diff options
Diffstat (limited to 'c++')
44 files changed, 611 insertions, 157 deletions
diff --git a/c++/Makefile.in b/c++/Makefile.in index 36364eb..c964e95 100644 --- a/c++/Makefile.in +++ b/c++/Makefile.in @@ -405,7 +405,6 @@ AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ AM_MAKEFLAGS = @AM_MAKEFLAGS@ AR = @AR@ -AS = @AS@ AUTOCONF = @AUTOCONF@ AUTOHEADER = @AUTOHEADER@ AUTOMAKE = @AUTOMAKE@ @@ -437,7 +436,6 @@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ DSYMUTIL = @DSYMUTIL@ DUMPBIN = @DUMPBIN@ -DYNAMIC_DIRS = @DYNAMIC_DIRS@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ @@ -461,11 +459,9 @@ GREP = @GREP@ H5_CFLAGS = @H5_CFLAGS@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ -H5_CXX_SHARED = @H5_CXX_SHARED@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ H5_LDFLAGS = @H5_LDFLAGS@ -H5_LONE_COLON = @H5_LONE_COLON@ H5_VERSION = @H5_VERSION@ HADDR_T = @HADDR_T@ HAVE_DMALLOC = @HAVE_DMALLOC@ @@ -528,7 +524,6 @@ R_INTEGER = @R_INTEGER@ R_LARGE = @R_LARGE@ SEARCH = @SEARCH@ SED = @SED@ -SETX = @SETX@ SET_MAKE = @SET_MAKE@ SHELL = @SHELL@ SIZE_T = @SIZE_T@ diff --git a/c++/examples/CMakeLists.txt b/c++/examples/CMakeLists.txt index 5ea51a4..ff375f3 100644 --- a/c++/examples/CMakeLists.txt +++ b/c++/examples/CMakeLists.txt @@ -35,7 +35,7 @@ set (tutr_examples foreach (example ${examples}) add_executable (cpp_ex_${example} ${HDF5_CPP_EXAMPLES_SOURCE_DIR}/${example}.cpp) TARGET_NAMING (cpp_ex_${example} ${LIB_TYPE}) - TARGET_C_PROPERTIES (cpp_ex_${example} " " " ") + TARGET_C_PROPERTIES (cpp_ex_${example} ${LIB_TYPE} " " " ") target_link_libraries (cpp_ex_${example} ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (cpp_ex_${example} PROPERTIES FOLDER examples/cpp) endforeach (example ${examples}) @@ -43,7 +43,7 @@ endforeach (example ${examples}) foreach (example ${tutr_examples}) add_executable (cpp_ex_${example} ${HDF5_CPP_EXAMPLES_SOURCE_DIR}/${example}.cpp) TARGET_NAMING (cpp_ex_${example} ${LIB_TYPE}) - TARGET_C_PROPERTIES (cpp_ex_${example} " " " ") + TARGET_C_PROPERTIES (cpp_ex_${example} ${LIB_TYPE} " " " ") target_link_libraries (cpp_ex_${example} ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (cpp_ex_${example} PROPERTIES FOLDER examples/cpp) endforeach (example ${tutr_examples}) diff --git a/c++/examples/Makefile.in b/c++/examples/Makefile.in index 734fdc8..c8d6b18 100644 --- a/c++/examples/Makefile.in +++ b/c++/examples/Makefile.in @@ -353,7 +353,6 @@ AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ AM_MAKEFLAGS = @AM_MAKEFLAGS@ AR = @AR@ -AS = @AS@ AUTOCONF = @AUTOCONF@ AUTOHEADER = @AUTOHEADER@ AUTOMAKE = @AUTOMAKE@ @@ -385,7 +384,6 @@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ DSYMUTIL = @DSYMUTIL@ DUMPBIN = @DUMPBIN@ -DYNAMIC_DIRS = @DYNAMIC_DIRS@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ @@ -409,11 +407,9 @@ GREP = @GREP@ H5_CFLAGS = @H5_CFLAGS@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ -H5_CXX_SHARED = @H5_CXX_SHARED@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ H5_LDFLAGS = @H5_LDFLAGS@ -H5_LONE_COLON = @H5_LONE_COLON@ H5_VERSION = @H5_VERSION@ HADDR_T = @HADDR_T@ HAVE_DMALLOC = @HAVE_DMALLOC@ @@ -476,7 +472,6 @@ R_INTEGER = @R_INTEGER@ R_LARGE = @R_LARGE@ SEARCH = @SEARCH@ SED = @SED@ -SETX = @SETX@ SET_MAKE = @SET_MAKE@ SHELL = @SHELL@ SIZE_T = @SIZE_T@ diff --git a/c++/examples/run-c++-ex.sh.in b/c++/examples/run-c++-ex.sh.in index 77ac36a..eae2782 100644 --- a/c++/examples/run-c++-ex.sh.in +++ b/c++/examples/run-c++-ex.sh.in @@ -34,7 +34,7 @@ EXIT_FAILURE=1 # Where the tool is installed. # default is relative path to installed location of the tools -prefix="${prefix:-../../../}" +prefix="${prefix:-@prefix@}" AR="@AR@" RANLIB="@RANLIB@" H5TOOL="h5c++" # The tool name diff --git a/c++/src/CMakeLists.txt b/c++/src/CMakeLists.txt index 513bbb6..2f3a0c4 100644 --- a/c++/src/CMakeLists.txt +++ b/c++/src/CMakeLists.txt @@ -84,7 +84,7 @@ set (CPP_HDRS ) add_library (${HDF5_CPP_LIB_TARGET} ${LIB_TYPE} ${CPP_SRCS} ${CPP_HDRS}) -TARGET_C_PROPERTIES (${HDF5_CPP_LIB_TARGET} " " " ") +TARGET_C_PROPERTIES (${HDF5_CPP_LIB_TARGET} ${LIB_TYPE} " " " ") target_link_libraries (${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET}) set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_CPP_LIB_TARGET}") H5_SET_LIB_OPTIONS (${HDF5_CPP_LIB_TARGET} ${HDF5_CPP_LIB_NAME} ${LIB_TYPE}) diff --git a/c++/src/H5AbstractDs.cpp b/c++/src/H5AbstractDs.cpp index 0e6ac00..d59c1eb 100644 --- a/c++/src/H5AbstractDs.cpp +++ b/c++/src/H5AbstractDs.cpp @@ -21,6 +21,7 @@ #include "H5PropList.h" #include "H5Object.h" #include "H5AbstractDs.h" +#include "H5DataSpace.h" #include "H5DcreatProp.h" #include "H5CommonFG.h" #include "H5Alltypes.h" @@ -124,8 +125,9 @@ DataType AbstractDs::getDataType() const // depending on which object invokes getDataType. Then, create and // return the DataType object try { - DataType datatype(p_get_type()); - return(datatype); + DataType datatype; + f_DataType_setId(&datatype, p_get_type()); + return(datatype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getDataType", E.getDetailMsg()); @@ -150,8 +152,9 @@ ArrayType AbstractDs::getArrayType() const // depending on which object invokes getArrayType. Then, create and // return the ArrayType object try { - ArrayType arraytype(p_get_type()); - return(arraytype); + ArrayType arraytype; + f_DataType_setId(&arraytype, p_get_type()); + return(arraytype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getArrayType", E.getDetailMsg()); @@ -176,8 +179,9 @@ CompType AbstractDs::getCompType() const // depending on which object invokes getCompType. Then, create and // return the CompType object try { - CompType comptype(p_get_type()); - return(comptype); + CompType comptype; + f_DataType_setId(&comptype, p_get_type()); + return(comptype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getCompType", E.getDetailMsg()); @@ -202,8 +206,9 @@ EnumType AbstractDs::getEnumType() const // depending on which object invokes getEnumType. Then, create and // return the EnumType object try { - EnumType enumtype(p_get_type()); - return(enumtype); + EnumType enumtype; + f_DataType_setId(&enumtype, p_get_type()); + return(enumtype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getEnumType", E.getDetailMsg()); @@ -228,8 +233,9 @@ IntType AbstractDs::getIntType() const // depending on which object invokes getIntType. Then, create and // return the IntType object try { - IntType inttype(p_get_type()); - return(inttype); + IntType inttype; + f_DataType_setId(&inttype, p_get_type()); + return(inttype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getIntType", E.getDetailMsg()); @@ -254,8 +260,9 @@ FloatType AbstractDs::getFloatType() const // depending on which object invokes getFloatType. Then, create and // return the FloatType object try { - FloatType floatype(p_get_type()); - return(floatype); + FloatType floatype; + f_DataType_setId(&floatype, p_get_type()); + return(floatype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getFloatType", E.getDetailMsg()); @@ -280,8 +287,9 @@ StrType AbstractDs::getStrType() const // depending on which object invokes getStrType. Then, create and // return the StrType object try { - StrType strtype(p_get_type()); - return(strtype); + StrType strtype; + f_DataType_setId(&strtype, p_get_type()); + return(strtype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getStrType", E.getDetailMsg()); @@ -306,8 +314,9 @@ VarLenType AbstractDs::getVarLenType() const // depending on which object invokes getVarLenType. Then, create and // return the VarLenType object try { - VarLenType varlentype(p_get_type()); - return(varlentype); + VarLenType varlentype; + f_DataType_setId(&varlentype, p_get_type()); + return(varlentype); } catch (DataSetIException E) { throw DataTypeIException("DataSet::getVarLenType", E.getDetailMsg()); diff --git a/c++/src/H5AbstractDs.h b/c++/src/H5AbstractDs.h index 8ed7967..810dc8b 100644 --- a/c++/src/H5AbstractDs.h +++ b/c++/src/H5AbstractDs.h @@ -28,6 +28,7 @@ class FloatType; class IntType; class StrType; class VarLenType; +class DataSpace; /*! \class AbstractDs \brief AbstractDs is an abstract base class, inherited by Attribute diff --git a/c++/src/H5ArrayType.h b/c++/src/H5ArrayType.h index 511126e..6577a6e 100644 --- a/c++/src/H5ArrayType.h +++ b/c++/src/H5ArrayType.h @@ -49,7 +49,6 @@ class H5_DLLCPP ArrayType : public DataType { // Noop destructor virtual ~ArrayType(); - protected: // Default constructor ArrayType(); diff --git a/c++/src/H5Attribute.cpp b/c++/src/H5Attribute.cpp index 6b5c753..0bfdff8 100644 --- a/c++/src/H5Attribute.cpp +++ b/c++/src/H5Attribute.cpp @@ -74,7 +74,8 @@ Attribute::Attribute(const Attribute& original) : AbstractDs(), IdComponent() //-------------------------------------------------------------------------- Attribute::Attribute(const hid_t existing_id) : AbstractDs(), IdComponent() { - id = existing_id; + id = existing_id; + incRefCount(); // increment number of references to this id } //-------------------------------------------------------------------------- @@ -270,8 +271,9 @@ DataSpace Attribute::getSpace() const // If the dataspace id is valid, create and return the DataSpace object if( dataspace_id > 0 ) { - DataSpace dataspace( dataspace_id ); - return( dataspace ); + DataSpace dataspace; + f_DataSpace_setId(&dataspace, dataspace_id); + return(dataspace); } else { diff --git a/c++/src/H5Attribute.h b/c++/src/H5Attribute.h index f57b922..eced64e 100644 --- a/c++/src/H5Attribute.h +++ b/c++/src/H5Attribute.h @@ -31,6 +31,16 @@ namespace H5 { */ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent { public: + + // Copy constructor: makes a copy of an existing Attribute object. + Attribute( const Attribute& original ); + + // Default constructor + Attribute(); + + // Creates a copy of an existing attribute using the attribute id + Attribute( const hid_t attr_id ); + // Closes this attribute. virtual void close(); @@ -70,15 +80,6 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent { ///\brief Returns this class name. virtual H5std_string fromClass () const { return("Attribute"); } - // Creates a copy of an existing attribute using the attribute id - Attribute( const hid_t attr_id ); - - // Copy constructor: makes a copy of an existing Attribute object. - Attribute( const Attribute& original ); - - // Default constructor - Attribute(); - // Gets the attribute id. virtual hid_t getId() const; @@ -109,6 +110,10 @@ class H5_DLLCPP Attribute : public AbstractDs, public IdComponent { // do not inherit H5Object::renameAttr void renameAttr() {} + + // Friend function to set Attribute id. For library use only. + friend void f_Attribute_setId(Attribute* attr, hid_t new_id); + }; #ifndef H5_NO_NAMESPACE } diff --git a/c++/src/H5CommonFG.cpp b/c++/src/H5CommonFG.cpp index 3aa0386..dbe26b4 100644 --- a/c++/src/H5CommonFG.cpp +++ b/c++/src/H5CommonFG.cpp @@ -14,6 +14,7 @@ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include <string> +#include <iostream> #include "H5Include.h" #include "H5Exception.h" @@ -33,9 +34,6 @@ #include "H5Alltypes.h" #include "H5private.h" // for HDstrcpy -#include <iostream> -using namespace std; - // There are a few comments that are common to most of the functions // defined in this file so they are listed here. // - getLocId is called by all functions, that call a C API, to get @@ -51,6 +49,7 @@ using namespace std; #ifndef H5_NO_NAMESPACE namespace H5 { +using namespace std; #endif //-------------------------------------------------------------------------- @@ -100,7 +99,9 @@ Group CommonFG::createGroup( const char* name, size_t size_hint ) const throwException("createGroup", "H5Gcreate2 failed"); // No failure, create and return the Group object - Group group( group_id ); + Group group; + CommonFG *ptr = &group; + ptr->p_setId(group_id); return( group ); } @@ -136,7 +137,9 @@ Group CommonFG::openGroup( const char* name ) const throwException("openGroup", "H5Gopen2 failed"); // No failure, create and return the Group object - Group group( group_id ); + Group group; + CommonFG *ptr = &group; + ptr->p_setId(group_id); return( group ); } @@ -178,7 +181,8 @@ DataSet CommonFG::createDataSet( const char* name, const DataType& data_type, co throwException("createDataSet", "H5Dcreate2 failed"); // No failure, create and return the DataSet object - DataSet dataset( dataset_id ); + DataSet dataset; + f_DataSet_setId(&dataset, dataset_id); return( dataset ); } @@ -213,7 +217,8 @@ DataSet CommonFG::openDataSet( const char* name ) const throwException("openDataSet", "H5Dopen2 failed"); // No failure, create and return the DataSet object - DataSet dataset( dataset_id ); + DataSet dataset; + f_DataSet_setId(&dataset, dataset_id); return( dataset ); } @@ -576,7 +581,8 @@ DataType CommonFG::openDataType( const char* name ) const throwException("openDataType", "H5Topen2 failed"); // No failure, create and return the DataType object - DataType data_type(type_id); + DataType data_type; + f_DataType_setId(&data_type, type_id); return(data_type); } @@ -611,7 +617,8 @@ ArrayType CommonFG::openArrayType( const char* name ) const throwException("openArrayType", "H5Topen2 failed"); // No failure, create and return the ArrayType object - ArrayType array_type (type_id); + ArrayType array_type; + f_DataType_setId(&array_type, type_id); return(array_type); } @@ -646,7 +653,8 @@ CompType CommonFG::openCompType( const char* name ) const throwException("openCompType", "H5Topen2 failed"); // No failure, create and return the CompType object - CompType comp_type(type_id); + CompType comp_type; + f_DataType_setId(&comp_type, type_id); return(comp_type); } @@ -681,7 +689,8 @@ EnumType CommonFG::openEnumType( const char* name ) const throwException("openEnumType", "H5Topen2 failed"); // No failure, create and return the EnumType object - EnumType enum_type(type_id); + EnumType enum_type; + f_DataType_setId(&enum_type, type_id); return(enum_type); } @@ -716,7 +725,8 @@ IntType CommonFG::openIntType( const char* name ) const throwException("openIntType", "H5Topen2 failed"); // No failure, create and return the IntType object - IntType int_type(type_id); + IntType int_type; + f_DataType_setId(&int_type, type_id); return(int_type); } @@ -751,7 +761,8 @@ FloatType CommonFG::openFloatType( const char* name ) const throwException("openFloatType", "H5Topen2 failed"); // No failure, create and return the FloatType object - FloatType float_type(type_id); + FloatType float_type; + f_DataType_setId(&float_type, type_id); return(float_type); } @@ -786,7 +797,8 @@ StrType CommonFG::openStrType( const char* name ) const throwException("openStrType", "H5Topen2 failed"); // No failure, create and return the StrType object - StrType str_type(type_id); + StrType str_type; + f_DataType_setId(&str_type, type_id); return(str_type); } @@ -821,7 +833,8 @@ VarLenType CommonFG::openVarLenType( const char* name ) const throwException("openVarLenType", "H5Topen2 failed"); // No failure, create and return the VarLenType object - VarLenType varlen_type(type_id); + VarLenType varlen_type; + f_DataType_setId(&varlen_type, type_id); return(varlen_type); } @@ -1100,6 +1113,58 @@ H5O_type_t CommonFG::childObjType(hsize_t index, H5_index_t index_type, H5_iter_ return(objtype); } +//-------------------------------------------------------------------------- +// Function: CommonFG::childObjVersion +///\brief Returns the object header version of an object in this file/group, +/// given the object's name. +///\param objname - IN: Name of the object +///\return Object version, which can have the following values: +/// \li \c H5O_VERSION_1 +/// \li \c H5O_VERSION_2 +///\exception H5::FileIException or H5::GroupIException +/// Exception will be thrown when: +/// - an error returned by the C API +/// - version number is not one of the valid values above +// Programmer Binh-Minh Ribler - April, 2014 +//-------------------------------------------------------------------------- +unsigned CommonFG::childObjVersion(const char* objname) const +{ + H5O_info_t objinfo; + unsigned version = 0; + + // Use C API to get information of the object + herr_t ret_value = H5Oget_info_by_name(getLocId(), objname, &objinfo, H5P_DEFAULT); + + // Throw exception if C API returns failure + if (ret_value < 0) + throwException("childObjVersion", "H5Oget_info_by_name failed"); + // Return a valid version or throw an exception for invalid value + else + { + version = objinfo.hdr.version; + if (version != H5O_VERSION_1 && version != H5O_VERSION_2) + throwException("childObjVersion", "Invalid version for object"); + } + return(version); +} + +//-------------------------------------------------------------------------- +// Function: CommonFG::childObjVersion +///\brief This is an overloaded member function, provided for convenience. +/// It takes an \a H5std_string for the object's name. +///\brief Returns the type of an object in this group, given the +/// object's name. +///\param objname - IN: Name of the object (H5std_string&) +///\exception H5::FileIException or H5::GroupIException +// Programmer Binh-Minh Ribler - April, 2014 +//-------------------------------------------------------------------------- +unsigned CommonFG::childObjVersion(const H5std_string& objname) const +{ + // Use overloaded function + unsigned version = childObjVersion(objname.c_str()); + return(version); +} + #ifndef H5_NO_DEPRECATED_SYMBOLS #ifndef DOXYGEN_SHOULD_SKIP_THIS //-------------------------------------------------------------------------- @@ -1172,6 +1237,7 @@ H5G_obj_t CommonFG::getObjTypeByIdx(hsize_t idx, H5std_string& type_name) const } return (obj_type); } + #endif // DOXYGEN_SHOULD_SKIP_THIS #endif /* H5_NO_DEPRECATED_SYMBOLS */ @@ -1189,6 +1255,37 @@ CommonFG::CommonFG() {} // Programmer Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- CommonFG::~CommonFG() {} + +//-------------------------------------------------------------------------- +// Function: f_DataType_setId - friend +// Purpose: This function is friend to class H5::DataType so that it +// can set DataType::id in order to work around a problem +// described in the JIRA issue HDFFV-7947. +// Applications shouldn't need to use it. +// param dtype - IN/OUT: DataType object to be changed +// param new_id - IN: New id to set +// Programmer Binh-Minh Ribler - 2015 +//-------------------------------------------------------------------------- +void f_DataType_setId(DataType* dtype, hid_t new_id) +{ + dtype->id = new_id; +} + +//-------------------------------------------------------------------------- +// Function: f_DataSet_setId - friend +// Purpose: This function is friend to class H5::DataSet so that it +// can set DataSet::id in order to work around a problem +// described in the JIRA issue HDFFV-7947. +// Applications shouldn't need to use it. +// param dset - IN/OUT: DataSet object to be changed +// param new_id - IN: New id to set +// Programmer Binh-Minh Ribler - 2015 +//-------------------------------------------------------------------------- +void f_DataSet_setId(DataSet* dset, hid_t new_id) +{ + dset->id = new_id; +} + #endif // DOXYGEN_SHOULD_SKIP_THIS #ifndef H5_NO_NAMESPACE diff --git a/c++/src/H5CommonFG.h b/c++/src/H5CommonFG.h index 5c8a142..d36d78c 100644 --- a/c++/src/H5CommonFG.h +++ b/c++/src/H5CommonFG.h @@ -21,6 +21,7 @@ namespace H5 { #endif +// Class forwarding class Group; class H5File; class ArrayType; @@ -70,6 +71,11 @@ class H5_DLLCPP CommonFG { H5O_type_t childObjType(const char* objname) const; H5O_type_t childObjType(hsize_t index, H5_index_t index_type=H5_INDEX_NAME, H5_iter_order_t order=H5_ITER_INC, const char* objname=".") const; + // Returns the object header version of an object in this file or group, + // given the object's name. + unsigned childObjVersion(const char* objname) const; + unsigned childObjVersion(const H5std_string& objname) const; + #ifndef H5_NO_DEPRECATED_SYMBOLS // Returns the type of an object in this group, given the // object's index. @@ -159,6 +165,10 @@ class H5_DLLCPP CommonFG { // Noop destructor. virtual ~CommonFG(); + + protected: + virtual void p_setId(const hid_t new_id) = 0; + #endif // DOXYGEN_SHOULD_SKIP_THIS }; // end of CommonFG declaration diff --git a/c++/src/H5CompType.cpp b/c++/src/H5CompType.cpp index 191f004..393aafc 100644 --- a/c++/src/H5CompType.cpp +++ b/c++/src/H5CompType.cpp @@ -227,7 +227,8 @@ hid_t CompType::p_get_member_type(unsigned member_num) const DataType CompType::getMemberDataType( unsigned member_num ) const { try { - DataType datatype(p_get_member_type(member_num)); + DataType datatype; + f_DataType_setId(&datatype, p_get_member_type(member_num)); return(datatype); } catch (DataTypeIException E) { @@ -248,6 +249,7 @@ ArrayType CompType::getMemberArrayType( unsigned member_num ) const { try { ArrayType arraytype(p_get_member_type(member_num)); + f_DataType_setId(&arraytype, p_get_member_type(member_num)); return(arraytype); } catch (DataTypeIException E) { @@ -268,6 +270,7 @@ CompType CompType::getMemberCompType( unsigned member_num ) const { try { CompType comptype(p_get_member_type(member_num)); + f_DataType_setId(&comptype, p_get_member_type(member_num)); return(comptype); } catch (DataTypeIException E) { @@ -288,6 +291,7 @@ EnumType CompType::getMemberEnumType( unsigned member_num ) const { try { EnumType enumtype(p_get_member_type(member_num)); + f_DataType_setId(&enumtype, p_get_member_type(member_num)); return(enumtype); } catch (DataTypeIException E) { @@ -308,6 +312,7 @@ IntType CompType::getMemberIntType( unsigned member_num ) const { try { IntType inttype(p_get_member_type(member_num)); + f_DataType_setId(&inttype, p_get_member_type(member_num)); return(inttype); } catch (DataTypeIException E) { @@ -328,6 +333,7 @@ FloatType CompType::getMemberFloatType( unsigned member_num ) const { try { FloatType floatype(p_get_member_type(member_num)); + f_DataType_setId(&floatype, p_get_member_type(member_num)); return(floatype); } catch (DataTypeIException E) { @@ -348,6 +354,7 @@ StrType CompType::getMemberStrType( unsigned member_num ) const { try { StrType strtype(p_get_member_type(member_num)); + f_DataType_setId(&strtype, p_get_member_type(member_num)); return(strtype); } catch (DataTypeIException E) { @@ -368,6 +375,7 @@ VarLenType CompType::getMemberVarLenType( unsigned member_num ) const { try { VarLenType varlentype(p_get_member_type(member_num)); + f_DataType_setId(&varlentype, p_get_member_type(member_num)); return(varlentype); } catch (DataTypeIException E) { diff --git a/c++/src/H5DataSet.cpp b/c++/src/H5DataSet.cpp index 0374d95..717ef88 100644 --- a/c++/src/H5DataSet.cpp +++ b/c++/src/H5DataSet.cpp @@ -63,6 +63,7 @@ DataSet::DataSet() : H5Object(), AbstractDs(), id(H5I_INVALID_HID) {} DataSet::DataSet(const hid_t existing_id) : H5Object(), AbstractDs() { id = existing_id; + incRefCount(); // increment number of references to this id } //-------------------------------------------------------------------------- @@ -137,7 +138,8 @@ DataSpace DataSet::getSpace() const throw DataSetIException("DataSet::getSpace", "H5Dget_space failed"); } //create dataspace object using the existing id then return the object - DataSpace data_space( dataspace_id ); + DataSpace data_space; + f_DataSpace_setId(&data_space, dataspace_id); return( data_space ); } @@ -170,8 +172,8 @@ DSetCreatPropList DataSet::getCreatePlist() const throw DataSetIException("DataSet::getCreatePlist", "H5Dget_create_plist failed"); } // create and return the DSetCreatPropList object - DSetCreatPropList create_plist( create_plist_id ); - return( create_plist ); + DSetCreatPropList create_plist(create_plist_id); // ok to use existing id const + return(create_plist); } //-------------------------------------------------------------------------- diff --git a/c++/src/H5DataSet.h b/c++/src/H5DataSet.h index 529466a..b2544a2 100644 --- a/c++/src/H5DataSet.h +++ b/c++/src/H5DataSet.h @@ -30,6 +30,7 @@ namespace H5 { */ class H5_DLLCPP DataSet : public H5Object, public AbstractDs { public: + // Close this dataset. virtual void close(); @@ -125,6 +126,10 @@ class H5_DLLCPP DataSet : public H5Object, public AbstractDs { // 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; + + // Friend function to set DataSet id. For library use only. + friend void f_DataSet_setId(DataSet* dset, hid_t new_id); + }; #ifndef H5_NO_NAMESPACE } diff --git a/c++/src/H5DataSpace.cpp b/c++/src/H5DataSpace.cpp index 761a454..d9c262d 100644 --- a/c++/src/H5DataSpace.cpp +++ b/c++/src/H5DataSpace.cpp @@ -85,6 +85,7 @@ DataSpace::DataSpace( int rank, const hsize_t * dims, const hsize_t * maxdims) : DataSpace::DataSpace(const hid_t existing_id) : IdComponent() { id = existing_id; + incRefCount(); // increment number of references to this id } //-------------------------------------------------------------------------- diff --git a/c++/src/H5DataSpace.h b/c++/src/H5DataSpace.h index b007fd0..a43cecd 100644 --- a/c++/src/H5DataSpace.h +++ b/c++/src/H5DataSpace.h @@ -129,6 +129,9 @@ class H5_DLLCPP DataSpace : public IdComponent { private: hid_t id; // HDF5 dataspace id + + // Friend function to set DataSpace id. For library use only. + friend void f_DataSpace_setId(DataSpace *dspace, hid_t new_id); }; #ifndef H5_NO_NAMESPACE } diff --git a/c++/src/H5DataType.cpp b/c++/src/H5DataType.cpp index c4b1694..cdcd1e6 100644 --- a/c++/src/H5DataType.cpp +++ b/c++/src/H5DataType.cpp @@ -71,6 +71,7 @@ DataType::DataType() : H5Object(), id(H5I_INVALID_HID) {} DataType::DataType(const hid_t existing_id) : H5Object() { id = existing_id; + incRefCount(); // increment number of references to this id } //-------------------------------------------------------------------------- @@ -105,7 +106,7 @@ DataType::DataType( const H5T_class_t type_class, size_t size ) : H5Object() // Jul, 2008 // Added for application convenience. //-------------------------------------------------------------------------- -DataType::DataType(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist) : H5Object(), id(H5I_INVALID_HID) +DataType::DataType(const H5Location& loc, const void* ref, H5R_type_t ref_type, const PropList& plist) : H5Object() { id = H5Location::p_dereference(loc.getId(), ref, ref_type, plist, "constructor - by dereference"); } @@ -141,6 +142,27 @@ DataType::DataType(const DataType& original) : H5Object() } //-------------------------------------------------------------------------- +// Function: DataType overloaded constructor +///\brief Creates a integer type using a predefined type +///\param pred_type - IN: Predefined datatype +///\exception H5::DataTypeIException +// Programmer Binh-Minh Ribler - 2000 +// Description +// Copying the type so that when a predefined type is passed in, +// a copy of it is made, not just a duplicate of the HDF5 id. +// Note: calling DataType::copy will invoke DataType::close() +// unnecessarily and will produce undefined behavior. +// -BMR, Apr 2015 +//-------------------------------------------------------------------------- +DataType::DataType(const PredType& pred_type) : H5Object() +{ + // call C routine to copy the datatype + id = H5Tcopy( pred_type.getId() ); + if (id < 0) + throw DataTypeIException("DataType constructor", "H5Tcopy failed"); +} + +//-------------------------------------------------------------------------- // Function: DataType::copy ///\brief Copies an existing datatype to this datatype object ///\param like_type - IN: Datatype to be copied @@ -203,11 +225,22 @@ void DataType::copy(const DataSet& dset) // Makes a copy of the type on the right hand side and stores // the new id in the left hand side object. // Programmer Binh-Minh Ribler - 2000 +// Modification +// Changed operator= to simply copy the id of rhs instead of +// calling H5Tcopy because, when the operator= is invoked, a +// different datatype id is created and it won't have the same +// characteristics as the original one, specifically, if the +// rhs represents a named datatype, "this" would still be a +// transient datatype. +// BMR - Mar, 2015 //-------------------------------------------------------------------------- DataType& DataType::operator=( const DataType& rhs ) { if (this != &rhs) - copy(rhs); + { + id = rhs.id; + incRefCount(); // increment number of references to this id + } return(*this); } @@ -463,8 +496,9 @@ DataType DataType::getSuper() const // the base type, otherwise, raise exception if( base_type_id > 0 ) { - DataType base_type( base_type_id ); - return( base_type ); + DataType base_type; + base_type.p_setId(base_type_id); + return(base_type); } else { diff --git a/c++/src/H5DataType.h b/c++/src/H5DataType.h index 064bfe1..6c8a312 100644 --- a/c++/src/H5DataType.h +++ b/c++/src/H5DataType.h @@ -36,6 +36,9 @@ class H5_DLLCPP DataType : public H5Object { // Copy constructor: makes a copy of the original object DataType( const DataType& original ); + // Creates a copy of a predefined type + DataType(const PredType& pred_type); + // Creates a datatype by way of dereference. DataType(const H5Location& loc, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT); DataType(const Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT, const PropList& plist = PropList::DEFAULT); @@ -133,6 +136,9 @@ class H5_DLLCPP DataType : public H5Object { #endif // DOXYGEN_SHOULD_SKIP_THIS private: + // Friend function to set DataType id. For library use only. + friend void f_DataType_setId(DataType* dtype, hid_t new_id); + void p_commit(hid_t loc_id, const char* name); }; #ifndef H5_NO_NAMESPACE diff --git a/c++/src/H5FaccProp.cpp b/c++/src/H5FaccProp.cpp index 5696742..5ce9d8e 100644 --- a/c++/src/H5FaccProp.cpp +++ b/c++/src/H5FaccProp.cpp @@ -40,10 +40,10 @@ FileAccPropList::FileAccPropList() : PropList( H5P_FILE_ACCESS ) {} //-------------------------------------------------------------------------- // Function: FileAccPropList copy constructor ///\brief Copy Constructor: makes a copy of the original -/// FileAccPropList object. +///\param original - IN: FileAccPropList instance to copy // Programmer: Binh-Minh Ribler - 2000 //-------------------------------------------------------------------------- -FileAccPropList::FileAccPropList(const FileAccPropList& orig) : PropList(orig) {} +FileAccPropList::FileAccPropList(const FileAccPropList& original) : PropList(original) {} //-------------------------------------------------------------------------- // Function: FileAccPropList overloaded constructor @@ -664,6 +664,67 @@ unsigned FileAccPropList::getGcReferences() const } //-------------------------------------------------------------------------- +// Function: FileAccPropList::setLibverBounds +///\brief Sets bounds on versions of library format to be used when creating +/// or writing objects. +///\param libver_low - IN: Earliest version of the library that will be +/// used for creating or writing objects +///\param libver_high - IN: Latest version of the library that will be +///\exception H5::PropListIException +///\par Description +/// Valid values of \a libver_low are as follows: +/// \li \c H5F_LIBVER_EARLIEST (Default) +/// \li \c H5F_LIBVER_18 +/// \li \c H5F_LIBVER_LATEST +/// +/// Valid values of \a libver_high are as follows: +/// \li \c H5F_LIBVER_18 +/// \li \c H5F_LIBVER_LATEST (Default) +/// +/// For more details, please refer to +/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetLibverBounds +// Programmer: Binh-Minh Ribler - March, 2015 +//-------------------------------------------------------------------------- +void FileAccPropList::setLibverBounds(H5F_libver_t libver_low, H5F_libver_t libver_high) const +{ + herr_t ret_value = H5Pset_libver_bounds(id, libver_low, libver_high); + if (ret_value < 0) + { + throw PropListIException("FileAccPropList::setLibverBounds", "H5Pset_libver_bounds failed"); + } +} + +//-------------------------------------------------------------------------- +// Function: FileAccPropList::getLibverBounds +///\brief Gets the current settings for the library version format bounds +/// from a file access property list. +///\param libver_low - OUT: Earliest version of the library that will be +/// used for creating or writing objects +///\param libver_high - OUT: Latest version of the library that will be +/// used for creating or writing objects +///\exception H5::PropListIException +///\par Description +/// On success, the argument \a libver_low can have the following +/// values: +/// \li \c H5F_LIBVER_EARLIEST +/// \li \c H5F_LIBVER_18 +/// \li \c H5F_LIBVER_LATEST +/// +/// and \a libver_high: +/// \li \c H5F_LIBVER_18 +/// \li \c H5F_LIBVER_LATEST +// Programmer: Binh-Minh Ribler - March, 2015 +//-------------------------------------------------------------------------- +void FileAccPropList::getLibverBounds(H5F_libver_t& libver_low, H5F_libver_t& libver_high) const +{ + herr_t ret_value = H5Pget_libver_bounds(id, &libver_low, &libver_high); + if( ret_value < 0 ) + { + throw PropListIException("FileAccPropList::getLibverBounds", "H5Pget_libver_bounds failed"); + } +} + +//-------------------------------------------------------------------------- // Function: FileAccPropList destructor ///\brief Noop destructor // Programmer Binh-Minh Ribler - 2000 diff --git a/c++/src/H5FaccProp.h b/c++/src/H5FaccProp.h index 861ac4c..fddc446 100644 --- a/c++/src/H5FaccProp.h +++ b/c++/src/H5FaccProp.h @@ -126,6 +126,13 @@ class H5_DLLCPP FileAccPropList : public PropList { // Returns garbage collecting references setting. unsigned getGcReferences() const; + // Sets bounds on versions of library format to be used when creating + // or writing objects. + void setLibverBounds(H5F_libver_t libver_low, H5F_libver_t libver_high) const; + + // Gets the current settings for the library version format bounds. + void getLibverBounds(H5F_libver_t& libver_low, H5F_libver_t& libver_high) const; + ///\brief Returns this class name. virtual H5std_string fromClass () const { return("FileAccPropList"); } diff --git a/c++/src/H5File.cpp b/c++/src/H5File.cpp index e0a0da5..fc802d0 100644 --- a/c++/src/H5File.cpp +++ b/c++/src/H5File.cpp @@ -158,6 +158,25 @@ void H5File::p_get_file(const char* name, unsigned int flags, const FileCreatPro #endif // DOXYGEN_SHOULD_SKIP_THIS //-------------------------------------------------------------------------- +// Function: H5File overloaded constructor +///\brief Creates an H5File object using an existing file id. +///\param existing_id - IN: Id of an existing file +// Programmer Binh-Minh Ribler - 2015 +// Description +// Mar 29, 2015 +// Added in responding to a request from user Jason Newton. +// However, it is not recommended to use the private member "id" +// in applications. Unlike other situations, where similar +// constructor is needed by the library in order to return +// an object, H5File doesn't need it. -BMR (HDFFV-8766 partially) +//-------------------------------------------------------------------------- +H5File::H5File(hid_t existing_id) : H5Location(), CommonFG() +{ + id = existing_id; + incRefCount(); // increment number of references to this id +} + +//-------------------------------------------------------------------------- // Function: H5File copy constructor ///\brief Copy constructor: makes a copy of the original /// H5File object. @@ -225,6 +244,13 @@ bool H5File::isHdf5(const H5std_string& name ) //-------------------------------------------------------------------------- void H5File::openFile(const char* name, unsigned int flags, const FileAccPropList& access_plist) { + try { + close(); + } + catch (Exception close_error) { + throw FileIException("H5File::openFile", close_error.getDetailMsg()); + } + hid_t access_plist_id = access_plist.getId(); id = H5Fopen (name, flags, access_plist_id); if (id < 0) // throw an exception when open fails @@ -379,25 +405,6 @@ ssize_t H5File::getObjCount(unsigned types) const } //-------------------------------------------------------------------------- -// Function: H5File::getObjCount -///\brief This is an overloaded member function, provided for convenience. -/// It takes no parameter and returns the object count of all -/// object types. -///\return Number of opened object IDs -///\exception H5::FileIException -// Programmer Binh-Minh Ribler - May 2004 -//-------------------------------------------------------------------------- -ssize_t H5File::getObjCount() const -{ - ssize_t num_objs = H5Fget_obj_count(id, H5F_OBJ_ALL); - if( num_objs < 0 ) - { - throw FileIException("H5File::getObjCount", "H5Fget_obj_count failed"); - } - return (num_objs); -} - -//-------------------------------------------------------------------------- // Function: H5File::getObjIDs ///\brief Retrieves a list of opened object IDs (files, datasets, /// groups and datatypes) in the same file. diff --git a/c++/src/H5File.h b/c++/src/H5File.h index 0ef85b5..939ac8e 100644 --- a/c++/src/H5File.h +++ b/c++/src/H5File.h @@ -59,8 +59,7 @@ class H5_DLLCPP H5File : public H5Location, public CommonFG { // Returns the number of opened object IDs (files, datasets, groups // and datatypes) in the same file. - ssize_t getObjCount(unsigned types) const; - ssize_t getObjCount() const; + ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const; // Retrieves a list of opened object IDs (files, datasets, groups // and datatypes) in the same file. @@ -84,6 +83,10 @@ class H5_DLLCPP H5File : public H5Location, public CommonFG { // Gets the file id virtual hid_t getLocId() const; + // Creates an H5File using an existing file id. Not recommended + // in applications. + H5File(hid_t existing_id); + #endif // DOXYGEN_SHOULD_SKIP_THIS ///\brief Returns this class name. diff --git a/c++/src/H5Group.cpp b/c++/src/H5Group.cpp index 8b22458..4d1d61c 100644 --- a/c++/src/H5Group.cpp +++ b/c++/src/H5Group.cpp @@ -85,6 +85,7 @@ hid_t Group::getLocId() const Group::Group(const hid_t existing_id) : H5Object(), CommonFG() { id = existing_id; + incRefCount(); // increment number of references to this id } //-------------------------------------------------------------------------- diff --git a/c++/src/H5IdComponent.cpp b/c++/src/H5IdComponent.cpp index 54813ea..c01d41e 100644 --- a/c++/src/H5IdComponent.cpp +++ b/c++/src/H5IdComponent.cpp @@ -46,6 +46,11 @@ namespace H5 { //-------------------------------------------------------------------------- IdComponent::IdComponent(const hid_t h5_id) {} +//void IdComponent::p_setId(const hid_t new_id) +//{ + //p_setId(new_id); +//} + //-------------------------------------------------------------------------- // Function: IdComponent copy constructor // Purpose: This noop copy constructor is removed as a result of the data diff --git a/c++/src/H5IdComponent.h b/c++/src/H5IdComponent.h index f9fd56e..068fb74 100644 --- a/c++/src/H5IdComponent.h +++ b/c++/src/H5IdComponent.h @@ -104,6 +104,7 @@ class H5_DLLCPP IdComponent { // Sets the identifier of this object to a new value. - this one // doesn't increment reference count virtual void p_setId(const hid_t new_id) = 0; + //virtual void p_setId(const hid_t new_id); #endif // DOXYGEN_SHOULD_SKIP_THIS diff --git a/c++/src/H5Include.h b/c++/src/H5Include.h index 87cb182..1e0e952 100644 --- a/c++/src/H5Include.h +++ b/c++/src/H5Include.h @@ -28,3 +28,15 @@ typedef int bool; const bool false = 0; const bool true = 1; #endif + +// These are defined in H5Opkg.h, which should not be included in the C++ API, +// so re-define them here for now. + +/* Initial version of the object header format */ +#define H5O_VERSION_1 1 + +/* Revised version - leaves out reserved bytes and alignment padding, and adds + * magic number as prefix and checksum as suffix for all chunks. + */ +#define H5O_VERSION_2 2 + diff --git a/c++/src/H5IntType.h b/c++/src/H5IntType.h index 95fa642..e28f5c2 100644 --- a/c++/src/H5IntType.h +++ b/c++/src/H5IntType.h @@ -24,7 +24,7 @@ namespace H5 { //! Class IntType operates on HDF5 integer datatype. class H5_DLLCPP IntType : public AtomType { public: - // Creates a integer type using a predefined type + // Creates an integer type using a predefined type IntType(const PredType& pred_type); // Gets the integer datatype of the specified dataset diff --git a/c++/src/H5Location.cpp b/c++/src/H5Location.cpp index 5cece19..5100e12 100644 --- a/c++/src/H5Location.cpp +++ b/c++/src/H5Location.cpp @@ -126,8 +126,9 @@ Attribute H5Location::createAttribute( const char* name, const DataType& data_ty // If the attribute id is valid, create and return the Attribute object if( attr_id > 0 ) { - Attribute attr( attr_id ); - return( attr ); + Attribute attr; + f_Attribute_setId(&attr, attr_id); + return( attr ); } else throw AttributeIException(inMemFunc("createAttribute"), "H5Acreate2 failed"); @@ -158,8 +159,9 @@ Attribute H5Location::openAttribute( const char* name ) const hid_t attr_id = H5Aopen(getId(), name, H5P_DEFAULT); if( attr_id > 0 ) { - Attribute attr( attr_id ); - return( attr ); + Attribute attr; + f_Attribute_setId(&attr, attr_id); + return( attr ); } else { @@ -193,12 +195,13 @@ Attribute H5Location::openAttribute( const unsigned int idx ) const H5_ITER_INC, (hsize_t)idx, H5P_DEFAULT, H5P_DEFAULT); if( attr_id > 0 ) { - Attribute attr( attr_id ); - return( attr ); + Attribute attr; + f_Attribute_setId(&attr, attr_id); + return(attr); } else { - throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen_by_idx failed"); + throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen_by_idx failed"); } } @@ -904,6 +907,12 @@ H5O_type_t H5Location::p_get_ref_obj_type(void *ref, H5R_type_t ref_type) const ///\return DataSpace object ///\exception H5::ReferenceException // Programmer Binh-Minh Ribler - May, 2004 +// Modification +// Mar 29, 2015 +// Used friend function to set id for DataSpace instead of the +// existing id constructor or the setId method to avoid incrementing +// ref count, as a work-around for a problem described in the JIRA +// issue HDFFV-7947. -BMR //-------------------------------------------------------------------------- DataSpace H5Location::getRegion(void *ref, H5R_type_t ref_type) const { @@ -913,8 +922,9 @@ DataSpace H5Location::getRegion(void *ref, H5R_type_t ref_type) const throw ReferenceException(inMemFunc("getRegion"), "H5Rget_region failed"); } try { - DataSpace dataspace(space_id); - return(dataspace); + DataSpace dataspace; + f_DataSpace_setId(&dataspace, space_id); + return(dataspace); } catch (DataSpaceIException E) { throw ReferenceException(inMemFunc("getRegion"), E.getDetailMsg()); @@ -929,6 +939,36 @@ DataSpace H5Location::getRegion(void *ref, H5R_type_t ref_type) const //-------------------------------------------------------------------------- H5Location::~H5Location() {} +//-------------------------------------------------------------------------- +// Function: f_Attribute_setId - friend +// Purpose: This function is friend to class H5::Attribute so that it +// can set Attribute::id in order to work around a problem +// described in the JIRA issue HDFFV-7947. +// Applications shouldn't need to use it. +// param attr - IN/OUT: Attribute object to be changed +// param new_id - IN: New id to set +// Programmer Binh-Minh Ribler - 2015 +//-------------------------------------------------------------------------- +void f_Attribute_setId(Attribute* attr, hid_t new_id) +{ + attr->id = new_id; +} + +//-------------------------------------------------------------------------- +// Function: f_DataSpace_setId - friend +// Purpose: This function is friend to class H5::DataSpace so that it can +// can set DataSpace::id in order to work around a problem +// described in the JIRA issue HDFFV-7947. +// Applications shouldn't need to use it. +// param dspace - IN/OUT: DataSpace object to be changed +// param new_id - IN: New id to set +// Programmer Binh-Minh Ribler - 2015 +//-------------------------------------------------------------------------- +void f_DataSpace_setId(DataSpace* dspace, hid_t new_id) +{ + dspace->id = new_id; +} + #endif // DOXYGEN_SHOULD_SKIP_THIS #ifndef H5_NO_NAMESPACE diff --git a/c++/src/H5Location.h b/c++/src/H5Location.h index 15b9ffd..79a8d5c 100644 --- a/c++/src/H5Location.h +++ b/c++/src/H5Location.h @@ -151,7 +151,7 @@ class H5_DLLCPP H5Location : public IdComponent { H5Location(const hid_t loc_id); // Copy constructor. - H5Location(const H5Location& original); + // H5Location(const H5Location& original); // Creates a reference to an HDF5 object or a dataset region. void p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const; @@ -167,6 +167,10 @@ class H5_DLLCPP H5Location : public IdComponent { // Retrieves the type of object that an object reference points to. H5O_type_t p_get_ref_obj_type(void *ref, H5R_type_t ref_type) const; + // Sets the identifier of this object to a new value. - this one + // doesn't increment reference count + virtual void p_setId(const hid_t new_id) = 0; + #endif // DOXYGEN_SHOULD_SKIP_THIS // Noop destructor. diff --git a/c++/src/H5PropList.cpp b/c++/src/H5PropList.cpp index 1d7d1ba..70ec629 100644 --- a/c++/src/H5PropList.cpp +++ b/c++/src/H5PropList.cpp @@ -258,6 +258,7 @@ void PropList::p_setId(const hid_t new_id) // reset object's id to the given id id = new_id; } + #endif // DOXYGEN_SHOULD_SKIP_THIS //-------------------------------------------------------------------------- diff --git a/c++/src/H5VarLenType.h b/c++/src/H5VarLenType.h index 40c597f..672b3db 100644 --- a/c++/src/H5VarLenType.h +++ b/c++/src/H5VarLenType.h @@ -40,7 +40,6 @@ class H5_DLLCPP VarLenType : public DataType { // Noop destructor virtual ~VarLenType(); - protected: // Default constructor VarLenType(); }; diff --git a/c++/src/Makefile.am b/c++/src/Makefile.am index 7c1f497..cdef7bf 100644 --- a/c++/src/Makefile.am +++ b/c++/src/Makefile.am @@ -30,12 +30,6 @@ 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) $(AM_LDFLAGS) -# Shared C++ libraries aren't universally supported. -if CXX_SHARED_CONDITIONAL -else - AM_LDFLAGS+=-static -endif - bin_SCRIPTS=h5c++ # Source files for the library diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in index 19e4e22..3afedda 100644 --- a/c++/src/Makefile.in +++ b/c++/src/Makefile.in @@ -103,9 +103,6 @@ DIST_COMMON = $(top_srcdir)/config/commence.am \ $(srcdir)/Makefile.am $(top_srcdir)/bin/mkinstalldirs \ $(srcdir)/h5c++.in $(top_srcdir)/bin/depcomp \ $(include_HEADERS) $(top_srcdir)/bin/test-driver - -# Shared C++ libraries aren't universally supported. -@CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static TESTS = subdir = c++/src ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 @@ -416,10 +413,9 @@ AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@ AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@ AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ -AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1) +AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ AM_MAKEFLAGS = @AM_MAKEFLAGS@ AR = @AR@ -AS = @AS@ AUTOCONF = @AUTOCONF@ AUTOHEADER = @AUTOHEADER@ AUTOMAKE = @AUTOMAKE@ @@ -451,7 +447,6 @@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ DSYMUTIL = @DSYMUTIL@ DUMPBIN = @DUMPBIN@ -DYNAMIC_DIRS = @DYNAMIC_DIRS@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ @@ -475,11 +470,9 @@ GREP = @GREP@ H5_CFLAGS = @H5_CFLAGS@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ -H5_CXX_SHARED = @H5_CXX_SHARED@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ H5_LDFLAGS = @H5_LDFLAGS@ -H5_LONE_COLON = @H5_LONE_COLON@ H5_VERSION = @H5_VERSION@ HADDR_T = @HADDR_T@ HAVE_DMALLOC = @HAVE_DMALLOC@ @@ -542,7 +535,6 @@ R_INTEGER = @R_INTEGER@ R_LARGE = @R_LARGE@ SEARCH = @SEARCH@ SED = @SED@ -SETX = @SETX@ SET_MAKE = @SET_MAKE@ SHELL = @SHELL@ SIZE_T = @SIZE_T@ @@ -678,7 +670,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 # After making changes, run bin/reconfigure to update other configure related # files like Makefile.in. LT_VERS_INTERFACE = 6 -LT_VERS_REVISION = 206 +LT_VERS_REVISION = 207 LT_VERS_AGE = 0 # This is our main target diff --git a/c++/src/h5c++.in b/c++/src/h5c++.in index a4aaf52..069842a 100644 --- a/c++/src/h5c++.in +++ b/c++/src/h5c++.in @@ -333,7 +333,7 @@ if test "x$do_link" = "xyes"; then hpux*) flag="-Wl,+b -Wl," ;; freebsd*|solaris*) flag="-R" ;; rs6000*|aix*) flag="-L" ;; - irix*|sgi) flag="-rpath " ;; + sgi) flag="-rpath " ;; *) flag="" ;; esac diff --git a/c++/test/CMakeLists.txt b/c++/test/CMakeLists.txt index fe463fa..dcdf3a3 100644 --- a/c++/test/CMakeLists.txt +++ b/c++/test/CMakeLists.txt @@ -36,7 +36,7 @@ configure_file (${HDF5_CPP_TEST_SOURCE_DIR}/H5srcdir_str.h.in H5srcdir_str.h @O add_executable (cpp_testhdf5 ${CPP_TEST_SRCS} ) TARGET_NAMING (cpp_testhdf5 ${LIB_TYPE}) -TARGET_C_PROPERTIES (cpp_testhdf5 " " " ") +TARGET_C_PROPERTIES (cpp_testhdf5 ${LIB_TYPE} " " " ") target_link_libraries (cpp_testhdf5 ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET} diff --git a/c++/test/Makefile.am b/c++/test/Makefile.am index 2717e9c..705ec72 100644 --- a/c++/test/Makefile.am +++ b/c++/test/Makefile.am @@ -23,12 +23,6 @@ include $(top_srcdir)/config/commence.am # Include src, test, and c++/src directories AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/c++/src -# Shared C++ libraries aren't universally supported. -if CXX_SHARED_CONDITIONAL -else - AM_LDFLAGS+=-static -endif - # These are our main targets. They should be listed in the order to be # executed, generally most specific tests to least specific tests. TEST_PROG=testhdf5 diff --git a/c++/test/Makefile.in b/c++/test/Makefile.in index 709a97e..8711eef 100644 --- a/c++/test/Makefile.in +++ b/c++/test/Makefile.in @@ -99,9 +99,6 @@ DIST_COMMON = $(top_srcdir)/config/commence.am \ $(srcdir)/Makefile.am $(top_srcdir)/bin/mkinstalldirs \ $(srcdir)/H5srcdir_str.h.in $(top_srcdir)/bin/depcomp \ $(top_srcdir)/bin/test-driver - -# Shared C++ libraries aren't universally supported. -@CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static check_PROGRAMS = $(am__EXEEXT_1) TESTS = $(am__EXEEXT_1) subdir = c++/test @@ -407,10 +404,9 @@ AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src \ AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@ AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@ AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ -AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1) +AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ AM_MAKEFLAGS = @AM_MAKEFLAGS@ AR = @AR@ -AS = @AS@ AUTOCONF = @AUTOCONF@ AUTOHEADER = @AUTOHEADER@ AUTOMAKE = @AUTOMAKE@ @@ -442,7 +438,6 @@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ DSYMUTIL = @DSYMUTIL@ DUMPBIN = @DUMPBIN@ -DYNAMIC_DIRS = @DYNAMIC_DIRS@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ @@ -466,11 +461,9 @@ GREP = @GREP@ H5_CFLAGS = @H5_CFLAGS@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ -H5_CXX_SHARED = @H5_CXX_SHARED@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ H5_LDFLAGS = @H5_LDFLAGS@ -H5_LONE_COLON = @H5_LONE_COLON@ H5_VERSION = @H5_VERSION@ HADDR_T = @HADDR_T@ HAVE_DMALLOC = @HAVE_DMALLOC@ @@ -533,7 +526,6 @@ R_INTEGER = @R_INTEGER@ R_LARGE = @R_LARGE@ SEARCH = @SEARCH@ SED = @SED@ -SETX = @SETX@ SET_MAKE = @SET_MAKE@ SHELL = @SHELL@ SIZE_T = @SIZE_T@ diff --git a/c++/test/dsets.cpp b/c++/test/dsets.cpp index e5c8bf0..9f1916d 100644 --- a/c++/test/dsets.cpp +++ b/c++/test/dsets.cpp @@ -59,11 +59,9 @@ const H5std_string DSET_BOGUS_NAME ("bogus"); /* Temporary filter IDs used for testing */ const int H5Z_FILTER_BOGUS = 305; -#if 0 // UNUSED variables caused warning, so duplicated below with NULL instead static size_t filter_bogus(unsigned int flags, size_t cd_nelmts, const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf); -#endif -static size_t filter_bogus(size_t nbytes); +// UNUSED variables caused warning, but taking them out caused failure. /*------------------------------------------------------------------------- * Function: test_create @@ -461,12 +459,10 @@ const H5Z_class2_t H5Z_BOGUS[1] = {{ *------------------------------------------------------------------------- */ static size_t -#if 0 // UNUSED variables caused warning, so duplicated below with NULL instead filter_bogus(unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[], size_t nbytes, size_t *buf_size, void **buf) -#endif -filter_bogus(size_t nbytes) +// UNUSED variables caused warning, but taking them out caused failure. { return nbytes; } diff --git a/c++/test/tattr.cpp b/c++/test/tattr.cpp index 407e6a8..c9422ce 100644 --- a/c++/test/tattr.cpp +++ b/c++/test/tattr.cpp @@ -741,12 +741,26 @@ static void test_attr_compound_read() // Verify name H5std_string attr_name = attr.getName(); verify_val(attr_name, ATTR4_NAME, "Attribute::getName", __LINE__, __FILE__); - PASSED(); } // end try block catch (Exception E) { issue_fail_msg("test_attr_compound_read()", __LINE__, __FILE__, E.getCDetailMsg()); } + + try + { + // Now, try truncating the file to make sure reference counting is good. + // If any references to ids in the previous block are left unterminated, + // the truncating will fail, because the file will not be closed in + // the file.close() above. + H5File file1(FILE_COMPOUND, H5F_ACC_TRUNC); + + PASSED(); + } // end try block + + catch (FileIException E) { + issue_fail_msg("test_attr_compound_read()", __LINE__, __FILE__, "Unable to truncate file, possibly because some objects are left opened"); + } } // test_attr_compound_read() /**************************************************************** diff --git a/c++/test/tcompound.cpp b/c++/test/tcompound.cpp index 156f438..dbf2f0c 100644 --- a/c++/test/tcompound.cpp +++ b/c++/test/tcompound.cpp @@ -780,7 +780,7 @@ static void test_compound_set_size() CompType dtype_tmp = file.openCompType("dtype"); // Make a copy of the data type - dtype = dtype_tmp; + dtype.copy(dtype_tmp); // Verify that the compound is not packed // packed = dtype_tmp.packed(); // not until C library provides API diff --git a/c++/test/tfile.cpp b/c++/test/tfile.cpp index ad5e6fc..f3bbb16 100644 --- a/c++/test/tfile.cpp +++ b/c++/test/tfile.cpp @@ -330,6 +330,32 @@ static void test_file_open() verify_val(iparm1, F2_SYM_INTERN_K, "FileCreatPropList::getSymk", __LINE__, __FILE__); verify_val(iparm2, F2_SYM_LEAF_K, "FileCreatPropList::getSymk", __LINE__, __FILE__); + // Test H5File constructor with existing file id + H5File file2(file1.getId()); + file1.close(); + + // Try truncating the file, and it should fail because the file is + // still opened with file2. + try { + H5File file3 (FILE2, H5F_ACC_TRUNC); // should throw E + + // Should FAIL but didn't, so throw an invalid action exception + throw InvalidActionException("H5File constructor", "Attempt truncating an opened file."); + } + catch( FileIException E ) // catching H5F_ACC_TRUNC on opened file + {} // do nothing, FAIL expected + + // Now, really close the file. + file2.close(); + + // Truncating should succeed now. + H5File file3(FILE2, H5F_ACC_TRUNC); + + // Opening another file to file3 object, FILE2 should be closed, so + // the next attempt to truncate FILE2 should succeed. + file3.openFile(FILE1, H5F_ACC_RDONLY); + H5File file4(FILE2, H5F_ACC_TRUNC); + PASSED(); } // end of try block @@ -501,6 +527,7 @@ const H5std_string FATTR1_NAME ("file attribute 1"); const H5std_string FATTR2_NAME ("file attribute 2"); int fattr_data[ATTR1_DIM1]={512,-234,98123}; /* Test data for file attribute */ int dattr_data[ATTR1_DIM1]={256,-123,1000}; /* Test data for dataset attribute */ + static void test_file_attribute() { int rdata[ATTR1_DIM1]; @@ -602,6 +629,119 @@ static void test_file_attribute() } } // test_file_attribute() +const H5std_string FILE6("tfile5.h5"); +const H5std_string ROOTGROUP("/"); +const H5std_string GROUP1("/G1"); +const H5std_string SUBGROUP3("/G1/G3"); + +/*------------------------------------------------------------------------- + * Function: test_libver_bounds_real + * + * Purpose: Verify that a file created and modified with the + * specified libver bounds has the specified object header + * versions for the right objects. + * + * Return: None + * + * Programmer: Binh-Minh Ribler (use C version) + * March, 2015 + * + *------------------------------------------------------------------------- + */ +static void test_libver_bounds_real( + H5F_libver_t libver_create, unsigned oh_vers_create, + H5F_libver_t libver_mod, unsigned oh_vers_mod) +{ + try { + + /* + * Create a new file using the default creation property and access property + * with latest library version. + */ + FileAccPropList fapl; + fapl.setLibverBounds(libver_create, H5F_LIBVER_LATEST); + H5File file(FILE6, H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, fapl); + + /* + * Make sure the root group has the correct object header version + */ + unsigned obj_version = file.childObjVersion(ROOTGROUP); + verify_val(obj_version, oh_vers_create, "H5File::childObjVersion", __LINE__, __FILE__); + + /* + * Reopen the file and make sure the root group still has the correct version + */ + file.close(); + + fapl.setLibverBounds(libver_mod, H5F_LIBVER_LATEST); + + file.openFile(FILE6, H5F_ACC_RDWR, fapl); + + obj_version = file.childObjVersion(ROOTGROUP); + verify_val(obj_version, oh_vers_create, "H5File::childObjVersion", __LINE__, __FILE__); + + /* + * Create a group named "/G1" in the file, and make sure it has the correct + * object header version + */ + Group group = file.createGroup(GROUP1); + + obj_version = file.childObjVersion(GROUP1); + verify_val(obj_version, oh_vers_mod, "H5File::childObjVersion", __LINE__, __FILE__); + + group.close(); // close "/G1" + + /* + * Create a group named "/G1/G3" in the file, and make sure it has the + * correct object header version + */ + group = file.createGroup(SUBGROUP3); + + obj_version = group.childObjVersion(SUBGROUP3); + verify_val(obj_version, oh_vers_mod, "H5File::childObjVersion", __LINE__, __FILE__); + + group.close(); // close "/G1/G3" + + /* + * Make sure the root group still has the correct object header version + */ + obj_version = file.childObjVersion(ROOTGROUP); + verify_val(obj_version, oh_vers_create, "H5File::childObjVersion", __LINE__, __FILE__); + + // Everything should be closed as they go out of scope + } // end of try block + + catch (Exception E) { + issue_fail_msg("test_libver_bounds_real()", __LINE__, __FILE__, E.getCDetailMsg()); + } + +} /* end test_libver_bounds_real() */ + +/*------------------------------------------------------------------------- + * + * Function: test_libver_bounds + * + * Purpose: Verify that a file created and modified with various + * libver bounds is handled correctly. + * + * Return: None + * + * Programmer: Binh-Minh Ribler (use C version) + * March 2015 + * + *------------------------------------------------------------------------- + */ +static void test_libver_bounds() +{ + // Output message about test being performed + SUBTEST("Setting library version bounds"); + + /* Run the tests */ + test_libver_bounds_real(H5F_LIBVER_EARLIEST, H5O_VERSION_1, H5F_LIBVER_LATEST, H5O_VERSION_2); + test_libver_bounds_real(H5F_LIBVER_LATEST, H5O_VERSION_2, H5F_LIBVER_EARLIEST, H5O_VERSION_1); + PASSED(); +} /* end test_libver_bounds() */ + /*------------------------------------------------------------------------- * Function: test_file * @@ -629,6 +769,7 @@ void test_file() test_file_size(); // Test file size test_file_name(); // Test getting file's name test_file_attribute(); // Test file attribute feature + test_libver_bounds(); // Test format version } // test_file() @@ -655,4 +796,5 @@ void cleanup_file() HDremove(FILE3.c_str()); HDremove(FILE4.c_str()); HDremove(FILE5.c_str()); + HDremove(FILE6.c_str()); } // cleanup_file diff --git a/c++/test/tobject.cpp b/c++/test/tobject.cpp index c74d34a..2381ec2 100644 --- a/c++/test/tobject.cpp +++ b/c++/test/tobject.cpp @@ -182,20 +182,38 @@ static void test_get_objname_ontypes() // Create a datatype and save it IntType inttype(PredType::STD_B8LE); + inttype.commit(file, "INT type of STD_B8LE"); + // Close the type then open it again to test getting its name + inttype.close(); + inttype = file.openIntType("INT type of STD_B8LE"); + + // Get and verify its name + H5std_string inttype_name = inttype.getObjName(); + verify_val(inttype_name, "/INT type of STD_B8LE", "DataType::getObjName", __LINE__, __FILE__); + + // Make copy of a predefined type and save it DataType dtype(PredType::STD_B8LE); dtype.commit(file, "STD_B8LE"); + // Close the data type and file + dtype.close(); + file.close(); + + // Re-open the file and the data type to test getting its name + file.openFile(FILE_OBJECTS, H5F_ACC_RDWR); + dtype = file.openDataType("STD_B8LE"); + // Get and verify its name H5std_string type_name = dtype.getObjName(); - verify_val(type_name, "/STD_B8LE", "DataSet::getObjName", __LINE__, __FILE__); + verify_val(type_name, "/STD_B8LE", "DataType::getObjName", __LINE__, __FILE__); // Test getting type's name from copied type DataType copied_type; copied_type.copy(dtype); copied_type.commit(file, "copy of STD_B8LE"); type_name = copied_type.getObjName(); - verify_val(type_name, "/copy of STD_B8LE", "DataSet::getObjName", __LINE__, __FILE__); + verify_val(type_name, "/copy of STD_B8LE", "DataType::getObjName", __LINE__, __FILE__); // Test copying an integer predefined type IntType new_int_type(PredType::NATIVE_INT); @@ -203,8 +221,8 @@ static void test_get_objname_ontypes() // Name this datatype new_int_type.commit(grp, "IntType NATIVE_INT"); ssize_t name_len = new_int_type.getObjName(type_name); // default len - verify_val(name_len, (ssize_t)HDstrlen("/typetests/IntType NATIVE_INT"), "DataSet::getObjName", __LINE__, __FILE__); - verify_val(type_name, "/typetests/IntType NATIVE_INT", "DataSet::getObjName", __LINE__, __FILE__); + verify_val(name_len, (ssize_t)HDstrlen("/typetests/IntType NATIVE_INT"), "DataType::getObjName", __LINE__, __FILE__); + verify_val(type_name, "/typetests/IntType NATIVE_INT", "DataType::getObjName", __LINE__, __FILE__); // Close everything or they can be closed when objects go out of scope dtype.close(); diff --git a/c++/test/ttypes.cpp b/c++/test/ttypes.cpp index 004723f..2e64051 100644 --- a/c++/test/ttypes.cpp +++ b/c++/test/ttypes.cpp @@ -283,10 +283,16 @@ static void test_query() tid2.close(); file.close(); + // Try truncating the file to make sure reference counting is good. + // If any references to ids of tid1 and tid2 are left unterminated, + // the truncating will fail, because the file will not be closed in + // the file.close() above. + H5File file1(FILENAME[2], H5F_ACC_TRUNC); + PASSED(); } // end of try block catch (Exception E) { - issue_fail_msg("test_query", __LINE__, __FILE__, E.getCDetailMsg()); + issue_fail_msg("test_query", __LINE__, __FILE__, E.getCDetailMsg()); } } // test_query @@ -467,27 +473,20 @@ static void test_named () trans_type.setPrecision(256); trans_type.close(); - /* - * Close the committed type and reopen it. It should return a named type. -* This had something to do with the way IntType was returned and assigned -and caused itype.committed not working correctly. So, use another_type for -now. + // Close the committed type and reopen it. It should be a named type. itype.close(); itype = file.openIntType("native-int"); iscommitted = itype.committed(); -*/ - IntType another_type = file.openIntType("native-int"); - iscommitted = another_type.committed(); if (!iscommitted) throw InvalidActionException("IntType::committed()", "Opened named types should be named types!"); // Create a dataset that uses the named type, then get the dataset's // datatype and make sure it's a named type. - DataSet dset = file.createDataSet("dset1", another_type, space); + DataSet dset = file.createDataSet("dset1", itype, space); ds_type = new DataType(dset.getDataType()); iscommitted = ds_type->committed(); if (!iscommitted) - throw InvalidActionException("IntType::committed()", "1 Dataset type should be named type!"); + throw InvalidActionException("IntType::committed()", "Dataset type should be named type!"); dset.close(); ds_type->close(); delete ds_type; |