541 from dongjoon-hyun/SPARK-13702.
* [ML] testEstimatorAndModelReadWrite should call checkModelDataYanbo Liang2016-03-082-1/+5
| | | | | | | | | | | | | ## What changes were proposed in this pull request? Although we defined ```checkModelData``` in [```read/write``` test](https://github.com/apache/spark/blob/master/mllib/src/test/scala/org/apache/spark/ml/regression/LinearRegressionSuite.scala#L994) of ML estimators/models and pass it to ```testEstimatorAndModelReadWrite```, ```testEstimatorAndModelReadWrite``` omits to call ```checkModelData``` to check the equality of model data. So actually we did not run the check of model data equality for all test cases currently, we should fix it. BTW, fix the bug of LDA read/write test which did not set ```docConcentration```. This bug should have failed test, but it does not complain because we did not run ```checkModelData``` actually. cc jkbradley mengxr ## How was this patch tested? No new unit test, should pass the exist ones. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11513 from yanboliang/ml-check-model-data.
* [SPARK-13715][MLLIB] Remove last usages of jblas in testsSean Owen2016-03-087-118/+106
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? Remove last usage of jblas, in tests ## How was this patch tested? Jenkins tests -- the same ones that are being modified. Author: Sean Owen <sowen@cloudera.com> Closes #11560 from srowen/SPARK-13715.
* [SPARK-13665][SQL] Separate the concerns of HadoopFsRelationMichael Armbrust2016-03-072-76/+67
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | `HadoopFsRelation` is used for reading most files into Spark SQL. However today this class mixes the concerns of file management, schema reconciliation, scan building, bucketing, partitioning, and writing data. As a result, many data sources are forced to reimplement the same functionality and the various layers have accumulated a fair bit of inefficiency. This PR is a first cut at separating this into several components / interfaces that are each described below. Additionally, all implementations inside of Spark (parquet, csv, json, text, orc, svmlib) have been ported to the new API `FileFormat`. External libraries, such as spark-avro will also need to be ported to work with Spark 2.0. ### HadoopFsRelation A simple `case class` that acts as a container for all of the metadata required to read from a datasource. All discovery, resolution and merging logic for schemas and partitions has been removed. This an internal representation that no longer needs to be exposed to developers. ```scala case class HadoopFsRelation( sqlContext: SQLContext, location: FileCatalog, partitionSchema: StructType, dataSchema: StructType, bucketSpec: Option[BucketSpec], fileFormat: FileFormat, options: Map[String, String]) extends BaseRelation ``` ### FileFormat The primary interface that will be implemented by each different format including external libraries. Implementors are responsible for reading a given format and converting it into `InternalRow` as well as writing out an `InternalRow`. A format can optionally return a schema that is inferred from a set of files. ```scala trait FileFormat { def inferSchema( sqlContext: SQLContext, options: Map[String, String], files: Seq[FileStatus]): Option[StructType] def prepareWrite( sqlContext: SQLContext, job: Job, options: Map[String, String], dataSchema: StructType): OutputWriterFactory def buildInternalScan( sqlContext: SQLContext, dataSchema: StructType, requiredColumns: Array[String], filters: Array[Filter], bucketSet: Option[BitSet], inputFiles: Array[FileStatus], broadcastedConf: Broadcast[SerializableConfiguration], options: Map[String, String]): RDD[InternalRow] } ``` The current interface is based on what was required to get all the tests passing again, but still mixes a couple of concerns (i.e. `bucketSet` is passed down to the scan instead of being resolved by the planner). Additionally, scans are still returning `RDD`s instead of iterators for single files. In a future PR, bucketing should be removed from this interface and the scan should be isolated to a single file. ### FileCatalog This interface is used to list the files that make up a given relation, as well as handle directory based partitioning. ```scala trait FileCatalog { def paths: Seq[Path] def partitionSpec(schema: Option[StructType]): PartitionSpec def allFiles(): Seq[FileStatus] def getStatus(path: Path): Array[FileStatus] def refresh(): Unit } ``` Currently there are two implementations: - `HDFSFileCatalog` - based on code from the old `HadoopFsRelation`. Infers partitioning by recursive listing and caches this data for performance - `HiveFileCatalog` - based on the above, but it uses the partition spec from the Hive Metastore. ### ResolvedDataSource Produces a logical plan given the following description of a Data Source (which can come from DataFrameReader or a metastore): - `paths: Seq[String] = Nil` - `userSpecifiedSchema: Option[StructType] = None` - `partitionColumns: Array[String] = Array.empty` - `bucketSpec: Option[BucketSpec] = None` - `provider: String` - `options: Map[String, String]` This class is responsible for deciding which of the Data Source APIs a given provider is using (including the non-file based ones). All reconciliation of partitions, buckets, schema from metastores or inference is done here. ### DataSourceAnalysis / DataSourceStrategy Responsible for analyzing and planning reading/writing of data using any of the Data Source APIs, including: - pruning the files from partitions that will be read based on filters. - appending partition columns* - applying additional filters when a data source can not evaluate them internally. - constructing an RDD that is bucketed correctly when required* - sanity checking schema match-up and other analysis when writing. *In the future we should do that following: - Break out file handling into its own Strategy as its sufficiently complex / isolated. - Push the appending of partition columns down in to `FileFormat` to avoid an extra copy / unvectorization. - Use a custom RDD for scans instead of `SQLNewNewHadoopRDD2` Author: Michael Armbrust <michael@databricks.com> Author: Wenchen Fan <wenchen@databricks.com> Closes #11509 from marmbrus/fileDataSource.
* [SPARK-13036][SPARK-13318][SPARK-13319] Add save/load for feature.pyXusen Yin2016-03-042-3/+45
| | | | | | | | | | Add save/load for feature.py. Meanwhile, add save/load for `ElementwiseProduct` in Scala side and fix a bug of missing `setDefault` in `VectorSlicer` and `StopWordsRemover`. In this PR I ignore the `RFormula` and `RFormulaModel` because its Scala implementation is pending in https://github.com/apache/spark/pull/9884. I'll add them in this PR if https://github.com/apache/spark/pull/9884 gets merged first. Or add a follow-up JIRA for `RFormula`. Author: Xusen Yin <yinxusen@gmail.com> Closes #11203 from yinxusen/SPARK-13036.
* [SPARK-13646][MLLIB] QuantileDiscretizer counts dataset twice in get…Abou Haydar Elias2016-03-041-1/+1
| | | | | | | | | | | ## What changes were proposed in this pull request? It avoids counting the dataframe twice. Author: Abou Haydar Elias <abouhaydar.elias@gmail.com> Author: Elie A <abouhaydar.elias@gmail.com> Closes #11491 from eliasah/quantile-discretizer-patch.
* [MINOR] Fix typos in comments and testcase name of codeDongjoon Hyun2016-03-031-1/+1
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR fixes typos in comments and testcase name of code. ## How was this patch tested? manual. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11481 from dongjoon-hyun/minor_fix_typos_in_code.
* [MINOR][ML][DOC] Remove duplicated periods at the end of some sharedParamYanbo Liang2016-03-032-15/+15
| | | | | | | | | | | | ## What changes were proposed in this pull request? Remove duplicated periods at the end of some sharedParams in ScalaDoc, such as [here](https://github.com/apache/spark/pull/11344/files#diff-9edc669edcf2c0c7cf1efe4a0a57da80L367) cc mengxr srowen ## How was this patch tested? Documents change, no test. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11344 from yanboliang/shared-cleanup.
* [SPARK-13583][CORE][STREAMING] Remove unused imports and add checkstyle ruleDongjoon Hyun2016-03-0334-44/+18
| | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? After SPARK-6990, `dev/lint-java` keeps Java code healthy and helps PR review by saving much time. This issue aims remove unused imports from Java/Scala code and add `UnusedImports` checkstyle rule to help developers. ## How was this patch tested? ``` ./dev/lint-java ./build/sbt compile ``` Author: Dongjoon Hyun <dongjoon@apache.org> Closes #11438 from dongjoon-hyun/SPARK-13583.
* [SPARK-13423][WIP][CORE][SQL][STREAMING] Static analysis fixes for 2.xSean Owen2016-03-0327-55/+61
| | | | | | | | | | | | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Make some cross-cutting code improvements according to static analysis. These are individually up for discussion since they exist in separate commits that can be reverted. The changes are broadly: - Inner class should be static - Mismatched hashCode/equals - Overflow in compareTo - Unchecked warnings - Misuse of assert, vs junit.assert - get(a) + getOrElse(b) -> getOrElse(a,b) - Array/String .size -> .length (occasionally, -> .isEmpty / .nonEmpty) to avoid implicit conversions - Dead code - tailrec - exists(_ == ) -> contains find + nonEmpty -> exists filter + size -> count - reduce(_+_) -> sum map + flatten -> map The most controversial may be .size -> .length simply because of its size. It is intended to avoid implicits that might be expensive in some places. ## How was the this patch tested? Existing Jenkins unit tests. Author: Sean Owen <sowen@cloudera.com> Closes #11292 from srowen/SPARK-13423.
* [SPARK-12811][ML] Estimator for Generalized Linear Models(GLMs)Yanbo Liang2016-03-014-4/+1094
| | | | | | | | | | Estimator for Generalized Linear Models(GLMs) which will be solved by IRLS. cc mengxr Author: Yanbo Liang <ybliang8@gmail.com> Closes #11136 from yanboliang/spark-12811.
* [SPARK-13506][MLLIB] Fix the wrong parameter in R code comment in ↵Zheng RuiFeng2016-02-291-1/+2
| | | | | | | | | | | | | | | | | | AssociationRulesSuite JIRA: https://issues.apache.org/jira/browse/SPARK-13506 ## What changes were proposed in this pull request? just chang R Snippet Comment in AssociationRulesSuite ## How was this patch tested? unit test passsed Author: Zheng RuiFeng <ruifengz@foxmail.com> Closes #11387 from zhengruifeng/ars.
* [SPARK-13545][MLLIB][PYSPARK] Make MLlib LogisticRegressionWithLBFGS's ↵Yanbo Liang2016-02-291-0/+4
| | | | | | | | | | | | | | | | | default parameters consistent in Scala and Python ## What changes were proposed in this pull request? * The default value of ```regParam``` of PySpark MLlib ```LogisticRegressionWithLBFGS``` should be consistent with Scala which is ```0.0```. (This is also consistent with ML ```LogisticRegression```.) * BTW, if we use a known updater(L1 or L2) for binary classification, ```LogisticRegressionWithLBFGS``` will call the ML implementation. We should update the API doc to clarifying ```numCorrections``` will have no effect if we fall into that route. * Make a pass for all parameters of ```LogisticRegressionWithLBFGS```, others are set properly. cc mengxr dbtsai ## How was this patch tested? No new tests, it should pass all current tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11424 from yanboliang/spark-13545.
* [SPARK-12634][PYSPARK][DOC] PySpark tree parameter desc to consistent formatBryan Cutler2016-02-264-132/+140
| | | | | | | | | | | Part of task for [SPARK-11219](https://issues.apache.org/jira/browse/SPARK-11219) to make PySpark MLlib parameter description formatting consistent. This is for the tree module. closes #10601 Author: Bryan Cutler <cutlerb@gmail.com> Author: vijaykiran <mail@vijaykiran.com> Closes #11353 from BryanCutler/param-desc-consistent-tree-SPARK-12634.
* [SPARK-13457][SQL] Removes DataFrame RDD operationsCheng Lian2016-02-2750-99/+117
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? This is another try of PR #11323. This PR removes DataFrame RDD operations except for `foreach` and `foreachPartitions` (they are actions rather than transformations). Original calls are now replaced by calls to methods of `DataFrame.rdd`. PR #11323 was reverted because it introduced a regression: both `DataFrame.foreach` and `DataFrame.foreachPartitions` wrap underlying RDD operations with `withNewExecutionId` to track Spark jobs. But they are removed in #11323. ## How was the this patch tested? No extra tests are added. Existing tests should do the work. Author: Cheng Lian <lian@databricks.com> Closes #11388 from liancheng/remove-df-rdd-ops.
* [SPARK-13028] [ML] Add MaxAbsScaler to ML.feature as a transformerYuhao Yang2016-02-252-0/+246
| | | | | | | | | | | | | | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-13028 MaxAbsScaler works in a very similar way as MinMaxScaler, but scales in a way that the training data lies within the range [-1, 1] by dividing through the largest maximum value in each feature. The motivation to use this scaling includes robustness to very small standard deviations of features and preserving zero entries in sparse data. Unlike StandardScaler and MinMaxScaler, MaxAbsScaler does not shift/center the data, and thus does not destroy any sparsity. Something similar from sklearn: http://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.MaxAbsScaler.html#sklearn.preprocessing.MaxAbsScaler Author: Yuhao Yang <hhbyyh@gmail.com> Closes #10939 from hhbyyh/maxabs and squashes the following commits: fd8bdcd [Yuhao Yang] add tag and some optimization on fit 648fced [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into maxabs 75bebc2 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into maxabs cb10bb6 [Yuhao Yang] remove minmax 91ef8f3 [Yuhao Yang] ut added 8ab0747 [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into maxabs a9215b5 [Yuhao Yang] max abs scaler
* [SPARK-12874][ML] ML StringIndexer does not protect itself from column name ↵Yu ISHIKAWA2016-02-252-0/+12
| | | | | | | | | | | | | | | | duplication ## What changes were proposed in this pull request? ML StringIndexer does not protect itself from column name duplication. We should still improve a way to validate a schema of `StringIndexer` and `StringIndexerModel`. However, it would be great to fix at another issue. ## How was this patch tested? unit test Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #11370 from yu-iskw/SPARK-12874.
* Revert "[SPARK-13457][SQL] Removes DataFrame RDD operations"Davies Liu2016-02-2549-116/+98
| | | | This reverts commit 157fe64f3ecbd13b7286560286e50235eecfe30e.
* [SPARK-13457][SQL] Removes DataFrame RDD operationsCheng Lian2016-02-2549-98/+116
| | | | | | | | | | | | | | ## What changes were proposed in this pull request? This PR removes DataFrame RDD operations. Original calls are now replaced by calls to methods of `DataFrame.rdd`. ## How was the this patch tested? No extra tests are added. Existing tests should do the work. Author: Cheng Lian <lian@databricks.com> Closes #11323 from liancheng/remove-df-rdd-ops.
* [SPARK-13490][ML] ML LinearRegression should cache standardization param valueYanbo Liang2016-02-251-1/+2
| | | | | | | | | | | | | ## What changes were proposed in this pull request? Like #11027 for ```LogisticRegression```, ```LinearRegression``` with L1 regularization should also cache the value of the ```standardization``` rather than re-fetching it from the ```ParamMap``` for every OWLQN iteration. cc srowen ## How was this patch tested? No extra tests are added. It should pass all existing tests. Author: Yanbo Liang <ybliang8@gmail.com> Closes #11367 from yanboliang/spark-13490.
* [SPARK-13444][MLLIB] QuantileDiscretizer chooses bad splits on large DataFramesOliver Pierson2016-02-252-2/+29
| | | | | | | | | | | | | | | | | | ## What changes were proposed in this pull request? Change line 113 of QuantileDiscretizer.scala to `val requiredSamples = math.max(numBins * numBins, 10000.0)` so that `requiredSamples` is a `Double`. This will fix the division in line 114 which currently results in zero if `requiredSamples < dataset.count` ## How was the this patch tested? Manual tests. I was having a problems using QuantileDiscretizer with my a dataset and after making this change QuantileDiscretizer behaves as expected. Author: Oliver Pierson <ocp@gatech.edu> Author: Oliver Pierson <opierson@umd.edu> Closes #11319 from oliverpierson/SPARK-13444.
* [SPARK-13011] K-means wrapper in SparkRXusen Yin2016-02-232-3/+94
| | | | | | | | https://issues.apache.org/jira/browse/SPARK-13011 Author: Xusen Yin <yinxusen@gmail.com> Closes #11124 from yinxusen/SPARK-13011.
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