develop JNI export references and java updates (#467)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

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

java/src/hdf/hdf5lib/H5.java

@@ -512,8 +512,8 @@ public synchronized static native int H5set_free_list_limits(int reg_global_lim,
      *
      * @param file_export_name
      *            The file name to export data into.
-     * @param file_name
-     *            The name of the HDF5 file containing the dataset.
+     * @param file_id
+     *            The identifier of the HDF5 file containing the dataset.
      * @param object_path
      *            The full path of the dataset to be exported.
      * @param binary_order
@@ -525,9 +525,30 @@ public synchronized static native int H5set_free_list_limits(int reg_global_lim,
      * @exception HDF5LibraryException
      *                - Error from the HDF-5 Library.
      **/
-    public synchronized static native void H5export_dataset(String file_export_name, String file_name,
+    public synchronized static native void H5export_dataset(String file_export_name, long file_id,
             String object_path, int binary_order) throws HDF5LibraryException;
 
+    /**
+     * H5export_attribute is a utility function to save data in a file.
+     *
+     * @param file_export_name
+     *            The file name to export data into.
+     * @param dataset_id
+     *            The identifier of the dataset containing the attribute.
+     * @param attribute_name
+     *            The attribute to be exported.
+     * @param binary_order
+     *            99 - export data as text.
+     *            1 - export data as binary Native Order.
+     *            2 - export data as binary Little Endian.
+     *            3 - export data as binary Big Endian.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5export_attribute(String file_export_name, long dataset_id,
+            String attribute_name, int binary_order) throws HDF5LibraryException;
+
     /**
      * H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled.
      *

java/src/hdf/hdf5lib/HDF5Constants.java

@@ -55,15 +55,15 @@ public class HDF5Constants {
     public static final int H5_INDEX_CRT_ORDER = H5_INDEX_CRT_ORDER();
     /** indices on links, number of indices defined */
     public static final int H5_INDEX_N = H5_INDEX_N();
-    /** */
+    /** Common iteration orders, Unknown order */
     public static final int H5_ITER_UNKNOWN = H5_ITER_UNKNOWN();
-    /** */
+    /** Common iteration orders, Increasing order */
     public static final int H5_ITER_INC = H5_ITER_INC();
-    /** */
+    /** Common iteration orders, Decreasing order */
     public static final int H5_ITER_DEC = H5_ITER_DEC();
-    /** */
+    /** Common iteration orders, No particular order, whatever is fastest */
     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();
     /** */
     public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION();

java/src/hdf/hdf5lib/HDF5GroupInfo.java

@@ -90,32 +90,44 @@ public void reset() {
         linklen = 0;
     }
 
-    /** fileno accessors */
+    /** fileno accessors
+     * @return the file number if successful
+     */
     public long[] getFileno() {
         return fileno;
     }
 
-    /** accessors */
+    /** accessors
+     * @return the object number if successful
+     */
     public long[] getObjno() {
         return objno;
     }
 
-    /** accessors */
+    /** accessors
+     * @return type of group if successful
+     */
     public int getType() {
         return type;
     }
 
-    /** accessors */
+    /** accessors
+     * @return the number of links in the group if successful
+     */
     public int getNlink() {
         return nlink;
     }
 
-    /** accessors */
+    /** accessors
+     * @return the modified time value if successful
+     */
     public long getMtime() {
         return mtime;
     }
 
-    /** accessors */
+    /** accessors
+     * @return a length of link name if successful
+     */
     public int getLinklen() {
         return linklen;
     }

java/src/hdf/hdf5lib/HDFArray.java

@@ -827,12 +827,10 @@ public ArrayDescriptor(Object anArray) throws HDF5Exception
         else if (NT == 'S') {
             NTsize = 2;
         }
-        else if ((NT == 'I')
-                || (NT == 'F')) {
+        else if ((NT == 'I') || (NT == 'F')) {
             NTsize = 4;
         }
-        else if ((NT == 'J')
-                || (NT == 'D')) {
+        else if ((NT == 'J') || (NT == 'D')) {
             NTsize = 8;
         }
         else if (css.startsWith("Ljava.lang.Byte")) {
@@ -925,8 +923,8 @@ public void dumpInfo()
         System.out.println("Type: " + theType);
         System.out.println("Class: " + theClass);
         System.out.println("NT: " + NT + " NTsize: " + NTsize);
-        System.out
-                .println("Array has " + dims + " dimensions (" + totalSize + " bytes, " + totalElements + " elements)");
+        System.out.println("Array has " + dims + " dimensions (" + totalSize
+                + " bytes, " + totalElements + " elements)");
         int i;
         for (i = 0; i <= dims; i++) {
             Class tc = objs[i].getClass();

java/src/hdf/hdf5lib/structs/H5_ih_info_t.java

@@ -20,9 +20,9 @@
  */
 public class H5_ih_info_t implements Serializable {
     private static final long serialVersionUID = -142238015615462707L;
-    /** */
-    public long     index_size;     /* btree and/or list */
-    /** */
+    /** btree and/or list size of index */
+    public long     index_size;
+    /** btree and/or list size of hp */
     public long     heap_size;
 
     H5_ih_info_t (long index_size, long heap_size)