SonarQube fixes.

karlnicholas · karlnicholas · commit 31b685399e41 · 2025-07-26T10:48:03.000-04:00
diff --git a/src/main/java/org/hdf5javalib/dataclass/HdfReference.java b/src/main/java/org/hdf5javalib/dataclass/HdfReference.java
@@ -1,7 +1,6 @@
 package org.hdf5javalib.dataclass;
 
 import org.hdf5javalib.datatype.ReferenceDatatype;
-import org.hdf5javalib.hdffile.infrastructure.HdfGlobalHeap;
 
 import java.nio.ByteBuffer;
 import java.util.Arrays;
@@ -21,14 +20,6 @@ public HdfReference(byte[] bytes, ReferenceDatatype datatype) {
         this.datatype = datatype;
     }
 
-    public HdfReference(byte[] bytes, ReferenceDatatype datatype, HdfGlobalHeap globalHeap) {
-        if (bytes == null || bytes.length == 0) throw new IllegalArgumentException("Bytes cannot be null or empty");
-        if (datatype == null) throw new IllegalArgumentException("Datatype cannot be null");
-        this.bytes = bytes;
-        this.datatype = datatype;
-    }
-
-
     public byte[] getBytes() {
         return bytes.clone();
     }
@@ -40,10 +31,6 @@ public ReferenceDatatype getDatatype() {
     @Override
     public String toString() {
         return datatype.toString(bytes);
-//        StringBuilder sb = new StringBuilder();
-//        for (byte b : bytes) sb.append(String.format("%02X", b));
-//        String base = "Reference[" + ReferenceDatatype.getReferenceType(datatype.getClassBitField()).getDescription() + "]=" + sb;
-//        return base;
     }
 
     @Override
diff --git a/src/main/java/org/hdf5javalib/dataclass/reference/HdfAttributeReference.java b/src/main/java/org/hdf5javalib/dataclass/reference/HdfAttributeReference.java
@@ -1,7 +1,6 @@
 package org.hdf5javalib.dataclass.reference;
 
 import org.hdf5javalib.datatype.ReferenceDatatype;
-import org.hdf5javalib.hdfjava.HdfDataFile;
 import org.hdf5javalib.utils.HdfDataHolder;
 
 public class HdfAttributeReference implements HdfReferenceInstance {
diff --git a/src/main/java/org/hdf5javalib/dataclass/reference/HdfDatasetRegionReference.java b/src/main/java/org/hdf5javalib/dataclass/reference/HdfDatasetRegionReference.java
@@ -5,7 +5,6 @@
 import org.hdf5javalib.datatype.ReferenceDatatype;
 import org.hdf5javalib.hdfjava.HdfBTree;
 import org.hdf5javalib.hdfjava.HdfBTreeNode;
-import org.hdf5javalib.hdfjava.HdfDataFile;
 import org.hdf5javalib.hdfjava.HdfDataObject;
 import org.hdf5javalib.utils.HdfDataHolder;
 
diff --git a/src/main/java/org/hdf5javalib/dataclass/reference/HdfObjectReference.java b/src/main/java/org/hdf5javalib/dataclass/reference/HdfObjectReference.java
@@ -8,7 +8,6 @@
 import org.hdf5javalib.hdffile.metadata.HdfSuperblock;
 import org.hdf5javalib.hdfjava.HdfBTree;
 import org.hdf5javalib.hdfjava.HdfBTreeNode;
-import org.hdf5javalib.hdfjava.HdfDataFile;
 import org.hdf5javalib.hdfjava.HdfDataObject;
 import org.hdf5javalib.utils.HdfDataHolder;
 
diff --git a/src/main/java/org/hdf5javalib/dataclass/reference/HdfReferenceInstance.java b/src/main/java/org/hdf5javalib/dataclass/reference/HdfReferenceInstance.java
@@ -1,6 +1,5 @@
 package org.hdf5javalib.dataclass.reference;
 
-import org.hdf5javalib.hdfjava.HdfDataFile;
 import org.hdf5javalib.utils.HdfDataHolder;
 
 public interface HdfReferenceInstance {
diff --git a/src/main/java/org/hdf5javalib/datatype/ArrayDatatype.java b/src/main/java/org/hdf5javalib/datatype/ArrayDatatype.java
@@ -211,17 +211,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as ArrayDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || datatype.requiresGlobalHeap(required);
-    }
-
     /**
      * Converts the byte array to a string representation of the array elements.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/BitFieldDatatype.java b/src/main/java/org/hdf5javalib/datatype/BitFieldDatatype.java
@@ -156,17 +156,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as BitFieldDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || false;
-    }
-
     /**
      * Checks if the bitfield uses big-endian byte order.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/CompoundDatatype.java b/src/main/java/org/hdf5javalib/datatype/CompoundDatatype.java
@@ -322,20 +322,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required for any member, false otherwise
-     * @return true if any member requires a global heap, false otherwise
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        for (CompoundMemberDatatype member : members) {
-            required = member.requiresGlobalHeap(required);
-        }
-        return required;
-    }
-
     /**
      * Converts byte data to a POJO or record instance of the specified class using reflection.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/CompoundMemberDatatype.java b/src/main/java/org/hdf5javalib/datatype/CompoundMemberDatatype.java
@@ -281,17 +281,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         return datatype.getInstance(clazz, bytes);
     }
 
-    /**
-     * Indicates whether a global heap is required for the member's base datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return true if the base datatype requires a global heap, false otherwise
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return datatype.requiresGlobalHeap(required);
-    }
-
     /**
      * Sets the global heap for the member's base datatype.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/Datatype.java b/src/main/java/org/hdf5javalib/datatype/Datatype.java
@@ -65,14 +65,6 @@ public interface Datatype {
      */
     <T> T getInstance(Class<T> clazz, byte[] bytes);
 
-    /**
-     * Indicates whether the datatype requires a global heap.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return true if the datatype requires a global heap, false otherwise
-     */
-    boolean requiresGlobalHeap(boolean required);
-
     /**
      * Sets the global heap for the datatype.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/EnumDatatype.java b/src/main/java/org/hdf5javalib/datatype/EnumDatatype.java
@@ -221,17 +221,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as EnumDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || datatype.requiresGlobalHeap(required);
-    }
-
     /**
      * Converts the byte array to the corresponding enumeration name.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/FixedPointDatatype.java b/src/main/java/org/hdf5javalib/datatype/FixedPointDatatype.java
@@ -469,17 +469,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as FixedPointDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || false;
-    }
-
     /**
      * Sets the global heap for this datatype (no-op for FixedPointDatatype).
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/FloatingPointDatatype.java b/src/main/java/org/hdf5javalib/datatype/FloatingPointDatatype.java
@@ -217,17 +217,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as FloatingPointDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || false;
-    }
-
     /**
      * Converts the byte array to a Float value.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/OpaqueDatatype.java b/src/main/java/org/hdf5javalib/datatype/OpaqueDatatype.java
@@ -192,17 +192,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as OpaqueDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || false;
-    }
-
     /**
      * Converts the byte array to a hexadecimal string representation.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/ReferenceDatatype.java b/src/main/java/org/hdf5javalib/datatype/ReferenceDatatype.java
@@ -132,12 +132,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        ReferenceType type = getReferenceType(classBitField);
-        return required || type == ReferenceType.DATASET_REGION1 || type == ReferenceType.DATASET_REGION2;
-    }
-
     /**
      * Retrieves the reference type value from the class bit field.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/StringDatatype.java b/src/main/java/org/hdf5javalib/datatype/StringDatatype.java
@@ -132,17 +132,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as StringDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || false;
-    }
-
     /**
      * Converts the byte array to a string, handling padding and termination based on the padding type.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/TimeDatatype.java b/src/main/java/org/hdf5javalib/datatype/TimeDatatype.java
@@ -144,17 +144,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return false, as TimeDatatype does not require a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required;
-    }
-
     /**
      * Checks if the time datatype uses big-endian byte order.
      *
diff --git a/src/main/java/org/hdf5javalib/datatype/VariableLengthDatatype.java b/src/main/java/org/hdf5javalib/datatype/VariableLengthDatatype.java
@@ -151,17 +151,6 @@ public <T> T getInstance(Class<T> clazz, byte[] bytes) {
         throw new UnsupportedOperationException("Unknown type: " + clazz);
     }
 
-    /**
-     * Indicates whether a global heap is required for this datatype.
-     *
-     * @param required true if the global heap is required, false otherwise
-     * @return true, as VariableLengthDatatype requires a global heap
-     */
-    @Override
-    public boolean requiresGlobalHeap(boolean required) {
-        return required || true;
-    }
-
     /**
      * Converts the byte array to a string representation, handling strings or sequences.
      *
diff --git a/src/main/java/org/hdf5javalib/package-info.java b/src/main/java/org/hdf5javalib/package-info.java
@@ -0,0 +1,21 @@
+/**
+ * A pure Java library for reading HDF5 files, providing support for datasets in the root group, including compound datasets,
+ * scalars, vectors, and multi-dimensional datasets. It handles various datatypes such as fixed-point, floating-point, and strings,
+ * and is compatible with HDF5 files generated by the C++ HDF5 library.
+ *
+ * <p>This package enables Java developers to access and manipulate HDF5 data without requiring external native libraries,
+ * making it suitable for scientific computing, data analysis, and applications dealing with large hierarchical datasets.</p>
+ *
+ * <p>Key features include:
+ * <ul>
+ *   <li>Reading of root-group datasets with robust datatype support.</li>
+ *   <li>No external dependencies beyond Java 17 or higher.</li>
+ *   <li>Maven integration for easy inclusion in projects.</li>
+ * </ul>
+ * </p>
+ *
+ * <p>For detailed usage examples and reading capabilities, refer to the project documentation.</p>
+ *
+ * @since 0.1.3
+ */
+package org.hdf5javalib;
diff --git a/src/test/java/org/hdf5javalib/examples/h5ex_t/H5exTReadTest.java b/src/test/java/org/hdf5javalib/examples/h5ex_t/H5exTReadTest.java
@@ -1,6 +1,9 @@
 package org.hdf5javalib.examples.h5ex_t;
 
-import org.hdf5javalib.dataclass.*;
+import org.hdf5javalib.dataclass.HdfCompound;
+import org.hdf5javalib.dataclass.HdfCompoundMember;
+import org.hdf5javalib.dataclass.HdfData;
+import org.hdf5javalib.dataclass.HdfVariableLength;
 import org.hdf5javalib.dataclass.reference.HdfReferenceInstance;
 import org.hdf5javalib.datasource.TypedDataSource;
 import org.hdf5javalib.datatype.*;
diff --git a/src/test/java/org/hdf5javalib/examples/read/CompoundReadTest.java b/src/test/java/org/hdf5javalib/examples/read/CompoundReadTest.java
@@ -3,14 +3,13 @@
 import org.hdf5javalib.dataclass.HdfCompound;
 import org.hdf5javalib.dataclass.HdfData;
 import org.hdf5javalib.datasource.TypedDataSource;
+import org.hdf5javalib.datatype.CompoundDatatype;
 import org.hdf5javalib.examples.ResourceLoader;
 import org.hdf5javalib.hdfjava.HdfDataset;
-import org.hdf5javalib.datatype.CompoundDatatype;
 import org.hdf5javalib.hdfjava.HdfFileReader;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
-import java.io.IOException;
 import java.math.BigDecimal;
 import java.math.BigInteger;
 import java.nio.ByteBuffer;
diff --git a/src/test/java/org/hdf5javalib/examples/read/SeparateTypesReadTest.java b/src/test/java/org/hdf5javalib/examples/read/SeparateTypesReadTest.java
@@ -15,7 +15,8 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertArrayEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class SeparateTypesReadTest {
 
