Develop HDFFV-11310 (#1811)

* Rework java vl check in read/write. Handle old refs in h5dump

* Committing clang-format changes

* Java changes allow default VL reads

* Fix JNI utility for old refs

* HDFFV-11310 - implement vlen read/write for atomic types.

* format check fix

* Mostly format fixes

* More format issues

* Two format changes

* Use JNI names for sizeof

* format change

* fix size typo

* Change to older method to initialize list

* remove unused var

* format fix

* switch writeVL functions to use datatype instead of java type

* Add VL option to generic read/write check

* Correct function name typo

* Add JIRA issue

* Correct note to match change in code.

* HDFFV-11318 add VL references as byte arrays

* Add release note and format changes

* Another format update

* Fix unreleased allocations

* Fix format

* format correction

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

3 files changed, 68 insertions, 26 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 905a092..12e5f87 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1242,6 +1242,10 @@ public class H5 implements java.io.Serializable {
             log.trace("H5Aread_string type");
             status = H5Aread_string(attr_id, mem_type_id, (String[])obj);
         }
+        else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
+            log.trace("H5AreadVL type");
+            status = H5AreadVL(attr_id, mem_type_id, (Object[])obj);
+        }
         else {
             // Create a data buffer to hold the data into a Java Array
             HDFArray theArray = new HDFArray(obj);
@@ -1788,6 +1792,10 @@ public class H5 implements java.io.Serializable {
             log.trace("H5Dwrite_string type");
             status = H5Awrite_string(attr_id, mem_type_id, (String[])obj);
         }
+        else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
+            log.trace("H5AwriteVL type");
+            status = H5AwriteVL(attr_id, mem_type_id, (Object[])obj);
+        }
         else {
             HDFArray theArray = new HDFArray(obj);
             byte[] buf        = theArray.byteify();
@@ -2772,6 +2780,11 @@ public class H5 implements java.io.Serializable {
             status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
                                     (String[])obj);
         }
+        else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
+            log.trace("H5DreadVL type");
+            status =
+                H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[])obj);
+        }
         else {
             // Create a data buffer to hold the data into a Java Array
             HDFArray theArray = new HDFArray(obj);
@@ -3450,6 +3463,11 @@ public class H5 implements java.io.Serializable {
             status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
                                      (String[])obj);
         }
+        else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
+            log.trace("H5DwriteVL type");
+            status = H5DwriteVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
+                                (Object[])obj);
+        }
         else {
             HDFArray theArray = new HDFArray(obj);
             byte[] buf        = theArray.byteify();
@@ -9356,9 +9374,8 @@ public class H5 implements java.io.Serializable {
         byte[] buf        = theArray.emptyBytes();
 
         int status = H5Pget_fill_value(plist_id, type_id, buf);
-        if (status >= 0) {
+        if (status >= 0)
             obj = theArray.arrayify(buf);
-        }
 
         return status;
     }
@@ -11018,8 +11035,6 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Rdestroy(byte[] ref_ptr)
         throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
-    // Info //
-
     /**
      * H5Rget_type retrieves the type of a reference.
      *
@@ -11076,8 +11091,6 @@ public class H5 implements java.io.Serializable {
     public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
         throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
-    // Dereference //
-
     /**
      * H5Ropen_object opens that object and returns an identifier.
      * The object opened with this function should be closed when it is no longer needed
@@ -11224,8 +11237,6 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
         throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
-    // Get name //
-
     /**
      * H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
      *
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index b0c639c..5995246 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -16,7 +16,7 @@ package hdf.hdf5lib;
 import hdf.hdf5lib.structs.H5O_token_t;
 
 /**
- * /** This class contains C constants and enumerated types of HDF5 library. The
+ * This class contains C constants and enumerated types of HDF5 library. The
  * values of these constants are obtained from the library by calling J2C(int
  * jconstant), where jconstant is any of the private constants which start their
  * name with "JH5" need to be converted.
@@ -62,31 +62,62 @@ public class HDF5Constants {
     public static final int H5_ITER_NATIVE = H5_ITER_NATIVE();
     /** Common iteration orders, Number of iteration orders */
     public static final int H5_ITER_N = H5_ITER_N();
-    /** */
+    /** The version of the H5AC_cache_config_t in use */
     public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION();
-    /** */
+    /** The maximum length of the trace file path */
     public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN();
-    /** */
+    /**
+     *    When metadata_write_strategy is set to this value, only process
+     *    zero is allowed to write dirty metadata to disk.  All other
+     *    processes must retain dirty metadata until they are informed at
+     *    a sync point that the dirty metadata in question has been written
+     *    to disk.
+     */
     public static final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY =
         H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY();
-    /** */
+    /**
+     *    In the distributed metadata write strategy, process zero still makes
+     *    the decisions as to what entries should be flushed, but the actual
+     *    flushes are distributed across the processes in the computation to
+     *    the extent possible.
+     */
     public static final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED =
         H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED();
-    /** */
+    /** Don't attempt to increase the size of the cache automatically */
     public static final int H5C_incr_off = H5C_incr_off();
-    /** */
+    /**
+     *  Attempt to increase the size of the cache
+     *              whenever the average hit rate over the last epoch drops
+     *              below the value supplied in the lower_hr_threshold
+     *              field
+     */
     public static final int H5C_incr_threshold = H5C_incr_threshold();
-    /** */
+    /** Don't perform flash increases in the size of the cache */
     public static final int H5C_flash_incr_off = H5C_flash_incr_off();
-    /** */
+    /** increase the current maximum cache size by x * flash_multiple less any free space in the cache */
     public static final int H5C_flash_incr_add_space = H5C_flash_incr_add_space();
-    /** */
+    /** Don't attempt to decrease the size of the cache automatically */
     public static final int H5C_decr_off = H5C_decr_off();
-    /** */
+    /**
+     *  Attempt to decrease the size of the cache
+     *              whenever the average hit rate over the last epoch rises
+     *              above the value supplied in the upper_hr_threshold
+     *              field
+     */
     public static final int H5C_decr_threshold = H5C_decr_threshold();
-    /** */
+    /**
+     *  At the end of each epoch, search the cache for
+     *              entries that have not been accessed for at least the number
+     *              of epochs specified in the epochs_before_eviction field, and
+     *              evict these entries
+     */
     public static final int H5C_decr_age_out = H5C_decr_age_out();
-    /** */
+    /**
+     *  Same as age_out, but we only
+     *              attempt to reduce the cache size when the hit rate observed
+     *              over the last epoch exceeds the value provided in the
+     *              upper_hr_threshold field
+     */
     public static final int H5C_decr_age_out_with_threshold = H5C_decr_age_out_with_threshold();
     /** */
     public static final int H5D_CHUNK_IDX_BTREE = H5D_CHUNK_IDX_BTREE();
@@ -912,11 +943,11 @@ public class HDF5Constants {
     /** */
     public static final int H5R_MAXTYPE = H5R_MAXTYPE();
     /** */
-    public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
+    public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
     /** */
     public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
     /** */
-    public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
+    public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
     /** */
     public static final int H5R_OBJECT = H5R_OBJECT();
     /** */
@@ -2395,11 +2426,11 @@ public class HDF5Constants {
 
     private static native final int H5R_MAXTYPE();
 
-    private static native final int H5R_REF_BUF_SIZE();
+    private static native final int H5R_DSET_REG_REF_BUF_SIZE();
 
     private static native final int H5R_OBJ_REF_BUF_SIZE();
 
-    private static native final int H5R_DSET_REG_REF_BUF_SIZE();
+    private static native final int H5R_REF_BUF_SIZE();
 
     private static native final int H5R_OBJECT();
 
diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java
index 220cfb6..880f003 100644
--- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java
+++ b/java/src/hdf/hdf5lib/HDF5GroupInfo.java
@@ -158,7 +158,7 @@ public class HDF5GroupInfo {
     public long getOID() { return objno[0]; }
 
     /**
-     * /** Converts this object to a String representation.
+     * Converts this object to a String representation.
      *
      * @return a string representation of this object
      */