From 9d69a2540d7ecda32d1dd2f9ae215ce174f9ca97 Mon Sep 17 00:00:00 2001
From: qaate47 <antoine.willerval@the-qa-company.com>
Date: Wed, 27 Jul 2022 11:27:36 +0200
Subject: [PATCH] update JLargeArrays to 1.7-SNAPSHOT and fix #167
 https://gitlab.com/visnow.org/JLargeArrays/-/packages

---
 hdt-java-core/pom.xml                         | 10 +++++++--
 .../compact/sequence/SequenceLog64Big.java    | 21 +++++++------------
 .../java/org/rdfhdt/hdt/util/io/IOUtil.java   |  2 +-
 .../hdt/compact/sequence/LargeArrayTest.java  | 20 ++++++++++++++++++
 4 files changed, 37 insertions(+), 16 deletions(-)
 create mode 100644 hdt-java-core/src/test/java/org/rdfhdt/hdt/compact/sequence/LargeArrayTest.java

diff --git a/hdt-java-core/pom.xml b/hdt-java-core/pom.xml
index 195a0de9..e457fead 100644
--- a/hdt-java-core/pom.xml
+++ b/hdt-java-core/pom.xml
@@ -49,8 +49,9 @@
             <artifactId>jena-arq</artifactId>
         </dependency>
         <dependency>
-            <groupId>pl.edu.icm</groupId>
+            <groupId>org.visnow</groupId>
             <artifactId>JLargeArrays</artifactId>
+            <version>1.7-20220624.150242-7</version>
         </dependency>
         <dependency>
             <groupId>pl.pragmatists</groupId>
@@ -63,7 +64,12 @@
 		    <version>1.6</version>
 		</dependency>		        
     </dependencies>
-
+    <repositories>
+        <repository>
+            <id>gitlab-maven</id>
+            <url>https://gitlab.com/api/v4/projects/375779/packages/maven</url>
+        </repository>
+    </repositories>
     <build>
         <plugins>
             <plugin>
diff --git a/hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64Big.java b/hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64Big.java
index 3121ea54..db536827 100644
--- a/hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64Big.java
+++ b/hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64Big.java
@@ -44,9 +44,8 @@
 import org.rdfhdt.hdt.util.crc.CRCInputStream;
 import org.rdfhdt.hdt.util.crc.CRCOutputStream;
 import org.rdfhdt.hdt.util.io.IOUtil;
-
-import pl.edu.icm.jlargearrays.LongLargeArray;
-import pl.edu.icm.jlargearrays.LargeArrayUtils;
+import org.visnow.jlargearrays.LargeArrayUtils;
+import org.visnow.jlargearrays.LongLargeArray;
 
 /**
  * @author mario.arias,Lyudmila Balakireva
@@ -55,8 +54,8 @@
 public class SequenceLog64Big implements DynamicSequence { 
 	private static final byte W = 64;
 	private static final int INDEX = 1073741824;
-	
-    LongLargeArray data;
+
+	LongLargeArray data;
 	private int numbits;
 	private long numentries=0;
 	private long maxvalue;
@@ -77,7 +76,7 @@ public SequenceLog64Big(int numbits, long capacity) {
 		long size = numWordsFor(numbits, capacity);
 		LongLargeArray.setMaxSizeOf32bitArray(SequenceLog64Big.INDEX);
 		
-		data = new LongLargeArray(Math.max((int)size,1)); 
+		data = new LongLargeArray(Math.max(size,1));
 	}
 	
 	public SequenceLog64Big(int numbits, long capacity, boolean initialize) {
@@ -158,11 +157,7 @@ private void resizeArray(long size) {
 		//data = Arrays.copyOf(data, size);
 		if(size > 0) {
 			LongLargeArray a = new LongLargeArray(size);
-			if (size < data.length()) {
-				LargeArrayUtils.arraycopy(data, 0, a, 0, size);
-			} else {
-				LargeArrayUtils.arraycopy(data, 0, a, 0, data.length());
-			}
+			LargeArrayUtils.arraycopy(data, 0, a, 0, Math.min(size, data.length()));
 			data = a;
 		}else{
 			this.numentries = 0;
@@ -182,7 +177,7 @@ public void add(Iterator<Long> elements) {
 		// Count and calculate number of bits needed per element.
 		while(elements.hasNext()) {
 			long val = elements.next();
-			max = val>max ? val : max;
+			max = Math.max(val, max);
 			numentries++;
 		}
 		
@@ -208,7 +203,7 @@ public void addIntegers(ArrayList<Integer> elements) {
 		// Count and calculate number of bits needed per element.
 		for (int i=0;i<elements.size();i++){
 			long val = elements.get(i).longValue();
-			max = val>max ? val : max;
+			max = Math.max(val, max);
 			numentries++;
 		}
 		
diff --git a/hdt-java-core/src/main/java/org/rdfhdt/hdt/util/io/IOUtil.java b/hdt-java-core/src/main/java/org/rdfhdt/hdt/util/io/IOUtil.java
index f4275796..bbd84658 100644
--- a/hdt-java-core/src/main/java/org/rdfhdt/hdt/util/io/IOUtil.java
+++ b/hdt-java-core/src/main/java/org/rdfhdt/hdt/util/io/IOUtil.java
@@ -30,7 +30,7 @@
 import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
 import org.rdfhdt.hdt.listener.ProgressListener;
 import org.rdfhdt.hdt.util.string.ByteStringUtil;
-import pl.edu.icm.jlargearrays.LargeArrayUtils;
+import org.visnow.jlargearrays.LargeArrayUtils;
 
 import java.io.*;
 import java.net.URL;
diff --git a/hdt-java-core/src/test/java/org/rdfhdt/hdt/compact/sequence/LargeArrayTest.java b/hdt-java-core/src/test/java/org/rdfhdt/hdt/compact/sequence/LargeArrayTest.java
new file mode 100644
index 00000000..4eeaee88
--- /dev/null
+++ b/hdt-java-core/src/test/java/org/rdfhdt/hdt/compact/sequence/LargeArrayTest.java
@@ -0,0 +1,20 @@
+package org.rdfhdt.hdt.compact.sequence;
+
+import org.junit.Test;
+import org.visnow.jlargearrays.LargeArray;
+import org.visnow.jlargearrays.LongLargeArray;
+
+public class LargeArrayTest {
+
+	@Test
+	public void allocationTest() {
+		int old = LargeArray.getMaxSizeOf32bitArray();
+		try {
+			LargeArray.setMaxSizeOf32bitArray(100);
+			long size = LargeArray.getMaxSizeOf32bitArray() + 2L;
+			new LongLargeArray(size);
+		} finally {
+			LargeArray.setMaxSizeOf32bitArray(old);
+		}
+	}
+}