Merge pull request #381 from apache/SpotBugs_Fixes

Fixes problems found when running latest version of SpotBugs.

README.md

@@ -92,12 +92,23 @@ See the pom.xml file for test dependencies.
 
 Building and running tests using JDK 8 should not be a problem. 
 
-However, with JDK 9+, and Eclipse version up to and including 4.22.0 (2021-12), Eclipse fails to translate the required JPMS JVM arguments specified in the POM into the *.classpath* file, causing illegal reflection access errors.
+However, with JDK 9+, and Eclipse versions up to and including 4.22.0 (2021-12), Eclipse fails to translate the required JPMS JVM arguments specified in the POM compiler or surefire plugins into the *.classpath* file, causing illegal reflection access errors 
+[eclipse-m2e/m2e-core Bug 543631](https://github.com/eclipse-m2e/m2e-core/issues/129).
 
 There are two ways to fix this:
 
-#### Manually update *.classpath* file:
-Open the *.classpath* file in a text editor and insert the following *classpathentry* element (this assumes JDK11, change to suit) then *refresh*.:
+#### Method 1: Manually update *.classpath* file:
+Open the *.classpath* file in a text editor and find the following *classpathentry* element (this assumes JDK11, change to suit):
+
+```
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
+		<attributes>
+			<attribute name="module" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+```
+Then edit it as follows:
 
 ```
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
@@ -109,8 +120,9 @@ Open the *.classpath* file in a text editor and insert the following *classpathe
 		</attributes>
 	</classpathentry>
 ```
+Finally, *refresh*.
 
-#### Manually update *Module Dependencies*
+#### Method 2: Manually update *Module Dependencies*
 
 In Eclipse, open the project *Properties / Java Build Path / Module Dependencies ...*
 

src/main/java/org/apache/datasketches/Util.java

@@ -33,6 +33,7 @@
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.util.Objects;
 
 /**
  * Common utility functions.
@@ -846,13 +847,15 @@ public static boolean isLessThanUnsigned(final long n1, final long n2) {
    * @return the absolute path of the given resource file's shortName.
    */
   public static String getResourcePath(final String shortFileName) {
+    Objects.requireNonNull(shortFileName, "input parameter " + shortFileName + " cannot be null.");
     try {
       final URL url = Util.class.getClassLoader().getResource(shortFileName);
+      Objects.requireNonNull(url, "resource " + shortFileName + " could not be acquired.");
       final URI uri = url.toURI();
       //decodes any special characters
       final String path = uri.isAbsolute() ? Paths.get(uri).toAbsolutePath().toString() : uri.getPath();
       return path;
-    } catch (final NullPointerException | URISyntaxException e) {
+    } catch (final URISyntaxException e) {
       throw new SketchesArgumentException("Cannot find resource: " + shortFileName + LS + e);
     }
   }

src/main/java/org/apache/datasketches/fdt/FdtSketch.java

@@ -82,6 +82,23 @@ public FdtSketch(final double threshold, final double rse) {
     super(computeLgK(threshold, rse));
   }
 
+  /**
+   * Copy Constructor
+   * @param sketch the sketch to copy
+   */
+  public FdtSketch(final FdtSketch sketch) {
+    super(sketch);
+  }
+
+  /**
+   * @return a deep copy of this sketch
+   */
+  @SuppressWarnings("unchecked")
+  @Override
+  public FdtSketch copy() {
+    return new FdtSketch(this);
+  }
+
   /**
    * Update the sketch with the given string array tuple.
    * @param tuple the given string array tuple.

src/main/java/org/apache/datasketches/fdt/PostProcessor.java

@@ -58,7 +58,7 @@ public class PostProcessor {
    * @param sep the separator character
    */
   public PostProcessor(final FdtSketch sketch, final Group group, final char sep) {
-    this.sketch = sketch;
+    this.sketch = sketch.copy();
     this.sep = sep;
     final int numEntries = sketch.getRetainedEntries();
     mapArrSize = ceilingPowerOf2((int)(numEntries / 0.75));

src/main/java/org/apache/datasketches/quantiles/DirectUpdateDoublesSketch.java

@@ -42,6 +42,7 @@
 import static org.apache.datasketches.quantiles.Util.computeBitPattern;
 
 import org.apache.datasketches.Family;
+import org.apache.datasketches.SketchesArgumentException;
 import org.apache.datasketches.memory.MemoryRequestServer;
 import org.apache.datasketches.memory.WritableMemory;
 
@@ -250,6 +251,11 @@ private WritableMemory growCombinedMemBuffer(final int itemSpaceNeeded) {
     assert needBytes > memBytes;
 
     memReqSvr = (memReqSvr == null) ? mem_.getMemoryRequestServer() : memReqSvr;
+    if (memReqSvr == null) {
+      throw new SketchesArgumentException(
+          "A request for more memory has been denied, "
+          + "or a default MemoryRequestServer has not been provided. Must abort. ");
+    }
 
     final WritableMemory newMem = memReqSvr.request(mem_, needBytes);
 

src/main/java/org/apache/datasketches/theta/AnotBimpl.java

@@ -78,7 +78,6 @@ public void setA(final Sketch skA) {
 
     //process A
     hashArr_ = getHashArrA(skA);
-    hashArr_ = (hashArr_ == null) ? new long[0] : hashArr_;
     empty_ = false;
     thetaLong_ = skA.getThetaLong();
     curCount_ = hashArr_.length;
@@ -94,7 +93,6 @@ public void notB(final Sketch skB) {
 
     //process B
     hashArr_ = getResultHashArr(thetaLong_, curCount_, hashArr_, skB);
-    hashArr_ = (hashArr_ == null) ? new long[0] : hashArr_;
     curCount_ = hashArr_.length;
     empty_ = curCount_ == 0 && thetaLong_ == Long.MAX_VALUE;
   }
@@ -135,7 +133,7 @@ public CompactSketch aNotB(final Sketch skA, final Sketch skB, final boolean dst
 
     //process A
     final long[] hashArrA = getHashArrA(skA);
-    final int countA = (hashArrA == null) ? 0 : hashArrA.length;
+    final int countA = hashArrA.length;
 
 
     //process B

src/main/java/org/apache/datasketches/tuple/QuickSelectSketch.java

@@ -134,6 +134,24 @@ private enum Flags { IS_BIG_ENDIAN, IS_IN_SAMPLING_MODE, IS_EMPTY, HAS_ENTRIES,
     setRebuildThreshold();
   }
 
+  /**
+   * Copy constructor
+   * @param sketch the QuickSelectSketch to be copied.
+   */
+  QuickSelectSketch(final QuickSelectSketch<S> sketch) {
+    nomEntries_ = sketch.nomEntries_;
+    lgCurrentCapacity_ = sketch.lgCurrentCapacity_;
+    lgResizeFactor_ = sketch.lgResizeFactor_;
+    count_ = sketch.count_;
+    samplingProbability_ = sketch.samplingProbability_;
+    rebuildThreshold_ = sketch.rebuildThreshold_;
+    thetaLong_ = sketch.thetaLong_;
+    empty_ = sketch.empty_;
+    summaryFactory_ = sketch.summaryFactory_;
+    hashTable_ = sketch.hashTable_.clone();
+    summaryTable_ = Util.copySummaryArray(sketch.summaryTable_);
+  }
+
   /**
    * This is to create an instance of a QuickSelectSketch given a serialized form
    * @param mem Memory object with serialized QukckSelectSketch
@@ -205,6 +223,13 @@ private enum Flags { IS_BIG_ENDIAN, IS_IN_SAMPLING_MODE, IS_EMPTY, HAS_ENTRIES,
     setRebuildThreshold();
   }
 
+  /**
+   * @return a deep copy of this sketch
+   */
+  QuickSelectSketch<S> copy() {
+    return new QuickSelectSketch<S>(this);
+  }
+
   long[] getHashTable() {
     return hashTable_;
   }

src/main/java/org/apache/datasketches/tuple/UpdatableSketch.java

@@ -75,6 +75,23 @@ public UpdatableSketch(final Memory srcMem, final SummaryDeserializer<S> deseria
     super(srcMem, deserializer, summaryFactory);
   }
 
+  /**
+   * Copy Constructor
+   * @param sketch the sketch to copy
+   */
+  public UpdatableSketch(final UpdatableSketch<U, S> sketch) {
+    super(sketch);
+  }
+
+  /**
+   * @return a deep copy of this sketch
+   */
+  @SuppressWarnings("unchecked")
+  @Override
+  public UpdatableSketch<U,S> copy() {
+    return new UpdatableSketch<U,S>(this);
+  }
+
   /**
    * Updates this sketch with a long key and U value.
    * The value is passed to update() method of the Summary object associated with the key

src/main/java/org/apache/datasketches/tuple/Util.java

@@ -137,12 +137,20 @@ public static long stringArrHash(final String[] strArray) {
     return hashCharArr(s.toCharArray(), 0, s.length(), PRIME);
   }
 
+  /**
+   * Will copy compact summary arrays as well as hashed summary tables (with nulls).
+   * @param <S> type of summary
+   * @param summaryArr the given summary array or table
+   * @return the copy
+   */
   @SuppressWarnings("unchecked")
   public static <S extends Summary> S[] copySummaryArray(final S[] summaryArr) {
     final int len = summaryArr.length;
     final S[] tmpSummaryArr = newSummaryArray(summaryArr, len);
     for (int i = 0; i < len; i++) {
-      tmpSummaryArr[i] = (S) summaryArr[i].copy();
+      final S summary = summaryArr[i];
+      if (summary == null) { continue; }
+      tmpSummaryArr[i] = (S) summary.copy();
     }
     return tmpSummaryArr;
   }

src/main/java/org/apache/datasketches/tuple/strings/ArrayOfStringsSketch.java

@@ -73,6 +73,23 @@ public ArrayOfStringsSketch(final Memory mem) {
     super(mem, new ArrayOfStringsSummaryDeserializer(), new ArrayOfStringsSummaryFactory());
   }
 
+  /**
+   * Copy Constructor
+   * @param sketch the sketch to copy
+   */
+  public ArrayOfStringsSketch(final ArrayOfStringsSketch sketch) {
+    super(sketch);
+  }
+
+  /**
+   * @return a deep copy of this sketch
+   */
+  @SuppressWarnings("unchecked")
+  @Override
+  public ArrayOfStringsSketch copy() {
+    return new ArrayOfStringsSketch(this);
+  }
+
   /**
    * Updates the sketch with String arrays for both key and value.
    * @param strArrKey the given String array key

src/test/java/org/apache/datasketches/UtilTest.java

@@ -89,7 +89,7 @@ public void numTrailingOnes() {
   public void checkBoundsTest() {
     Util.checkBounds(999, 2, 1000);
   }
-  
+
   @Test
   public void checkIsPowerOf2() {
     Assert.assertEquals(isPowerOf2(0), false);
@@ -396,7 +396,7 @@ public void resourcefileExists() {
     assertTrue(file.exists());
   }
 
-  @Test(expectedExceptions = SketchesArgumentException.class)
+  @Test(expectedExceptions = NullPointerException.class)
   public void resourceFileNotFound() {
     final String shortFileName = "cpc-empty.sk";
     getResourceFile(shortFileName + "123");
@@ -409,7 +409,7 @@ public void resourceBytesCorrect() {
     assertTrue(bytes.length == 8);
   }
 
-  @Test(expectedExceptions = SketchesArgumentException.class)
+  @Test(expectedExceptions = NullPointerException.class)
   public void resourceBytesFileNotFound() {
     final String shortFileName = "cpc-empty.sk";
     getResourceBytes(shortFileName + "123");

src/test/java/org/apache/datasketches/fdt/FdtSketchTest.java

@@ -151,6 +151,17 @@ public void checkEstimatingPostProcessing() {
     }
   }
 
+  @Test
+  public void checkCopyCtor() {
+    final int lgK = 14;
+    final FdtSketch sk = new FdtSketch(lgK);
+
+    final String[] nodesArr = {"abc", "def" };
+    sk.update(nodesArr);
+    assertEquals(sk.getRetainedEntries(), 1);
+    final FdtSketch sk2 = sk.copy();
+    assertEquals(sk2.getRetainedEntries(), 1);
+  }
 
   @Test
   public void printlnTest() {

src/test/java/org/apache/datasketches/quantiles/DoublesSketchTest.java

@@ -152,15 +152,17 @@ public void directSketchShouldMoveOntoHeapEventually() {
 
   @Test
   public void directSketchShouldMoveOntoHeapEventually2() {
-    try (WritableHandle wdh = WritableMemory.allocateDirect(50)) {
+    int i = 0;
+    try (WritableHandle wdh =
+        WritableMemory.allocateDirect(50, ByteOrder.LITTLE_ENDIAN, new DefaultMemoryRequestServer())) {
       WritableMemory mem = wdh.getWritable();
       UpdateDoublesSketch sketch = DoublesSketch.builder().build(mem);
       Assert.assertTrue(sketch.isSameResource(mem));
-      for (int i = 0; i < 1000; i++) {
-        try {
+      for (; i < 1000; i++) {
+        if (sketch.isSameResource(mem)) {
           sketch.update(i);
-          if (sketch.isSameResource(mem)) { continue; }
-        } catch (NullPointerException e) {
+        } else {
+          System.out.println("MOVED at i = " + i);
           break;
         }
       }

src/test/java/org/apache/datasketches/sampling/VarOptItemsSketchTest.java

@@ -515,17 +515,9 @@ public void checkReset() {
     for (int i = 0; i < (2 * k); ++i) {
       sketch.update("a", 100.0 + i);
     }
-
     assertEquals(sketch.getN(), 2 * k);
     assertEquals(sketch.getHRegionCount(), 0);
     assertEquals(sketch.getRRegionCount(), k);
-    try {
-      sketch.getMark(0);
-      fail();
-    } catch (final NullPointerException e) {
-      // expected
-    }
-
     sketch.reset();
     assertEquals(sketch.getN(), 0);
     assertEquals(sketch.getHRegionCount(), 0);

src/test/java/org/apache/datasketches/theta/CornerCaseThetaSetOperationsTest.java

@@ -115,7 +115,7 @@ public void emptyDegenerate() {
   }
 
   @Test
-  public void EmptyEstimation() {
+  public void emptyEstimation() {
     UpdateSketch thetaA = getSketch(SkType.EMPTY, 0, 0);
     UpdateSketch thetaB = getSketch(SkType.ESTIMATION, LOWP, LT_LOWP_V);
     final double expectedIntersectTheta = 1.0;
@@ -301,7 +301,7 @@ public void estimationEstimation() {
   //=================================
 
   @Test
-  public void DegenerateEmpty() {
+  public void degenerateEmpty() {
     UpdateSketch thetaA = getSketch(SkType.DEGENERATE, LOWP, GT_LOWP_V); //entries = 0
     UpdateSketch thetaB = getSketch(SkType.EMPTY, 0, 0);
     final double expectedIntersectTheta = 1.0;
@@ -321,7 +321,7 @@ public void DegenerateEmpty() {
   }
 
   @Test
-  public void DegenerateExact() {
+  public void degenerateExact() {
     UpdateSketch thetaA = getSketch(SkType.DEGENERATE,  LOWP, GT_LOWP_V); //entries = 0
     UpdateSketch thetaB = getSketch(SkType.EXACT, 0, LT_LOWP_V);
     final double expectedIntersectTheta = LOWP_THETA;
@@ -341,7 +341,7 @@ public void DegenerateExact() {
   }
 
   @Test
-  public void DegenerateDegenerate() {
+  public void degenerateDegenerate() {
     UpdateSketch thetaA = getSketch(SkType.DEGENERATE, MIDP, GT_MIDP_V); //entries = 0
     UpdateSketch thetaB = getSketch(SkType.DEGENERATE, LOWP, GT_LOWP_V);
     final double expectedIntersectTheta = LOWP_THETA;
@@ -361,7 +361,7 @@ public void DegenerateDegenerate() {
   }
 
   @Test
-  public void DegenerateEstimation() {
+  public void degenerateEstimation() {
     UpdateSketch thetaA = getSketch(SkType.DEGENERATE, MIDP, GT_MIDP_V); //entries = 0
     UpdateSketch thetaB = getSketch(SkType.ESTIMATION, LOWP, LT_LOWP_V);
     final double expectedIntersectTheta = LOWP_THETA;

src/test/java/org/apache/datasketches/theta/HeapifyWrapSerVer1and2Test.java

@@ -378,7 +378,7 @@ public void checkWrapCompactSketchGivenDefaultSeed() {
     assertEquals(sv3cskResult.getEstimate(), sv3usk.getEstimate());
     assertEquals(sv3cskResult.getSeedHash(), seedHash);
     assertFalse(sv3cskResult.isDirect());
-    try { wh.close(); } catch (Exception e) {}
+    try { wh.close(); } catch (Exception e) {/* ignore */}
   }
 
   @Test