path: root/c++/src/H5Object.cpp

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include <string>

#include "H5private.h"        // for HDmemset
#include "H5Include.h"
#include "H5Exception.h"
#include "H5IdComponent.h"
#include "H5PropList.h"
#include "H5FaccProp.h"
#include "H5FcreatProp.h"
#include "H5OcreatProp.h"
#include "H5DcreatProp.h"
#include "H5DxferProp.h"
#include "H5LcreatProp.h"
#include "H5LaccProp.h"
#include "H5Location.h"
#include "H5Object.h"
#include "H5DataType.h"
#include "H5DataSpace.h"
#include "H5AbstractDs.h"
#include "H5CommonFG.h"
#include "H5Group.h"
#include "H5File.h"
#include "H5DataSet.h"
#include "H5Attribute.h"

namespace H5 {

#ifndef DOXYGEN_SHOULD_SKIP_THIS
// userAttrOpWrpr simply interfaces between the user's function and the
// C library function H5Aiterate2; used to resolve the different prototype
// problem.  May be moved to Iterator later.
extern "C" herr_t userAttrOpWrpr(hid_t loc_id, const char *attr_name,
    const H5A_info_t *ainfo, void *op_data)
{
    H5std_string s_attr_name = H5std_string(attr_name);
    UserData4Aiterate* myData = reinterpret_cast<UserData4Aiterate *> (op_data);
    myData->op(*myData->location, s_attr_name, myData->opData);
    return 0;
}

//--------------------------------------------------------------------------
// Function:    H5Object default constructor (protected)
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Object::H5Object() : 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->p_setId(new_id);
}
#endif

//--------------------------------------------------------------------------
// Function:    H5Object::createAttribute
///\brief       Creates an attribute for a group, dataset, or named datatype.
///\param       name - IN: Name of the attribute
///\param       data_type - IN: Datatype for the attribute
///\param       data_space - IN: Dataspace for the attribute - only simple
///             dataspaces are allowed at this time
///\param       create_plist - IN: Creation property list - default to
///             PropList::DEFAULT
///\return      Attribute instance
///\exception   H5::AttributeIException
///\par Description
///             The attribute name specified in \a name must be unique.
///             Attempting to create an attribute with the same name as an
///             existing attribute will raise an exception, leaving the
///             pre-existing attribute intact. To overwrite an existing
///             attribute with a new attribute of the same name, first
///             delete the existing one with \c H5Object::removeAttr, then
///             recreate it with this function.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::createAttribute(const char* name, const DataType& data_type, const DataSpace& data_space, const PropList& create_plist) const
{
    hid_t type_id = data_type.getId();
    hid_t space_id = data_space.getId();
    hid_t plist_id = create_plist.getId();
    hid_t attr_id = H5Acreate2(getId(), name, type_id, space_id, plist_id, H5P_DEFAULT);

    // If the attribute id is valid, create and return the Attribute object
    if (attr_id > 0)
    {
        Attribute attr;
        f_Attribute_setId(&attr, attr_id);
        return(attr);
    }
    else
        throw AttributeIException(inMemFunc("createAttribute"), "H5Acreate2 failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::createAttribute
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for \a name.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::createAttribute(const H5std_string& name, const DataType& data_type, const DataSpace& data_space, const PropList& create_plist) const
{
    return(createAttribute(name.c_str(), data_type, data_space, create_plist));
}

//--------------------------------------------------------------------------
// Function:    H5Object::openAttribute
///\brief       Opens an attribute given its name.
///\param       name - IN: Name of the attribute
///\return      Attribute instance
///\exception   H5::AttributeIException
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute(const char* name) const
{
    hid_t attr_id = H5Aopen(getId(), name, H5P_DEFAULT);
    if (attr_id > 0)
    {
        Attribute attr;
        f_Attribute_setId(&attr, attr_id);
        return(attr);
    }
    else
    {
        throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen failed");
    }
}

//--------------------------------------------------------------------------
// Function:    H5Object::openAttribute
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for \a name.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute(const H5std_string& name) const
{
    return(openAttribute(name.c_str()));
}

//--------------------------------------------------------------------------
// Function:    H5Object::openAttribute
///\brief       Opens an attribute given its index.
///\param       idx - IN: Index of the attribute, a 0-based, non-negative integer
///\return      Attribute instance
///\exception   H5::AttributeIException
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute(const unsigned int idx) const
{
    hid_t attr_id = H5Aopen_by_idx(getId(), ".", H5_INDEX_CRT_ORDER,
              H5_ITER_INC, static_cast<hsize_t>(idx), H5P_DEFAULT, H5P_DEFAULT);
    if (attr_id > 0)
    {
        Attribute attr;
        f_Attribute_setId(&attr, attr_id);
        return(attr);
    }
    else
    {
        throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen_by_idx failed");
    }
}

//--------------------------------------------------------------------------
// Function:    H5Object::iterateAttrs
///\brief       Iterates a user's function over all the attributes of an H5
///             object, which may be a group, dataset or named datatype.
///\param       user_op - IN: User's function to operate on each attribute
///\param       _idx - IN/OUT: Starting (IN) and ending (OUT) attribute indices
///\param       op_data - IN: User's data to pass to user's operator function
///\return      Returned value of the last operator if it was non-zero, or
///             zero if all attributes were processed
///\exception   H5::AttributeIException
///\par Description
///             The signature of user_op is
///             void (*)(H5::H5Location&, H5std_string, void*).
///             For information, please refer to the H5Aiterate2 API in
///             the HDF5 C Reference Manual.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int H5Object::iterateAttrs(attr_operator_t user_op, unsigned *_idx, void *op_data)
{
    // store the user's function and data
    UserData4Aiterate* userData = new UserData4Aiterate;
    userData->opData = op_data;
    userData->op = user_op;
    userData->location = this;

    // call the C library routine H5Aiterate2 to iterate the attributes
    hsize_t idx = _idx ? static_cast<hsize_t>(*_idx) : 0;
    int ret_value = H5Aiterate2(getId(), H5_INDEX_NAME, H5_ITER_INC, &idx,
                         userAttrOpWrpr, static_cast<void *>(userData));

    // release memory
    delete userData;

    if (ret_value >= 0) {
        /* Pass back update index value to calling code */
        if (_idx)
            *_idx = static_cast<unsigned>(idx);
        return(ret_value);
    }
    else  // raise exception when H5Aiterate returns a negative value
        throw AttributeIException(inMemFunc("iterateAttrs"), "H5Aiterate2 failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::getInfo
///\brief       Retrieves information about an HDF5 object.
///\param       objinfo - OUT: Struct containing the object info
///\param       fields  - IN: Indicates the group of information to be retrieved
///\par Description
///             Valid values of \a fields are as follows:
///             \li \c H5O_INFO_BASIC (default)
///             \li \c H5O_INFO_TIME
///             \li \c H5O_INFO_NUM_ATTRS
///             \li \c H5O_INFO_HDR
///             \li \c H5O_INFO_META_SIZE
///             \li \c H5O_INFO_ALL
// July, 2018
//--------------------------------------------------------------------------
void H5Object::getInfo(H5O_info_t& objinfo, unsigned fields) const
{

    // Use C API to get information of the object
    herr_t ret_value = H5Oget_info2(getId(), &objinfo, fields);

    // Throw exception if C API returns failure
    if (ret_value < 0)
        throwException(inMemFunc("getInfo"), "H5Oget_info2 failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::getInfo
///\brief       Retrieves information about an HDF5 object given its name.
///\param       name    - IN: Name of the object to be queried - \c char *
///\param       objinfo - OUT: Struct containing the object info
///\param       fields  - IN: Indicates the group of information to be retrieved
///                           - default to H5O_INFO_BASIC
///\param       lapl - IN: Link access property list
///\par Description
///             Valid values of \a fields are as follows:
///             \li \c H5O_INFO_BASIC (default)
///             \li \c H5O_INFO_TIME
///             \li \c H5O_INFO_NUM_ATTRS
///             \li \c H5O_INFO_HDR
///             \li \c H5O_INFO_META_SIZE
///             \li \c H5O_INFO_ALL
// July, 2018
//--------------------------------------------------------------------------
void H5Object::getInfo(const char* name, H5O_info_t& objinfo, unsigned fields, const LinkAccPropList& lapl) const
{
    // Use C API to get information of the object
    herr_t ret_value = H5Oget_info_by_name2(getId(), name, &objinfo, fields, lapl.getId());

    // Throw exception if C API returns failure
    if (ret_value < 0)
        throwException(inMemFunc("getInfo"), "H5Oget_info_by_name2 failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::getInfo
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for \a name.
///\param       name    - IN: Name of the object to be queried - \c H5std_string
///\param       objinfo - OUT: Struct containing the object info
///\param       fields  - IN: Indicates the group of information to be retrieved
///                           - default to H5O_INFO_BASIC
///\param       lapl - IN: Link access property list
// July, 2018
//--------------------------------------------------------------------------
void H5Object::getInfo(const H5std_string& name, H5O_info_t& objinfo, unsigned fields, const LinkAccPropList& lapl) const
{
    getInfo(name.c_str(), objinfo, fields, lapl);
}

//--------------------------------------------------------------------------
// Function:    H5Object::getInfo
///\brief       Retrieves information about an HDF5 object given its index.
///\param       grp_name - IN: Group name where the object belongs - \c char *
///\param       idx_type - IN: Type of index
///\param       order   - IN: Order to traverse
///\param       idx     - IN: Object position
///\param       objinfo - OUT: Struct containing the object info
///\param       fields  - IN: Indicates the group of information to be retrieved
///                           - default to H5O_INFO_BASIC
///\param       lapl    - IN: Link access property list
///\par Description
///             Valid values of \a fields are as follows:
///             \li \c H5O_INFO_BASIC (default)
///             \li \c H5O_INFO_TIME
///             \li \c H5O_INFO_NUM_ATTRS
///             \li \c H5O_INFO_HDR
///             \li \c H5O_INFO_META_SIZE
///             \li \c H5O_INFO_ALL
// July, 2018
//--------------------------------------------------------------------------
void H5Object::getInfo(const char* grp_name, H5_index_t idx_type,
     H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, unsigned fields,
     const LinkAccPropList& lapl) const
{
    // Use C API to get information of the object
    herr_t ret_value = H5Oget_info_by_idx2(getId(), grp_name, idx_type, order,
                       idx, &objinfo, fields, lapl.getId());

    // Throw exception if C API returns failure
    if (ret_value < 0)
        throwException(inMemFunc("getInfo"), "H5Oget_info_by_idx2 failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::getInfo
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for \a name.
///\param       name    - IN: Name of the object to be queried - \c H5std_string
///\param       objinfo - OUT: Struct containing the object info
///\param       fields  - IN: Indicates a group of information to be retrieved
///                           - default to H5O_INFO_BASIC
///\param       lapl - IN: Link access property list
// July, 2018
//--------------------------------------------------------------------------
void H5Object::getInfo(const H5std_string& grp_name, H5_index_t idx_type,
     H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, unsigned fields,
     const LinkAccPropList& lapl) const
{
    getInfo(grp_name.c_str(), idx_type, order, idx, objinfo, fields, lapl);
}

//--------------------------------------------------------------------------
// Function:    H5Object::objVersion
///\brief       Returns the header version of this HDF5 object.
///\return      Object version, which can have the following values:
///             \li \c H5O_VERSION_1
///             \li \c H5O_VERSION_2
///\exception   H5::ObjHeaderIException
///             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 - December, 2016
//--------------------------------------------------------------------------
unsigned H5Object::objVersion() const
{
    H5O_info_t objinfo;
    unsigned version = 0;

    // Use C API to get information of the object
    herr_t ret_value = H5Oget_info2(getId(), &objinfo, H5O_INFO_HDR);

    // Throw exception if C API returns failure
    if (ret_value < 0)
        throw Exception(inMemFunc("objVersion"), "H5Oget_info 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)
            throw ObjHeaderIException("objVersion", "Invalid version for object");
    }
    return(version);
}

//--------------------------------------------------------------------------
// Function:    H5Object::getNumAttrs
///\brief       Returns the number of attributes attached to this HDF5 object.
///\return      Number of attributes
///\exception   H5::AttributeIException
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int H5Object::getNumAttrs() const
{
    H5O_info_t oinfo;    /* Object info */

    if(H5Oget_info2(getId(), &oinfo, H5O_INFO_NUM_ATTRS) < 0)
        throw AttributeIException(inMemFunc("getNumAttrs"), "H5Oget_info failed");
    else
        return(static_cast<int>(oinfo.num_attrs));
}

//--------------------------------------------------------------------------
// Function:    H5Object::attrExists
///\brief       Checks whether the named attribute exists at this location.
///\param       name - IN: Name of the attribute to be queried
///\exception   H5::AttributeIException
// Programmer   Binh-Minh Ribler - 2013
//--------------------------------------------------------------------------
bool H5Object::attrExists(const char* name) const
{
    // Call C routine H5Aexists to determine whether an attribute exists
    // at this location, which could be specified by a file, group, dataset,
    // or named datatype.
    herr_t ret_value = H5Aexists(getId(), name);
    if (ret_value > 0)
        return true;
    else if(ret_value == 0)
        return false;
    else // Raise exception when H5Aexists returns a negative value
        throw AttributeIException(inMemFunc("attrExists"), "H5Aexists failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::attrExists
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for \a name.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
bool H5Object::attrExists(const H5std_string& name) const
{
    return(attrExists(name.c_str()));
}

//--------------------------------------------------------------------------
// Function:    H5Object::removeAttr
///\brief       Removes the named attribute from this object.
///\param       name - IN: Name of the attribute to be removed
///\exception   H5::AttributeIException
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5Object::removeAttr(const char* name) const
{
    herr_t ret_value = H5Adelete(getId(), name);
    if (ret_value < 0)
        throw AttributeIException(inMemFunc("removeAttr"), "H5Adelete failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::removeAttr
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for \a name.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5Object::removeAttr(const H5std_string& name) const
{
    removeAttr(name.c_str());
}

//--------------------------------------------------------------------------
// Function:    H5Object::renameAttr
///\brief       Renames the named attribute from this object.
///\param       oldname - IN: Name of the attribute to be renamed
///\param       newname - IN: New name ame of the attribute
///\exception   H5::AttributeIException
// Programmer   Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
void H5Object::renameAttr(const char* oldname, const char* newname) const
{
    herr_t ret_value = H5Arename(getId(), oldname, newname);
    if (ret_value < 0)
        throw AttributeIException(inMemFunc("renameAttr"), "H5Arename failed");
}

//--------------------------------------------------------------------------
// Function:    H5Object::renameAttr
///\brief       This is an overloaded member function, provided for convenience.
///             It differs from the above function in that it takes
///             a reference to an \c H5std_string for the names.
// Programmer   Binh-Minh Ribler - Mar, 2005
//--------------------------------------------------------------------------
void H5Object::renameAttr(const H5std_string& oldname, const H5std_string& newname) const
{
    renameAttr (oldname.c_str(), newname.c_str());
}

//--------------------------------------------------------------------------
// Function:    getObjName
///\brief       Given an id, returns the type of the object.
///\return      The name of the object
// Programmer   Binh-Minh Ribler - Mar, 2014
//--------------------------------------------------------------------------
ssize_t H5Object::getObjName(char *obj_name, size_t buf_size) const
{
    // H5Iget_name will get buf_size-1 chars of the name to null terminate it
    ssize_t name_size = H5Iget_name(getId(), obj_name, buf_size);

    // If H5Iget_name returns a negative value, raise an exception
    if (name_size < 0)
     {
        throw Exception(inMemFunc("getObjName"), "H5Iget_name failed");
    }
    else if (name_size == 0)
     {
        throw Exception(inMemFunc("getObjName"), "Object must have a name, but name length is 0");
    }
    // Return length of the name
    return(name_size);
}

//--------------------------------------------------------------------------
// Function:    H5Object::getObjName
///\brief       Returns the name of this object as an \a H5std_string.
///\return      Name of the object
///\exception   H5::Exception
// Programmer   Binh-Minh Ribler - Mar, 2014
//--------------------------------------------------------------------------
H5std_string H5Object::getObjName() const
{
    H5std_string obj_name(""); // object name to return

    // Preliminary call to get the size of the object name
    ssize_t name_size = H5Iget_name(getId(), NULL, static_cast<size_t>(0));

    // If H5Iget_name failed, throw exception
    if (name_size < 0)
     {
        throw Exception(inMemFunc("getObjName"), "H5Iget_name failed");
    }
    else if (name_size == 0)
     {
        throw Exception(inMemFunc("getObjName"), "Object must have a name, but name length is 0");
    }
    // Object's name exists, retrieve it
    else if (name_size > 0)
     {
        char* name_C = new char[name_size+1];  // temporary C-string
        HDmemset(name_C, 0, name_size+1); // clear buffer

        // Use overloaded function
        name_size = getObjName(name_C, name_size+1);

        // Convert the C object name to return
        obj_name = name_C;

        // Clean up resource
        delete []name_C;
    }
    // Return object's name
    return(obj_name);
}

//--------------------------------------------------------------------------
// Function:    H5Object::getObjName
///\brief       Gets the name of this object, returning its length.
///\param       obj_name - OUT: Buffer for the name string as \a H5std_string
///\param       len  -  IN: Desired length of the name, default to 0
///\return      Actual length of the object name
///\exception   H5::Exception
///\par Description
///             This function retrieves the object's name as an std string.
///             buf_size can specify a specific length or default to 0, in
///             which case the entire name will be retrieved.
// Programmer   Binh-Minh Ribler - Mar, 2014
//--------------------------------------------------------------------------
ssize_t H5Object::getObjName(H5std_string& obj_name, size_t len) const
{
    ssize_t name_size = 0;

    // If no length is provided, get the entire object name
    if (len == 0)
     {
        obj_name = getObjName();
        name_size = obj_name.length();
    }
    // If length is provided, get that number of characters in name
    else
     {
        char* name_C = new char[len+1];  // temporary C-string
        HDmemset(name_C, 0, len+1); // clear buffer

        // Use overloaded function
        name_size = getObjName(name_C, len+1);

        // Convert the C object name to return
        obj_name = name_C;

        // Clean up resource
        delete []name_C;
    }
    // Otherwise, keep obj_name intact

    // Return name size
    return(name_size);
}

#ifndef DOXYGEN_SHOULD_SKIP_THIS
//--------------------------------------------------------------------------
// Function:    H5Object destructor
///\brief       Noop destructor.
// Programmer   Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
H5Object::~H5Object() {}
#endif // DOXYGEN_SHOULD_SKIP_THIS

} // end namespace