Fix set0 with LongArrayDisk

hdt-java-core/src/main/java/org/rdfhdt/hdt/util/disk/LongArrayDisk.java

@@ -20,6 +20,7 @@
 
 package org.rdfhdt.hdt.util.disk;
 
+import org.rdfhdt.hdt.util.BitUtil;
 import org.rdfhdt.hdt.util.io.CloseMappedByteBuffer;
 import org.rdfhdt.hdt.util.io.IOUtil;
 
@@ -139,9 +140,11 @@ public long length() {
         return size;
     }
 
-    public void set0(long start, long end) {
+    public void set0(long startIndex, long endIndex) {
+        long start = startIndex * 8L;
+        long end = endIndex * 8L;
+
         if (start >= end) {
-            // TODO: trim the file after end
             return;
         }
         int startBlock = (int) (start / MAPPING_SIZE);
@@ -166,15 +169,21 @@ public void set0(long start, long end) {
                 startBuffer = 0;
             }
             if (i == endBlock) {
-                endBuffer = (int) (end % MAPPING_SIZE);
+                if (end % MAPPING_SIZE == 0) {
+                    endBuffer = (int) MAPPING_SIZE;
+                } else {
+                    endBuffer = (int) (end % MAPPING_SIZE);
+                }
             } else {
                 endBuffer = capacity;
             }
 
-            int toWrite = (endBuffer - startBuffer) * 8;
+            assert endBuffer > startBuffer : "start after end " + startBuffer + " -> " + endBuffer;
+
+            int toWrite = endBuffer - startBuffer;
 
             while (toWrite > 0) {
-                mapping.position(startBuffer * 8);
+                mapping.position(startBuffer);
                 int w = Math.min(toWrite, zeros.length);
 
                 mapping.put(zeros, 0, w);
@@ -214,6 +223,9 @@ public void resize(long newSize) throws IOException {
             IOUtil.closeAll(this.mappings);
             this.mappings = null;
 
+            // resize the file to the new size
+            channel.truncate(sizeBit);
+
             for (int block = 0; block < blocks; block++) {
                 long sizeMapping;
                 if (block + 1 == blocks && sizeBit % MAPPING_SIZE != 0) {
@@ -223,6 +235,7 @@ public void resize(long newSize) throws IOException {
                 }
                 mappings[block] = IOUtil.mapChannel(location.toAbsolutePath().toString(), channel, FileChannel.MapMode.READ_WRITE, block * MAPPING_SIZE, sizeMapping);
             }
+
             // close previous mapping
             this.mappings = mappings;
 

hdt-java-core/src/test/java/org/rdfhdt/hdt/util/disk/LongArrayDiskTest.java

@@ -18,6 +18,7 @@
 import java.util.stream.IntStream;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 public class LongArrayDiskTest  extends AbstractMapMemoryTest {
 
@@ -103,5 +104,55 @@ public void resizeTest() throws IOException {
             assertEquals(array.get(3), 4);
         }
     }
+    @Test
+    public void largeResizeTest() throws IOException {
+        Path root = tempDir.getRoot().toPath();
+
+        long[] tests = {7, 5, 9, 2};
+
+        Path arrFile = root.resolve("arr");
+        try {
+            long endSize;
+            try (LongArrayDisk array = new LongArrayDisk(arrFile, 100)) {
+                // add check value after the resizes/loading
+                for (int i = 0; i < tests.length; i++) {
+                    array.set(i, tests[i]);
+                }
+
+                // resize from 10^3 to 10^9 to see the usage of multiple mappings in set0
+                for (int i = 10; i < 30; i++) {
+                    array.resize(1L << i);
+                }
+
+                // store the size
+                endSize = array.length();
+            }
+
+            assertEquals("array size and file size aren't matching!", endSize * 8L, Files.size(arrFile));
+
+            long endSize2;
 
+            try (LongArrayDisk array = new LongArrayDisk(arrFile, endSize, false)) {
+                // resize to a lower size to test the file truncating
+                array.resize(1L << 10);
+
+                // store the new size
+                endSize2 = array.length();
+            }
+
+            assertEquals("new array size and file size aren't matching!", endSize2 * 8L, Files.size(arrFile));
+
+            assertTrue("old array size isn't bigger than the new size, bad test?", endSize2 < endSize);
+
+            try (LongArrayDisk array = new LongArrayDisk(arrFile, endSize2, false)) {
+                // assert that the reloading/resizing didn't cancelled some values
+                for (int i = 0; i < tests.length; i++) {
+                    assertEquals(tests[i], array.get(i));
+                }
+            }
+        } finally {
+            Files.deleteIfExists(arrFile);
+        }
+
+    }
 }