Updates for v2 arch

Author: karlnicholas

src/main/java/org/hdf5javalib/dataclass/reference/HdfObjectReference.java

@@ -113,6 +113,9 @@ public HdfObjectReference(byte[] bytes, ReferenceDatatype dt, boolean external)
 //            } else {
 //                objectPathString = hdfDataObject.getObjectPath();
 //            }
+            if ( hdfDataObject == null ) {
+                throw new IllegalStateException("DataObject for reference not found for: " + localHdfFixedPoint);
+            }
             String objectPathString = hdfDataObject.getObjectPath();
 
             this.hdfDataHolder = HdfDataHolder.ofScalar(

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

@@ -47,8 +47,8 @@ private void run() {
             // List all .h5 files in HDF5Examples resources directory
             // ATL03_20250302235544_11742607_006_01
 //            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/ATL03_20250302235544_11742607_007_01.h5");
+            Path dirPath = Paths.get("c:/users/karln/Downloads/ATL03_20250302235544_11742607_006_01.h5");
             processFile(dirPath);
         } catch (Exception e) {
             throw new IllegalStateException(e);

src/main/java/org/hdf5javalib/hdffile/dataobjects/HdfObjectHeaderPrefix.java

@@ -26,9 +26,10 @@ public abstract class HdfObjectHeaderPrefix {
     protected HdfObjectHeaderPrefix(
             List<HdfMessage> headerMessages,
             HdfFixedPoint offset,
-            long objectHeaderSize,
-            HdfDataFile hdfDataFile,
-            int OBJECT_HREADER_PREFIX_HEADER_SIZE
+            long objectHeaderSize
+//            ,
+//            HdfDataFile hdfDataFile,
+//            int OBJECT_HREADER_PREFIX_HEADER_SIZE
     ) {
         this.headerMessages = headerMessages;
         this.objectHeaderSize = objectHeaderSize;

src/main/java/org/hdf5javalib/hdffile/dataobjects/HdfObjectHeaderPrefixV1.java

@@ -47,7 +47,9 @@ public class HdfObjectHeaderPrefixV1 extends HdfObjectHeaderPrefix {
     public HdfObjectHeaderPrefixV1(int version, long objectReferenceCount, long objectHeaderSize, List<HdfMessage> headerMessages,
                                    HdfDataFile hdfDataFile, HdfFixedPoint offset
     ) {
-        super(headerMessages, offset, objectHeaderSize, hdfDataFile, OBJECT_HEADER_PREFIX_HEADER_SIZE);
+        super(headerMessages, offset, objectHeaderSize
+//                , hdfDataFile, OBJECT_HEADER_PREFIX_HEADER_SIZE
+        );
         this.version = version;
         this.objectReferenceCount = objectReferenceCount;
     }

src/main/java/org/hdf5javalib/hdffile/dataobjects/HdfObjectHeaderPrefixV2.java

@@ -37,7 +37,9 @@ public HdfObjectHeaderPrefixV2(
     ) {
         super(headerMessages,
                 HdfWriteUtils.hdfFixedPointFromValue(offset, hdfDataFile.getSuperblock().getFixedPointDatatypeForLength()),
-            objectHeaderSize, hdfDataFile, (int) prefixSize);
+            objectHeaderSize
+//                , hdfDataFile, (int) prefixSize
+        );
         this.flags = flags;
         this.checksum = checksum;
         this.accessTime = accessTime;

src/main/java/org/hdf5javalib/hdfjava/HdfFileReader.java

@@ -27,6 +27,7 @@
 import java.time.Instant;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicReference;
+import java.util.function.Function;
 
 import static org.hdf5javalib.datatype.FixedPointDatatype.BIT_MULTIPLIER;
 import static org.hdf5javalib.hdffile.dataobjects.HdfObjectHeaderPrefixV1.*;
@@ -624,7 +625,9 @@ private static HdfBTreeV1ForGroup readFromSeekableByteChannelRecursiveForGroups(
         for (int i = 0; i < entriesUsed; i++) {
             HdfFixedPoint childPointer = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, entriesBuffer);
             HdfFixedPoint key = HdfReadUtils.readHdfFixedPointFromBuffer(hdfLength, entriesBuffer);
+            long filePosAfterEntriesBlock = fileChannel.position();
             long childAddress = childPointer.getInstance(Long.class);
+            fileChannel.position(childAddress);
 
             HdfGroupForGroupBTreeEntry entry;
             if (nodeLevel == 1) {
@@ -636,6 +639,7 @@ private static HdfBTreeV1ForGroup readFromSeekableByteChannelRecursiveForGroups(
                 HdfGroupSymbolTableNode child = readSnodFromSeekableByteChannel(fileChannel, hdfDataFile);
                 entry = new HdfGroupForGroupBTreeEntry(key, childPointer, null, child); // Assuming entry constructor accepts Object for last param
             }
+            fileChannel.position(filePosAfterEntriesBlock);
             entries.add(entry);
         }
         return currentNode;
@@ -989,13 +993,15 @@ protected static HdfObjectHeaderPrefixV1 readObjectHeader(
                 HdfMessage.readMessagesFromByteBuffer(fileChannel, objectHeaderSize, hdfDataFile, HdfMessage.V1_OBJECT_HEADER_READ_PREFIX)
         );
 
-        for (HdfMessage hdfMessage : dataObjectHeaderMessages) {
-            if (hdfMessage instanceof ObjectHeaderContinuationMessage objectHeaderContinuationMessage) {
-                dataObjectHeaderMessages.addAll(HdfMessage.parseContinuationMessage(fileChannel, objectHeaderContinuationMessage, hdfDataFile, HdfMessage.V1_OBJECT_HEADER_READ_PREFIX));
-
-                break;
-            }
-        }
+//        for (HdfMessage hdfMessage : dataObjectHeaderMessages) {
+//            if (hdfMessage instanceof ObjectHeaderContinuationMessage objectHeaderContinuationMessage) {
+//                dataObjectHeaderMessages.addAll(HdfMessage.parseContinuationMessage(fileChannel, objectHeaderContinuationMessage, hdfDataFile, HdfMessage.V1_OBJECT_HEADER_READ_PREFIX));
+//
+//                break;
+//            }
+//        }
+        // --- 6. Handle Continuation Messages ---
+        parseContinuationMessages(fileChannel, HdfMessage.V1_OBJECT_HEADER_READ_PREFIX, dataObjectHeaderMessages, hdfDataFile);
 
         // Create the instance
         return new HdfObjectHeaderPrefixV1(
@@ -1096,15 +1102,17 @@ static HdfObjectHeaderPrefixV2 readV2ObjectHeader(SeekableByteChannel fileChanne
         // Here you would typically verify the checksum against the header chunk data.
 
         // --- 6. Handle Continuation Messages ---
-        parseContinuationMessages(fileChannel, flags, dataObjectHeaderMessages, hdfDataFile);
+        Function<ByteBuffer, HdfMessage.OBJECT_HEADER_PREFIX> prefixReader = (flags & 0b00000100) > 0 ? HdfMessage.V2OBJECT_HEADER_READ_PREFIX_WITHORDER : HdfMessage.V2_OBJECT_HEADER_READ_PREFIX;
+;
+        parseContinuationMessages(fileChannel, prefixReader, dataObjectHeaderMessages, hdfDataFile);
         // --- 7. Create the V2 Header Prefix Instance ---
         return new HdfObjectHeaderPrefixV2(flags, sizeOfChunk0, checksum,
                 accessTime, modificationTime, changeTime, birthTime,
                 maxCompactAttributes, minDenseAttributes,
                 dataObjectHeaderMessages, hdfDataFile, objectHeaderAddress, prefixSize);
     }
 
-    private static void parseContinuationMessages(SeekableByteChannel fileChannel, int flags, List<HdfMessage> currentMessages, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
+    private static void parseContinuationMessages(SeekableByteChannel fileChannel, Function<ByteBuffer, HdfMessage.OBJECT_HEADER_PREFIX> prefixReader, List<HdfMessage> currentMessages, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
         // Use a queue to process messages iteratively instead of recursively
         Queue<HdfMessage> messageQueue = new LinkedList<>(currentMessages);
 
@@ -1116,7 +1124,7 @@ private static void parseContinuationMessages(SeekableByteChannel fileChannel, i
                         fileChannel,
                         objectHeaderContinuationMessage,
                         hdfDataFile,
-                        (flags & 0b00000100) > 0 ? HdfMessage.V2OBJECT_HEADER_READ_PREFIX_WITHORDER : HdfMessage.V2_OBJECT_HEADER_READ_PREFIX
+                        prefixReader
                 );
                 // Add new messages to the queue for further processing
                 messageQueue.addAll(newContinuationMessages);

src/test/java/org/hdf5javalib/examples/read/CompoundReadTest.java

@@ -92,7 +92,7 @@ static void registerCustomConverter() {
         CompoundDatatype.addConverter(MonitoringData.class, (bytes, datatype) -> {
             MonitoringData monitoringData = new MonitoringData();
             for (CompoundMemberDatatype member : datatype.getMembers()) {
-                byte[] memberBytes = Arrays.copyOfRange(bytes, member.getOffset(), member.getOffset() + member.getSize());
+                byte[] memberBytes = Arrays.copyOfRange(bytes, Math.toIntExact(member.getOffset()), Math.toIntExact(member.getOffset() + member.getSize()));
                 switch (member.getName()) {
                     case "recordId" -> {
                         long recordId = member.getInstance(Long.class, memberBytes);