[svn-r17238] Purpose: Fix bug and improve readability

Description:
    - Revised DataSet::write to pass in correct string buffer
    - Added member function DataSet::getInMemDataSize() to simplify
      getting the dataset's data size in memory.
    - Added private functions for reading fixed- and variable-length
      string data: p_read_fixed_len and p_read_variable_len.
    - Added tests to write/read array of strings to datasets.

Platforms tested:
    Linux/32 2.6 (jam)
    FreeBSD/64 6.3 (liberty)
    SunOS 5.10 (linew)

6 files changed, 214 insertions, 26 deletions

diff --git a/c++/src/H5AbstractDs.cpp b/c++/src/H5AbstractDs.cpp
index a61cc88..19eeb33 100644
--- a/c++/src/H5AbstractDs.cpp
+++ b/c++/src/H5AbstractDs.cpp
@@ -25,6 +25,11 @@
 #include "H5CommonFG.h"
 #include "H5Alltypes.h"
 
+#include <iostream> // remove when done
+
+    using std::cerr;
+    using std::endl;
+
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
 #endif
diff --git a/c++/src/H5AbstractDs.h b/c++/src/H5AbstractDs.h
index c98e5e1..1d04d6c 100644
--- a/c++/src/H5AbstractDs.h
+++ b/c++/src/H5AbstractDs.h
@@ -51,6 +51,9 @@ class H5_DLLCPP AbstractDs {
 	StrType getStrType() const;
 	VarLenType getVarLenType() const;
 
+	// Gets the size in memory of this abstract dataset.
+	virtual size_t getInMemDataSize() const = 0;
+
 	// Gets the dataspace of this abstract dataset - pure virtual.
 	virtual DataSpace getSpace() const = 0;
 
diff --git a/c++/src/H5Attribute.cpp b/c++/src/H5Attribute.cpp
index b1ab73e..6de5e63 100644
--- a/c++/src/H5Attribute.cpp
+++ b/c++/src/H5Attribute.cpp
@@ -198,35 +198,37 @@ void Attribute::read(const DataType& mem_type, H5std_string& strg) const
 //--------------------------------------------------------------------------
 size_t Attribute::getInMemDataSize() const
 {
+    char *func = "Attribute::getInMemDataSize";
+
     // Get the data type of this attribute
     hid_t mem_type_id = H5Aget_type(id);
-    if (mem_type_id <= 0)
+    if( mem_type_id < 0 )
     {
-	throw AttributeIException("Attribute::getInMemDataSize", "H5Aget_type failed");
+	throw AttributeIException(func, "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::getInMemDataSize", "H5Tget_native_type failed");
+	throw AttributeIException(func, "H5Tget_native_type failed");
     }
     size_t type_size = H5Tget_size(native_type);
     if (type_size == 0)
     {
-	throw AttributeIException("Attribute::getInMemDataSize", "H5Tget_size failed");
+	throw AttributeIException(func, "H5Tget_size failed");
     }
 
     // Get number of elements of the attribute
     hid_t space_id = H5Aget_space(id);
     if (space_id < 0)
     {
-	throw AttributeIException("Attribute::getInMemDataSize", "H5Aget_space failed");
+	throw AttributeIException(func, "H5Aget_space failed");
     }
     hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
     if (num_elements < 0)
     {
-	throw AttributeIException("Attribute::getInMemDataSize", "H5Sget_simple_extent_npoints failed");
+	throw AttributeIException(func, "H5Sget_simple_extent_npoints failed");
     }
 
     // Calculate and return the size of the data
diff --git a/c++/src/H5Attribute.h b/c++/src/H5Attribute.h
index abece10..284e5bc 100644
--- a/c++/src/H5Attribute.h
+++ b/c++/src/H5Attribute.h
@@ -38,10 +38,10 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent {
 	virtual DataSpace getSpace() const;
 
 	// Returns the amount of storage size required for this attribute.
-	hsize_t getStorageSize() const;
+	virtual hsize_t getStorageSize() const;
 
 	// Returns the in memory size of this attribute's data.
-	size_t getInMemDataSize() const;
+	virtual size_t getInMemDataSize() const;
 
 	// Reads data from this attribute.
 	void read( const DataType& mem_type, void *buf ) const;
@@ -82,7 +82,7 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent {
 	// sub-types
 	virtual hid_t p_get_type() const;
 
-	// Reads variable or fixed len strings
+	// Reads variable or fixed len strings from this attribute.
 	void p_read_variable_len(const DataType& mem_type, H5std_string& strg) const;
 	void p_read_fixed_len(const DataType& mem_type, H5std_string& strg) const;
 
diff --git a/c++/src/H5DataSet.cpp b/c++/src/H5DataSet.cpp
index 494d3ea..cddb5d4 100644
--- a/c++/src/H5DataSet.cpp
+++ b/c++/src/H5DataSet.cpp
@@ -37,6 +37,7 @@
 #include "H5File.h"
 #include "H5Attribute.h"
 #include "H5DataSet.h"
+#include "H5private.h"		// for HDfree
 
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
@@ -220,6 +221,53 @@ hsize_t DataSet::getStorageSize() const
 }
 
 //--------------------------------------------------------------------------
+// Function:	DataSet::getInMemDataSize
+///\brief	Gets the size in memory of the dataset's data.
+///\return	Size of data (in memory)
+///\exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Apr 2009
+//--------------------------------------------------------------------------
+size_t DataSet::getInMemDataSize() const
+{
+    char *func = "DataSet::getInMemDataSize";
+
+    // Get the data type of this dataset
+    hid_t mem_type_id = H5Dget_type(id);
+    if( mem_type_id < 0 )
+    {
+	throw DataSetIException(func, "H5Dget_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 DataSetIException(func, "H5Tget_native_type failed");
+    }
+    size_t type_size = H5Tget_size(native_type);
+    if (type_size == 0)
+    {
+	throw DataSetIException(func, "H5Tget_size failed");
+    }
+
+    // Get number of elements of the dataset
+    hid_t space_id = H5Dget_space(id); // first get its data space
+    if (space_id < 0)
+    {
+	throw DataSetIException(func, "H5Dget_space failed");
+    }
+    hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
+    if (num_elements < 0)
+    {
+	throw DataSetIException(func, "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:	DataSet::getOffset
 ///\brief	Returns the address of this dataset in the file.
 ///\return	Address of dataset
@@ -364,20 +412,45 @@ void DataSet::read( void* buf, const DataType& mem_type, const DataSpace& mem_sp
 // Function:	DataSet::read
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It takes a reference to a \c std::string for the buffer.
+///\param	buf - IN: Buffer for read data
+///\param	mem_type - IN: Memory datatype
+///\param	mem_space - IN: Memory dataspace
+///\param	file_space - IN: Dataset's dataspace in the file
+///\param	xfer_plist - IN: Transfer property list for this I/O operation
+///\exception	H5::DataSetIException
 // Programmer	Binh-Minh Ribler - 2000
-//--------------------------------------------------------------------------
-void DataSet::read( H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
+// Modification
+//	Jul 2009
+//		Follow the change to Attribute::read and use the following
+//		private functions to read datasets with fixed- and
+//		variable-length string:
+//			DataSet::p_read_fixed_len and
+//			DataSet::p_read_variable_len
+//--------------------------------------------------------------------------
+void DataSet::read(H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist) const
 {
-   // Allocate C character string for reading
-   size_t size = mem_type.getSize();
-   char* strg_C = new char[size+1];  // temporary C-string for C API
+    // Check if this dataset 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 DataSetIException("DataSet::read", "H5Tis_variable_str failed");
+    }
 
-   // Use the overloaded member to read
-   read(strg_C, mem_type, mem_space, file_space, xfer_plist);
+    // Obtain identifiers for C API
+    hid_t mem_type_id = mem_type.getId();
+    hid_t mem_space_id = mem_space.getId();
+    hid_t file_space_id = file_space.getId();
+    hid_t xfer_plist_id = xfer_plist.getId();
 
-   // Get the String and clean up
-   strg = strg_C;
-   delete []strg_C;
+    if (!is_variable_len)       // only allocate for fixed-len string
+    {
+        p_read_fixed_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg);
+    }
+    else
+    {
+        p_read_variable_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg);
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -416,15 +489,46 @@ void DataSet::write( const void* buf, const DataType& mem_type, const DataSpace&
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It takes a reference to a \c std::string for the buffer.
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	Jul 2009
+//		Modified to pass the buffer into H5Dwrite properly depending
+//		whether the dataset has variable- or fixed-length string.
 //--------------------------------------------------------------------------
 void DataSet::write( const H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) 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 DataSetIException("DataSet::write", "H5Tis_variable_str failed");
+    }
+
+   // Obtain identifiers for C API
+   hid_t mem_type_id = mem_type.getId();
+   hid_t mem_space_id = mem_space.getId();
+   hid_t file_space_id = file_space.getId();
+   hid_t xfer_plist_id = xfer_plist.getId();
+
+    // 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;
 
-   // Use the overloaded member
-   write(strg_C, mem_type, mem_space, file_space, xfer_plist);
+    // Pass string in differently depends on variable or fixed length
+    if (!is_variable_len)
+    {
+        ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C );
+    }
+    else
+    {
+        // passing string argument by address
+        ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C );
+    }
+    if (ret_value < 0)
+    {
+        throw DataSetIException("DataSet::write", "H5Dwrite failed");
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -586,7 +690,74 @@ hid_t DataSet::getId() const
 }
 
 //--------------------------------------------------------------------------
-// Function:    DataSet::p_setId
+// Function:	DataSet::p_read_fixed_len (private)
+// brief	Reads a fixed length \a H5std_string from an dataset.
+// param	mem_type  - IN: DataSet datatype (in memory)
+// param	strg      - IN: Buffer for read string
+// exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Jul, 2009
+// Modification
+//	Jul 2009
+//		Added in follow to the change in Attribute::read
+//--------------------------------------------------------------------------
+void DataSet::p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const
+{
+    // Only allocate for fixed-len string.
+
+    // Get the size of the dataset's data
+    size_t attr_size = getInMemDataSize();
+
+    // If there is data, allocate buffer and read it.
+    if (attr_size > 0)
+    {
+	char *strg_C = NULL;
+
+	strg_C = new char [(size_t)attr_size+1];
+	herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C);
+
+	if( ret_value < 0 )
+	{
+	    delete []strg_C;	// de-allocate for fixed-len string
+	    throw DataSetIException("DataSet::read", "H5Dread failed for fixed length string");
+	}
+
+	// Get string from the C char* and release resource allocated locally
+	strg = strg_C;
+	delete []strg_C;
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataSet::p_read_variable_len (private)
+// brief	Reads a variable length \a H5std_string from an dataset.
+// param	mem_type  - IN: DataSet datatype (in memory)
+// param	strg      - IN: Buffer for read string
+// exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Jul, 2009
+// Modification
+//	Jul 2009
+//		Added in follow to the change in Attribute::read
+//--------------------------------------------------------------------------
+void DataSet::p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const
+{
+    // Prepare and call C API to read dataset.
+    char *strg_C;
+
+    // Read dataset, no allocation for variable-len string; C library will
+    herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C);
+
+    if( ret_value < 0 )
+    {
+	throw DataSetIException("DataSet::read", "H5Dread failed for variable length string");
+    }
+
+    // Get string from the C char* and release resource allocated by C API
+    strg = strg_C;
+    HDfree(strg_C);
+}
+
+//--------------------------------------------------------------------------
+// Function:    DataSet::p_setId (private)
 ///\brief       Sets the identifier of this object to a new value.
 ///
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
diff --git a/c++/src/H5DataSet.h b/c++/src/H5DataSet.h
index f26d775..3d9183d 100644
--- a/c++/src/H5DataSet.h
+++ b/c++/src/H5DataSet.h
@@ -49,7 +49,10 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
 	void getSpaceStatus(H5D_space_status_t& status) const;
 
 	// Returns the amount of storage size required for this dataset.
-	hsize_t getStorageSize() const;
+	virtual hsize_t getStorageSize() const;
+
+	// Returns the in memory size of this attribute's data.
+	virtual size_t getInMemDataSize() const;
 
 	// Returns the number of bytes required to store VL data.
 	hsize_t getVlenBufSize( DataType& type, DataSpace& space ) const;
@@ -113,6 +116,10 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
         // sub-types
 	virtual hid_t p_get_type() const;
 
+	// Reads variable or fixed len strings from this dataset.
+	void p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const;
+	void p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const;
+
    protected:
         // Sets the dataset id.
         virtual void p_setId(const hid_t new_id);