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>

7 files changed, 118 insertions, 19 deletions

diff --git a/java/test/CMakeLists.txt b/java/test/CMakeLists.txt
index c791c79..10f9d52 100644
--- a/java/test/CMakeLists.txt
+++ b/java/test/CMakeLists.txt
@@ -96,6 +96,8 @@ HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_
 HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_DIR}/h5ex_g_iterateO2.hdf" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
 HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_reg.h5" "${PROJECT_BINARY_DIR}/trefer_reg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
 HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_attr.h5" "${PROJECT_BINARY_DIR}/trefer_attr.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
+HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tdatareg.h5" "${PROJECT_BINARY_DIR}/tdatareg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
+HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tattrreg.h5" "${PROJECT_BINARY_DIR}/tattrreg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
 
 add_custom_target(${HDF5_JAVA_TEST_LIB_TARGET}_files ALL COMMENT "Copying files needed by ${HDF5_JAVA_TEST_LIB_TARGET} tests" DEPENDS ${${HDF5_JAVA_TEST_LIB_TARGET}_files_list})
 
@@ -213,6 +215,8 @@ if (HDF5_TEST_JAVA AND HDF5_TEST_SERIAL)
         HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_DIR}/${voltest}/h5ex_g_iterateO2.hdf" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
         HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_reg.h5" "${PROJECT_BINARY_DIR}/${voltest}/trefer_reg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
         HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_attr.h5" "${PROJECT_BINARY_DIR}/${voltest}/trefer_attr.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
+        HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tdatareg.h5" "${PROJECT_BINARY_DIR}/${voltest}/tdatareg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
+        HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tattrreg.h5" "${PROJECT_BINARY_DIR}/${voltest}/tattrreg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
 
         add_custom_target(${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files ALL COMMENT "Copying files needed by ${HDF5_JAVA_TEST_LIB_TARGET} tests" DEPENDS ${${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files_list})
 
diff --git a/java/test/TestH5.java b/java/test/TestH5.java
index c4f298e..1f298f3 100644
--- a/java/test/TestH5.java
+++ b/java/test/TestH5.java
@@ -49,9 +49,13 @@ public class TestH5 {
     @Rule public TestName testname = new TestName();
     private static final String H5_FILE = "testData.h5";
     private static final String EXPORT_FILE = "testExport.txt";
-    private static final String H5_DREG_FILE = "trefer_reg.h5";
-    private static final String EXPORT_DREG_FILE = "testExportReg.txt";
-    private static final String H5_AREG_FILE = "trefer_attr.h5";
+    private static final String H5_REGION_FILE = "trefer_reg.h5";
+    private static final String EXPORT_REGION_FILE = "testExportReg.txt";
+    private static final String H5_ATTR_FILE = "trefer_attr.h5";
+    private static final String EXPORT_ATTR_FILE = "testExportAttr.txt";
+    private static final String H5_DREG_FILE = "tdatareg.h5";
+    private static final String EXPORT_DREG_FILE = "testExportDReg.txt";
+    private static final String H5_AREG_FILE = "tattrreg.h5";
     private static final String EXPORT_AREG_FILE = "testExportAReg.txt";
     private static final int DIM_X = 4;
     private static final int DIM_Y = 6;
@@ -129,7 +133,7 @@ public class TestH5 {
     public void _openH5File(String filename, String dsetname) {
        try {
            H5fid = H5.H5Fopen(filename,
-                   HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
+                   HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
@@ -162,6 +166,7 @@ public class TestH5 {
     @After
     public void closeH5File() throws HDF5LibraryException {
         _closeH5File();
+        assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
         System.out.println();
     }
 
@@ -415,8 +420,10 @@ public class TestH5 {
 
         _closeH5File();
 
+        _openH5File(H5_FILE, "/dset");
+
         try {
-            H5.H5export_dataset(EXPORT_FILE, H5_FILE, "/dset", 99);
+            H5.H5export_dataset(EXPORT_FILE, H5fid, "/dset", 99);
         }
         catch (HDF5LibraryException err) {
             err.printStackTrace();
@@ -454,6 +461,86 @@ public class TestH5 {
     }
 
     @Test
+    public void testH5export_region() {
+        int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
+                111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
+                186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
+                207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
+        int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
+        String objName = "/Dataset1";
+
+        _openH5File(H5_REGION_FILE, objName);
+
+        try {
+            H5.H5export_dataset(EXPORT_REGION_FILE, H5fid, objName, 99);
+        }
+        catch (HDF5LibraryException err) {
+            err.printStackTrace();
+            fail("H5export_dataset failed: " + err);
+        }
+
+        File file = new File(EXPORT_REGION_FILE);
+
+        try {
+            Reader reader = new FileReader(EXPORT_REGION_FILE);
+            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
+            int indx = 0;
+            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
+                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
+                    dset_indata[indx] = (int)streamTokenizer.nval;
+                    indx++;
+                }
+            }
+            reader.close();
+        }
+        catch (IOException err) {
+            err.printStackTrace();
+            fail("read file failed: " + err);
+        }
+        for(int row = 0; row < DIM_X; row++)
+            assertTrue("testH5export_region: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
+    }
+
+    @Test
+    public void testH5export_attribute() {
+        int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
+        int[] dset_indata = new int[DIM_ATTR];
+        String objName = "/Dataset3";
+
+        _openH5File(H5_ATTR_FILE, objName);
+
+        try {
+            H5.H5export_dataset(EXPORT_ATTR_FILE, H5did, objName, 99);
+        }
+        catch (HDF5LibraryException err) {
+            err.printStackTrace();
+            fail("H5export_dataset failed: " + err);
+        }
+
+        File file = new File(EXPORT_ATTR_FILE);
+
+        try {
+            Reader reader = new FileReader(EXPORT_ATTR_FILE);
+            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
+            int indx = 0;
+            int jndx = 0;
+            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
+                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
+                    dset_indata[indx] = (int)streamTokenizer.nval;
+                    indx++;
+                }
+            }
+            reader.close();
+        }
+        catch (IOException err) {
+            err.printStackTrace();
+            fail("read file failed: " + err);
+        }
+        for(int row = 0; row < DIM_X; row++)
+            assertTrue("testH5export_attribute: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
+    }
+
+    @Test
     public void testH5export_regdataset() {
         int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
                 111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
@@ -465,7 +552,7 @@ public class TestH5 {
         _openH5File(H5_DREG_FILE, objName);
 
         try {
-            H5.H5export_dataset(EXPORT_DREG_FILE, H5_DREG_FILE, objName, 99);
+            H5.H5export_dataset(EXPORT_DREG_FILE, H5fid, objName, 99);
         }
         catch (HDF5LibraryException err) {
             err.printStackTrace();
@@ -491,23 +578,27 @@ public class TestH5 {
             fail("read file failed: " + err);
         }
         for(int row = 0; row < DIM_X; row++)
-            assertTrue("H5export_dataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
+            assertTrue("testH5export_regdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
     }
 
     @Test
     public void testH5export_attrdataset() {
-        int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
-        int[] dset_indata = new int[DIM_ATTR];
-        String objName = "/Dataset3";
+        int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
+                111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
+                186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
+                207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
+        int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
+        String dsetName = "/Dataset1";
+        String objName = "Attribute1";
 
-        _openH5File(H5_AREG_FILE, objName);
+        _openH5File(H5_AREG_FILE, dsetName);
 
         try {
-            H5.H5export_dataset(EXPORT_AREG_FILE, H5_AREG_FILE, objName, 99);
+            H5.H5export_attribute(EXPORT_AREG_FILE, H5did, objName, 99);
         }
         catch (HDF5LibraryException err) {
             err.printStackTrace();
-            fail("H5export_dataset failed: " + err);
+            fail("H5export_attribute failed: " + err);
         }
 
         File file = new File(EXPORT_AREG_FILE);
@@ -530,6 +621,6 @@ public class TestH5 {
             fail("read file failed: " + err);
         }
         for(int row = 0; row < DIM_X; row++)
-            assertTrue("H5export_dataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
+            assertTrue("testH5export_attrdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
     }
 }
diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java
index 863ce79..dac3a9c 100644
--- a/java/test/TestH5D.java
+++ b/java/test/TestH5D.java
@@ -197,7 +197,7 @@ public class TestH5D {
     private final void _openH5file(String filename, String dsetname, long dapl) {
        try {
            H5fid = H5.H5Fopen(filename,
-                   HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
+                   HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
diff --git a/java/test/TestH5Rref.java b/java/test/TestH5Rref.java
index aeec64f..cbdabdd 100644
--- a/java/test/TestH5Rref.java
+++ b/java/test/TestH5Rref.java
@@ -53,7 +53,7 @@ public class TestH5Rref {
     public void openH5file(String filename, String dsetname) {
        try {
            H5fid = H5.H5Fopen(filename,
-                   HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
+                   HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
diff --git a/java/test/TestH5T.java b/java/test/TestH5T.java
index c882f8e..ed4e2a9 100644
--- a/java/test/TestH5T.java
+++ b/java/test/TestH5T.java
@@ -206,7 +206,7 @@ public class TestH5T {
 
     @Test
     public void testH5Tenum_functions() {
-        long       filetype_id =HDF5Constants.H5I_INVALID_HID;
+        long       filetype_id = HDF5Constants.H5I_INVALID_HID;
         String    enum_type ="Enum_type";
         byte[]    enum_val = new byte[1];
         String    enum_name = null;
@@ -398,7 +398,7 @@ public class TestH5T {
 
     @Test
     public void testH5Tcompound_functions() {
-        long       filetype_id =HDF5Constants.H5I_INVALID_HID;
+        long       filetype_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a compound datatype
         try {
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 81ce13b..3774cbd 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -252,6 +252,8 @@ COPY_DATAFILES_TO_BLDDIR()
     $CP -f $HDFTEST_HOME/h5ex_g_iterate.orig $BLDDIR/h5ex_g_iterateO2.hdf
     $CP -f $TOOLS_TESTFILES/trefer_reg.h5 $BLDDIR/trefer_reg.h5
     $CP -f $TOOLS_TESTFILES/trefer_attr.h5 $BLDDIR/trefer_attr.h5
+    $CP -f $TOOLS_TESTFILES/tdatareg.h5 $BLDDIR/tdatareg.h5
+    $CP -f $TOOLS_TESTFILES/tattrreg.h5 $BLDDIR/tattrreg.h5
 }
 
 CLEAN_DATAFILES_AND_BLDDIR()
diff --git a/java/test/testfiles/JUnit-TestH5.txt b/java/test/testfiles/JUnit-TestH5.txt
index 59765d9..fb50a57 100644
--- a/java/test/testfiles/JUnit-TestH5.txt
+++ b/java/test/testfiles/JUnit-TestH5.txt
@@ -1,4 +1,5 @@
 JUnit version 4.11
+.testH5export_region
 .testH5get_libversion_null_param
 .testJ2C
 .testH5export_dataset
@@ -7,6 +8,7 @@ JUnit version 4.11
 .testH5garbage_collect
 .testH5error_off
 .testH5export_regdataset
+.testH5export_attribute
 .serializeToDisk
 .testH5open
 .testH5check_version
@@ -15,5 +17,5 @@ JUnit version 4.11
 
 Time:  XXXX
 
-OK (13 tests)
+OK (15 tests)