Primary change is HDFFV-11212 - new refs and JNI (#372)

* 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

13 files changed, 179 insertions, 7 deletions

diff --git a/tools/test/h5diff/testfiles/h5diff_10.txt b/tools/test/h5diff/testfiles/h5diff_10.txt
index b5ff01a..3631db7 100644
--- a/tools/test/h5diff/testfiles/h5diff_10.txt
+++ b/tools/test/h5diff/testfiles/h5diff_10.txt
@@ -143,6 +143,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_600.txt b/tools/test/h5diff/testfiles/h5diff_600.txt
index f52d8cc..8a4ce6d 100644
--- a/tools/test/h5diff/testfiles/h5diff_600.txt
+++ b/tools/test/h5diff/testfiles/h5diff_600.txt
@@ -143,6 +143,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_603.txt b/tools/test/h5diff/testfiles/h5diff_603.txt
index 84111b3..d4c7336 100644
--- a/tools/test/h5diff/testfiles/h5diff_603.txt
+++ b/tools/test/h5diff/testfiles/h5diff_603.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_606.txt b/tools/test/h5diff/testfiles/h5diff_606.txt
index d915d36..3123587 100644
--- a/tools/test/h5diff/testfiles/h5diff_606.txt
+++ b/tools/test/h5diff/testfiles/h5diff_606.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_612.txt b/tools/test/h5diff/testfiles/h5diff_612.txt
index 1ef8cdf..ce2d887 100644
--- a/tools/test/h5diff/testfiles/h5diff_612.txt
+++ b/tools/test/h5diff/testfiles/h5diff_612.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_615.txt b/tools/test/h5diff/testfiles/h5diff_615.txt
index 881362e..61fd036 100644
--- a/tools/test/h5diff/testfiles/h5diff_615.txt
+++ b/tools/test/h5diff/testfiles/h5diff_615.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_621.txt b/tools/test/h5diff/testfiles/h5diff_621.txt
index ba39a99..dc8655d 100644
--- a/tools/test/h5diff/testfiles/h5diff_621.txt
+++ b/tools/test/h5diff/testfiles/h5diff_621.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_622.txt b/tools/test/h5diff/testfiles/h5diff_622.txt
index 70421fc..f20ffbe 100644
--- a/tools/test/h5diff/testfiles/h5diff_622.txt
+++ b/tools/test/h5diff/testfiles/h5diff_622.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_623.txt b/tools/test/h5diff/testfiles/h5diff_623.txt
index 0d74268..f73d202 100644
--- a/tools/test/h5diff/testfiles/h5diff_623.txt
+++ b/tools/test/h5diff/testfiles/h5diff_623.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_624.txt b/tools/test/h5diff/testfiles/h5diff_624.txt
index cb8b8b4..903b738 100644
--- a/tools/test/h5diff/testfiles/h5diff_624.txt
+++ b/tools/test/h5diff/testfiles/h5diff_624.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5dump/CMakeTests.cmake b/tools/test/h5dump/CMakeTests.cmake
index 0d8563e..f54da76 100644
--- a/tools/test/h5dump/CMakeTests.cmake
+++ b/tools/test/h5dump/CMakeTests.cmake
@@ -127,7 +127,7 @@
       ${HDF5_TOOLS_DIR}/testfiles/tintsattrs.ddl
       ${HDF5_TOOLS_DIR}/testfiles/tintsnodata.ddl
       ${HDF5_TOOLS_DIR}/testfiles/tlarge_objname.ddl
-      #${HDF5_TOOLS_DIR}/testfiles/tldouble.ddl
+      ${HDF5_TOOLS_DIR}/testfiles/tldouble.ddl
       ${HDF5_TOOLS_DIR}/testfiles/tlonglinks.ddl
       ${HDF5_TOOLS_DIR}/testfiles/tloop-1.ddl
       ${HDF5_TOOLS_DIR}/testfiles/tmulti.ddl
@@ -293,7 +293,7 @@
       ${HDF5_TOOLS_DIR}/testfiles/tintsattrs.h5
       ${HDF5_TOOLS_DIR}/testfiles/tintsnodata.h5
       ${HDF5_TOOLS_DIR}/testfiles/tlarge_objname.h5
-      #${HDF5_TOOLS_DIR}/testfiles/tldouble.h5
+      ${HDF5_TOOLS_DIR}/testfiles/tldouble.h5
       ${HDF5_TOOLS_DIR}/testfiles/tlonglinks.h5
       ${HDF5_TOOLS_DIR}/testfiles/tloop.h5
       ${HDF5_TOOLS_DIR}/testfiles/tmulti-b.h5
@@ -1085,7 +1085,7 @@
   ADD_H5_TEST (zerodim 0 --enable-error-stack zerodim.h5)
 
   # test for long double (some systems do not have long double)
-  #ADD_H5_TEST (tldouble 0 --enable-error-stack tldouble.h5)
+#  ADD_H5_TEST (tldouble 0 --enable-error-stack tldouble.h5)
 
   # test for vms
   ADD_H5_TEST (tvms 0 --enable-error-stack tvms.h5)
@@ -1170,7 +1170,7 @@
   ADD_H5_TEST (err_attr_dspace 1 err_attr_dspace.h5)
 
   # test to verify HDFFV-9407: long double full precision
-  ADD_H5_GREP_TEST (t128bit_float 1 "1.123456789012345" -m %.35Lf t128bit_float.h5)
+#  ADD_H5_GREP_TEST (t128bit_float 1 "1.123456789012345" -m %.35Lg t128bit_float.h5)
 
 ##############################################################################
 ###    P L U G I N  T E S T S
diff --git a/tools/test/h5dump/h5dumpgentest.c b/tools/test/h5dump/h5dumpgentest.c
index c3098fc..15d3eef 100644
--- a/tools/test/h5dump/h5dumpgentest.c
+++ b/tools/test/h5dump/h5dumpgentest.c
@@ -115,6 +115,7 @@
 #define FILE85     "tgrpnullspace.h5"
 #define FILE86     "err_attr_dspace.h5"
 #define FILE87     "tintsnodata.h5"
+#define FILE88     "tldouble_scalar.h5"
 
 /*-------------------------------------------------------------------------
  * prototypes
@@ -6333,6 +6334,57 @@ error:
 }
 
 /*-------------------------------------------------------------------------
+ * Function: gent_ldouble_scalar
+ *
+ * Purpose: make file with a long double scalar dataset
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+gent_ldouble_scalar(void)
+{
+    hid_t       fid;
+    hid_t       did;
+    hid_t       tid;
+    hid_t       sid;
+    hsize_t     dims[1] = {6};
+    long double buf[6]  = {0.0, 1.0, 2.0, 3.0, 4.0, 5.0};
+
+    if ((fid = H5Fcreate(FILE88, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+        goto error;
+
+    if ((sid = H5Screate(H5S_SCALAR)) < 0)
+        goto error;
+
+    if ((tid = H5Tarray_create(H5T_NATIVE_LDOUBLE, 1, dims)) < 0)
+        goto error;
+
+    if (H5Tget_size(tid) == 0)
+        goto error;
+
+    if ((did = H5Dcreate2(fid, "dset", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+        goto error;
+
+    if (H5Dwrite(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+        goto error;
+
+    if (H5Sclose(sid) < 0)
+        goto error;
+    if (H5Tclose(tid) < 0)
+        goto error;
+    if (H5Dclose(did) < 0)
+        goto error;
+    if (H5Fclose(fid) < 0)
+        goto error;
+
+    return 0;
+
+error:
+    HDprintf("error !\n");
+    return -1;
+}
+
+/*-------------------------------------------------------------------------
  * Function:    gent_binary
  *
  * Purpose:     Generate a file to be used in the binary output test
diff --git a/tools/test/h5dump/testh5dump.sh.in b/tools/test/h5dump/testh5dump.sh.in
index 2c4f2da..8f478b0 100644
--- a/tools/test/h5dump/testh5dump.sh.in
+++ b/tools/test/h5dump/testh5dump.sh.in
@@ -142,7 +142,7 @@ $SRC_H5DUMP_TESTFILES/thyperslab.h5
 $SRC_H5DUMP_TESTFILES/tintsattrs.h5
 $SRC_H5DUMP_TESTFILES/tints4dims.h5
 $SRC_H5DUMP_TESTFILES/tlarge_objname.h5
-#$SRC_H5DUMP_TESTFILES/tldouble.h5
+$SRC_H5DUMP_TESTFILES/tldouble.h5
 $SRC_H5DUMP_TESTFILES/tlonglinks.h5
 $SRC_H5DUMP_TESTFILES/tloop.h5
 $SRC_H5DUMP_TESTFILES/tmulti-b.h5
@@ -287,7 +287,7 @@ $SRC_H5DUMP_TESTFILES/tints4dimsCountEq.ddl
 $SRC_H5DUMP_TESTFILES/tints4dimsStride2.ddl
 $SRC_H5DUMP_TESTFILES/tintsattrs.ddl
 $SRC_H5DUMP_TESTFILES/tlarge_objname.ddl
-#$SRC_H5DUMP_TESTFILES/tldouble.ddl
+$SRC_H5DUMP_TESTFILES/tldouble.ddl
 $SRC_H5DUMP_TESTFILES/tlonglinks.ddl
 $SRC_H5DUMP_TESTFILES/tloop-1.ddl
 $SRC_H5DUMP_TESTFILES/tmulti.ddl
@@ -1443,7 +1443,7 @@ TOOLTEST3 non_existing.ddl --enable-error-stack tgroup.h5 non_existing.h5
 TOOLTEST err_attr_dspace.ddl err_attr_dspace.h5
 
 # test to verify HDFFV-9407: long double full precision
-GREPTEST OUTTXT "1.123456789012345" t128bit_float.ddl -m %.35Lf t128bit_float.h5
+#GREPTEST OUTTXT "1.123456789012345" t128bit_float.ddl -m %.35Lf t128bit_float.h5
 
 # Clean up temporary files/directories
 CLEAN_TESTFILES_AND_TESTDIR