Merge branch 'develop' into feature/coding_standardsfeature/coding_standards

10 files changed, 54 insertions, 65 deletions

diff --git a/java/examples/intro/CMakeLists.txt b/java/examples/intro/CMakeLists.txt
index e60af88..867740b 100644
--- a/java/examples/intro/CMakeLists.txt
+++ b/java/examples/intro/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.10)
+cmake_minimum_required (VERSION 3.12)
 project (HDFJAVA_EXAMPLES_INTRO Java)
 
 set (CMAKE_VERBOSE_MAKEFILE 1)
@@ -13,7 +13,7 @@ set (HDF_JAVA_EXAMPLES
     H5_ReadWrite
 )
 
-if (WIN32 OR MINGW)
+if (WIN32)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
@@ -45,19 +45,7 @@ foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH})
   set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}")
 endforeach ()
 
-foreach (example ${HDF_JAVA_OBJECT_EXAMPLES})
-  file (WRITE ${PROJECT_BINARY_DIR}/${example}_Manifest.txt
-  "Main-Class: examples.intro.${example}
-"
-  )
-  add_jar (${example} MANIFEST ${PROJECT_BINARY_DIR}/${example}_Manifest.txt ${example}.java)
-  get_target_property (${example}_JAR_FILE ${example} JAR_FILE)
-#  install_jar (${example} ${HJAVA_INSTALL_DATA_DIR}/examples examples)
-  get_target_property (${example}_CLASSPATH ${example} CLASSDIR)
-  add_dependencies (${example} ${HDFJAVA_H5_LIB_TARGET})
-endforeach ()
-
-if (BUILD_TESTING)
+if (BUILD_TESTING AND HDF5_TEST_EXAMPLES AND HDF5_TEST_SERIAL)
   get_property (target_name TARGET ${HDF5_JAVA_JNI_LIB_TARGET} PROPERTY OUTPUT_NAME)
   set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${target_name}$<$<CONFIG:Debug>:${CMAKE_DEBUG_POSTFIX}>;")
 
@@ -89,7 +77,9 @@ if (BUILD_TESTING)
             -D "TEST_REFERENCE=intro/${example}.txt"
             -P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
     )
-    set_tests_properties (JAVA_intro-${example} PROPERTIES DEPENDS JAVA_intro-${example}-copy-objects)
+    set_tests_properties (JAVA_intro-${example} PROPERTIES
+        DEPENDS JAVA_intro-${example}-copy-objects
+    )
   endforeach ()
 
 endif ()
diff --git a/java/examples/intro/H5_CreateAttribute.java b/java/examples/intro/H5_CreateAttribute.java
index 68749b1..949a770 100644
--- a/java/examples/intro/H5_CreateAttribute.java
+++ b/java/examples/intro/H5_CreateAttribute.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -28,10 +27,10 @@ public class H5_CreateAttribute {
     private static String DATASETATTRIBUTE = "Units";
 
     private static void CreateDatasetAttribute() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
-        long attribute_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long attribute_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims1 = { DIM_X, DIM_Y };
         long[] dims = { 2 };
         int[] attr_data = { 100, 200 };
diff --git a/java/examples/intro/H5_CreateDataset.java b/java/examples/intro/H5_CreateDataset.java
index 3572a31..f938be2 100644
--- a/java/examples/intro/H5_CreateDataset.java
+++ b/java/examples/intro/H5_CreateDataset.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -27,9 +26,9 @@ public class H5_CreateDataset {
     private static final int DIM_Y = 6;
 
     private static void CreateDataset() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
 
         // Create a new file using default properties.
diff --git a/java/examples/intro/H5_CreateFile.java b/java/examples/intro/H5_CreateFile.java
index a8c87ea..d48ba6c 100644
--- a/java/examples/intro/H5_CreateFile.java
+++ b/java/examples/intro/H5_CreateFile.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -24,7 +23,7 @@ public class H5_CreateFile {
     static final String FILENAME = "H5_CreateFile.h5";
 
     private static void CreateFile() {
-        long file_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/intro/H5_CreateGroup.java b/java/examples/intro/H5_CreateGroup.java
index 9359605..c0bb954 100644
--- a/java/examples/intro/H5_CreateGroup.java
+++ b/java/examples/intro/H5_CreateGroup.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -25,8 +24,8 @@ public class H5_CreateGroup {
     private static String GROUPNAME = "MyGroup";
 
     private static void CreateGroup() {
-        long file_id = -1;
-        long group_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/intro/H5_CreateGroupAbsoluteRelative.java b/java/examples/intro/H5_CreateGroupAbsoluteRelative.java
index ddc069f..f2c6168 100644
--- a/java/examples/intro/H5_CreateGroupAbsoluteRelative.java
+++ b/java/examples/intro/H5_CreateGroupAbsoluteRelative.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -27,10 +26,10 @@ public class H5_CreateGroupAbsoluteRelative {
     private static String GROUPNAME_B = "GroupB";
 
     private static void CreateGroupAbsoluteAndRelative() {
-        long file_id = -1;
-        long group1_id = -1;
-        long group2_id = -1;
-        long group3_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group1_id = HDF5Constants.H5I_INVALID_HID;
+        long group2_id = HDF5Constants.H5I_INVALID_HID;
+        long group3_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/intro/H5_CreateGroupDataset.java b/java/examples/intro/H5_CreateGroupDataset.java
index bdb0546..f1d1cba 100644
--- a/java/examples/intro/H5_CreateGroupDataset.java
+++ b/java/examples/intro/H5_CreateGroupDataset.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -32,12 +31,12 @@ public class H5_CreateGroupDataset {
     private static final int DIM2_Y = 10;
 
     private static void h5_crtgrpd() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
-        long group_id = -1;
-        long group1_id = -1;
-        long group2_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
+        long group1_id = HDF5Constants.H5I_INVALID_HID;
+        long group2_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset1_data = new int[DIM1_X][DIM1_Y];
         int[][] dset2_data = new int[DIM2_X][DIM2_Y];
         long[] dims1 = { DIM1_X, DIM1_Y };
@@ -108,7 +107,7 @@ public class H5_CreateGroupDataset {
         try {
             if (dataspace_id >= 0)
                 H5.H5Sclose(dataspace_id);
-            dataspace_id = -1;
+            dataspace_id = HDF5Constants.H5I_INVALID_HID;
         }
         catch (Exception e) {
             e.printStackTrace();
@@ -118,7 +117,7 @@ public class H5_CreateGroupDataset {
         try {
             if (dataset_id >= 0)
                 H5.H5Dclose(dataset_id);
-            dataset_id = -1;
+            dataset_id = HDF5Constants.H5I_INVALID_HID;
         }
         catch (Exception e) {
             e.printStackTrace();
diff --git a/java/examples/intro/H5_ReadWrite.java b/java/examples/intro/H5_ReadWrite.java
index 5a7dabc..67e1ac5 100644
--- a/java/examples/intro/H5_ReadWrite.java
+++ b/java/examples/intro/H5_ReadWrite.java
@@ -1,12 +1,11 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -27,9 +26,9 @@ public class H5_ReadWrite {
     private static final int DIM_Y = 6;
 
     private static void ReadWriteDataset() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
index 1886485..a095f27 100644
--- a/java/examples/intro/JavaIntroExample.sh.in
+++ b/java/examples/intro/JavaIntroExample.sh.in
@@ -1,13 +1,12 @@
 #! /bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
@@ -15,6 +14,7 @@
 top_builddir=@top_builddir@
 top_srcdir=@top_srcdir@
 srcdir=@srcdir@
+IS_DARWIN="@H5_IS_DARWIN@"
 
 TESTNAME=EX_Intro
 EXIT_SUCCESS=0
@@ -33,8 +33,8 @@ nerrors=0
 
 # where the libs exist
 HDFLIB_HOME="$top_srcdir/java/lib"
-BLDLIBDIR="$top_builddir/hdf5/lib"
 BLDDIR="."
+BLDLIBDIR="$BLDDIR/testlibs"
 HDFTEST_HOME="$top_srcdir/java/examples/intro"
 JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
 TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar
@@ -54,8 +54,8 @@ $top_builddir/java/src/jni/.libs/libhdf5_java.*
 $top_builddir/java/src/$JARFILE
 "
 LIST_JAR_TESTFILES="
-$HDFLIB_HOME/slf4j-api-1.7.25.jar
-$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
+$HDFLIB_HOME/slf4j-api-1.7.33.jar
+$HDFLIB_HOME/ext/slf4j-simple-1.7.33.jar
 "
 LIST_DATA_FILES="
 $HDFTEST_HOME/../testfiles/examples.intro.H5_CreateDataset.txt
@@ -99,6 +99,13 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    if [ "$IS_DARWIN" = "yes" ]; then
+       (cd $BLDLIBDIR; \
+         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}'`; \
+         echo $exist_path; \
+         install_name_tool -change $exist_path @rpath/libhdf5.dylib libhdf5_java.dylib)
+    fi
     # copy jar files. Used -f to make sure get a new copy
     for tstfile in $COPY_JARTESTFILES
     do
@@ -198,7 +205,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@
 COPY_LIBFILES_TO_BLDLIBDIR
 COPY_DATAFILES_TO_BLDDIR
 
-CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE""
+CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.33.jar:"$BLDLIBDIR"/slf4j-simple-1.7.33.jar:"$TESTJARFILE""
 
 TEST=/usr/bin/test
 if [ ! -x /usr/bin/test ]
diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am
index 33f44c2..741f122 100644
--- a/java/examples/intro/Makefile.am
+++ b/java/examples/intro/Makefile.am
@@ -1,12 +1,11 @@
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 ##
@@ -28,13 +27,13 @@ classes:
 
 pkgpath = examples/intro
 hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
-CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
+CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.33.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.33.jar:$$CLASSPATH
 
 jarfile = jar$(PACKAGE_TARNAME)intro.jar
 
 AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation
 
-TESTPACKAGE = 
+TESTPACKAGE =
 
 noinst_JAVA = \
     H5_CreateAttribute.java \