SonarQube cleanup - bugs cleanup

Author: karlnicholas

src/main/java/org/hdf5javalib/examples/hdf5examples/HDF5Debug.java

@@ -49,7 +49,11 @@ private void run() {
 //            Path dirPath = Paths.get(Objects.requireNonNull(HDF5Debug.class.getClassLoader().getResource("HDF5Examples/h5ex_g_compact2.h5")).toURI());
 //            Path dirPath = Paths.get("c:/users/karln/Downloads/ATL03_20250302235544_11742607_007_01.h5");
 //            Path dirPath = Paths.get("c:/users/karln/Downloads/ATL03_20250302235544_11742607_006_01.h5");
-            Path dirPath = Paths.get("c:/users/karln/Downloads/SMAP_L1B_TB_57204_D_20251016T224815_R19240_001.h5");
+//            Path dirPath = Paths.get("c:/users/karln/Downloads/SMAP_L1B_TB_57204_D_20251016T224815_R19240_001.h5");
+//            Path dirPath = Paths.get("c:/users/karln/Downloads/ATL08_20250610011615_13002704_007_01.h5");
+            Path dirPath = Paths.get("c:/users/karln/Downloads/SMAP_L2_SM_P_55348_A_20250612T001323_R19240_001.h5");
+
+
             processFile(dirPath);
         } catch (Exception e) {
             throw new IllegalStateException(e);

src/main/java/org/hdf5javalib/hdffile/dataobjects/messages/HdfMessage.java

@@ -244,6 +244,7 @@ protected static HdfMessage parseHeaderMessage(MessageType type, int flags, byte
             case OBJECT_MODIFICATION_TIME_MESSAGE -> ObjectModificationTimeMessage.parseHeaderMessage(flags, data, hdfDataFile);
             case BTREE_K_VALUES_MESSAGE -> BTreeKValuesMessage.parseHeaderMessage(flags, data, hdfDataFile);
             case ATTRIBUTE_INFO_MESSAGE -> AttributeInfoMessage.parseHeaderMessage(flags, data, hdfDataFile);
+            case OBJECT_REFERENCE_COUNT_MESSAGE ->  ObjectReferenceCountMessage.parseHeaderMessage(flags, data, hdfDataFile);
             default -> throw new IllegalArgumentException("Unknown message type: " + type);
         };
     }

src/main/java/org/hdf5javalib/hdffile/dataobjects/messages/ObjectReferenceCountMessage.java

@@ -0,0 +1,64 @@
+package org.hdf5javalib.hdffile.dataobjects.messages;
+
+import org.hdf5javalib.hdfjava.HdfDataFile;
+
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.util.Arrays;
+
+public class ObjectReferenceCountMessage extends HdfMessage {
+    /**
+     * The version of the fill value message format.
+     */
+    private final int version;
+    private final long referenceCount;
+
+    /**
+     * Public constructor
+     * @param version Message version
+     * @param referenceCount referenceCount in Message
+     * @param sizeMessageData size of message data
+     * @param messageFlags messageflags
+     */
+    public ObjectReferenceCountMessage(int version, long referenceCount, int sizeMessageData, int messageFlags) {
+        super(MessageType.OBJECT_REFERENCE_COUNT_MESSAGE, sizeMessageData, messageFlags);
+        this.version = version;
+        this.referenceCount = referenceCount;
+    }
+
+    /**
+     * Parses a FillValueMessage from the provided data and file context.
+     *
+     * @param flags       message flags
+     * @param data        the byte array containing the message data
+     * @param hdfDataFile the HDF5 file context for additional resources
+     * @return a new FillValueMessage instance parsed from the data
+     */
+    public static HdfMessage parseHeaderMessage(int flags, byte[] data, HdfDataFile hdfDataFile) {
+        ByteBuffer buffer = ByteBuffer.wrap(data).order(ByteOrder.LITTLE_ENDIAN);
+
+        // Parse the first 4 bytes
+        int version = Byte.toUnsignedInt(buffer.get());
+        long referenceCount = Integer.toUnsignedLong(buffer.getInt());
+        return new ObjectReferenceCountMessage(version, referenceCount, flags, data.length);
+    }
+
+    /**
+     * Returns a string representation of this FillValueMessage.
+     *
+     * @return a string describing the message size, version, allocation times, and fill value details
+     */
+    @Override
+    public String toString() {
+        return "ObjectReferenceCountMessage(" + (getSizeMessageData() + HDF_MESSAGE_PREAMBLE_SIZE) + "){" +
+                "version=" + version +
+                ", referenceCount=" + referenceCount +
+                '}';
+    }
+
+
+    @Override
+    public void writeMessageToByteBuffer(ByteBuffer buffer) {
+        // not implemented
+    }
+}