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From jkbrad...@apache.org
Subject spark git commit: [SPARK-11605][MLLIB] ML 1.6 QA: API: Java compatibility, docs
Date Tue, 08 Dec 2015 19:46:31 GMT
Repository: spark
Updated Branches:
  refs/heads/master 4bcb89494 -> 5cb469505


[SPARK-11605][MLLIB] ML 1.6 QA: API: Java compatibility, docs

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.


Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/5cb46950
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/5cb46950
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/5cb46950

Branch: refs/heads/master
Commit: 5cb4695051e3dac847b1ea14d62e54dcf672c31c
Parents: 4bcb894
Author: Yuhao Yang <hhbyyh@gmail.com>
Authored: Tue Dec 8 11:46:26 2015 -0800
Committer: Joseph K. Bradley <joseph@databricks.com>
Committed: Tue Dec 8 11:46:26 2015 -0800

----------------------------------------------------------------------
 .../examples/mllib/StreamingTestExample.scala   |  4 +-
 .../spark/mllib/stat/test/StreamingTest.scala   | 50 ++++++++++++++++----
 .../mllib/tree/model/treeEnsembleModels.scala   |  6 ++-
 .../spark/mllib/stat/JavaStatisticsSuite.java   | 38 +++++++++++++--
 .../spark/mllib/stat/StreamingTestSuite.scala   | 25 +++++-----
 5 files changed, 96 insertions(+), 27 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/spark/blob/5cb46950/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
----------------------------------------------------------------------
diff --git a/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
b/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
index b6677c6..49f5df3 100644
--- a/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
+++ b/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
@@ -18,7 +18,7 @@
 package org.apache.spark.examples.mllib
 
 import org.apache.spark.SparkConf
-import org.apache.spark.mllib.stat.test.StreamingTest
+import org.apache.spark.mllib.stat.test.{BinarySample, StreamingTest}
 import org.apache.spark.streaming.{Seconds, StreamingContext}
 import org.apache.spark.util.Utils
 
@@ -66,7 +66,7 @@ object StreamingTestExample {
 
     // $example on$
     val data = ssc.textFileStream(dataDir).map(line => line.split(",") match {
-      case Array(label, value) => (label.toBoolean, value.toDouble)
+      case Array(label, value) => BinarySample(label.toBoolean, value.toDouble)
     })
 
     val streamingTest = new StreamingTest()

http://git-wip-us.apache.org/repos/asf/spark/blob/5cb46950/mllib/src/main/scala/org/apache/spark/mllib/stat/test/StreamingTest.scala
----------------------------------------------------------------------
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/stat/test/StreamingTest.scala b/mllib/src/main/scala/org/apache/spark/mllib/stat/test/StreamingTest.scala
index 75c6a51..e990fe0 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/stat/test/StreamingTest.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/stat/test/StreamingTest.scala
@@ -17,13 +17,31 @@
 
 package org.apache.spark.mllib.stat.test
 
+import scala.beans.BeanInfo
+
 import org.apache.spark.Logging
 import org.apache.spark.annotation.{Experimental, Since}
-import org.apache.spark.rdd.RDD
+import org.apache.spark.streaming.api.java.JavaDStream
 import org.apache.spark.streaming.dstream.DStream
 import org.apache.spark.util.StatCounter
 
 /**
+ * Class that represents the group and value of a sample.
+ *
+ * @param isExperiment if the sample is of the experiment group.
+ * @param value numeric value of the observation.
+ */
+@Since("1.6.0")
+@BeanInfo
+case class BinarySample @Since("1.6.0") (
+    @Since("1.6.0") isExperiment: Boolean,
+    @Since("1.6.0") value: Double) {
+  override def toString: String = {
+    s"($isExperiment, $value)"
+  }
+}
+
+/**
  * :: Experimental ::
  * Performs online 2-sample significance testing for a stream of (Boolean, Double) pairs.
The
  * Boolean identifies which sample each observation comes from, and the Double is the numeric
value
@@ -83,13 +101,13 @@ class StreamingTest @Since("1.6.0") () extends Logging with Serializable
{
   /**
    * Register a [[DStream]] of values for significance testing.
    *
-   * @param data stream of (key,value) pairs where the key denotes group membership (true
=
-   *             experiment, false = control) and the value is the numerical metric to test
for
-   *             significance
+   * @param data stream of BinarySample(key,value) pairs where the key denotes group membership
+   *             (true = experiment, false = control) and the value is the numerical metric
to
+   *             test for significance
    * @return stream of significance testing results
    */
   @Since("1.6.0")
-  def registerStream(data: DStream[(Boolean, Double)]): DStream[StreamingTestResult] = {
+  def registerStream(data: DStream[BinarySample]): DStream[StreamingTestResult] = {
     val dataAfterPeacePeriod = dropPeacePeriod(data)
     val summarizedData = summarizeByKeyAndWindow(dataAfterPeacePeriod)
     val pairedSummaries = pairSummaries(summarizedData)
@@ -97,9 +115,22 @@ class StreamingTest @Since("1.6.0") () extends Logging with Serializable
{
     testMethod.doTest(pairedSummaries)
   }
 
+  /**
+   * Register a [[JavaDStream]] of values for significance testing.
+   *
+   * @param data stream of BinarySample(isExperiment,value) pairs where the isExperiment
denotes
+   *             group (true = experiment, false = control) and the value is the numerical
metric
+   *             to test for significance
+   * @return stream of significance testing results
+   */
+  @Since("1.6.0")
+  def registerStream(data: JavaDStream[BinarySample]): JavaDStream[StreamingTestResult] =
{
+    JavaDStream.fromDStream(registerStream(data.dstream))
+  }
+
   /** Drop all batches inside the peace period. */
   private[stat] def dropPeacePeriod(
-      data: DStream[(Boolean, Double)]): DStream[(Boolean, Double)] = {
+      data: DStream[BinarySample]): DStream[BinarySample] = {
     data.transform { (rdd, time) =>
       if (time.milliseconds > data.slideDuration.milliseconds * peacePeriod) {
         rdd
@@ -111,9 +142,10 @@ class StreamingTest @Since("1.6.0") () extends Logging with Serializable
{
 
   /** Compute summary statistics over each key and the specified test window size. */
   private[stat] def summarizeByKeyAndWindow(
-      data: DStream[(Boolean, Double)]): DStream[(Boolean, StatCounter)] = {
+      data: DStream[BinarySample]): DStream[(Boolean, StatCounter)] = {
+    val categoryValuePair = data.map(sample => (sample.isExperiment, sample.value))
     if (this.windowSize == 0) {
-      data.updateStateByKey[StatCounter](
+      categoryValuePair.updateStateByKey[StatCounter](
         (newValues: Seq[Double], oldSummary: Option[StatCounter]) => {
           val newSummary = oldSummary.getOrElse(new StatCounter())
           newSummary.merge(newValues)
@@ -121,7 +153,7 @@ class StreamingTest @Since("1.6.0") () extends Logging with Serializable
{
         })
     } else {
       val windowDuration = data.slideDuration * this.windowSize
-      data
+      categoryValuePair
         .groupByKeyAndWindow(windowDuration)
         .mapValues { values =>
           val summary = new StatCounter()

http://git-wip-us.apache.org/repos/asf/spark/blob/5cb46950/mllib/src/main/scala/org/apache/spark/mllib/tree/model/treeEnsembleModels.scala
----------------------------------------------------------------------
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/tree/model/treeEnsembleModels.scala
b/mllib/src/main/scala/org/apache/spark/mllib/tree/model/treeEnsembleModels.scala
index 3f427f0..feabcee 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/tree/model/treeEnsembleModels.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/tree/model/treeEnsembleModels.scala
@@ -25,7 +25,7 @@ import org.json4s.JsonDSL._
 import org.json4s.jackson.JsonMethods._
 
 import org.apache.spark.{Logging, SparkContext}
-import org.apache.spark.annotation.Since
+import org.apache.spark.annotation.{DeveloperApi, Since}
 import org.apache.spark.api.java.JavaRDD
 import org.apache.spark.mllib.linalg.Vector
 import org.apache.spark.mllib.regression.LabeledPoint
@@ -186,6 +186,7 @@ class GradientBoostedTreesModel @Since("1.2.0") (
 object GradientBoostedTreesModel extends Loader[GradientBoostedTreesModel] {
 
   /**
+   * :: DeveloperApi ::
    * Compute the initial predictions and errors for a dataset for the first
    * iteration of gradient boosting.
    * @param data: training data.
@@ -196,6 +197,7 @@ object GradientBoostedTreesModel extends Loader[GradientBoostedTreesModel]
{
    *         corresponding to every sample.
    */
   @Since("1.4.0")
+  @DeveloperApi
   def computeInitialPredictionAndError(
       data: RDD[LabeledPoint],
       initTreeWeight: Double,
@@ -209,6 +211,7 @@ object GradientBoostedTreesModel extends Loader[GradientBoostedTreesModel]
{
   }
 
   /**
+   * :: DeveloperApi ::
    * Update a zipped predictionError RDD
    * (as obtained with computeInitialPredictionAndError)
    * @param data: training data.
@@ -220,6 +223,7 @@ object GradientBoostedTreesModel extends Loader[GradientBoostedTreesModel]
{
    *         corresponding to each sample.
    */
   @Since("1.4.0")
+  @DeveloperApi
   def updatePredictionError(
     data: RDD[LabeledPoint],
     predictionAndError: RDD[(Double, Double)],

http://git-wip-us.apache.org/repos/asf/spark/blob/5cb46950/mllib/src/test/java/org/apache/spark/mllib/stat/JavaStatisticsSuite.java
----------------------------------------------------------------------
diff --git a/mllib/src/test/java/org/apache/spark/mllib/stat/JavaStatisticsSuite.java b/mllib/src/test/java/org/apache/spark/mllib/stat/JavaStatisticsSuite.java
index 4795809..66b2cea 100644
--- a/mllib/src/test/java/org/apache/spark/mllib/stat/JavaStatisticsSuite.java
+++ b/mllib/src/test/java/org/apache/spark/mllib/stat/JavaStatisticsSuite.java
@@ -18,34 +18,49 @@
 package org.apache.spark.mllib.stat;
 
 import java.io.Serializable;
-
 import java.util.Arrays;
+import java.util.List;
 
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
+import static org.apache.spark.streaming.JavaTestUtils.*;
 import static org.junit.Assert.assertEquals;
 
+import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaDoubleRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.mllib.linalg.Vectors;
 import org.apache.spark.mllib.regression.LabeledPoint;
+import org.apache.spark.mllib.stat.test.BinarySample;
 import org.apache.spark.mllib.stat.test.ChiSqTestResult;
 import org.apache.spark.mllib.stat.test.KolmogorovSmirnovTestResult;
+import org.apache.spark.mllib.stat.test.StreamingTest;
+import org.apache.spark.streaming.Duration;
+import org.apache.spark.streaming.api.java.JavaDStream;
+import org.apache.spark.streaming.api.java.JavaStreamingContext;
 
 public class JavaStatisticsSuite implements Serializable {
   private transient JavaSparkContext sc;
+  private transient JavaStreamingContext ssc;
 
   @Before
   public void setUp() {
-    sc = new JavaSparkContext("local", "JavaStatistics");
+    SparkConf conf = new SparkConf()
+      .setMaster("local[2]")
+      .setAppName("JavaStatistics")
+      .set("spark.streaming.clock", "org.apache.spark.util.ManualClock");
+    sc = new JavaSparkContext(conf);
+    ssc = new JavaStreamingContext(sc, new Duration(1000));
+    ssc.checkpoint("checkpoint");
   }
 
   @After
   public void tearDown() {
-    sc.stop();
+    ssc.stop();
+    ssc = null;
     sc = null;
   }
 
@@ -76,4 +91,21 @@ public class JavaStatisticsSuite implements Serializable {
       new LabeledPoint(0.0, Vectors.dense(2.4, 8.1))));
     ChiSqTestResult[] testResults = Statistics.chiSqTest(data);
   }
+
+  @Test
+  public void streamingTest() {
+    List<BinarySample> trainingBatch = Arrays.asList(
+      new BinarySample(true, 1.0),
+      new BinarySample(false, 2.0));
+    JavaDStream<BinarySample> training =
+      attachTestInputStream(ssc, Arrays.asList(trainingBatch, trainingBatch), 2);
+    int numBatches = 2;
+    StreamingTest model = new StreamingTest()
+      .setWindowSize(0)
+      .setPeacePeriod(0)
+      .setTestMethod("welch");
+    model.registerStream(training);
+    attachTestOutputStream(training);
+    runStreams(ssc, numBatches, numBatches);
+  }
 }

http://git-wip-us.apache.org/repos/asf/spark/blob/5cb46950/mllib/src/test/scala/org/apache/spark/mllib/stat/StreamingTestSuite.scala
----------------------------------------------------------------------
diff --git a/mllib/src/test/scala/org/apache/spark/mllib/stat/StreamingTestSuite.scala b/mllib/src/test/scala/org/apache/spark/mllib/stat/StreamingTestSuite.scala
index d3e9ef4..3c657c8 100644
--- a/mllib/src/test/scala/org/apache/spark/mllib/stat/StreamingTestSuite.scala
+++ b/mllib/src/test/scala/org/apache/spark/mllib/stat/StreamingTestSuite.scala
@@ -18,7 +18,8 @@
 package org.apache.spark.mllib.stat
 
 import org.apache.spark.SparkFunSuite
-import org.apache.spark.mllib.stat.test.{StreamingTest, StreamingTestResult, StudentTTest,
WelchTTest}
+import org.apache.spark.mllib.stat.test.{StreamingTest, StreamingTestResult, StudentTTest,
+  WelchTTest, BinarySample}
 import org.apache.spark.streaming.TestSuiteBase
 import org.apache.spark.streaming.dstream.DStream
 import org.apache.spark.util.StatCounter
@@ -48,7 +49,7 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
 
     // setup and run the model
     val ssc = setupStreams(
-      input, (inputDStream: DStream[(Boolean, Double)]) => model.registerStream(inputDStream))
+      input, (inputDStream: DStream[BinarySample]) => model.registerStream(inputDStream))
     val outputBatches = runStreams[StreamingTestResult](ssc, numBatches, numBatches)
 
     assert(outputBatches.flatten.forall(res =>
@@ -75,7 +76,7 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
 
     // setup and run the model
     val ssc = setupStreams(
-      input, (inputDStream: DStream[(Boolean, Double)]) => model.registerStream(inputDStream))
+      input, (inputDStream: DStream[BinarySample]) => model.registerStream(inputDStream))
     val outputBatches = runStreams[StreamingTestResult](ssc, numBatches, numBatches)
 
     assert(outputBatches.flatten.forall(res =>
@@ -102,7 +103,7 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
 
     // setup and run the model
     val ssc = setupStreams(
-      input, (inputDStream: DStream[(Boolean, Double)]) => model.registerStream(inputDStream))
+      input, (inputDStream: DStream[BinarySample]) => model.registerStream(inputDStream))
     val outputBatches = runStreams[StreamingTestResult](ssc, numBatches, numBatches)
 
 
@@ -130,7 +131,7 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
 
     // setup and run the model
     val ssc = setupStreams(
-      input, (inputDStream: DStream[(Boolean, Double)]) => model.registerStream(inputDStream))
+      input, (inputDStream: DStream[BinarySample]) => model.registerStream(inputDStream))
     val outputBatches = runStreams[StreamingTestResult](ssc, numBatches, numBatches)
 
     assert(outputBatches.flatten.forall(res =>
@@ -157,7 +158,7 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
     // setup and run the model
     val ssc = setupStreams(
       input,
-      (inputDStream: DStream[(Boolean, Double)]) => model.summarizeByKeyAndWindow(inputDStream))
+      (inputDStream: DStream[BinarySample]) => model.summarizeByKeyAndWindow(inputDStream))
     val outputBatches = runStreams[(Boolean, StatCounter)](ssc, numBatches, numBatches)
     val outputCounts = outputBatches.flatten.map(_._2.count)
 
@@ -190,7 +191,7 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
 
     // setup and run the model
     val ssc = setupStreams(
-      input, (inputDStream: DStream[(Boolean, Double)]) => model.dropPeacePeriod(inputDStream))
+      input, (inputDStream: DStream[BinarySample]) => model.dropPeacePeriod(inputDStream))
     val outputBatches = runStreams[(Boolean, Double)](ssc, numBatches, numBatches)
 
     assert(outputBatches.flatten.length == (numBatches - peacePeriod) * pointsPerBatch)
@@ -210,11 +211,11 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
       .setPeacePeriod(0)
 
     val input = generateTestData(numBatches, pointsPerBatch, meanA, stdevA, meanB, stdevB,
42)
-      .map(batch => batch.filter(_._1)) // only keep one test group
+      .map(batch => batch.filter(_.isExperiment)) // only keep one test group
 
     // setup and run the model
     val ssc = setupStreams(
-      input, (inputDStream: DStream[(Boolean, Double)]) => model.registerStream(inputDStream))
+      input, (inputDStream: DStream[BinarySample]) => model.registerStream(inputDStream))
     val outputBatches = runStreams[StreamingTestResult](ssc, numBatches, numBatches)
 
     assert(outputBatches.flatten.forall(result => (result.pValue - 1.0).abs < 0.001))
@@ -228,13 +229,13 @@ class StreamingTestSuite extends SparkFunSuite with TestSuiteBase {
       stdevA: Double,
       meanB: Double,
       stdevB: Double,
-      seed: Int): (IndexedSeq[IndexedSeq[(Boolean, Double)]]) = {
+      seed: Int): (IndexedSeq[IndexedSeq[BinarySample]]) = {
     val rand = new XORShiftRandom(seed)
     val numTrues = pointsPerBatch / 2
     val data = (0 until numBatches).map { i =>
-      (0 until numTrues).map { idx => (true, meanA + stdevA * rand.nextGaussian())} ++
+      (0 until numTrues).map { idx => BinarySample(true, meanA + stdevA * rand.nextGaussian())}
++
         (pointsPerBatch / 2 until pointsPerBatch).map { idx =>
-          (false, meanB + stdevB * rand.nextGaussian())
+          BinarySample(false, meanB + stdevB * rand.nextGaussian())
         }
     }
 


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