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

1 files changed, 27 insertions, 1 deletions

diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 2eabdf0..8c22c5a 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -46,6 +46,8 @@ HDFLIB_HOME="$top_srcdir/java/lib"
 BLDDIR="."
 BLDLIBDIR="$BLDDIR/testlibs"
 HDFTEST_HOME="$top_srcdir/java/test"
+TOOLS_TESTFILES="$top_srcdir/tools/testfiles"
+
 JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
 TESTJARFILE=jar@PACKAGE_TARNAME@test.jar
 test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
@@ -93,6 +95,7 @@ $HDFTEST_HOME/testfiles/JUnit-TestH5Lparams.txt
 $HDFTEST_HOME/testfiles/JUnit-TestH5Lbasic.txt
 $HDFTEST_HOME/testfiles/JUnit-TestH5Lcreate.txt
 $HDFTEST_HOME/testfiles/JUnit-TestH5R.txt
+$HDFTEST_HOME/testfiles/JUnit-TestH5Rref.txt
 $HDFTEST_HOME/testfiles/JUnit-TestH5P.txt
 $HDFTEST_HOME/testfiles/JUnit-TestH5PData.txt
 $HDFTEST_HOME/testfiles/JUnit-TestH5Pfapl.txt
@@ -146,7 +149,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then 
+    if [ "$IS_DARWIN" = "yes" ]; then
        (cd testlibs; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -248,6 +251,8 @@ COPY_DATAFILES_TO_BLDDIR()
     $CP -f $HDFTEST_HOME/h5ex_g_iterate.orig $BLDDIR/h5ex_g_iterateL2.hdf
     $CP -f $HDFTEST_HOME/h5ex_g_iterate.orig $BLDDIR/h5ex_g_iterateO1.hdf
     $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
 }
 
 CLEAN_DATAFILES_AND_BLDDIR()
@@ -768,6 +773,27 @@ else
     test yes = "$verbose" && $DIFF JUnit-TestH5R.txt JUnit-TestH5R.out |sed 's/^/    /'
 fi
 
+echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5Rref"
+TESTING JUnit-TestH5Rref
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5Rref > JUnit-TestH5Rref.ext)
+
+# Extract file name, line number, version and thread IDs because they may be different
+sed -e 's/thread [0-9]*/thread (IDs)/' -e 's/: .*\.c /: (file name) /' \
+    -e 's/line [0-9]*/line (number)/' \
+    -e 's/Time: [0-9]*[\.,[0-9]*]*/Time:  XXXX/' \
+    -e 's/v[1-9]*\.[0-9]*\./version (number)\./' \
+    -e 's/[1-9]*\.[0-9]*\.[0-9]*[^)]*/version (number)/' \
+    JUnit-TestH5Rref.ext > JUnit-TestH5Rref.out
+
+if diff JUnit-TestH5Rref.out JUnit-TestH5Rref.txt > /dev/null; then
+    echo "  PASSED      JUnit-TestH5Rref"
+else
+    echo "**FAILED**    JUnit-TestH5Rref"
+    echo "    Expected result differs from actual result"
+    nerrors="`expr $nerrors + 1`"
+    test yes = "$verbose" && $DIFF JUnit-TestH5Rref.txt JUnit-TestH5Rref.out |sed 's/^/    /'
+fi
+
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5P"
 TESTING JUnit-TestH5P
 ($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5P > JUnit-TestH5P.ext)