Merge branch 'master' of github.com:apache/spark into sql-tests-refactor

Author: Andrew Or

mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAModel.scala

@@ -26,7 +26,7 @@ import org.json4s.jackson.JsonMethods._
 
 import org.apache.spark.SparkContext
 import org.apache.spark.annotation.Experimental
-import org.apache.spark.api.java.JavaPairRDD
+import org.apache.spark.api.java.{JavaPairRDD, JavaRDD}
 import org.apache.spark.graphx.{Edge, EdgeContext, Graph, VertexId}
 import org.apache.spark.mllib.linalg.{Matrices, Matrix, Vector, Vectors}
 import org.apache.spark.mllib.util.{Loader, Saveable}
@@ -228,6 +228,11 @@ class LocalLDAModel private[clustering] (
     docConcentration, topicConcentration, topicsMatrix.toBreeze.toDenseMatrix, gammaShape, k,
     vocabSize)
 
+  /** Java-friendly version of [[logLikelihood]] */
+  def logLikelihood(documents: JavaPairRDD[java.lang.Long, Vector]): Double = {
+    logLikelihood(documents.rdd.asInstanceOf[RDD[(Long, Vector)]])
+  }
+
   /**
    * Calculate an upper bound bound on perplexity.  (Lower is better.)
    * See Equation (16) in original Online LDA paper.
@@ -242,6 +247,11 @@ class LocalLDAModel private[clustering] (
     -logLikelihood(documents) / corpusTokenCount
   }
 
+  /** Java-friendly version of [[logPerplexity]] */
+  def logPerplexity(documents: JavaPairRDD[java.lang.Long, Vector]): Double = {
+    logPerplexity(documents.rdd.asInstanceOf[RDD[(Long, Vector)]])
+  }
+
   /**
    * Estimate the variational likelihood bound of from `documents`:
    *    log p(documents) >= E_q[log p(documents)] - E_q[log q(documents)]
@@ -341,8 +351,14 @@ class LocalLDAModel private[clustering] (
     }
   }
 
-}
+  /** Java-friendly version of [[topicDistributions]] */
+  def topicDistributions(
+      documents: JavaPairRDD[java.lang.Long, Vector]): JavaPairRDD[java.lang.Long, Vector] = {
+    val distributions = topicDistributions(documents.rdd.asInstanceOf[RDD[(Long, Vector)]])
+    JavaPairRDD.fromRDD(distributions.asInstanceOf[RDD[(java.lang.Long, Vector)]])
+  }
 
+}
 
 @Experimental
 object LocalLDAModel extends Loader[LocalLDAModel] {
@@ -657,6 +673,13 @@ class DistributedLDAModel private[clustering] (
     }
   }
 
+  /** Java-friendly version of [[topTopicsPerDocument]] */
+  def javaTopTopicsPerDocument(
+      k: Int): JavaRDD[(java.lang.Long, Array[Int], Array[java.lang.Double])] = {
+    val topics = topTopicsPerDocument(k)
+    topics.asInstanceOf[RDD[(java.lang.Long, Array[Int], Array[java.lang.Double])]].toJavaRDD()
+  }
+
   // TODO:
   // override def topicDistributions(documents: RDD[(Long, Vector)]): RDD[(Long, Vector)] = ???
 

mllib/src/main/scala/org/apache/spark/mllib/stat/Statistics.scala

@@ -20,7 +20,7 @@ package org.apache.spark.mllib.stat
 import scala.annotation.varargs
 
 import org.apache.spark.annotation.Experimental
-import org.apache.spark.api.java.JavaRDD
+import org.apache.spark.api.java.{JavaRDD, JavaDoubleRDD}
 import org.apache.spark.mllib.linalg.distributed.RowMatrix
 import org.apache.spark.mllib.linalg.{Matrix, Vector}
 import org.apache.spark.mllib.regression.LabeledPoint
@@ -178,6 +178,9 @@ object Statistics {
     ChiSqTest.chiSquaredFeatures(data)
   }
 
+  /** Java-friendly version of [[chiSqTest()]] */
+  def chiSqTest(data: JavaRDD[LabeledPoint]): Array[ChiSqTestResult] = chiSqTest(data.rdd)
+
   /**
    * Conduct the two-sided Kolmogorov-Smirnov (KS) test for data sampled from a
    * continuous distribution. By comparing the largest difference between the empirical cumulative
@@ -212,4 +215,15 @@ object Statistics {
     : KolmogorovSmirnovTestResult = {
     KolmogorovSmirnovTest.testOneSample(data, distName, params: _*)
   }
+
+  /** Java-friendly version of [[kolmogorovSmirnovTest()]] */
+  @varargs
+  def kolmogorovSmirnovTest(
+      data: JavaDoubleRDD,
+      distName: String,
+      params: java.lang.Double*): KolmogorovSmirnovTestResult = {
+    val javaParams = params.asInstanceOf[Seq[Double]]
+    KolmogorovSmirnovTest.testOneSample(data.rdd.asInstanceOf[RDD[Double]],
+      distName, javaParams: _*)
+  }
 }

mllib/src/test/java/org/apache/spark/mllib/clustering/JavaLDASuite.java

@@ -124,6 +124,10 @@ public Boolean call(Tuple2<Long, Vector> tuple2) {
         }
     });
     assertEquals(topicDistributions.count(), nonEmptyCorpus.count());
+
+    // Check: javaTopTopicsPerDocuments
+    JavaRDD<scala.Tuple3<java.lang.Long, int[], java.lang.Double[]>> topTopics =
+      model.javaTopTopicsPerDocument(3);
   }
 
   @Test
@@ -160,11 +164,31 @@ public void OnlineOptimizerCompatibility() {
     assertEquals(roundedLocalTopicSummary.length, k);
   }
 
+  @Test
+  public void localLdaMethods() {
+    JavaRDD<Tuple2<Long, Vector>> docs = sc.parallelize(toyData, 2);
+    JavaPairRDD<Long, Vector> pairedDocs = JavaPairRDD.fromJavaRDD(docs);
+
+    // check: topicDistributions
+    assertEquals(toyModel.topicDistributions(pairedDocs).count(), pairedDocs.count());
+
+    // check: logPerplexity
+    double logPerplexity = toyModel.logPerplexity(pairedDocs);
+
+    // check: logLikelihood.
+    ArrayList<Tuple2<Long, Vector>> docsSingleWord = new ArrayList<Tuple2<Long, Vector>>();
+    docsSingleWord.add(new Tuple2<Long, Vector>(Long.valueOf(0), Vectors.dense(1.0, 0.0, 0.0)));
+    JavaPairRDD<Long, Vector> single = JavaPairRDD.fromJavaRDD(sc.parallelize(docsSingleWord));
+    double logLikelihood = toyModel.logLikelihood(single);
+  }
+
   private static int tinyK = LDASuite$.MODULE$.tinyK();
   private static int tinyVocabSize = LDASuite$.MODULE$.tinyVocabSize();
   private static Matrix tinyTopics = LDASuite$.MODULE$.tinyTopics();
   private static Tuple2<int[], double[]>[] tinyTopicDescription =
       LDASuite$.MODULE$.tinyTopicDescription();
   private JavaPairRDD<Long, Vector> corpus;
+  private LocalLDAModel toyModel = LDASuite$.MODULE$.toyModel();
+  private ArrayList<Tuple2<Long, Vector>> toyData = LDASuite$.MODULE$.javaToyData();
 
 }

mllib/src/test/java/org/apache/spark/mllib/stat/JavaStatisticsSuite.java

@@ -27,7 +27,12 @@
 import static org.junit.Assert.assertEquals;
 
 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.ChiSqTestResult;
+import org.apache.spark.mllib.stat.test.KolmogorovSmirnovTestResult;
 
 public class JavaStatisticsSuite implements Serializable {
   private transient JavaSparkContext sc;
@@ -53,4 +58,21 @@ public void testCorr() {
     // Check default method
     assertEquals(corr1, corr2);
   }
+
+  @Test
+  public void kolmogorovSmirnovTest() {
+    JavaDoubleRDD data = sc.parallelizeDoubles(Lists.newArrayList(0.2, 1.0, -1.0, 2.0));
+    KolmogorovSmirnovTestResult testResult1 = Statistics.kolmogorovSmirnovTest(data, "norm");
+    KolmogorovSmirnovTestResult testResult2 = Statistics.kolmogorovSmirnovTest(
+      data, "norm", 0.0, 1.0);
+  }
+
+  @Test
+  public void chiSqTest() {
+    JavaRDD<LabeledPoint> data = sc.parallelize(Lists.newArrayList(
+      new LabeledPoint(0.0, Vectors.dense(0.1, 2.3)),
+      new LabeledPoint(1.0, Vectors.dense(1.5, 5.1)),
+      new LabeledPoint(0.0, Vectors.dense(2.4, 8.1))));
+    ChiSqTestResult[] testResults = Statistics.chiSqTest(data);
+  }
 }

mllib/src/test/scala/org/apache/spark/mllib/clustering/LDASuite.scala

@@ -17,6 +17,8 @@
 
 package org.apache.spark.mllib.clustering
 
+import java.util.{ArrayList => JArrayList}
+
 import breeze.linalg.{DenseMatrix => BDM, argtopk, max, argmax}
 
 import org.apache.spark.SparkFunSuite
@@ -575,6 +577,17 @@ private[clustering] object LDASuite {
     Vectors.sparse(6, Array(4, 5), Array(1, 1))
   ).zipWithIndex.map { case (wordCounts, docId) => (docId.toLong, wordCounts) }
 
+  /** Used in the Java Test Suite */
+  def javaToyData: JArrayList[(java.lang.Long, Vector)] = {
+    val javaData = new JArrayList[(java.lang.Long, Vector)]
+    var i = 0
+    while (i < toyData.size) {
+      javaData.add((toyData(i)._1, toyData(i)._2))
+      i += 1
+    }
+    javaData
+  }
+
   def toyModel: LocalLDAModel = {
     val k = 2
     val vocabSize = 6

python/pyspark/sql/context.py

@@ -39,7 +39,7 @@
 try:
     import pandas
     has_pandas = True
-except ImportError:
+except Exception:
     has_pandas = False
 
 __all__ = ["SQLContext", "HiveContext", "UDFRegistration"]