1 10 HDFFV-11310 implement JNI VL support for primitive types (#1858)

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

* HDFFV-11310 - VL read/write function for primitive types

* Add read/write VL option

* fix function name typo

* remove debugging prints

* Remove more debugging code

* Correct note to match change in code.

* HDFFV-11318 add VL references as byte arrays

* Fix unreleased allocations, fix debug

* Fix format

* Fix formatting

* Correct typo

2 files changed, 28 insertions, 6 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index b95495a..e96cf06 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -246,7 +246,7 @@ public class H5 implements java.io.Serializable {
      *
      * Make sure to update the versions number when a different library is used.
      */
-    public final static int LIB_VERSION[] = {1, 10, 9};
+    public final static int LIB_VERSION[] = {1, 10, 10};
 
     /**
      *  add system property to load library by path
@@ -1267,6 +1267,10 @@ 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);
@@ -1813,6 +1817,10 @@ 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();
@@ -2797,6 +2805,11 @@ 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);
@@ -3472,6 +3485,11 @@ 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();
@@ -6468,7 +6486,7 @@ public class H5 implements java.io.Serializable {
 
     /**
      * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and
-     *relative name.
+     * relative name.
      *
      * @param loc_id
      *            IN: File or group identifier specifying location of group in which object is located
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 7c02af9..bcf3eab 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -81,7 +81,8 @@ public class HDF5Constants {
         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
+    /**
+     *  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
@@ -93,19 +94,22 @@ public class HDF5Constants {
     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
+    /**
+     *  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
+    /**
+     *  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
+    /**
+     *  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