## What changes were proposed in this pull request?
Refactor All Java Tests that use SparkSession, to extend SharedSparkSesion
## How was this patch tested?
Existing Tests
Author: Sandeep Singh <sandeep@techaddict.me>
Closes#13101 from techaddict/SPARK-15296.
## What changes were proposed in this pull request?
It seems most of Python examples were changed to use SparkSession by https://github.com/apache/spark/pull/12809. This PR said both examples below:
- `simple_params_example.py`
- `aft_survival_regression.py`
are not changed because it dose not work. It seems `aft_survival_regression.py` is changed by https://github.com/apache/spark/pull/13050 but `simple_params_example.py` is not yet.
This PR corrects the example and make this use SparkSession.
In more detail, it seems `threshold` is replaced to `thresholds` here and there by 5a23213c14. However, when it calls `lr.fit(training, paramMap)` this overwrites the values. So, `threshold` was 5 and `thresholds` becomes 5.5 (by `1 / (1 + thresholds(0) / thresholds(1)`).
According to the comment below. this is not allowed, 354f8f11bd/mllib/src/main/scala/org/apache/spark/ml/classification/LogisticRegression.scala (L58-L61).
So, in this PR, it sets the equivalent value so that this does not throw an exception.
## How was this patch tested?
Manully (`mvn package -DskipTests && spark-submit simple_params_example.py`)
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#13135 from HyukjinKwon/SPARK-15031.
## What changes were proposed in this pull request?
I use Intellj-IDEA to search usage of deprecate SparkContext.accumulator in the whole spark project, and update the code.(except those test code for accumulator method itself)
## How was this patch tested?
Exisiting unit tests
Author: WeichenXu <WeichenXu123@outlook.com>
Closes#13112 from WeichenXu123/update_accuV2_in_mllib.
## What changes were proposed in this pull request?
Update the unit test code, examples, and documents to remove calls to deprecated method `dataset.registerTempTable`.
## How was this patch tested?
This PR only changes the unit test code, examples, and comments. It should be safe.
This is a follow up of PR https://github.com/apache/spark/pull/12945 which was merged.
Author: Sean Zhong <seanzhong@databricks.com>
Closes#13098 from clockfly/spark-15171-remove-deprecation.
## What changes were proposed in this pull request?
Once SPARK-14487 and SPARK-14549 are merged, we will migrate to use the new vector and matrix type in the new ml pipeline based apis.
## How was this patch tested?
Unit tests
Author: DB Tsai <dbt@netflix.com>
Author: Liang-Chi Hsieh <simonh@tw.ibm.com>
Author: Xiangrui Meng <meng@databricks.com>
Closes#12627 from dbtsai/SPARK-14615-NewML.
## What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
copy & paste example in ml-collaborative-filtering.html into spark-shell, we see the following errors.
scala> case class Rating(userId: Int, movieId: Int, rating: Float, timestamp: Long)
defined class Rating
scala> object Rating {
def parseRating(str: String): Rating = { | val fields = str.split("::") | assert(fields.size == 4) | Rating(fields(0).toInt, fields(1).toInt, fields(2).toFloat, fields(3).toLong) | }
}
<console>:29: error: Rating.type does not take parameters
Rating(fields(0).toInt, fields(1).toInt, fields(2).toFloat, fields(3).toLong)
^
In standard scala repl, it has the same error.
Scala/spark-shell repl has some quirks (e.g. packages are also not well supported).
The reason of errors is that scala/spark-shell repl discards previous definitions when we define the Object with the same class name. Solution: We can rename the Object Rating.
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Manually test it: 1). ./bin/run-example ALSExample
2). copy & paste example in the generated document. It works fine.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#13110 from wangmiao1981/repl.
## What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
Add guide doc and examples for GaussianMixture in Spark.ml in Java, Scala and Python.
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Manual compile and test all examples
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#12788 from wangmiao1981/example.
## What changes were proposed in this pull request?
Add Scala/Java/Python examples for ```GeneralizedLinearRegression```.
## How was this patch tested?
They are examples and have been tested offline.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#12754 from yanboliang/spark-14979.
## What changes were proposed in this pull request?
Deprecates registerTempTable and add dataset.createTempView, dataset.createOrReplaceTempView.
## How was this patch tested?
Unit tests.
Author: Sean Zhong <seanzhong@databricks.com>
Closes#12945 from clockfly/spark-15171.
## What changes were proposed in this pull request?
1, Use `SparkSession` according to [SPARK-15031](https://issues.apache.org/jira/browse/SPARK-15031)
2, Update indent for `SparkContext` according to [SPARK-15134](https://issues.apache.org/jira/browse/SPARK-15134)
3, BTW, remove some duplicate space and add missing '.'
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#13050 from zhengruifeng/use_sparksession.
## What changes were proposed in this pull request?
Renaming the streaming-kafka artifact to include kafka version, in anticipation of needing a different artifact for later kafka versions
## How was this patch tested?
Unit tests
Author: cody koeninger <cody@koeninger.org>
Closes#12946 from koeninger/SPARK-15085.
## What changes were proposed in this pull request?
This fixes compile errors.
## How was this patch tested?
Pass the Jenkins tests.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#13053 from dongjoon-hyun/hotfix_sqlquerysuite.
## What changes were proposed in this pull request?
1,create a libsvm-type dataset for lda: `data/mllib/sample_lda_libsvm_data.txt`
2,add python example
3,directly read the datafile in examples
4,BTW, change to `SparkSession` in `aft_survival_regression.py`
## How was this patch tested?
manual tests
`./bin/spark-submit examples/src/main/python/ml/lda_example.py`
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12927 from zhengruifeng/lda_pe.
## What changes were proposed in this pull request?
Python example for ml.kmeans already exists, but not included in user guide.
1,small changes like: `example_on` `example_off`
2,add it to user guide
3,update examples to directly read datafile
## How was this patch tested?
manual tests
`./bin/spark-submit examples/src/main/python/ml/kmeans_example.py
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12925 from zhengruifeng/km_pe.
## What changes were proposed in this pull request?
1, add BisectingKMeans to ml-clustering.md
2, add the missing Scala BisectingKMeansExample
3, create a new datafile `data/mllib/sample_kmeans_data.txt`
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11844 from zhengruifeng/doc_bkm.
## What changes were proposed in this pull request?
1, Add python example for OneVsRest
2, remove args-parsing
## How was this patch tested?
manual tests
`./bin/spark-submit examples/src/main/python/ml/one_vs_rest_example.py`
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12920 from zhengruifeng/ovr_pe.
This PR removes `sqlContext` in examples. Actual usage was all replaced in https://github.com/apache/spark/pull/12809 but there are some in comments.
Manual style checking.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#13006 from HyukjinKwon/minor-docs.
## What changes were proposed in this pull request?
* Since Spark has supported native csv reader, it does not necessary to use the third party ```spark-csv``` in ```examples/src/main/r/data-manipulation.R```. Meanwhile, remove all ```spark-csv``` usage in SparkR.
* Running R applications through ```sparkR``` is not supported as of Spark 2.0, so we change to use ```./bin/spark-submit``` to run the example.
## How was this patch tested?
Offline test.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#13005 from yanboliang/r-df-examples.
Cleans up ALS examples by removing unnecessary casts to double for `rating` and `prediction` columns, since `RegressionEvaluator` now supports `Double` & `Float` input types.
## How was this patch tested?
Manual compile and run with `run-example ml.ALSExample` and `spark-submit examples/src/main/python/ml/als_example.py`.
Author: Nick Pentreath <nickp@za.ibm.com>
Closes#12892 from MLnick/als-examples-cleanup.
## What changes were proposed in this pull request?
Add the missing python example for QuantileDiscretizer
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12281 from zhengruifeng/discret_pe.
## What changes were proposed in this pull request?
This issue addresses the comments in SPARK-15031 and also fix java-linter errors.
- Use multiline format in SparkSession builder patterns.
- Update `binary_classification_metrics_example.py` to use `SparkSession`.
- Fix Java Linter errors (in SPARK-13745, SPARK-15031, and so far)
## How was this patch tested?
After passing the Jenkins tests and run `dev/lint-java` manually.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12911 from dongjoon-hyun/SPARK-15134.
## What changes were proposed in this pull request?
Removing the `withHiveSupport` method of `SparkSession`, instead use `enableHiveSupport`
## How was this patch tested?
ran tests locally
Author: Sandeep Singh <sandeep@techaddict.me>
Closes#12851 from techaddict/SPARK-15072.
## What changes were proposed in this pull request?
This PR aims to update Scala/Python/Java examples by replacing `SQLContext` with newly added `SparkSession`.
- Use **SparkSession Builder Pattern** in 154(Scala 55, Java 52, Python 47) files.
- Add `getConf` in Python SparkContext class: `python/pyspark/context.py`
- Replace **SQLContext Singleton Pattern** with **SparkSession Singleton Pattern**:
- `SqlNetworkWordCount.scala`
- `JavaSqlNetworkWordCount.java`
- `sql_network_wordcount.py`
Now, `SQLContexts` are used only in R examples and the following two Python examples. The python examples are untouched in this PR since it already fails some unknown issue.
- `simple_params_example.py`
- `aft_survival_regression.py`
## How was this patch tested?
Manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12809 from dongjoon-hyun/SPARK-15031.
## What changes were proposed in this pull request?
Add python3 compatibility in python examples
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12868 from zhengruifeng/fix_gmm_py.
## What changes were proposed in this pull request?
This is a python port of corresponding Scala builder pattern code. `sql.py` is modified as a target example case.
## How was this patch tested?
Manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12860 from dongjoon-hyun/SPARK-15084.
## What changes were proposed in this pull request?
Users should use the builder pattern instead.
## How was this patch tested?
Jenks.
Author: Andrew Or <andrew@databricks.com>
Closes#12873 from andrewor14/spark-session-constructor.
## What changes were proposed in this pull request?
Now, `SQLContext` is used for backward-compatibility, we had better use `SparkSession` in Spark 2.0 examples.
## How was this patch tested?
It's just example change. After building, run `bin/run-example org.apache.spark.examples.sql.RDDRelation`.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12808 from dongjoon-hyun/rddrelation.
## What changes were proposed in this pull request?
In spark.ml document, the LogisticRegression scala example uses sqlCtx. It is inconsistent with java and python examples which use sqlContext. In addition, a user can't copy & paste to run the example in spark-shell as sqlCtx doesn't exist in spark-shell while sqlContext exists.
Change the scala example referred by the spark.ml example.
## How was this patch tested?
Compile the example scala file and it passes compilation.
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#12717 from wangmiao1981/doc.
Spark's published POMs are supposed to be flattened and not contain variable substitution (see SPARK-3812), but the dummy dependency that was required for this was accidentally removed. We should re-introduce this dependency in order to fix an issue where the un-flattened POMs cause the wrong dependencies to be included in Scala 2.10 published POMs.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#12706 from JoshRosen/SPARK-14925-published-poms-should-be-flattened.
## What changes were proposed in this pull request?
Add the missing python example for VectorSlicer
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12282 from zhengruifeng/vecslicer_pe.
## What changes were proposed in this pull request?
Use Long.parseLong which returns a primative.
Use a series of appends() reduces the creation of an extra StringBuilder type
## How was this patch tested?
Unit tests
Author: Azeem Jiva <azeemj@gmail.com>
Closes#12520 from javawithjiva/minor.
## What changes were proposed in this pull request?
This removes the class `HiveContext` itself along with all code usages associated with it. The bulk of the work was already done in #12485. This is mainly just code cleanup and actually removing the class.
Note: A couple of things will break after this patch. These will be fixed separately.
- the python HiveContext
- all the documentation / comments referencing HiveContext
- there will be no more HiveContext in the REPL (fixed by #12589)
## How was this patch tested?
No change in functionality.
Author: Andrew Or <andrew@databricks.com>
Closes#12585 from andrewor14/delete-hive-context.
First, make all dependencies in the examples module provided, and explicitly
list a couple of ones that somehow are promoted to compile by maven. This
means that to run streaming examples, the streaming connector package needs
to be provided to run-examples using --packages or --jars, just like regular
apps.
Also, remove a couple of outdated examples. HBase has had Spark bindings for
a while and is even including them in the HBase distribution in the next
version, making the examples obsolete. The same applies to Cassandra, which
seems to have a proper Spark binding library already.
I just tested the build, which passes, and ran SparkPi. The examples jars
directory now has only two jars:
```
$ ls -1 examples/target/scala-2.11/jars/
scopt_2.11-3.3.0.jar
spark-examples_2.11-2.0.0-SNAPSHOT.jar
```
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#12544 from vanzin/SPARK-14744.
## What changes were proposed in this pull request?
This issue aims to fix some errors in R examples and make them up-to-date in docs and example modules.
- Remove the wrong usage of `map`. We need to use `lapply` in `sparkR` if needed. However, `lapply` is private so far. The corrected example will be added later.
- Fix the wrong example in Section `Generic Load/Save Functions` of `docs/sql-programming-guide.md` for consistency
- Fix datatypes in `sparkr.md`.
- Update a data result in `sparkr.md`.
- Replace deprecated functions to remove warnings: jsonFile -> read.json, parquetFile -> read.parquet
- Use up-to-date R-like functions: loadDF -> read.df, saveDF -> write.df, saveAsParquetFile -> write.parquet
- Replace `SparkR DataFrame` with `SparkDataFrame` in `dataframe.R` and `data-manipulation.R`.
- Other minor syntax fixes and a typo.
## How was this patch tested?
Manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12649 from dongjoon-hyun/SPARK-14883.
## What changes were proposed in this pull request?
Java `sampleByKey` methods should accept `Map` with `java.lang.Double` values
## How was this patch tested?
Existing (updated) Jenkins tests
Author: Sean Owen <sowen@cloudera.com>
Closes#12637 from srowen/SPARK-14873.
## What changes were proposed in this pull request?
`JavaStreamingContext.awaitTermination` methods should be declared as `throws[InterruptedException]` so that this exception can be handled in Java code. Note this is not just a doc change, but an API change, since now (in Java) the method has a checked exception to handle. All await-like methods in Java APIs behave this way, so seems worthwhile for 2.0.
## How was this patch tested?
Jenkins tests
Author: Sean Owen <sowen@cloudera.com>
Closes#12418 from srowen/SPARK-8393.
## What changes were proposed in this pull request?
Currently, the docs for TF-IDF only refer to using HashingTF with IDF. However, CountVectorizer can also be used. We should probably amend the user guide and examples to show this.
## How was this patch tested?
unit tests and doc generation
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#12454 from hhbyyh/tfdoc.
## What changes were proposed in this pull request?
Move the spark-examples.jar from being in examples/target to examples/target/scala-2.11/jars
## How was this patch tested?
Built distribution to make sure examples jar was being included in the tarball.
Ran run-example to make sure examples were run.
Author: Mark Grover <mark@apache.org>
Closes#12476 from markgrover/spark-14711.
## What changes were proposed in this pull request?
Add the missing python example for ChiSqSelector
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12283 from zhengruifeng/chi2_pe.
## What changes were proposed in this pull request?
https://issues.apache.org/jira/browse/SPARK-14299
Delete duplications in scala/examples/ml.
TrainValidationSplitExample.scala --> ModelSelectionViaTrainValidationSplitExample
CrossValidatorExample.scala --> ModelSelectionViaCrossValidationExample
## How was this patch tested?
Existing tests passed.
(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)
Author: Xusen Yin <yinxusen@gmail.com>
Closes#12366 from yinxusen/SPARK-14299-2.
## What changes were proposed in this pull request?
This PR removes
- Inappropriate type notations
For example, from
```scala
words.foreachRDD { (rdd: RDD[String], time: Time) =>
...
```
to
```scala
words.foreachRDD { (rdd, time) =>
...
```
- Extra anonymous closure within functional transformations.
For example,
```scala
.map(item => {
...
})
```
which can be just simply as below:
```scala
.map { item =>
...
}
```
and corrects some obvious style nits.
## How was this patch tested?
This was tested after adding rules in `scalastyle-config.xml`, which ended up with not finding all perfectly.
The rules applied were below:
- For the first correction,
```xml
<check customId="NoExtraClosure" level="error" class="org.scalastyle.file.RegexChecker" enabled="true">
<parameters><parameter name="regex">(?m)\.[a-zA-Z_][a-zA-Z0-9]*\(\s*[^,]+s*=>\s*\{[^\}]+\}\s*\)</parameter></parameters>
</check>
```
```xml
<check customId="NoExtraClosure" level="error" class="org.scalastyle.file.RegexChecker" enabled="true">
<parameters><parameter name="regex">\.[a-zA-Z_][a-zA-Z0-9]*\s*[\{|\(]([^\n>,]+=>)?\s*\{([^()]|(?R))*\}^[,]</parameter></parameters>
</check>
```
- For the second correction
```xml
<check customId="TypeNotation" level="error" class="org.scalastyle.file.RegexChecker" enabled="true">
<parameters><parameter name="regex">\.[a-zA-Z_][a-zA-Z0-9]*\s*[\{|\(]\s*\([^):]*:R))*\}^[,]</parameter></parameters>
</check>
```
**Those rules were not added**
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#12413 from HyukjinKwon/SPARK-style.
## What changes were proposed in this pull request?
This PR removes extra anonymous closure within functional transformations.
For example,
```scala
.map(item => {
...
})
```
which can be just simply as below:
```scala
.map { item =>
...
}
```
## How was this patch tested?
Related unit tests and `sbt scalastyle`.
Author: hyukjinkwon <gurwls223@gmail.com>
Closes#12382 from HyukjinKwon/minor-extra-closers.
jira: https://issues.apache.org/jira/browse/SPARK-13089
Add section in ml-classification.md for NaiveBayes DataFrame-based API, plus example code (using include_example to clip code from examples/ folder files).
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#11015 from hhbyyh/naiveBayesDoc.
## What changes were proposed in this pull request?
Add python CountVectorizerExample
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11917 from zhengruifeng/cv_pe.
## What changes were proposed in this pull request?
According to the [Spark Code Style Guide](https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide) and [Scala Style Guide](http://docs.scala-lang.org/style/control-structures.html#curlybraces), we had better enforce the following rule.
```
case: Always omit braces in case clauses.
```
This PR makes a new ScalaStyle rule, 'OmitBracesInCase', and enforces it to the code.
## How was this patch tested?
Pass the Jenkins tests (including Scala style checking)
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12280 from dongjoon-hyun/SPARK-14508.
## What changes were proposed in this pull request?
Fixes to eliminate warnings during package and doc builds.
## How was this patch tested?
Existing unit tests
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#12263 from jkbradley/warning-cleanups.
## What changes were proposed in this pull request?
This PR updates MLlib APIs to accept `Dataset[_]` as input where `DataFrame` was the input type. This PR doesn't change the output type. In Java, `Dataset[_]` maps to `Dataset<?>`, which includes `Dataset<Row>`. Some implementations were changed in order to return `DataFrame`. Tests and examples were updated. Note that this is a breaking change for subclasses of Transformer/Estimator.
Lol, we don't have to rename the input argument, which has been `dataset` since Spark 1.2.
TODOs:
- [x] update MiMaExcludes (seems all covered by explicit filters from SPARK-13920)
- [x] Python
- [x] add a new test to accept Dataset[LabeledPoint]
- [x] remove unused imports of Dataset
## How was this patch tested?
Exiting unit tests with some modifications.
cc: rxin jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Closes#12274 from mengxr/SPARK-14500.
## What changes were proposed in this pull request?
example does not work wo DataFrame import
## How was this patch tested?
example doc only
example does not work wo DataFrame import
Author: Örjan Lundberg <orjan.lundberg@gmail.com>
Closes#12277 from oluies/patch-1.
## What changes were proposed in this pull request?
This fix tries to remove duplicate Java code in examples/mllib and examples/ml. The following changes have been made:
```
deleted: ml/JavaCrossValidatorExample.java (duplicate of JavaModelSelectionViaCrossValidationExample.java)
deleted: ml/JavaTrainValidationSplitExample.java (duplicated of JavaModelSelectionViaTrainValidationSplitExample.java)
deleted: mllib/JavaFPGrowthExample.java (duplicate of JavaSimpleFPGrowth.java)
deleted: mllib/JavaLDAExample.java (duplicate of JavaLatentDirichletAllocationExample.java)
deleted: mllib/JavaKMeans.java (merged with JavaKMeansExample.java)
deleted: mllib/JavaLR.java (duplicate of JavaLinearRegressionWithSGDExample.java)
updated: mllib/JavaKMeansExample.java (merged with mllib/JavaKMeans.java)
```
## How was this patch tested?
Existing tests passed.
Author: Yong Tang <yong.tang.github@outlook.com>
Closes#12143 from yongtang/SPARK-14301.
## What changes were proposed in this pull request?
add three python examples
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12063 from zhengruifeng/dct_pe.
## What changes were proposed in this pull request?
According to the [Spark Code Style Guide](https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide#SparkCodeStyleGuide-Indentation), this PR adds a new scalastyle rule to prevent the followings.
```
/** In Spark, we don't use the ScalaDoc style so this
* is not correct.
*/
```
## How was this patch tested?
Pass the Jenkins tests (including `lint-scala`).
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12221 from dongjoon-hyun/SPARK-14444.
This change modifies the "assembly/" module to just copy needed
dependencies to its build directory, and modifies the packaging
script to pick those up (and remove duplicate jars packages in the
examples module).
I also made some minor adjustments to dependencies to remove some
test jars from the final packaging, and remove jars that conflict with each
other when packaged separately (e.g. servlet api).
Also note that this change restores guava in applications' classpaths, even
though it's still shaded inside Spark. This is now needed for the Hadoop
libraries that are packaged with Spark, which now are not processed by
the shade plugin.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#11796 from vanzin/SPARK-13579.
## What changes were proposed in this pull request?
This PR contains the following 5 types of maintenance fix over 59 files (+94 lines, -93 lines).
- Fix typos(exception/log strings, testcase name, comments) in 44 lines.
- Fix lint-java errors (MaxLineLength) in 6 lines. (New codes after SPARK-14011)
- Use diamond operators in 40 lines. (New codes after SPARK-13702)
- Fix redundant semicolon in 5 lines.
- Rename class `InferSchemaSuite` to `CSVInferSchemaSuite` in CSVInferSchemaSuite.scala.
## How was this patch tested?
Manual and pass the Jenkins tests.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12139 from dongjoon-hyun/SPARK-14355.
## What changes were proposed in this pull request?
This PR aims to fix all Scala-Style multiline comments into Java-Style multiline comments in Scala codes.
(All comment-only changes over 77 files: +786 lines, −747 lines)
## How was this patch tested?
Manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12130 from dongjoon-hyun/use_multiine_javadoc_comments.
## What changes were proposed in this pull request?
Typo fixes. No functional changes.
## How was this patch tested?
Built the sources and ran with samples.
Author: Jacek Laskowski <jacek@japila.pl>
Closes#11802 from jaceklaskowski/typo-fixes.
## What changes were proposed in this pull request?
This PR fixes some newly added java-lint errors(unused-imports, line-lengsth).
## How was this patch tested?
Pass the Jenkins tests.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11968 from dongjoon-hyun/SPARK-14167.
## What changes were proposed in this pull request?
This PR removes all docs about the old streaming-akka, streaming-zeromq, streaming-mqtt and streaming-twitter projects since I have already copied them to https://github.com/spark-packages
Also remove mqtt_wordcount.py that I forgot to remove previously.
## How was this patch tested?
Jenkins PR Build.
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#11824 from zsxwing/remove-doc.
## What changes were proposed in this pull request?
This PR moves flume back to Spark as per the discussion in the dev mail-list.
## How was this patch tested?
Existing Jenkins tests.
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#11895 from zsxwing/move-flume-back.
Replace example code in mllib-feature-extraction.md using include_example
https://issues.apache.org/jira/browse/SPARK-13017
The example code in the user guide is embedded in the markdown and hence it is not easy to test. It would be nice to automatically test them. This JIRA is to discuss options to automate example code testing and see what we can do in Spark 1.6.
Goal is to move actual example code to spark/examples and test compilation in Jenkins builds. Then in the markdown, we can reference part of the code to show in the user guide. This requires adding a Jekyll tag that is similar to https://github.com/jekyll/jekyll/blob/master/lib/jekyll/tags/include.rb, e.g., called include_example.
`{% include_example scala/org/apache/spark/examples/mllib/TFIDFExample.scala %}`
Jekyll will find `examples/src/main/scala/org/apache/spark/examples/mllib/TFIDFExample.scala` and pick code blocks marked "example" and replace code block in
`{% highlight %}`
in the markdown.
See more sub-tasks in parent ticket: https://issues.apache.org/jira/browse/SPARK-11337
Author: Xin Ren <iamshrek@126.com>
Closes#11142 from keypointt/SPARK-13017.
## What changes were proposed in this pull request?
This PR for ticket SPARK-13019 is based on previous PR(https://github.com/apache/spark/pull/11108).
Since PR(https://github.com/apache/spark/pull/11108) is breaking scala-2.10 build, more work is needed to fix build errors.
What I did new in this PR is adding keyword argument for 'fractions':
` val approxSample = data.sampleByKey(withReplacement = false, fractions = fractions)`
` val exactSample = data.sampleByKeyExact(withReplacement = false, fractions = fractions)`
I reopened ticket on JIRA but sorry I don't know how to reopen a GitHub pull request, so I just submitting a new pull request.
## How was this patch tested?
Manual build testing on local machine, build based on scala-2.10.
Author: Xin Ren <iamshrek@126.com>
Closes#11901 from keypointt/SPARK-13019.
https://issues.apache.org/jira/browse/SPARK-13019
The example code in the user guide is embedded in the markdown and hence it is not easy to test. It would be nice to automatically test them. This JIRA is to discuss options to automate example code testing and see what we can do in Spark 1.6.
Goal is to move actual example code to spark/examples and test compilation in Jenkins builds. Then in the markdown, we can reference part of the code to show in the user guide. This requires adding a Jekyll tag that is similar to https://github.com/jekyll/jekyll/blob/master/lib/jekyll/tags/include.rb, e.g., called include_example.
`{% include_example scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala %}`
Jekyll will find `examples/src/main/scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala` and pick code blocks marked "example" and replace code block in
`{% highlight %}`
in the markdown.
See more sub-tasks in parent ticket: https://issues.apache.org/jira/browse/SPARK-11337
Author: Xin Ren <iamshrek@126.com>
Closes#11108 from keypointt/SPARK-13019.
## What changes were proposed in this pull request?
[Spark Coding Style Guide](https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide) has 100-character limit on lines, but it's disabled for Java since 11/09/15. This PR enables **LineLength** checkstyle again. To help that, this also introduces **RedundantImport** and **RedundantModifier**, too. The following is the diff on `checkstyle.xml`.
```xml
- <!-- TODO: 11/09/15 disabled - the lengths are currently > 100 in many places -->
- <!--
<module name="LineLength">
<property name="max" value="100"/>
<property name="ignorePattern" value="^package.*|^import.*|a href|href|http://|https://|ftp://"/>
</module>
- -->
<module name="NoLineWrap"/>
<module name="EmptyBlock">
<property name="option" value="TEXT"/>
-167,5 +164,7
</module>
<module name="CommentsIndentation"/>
<module name="UnusedImports"/>
+ <module name="RedundantImport"/>
+ <module name="RedundantModifier"/>
```
## How was this patch tested?
Currently, `lint-java` is disabled in Jenkins. It needs a manual test.
After passing the Jenkins tests, `dev/lint-java` should passes locally.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11831 from dongjoon-hyun/SPARK-14011.
## What changes were proposed in this pull request?
Fix some nits discussed in https://github.com/apache/spark/pull/11776#issuecomment-198207419
use !rdd.isEmpty instead of rdd.count > 0
use static instead of AtomicInteger
remove unneeded "throws Exception"
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11821 from zhengruifeng/je_fix.
## 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.
## What changes were proposed in this pull request?
Add the java example of StreamingTest
## How was this patch tested?
manual tests in CLI: bin/run-example mllib.JavaStreamingTestExample dataDir 5 100
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11776 from zhengruifeng/streaming_je.
As part of the goal to stop creating assemblies in Spark, this change
modifies the mvn and sbt builds to not create an assembly for examples.
Instead, dependencies are copied to the build directory (under
target/scala-xx/jars), and in the final archive, into the "examples/jars"
directory.
To avoid having to deal too much with Windows batch files, I made examples
run through the launcher library; the spark-submit launcher now has a
special mode to run examples, which adds all the necessary jars to the
spark-submit command line, and replaces the bash and batch scripts that
were used to run examples. The scripts are now just a thin wrapper around
spark-submit; another advantage is that now all spark-submit options are
supported.
There are a few glitches; in the mvn build, a lot of duplicated dependencies
get copied, because they are promoted to "compile" scope due to extra
dependencies in the examples module (such as HBase). In the sbt build,
all dependencies are copied, because there doesn't seem to be an easy
way to filter things.
I plan to clean some of this up when the rest of the tasks are finished.
When the main assembly is replaced with jars, we can remove duplicate jars
from the examples directory during packaging.
Tested by running SparkPi in: maven build, sbt build, dist created by
make-distribution.sh.
Finally: note that running the "assembly" target in sbt doesn't build
the examples anymore. You need to run "package" for that.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#11452 from vanzin/SPARK-13576.
## What changes were proposed in this pull request?
Currently there are a few sub-projects, each for integrating with different external sources for Streaming. Now that we have better ability to include external libraries (spark packages) and with Spark 2.0 coming up, we can move the following projects out of Spark to https://github.com/spark-packages
- streaming-flume
- streaming-akka
- streaming-mqtt
- streaming-zeromq
- streaming-twitter
They are just some ancillary packages and considering the overhead of maintenance, running tests and PR failures, it's better to maintain them out of Spark. In addition, these projects can have their different release cycles and we can release them faster.
I have already copied these projects to https://github.com/spark-packages
## How was this patch tested?
Jenkins tests
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#11672 from zsxwing/remove-external-pkg.
## 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.
## 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 1deecd8d9c )
## How was this patch tested?
Jenkins tests
Author: Sean Owen <sowen@cloudera.com>
Closes#11657 from srowen/SPARK-13823.
## 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.
JIRA: https://issues.apache.org/jira/browse/SPARK-13814
## What changes were proposed in this pull request?
delete unnecessary imports in python examples files
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11651 from zhengruifeng/del_import_pe.
## What changes were proposed in this pull request?
PR #11443 temporarily disabled MiMA check, this PR re-enables it.
One extra change is that `object DataFrame` is also removed. The only purpose of introducing `object DataFrame` was to use it as an internal factory for creating `Dataset[Row]`. By replacing this internal factory with `Dataset.newDataFrame`, both `DataFrame` and `DataFrame$` are entirely removed from the API, so that we can simply put a `MissingClassProblem` filter in `MimaExcludes.scala` for most DataFrame API changes.
## How was this patch tested?
Tested by MiMA check triggered by Jenkins.
Author: Cheng Lian <lian@databricks.com>
Closes#11656 from liancheng/re-enable-mima.
## What changes were proposed in this pull request?
Fix build failure introduced in #11392 (change `DataFrame` -> `Dataset<Row>`).
## How was this patch tested?
Existing build/unit tests
Author: Nick Pentreath <nick.pentreath@gmail.com>
Closes#11653 from MLnick/java-maxabs-example-fix.
## What changes were proposed in this pull request?
jira: https://issues.apache.org/jira/browse/SPARK-13512
Add example and doc for ml.feature.MaxAbsScaler.
## How was this patch tested?
unit tests
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#11392 from hhbyyh/maxabsdoc.
JIRA: https://issues.apache.org/jira/browse/SPARK-13672
## What changes were proposed in this pull request?
add two python examples of BisectingKMeans for ml and mllib
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11515 from zhengruifeng/mllib_bkm_pe.
## 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.
## 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.
## What changes were proposed in this pull request?
This pull request adds a python example for train validation split.
## How was this patch tested?
This was style tested through lint-python, generally tested with ./dev/run-tests, and run in notebook and shell environments. It was viewed in docs locally with jekyll serve.
This contribution is my original work and I license it to Spark under its open source license.
Author: JeremyNixon <jnixon2@gmail.com>
Closes#11547 from JeremyNixon/tvs_example.
## 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.
## What changes were proposed in this pull request?
This issue fixes the following potential bugs and Java coding style detected by Coverity and Checkstyle.
- Implement both null and type checking in equals functions.
- Fix wrong type casting logic in SimpleJavaBean2.equals.
- Add `implement Cloneable` to `UTF8String` and `SortedIterator`.
- Remove dereferencing before null check in `AbstractBytesToBytesMapSuite`.
- Fix coding style: Add '{}' to single `for` statement in mllib examples.
- Remove unused imports in `ColumnarBatch` and `JavaKinesisStreamSuite`.
- Remove unused fields in `ChunkFetchIntegrationSuite`.
- Add `stop()` to prevent resource leak.
Please note that the last two checkstyle errors exist on newly added commits after [SPARK-13583](https://issues.apache.org/jira/browse/SPARK-13583).
## How was this patch tested?
manual via `./dev/lint-java` and Coverity site.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11530 from dongjoon-hyun/SPARK-13692.
## What changes were proposed in this pull request?
Added the conversion to int for the 'happiness value' read from the file. Otherwise, later on line 75 the multiplication will multiply a string by a number, yielding values like "-2-2" instead of -4.
## How was this patch tested?
Tested manually.
Author: Yury Liavitski <seconds.before@gmail.com>
Author: Yury Liavitski <yury.liavitski@il111.ice.local>
Closes#11540 from heliocentrist/fix-sentiment-value-type.
## 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.
Replace example code in mllib-clustering.md using include_example
https://issues.apache.org/jira/browse/SPARK-13013
The example code in the user guide is embedded in the markdown and hence it is not easy to test. It would be nice to automatically test them. This JIRA is to discuss options to automate example code testing and see what we can do in Spark 1.6.
Goal is to move actual example code to spark/examples and test compilation in Jenkins builds. Then in the markdown, we can reference part of the code to show in the user guide. This requires adding a Jekyll tag that is similar to https://github.com/jekyll/jekyll/blob/master/lib/jekyll/tags/include.rb, e.g., called include_example.
`{% include_example scala/org/apache/spark/examples/mllib/KMeansExample.scala %}`
Jekyll will find `examples/src/main/scala/org/apache/spark/examples/mllib/KMeansExample.scala` and pick code blocks marked "example" and replace code block in
`{% highlight %}`
in the markdown.
See more sub-tasks in parent ticket: https://issues.apache.org/jira/browse/SPARK-11337
Author: Xin Ren <iamshrek@126.com>
Closes#11116 from keypointt/SPARK-13013.
## 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.
## 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.
## What changes were proposed in this pull request?
#11479 [SPARK-13627] broke 2.10 compatibility: [2.10-Build](https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Compile/job/spark-master-compile-maven-scala-2.10/292/console)
At this moment, we need to support both 2.10 and 2.11.
This PR recovers some deprecated methods which were replace by [SPARK-13627].
## How was this patch tested?
Jenkins build: Both 2.10, 2.11.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11488 from dongjoon-hyun/hotfix_compatibility_with_2.10.
## What changes were proposed in this pull request?
This PR aims to fix the following deprecation warnings.
* MethodSymbolApi.paramss--> paramLists
* AnnotationApi.tpe -> tree.tpe
* BufferLike.readOnly -> toList.
* StandardNames.nme -> termNames
* scala.tools.nsc.interpreter.AbstractFileClassLoader -> scala.reflect.internal.util.AbstractFileClassLoader
* TypeApi.declarations-> decls
## How was this patch tested?
Check the compile build log and pass the tests.
```
./build/sbt
```
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11479 from dongjoon-hyun/SPARK-13627.
## What changes were proposed in this pull request?
Twitter Algebird deprecated `apply` in HyperLogLog.scala.
```
deprecated("Use toHLL", since = "0.10.0 / 2015-05")
def apply[T <% Array[Byte]](t: T) = create(t)
```
This PR replace the deprecated usage `apply` with new `create`
according to the upstream change.
## How was this patch tested?
manual.
```
/bin/spark-submit --class org.apache.spark.examples.streaming.TwitterAlgebirdHLL examples/target/scala-2.11/spark-examples-2.0.0-SNAPSHOT-hadoop2.2.0.jar
```
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11451 from dongjoon-hyun/replace_deprecated_hll_apply.
JIRA: https://issues.apache.org/jira/browse/SPARK-13550
## What changes were proposed in this pull request?
Just add a java example for ml.clustering.BisectingKMeans
## How was this patch tested?
manual tests were done.
(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11428 from zhengruifeng/ml_bkm_je.
JIRA: https://issues.apache.org/jira/browse/SPARK-13551
## What changes were proposed in this pull request?
Fix wrong comment and remove meanless lines in mllib.JavaBisectingKMeansExample
## How was this patch tested?
manual test
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11429 from zhengruifeng/mllib_bkm_je.
## What changes were proposed in this pull request?
This PR replaces example codes in `mllib-linear-methods.md` using `include_example`
by doing the followings:
* Extracts the example codes(Scala,Java,Python) as files in `example` module.
* Merges some dialog-style examples into a single file.
* Hide redundant codes in HTML for the consistency with other docs.
## How was the this patch tested?
manual test.
This PR can be tested by document generations, `SKIP_API=1 jekyll build`.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11320 from dongjoon-hyun/SPARK-11381.
## 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.
## 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.
This pull request uses {%include_example%} to add an example for the python cross validator to ml-guide.
Author: JeremyNixon <jnixon2@gmail.com>
Closes#11240 from JeremyNixon/pipeline_include_example.
Refine naive Bayes example by checking model after loading it
Author: movelikeriver <mars.lenjoy@gmail.com>
Closes#11125 from movelikeriver/naive_bayes.
Replaced example example code in mllib-dimensionality-reduction.md using
include_example
Author: Devaraj K <devaraj@apache.org>
Closes#11132 from devaraj-kavali/SPARK-13016.
Phase 1: update plugin versions, test dependencies, some example and third-party versions
Author: Sean Owen <sowen@cloudera.com>
Closes#11206 from srowen/SPARK-13324.
https://issues.apache.org/jira/browse/SPARK-12953
fix error when run RDDRelation.main():
"path file:/Users/sjk/pair.parquet already exists"
Set DataFrameWriter's mode to SaveMode.Overwrite
Author: shijinkui <shijinkui666@163.com>
Closes#10864 from shijinkui/set_mode.
This documents the implementation of ALS in `spark.ml` with example code in scala, java and python.
Author: BenFradet <benjamin.fradet@gmail.com>
Closes#10411 from BenFradet/SPARK-12247.
Replace example code in mllib-pmml-model-export.md using include_example
https://issues.apache.org/jira/browse/SPARK-13018
The example code in the user guide is embedded in the markdown and hence it is not easy to test. It would be nice to automatically test them. This JIRA is to discuss options to automate example code testing and see what we can do in Spark 1.6.
Goal is to move actual example code to spark/examples and test compilation in Jenkins builds. Then in the markdown, we can reference part of the code to show in the user guide. This requires adding a Jekyll tag that is similar to https://github.com/jekyll/jekyll/blob/master/lib/jekyll/tags/include.rb, e.g., called include_example.
`{% include_example scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala %}`
Jekyll will find `examples/src/main/scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala` and pick code blocks marked "example" and replace code block in
`{% highlight %}`
in the markdown.
See more sub-tasks in parent ticket: https://issues.apache.org/jira/browse/SPARK-11337
Author: Xin Ren <iamshrek@126.com>
Closes#11126 from keypointt/SPARK-13018.
JIRA: https://issues.apache.org/jira/browse/SPARK-12363
This issue is pointed by yanboliang. When `setRuns` is removed from PowerIterationClustering, one of the tests will be failed. I found that some `dstAttr`s of the normalized graph are not correct values but 0.0. By setting `TripletFields.All` in `mapTriplets` it can work.
Author: Liang-Chi Hsieh <viirya@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>
Closes#10539 from viirya/fix-poweriter.
This patch changes Spark's build to make Scala 2.11 the default Scala version. To be clear, this does not mean that Spark will stop supporting Scala 2.10: users will still be able to compile Spark for Scala 2.10 by following the instructions on the "Building Spark" page; however, it does mean that Scala 2.11 will be the default Scala version used by our CI builds (including pull request builds).
The Scala 2.11 compiler is faster than 2.10, so I think we'll be able to look forward to a slight speedup in our CI builds (it looks like it's about 2X faster for the Maven compile-only builds, for instance).
After this patch is merged, I'll update Jenkins to add new compile-only jobs to ensure that Scala 2.10 compilation doesn't break.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10608 from JoshRosen/SPARK-6363.
Fix Java function API methods for flatMap and mapPartitions to require producing only an Iterator, not Iterable. Also fix DStream.flatMap to require a function producing TraversableOnce only, not Traversable.
CC rxin pwendell for API change; tdas since it also touches streaming.
Author: Sean Owen <sowen@cloudera.com>
Closes#10413 from srowen/SPARK-3369.
Without importing the print_function, the lines later on like ```print("Usage: direct_kafka_wordcount.py <broker_list> <topic>", file=sys.stderr)``` fail when using python2.*. Import fixes that problem and doesn't break anything on python3 either.
Author: Mark Grover <mark@apache.org>
Closes#10872 from markgrover/python2_compat.
Include the following changes:
1. Add "streaming-akka" project and org.apache.spark.streaming.akka.AkkaUtils for creating an actorStream
2. Remove "StreamingContext.actorStream" and "JavaStreamingContext.actorStream"
3. Update the ActorWordCount example and add the JavaActorWordCount example
4. Make "streaming-zeromq" depend on "streaming-akka" and update the codes accordingly
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#10744 from zsxwing/streaming-akka-2.
This pull request removes the external block store API. This is rarely used, and the file system interface is actually a better, more standard way to interact with external storage systems.
There are some other things to remove also, as pointed out by JoshRosen. We will do those as follow-up pull requests.
Author: Reynold Xin <rxin@databricks.com>
Closes#10752 from rxin/remove-offheap.
Fix the style violation (space before , and :).
This PR is a followup for #10643.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#10685 from sarutak/SPARK-12692-followup-streaming.
PySpark MLlib ```GaussianMixtureModel``` should support single instance ```predict/predictSoft``` just like Scala do.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#10552 from yanboliang/spark-12603.
According to the documentation the sortByKey method does not take a lambda as an argument, thus the example is flawed. Removed the argument completely as this will default to ascending sort.
Author: Udo Klein <git@blinkenlight.net>
Closes#10640 from udoklein/patch-1.
This is a hotfix for a build bug introduced by the Netty exclusion changes in #10672. We can't exclude `io.netty:netty` because Akka depends on it. There's not a direct conflict between `io.netty:netty` and `io.netty:netty-all`, because the former puts classes in the `org.jboss.netty` namespace while the latter uses the `io.netty` namespace. However, there still is a conflict between `org.jboss.netty:netty` and `io.netty:netty`, so we need to continue to exclude the JBoss version of that artifact.
While the diff here looks somewhat large, note that this is only a revert of a some of the changes from #10672. You can see the net changes in pom.xml at 3119206b71...5211ab8 (diff-600376dffeb79835ede4a0b285078036)
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10693 from JoshRosen/netty-hotfix.
Netty classes are published under multiple artifacts with different names, so our build needs to exclude the `io.netty:netty` and `org.jboss.netty:netty` versions of the Netty artifact. However, our existing exclusions were incomplete, leading to situations where duplicate Netty classes would wind up on the classpath and cause compile errors (or worse).
This patch fixes the exclusion issue by adding more exclusions and uses Maven Enforcer's [banned dependencies](https://maven.apache.org/enforcer/enforcer-rules/bannedDependencies.html) rule to prevent these classes from accidentally being reintroduced. I also updated `dev/test-dependencies.sh` to run `mvn validate` so that the enforcer rules can run as part of pull request builds.
/cc rxin srowen pwendell. I'd like to backport at least the exclusion portion of this fix to `branch-1.5` in order to fix the documentation publishing job, which fails nondeterministically due to incompatible versions of Netty classes taking precedence on the compile-time classpath.
Author: Josh Rosen <rosenville@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10672 from JoshRosen/enforce-netty-exclusions.
Fix the style violation (space before , and :).
This PR is a followup for #10643.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#10684 from sarutak/SPARK-12692-followup-mllib.
Replace Guava `Optional` with (an API clone of) Java 8 `java.util.Optional` (edit: and a clone of Guava `Optional`)
See also https://github.com/apache/spark/pull/10512
Author: Sean Owen <sowen@cloudera.com>
Closes#10513 from srowen/SPARK-4819.
Fix most build warnings: mostly deprecated API usages. I'll annotate some of the changes below. CC rxin who is leading the charge to remove the deprecated APIs.
Author: Sean Owen <sowen@cloudera.com>
Closes#10570 from srowen/SPARK-12618.
This PR includes the following changes:
1. Rename `ActorReceiver` to `ActorReceiverSupervisor`
2. Remove `ActorHelper`
3. Add a new `ActorReceiver` for Scala and `JavaActorReceiver` for Java
4. Add `JavaActorWordCount` example
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#10457 from zsxwing/java-actor-stream.
I looked at each case individually and it looks like they can all be removed. The only one that I had to think twice was toArray (I even thought about un-deprecating it, until I realized it was a problem in Java to have toArray returning java.util.List).
Author: Reynold Xin <rxin@databricks.com>
Closes#10569 from rxin/SPARK-12615.
We switched to TorrentBroadcast in Spark 1.1, and HttpBroadcast has been undocumented since then. It's time to remove it in Spark 2.0.
Author: Reynold Xin <rxin@databricks.com>
Closes#10531 from rxin/SPARK-12588.
This PR adds Scala, Java and Python examples to show how to use Accumulator and Broadcast in Spark Streaming to support checkpointing.
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#10385 from zsxwing/accumulator-broadcast-example.
Example of joining a static RDD of word sentiments to a streaming RDD of Tweets in order to demo the usage of the transform() method.
Author: Jeff L <sha0lin@alumni.carnegiemellon.edu>
Closes#8431 from Agent007/SPARK-9057.
String.split accepts a regular expression, so we should escape "." and "|".
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#10361 from zsxwing/reg-bug.
We have DataFrame example for SparkR, we also need to add ML example under ```examples/src/main/r```.
cc mengxr jkbradley shivaram
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#10324 from yanboliang/spark-12364.
This PR includes only an example code in order to finish it quickly.
I'll send another PR for the docs soon.
Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com>
Closes#9952 from yu-iskw/SPARK-6518.
Rename ```weights``` to ```coefficients``` for examples/DeveloperApiExample.
cc mengxr jkbradley
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#10280 from yanboliang/spark-coefficients.
Since ```Dataset``` has a new meaning in Spark 1.6, we should rename it to avoid confusion.
#9873 finished the work of Scala example, here we focus on the Python one.
Move dataset_example.py to ```examples/ml``` and rename to ```dataframe_example.py```.
BTW, fix minor missing issues of #9873.
cc mengxr
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#9957 from yanboliang/SPARK-11978.
* ```jsonFile``` should support multiple input files, such as:
```R
jsonFile(sqlContext, c(“path1”, “path2”)) # character vector as arguments
jsonFile(sqlContext, “path1,path2”)
```
* Meanwhile, ```jsonFile``` has been deprecated by Spark SQL and will be removed at Spark 2.0. So we mark ```jsonFile``` deprecated and use ```read.json``` at SparkR side.
* Replace all ```jsonFile``` with ```read.json``` at test_sparkSQL.R, but still keep jsonFile test case.
* If this PR is accepted, we should also make almost the same change for ```parquetFile```.
cc felixcheung sun-rui shivaram
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#10145 from yanboliang/spark-12146.
Adding ability to define an initial state RDD for use with updateStateByKey PySpark. Added unit test and changed stateful_network_wordcount example to use initial RDD.
Author: Bryan Cutler <bjcutler@us.ibm.com>
Closes#10082 from BryanCutler/initial-rdd-updateStateByKey-SPARK-11713.
SPARK-12244:
Based on feedback from early users and personal experience attempting to explain it, the name trackStateByKey had two problem.
"trackState" is a completely new term which really does not give any intuition on what the operation is
the resultant data stream of objects returned by the function is called in docs as the "emitted" data for the lack of a better.
"mapWithState" makes sense because the API is like a mapping function like (Key, Value) => T with State as an additional parameter. The resultant data stream is "mapped data". So both problems are solved.
SPARK-12245:
From initial experiences, not having the key in the function makes it hard to return mapped stuff, as the whole information of the records is not there. Basically the user is restricted to doing something like mapValue() instead of map(). So adding the key as a parameter.
Author: Tathagata Das <tathagata.das1565@gmail.com>
Closes#10224 from tdas/rename.
Documentation regarding the `IndexToString` label transformer with code snippets in Scala/Java/Python.
Author: BenFradet <benjamin.fradet@gmail.com>
Closes#10166 from BenFradet/SPARK-12159.
jira: https://issues.apache.org/jira/browse/SPARK-11605
Check Java compatibility for MLlib for this release.
fix:
1. `StreamingTest.registerStream` needs java friendly interface.
2. `GradientBoostedTreesModel.computeInitialPredictionAndError` and `GradientBoostedTreesModel.updatePredictionError` has java compatibility issue. Mark them as `developerAPI`.
TBD:
[updated] no fix for now per discussion.
`org.apache.spark.mllib.classification.LogisticRegressionModel`
`public scala.Option<java.lang.Object> getThreshold();` has wrong return type for Java invocation.
`SVMModel` has the similar issue.
Yet adding a `scala.Option<java.util.Double> getThreshold()` would result in an overloading error due to the same function signature. And adding a new function with different name seems to be not necessary.
cc jkbradley feynmanliang
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#10102 from hhbyyh/javaAPI.
jira: https://issues.apache.org/jira/browse/SPARK-10393
Since the logic of the text processing part has been moved to ML estimators/transformers, replace the related code in LDA Example with the ML pipeline.
Author: Yuhao Yang <hhbyyh@gmail.com>
Author: yuhaoyang <yuhao@zhanglipings-iMac.local>
Closes#8551 from hhbyyh/ldaExUpdate.
This reverts PR #10002, commit 78209b0cca.
The original PR wasn't tested on Jenkins before being merged.
Author: Cheng Lian <lian@databricks.com>
Closes#10200 from liancheng/revert-pr-10002.
Add ```SQLTransformer``` user guide, example code and make Scala API doc more clear.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#10006 from yanboliang/spark-11958.
Made new patch contaning only markdown examples moved to exmaple/folder.
Ony three java code were not shfted since they were contaning compliation error ,these classes are
1)StandardScale 2)NormalizerExample 3)VectorIndexer
Author: Xusen Yin <yinxusen@gmail.com>
Author: somideshmukh <somilde@us.ibm.com>
Closes#10002 from somideshmukh/SomilBranch1.33.
`ByteBuffer` doesn't guarantee all contents in `ByteBuffer.array` are valid. E.g, a ByteBuffer returned by `ByteBuffer.slice`. We should not use the whole content of `ByteBuffer` unless we know that's correct.
This patch fixed all places that use `ByteBuffer.array` incorrectly.
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#10083 from zsxwing/bytebuffer-array.
We should upgrade to SBT 0.13.9, since this is a requirement in order to use SBT's new Maven-style resolution features (which will be done in a separate patch, because it's blocked by some binary compatibility issues in the POM reader plugin).
I also upgraded Scalastyle to version 0.8.0, which was necessary in order to fix a Scala 2.10.5 compatibility issue (see https://github.com/scalastyle/scalastyle/issues/156). The newer Scalastyle is slightly stricter about whitespace surrounding tokens, so I fixed the new style violations.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10112 from JoshRosen/upgrade-to-sbt-0.13.9.
This replaces https://github.com/apache/spark/pull/9696
Invoke Checkstyle and print any errors to the console, failing the step.
Use Google's style rules modified according to
https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide
Some important checks are disabled (see TODOs in `checkstyle.xml`) due to
multiple violations being present in the codebase.
Suggest fixing those TODOs in a separate PR(s).
More on Checkstyle can be found on the [official website](http://checkstyle.sourceforge.net/).
Sample output (from [build 46345](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/46345/consoleFull)) (duplicated because I run the build twice with different profiles):
> Checkstyle checks failed at following occurrences:
[ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/UnsafeRowParquetRecordReader.java:[217,7] (coding) MissingSwitchDefault: switch without "default" clause.
> [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/SpecificParquetRecordReaderBase.java:[198,10] (modifier) ModifierOrder: 'protected' modifier out of order with the JLS suggestions.
> [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/UnsafeRowParquetRecordReader.java:[217,7] (coding) MissingSwitchDefault: switch without "default" clause.
> [ERROR] src/main/java/org/apache/spark/sql/execution/datasources/parquet/SpecificParquetRecordReaderBase.java:[198,10] (modifier) ModifierOrder: 'protected' modifier out of order with the JLS suggestions.
> [error] running /home/jenkins/workspace/SparkPullRequestBuilder2/dev/lint-java ; received return code 1
Also fix some of the minor violations that didn't require sweeping changes.
Apologies for the previous botched PRs - I finally figured out the issue.
cr: JoshRosen, pwendell
> I state that the contribution is my original work, and I license the work to the project under the project's open source license.
Author: Dmitry Erastov <derastov@gmail.com>
Closes#9867 from dskrvk/master.
Remove duplicate mllib example (DT/RF/GBT in Java/Python).
Since we have tutorial code for DT/RF/GBT classification/regression in Scala/Java/Python and example applications for DT/RF/GBT in Scala, so we mark these as duplicated and remove them.
mengxr
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#9954 from yanboliang/SPARK-11975.
jira: https://issues.apache.org/jira/browse/SPARK-11689
Add simple user guide for LDA under spark.ml and example code under examples/. Use include_example to include example code in the user guide markdown. Check SPARK-11606 for instructions.
Original PR is reverted due to document build error. https://github.com/apache/spark/pull/9722
mengxr feynmanliang yinxusen Sorry for the troubling.
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#9974 from hhbyyh/ldaMLExample.
ML ```LinearRegression``` use ```data/mllib/sample_libsvm_data.txt``` as dataset in examples and user guide doc, but it's actually classification dataset rather than regression dataset. We should use ```data/mllib/sample_linear_regression_data.txt``` instead.
The deeper causes is that ```LinearRegression``` with "normal" solver can not solve this dataset correctly, may be due to the ill condition and unreasonable label. This issue has been reported at [SPARK-11918](https://issues.apache.org/jira/browse/SPARK-11918).
It will confuse users if they run the example code but get exception, so we should make this change which can clearly illustrate the usage of ```LinearRegression``` algorithm.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#9905 from yanboliang/spark-11920.
We used the name `Dataset` to refer to `SchemaRDD` in 1.2 in ML pipelines and created this example file. Since `Dataset` has a new meaning in Spark 1.6, we should rename it to avoid confusion. This PR also removes support for dense format to simplify the example code.
cc: yinxusen
Author: Xiangrui Meng <meng@databricks.com>
Closes#9873 from mengxr/SPARK-11895.
jira: https://issues.apache.org/jira/browse/SPARK-11689
Add simple user guide for LDA under spark.ml and example code under examples/. Use include_example to include example code in the user guide markdown. Check SPARK-11606 for instructions.
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#9722 from hhbyyh/ldaMLExample.
jira: https://issues.apache.org/jira/browse/SPARK-11816
Currently I only fixed some obvious comments issue like
// scalastyle:off println
on the bottom.
Yet the style in examples is not quite consistent, like only half of the examples are with
// Example usage: ./bin/run-example mllib.FPGrowthExample \,
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#9808 from hhbyyh/exampleStyle.
The HP Fortify Opens Source Review team (https://www.hpfod.com/open-source-review-project) reported a handful of potential resource leaks that were discovered using their static analysis tool. We should fix the issues identified by their scan.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#9455 from JoshRosen/fix-potential-resource-leaks.
JIRA issue https://issues.apache.org/jira/browse/SPARK-11728.
The ml-ensembles.md file contains `OneVsRestExample`. Instead of writing new code files of two `OneVsRestExample`s, I use two existing files in the examples directory, they are `OneVsRestExample.scala` and `JavaOneVsRestExample.scala`.
Author: Xusen Yin <yinxusen@gmail.com>
Closes#9716 from yinxusen/SPARK-11728.
Use 2 seconds batch size as duration specified in JavaStreamingContext constructor is 2000 ms
Author: Rohan Bhanderi <rohan.bhanderi@sjsu.edu>
Closes#9714 from RohanBhanderi/patch-2.
Use LibSVM data source rather than MLUtils.loadLibSVMFile to load DataFrame, include:
* Use libSVM data source for all example codes under examples/ml, and remove unused import.
* Use libSVM data source for user guides under ml-*** which were omitted by #8697.
* Fix bug: We should use ```sqlContext.read().format("libsvm").load(path)``` at Java side, but the API doc and user guides misuse as ```sqlContext.read.format("libsvm").load(path)```.
* Code cleanup.
mengxr
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#9690 from yanboliang/spark-11723.
I have made the required changes and tested.
Kindly review the changes.
Author: Rishabh Bhardwaj <rbnext29@gmail.com>
Closes#9407 from rishabhbhardwaj/SPARK-11445.
Add Python example code for Multilayer Perceptron Classification, and make example code in user guide document testable. mengxr
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#9594 from yanboliang/spark-11629.
TODO
- [x] Add Java API
- [x] Add API tests
- [x] Add a function test
Author: Shixiong Zhu <shixiong@databricks.com>
Closes#9636 from zsxwing/java-track.
Current updateStateByKey provides stateful processing in Spark Streaming. It allows the user to maintain per-key state and manage that state using an updateFunction. The updateFunction is called for each key, and it uses new data and existing state of the key, to generate an updated state. However, based on community feedback, we have learnt the following lessons.
* Need for more optimized state management that does not scan every key
* Need to make it easier to implement common use cases - (a) timeout of idle data, (b) returning items other than state
The high level idea that of this PR
* Introduce a new API trackStateByKey that, allows the user to update per-key state, and emit arbitrary records. The new API is necessary as this will have significantly different semantics than the existing updateStateByKey API. This API will have direct support for timeouts.
* Internally, the system will keep the state data as a map/list within the partitions of the state RDDs. The new data RDDs will be partitioned appropriately, and for all the key-value data, it will lookup the map/list in the state RDD partition and create a new list/map of updated state data. The new state RDD partition will be created based on the update data and if necessary, with old data.
Here is the detailed design doc. Please take a look and provide feedback as comments.
https://docs.google.com/document/d/1NoALLyd83zGs1hNGMm0Pc5YOVgiPpMHugGMk6COqxxE/edit#heading=h.ph3w0clkd4em
This is still WIP. Major things left to be done.
- [x] Implement basic functionality of state tracking, with initial RDD and timeouts
- [x] Unit tests for state tracking
- [x] Unit tests for initial RDD and timeout
- [ ] Unit tests for TrackStateRDD
- [x] state creating, updating, removing
- [ ] emitting
- [ ] checkpointing
- [x] Misc unit tests for State, TrackStateSpec, etc.
- [x] Update docs and experimental tags
Author: Tathagata Das <tathagata.das1565@gmail.com>
Closes#9256 from tdas/trackStateByKey.
I have tested it on my local, it is working fine, please review
Author: sachin aggarwal <different.sachin@gmail.com>
Closes#9539 from agsachin/SPARK-11552-real.
I have made the required changes in mllib-naive-bayes.md/mllib-isotonic-regression.md and also verified them.
Kindle Review it.
Author: Rishabh Bhardwaj <rbnext29@gmail.com>
Closes#9353 from rishabhbhardwaj/SPARK-11383.
mengxr https://issues.apache.org/jira/browse/SPARK-11289
I make some changes in ML feature extractors. I.e. TF-IDF, Word2Vec, and CountVectorizer. I add new example code in spark/examples, hope it is the right place to add those examples.
Author: Xusen Yin <yinxusen@gmail.com>
Closes#9266 from yinxusen/SPARK-11289.
All prediction models should store `numFeatures` indicating the number of features the model was trained on. Default value of -1 added for backwards compatibility.
Author: sethah <seth.hendrickson16@gmail.com>
Closes#8675 from sethah/SPARK-9715.
This is a followup to #8499 which adds a Scalastyle rule to mandate the use of SparkHadoopUtil's JobContext accessor methods and fixes the existing violations.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#8521 from JoshRosen/SPARK-10330-part2.
`fitIntercept` is a command line option but not set in the main program.
dbtsai
Author: Shuo Xiang <sxiang@pinterest.com>
Closes#8510 from coderxiang/intercept and squashes the following commits:
57c9b7d [Shuo Xiang] fix not being able to set intercept in LR example
Replace `JavaConversions` implicits with `JavaConverters`
Most occurrences I've seen so far are necessary conversions; a few have been avoidable. None are in critical code as far as I see, yet.
Author: Sean Owen <sowen@cloudera.com>
Closes#8033 from srowen/SPARK-9613.
This PR includes the following fixes:
1. Use `range` instead of `xrange` in `queue_stream.py` to support Python 3.
2. Fix the issue that `utf8_decoder` will return `bytes` rather than `str` when receiving an empty `bytes` in Python 3.
3. Fix the commands in docs so that the user can copy them directly to the command line. The previous commands was broken in the middle of a path, so when copying to the command line, the path would be split to two parts by the extra spaces, which forces the user to fix it manually.
Author: zsxwing <zsxwing@gmail.com>
Closes#8315 from zsxwing/SPARK-9812.
Tiny modification to a few comments ```sbt publishLocal``` work again.
Author: Herman van Hovell <hvanhovell@questtec.nl>
Closes#8209 from hvanhovell/SPARK-9980.
Copied ML models must have the same parent of original ones
Author: lewuathe <lewuathe@me.com>
Author: Lewuathe <lewuathe@me.com>
Closes#7447 from Lewuathe/SPARK-9073.
This PR is based on #4229, thanks prabeesh.
Closes#4229
Author: Prabeesh K <prabsmails@gmail.com>
Author: zsxwing <zsxwing@gmail.com>
Author: prabs <prabsmails@gmail.com>
Author: Prabeesh K <prabeesh.k@namshi.com>
Closes#7833 from zsxwing/pr4229 and squashes the following commits:
9570bec [zsxwing] Fix the variable name and check null in finally
4a9c79e [zsxwing] Fix pom.xml indentation
abf5f18 [zsxwing] Merge branch 'master' into pr4229
935615c [zsxwing] Fix the flaky MQTT tests
47278c5 [zsxwing] Include the project class files
478f844 [zsxwing] Add unpack
5f8a1d4 [zsxwing] Make the maven build generate the test jar for Python MQTT tests
734db99 [zsxwing] Merge branch 'master' into pr4229
126608a [Prabeesh K] address the comments
b90b709 [Prabeesh K] Merge pull request #1 from zsxwing/pr4229
d07f454 [zsxwing] Register StreamingListerner before starting StreamingContext; Revert unncessary changes; fix the python unit test
a6747cb [Prabeesh K] wait for starting the receiver before publishing data
87fc677 [Prabeesh K] address the comments:
97244ec [zsxwing] Make sbt build the assembly test jar for streaming mqtt
80474d1 [Prabeesh K] fix
1f0cfe9 [Prabeesh K] python style fix
e1ee016 [Prabeesh K] scala style fix
a5a8f9f [Prabeesh K] added Python test
9767d82 [Prabeesh K] implemented Python-friendly class
a11968b [Prabeesh K] fixed python style
795ec27 [Prabeesh K] address comments
ee387ae [Prabeesh K] Fix assembly jar location of mqtt-assembly
3f4df12 [Prabeesh K] updated version
b34c3c1 [prabs] adress comments
3aa7fff [prabs] Added Python streaming mqtt word count example
b7d42ff [prabs] Mqtt streaming support in Python
This PR replaces the old "threshold" with a generalized "thresholds" Param. We keep getThreshold,setThreshold for backwards compatibility for binary classification.
Note that the primary author of this PR is holdenk
Author: Holden Karau <holden@pigscanfly.ca>
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#7909 from jkbradley/holdenk-SPARK-8069-add-cutoff-aka-threshold-to-random-forest and squashes the following commits:
3952977 [Joseph K. Bradley] fixed pyspark doc test
85febc8 [Joseph K. Bradley] made python unit tests a little more robust
7eb1d86 [Joseph K. Bradley] small cleanups
6cc2ed8 [Joseph K. Bradley] Fixed remaining merge issues.
0255e44 [Joseph K. Bradley] Many cleanups for thresholds, some more tests
7565a60 [Holden Karau] fix pep8 style checks, add a getThreshold method similar to our LogisticRegression.scala one for API compat
be87f26 [Holden Karau] Convert threshold to thresholds in the python code, add specialized support for Array[Double] to shared parems codegen, etc.
6747dad [Holden Karau] Override raw2prediction for ProbabilisticClassifier, fix some tests
25df168 [Holden Karau] Fix handling of thresholds in LogisticRegression
c02d6c0 [Holden Karau] No default for thresholds
5e43628 [Holden Karau] CR feedback and fixed the renamed test
f3fbbd1 [Holden Karau] revert the changes to random forest :(
51f581c [Holden Karau] Add explicit types to public methods, fix long line
f7032eb [Holden Karau] Fix a java test bug, remove some unecessary changes
adf15b4 [Holden Karau] rename the classifier suite test to ProbabilisticClassifierSuite now that we only have it in Probabilistic
398078a [Holden Karau] move the thresholding around a bunch based on the design doc
4893bdc [Holden Karau] Use numtrees of 3 since previous result was tied (one tree for each) and the switch from different max methods picked a different element (since they were equal I think this is ok)
638854c [Holden Karau] Add a scala RandomForestClassifierSuite test based on corresponding python test
e09919c [Holden Karau] Fix return type, I need more coffee....
8d92cac [Holden Karau] Use ClassifierParams as the head
3456ed3 [Holden Karau] Add explicit return types even though just test
a0f3b0c [Holden Karau] scala style fixes
6f14314 [Holden Karau] Since hasthreshold/hasthresholds is in root classifier now
ffc8dab [Holden Karau] Update the sharedParams
0420290 [Holden Karau] Allow us to override the get methods selectively
978e77a [Holden Karau] Move HasThreshold into classifier params and start defining the overloaded getThreshold/getThresholds functions
1433e52 [Holden Karau] Revert "try and hide threshold but chainges the API so no dice there"
1f09a2e [Holden Karau] try and hide threshold but chainges the API so no dice there
efb9084 [Holden Karau] move setThresholds only to where its used
6b34809 [Holden Karau] Add a test with thresholding for the RFCS
74f54c3 [Holden Karau] Fix creation of vote array
1986fa8 [Holden Karau] Setting the thresholds only makes sense if the underlying class hasn't overridden predict, so lets push it down.
2f44b18 [Holden Karau] Add a global default of null for thresholds param
f338cfc [Holden Karau] Wait that wasn't a good idea, Revert "Some progress towards unifying threshold and thresholds"
634b06f [Holden Karau] Some progress towards unifying threshold and thresholds
85c9e01 [Holden Karau] Test passes again... little fnur
099c0f3 [Holden Karau] Move thresholds around some more (set on model not trainer)
0f46836 [Holden Karau] Start adding a classifiersuite
f70eb5e [Holden Karau] Fix test compile issues
a7d59c8 [Holden Karau] Move thresholding into Classifier trait
5d999d2 [Holden Karau] Some more progress, start adding a test (maybe try and see if we can find a better thing to use for the base of the test)
1fed644 [Holden Karau] Use thresholds to scale scores in random forest classifcation
31d6bf2 [Holden Karau] Start threading the threshold info through
0ef228c [Holden Karau] Add hasthresholds
Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process.
I'll explain several of the changes inline in comments.
Author: Sean Owen <sowen@cloudera.com>
Closes#7862 from srowen/SPARK-9534 and squashes the following commits:
ea51618 [Sean Owen] Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process.
[SPARK-9149] Add an example of spark.ml KMeans - ASF JIRA https://issues.apache.org/jira/browse/SPARK-9149
jkbradley Should we support other data formats, such as TSV or CSV. I have implemented these examples which support only space separated file which is same as the example for `spark.mllib`'s `KMeans`.
Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com>
Closes#7697 from yu-iskw/SPARK-9149 and squashes the following commits:
7137bad [Yu ISHIKAWA] Fix the typo
56b9da2 [Yu ISHIKAWA] Fix the place of the wrong import statment
554e574 [Yu ISHIKAWA] Change the way to format input data in KMeansExample
e7a948a [Yu ISHIKAWA] Import spark.ml.clustering.KMeans
1901e0c [Yu ISHIKAWA] Change how to initialize an array for a DataFrame schema
d8043f5 [Yu ISHIKAWA] Return a value directly
d81bf55 [Yu ISHIKAWA] Fix a typo and its access specifiers
3e0862d [Yu ISHIKAWA] Make KMeansExample more simple
51ce9c1 [Yu ISHIKAWA] Make JavaKMeansExample more simple
a5a01e0 [Yu ISHIKAWA] Fix a Javadoc about the command to execute the example
b09ec13 [Yu ISHIKAWA] [SPARK-9149][ML][Examples] Add an example of spark.ml KMeans
Author: Jonathan Alter <jonalter@users.noreply.github.com>
Closes#7093 from jonalter/SPARK-7977 and squashes the following commits:
ccd44cc [Jonathan Alter] Changed println to log in ThreadingSuite
7fcac3e [Jonathan Alter] Reverting to println in ThreadingSuite
10724b6 [Jonathan Alter] Changing some printlns to logs in tests
eeec1e7 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
0b1dcb4 [Jonathan Alter] More println cleanup
aedaf80 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
925fd98 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
0c16fa3 [Jonathan Alter] Replacing some printlns with logs
45c7e05 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
5c8e283 [Jonathan Alter] Allowing println in audit-release examples
5b50da1 [Jonathan Alter] Allowing printlns in example files
ca4b477 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
83ab635 [Jonathan Alter] Fixing new printlns
54b131f [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
1cd8a81 [Jonathan Alter] Removing some unnecessary comments and printlns
b837c3a [Jonathan Alter] Disallowing println
Here are more examples on SparkR DataFrames including creating a Spark Contect and a SQL
context, loading data and simple data manipulation.
Author: Daniel Emaasit (PhD Student) <daniel.emaasit@gmail.com>
Closes#6668 from Emaasit/dan-dev and squashes the following commits:
3a97867 [Daniel Emaasit (PhD Student)] Used fewer rows for createDataFrame
f7227f9 [Daniel Emaasit (PhD Student)] Using command line arguments
a550f70 [Daniel Emaasit (PhD Student)] Used base R functions
33f9882 [Daniel Emaasit (PhD Student)] Renamed file
b6603e3 [Daniel Emaasit (PhD Student)] changed "Describe" function to "describe"
90565dd [Daniel Emaasit (PhD Student)] Deleted the getting-started file
b95a103 [Daniel Emaasit (PhD Student)] Deleted this file
cc55cd8 [Daniel Emaasit (PhD Student)] combined all the code into one .R file
c6933af [Daniel Emaasit (PhD Student)] changed variable name to SQLContext
8e0fe14 [Daniel Emaasit (PhD Student)] provided two options for creating DataFrames
2653573 [Daniel Emaasit (PhD Student)] Updates to a comment and variable name
275b787 [Daniel Emaasit (PhD Student)] Added the Apache License at the top of the file
2e8f724 [Daniel Emaasit (PhD Student)] Added the Apache License at the top of the file
486f44e [Daniel Emaasit (PhD Student)] Added the Apache License at the file
d705112 [Daniel Emaasit (PhD Student)] Created more examples on SparkR DataFrames
Author: zsxwing <zsxwing@gmail.com>
Closes#6830 from zsxwing/flume-python and squashes the following commits:
78dfdac [zsxwing] Fix the compile error in the test code
f1bf3c0 [zsxwing] Address TD's comments
0449723 [zsxwing] Add sbt goal streaming-flume-assembly/assembly
e93736b [zsxwing] Fix the test case for determine_modules_to_test
9d5821e [zsxwing] Fix pyspark_core dependencies
f9ee681 [zsxwing] Merge branch 'master' into flume-python
7a55837 [zsxwing] Add streaming_flume_assembly to run-tests.py
b96b0de [zsxwing] Merge branch 'master' into flume-python
ce85e83 [zsxwing] Fix incompatible issues for Python 3
01cbb3d [zsxwing] Add import sys
152364c [zsxwing] Fix the issue that StringIO doesn't work in Python 3
14ba0ff [zsxwing] Add flume-assembly for sbt building
b8d5551 [zsxwing] Merge branch 'master' into flume-python
4762c34 [zsxwing] Fix the doc
0336579 [zsxwing] Refactor Flume unit tests and also add tests for Python API
9f33873 [zsxwing] Add the Python API for Flume
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.
...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.
A Python example similar to the existing one for Scala.
Author: Bryan Cutler <bjcutler@us.ibm.com>
Closes#6884 from BryanCutler/streaming-queueStream-example-8444 and squashes the following commits:
435ba7e [Bryan Cutler] [SPARK-8444] Fixed style checks, increased sleep time to show empty queue
257abb0 [Bryan Cutler] [SPARK-8444] Stop context gracefully, Removed unused import, Added description comment
376ef6e [Bryan Cutler] [SPARK-8444] Fixed bug causing DStream.pprint to append empty parenthesis to output instead of blank line
1ff5f8b [Bryan Cutler] [SPARK-8444] Adding Python streaming example for queue_stream
All, this is a first attempt at refactoring `dev/run-tests` into Python. Initially I merely converted all Bash calls over to Python, then moved to a much more modular approach (more functions, moved the calls around, etc.). What is here is the initial culmination and should provide a great base to various downstream issues (e.g. SPARK-7016, modularize / parallelize testing, etc.). Would love comments / suggestions for this initial first step!
/cc srowen pwendell nchammas
Author: Brennon York <brennon.york@capitalone.com>
Closes#5694 from brennonyork/SPARK-7017 and squashes the following commits:
154ed73 [Brennon York] updated finding java binary if JAVA_HOME not set
3922a85 [Brennon York] removed necessary passed in variable
f9fbe54 [Brennon York] reverted doc test change
8135518 [Brennon York] removed the test check for documentation changes until jenkins can get updated
05d435b [Brennon York] added check for jekyll install
22edb78 [Brennon York] add check if jekyll isn't installed on the path
2dff136 [Brennon York] fixed pep8 whitespace errors
767a668 [Brennon York] fixed path joining issues, ensured docs actually build on doc changes
c42cf9a [Brennon York] unpack set operations with splat (*)
fb85a41 [Brennon York] fixed minor set bug
0379833 [Brennon York] minor doc addition to print the changed modules
aa03d9e [Brennon York] added documentation builds as a top level test component, altered high level project changes to properly execute core tests only when necessary, changed variable names for simplicity
ec1ae78 [Brennon York] minor name changes, bug fixes
b7c72b9 [Brennon York] reverting streaming context
03fdd7b [Brennon York] fixed the tuple () wraps around example lambda
705d12e [Brennon York] changed example to comply with pep3113 supporting python3
60b3d51 [Brennon York] prepend rather than append onto PATH
7d2f5e2 [Brennon York] updated python tests to remove unused variable
2898717 [Brennon York] added a change to streaming test to check if it only runs streaming tests
eb684b6 [Brennon York] fixed sbt_test_goals reference error
db7ae6f [Brennon York] reverted SPARK_HOME from start of command
1ecca26 [Brennon York] fixed merge conflicts
2fcdfc0 [Brennon York] testing targte branch dump on jenkins
1f607b1 [Brennon York] finalizing revisions to modular tests
8afbe93 [Brennon York] made error codes a global
0629de8 [Brennon York] updated to refactor and remove various small bugs, removed pep8 complaints
d90ab2d [Brennon York] fixed merge conflicts, ensured that for regular builds both core and sql tests always run
b1248dc [Brennon York] exec python rather than running python and exiting with return code
f9deba1 [Brennon York] python to python2 and removed newline
6d0a052 [Brennon York] incorporated merge conflicts with SPARK-7249
f950010 [Brennon York] removed building hive-0.12.0 per SPARK-6908
703f095 [Brennon York] fixed merge conflicts
b1ca593 [Brennon York] reverted the sparkR test
afeb093 [Brennon York] updated to make sparkR test fail
1dada6b [Brennon York] reverted pyspark test failure
9a592ec [Brennon York] reverted mima exclude issue, added pyspark test failure
d825aa4 [Brennon York] revert build break, add mima break
f041d8a [Brennon York] added space from commented import to now test build breaking
983f2a2 [Brennon York] comment out import to fail build test
2386785 [Brennon York] Merge remote-tracking branch 'upstream/master' into SPARK-7017
76335fb [Brennon York] reverted rat license issue for sparkconf
e4a96cc [Brennon York] removed the import error and added license error, fixed the way run-tests and run-tests.py report their error codes
56d3cb9 [Brennon York] changed test back and commented out import to break compile
b37328c [Brennon York] fixed typo and added default return is no error block was found in the environment
7613558 [Brennon York] updated to return the proper env variable for return codes
a5bd445 [Brennon York] reverted license, changed test in shuffle to fail
803143a [Brennon York] removed license file for SparkContext
b0b2604 [Brennon York] comment out import to see if build fails and returns properly
83e80ef [Brennon York] attempt at better python output when called from bash
c095fa6 [Brennon York] removed another wait() call
26e18e8 [Brennon York] removed unnecessary wait()
07210a9 [Brennon York] minor doc string change for java version with namedtuple update
ec03bf3 [Brennon York] added namedtuple for java version to add readability
2cb413b [Brennon York] upcased global variables, changes various calling methods from check_output to check_call
639f1e9 [Brennon York] updated with pep8 rules, fixed minor bugs, added run-tests file in bash to call the run-tests.py script
3c53a1a [Brennon York] uncomment the scala tests :)
6126c4f [Brennon York] refactored run-tests into python
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
Resolves [SPARK-7743](https://issues.apache.org/jira/browse/SPARK-7743).
Trivial changes of versions, package names, as well as a small issue in `ParquetTableOperations.scala`
```diff
- val readContext = getReadSupport(configuration).init(
+ val readContext = ParquetInputFormat.getReadSupportInstance(configuration).init(
```
Since ParquetInputFormat.getReadSupport was made package private in the latest release.
Thanks
-- Thomas Omans
Author: Thomas Omans <tomans@cj.com>
Closes#6597 from eggsby/SPARK-7743 and squashes the following commits:
2df0d1b [Thomas Omans] [SPARK-7743] [SQL] Upgrading parquet version to 1.7.0
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
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
Author: Ram Sriharsha <rsriharsha@hw11853.local>
Closes#6358 from harsha2010/SPARK-7387 and squashes the following commits:
63efda2 [Ram Sriharsha] more examples for classifier to distinguish mapreduce from spark properly
aeb6bb6 [Ram Sriharsha] Python Style Fix
54a500c [Ram Sriharsha] Merge branch 'master' into SPARK-7387
615e91c [Ram Sriharsha] cleanup
204c4e3 [Ram Sriharsha] Merge branch 'master' into SPARK-7387
7246d35 [Ram Sriharsha] [SPARK-7387][ml][doc] CrossValidator example code in Python
Author: Reynold Xin <rxin@databricks.com>
Closes#6480 from rxin/whitespace-example and squashes the following commits:
8a4a3d4 [Reynold Xin] [SPARK-7929] Remove Bagel examples & whitespace fix for examples.
Fix the bug that entering only 1 arg will cause array out of bounds exception in PageRank example.
Author: Li Yao <hnkfliyao@gmail.com>
Closes#6455 from lastland/patch-1 and squashes the following commits:
de06128 [Li Yao] Fix the bug that entering only 1 arg will cause array out of bounds exception.
Since `spark-streaming-kafka` now is published for both Scala 2.10 and 2.11, we can move `KafkaWordCount` and `DirectKafkaWordCount` from `examples/scala-2.10/src/` to `examples/src/` so that they will appear in `spark-examples-***-jar` for Scala 2.11.
Author: zsxwing <zsxwing@gmail.com>
Closes#6436 from zsxwing/SPARK-7895 and squashes the following commits:
c6052f1 [zsxwing] Update examples/pom.xml
0bcfa87 [zsxwing] Fix the sleep time
b9d1256 [zsxwing] Move Kafka examples from scala-2.10/src to src
Author: tedyu <yuzhihong@gmail.com>
Closes#6381 from ted-yu/master and squashes the following commits:
e2f0ea1 [tedyu] Close HBaseAdmin at the end of HBaseTest
Hi,
Following the discussion in http://apache-spark-developers-list.1001551.n3.nabble.com/python-converter-in-HBaseConverter-scala-spark-examples-td10001.html. I made some modification in three files in package examples:
1. HBaseConverters.scala: the new converter will converts all the records in an hbase results into a single string
2. hbase_input.py: as the value string may contain several records, we can use ast package to convert the string into dict
3. HBaseTest.scala: as the package examples use hbase 0.98.7 the original constructor HTableDescriptor is deprecated. The updation to new constructor is made
Author: GenTang <gen.tang86@gmail.com>
Closes#3920 from GenTang/master and squashes the following commits:
d2153df [GenTang] import JSONObject precisely
4802481 [GenTang] dump the result into a singl String
62df7f0 [GenTang] remove the comment
21de653 [GenTang] return the string in json format
15b1fe3 [GenTang] the modification of comments
5cbbcfc [GenTang] the improvement of pythonconverter
ceb31c5 [GenTang] the modification for adapting updation of hbase
3253b61 [GenTang] the modification accompanying the improvement of pythonconverter
Also moved all the deprecated functions into one place for SQLContext and DataFrame, and updated tests to use the new API.
Author: Reynold Xin <rxin@databricks.com>
Closes#6210 from rxin/df-writer-reader-jdbc and squashes the following commits:
7465c2c [Reynold Xin] Fixed unit test.
118e609 [Reynold Xin] Updated tests.
3441b57 [Reynold Xin] Updated javadoc.
13cdd1c [Reynold Xin] [SPARK-7654][SQL] Move JDBC into DataFrame's reader/writer interface.
Author: Reynold Xin <rxin@databricks.com>
Closes#6211 from rxin/mllib-reader and squashes the following commits:
79a2cb9 [Reynold Xin] [SPARK-7654][MLlib] Migrate MLlib to the DataFrame reader/writer API.
This patch introduces DataFrameWriter and DataFrameReader.
DataFrameReader interface, accessible through SQLContext.read, contains methods that create DataFrames. These methods used to reside in SQLContext. Example usage:
```scala
sqlContext.read.json("...")
sqlContext.read.parquet("...")
```
DataFrameWriter interface, accessible through DataFrame.write, implements a builder pattern to avoid the proliferation of options in writing DataFrame out. It currently implements:
- mode
- format (e.g. "parquet", "json")
- options (generic options passed down into data sources)
- partitionBy (partitioning columns)
Example usage:
```scala
df.write.mode("append").format("json").partitionBy("date").saveAsTable("myJsonTable")
```
TODO:
- [ ] Documentation update
- [ ] Move JDBC into reader / writer?
- [ ] Deprecate the old interfaces
- [ ] Move the generic load interface into reader.
- [ ] Update example code and documentation
Author: Reynold Xin <rxin@databricks.com>
Closes#6175 from rxin/reader-writer and squashes the following commits:
b146c95 [Reynold Xin] Deprecation of old APIs.
bd8abdf [Reynold Xin] Fixed merge conflict.
26abea2 [Reynold Xin] Added general load methods.
244fbec [Reynold Xin] Added equivalent to example.
4f15d92 [Reynold Xin] Added documentation for partitionBy.
7e91611 [Reynold Xin] [SPARK-7654][SQL] DataFrameReader and DataFrameWriter for input/output API.
Java and Scala examples for OneVsRest. Fixes the base classifier to be Logistic Regression and accepts the configuration parameters of the base classifier.
Author: Ram Sriharsha <rsriharsha@hw11853.local>
Closes#6115 from harsha2010/SPARK-7575 and squashes the following commits:
87ad3c7 [Ram Sriharsha] extra line
f5d9891 [Ram Sriharsha] Merge branch 'master' into SPARK-7575
7076084 [Ram Sriharsha] cleanup
dfd660c [Ram Sriharsha] cleanup
8703e4f [Ram Sriharsha] update doc
cb23995 [Ram Sriharsha] fix commandline options for JavaOneVsRestExample
69e91f8 [Ram Sriharsha] cleanup
7f4e127 [Ram Sriharsha] cleanup
d4c40d0 [Ram Sriharsha] Code Review fixes
461eb38 [Ram Sriharsha] cleanup
e0106d9 [Ram Sriharsha] Fix typo
935cf56 [Ram Sriharsha] Try to match Java and Scala Example Commandline options
5323ff9 [Ram Sriharsha] cleanup
196a59a [Ram Sriharsha] cleanup
6adfa0c [Ram Sriharsha] Style Fix
8cfc5d5 [Ram Sriharsha] [SPARK-7575] Example code for OneVsRest
The difference is because we previously don't fit the intercept in Spark 1.3. Here, we change the input `String` so that the probability of instance 6 can be classified as `1.0` without any ambiguity.
with lambda = 0.001 in current LOR implementation, the prediction is
```
(4, spark i j k) --> prob=[0.1596407738787411,0.8403592261212589], prediction=1.0
(5, l m n) --> prob=[0.8378325685476612,0.16216743145233883], prediction=0.0
(6, spark hadoop spark) --> prob=[0.0692663313297627,0.9307336686702373], prediction=1.0
(7, apache hadoop) --> prob=[0.9821575333444208,0.01784246665557917], prediction=0.0
```
and the training accuracy is
```
(0, a b c d e spark) --> prob=[0.0021342419881406746,0.9978657580118594], prediction=1.0
(1, b d) --> prob=[0.9959176174854043,0.004082382514595685], prediction=0.0
(2, spark f g h) --> prob=[0.0014541569986711233,0.9985458430013289], prediction=1.0
(3, hadoop mapreduce) --> prob=[0.9982978367343561,0.0017021632656438518], prediction=0.0
```
Author: DB Tsai <dbt@netflix.com>
Closes#6109 from dbtsai/lor-example and squashes the following commits:
ac63ce4 [DB Tsai] first commit
A param instance is strongly attached to an parent in the current implementation. So if we make a copy of an estimator or a transformer in pipelines and other meta-algorithms, it becomes error-prone to copy the params to the copied instances. In this PR, a param is identified by its parent's UID and the param name. So it becomes loosely attached to its parent and all its derivatives. The UID is preserved during copying or fitting. All components now have a default constructor and a constructor that takes a UID as input. I keep the constructors for Param in this PR to reduce the amount of diff and moved `parent` as a mutable field.
This PR still needs some clean-ups, and there are several spark.ml PRs pending. I'll try to get them merged first and then update this PR.
jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Closes#6019 from mengxr/SPARK-7407 and squashes the following commits:
c4c8120 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7407
520f0a2 [Xiangrui Meng] address comments
2569168 [Xiangrui Meng] fix tests
873caca [Xiangrui Meng] fix tests in OneVsRest; fix a racing condition in shouldOwn
409ea08 [Xiangrui Meng] minor updates
83a163c [Xiangrui Meng] update JavaDeveloperApiExample
5db5325 [Xiangrui Meng] update OneVsRest
7bde7ae [Xiangrui Meng] merge master
697fdf9 [Xiangrui Meng] update Bucketizer
7b4f6c2 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7407
629d402 [Xiangrui Meng] fix LRSuite
154516f [Xiangrui Meng] merge master
aa4a611 [Xiangrui Meng] fix examples/compile
a4794dd [Xiangrui Meng] change Param to use to reduce the size of diff
fdbc415 [Xiangrui Meng] all tests passed
c255f17 [Xiangrui Meng] fix tests in ParamsSuite
818e1db [Xiangrui Meng] merge master
e1160cf [Xiangrui Meng] fix tests
fbc39f0 [Xiangrui Meng] pass test:compile
108937e [Xiangrui Meng] pass compile
8726d39 [Xiangrui Meng] use parent uid in Param
eaeed35 [Xiangrui Meng] update Identifiable
As is, to specify this option on command line, you have to escape the angle brackets.
Author: Bryan Cutler <bjcutler@us.ibm.com>
Closes#6049 from BryanCutler/dataFormat-option-7522 and squashes the following commits:
b34afb4 [Bryan Cutler] [SPARK-7522] Removed angle brackets from dataFormat option
jira: https://issues.apache.org/jira/browse/SPARK-7475
Add a new argument to specify the algorithm applied to LDA, to exhibit the basic usage of LDAOptimizer.
cc jkbradley
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#6000 from hhbyyh/ldaExample and squashes the following commits:
0a7e2bc [Yuhao Yang] fix according to comments
5810b0f [Yuhao Yang] adjust ldaExample for online LDA
Otherwise it will throw exception:
```
Exception in thread "main" kafka.common.FailedToSendMessageException: Failed to send messages after 3 tries.
at kafka.producer.async.DefaultEventHandler.handle(DefaultEventHandler.scala:90)
at kafka.producer.Producer.send(Producer.scala:77)
at org.apache.spark.examples.streaming.KafkaWordCountProducer$.main(KafkaWordCount.scala:96)
at org.apache.spark.examples.streaming.KafkaWordCountProducer.main(KafkaWordCount.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:623)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
```
Author: jerryshao <saisai.shao@intel.com>
Closes#5936 from jerryshao/SPARK-7396 and squashes the following commits:
270bbe2 [jerryshao] Fix Kafka Produce throw Exception issue
This PR also makes some of the DataFrame to RDD methods private as the RDD class is private in 1.4
cc rxin pwendell
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#5949 from shivaram/sparkr-examples and squashes the following commits:
6c42fdc [Shivaram Venkataraman] Remove SparkR RDD examples, add dataframe examples
The following items are added to Python kmeans:
kmeans - setEpsilon, setInitializationSteps
KMeansModel - computeCost, k
Author: Hrishikesh Subramonian <hrishikesh.subramonian@flytxt.com>
Closes#5647 from FlytxtRnD/newPyKmeansAPI and squashes the following commits:
b9e451b [Hrishikesh Subramonian] set seed to fixed value in doc test
5fd3ced [Hrishikesh Subramonian] doc test corrections
20b3c68 [Hrishikesh Subramonian] python 3 fixes
4d4e695 [Hrishikesh Subramonian] added arguments in python tests
21eb84c [Hrishikesh Subramonian] Python Kmeans - setEpsilon, setInitializationSteps, k and computeCost added.
Author: Jihong MA <linlin200605@gmail.com>
Closes#5904 from JihongMA/SPARK-7357 and squashes the following commits:
7d6153a [Jihong MA] SPARK-7357 Improving HBaseTest example
With the previous syntax it could look like that the reduceByKey sums separately abscissas and ordinates of some 2D points. Perhaps in this way should be easier to understand the example, especially for who is starting the functional programming like me now.
Author: Niccolo Becchi <niccolo.becchi@gmail.com>
Author: pippobaudos <niccolo.becchi@gmail.com>
Closes#5875 from pippobaudos/patch-1 and squashes the following commits:
3bb3a47 [pippobaudos] renamed variables in LocalKMeans.scala and kmeans.py to simplify readability
2c2a7a2 [Niccolo Becchi] Update SparkKMeans.scala
This PR added `copy(extra: ParamMap): Params` to `Params`, which makes a copy of the current instance with a randomly generated uid and some extra param values. With this change, we only need to implement `fit` and `transform` without extra param values given the default implementation of `fit(dataset, extra)`:
~~~scala
def fit(dataset: DataFrame, extra: ParamMap): Model = {
copy(extra).fit(dataset)
}
~~~
Inside `fit` and `transform`, since only the embedded values are used, I added `$` as an alias for `getOrDefault` to make the code easier to read. For example, in `LinearRegression.fit` we have:
~~~scala
val effectiveRegParam = $(regParam) / yStd
val effectiveL1RegParam = $(elasticNetParam) * effectiveRegParam
val effectiveL2RegParam = (1.0 - $(elasticNetParam)) * effectiveRegParam
~~~
Meta-algorithm like `Pipeline` implements its own `copy(extra)`. So the fitted pipeline model stored all copied stages (no matter whether it is a transformer or a model).
Other changes:
* `Params$.inheritValues` is moved to `Params!.copyValues` and returns the target instance.
* `fittingParamMap` was removed because the `parent` carries this information.
* `validate` was renamed to `validateParams` to be more precise.
TODOs:
* [x] add tests for newly added methods
* [ ] update documentation
jkbradley dbtsai
Author: Xiangrui Meng <meng@databricks.com>
Closes#5820 from mengxr/SPARK-5956 and squashes the following commits:
7bef88d [Xiangrui Meng] address comments
05229c3 [Xiangrui Meng] assert -> assertEquals
b2927b1 [Xiangrui Meng] organize imports
f14456b [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5956
93e7924 [Xiangrui Meng] add tests for hasParam & copy
463ecae [Xiangrui Meng] merge master
2b954c3 [Xiangrui Meng] update Binarizer
465dd12 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5956
282a1a8 [Xiangrui Meng] fix test
819dd2d [Xiangrui Meng] merge master
b642872 [Xiangrui Meng] example code runs
5a67779 [Xiangrui Meng] examples compile
c76b4d1 [Xiangrui Meng] fix all unit tests
0f4fd64 [Xiangrui Meng] fix some tests
9286a22 [Xiangrui Meng] copyValues to trained models
53e0973 [Xiangrui Meng] move inheritValues to Params and rename it to copyValues
9ee004e [Xiangrui Meng] merge copy and copyWith; rename validate to validateParams
d882afc [Xiangrui Meng] test compile
f082a31 [Xiangrui Meng] make Params copyable and simply handling of extra params in all spark.ml components
Main change: Added isValid field to Param. Modified all usages to use isValid when relevant. Added helper methods in ParamValidate.
Also overrode Params.validate() in:
* CrossValidator + model
* Pipeline + model
I made a few updates for the elastic net patch:
* I changed "tol" to "convergenceTol"
* I added some documentation
This PR is Scala + Java only. Python will be in a follow-up PR.
CC: mengxr
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#5740 from jkbradley/enforce-validate and squashes the following commits:
ad9c6c1 [Joseph K. Bradley] re-generated sharedParams after merging with current master
76415e8 [Joseph K. Bradley] reverted convergenceTol to tol
af62f4b [Joseph K. Bradley] Removed changes to SparkBuild, python linalg. Fixed test failures. Renamed ParamValidate to ParamValidators. Removed explicit type from ParamValidators calls where possible.
bb2665a [Joseph K. Bradley] merged with elastic net pr
ecda302 [Joseph K. Bradley] fix rat tests, plus add a little doc
6895dfc [Joseph K. Bradley] small cleanups
069ac6d [Joseph K. Bradley] many cleanups
928fb84 [Joseph K. Bradley] Maybe done
a910ac7 [Joseph K. Bradley] still workin
6d60e2e [Joseph K. Bradley] Still workin
b987319 [Joseph K. Bradley] Partly done with adding checks, but blocking on adding checking functionality to Param
dbc9fb2 [Joseph K. Bradley] merged with master. enforcing Params.validate
I've added an interface to JavaUtils to do byte conversion and added hooks within Utils.scala to handle conversion within Spark code (like for time strings). I've added matching tests for size conversion, and then updated all deprecated configs and documentation as per SPARK-5933.
Author: Ilya Ganelin <ilya.ganelin@capitalone.com>
Closes#5574 from ilganeli/SPARK-5932 and squashes the following commits:
11f6999 [Ilya Ganelin] Nit fixes
49a8720 [Ilya Ganelin] Whitespace fix
2ab886b [Ilya Ganelin] Scala style
fc85733 [Ilya Ganelin] Got rid of floating point math
852a407 [Ilya Ganelin] [SPARK-5932] Added much improved overflow handling. Can now handle sizes up to Long.MAX_VALUE Petabytes instead of being capped at Long.MAX_VALUE Bytes
9ee779c [Ilya Ganelin] Simplified fraction matches
22413b1 [Ilya Ganelin] Made MAX private
3dfae96 [Ilya Ganelin] Fixed some nits. Added automatic conversion of old paramter for kryoserializer.mb to new values.
e428049 [Ilya Ganelin] resolving merge conflict
8b43748 [Ilya Ganelin] Fixed error in pattern matching for doubles
84a2581 [Ilya Ganelin] Added smoother handling of fractional values for size parameters. This now throws an exception and added a warning for old spark.kryoserializer.buffer
d3d09b6 [Ilya Ganelin] [SPARK-5932] Fixing error in KryoSerializer
fe286b4 [Ilya Ganelin] Resolved merge conflict
c7803cd [Ilya Ganelin] Empty lines
54b78b4 [Ilya Ganelin] Simplified byteUnit class
69e2f20 [Ilya Ganelin] Updates to code
f32bc01 [Ilya Ganelin] [SPARK-5932] Fixed error in API in SparkConf.scala where Kb conversion wasn't being done properly (was Mb). Added test cases for both timeUnit and ByteUnit conversion
f15f209 [Ilya Ganelin] Fixed conversion of kryo buffer size
0f4443e [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5932
35a7fa7 [Ilya Ganelin] Minor formatting
928469e [Ilya Ganelin] [SPARK-5932] Converted some longs to ints
5d29f90 [Ilya Ganelin] [SPARK-5932] Finished documentation updates
7a6c847 [Ilya Ganelin] [SPARK-5932] Updated spark.shuffle.file.buffer
afc9a38 [Ilya Ganelin] [SPARK-5932] Updated spark.broadcast.blockSize and spark.storage.memoryMapThreshold
ae7e9f6 [Ilya Ganelin] [SPARK-5932] Updated spark.io.compression.snappy.block.size
2d15681 [Ilya Ganelin] [SPARK-5932] Updated spark.executor.logs.rolling.size.maxBytes
1fbd435 [Ilya Ganelin] [SPARK-5932] Updated spark.broadcast.blockSize
eba4de6 [Ilya Ganelin] [SPARK-5932] Updated spark.shuffle.file.buffer.kb
b809a78 [Ilya Ganelin] [SPARK-5932] Updated spark.kryoserializer.buffer.max
0cdff35 [Ilya Ganelin] [SPARK-5932] Updated to use bibibytes in method names. Updated spark.kryoserializer.buffer.mb and spark.reducer.maxMbInFlight
475370a [Ilya Ganelin] [SPARK-5932] Simplified ByteUnit code, switched to using longs. Updated docs to clarify that we use kibi, mebi etc instead of kilo, mega
851d691 [Ilya Ganelin] [SPARK-5932] Updated memoryStringToMb to use new interfaces
a9f4fcf [Ilya Ganelin] [SPARK-5932] Added unit tests for unit conversion
747393a [Ilya Ganelin] [SPARK-5932] Added unit tests for ByteString conversion
09ea450 [Ilya Ganelin] [SPARK-5932] Added byte string conversion to Jav utils
5390fd9 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5932
db9a963 [Ilya Ganelin] Closing second spark context
1dc0444 [Ilya Ganelin] Added ref equality check
8c884fa [Ilya Ganelin] Made getOrCreate synchronized
cb0c6b7 [Ilya Ganelin] Doc updates and code cleanup
270cfe3 [Ilya Ganelin] [SPARK-6703] Documentation fixes
15e8dea [Ilya Ganelin] Updated comments and added MiMa Exclude
0e1567c [Ilya Ganelin] Got rid of unecessary option for AtomicReference
dfec4da [Ilya Ganelin] Changed activeContext to AtomicReference
733ec9f [Ilya Ganelin] Fixed some bugs in test code
8be2f83 [Ilya Ganelin] Replaced match with if
e92caf7 [Ilya Ganelin] [SPARK-6703] Added test to ensure that getOrCreate both allows creation, retrieval, and a second context if desired
a99032f [Ilya Ganelin] Spacing fix
d7a06b8 [Ilya Ganelin] Updated SparkConf class to add getOrCreate method. Started test suite implementation
Currently only added `createDirectStream` API, I'm not sure if `createRDD` is also needed, since some Java object needs to be wrapped in Python. Please help to review, thanks a lot.
Author: jerryshao <saisai.shao@intel.com>
Author: Saisai Shao <saisai.shao@intel.com>
Closes#4723 from jerryshao/direct-kafka-python-api and squashes the following commits:
a1fe97c [jerryshao] Fix rebase issue
eebf333 [jerryshao] Address the comments
da40f4e [jerryshao] Fix Python 2.6 Syntax error issue
5c0ee85 [jerryshao] Style fix
4aeac18 [jerryshao] Fix bug in example code
7146d86 [jerryshao] Add unit test
bf3bdd6 [jerryshao] Add more APIs and address the comments
f5b3801 [jerryshao] Small style fix
8641835 [Saisai Shao] Rebase and update the code
589c05b [Saisai Shao] Fix the style
d6fcb6a [Saisai Shao] Address the comments
dfda902 [Saisai Shao] Style fix
0f7d168 [Saisai Shao] Add the doc and fix some style issues
67e6880 [Saisai Shao] Fix test bug
917b0db [Saisai Shao] Add Python createRDD API for Kakfa direct stream
c3fc11d [jerryshao] Modify the docs
2c00936 [Saisai Shao] address the comments
3360f44 [jerryshao] Fix code style
e0e0f0d [jerryshao] Code clean and bug fix
338c41f [Saisai Shao] Add python API and example for direct kafka stream
jira: https://issues.apache.org/jira/browse/SPARK-7090
LDA was implemented with extensibility in mind. And with the development of OnlineLDA and Gibbs Sampling, we are collecting more detailed requirements from different algorithms.
As Joseph Bradley jkbradley proposed in https://github.com/apache/spark/pull/4807 and with some further discussion, we'd like to adjust the code structure a little to present the common interface and extension point clearly.
Basically class LDA would be a common entrance for LDA computing. And each LDA object will refer to a LDAOptimizer for the concrete algorithm implementation. Users can customize LDAOptimizer with specific parameters and assign it to LDA.
Concrete changes:
1. Add a trait `LDAOptimizer`, which defines the common iterface for concrete implementations. Each subClass is a wrapper for a specific LDA algorithm.
2. Move EMOptimizer to file LDAOptimizer and inherits from LDAOptimizer, rename to EMLDAOptimizer. (in case a more generic EMOptimizer comes in the future)
-adjust the constructor of EMOptimizer, since all the parameters should be passed in through initialState method. This can avoid unwanted confusion or overwrite.
-move the code from LDA.initalState to initalState of EMLDAOptimizer
3. Add property ldaOptimizer to LDA and its getter/setter, and EMLDAOptimizer is the default Optimizer.
4. Change the return type of LDA.run from DistributedLDAModel to LDAModel.
Further work:
add OnlineLDAOptimizer and other possible Optimizers once ready.
Author: Yuhao Yang <hhbyyh@gmail.com>
Closes#5661 from hhbyyh/ldaRefactor and squashes the following commits:
0e2e006 [Yuhao Yang] respond to review comments
08a45da [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaRefactor
e756ce4 [Yuhao Yang] solve mima exception
d74fd8f [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaRefactor
0bb8400 [Yuhao Yang] refactor LDA with Optimizer
ec2f857 [Yuhao Yang] protoptype for discussion
....py
Author: tedyu <yuzhihong@gmail.com>
Closes#5673 from tedyu/master and squashes the following commits:
ab7c72b [tedyu] SPARK-7107 Adjust indentation to pass Python style tests
6e25939 [tedyu] Adjust line length to be shorter than 100 characters
18d172a [tedyu] SPARK-7107 Add parameter for zookeeper.znode.parent to hbase_inputformat.py
This is a continuation of [https://github.com/apache/spark/pull/5530] (which was for Decision Trees), but for ensembles: Random Forests and Gradient-Boosted Trees. Please refer to the JIRA [https://issues.apache.org/jira/browse/SPARK-6113], the design doc linked from the JIRA, and the previous PR linked above for design discussions.
This PR follows the example set by the previous PR for Decision Trees. It includes a few cleanups to Decision Trees.
Note: There is one issue which will be addressed in a separate PR: Ensembles' component Models have no parent or fittingParamMap. I plan to submit a separate PR which makes those values in Model be Options. It does not matter much which PR gets merged first.
CC: mengxr manishamde codedeft chouqin
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#5626 from jkbradley/dt-api-ensembles and squashes the following commits:
729167a [Joseph K. Bradley] small cleanups based on code review
bbae2a2 [Joseph K. Bradley] Updated per all comments in code review
855aa9a [Joseph K. Bradley] scala style fix
ea3d901 [Joseph K. Bradley] Added GBT to spark.ml, with tests and examples
c0f30c1 [Joseph K. Bradley] Added random forests and test suites to spark.ml. Not tested yet. Need to add example as well
d045ebd [Joseph K. Bradley] some more updates, but far from done
ee1a10b [Joseph K. Bradley] Added files from old PR and did some initial updates.
To run Spark, default will read file from HDFS if we don't set the schema.
Author: linweizhong <linweizhong@huawei.com>
Closes#5684 from Sephiroth-Lin/pyspark_example_minor and squashes the following commits:
19fe145 [linweizhong] Update example sql.py, so that can read file correctly
This is a reopening of #4867.
A short summary of the issues resolved from the previous PR:
1. HTTPClient version mismatch: Selenium (used for UI tests) requires version 4.3.x, and Tachyon included 4.2.5 through a transitive dependency of its shaded thrift jar. To address this, Tachyon 0.6.3 will promote the transitive dependencies of the shaded jar so they can be excluded in spark.
2. Jackson-Mapper-ASL version mismatch: In lower versions of hadoop-client (ie. 1.0.4), version 1.0.1 is included. The parquet library used in spark sql requires version 1.8+. Its unclear to me why upgrading tachyon-client would cause this dependency to break. The solution was to exclude jackson-mapper-asl from hadoop-client.
It seems that the dependency management in spark-parent will not work on transitive dependencies, one way to make sure jackson-mapper-asl is included with the correct version is to add it as a top level dependency. The best solution would be to exclude the dependency in the modules which require a higher version, but that did not fix the unit tests. Any suggestions on the best way to solve this would be appreciated!
Author: Calvin Jia <jia.calvin@gmail.com>
Closes#5354 from calvinjia/upgrade_tachyon_0.6.3 and squashes the following commits:
0eefe4d [Calvin Jia] Handle httpclient version in maven dependency management. Remove httpclient version setting from profiles.
7c00dfa [Calvin Jia] Set httpclient version to 4.3.2 for selenium. Specify version of httpclient for sql/hive (previously 4.2.5 transitive dependency of libthrift).
9263097 [Calvin Jia] Merge master to test latest changes
dbfc1bd [Calvin Jia] Use Tachyon 0.6.4 for cleaner dependencies.
e2ff80a [Calvin Jia] Exclude the jetty and curator promoted dependencies from tachyon-client.
a3a29da [Calvin Jia] Update tachyon-client exclusions.
0ae6c97 [Calvin Jia] Change tachyon version to 0.6.3
a204df9 [Calvin Jia] Update make distribution tachyon version.
a93c94f [Calvin Jia] Exclude jackson-mapper-asl from hadoop client since it has a lower version than spark's expected version.
a8a923c [Calvin Jia] Exclude httpcomponents from Tachyon
910fabd [Calvin Jia] Update to master
eed9230 [Calvin Jia] Update tachyon version to 0.6.1.
11907b3 [Calvin Jia] Use TachyonURI for tachyon paths instead of strings.
71bf441 [Calvin Jia] Upgrade Tachyon client version to 0.6.0.
Author: Prabeesh K <prabeesh.k@namshi.com>
Closes#5653 from prabeesh/fix and squashes the following commits:
9d7a9f5 [Prabeesh K] fixed scala string interpolation error
This does a few clean-ups. With this PR, all spark.ml tree components have ```private[ml]``` constructors.
CC: mengxr
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#5567 from jkbradley/dt-api-dt2 and squashes the following commits:
2263b5b [Joseph K. Bradley] Added note about tree example issue.
bb9f610 [Joseph K. Bradley] Small cleanups after original tree API PR
It should load from `testInput` instead of `input` for test data.
Author: Liang-Chi Hsieh <viirya@gmail.com>
Closes#5594 from viirya/use_testinput and squashes the following commits:
5e8b174 [Liang-Chi Hsieh] Fix style.
b60b475 [Liang-Chi Hsieh] Use testInput.
This is a PR for cleaning up and finalizing the DecisionTree API. PRs for ensembles will follow once this is merged.
### Goal
Here is the description copied from the JIRA (for both trees and ensembles):
> **Issue**: The APIs for DecisionTree and ensembles (RandomForests and GradientBoostedTrees) have been experimental for a long time. The API has become very convoluted because trees and ensembles have many, many variants, some of which we have added incrementally without a long-term design.
> **Proposal**: This JIRA is for discussing changes required to finalize the APIs. After we discuss, I will make a PR to update the APIs and make them non-Experimental. This will require making many breaking changes; see the design doc for details.
> **[Design doc](https://docs.google.com/document/d/1rJ_DZinyDG3PkYkAKSsQlY0QgCeefn4hUv7GsPkzBP4)** : This outlines current issues and the proposed API.
Overall code layout:
* The old API in mllib.tree.* will remain the same.
* The new API will reside in ml.classification.* and ml.regression.*
### Summary of changes
Old API
* Exactly the same, except I made 1 method in Loss private (but that is not a breaking change since that method was introduced after the Spark 1.3 release).
New APIs
* Under Pipeline API
* The new API preserves functionality, except:
* New API does NOT store prob (probability of label in classification). I want to have it store the full vector of probabilities but feel that should be in a later PR.
* Use abstractions for parameters, estimators, and models to avoid code duplication
* Limit parameters to relevant algorithms
* For enum-like types, only expose Strings
* We can make these pluggable later on by adding new parameters. That is a far-future item.
Test suites
* I organized DecisionTreeSuite, but I made absolutely no changes to the tests themselves.
* The test suites for the new API only test (a) similarity with the results of the old API and (b) elements of the new API.
* After code is moved to this new API, we should move the tests from the old suites which test the internals.
### Details
#### Changed names
Parameters
* useNodeIdCache -> cacheNodeIds
#### Other changes
* Split: Changed categories to set instead of list
#### Non-decision tree changes
* AttributeGroup
* Added parentheses to toMetadata, toStructField methods (These were removed in a previous PR, but I ran into 1 issue with the Scala compiler not being able to disambiguate between a toMetadata method with no parentheses and a toMetadata method which takes 1 argument.)
* Attributes
* Renamed: toMetadata -> toMetadataImpl
* Added toMetadata methods which return ML metadata (keyed with “ML_ATTR”)
* NominalAttribute: Added getNumValues method which examines both numValues and values.
* Params.inheritValues: Checks whether the parent param really belongs to the child (to allow Estimator-Model pairs with different sets of parameters)
### Questions for reviewers
* Is "DecisionTreeClassificationModel" too long a name?
* Is this OK in the docs?
```
class DecisionTreeRegressor extends TreeRegressor[DecisionTreeRegressionModel] with DecisionTreeParams[DecisionTreeRegressor] with TreeRegressorParams[DecisionTreeRegressor]
```
### Future
We should open up the abstractions at some point. E.g., it would be useful to be able to set tree-related parameters in 1 place and then pass those to multiple tree-based algorithms.
Follow-up JIRAs will be (in this order):
* Tree ensembles
* Deprecate old tree code
* Move DecisionTree implementation code to new API.
* Move tests from the old suites which test the internals.
* Update programming guide
* Python API
* Change RandomForest* to always use bootstrapping, even when numTrees = 1
* Provide the probability of the predicted label for classification. After we move code to the new API and update it to maintain probabilities for all labels, then we can add the probabilities to the new API.
CC: mengxr manishamde codedeft chouqin MechCoder
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#5530 from jkbradley/dt-api-dt and squashes the following commits:
6aae255 [Joseph K. Bradley] Changed tree abstractions not to take type parameters, and for setters to return this.type instead
ec17947 [Joseph K. Bradley] Updates based on code review. Main changes were: moving public types from ml.impl.tree to ml.tree, modifying CategoricalSplit to take an Array of categories but store a Set internally, making more types sealed or final
5626c81 [Joseph K. Bradley] style fixes
f8fbd24 [Joseph K. Bradley] imported reorg of DecisionTreeSuite from old PR. small cleanups
7ef63ed [Joseph K. Bradley] Added DecisionTreeRegressor, test suites, and example (for real this time)
e11673f [Joseph K. Bradley] Added DecisionTreeRegressor, test suites, and example
119f407 [Joseph K. Bradley] added DecisionTreeClassifier example
0bdc486 [Joseph K. Bradley] fixed issues after param PR was merged
f9fbb60 [Joseph K. Bradley] Done with DecisionTreeClassifier, but no save/load yet. Need to add example as well
2532c9a [Joseph K. Bradley] partial move to spark.ml API, not done yet
c72c1a0 [Joseph K. Bradley] Copied changes for common items, plus DecisionTreeClassifier from original PR
This PR update PySpark to support Python 3 (tested with 3.4).
Known issue: unpickle array from Pyrolite is broken in Python 3, those tests are skipped.
TODO: ec2/spark-ec2.py is not fully tested with python3.
Author: Davies Liu <davies@databricks.com>
Author: twneale <twneale@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#5173 from davies/python3 and squashes the following commits:
d7d6323 [Davies Liu] fix tests
6c52a98 [Davies Liu] fix mllib test
99e334f [Davies Liu] update timeout
b716610 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
cafd5ec [Davies Liu] adddress comments from @mengxr
bf225d7 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
179fc8d [Davies Liu] tuning flaky tests
8c8b957 [Davies Liu] fix ResourceWarning in Python 3
5c57c95 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
4006829 [Davies Liu] fix test
2fc0066 [Davies Liu] add python3 path
71535e9 [Davies Liu] fix xrange and divide
5a55ab4 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
125f12c [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ed498c8 [Davies Liu] fix compatibility with python 3
820e649 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
e8ce8c9 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ad7c374 [Davies Liu] fix mllib test and warning
ef1fc2f [Davies Liu] fix tests
4eee14a [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
20112ff [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
59bb492 [Davies Liu] fix tests
1da268c [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ca0fdd3 [Davies Liu] fix code style
9563a15 [Davies Liu] add imap back for python 2
0b1ec04 [Davies Liu] make python examples work with Python 3
d2fd566 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
a716d34 [Davies Liu] test with python 3.4
f1700e8 [Davies Liu] fix test in python3
671b1db [Davies Liu] fix test in python3
692ff47 [Davies Liu] fix flaky test
7b9699f [Davies Liu] invalidate import cache for Python 3.3+
9c58497 [Davies Liu] fix kill worker
309bfbf [Davies Liu] keep compatibility
5707476 [Davies Liu] cleanup, fix hash of string in 3.3+
8662d5b [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
f53e1f0 [Davies Liu] fix tests
70b6b73 [Davies Liu] compile ec2/spark_ec2.py in python 3
a39167e [Davies Liu] support customize class in __main__
814c77b [Davies Liu] run unittests with python 3
7f4476e [Davies Liu] mllib tests passed
d737924 [Davies Liu] pass ml tests
375ea17 [Davies Liu] SQL tests pass
6cc42a9 [Davies Liu] rename
431a8de [Davies Liu] streaming tests pass
78901a7 [Davies Liu] fix hash of serializer in Python 3
24b2f2e [Davies Liu] pass all RDD tests
35f48fe [Davies Liu] run future again
1eebac2 [Davies Liu] fix conflict in ec2/spark_ec2.py
6e3c21d [Davies Liu] make cloudpickle work with Python3
2fb2db3 [Josh Rosen] Guard more changes behind sys.version; still doesn't run
1aa5e8f [twneale] Turned out `pickle.DictionaryType is dict` == True, so swapped it out
7354371 [twneale] buffer --> memoryview I'm not super sure if this a valid change, but the 2.7 docs recommend using memoryview over buffer where possible, so hoping it'll work.
b69ccdf [twneale] Uses the pure python pickle._Pickler instead of c-extension _pickle.Pickler. It appears pyspark 2.7 uses the pure python pickler as well, so this shouldn't degrade pickling performance (?).
f40d925 [twneale] xrange --> range
e104215 [twneale] Replaces 2.7 types.InstsanceType with 3.4 `object`....could be horribly wrong depending on how types.InstanceType is used elsewhere in the package--see http://bugs.python.org/issue8206
79de9d0 [twneale] Replaces python2.7 `file` with 3.4 _io.TextIOWrapper
2adb42d [Josh Rosen] Fix up some import differences between Python 2 and 3
854be27 [Josh Rosen] Run `futurize` on Python code:
7c5b4ce [Josh Rosen] Remove Python 3 check in shell.py.
