[svn-r19050] Description:

	Bring r18704:19049 from trunk to revise_chunks branch.

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
                w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                in production mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
        Mac OS X/32 10.6.3 (amazon) in debug mode
        Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
                in production mode

5 files changed, 285 insertions, 21 deletions

diff --git a/tools/h5copy/CMakeLists.txt b/tools/h5copy/CMakeLists.txt
new file mode 100644
index 0000000..61f5ef3
--- /dev/null
+++ b/tools/h5copy/CMakeLists.txt
@@ -0,0 +1,249 @@
+cmake_minimum_required (VERSION 2.8)
+PROJECT (HDF5_TOOLS_H5COPY)
+
+#-----------------------------------------------------------------------------
+# Setup include Directories
+#-----------------------------------------------------------------------------
+INCLUDE_DIRECTORIES (${HDF5_TOOLS_SOURCE_DIR}/lib)
+INCLUDE_DIRECTORIES (${HDF5_PROJECT_DIR}/test)
+
+# --------------------------------------------------------------------
+# Add the h5copy and test executables
+# --------------------------------------------------------------------
+ADD_EXECUTABLE (h5copy ${HDF5_TOOLS_H5COPY_SOURCE_DIR}/h5copy.c)
+H5_NAMING (h5copy)
+IF (WIN32)
+  IF (MSVC)
+    IF (NOT BUILD_SHARED_LIBS)
+      SET_TARGET_PROPERTIES (h5copy
+          PROPERTIES
+              LINK_FLAGS "/NODEFAULTLIB:MSVCRT"
+      ) 
+    ENDIF (NOT BUILD_SHARED_LIBS)
+  ENDIF (MSVC)
+ENDIF (WIN32)
+TARGET_LINK_LIBRARIES (h5copy  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+
+SET (H5_DEP_EXECUTABLES h5copy)
+
+IF (BUILD_TESTING)
+  IF (NOT BUILD_SHARED_LIBS)
+    ADD_EXECUTABLE (h5copygentest ${HDF5_TOOLS_H5COPY_SOURCE_DIR}/h5copygentest.c)
+    H5_NAMING (h5copygentest)
+    IF (WIN32)
+      IF (MSVC)
+        SET_TARGET_PROPERTIES (h5copygentest
+            PROPERTIES
+                LINK_FLAGS "/NODEFAULTLIB:MSVCRT"
+        ) 
+      ENDIF (MSVC)
+    ENDIF (WIN32)
+    TARGET_LINK_LIBRARIES (h5copygentest ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+
+    #ADD_TEST (NAME h5copygentest COMMAND $<TARGET_FILE:h5copygentest>)
+
+    SET (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES}
+        #h5copygentest
+    )
+  ENDIF (NOT BUILD_SHARED_LIBS)
+  
+  #-- Copy all the HDF5 files from the test directory into the source directory
+  SET (HDF5_REFERENCE_FILES
+      h5copy_extlinks_src.out.ls
+      h5copy_ref.out.ls
+      h5copytst.out.ls
+  )
+  SET (HDF5_REFERENCE_TEST_FILES
+      h5copy_extlinks_src.h5
+      h5copy_extlinks_trg.h5
+      h5copy_ref.h5
+      h5copytst.h5
+  )
+
+  FILE (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
+  FOREACH (ls_file ${HDF5_REFERENCE_FILES})
+    SET (lsdest "${PROJECT_BINARY_DIR}/testfiles/${ls_file}")
+    #MESSAGE (STATUS " Translating ${ls_file}")
+    ADD_CUSTOM_COMMAND (
+        TARGET     h5copy
+        POST_BUILD
+        COMMAND    ${XLATE_UTILITY}
+        ARGS       ${HDF5_TOOLS_H5COPY_SOURCE_DIR}/testfiles/${ls_file} ${lsdest} -l3
+    )
+  ENDFOREACH (ls_file ${HDF5_REFERENCE_FILES})
+
+  FOREACH (h5_file ${HDF5_REFERENCE_TEST_FILES})
+    SET (dest "${PROJECT_BINARY_DIR}/testfiles/${h5_file}")
+    #MESSAGE (STATUS " Copying ${h5_file}")
+    ADD_CUSTOM_COMMAND (
+        TARGET     h5copy
+        POST_BUILD
+        COMMAND    ${CMAKE_COMMAND}
+        ARGS       -E copy_if_different ${HDF5_TOOLS_H5COPY_SOURCE_DIR}/testfiles/${h5_file} ${dest}
+    )
+  ENDFOREACH (h5_file ${HDF5_REFERENCE_TEST_FILES})
+
+  # Test files
+  SET (HDF_FILE1 h5copytst)
+  SET (HDF_FILE2 h5copy_ref)
+  SET (HDF_EXT_SRC_FILE h5copy_extlinks_src)
+  SET (HDF_EXT_TRG_FILE h5copy_extlinks_trg)
+
+  MACRO (ADD_H5_TEST testname resultcode testfile vparam srcname dstname)
+  
+    IF (NOT "${ARGN}" STREQUAL "")
+      ADD_TEST (
+          NAME H5COPY-${testname}
+          COMMAND $<TARGET_FILE:h5copy> -f ${ARGN} -i ./testfiles/${testfile}.h5 -o ./testfiles/${testfile}.out.h5 -${vparam} -s ${srcname} -d ${dstname}
+      )
+    ELSE (NOT "${ARGN}" STREQUAL "")
+      ADD_TEST (
+          NAME H5COPY-${testname}
+          COMMAND $<TARGET_FILE:h5copy> -i ./testfiles/${testfile}.h5 -o ./testfiles/${testfile}.out.h5 -${vparam} -s ${srcname} -d ${dstname}
+      )
+    ENDIF (NOT "${ARGN}" STREQUAL "")
+    IF (NOT ${resultcode} STREQUAL "2")
+      ADD_TEST (
+          NAME H5COPY-DIFF_${testname}
+          COMMAND $<TARGET_FILE:h5diff> -q ./testfiles/${testfile}.h5 ./testfiles/${testfile}.out.h5 ${srcname} ${dstname}
+      )
+      IF (${resultcode} STREQUAL "1")
+        SET_TESTS_PROPERTIES (H5COPY-DIFF_${testname} PROPERTIES WILL_FAIL "true")
+      ENDIF (${resultcode} STREQUAL "1")
+    ENDIF (NOT ${resultcode} STREQUAL "2")
+  ENDMACRO (ADD_H5_TEST testname resultcode testfile vparam srcname dstname)
+
+
+  MACRO (ADD_H5LS_TEST file)
+    ADD_TEST (
+        NAME H5COPY-H5LS_${file}
+        COMMAND "${CMAKE_COMMAND}"
+            -D "TEST_PROGRAM=$<TARGET_FILE:h5ls>"
+            -D "TEST_ARGS=-Svr;./testfiles/${file}.out.h5"
+            -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+            -D "TEST_OUTPUT=./testfiles/${file}.out.out"
+            -D "TEST_EXPECT=0"
+            -D "TEST_REFERENCE=./testfiles/${file}.out.ls"
+            -D "TEST_MASK=true"
+            -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+    )
+  ENDMACRO (ADD_H5LS_TEST file)
+
+############# COPY OBJECTS ##############
+
+  # Remove any output file left over from previous test run
+  ADD_TEST (
+      NAME H5COPY-clear-objects
+      COMMAND    ${CMAKE_COMMAND}
+          -E remove 
+          ./testfiles/${HDF_FILE1}.out.h5
+          ./testfiles/${HDF_FILE1}.out.out
+  )
+  
+  # "Test copying various forms of datasets"
+  ADD_H5_TEST (simple 0 ${HDF_FILE1} v simple simple)
+  ADD_H5_TEST (chunk 0 ${HDF_FILE1} v chunk chunk)
+  ADD_H5_TEST (compact 0 ${HDF_FILE1} v compact compact)
+  ADD_H5_TEST (compound 0 ${HDF_FILE1} v compound compound)
+  ADD_H5_TEST (compressed 0 ${HDF_FILE1} v compressed compressed)
+  ADD_H5_TEST (named_vl 0 ${HDF_FILE1} v named_vl named_vl)
+  ADD_H5_TEST (nested_vl 0 ${HDF_FILE1} v nested_vl nested_vl)
+
+  # "Test copying dataset within group in source file to root of destination"
+  ADD_H5_TEST (simple_top 0 ${HDF_FILE1} v grp_dsets/simple simple_top)
+
+  # "Test copying & renaming dataset"
+  ADD_H5_TEST (rename 0 ${HDF_FILE1} v compound rename)
+
+  # "Test copying empty, 'full' & 'nested' groups"
+  ADD_H5_TEST (grp_empty 0 ${HDF_FILE1} v grp_empty grp_empty)
+  ADD_H5_TEST (grp_dsets 0 ${HDF_FILE1} v grp_dsets grp_dsets)
+  ADD_H5_TEST (grp_nested 0 ${HDF_FILE1} v grp_nested grp_nested)
+
+  # "Test copying dataset within group in source file to group in destination"
+  ADD_H5_TEST (simple_group 0 ${HDF_FILE1} v /grp_dsets/simple /grp_dsets/simple_group)
+
+  # "Test copying & renaming group"
+  ADD_H5_TEST (grp_rename 1 ${HDF_FILE1} v grp_dsets grp_rename)
+
+  # "Test copying 'full' group hierarchy into group in destination file"
+  ADD_H5_TEST (grp_dsets_rename 1 ${HDF_FILE1} v grp_dsets /grp_rename/grp_dsets)
+
+  # "Test copying objects into group hier. that doesn't exist yet in destination file"
+  ADD_H5_TEST (A_B1_simple 0 ${HDF_FILE1} vp simple /A/B1/simple)
+  ADD_H5_TEST (A_B2_simple2 0 ${HDF_FILE1} vp simple /A/B2/simple2)
+  ADD_H5_TEST (C_D_simple 0 ${HDF_FILE1} vp /grp_dsets/simple /C/D/simple)
+  ADD_H5_TEST (E_F_grp_dsets 1 ${HDF_FILE1} vp /grp_dsets /E/F/grp_dsets)
+  ADD_H5_TEST (G_H_grp_nested 1 ${HDF_FILE1} vp /grp_nested /G/H/grp_nested)
+
+  # Verify that the file created above is correct
+  ADD_H5LS_TEST (${HDF_FILE1})
+  
+############# COPY REFERENCES ##############
+
+  # Remove any output file left over from previous test run
+  ADD_TEST (
+      NAME H5COPY-clear-refs
+      COMMAND    ${CMAKE_COMMAND}
+          -E remove 
+          ./testfiles/${HDF_FILE2}.out.h5
+          ./testfiles/${HDF_FILE2}.out.out
+  )
+
+  # "Test copying object and region references"
+  ADD_H5_TEST (region_ref 2 ${HDF_FILE2} v / /COPY ref)
+
+  # Verify that the file created above is correct
+  ADD_H5LS_TEST (${HDF_FILE2})
+
+############# COPY EXT LINKS ############## 
+
+  # Remove any output file left over from previous test run
+  ADD_TEST (
+      NAME H5COPY-clear-ext-links
+      COMMAND    ${CMAKE_COMMAND}
+          -E remove 
+          ./testfiles/${HDF_EXT_SRC_FILE}.out.h5
+          ./testfiles/${HDF_EXT_SRC_FILE}.out.out
+  )
+
+  # "Test copying external link directly without -f ext"
+  ADD_H5_TEST (ext_link 2 ${HDF_EXT_SRC_FILE} v /group_ext/extlink_dset /copy1_dset)
+
+  # "Test copying external link directly with -f ext"
+  ADD_H5_TEST (ext_link_f 2 ${HDF_EXT_SRC_FILE} v /group_ext/extlink_dset /copy2_dset ext)
+
+  # "Test copying dangling external link (no obj) directly without -f ext"
+  ADD_H5_TEST (ext_dangle_noobj 0 ${HDF_EXT_SRC_FILE} v /group_ext/extlink_notyet1 /copy_dangle1_1)
+
+  # "Test copying dangling external link (no obj) directly with -f ext"
+  ADD_H5_TEST (ext_dangle_noobj_f 2 ${HDF_EXT_SRC_FILE} v /group_ext/extlink_notyet1 /copy_dangle1_2 ext)
+
+  # "Test copying dangling external link (no file) directly without -f ext"
+  ADD_H5_TEST (ext_dangle_nofile 0 ${HDF_EXT_SRC_FILE} v /group_ext/extlink_notyet2 /copy_dangle2_1)
+
+  # "Test copying dangling external link (no file) directly with -f ext"
+  ADD_H5_TEST (ext_dangle_nofile_f 2 ${HDF_EXT_SRC_FILE} v /group_ext/extlink_notyet2 /copy_dangle2_2 ext)
+
+  # "Test copying a group contains external links without -f ext"
+  ADD_H5_TEST (ext_link_group 2 ${HDF_EXT_SRC_FILE} v /group_ext /copy1_group)
+
+  # "Test copying a group contains external links with -f ext"
+  ADD_H5_TEST (ext_link_group_f 2 ${HDF_EXT_SRC_FILE} v /group_ext /copy2_group ext) 
+
+  # Verify that the file created above is correct
+  ADD_H5LS_TEST (${HDF_EXT_SRC_FILE})
+  
+ENDIF (BUILD_TESTING)
+
+#-----------------------------------------------------------------------------

+# Rules for Installation of tools using make Install target

+#-----------------------------------------------------------------------------

+INSTALL (
+    TARGETS
+        h5copy
+    RUNTIME DESTINATION
+        bin/tools
+    COMPONENT
+        toolsapplications
+)
diff --git a/tools/h5copy/Makefile.in b/tools/h5copy/Makefile.in
index 48052b3..0ac4799 100644
--- a/tools/h5copy/Makefile.in
+++ b/tools/h5copy/Makefile.in
@@ -192,12 +192,12 @@ INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 INSTRUMENT = @INSTRUMENT@
 INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@
+LARGEFILE = @LARGEFILE@
 LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
-LINUX_LFS = @LINUX_LFS@
 LIPO = @LIPO@
 LL_PATH = @LL_PATH@
 LN_S = @LN_S@
diff --git a/tools/h5copy/h5copy.c b/tools/h5copy/h5copy.c
index 0ea8e16..89cb5fb 100644
--- a/tools/h5copy/h5copy.c
+++ b/tools/h5copy/h5copy.c
@@ -19,8 +19,8 @@
 #include <string.h>
 #include <stdlib.h>
 
-const char *progname="h5copy";
-int   d_status;
+/* Name of tool */
+#define PROGRAMNAME "h5copy"
 
 /* command-line options: short and long-named parameters */
 static const char *s_opts = "d:f:hi:o:ps:vV";
@@ -176,7 +176,7 @@ static int parse_flag(const char* str_flag, unsigned *flag)
  }
  else
  {
-  error_msg(progname, "Error in input flag\n");
+  error_msg("Error in input flag\n");
   return -1;
  }
 
@@ -216,7 +216,9 @@ main (int argc, const char *argv[])
  int          li_ret;
  h5tool_link_info_t linkinfo;
 
- /* initialize h5tools lib */
+ h5tools_setprogname(PROGRAMNAME);
+ h5tools_setstatus(EXIT_SUCCESS);
+/* initialize h5tools lib */
  h5tools_init();
 
  /* Check for no command line parameters */
@@ -266,7 +268,7 @@ main (int argc, const char *argv[])
    break;
 
   case 'V':
-   print_version(progname);
+   print_version(h5tools_getprogname());
    leave(EXIT_SUCCESS);
    break;
 
@@ -286,28 +288,28 @@ main (int argc, const char *argv[])
 
  if (fname_src==NULL)
  {
-  error_msg(progname, "Input file name missing\n");
+  error_msg("Input file name missing\n");
   usage();
   leave(EXIT_FAILURE);
  }
 
  if (fname_dst==NULL)
  {
-  error_msg(progname, "Output file name missing\n");
+  error_msg("Output file name missing\n");
   usage();
   leave(EXIT_FAILURE);
  }
 
  if (oname_src==NULL)
  {
-  error_msg(progname, "Source object name missing\n");
+  error_msg("Source object name missing\n");
   usage();
   leave(EXIT_FAILURE);
  }
 
  if (oname_dst==NULL)
  {
-  error_msg(progname, "Destination object name missing\n");
+  error_msg("Destination object name missing\n");
   usage();
   leave(EXIT_FAILURE);
  }
@@ -324,7 +326,7 @@ main (int argc, const char *argv[])
  *-------------------------------------------------------------------------*/
  if (fid_src==-1)
  {
-  error_msg(progname, "Could not open input file <%s>...Exiting\n", fname_src);
+  error_msg("Could not open input file <%s>...Exiting\n", fname_src);
   if (fname_src)
    free(fname_src);
   leave(EXIT_FAILURE);
@@ -347,7 +349,7 @@ main (int argc, const char *argv[])
  *-------------------------------------------------------------------------*/
  if (fid_dst==-1)
  {
-  error_msg(progname, "Could not open output file <%s>...Exiting\n", fname_dst);
+  error_msg("Could not open output file <%s>...Exiting\n", fname_dst);
   if (fname_src)
    free(fname_src);
   if (fname_dst)
@@ -388,7 +390,7 @@ main (int argc, const char *argv[])
 
     /* Create link creation property list */
     if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
-        error_msg(progname, "Could not create link creation property list\n");
+        error_msg("Could not create link creation property list\n");
         goto error;
     } /* end if */
 
@@ -396,13 +398,13 @@ main (int argc, const char *argv[])
     if(parents) {
         /* Set the intermediate group creation property */
         if(H5Pset_create_intermediate_group(lcpl_id, 1) < 0) {
-            error_msg(progname, "Could not set property for creating parent groups\n");
+            error_msg("Could not set property for creating parent groups\n");
             goto error;
         } /* end if */
 
         /* Display some output if requested */
         if(verbose)
-            printf("%s: Creating parent groups\n", progname);
+            printf("%s: Creating parent groups\n", h5tools_getprogname());
     } /* end if */
 
 /*-------------------------------------------------------------------------
diff --git a/tools/h5copy/h5copygentest.c b/tools/h5copy/h5copygentest.c
index e52b700..26a2588 100644
--- a/tools/h5copy/h5copygentest.c
+++ b/tools/h5copy/h5copygentest.c
@@ -21,6 +21,9 @@
 #include "H5private.h"
 #include "h5tools.h"
 
+/* Name of tool */
+#define PROGRAMNAME "h5copygentest"
+
 /* HDF file names */
 #define HDF_FILE1                "h5copytst.h5"
 #define HDF_FILE1_NEW            "h5copytst_new.h5"
@@ -420,6 +423,10 @@ static herr_t gen_obj_ref(hid_t loc_id)
     hsize_t dims2[1]={2};
     int data[3] = {10,20,30};
     int status;
+    /*---------------------
+     * create obj references to the previously created objects.
+     * Passing -1 as reference is an object.*/
+    hobj_ref_t or_data[2];  /* write buffer */
     herr_t ret = SUCCEED;
 
     /*--------------
@@ -462,11 +469,6 @@ static herr_t gen_obj_ref(hid_t loc_id)
     }
      H5Gclose(oid);
 
-    /*---------------------
-     * create obj references to the previously created objects.
-     * Passing -1 as reference is an object.*/
-     hobj_ref_t or_data[2];  /* write buffer */
-
     status = H5Rcreate (&or_data[0], loc_id, OBJ_REF_DS, H5R_OBJECT, -1);
     if (status < 0)
     {
@@ -914,6 +916,9 @@ out:
 
 int main(void)
 {
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
     Test_Obj_Copy();
     Test_Ref_Copy();
     Test_Extlink_Copy();
diff --git a/tools/h5copy/testh5copy.sh b/tools/h5copy/testh5copy.sh
index ad731b6..029caf9 100644
--- a/tools/h5copy/testh5copy.sh
+++ b/tools/h5copy/testh5copy.sh
@@ -41,6 +41,7 @@ DIFF='diff -c'
 
 nerrors=0
 verbose=yes
+h5haveexitcode=yes	    # default is yes
 
 # The build (current) directory might be different than the source directory.
 if test -z "$srcdir"; then
@@ -51,6 +52,13 @@ OUTDIR=./testfiles
 
 test -d $OUTDIR || mkdir $OUTDIR
 
+# RUNSERIAL is used. Check if it can return exit code from executalbe correctly.
+if [ -n "$RUNSERIAL_NOEXITCODE" ]; then
+    echo "***Warning*** Serial Exit Code is not passed back to shell corretly."
+    echo "***Warning*** Exit code checking is skipped."
+    h5haveexitcode=no
+fi
+
 # Print a "SKIP" message
 SKIP() {
 	 TESTING $H5COPY $@
@@ -200,7 +208,7 @@ H5DIFFTEST_FAIL()
     $RUNSERIAL $H5DIFF_BIN -q "$@" 
     RET=$?
 
-    if [ $RET != 1 ] ; then
+    if [ $h5haveexitcode = 'yes' -a $RET != 1 ] ; then
          echo "*FAILED*"
          nerrors="`expr $nerrors + 1`"
     else