[svn-r16825] Description:

	Bring revisions 16636:16821 from trunk to revise_chunks branch

Tested on:
	FreeBSD/32 6.3 (duty)
	Mac OS X/32 10.5.6 (amazon)
	(h5committest not needed on this branch)

4 files changed, 183 insertions, 47 deletions

diff --git a/c++/src/H5Attribute.cpp b/c++/src/H5Attribute.cpp
index c90076c..a844b77 100644
--- a/c++/src/H5Attribute.cpp
+++ b/c++/src/H5Attribute.cpp
@@ -34,6 +34,7 @@
 #include "H5DataSpace.h"
 #include "H5File.h"
 #include "H5Attribute.h"
+#include "H5private.h"		// for HDfree
 
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
@@ -95,23 +96,40 @@ void Attribute::write( const DataType& mem_type, const void *buf ) const
 //--------------------------------------------------------------------------
 // Function:	Attribute::write
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It writes a \a std::string to this attribute.
+///		It writes a \a H5std_string to this attribute.
 ///\param	mem_type  - IN: Attribute datatype (in memory)
 ///\param	strg      - IN: Data to be written
 ///\exception	H5::AttributeIException
 // Programmer	Binh-Minh Ribler - Apr, 2003
 //--------------------------------------------------------------------------
-void Attribute::write( const DataType& mem_type, const H5std_string& strg ) const
+void Attribute::write(const DataType& mem_type, const H5std_string& strg) const
 {
-   // Convert string to C-string
-   const char* strg_C;
-   strg_C = strg.c_str();  // strg_C refers to the contents of strg as a C-str
+    // Check if this attribute has variable-len string or fixed-len string and
+    // proceed appropriately.
+    htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
+    if (is_variable_len < 0)
+    {
+	throw AttributeIException("Attribute::write", "H5Tis_variable_str failed");
+    }
+    // Convert string to C-string
+    const char* strg_C;
+    strg_C = strg.c_str();  // strg_C refers to the contents of strg as a C-str
+    herr_t ret_value = 0;
 
-   herr_t ret_value = H5Awrite( id, mem_type.getId(), &strg_C );
-   if( ret_value < 0 )
-   {
-      throw AttributeIException("Attribute::write", "H5Awrite failed");
-   }
+    // Pass string in differently depends on variable or fixed length
+    if (!is_variable_len)
+    {
+	ret_value = H5Awrite(id, mem_type.getId(), strg_C);
+    }
+    else
+    {
+	// passing third argument by address
+	ret_value = H5Awrite(id, mem_type.getId(), &strg_C);
+    }
+    if (ret_value < 0)
+    {
+	throw AttributeIException("Attribute::write", "H5Awrite failed");
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -127,14 +145,58 @@ void Attribute::read( const DataType& mem_type, void *buf ) const
    herr_t ret_value = H5Aread( id, mem_type.getId(), buf );
    if( ret_value < 0 )
    {
-      throw AttributeIException("Attribute::read", "H5Aread  failed");
+      throw AttributeIException("Attribute::read", "H5Aread failed");
    }
 }
 
 //--------------------------------------------------------------------------
+// Function:	Attribute::getInMemDataSize
+///\brief	Gets the size in memory of the attribute's data.
+///\exception	H5::AttributeIException
+// Programmer	Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+size_t Attribute::getInMemDataSize() const
+{
+    // Get the data type of this attribute
+    hid_t mem_type_id = H5Aget_type(id);
+    if (mem_type_id <= 0)
+    {
+	throw AttributeIException("Attribute::getDataSize", "H5Aget_type failed");
+    }
+
+    // Get the data type's size
+    hid_t native_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT);
+    if (native_type < 0)
+    {
+	throw AttributeIException("Attribute::read", "H5Tget_native_type failed");
+    }
+    size_t type_size = H5Tget_size(native_type);
+    if (type_size == 0)
+    {
+	throw AttributeIException("Attribute::read", "H5Tget_size failed");
+    }
+
+    // Get number of elements of the attribute
+    hid_t space_id = H5Aget_space(id);
+    if (space_id < 0)
+    {
+	throw AttributeIException("Attribute::read", "H5Aget_space failed");
+    }
+    hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
+    if (num_elements < 0)
+    {
+	throw AttributeIException("Attribute::read", "H5Sget_simple_extent_npoints failed");
+    }
+
+    // Calculate and return the size of the data
+    size_t data_size = type_size * num_elements;
+    return(data_size);
+}
+
+//--------------------------------------------------------------------------
 // Function:	Attribute::read
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It reads a \a std::string from this attribute.
+///		It reads a \a H5std_string from this attribute.
 ///\param	mem_type  - IN: Attribute datatype (in memory)
 ///\param	strg      - IN: Buffer for read string
 ///\exception	H5::AttributeIException
@@ -145,31 +207,72 @@ void Attribute::read( const DataType& mem_type, void *buf ) const
 //		space for the buffer.  Obtained the attribute size and
 //		allocated memory properly. - BMR
 //--------------------------------------------------------------------------
-void Attribute::read( const DataType& mem_type, H5std_string& strg ) const
+void Attribute::read(const DataType& mem_type, H5std_string& strg) const
 {
-   // Get the attribute size and allocate temporary C-string for C API
-   hsize_t attr_size = H5Aget_storage_size(id);
-   if (attr_size <= 0)
-   {
-      throw AttributeIException("Attribute::read", "Unable to get attribute size before reading");
-   }
-   char* strg_C = new char [(size_t)attr_size+1];
-   if (strg_C == NULL)
-   {
-      throw AttributeIException("Attribute::read", "Unable to allocate buffer to read the attribute");
-   }
 
-   // Call C API to get the attribute data, a string of chars
-   herr_t ret_value = H5Aread(id, mem_type.getId(), &strg_C);
-   if( ret_value < 0 )
-   {
-      throw AttributeIException("Attribute::read", "H5Aread failed");
-   }
+    // Check if this attribute has variable-len string or fixed-len string and
+    // proceed appropriately.
+    htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
+    if (is_variable_len < 0)
+    {
+	throw AttributeIException("Attribute::write", "H5Tis_variable_str failed");
+    }
+
+    // Prepare and call C API to read attribute.
+    char *strg_C;
+    herr_t ret_value = 0;
+    size_t attr_size;
+    if (!is_variable_len)	// only allocate for fixed-len string
+    {
+	// Get the size of the attribute's data
+	attr_size = getInMemDataSize();
+
+	if (attr_size > 0)
+	{
+	    strg_C = new char [(size_t)attr_size+1];
+	    if (strg_C == NULL)
+	    {
+		throw AttributeIException("Attribute::read",
+			"Unable to allocate buffer to read the attribute");
+	    }
+	    ret_value = H5Aread(id, mem_type.getId(), strg_C);
+	}
+	else
+	    HDstrcpy(strg_C, "");
+    }
+    else
+    {
+	// no allocation for variable-len string; C library will
+	ret_value = H5Aread(id, mem_type.getId(), &strg_C);
+    }
+    if( ret_value < 0 )
+    {
+	if (!is_variable_len)	// only de-allocate for fixed-len string
+	    delete []strg_C;
+	throw AttributeIException("Attribute::read", "H5Aread failed");
+    }
 
-   // Get 'string' from the C char* and release resource
-   strg_C[attr_size] = '\0';
-   strg = strg_C;
-   delete []strg_C;
+    if( ret_value < 0 )
+    {
+	if (!is_variable_len)	// only de-allocate for fixed-len string
+	    delete []strg_C;
+	throw AttributeIException("Attribute::read", "H5Aread failed");
+    }
+
+    // Get string from the C char* and release resource allocated locally
+    if (!is_variable_len)
+    {
+	if (strg_C != "")
+	    strg_C[attr_size] = '\0';
+	strg = strg_C;
+	delete []strg_C;
+    }
+    // Get string from the C char* and release resource allocated by C API
+    else
+    {
+	strg = strg_C;
+	HDfree(strg_C);
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -342,21 +445,21 @@ hid_t Attribute::getId() const
 ///\brief       Sets the identifier of this object to a new value.
 ///
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
-///             object fails
+///		object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
-//              that the current valid id of this object is properly closed.
-//              Then the object's id is reset to the new id.
+//		The underlaying reference counting in the C library ensures
+//		that the current valid id of this object is properly closed.
+//		Then the object's id is reset to the new id.
 // Programmer   Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void Attribute::p_setId(const hid_t new_id)
 {
     // handling references to this old id
     try {
-        close();
+	close();
     }
     catch (Exception close_error) {
-        throw AttributeIException("Attribute::p_setId", close_error.getDetailMsg());
+	throw AttributeIException("Attribute::p_setId", close_error.getDetailMsg());
     }
    // reset object's id to the given id
    id = new_id;
diff --git a/c++/src/H5Attribute.h b/c++/src/H5Attribute.h
index 9cf91ba..00a08a5 100644
--- a/c++/src/H5Attribute.h
+++ b/c++/src/H5Attribute.h
@@ -40,6 +40,9 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent {
 	// Returns the amount of storage size required for this attribute.
 	hsize_t getStorageSize() const;
 
+	// Returns the in memory size of this attribute's data.
+	size_t getInMemDataSize() const;
+
 	// Reads data from this attribute.
 	void read( const DataType& mem_type, void *buf ) const;
 	void read( const DataType& mem_type, H5std_string& strg ) const;
diff --git a/c++/src/Makefile.am b/c++/src/Makefile.am
index 3b1ed0d..c18b990 100644
--- a/c++/src/Makefile.am
+++ b/c++/src/Makefile.am
@@ -19,6 +19,7 @@
 #
 
 include $(top_srcdir)/config/commence.am
+include $(top_srcdir)/config/lt_vers.am
 
 # Include src directory
 INCLUDES=-I$(top_srcdir)/src
@@ -26,6 +27,9 @@ INCLUDES=-I$(top_srcdir)/src
 # This is our main target
 lib_LTLIBRARIES=libhdf5_cpp.la
 
+# Add libtool numbers to the HDF5 C++ library (from config/lt_vers.am)
+libhdf5_cpp_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
+
 # Shared C++ libraries aren't universally supported.
 if CXX_SHARED_CONDITIONAL
 else
diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in
index 9d50223..abe8590 100644
--- a/c++/src/Makefile.in
+++ b/c++/src/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.10.1 from Makefile.am.
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -54,7 +54,8 @@ host_triplet = @host@
 DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
 	$(srcdir)/Makefile.in $(srcdir)/h5c++.in \
 	$(top_srcdir)/config/commence.am \
-	$(top_srcdir)/config/conclude.am
+	$(top_srcdir)/config/conclude.am \
+	$(top_srcdir)/config/lt_vers.am
 TESTS =
 subdir = c++/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -83,6 +84,9 @@ am_libhdf5_cpp_la_OBJECTS = H5Exception.lo H5IdComponent.lo \
 	H5StrType.lo H5ArrayType.lo H5VarLenType.lo H5CompType.lo \
 	H5DataSet.lo H5CommonFG.lo H5Group.lo H5File.lo
 libhdf5_cpp_la_OBJECTS = $(am_libhdf5_cpp_la_OBJECTS)
+libhdf5_cpp_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
+	$(CXXFLAGS) $(libhdf5_cpp_la_LDFLAGS) $(LDFLAGS) -o $@
 binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
 SCRIPTS = $(bin_SCRIPTS)
 DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src
@@ -353,12 +357,21 @@ TRACE = perl $(top_srcdir)/bin/trace
 # *.clog are from the MPE option.
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog
 
+# Add libtool shared library version numbers to the HDF5 library
+# See libtool versioning documentation online.
+LT_VERS_INTERFACE = 6
+LT_VERS_REVISION = 29
+LT_VERS_AGE = 0
+
 # Include src directory
 INCLUDES = -I$(top_srcdir)/src
 
 # This is our main target
 lib_LTLIBRARIES = libhdf5_cpp.la
 
+# Add libtool numbers to the HDF5 C++ library (from config/lt_vers.am)
+libhdf5_cpp_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
+
 # Shared C++ libraries aren't universally supported.
 @CXX_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
 bin_SCRIPTS = h5c++
@@ -408,12 +421,12 @@ all: all-am
 
 .SUFFIXES:
 .SUFFIXES: .cpp .lo .o .obj
-$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir)/config/commence.am $(top_srcdir)/config/conclude.am $(am__configure_deps)
+$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir)/config/commence.am $(top_srcdir)/config/lt_vers.am $(top_srcdir)/config/conclude.am $(am__configure_deps)
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
-	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
-		&& exit 0; \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
 	      exit 1;; \
 	  esac; \
 	done; \
@@ -467,7 +480,7 @@ clean-libLTLIBRARIES:
 	  rm -f "$${dir}/so_locations"; \
 	done
 libhdf5_cpp.la: $(libhdf5_cpp_la_OBJECTS) $(libhdf5_cpp_la_DEPENDENCIES) 
-	$(CXXLINK) -rpath $(libdir) $(libhdf5_cpp_la_OBJECTS) $(libhdf5_cpp_la_LIBADD) $(LIBS)
+	$(libhdf5_cpp_la_LINK) -rpath $(libdir) $(libhdf5_cpp_la_OBJECTS) $(libhdf5_cpp_la_LIBADD) $(LIBS)
 install-binSCRIPTS: $(bin_SCRIPTS)
 	@$(NORMAL_INSTALL)
 	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
@@ -570,7 +583,7 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonemtpy = 1; } \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
 	      END { if (nonempty) { for (i in files) print i; }; }'`; \
 	mkid -fID $$unique
 tags: TAGS
@@ -762,6 +775,19 @@ uninstall-am: uninstall-binSCRIPTS uninstall-includeHEADERS \
 help:
 	@$(top_srcdir)/bin/makehelp
 
+# 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 files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+
 # Some C++ compilers/linkers (PGI?) create a directory named "ii_files" that
 # holds *.ii files, which are template entity instantiations.
 # This entire directory should be cleaned.