/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5Ocopy_ref.c
*
* Purpose: Object with references copying routines.
*
*-------------------------------------------------------------------------
*/
/****************/
/* Module Setup */
/****************/
#include "H5Omodule.h" /* This source code file is part of the H5O module */
#define H5R_FRIEND /* Suppress error about including H5Rpkg */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Fprivate.h" /* File */
#include "H5Iprivate.h" /* IDs */
#include "H5Lprivate.h" /* Links */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
#include "H5Rpkg.h" /* References */
#include "H5VLnative_private.h" /* Native VOL connector */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Package Typedefs */
/********************/
/********************/
/* Local Prototypes */
/********************/
static herr_t H5O__copy_obj_by_ref(H5O_loc_t *src_oloc, H5O_loc_t *dst_oloc, H5G_loc_t *dst_root_loc,
H5O_copy_t *cpy_info);
static herr_t H5O__copy_expand_ref_object1(H5O_loc_t *src_oloc, const void *buf_src, H5O_loc_t *dst_oloc,
H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count,
H5O_copy_t *cpy_info);
static herr_t H5O__copy_expand_ref_region1(H5O_loc_t *src_oloc, const void *buf_src, H5O_loc_t *dst_oloc,
H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count,
H5O_copy_t *cpy_info);
static herr_t H5O__copy_expand_ref_object2(H5O_loc_t *src_oloc, hid_t tid_src, const H5T_t *dt_src,
const void *buf_src, size_t nbytes_src, H5O_loc_t *dst_oloc,
H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count,
H5O_copy_t *cpy_info);
/*********************/
/* Package Variables */
/*********************/
/* Declare extern the free list to manage blocks of type conversion data */
H5FL_BLK_EXTERN(type_conv);
/*****************************/
/* Library Private Variables */
/*****************************/
/*******************/
/* Local Variables */
/*******************/
/*-------------------------------------------------------------------------
* Function: H5O__copy_obj_by_ref
*
* Purpose: Copy the object pointed to by src_oloc.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O__copy_obj_by_ref(H5O_loc_t *src_oloc, H5O_loc_t *dst_oloc, H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
HDassert(src_oloc);
HDassert(dst_oloc);
/* Perform the copy, or look up existing copy */
if ((ret_value = H5O_copy_header_map(src_oloc, dst_oloc, cpy_info, FALSE, NULL, NULL)) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
/* Check if a new valid object is copied to the destination */
if (H5F_addr_defined(dst_oloc->addr) && (ret_value > SUCCEED)) {
char tmp_obj_name[80];
H5G_name_t new_path;
H5O_loc_t new_oloc;
H5G_loc_t new_loc;
/* Set up group location for new object */
new_loc.oloc = &new_oloc;
new_loc.path = &new_path;
H5G_loc_reset(&new_loc);
new_oloc.file = dst_oloc->file;
new_oloc.addr = dst_oloc->addr;
/* Pick a default name for the new object */
HDsnprintf(tmp_obj_name, sizeof(tmp_obj_name), "~obj_pointed_by_%llu",
(unsigned long long)dst_oloc->addr);
/* Create a link to the newly copied object */
/* Note: since H5O_copy_header_map actually copied the target object, it
* must exist either in cache or on disk, therefore it is safe to not
* pass the obj_type and udata fields returned by H5O_copy_header_map.
* This could be changed in the future to slightly improve performance
* --NAF */
if (H5L_link(dst_root_loc, tmp_obj_name, &new_loc, cpy_info->lcpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to insert link")
H5G_loc_free(&new_loc);
} /* if (H5F_addr_defined(dst_oloc.addr)) */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O__copy_obj_by_ref() */
/*-------------------------------------------------------------------------
* Function: H5O__copy_expand_ref_object1
*
* Purpose: Copy the object pointed by a deprecated object reference.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O__copy_expand_ref_object1(H5O_loc_t *src_oloc, const void *buf_src, H5O_loc_t *dst_oloc,
H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count, H5O_copy_t *cpy_info)
{
const hobj_ref_t *src_ref = (const hobj_ref_t *)buf_src;
hobj_ref_t *dst_ref = (hobj_ref_t *)buf_dst;
const unsigned char zeros[H5R_OBJ_REF_BUF_SIZE] = {0};
size_t buf_size = H5R_OBJ_REF_BUF_SIZE;
size_t i; /* Local index variable */
size_t token_size = H5F_SIZEOF_ADDR(src_oloc->file);
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Making equivalent references in the destination file */
for (i = 0; i < ref_count; i++) {
const unsigned char *src_buf = (const unsigned char *)&src_ref[i];
unsigned char *dst_buf = (unsigned char *)&dst_ref[i];
H5O_token_t tmp_token = {0};
/* If data is not initialized, copy zeros and skip */
if (0 == HDmemcmp(src_buf, zeros, buf_size))
HDmemset(dst_buf, 0, buf_size);
else {
/* Set up for the object copy for the reference */
if (H5R__decode_token_obj_compat(src_buf, &buf_size, &tmp_token, token_size) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTDECODE, FAIL, "unable to decode src object address")
if (H5VL_native_token_to_addr(src_oloc->file, H5I_FILE, tmp_token, &src_oloc->addr) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTUNSERIALIZE, FAIL,
"can't deserialize object token into address")
if (!H5F_addr_defined(src_oloc->addr) || src_oloc->addr == 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "undefined reference pointer")
dst_oloc->addr = HADDR_UNDEF;
/* Attempt to copy object from source to destination file */
if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
/* Set the object reference info for the destination file */
if (H5VL_native_addr_to_token(dst_oloc->file, H5I_FILE, dst_oloc->addr, &tmp_token) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL, "can't serialize address into object token")
if (H5R__encode_token_obj_compat((const H5O_token_t *)&tmp_token, token_size, dst_buf,
&buf_size) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTDECODE, FAIL, "unable to encode dst object address")
} /* end else */
} /* end for */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O__copy_expand_ref_object1() */
/*-------------------------------------------------------------------------
* Function: H5O__copy_expand_ref_region1
*
* Purpose: Copy the object pointed by a deprecated region reference.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O__copy_expand_ref_region1(H5O_loc_t *src_oloc, const void *buf_src, H5O_loc_t *dst_oloc,
H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count, H5O_copy_t *cpy_info)
{
const hdset_reg_ref_t *src_ref = (const hdset_reg_ref_t *)buf_src;
hdset_reg_ref_t *dst_ref = (hdset_reg_ref_t *)buf_dst;
const unsigned char zeros[H5R_DSET_REG_REF_BUF_SIZE] = {0};
size_t buf_size = H5R_DSET_REG_REF_BUF_SIZE;
size_t i; /* Local index variable */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Making equivalent references in the destination file */
for (i = 0; i < ref_count; i++) {
const unsigned char *src_buf = (const unsigned char *)&src_ref[i];
unsigned char *dst_buf = (unsigned char *)&dst_ref[i];
unsigned char *data = NULL;
size_t data_size;
const uint8_t *p;
uint8_t *q;
/* If data is not initialized, copy zeros and skip */
if (0 == HDmemcmp(src_buf, zeros, buf_size))
HDmemset(dst_buf, 0, buf_size);
else {
/* Read from heap */
if (H5R__decode_heap(src_oloc->file, src_buf, &buf_size, &data, &data_size) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTDECODE, FAIL, "unable to decode dataset region information")
/* Get object address */
p = (const uint8_t *)data;
H5F_addr_decode(src_oloc->file, &p, &src_oloc->addr);
if (!H5F_addr_defined(src_oloc->addr) || src_oloc->addr == 0) {
H5MM_free(data);
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "undefined reference pointer")
}
dst_oloc->addr = HADDR_UNDEF;
/* Attempt to copy object from source to destination file */
if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0) {
H5MM_free(data);
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
} /* end if */
/* Serialize object addr */
q = (uint8_t *)data;
H5F_addr_encode(dst_oloc->file, &q, dst_oloc->addr);
/* Write to heap */
if (H5R__encode_heap(dst_oloc->file, dst_buf, &buf_size, data, (size_t)data_size) < 0) {
H5MM_free(data);
HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to encode dataset region information")
}
/* Free the buffer allocated in H5R__decode_heap() */
H5MM_free(data);
} /* end else */
} /* end for */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O__copy_expand_ref_region1() */
/*-------------------------------------------------------------------------
* Function: H5O__copy_expand_ref_object2
*
* Purpose: Copy the object pointed by a reference (object, region, attribute).
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O__copy_expand_ref_object2(H5O_loc_t *src_oloc, hid_t tid_src, const H5T_t *dt_src, const void *buf_src,
size_t nbytes_src, H5O_loc_t *dst_oloc, H5G_loc_t *dst_root_loc, void *buf_dst,
size_t ref_count, H5O_copy_t *cpy_info)
{
H5T_t *dt_mem = NULL; /* Memory datatype */
H5T_t *dt_dst = NULL; /* Destination datatype */
hid_t tid_mem = H5I_INVALID_HID; /* Datatype ID for memory datatype */
hid_t tid_dst = H5I_INVALID_HID; /* Datatype ID for memory datatype */
H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */
size_t i; /* Local index variable */
hbool_t reg_tid_src = (tid_src == H5I_INVALID_HID);
hid_t dst_loc_id = H5I_INVALID_HID;
void *conv_buf = NULL; /* Buffer for converting data */
size_t conv_buf_size = 0; /* Buffer size */
void *reclaim_buf = NULL; /* Buffer for reclaiming data */
H5S_t *buf_space = NULL; /* Dataspace describing buffer */
hsize_t buf_dim[1] = {ref_count}; /* Dimension for buffer */
size_t token_size = H5F_SIZEOF_ADDR(src_oloc->file);
const unsigned char zeros[H5R_REF_BUF_SIZE] = {0};
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Create datatype ID for src datatype. */
if ((tid_src == H5I_INVALID_HID) && (tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
/* create a memory copy of the reference datatype */
if (NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to copy")
if ((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0) {
(void)H5T_close_real(dt_mem);
HGOTO_ERROR(H5E_OHDR, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
} /* end if */
/* create reference datatype at the destination file */
if (NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to copy")
if (H5T_set_loc(dt_dst, H5F_VOL_OBJ(dst_oloc->file), H5T_LOC_DISK) < 0) {
(void)H5T_close_real(dt_dst);
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
} /* end if */
if ((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0) {
(void)H5T_close_real(dt_dst);
HGOTO_ERROR(H5E_OHDR, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
} /* end if */
/* Set up the conversion functions */
if (NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
if (NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
/* Use extra conversion buffer (TODO we should avoid using an extra buffer once the H5Ocopy code has been
* reworked) */
conv_buf_size = MAX(H5T_get_size(dt_src), H5T_get_size(dt_mem)) * ref_count;
if (NULL == (conv_buf = H5FL_BLK_MALLOC(type_conv, conv_buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer")
H5MM_memcpy(conv_buf, buf_src, nbytes_src);
/* Convert from source file to memory */
if (H5T_convert(tpath_src_mem, tid_src, tid_mem, ref_count, (size_t)0, (size_t)0, conv_buf, NULL) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCONVERT, FAIL, "datatype conversion failed")
/* Retrieve loc ID */
if ((dst_loc_id = H5F_get_id(dst_oloc->file)) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file or file object")
/* Making equivalent references in the destination file */
for (i = 0; i < ref_count; i++) {
H5R_ref_t *ref_ptr = (H5R_ref_t *)conv_buf;
H5R_ref_priv_t *ref = (H5R_ref_priv_t *)&ref_ptr[i];
/* Check for null reference - only expand reference if it is not null */
if (HDmemcmp(ref, zeros, H5R_REF_BUF_SIZE)) {
H5O_token_t tmp_token = {0};
/* Get src object address */
if (H5R__get_obj_token(ref, &tmp_token, &token_size) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to get object token")
if (H5VL_native_token_to_addr(src_oloc->file, H5I_FILE, tmp_token, &src_oloc->addr) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTUNSERIALIZE, FAIL,
"can't deserialize object token into address")
/* Attempt to copy object from source to destination file */
if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
/* Set dst object address */
if (H5VL_native_addr_to_token(dst_oloc->file, H5I_FILE, dst_oloc->addr, &tmp_token) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL, "can't serialize address into object token")
if (H5R__set_obj_token(ref, (const H5O_token_t *)&tmp_token, token_size) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set object token")
/* Do not set app_ref since references are released once the copy is done */
if (H5R__set_loc_id(ref, dst_loc_id, TRUE, FALSE) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set destination loc id")
} /* end if */
} /* end for */
/* Copy into another buffer, to reclaim memory later */
if (NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, conv_buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer")
H5MM_memcpy(reclaim_buf, conv_buf, conv_buf_size);
if (NULL == (buf_space = H5S_create_simple((unsigned)1, buf_dim, NULL)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
/* Convert from memory to destination file */
if (H5T_convert(tpath_mem_dst, tid_mem, tid_dst, ref_count, (size_t)0, (size_t)0, conv_buf, NULL) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCONVERT, FAIL, "datatype conversion failed")
H5MM_memcpy(buf_dst, conv_buf, nbytes_src);
/* Reclaim space from reference data */
if (H5T_reclaim(tid_mem, buf_space, reclaim_buf) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_BADITER, FAIL, "unable to reclaim reference data")
done:
if (buf_space && (H5S_close(buf_space) < 0))
HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "Can't close dataspace")
/* Don't decrement ID, we want to keep underlying datatype */
if (reg_tid_src && (tid_src > 0) && (NULL == H5I_remove(tid_src)))
HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if ((tid_mem > 0) && H5I_dec_ref(tid_mem) < 0)
HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if ((tid_dst > 0) && H5I_dec_ref(tid_dst) < 0)
HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if (reclaim_buf)
reclaim_buf = H5FL_BLK_FREE(type_conv, reclaim_buf);
if (conv_buf)
conv_buf = H5FL_BLK_FREE(type_conv, conv_buf);
if ((dst_loc_id != H5I_INVALID_HID) && (H5I_dec_ref(dst_loc_id) < 0))
HDONE_ERROR(H5E_OHDR, H5E_CANTDEC, FAIL, "unable to decrement refcount on location id")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O__copy_expand_ref_object2() */
/*-------------------------------------------------------------------------
* Function: H5O_copy_expand_ref
*
* Purpose: Copy the object pointed by a reference.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
herr_t
H5O_copy_expand_ref(H5F_t *file_src, hid_t tid_src, const H5T_t *dt_src, void *buf_src, size_t nbytes_src,
H5F_t *file_dst, void *buf_dst, H5O_copy_t *cpy_info)
{
H5O_loc_t dst_oloc; /* Copied object object location */
H5O_loc_t src_oloc; /* Temporary object location for source object */
H5G_loc_t dst_root_loc; /* The location of root group of the destination file */
size_t ref_count;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
/* Sanity checks */
HDassert(file_src);
HDassert(buf_src);
HDassert(file_dst);
HDassert(buf_dst);
HDassert(nbytes_src);
HDassert(cpy_info);
/* Initialize object locations */
H5O_loc_reset(&src_oloc);
H5O_loc_reset(&dst_oloc);
src_oloc.file = file_src;
dst_oloc.file = file_dst;
/* Set up the root group in the destination file */
if (NULL == (dst_root_loc.oloc = H5G_oloc(H5G_rootof(file_dst))))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get object location for root group")
if (NULL == (dst_root_loc.path = H5G_nameof(H5G_rootof(file_dst))))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get path for root group")
/* Determine # of reference elements to copy */
ref_count = nbytes_src / H5T_get_size(dt_src);
/* Copy object references */
switch (H5T_get_ref_type(dt_src)) {
case H5R_OBJECT1:
if (H5O__copy_expand_ref_object1(&src_oloc, buf_src, &dst_oloc, &dst_root_loc, buf_dst, ref_count,
cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "unable to expand H5R_OBJECT1 reference")
break;
case H5R_DATASET_REGION1:
if (H5O__copy_expand_ref_region1(&src_oloc, buf_src, &dst_oloc, &dst_root_loc, buf_dst, ref_count,
cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "unable to expand H5R_DATASET_REGION1 reference")
break;
case H5R_DATASET_REGION2:
case H5R_ATTR:
case H5R_OBJECT2:
if (H5O__copy_expand_ref_object2(&src_oloc, tid_src, dt_src, buf_src, nbytes_src, &dst_oloc,
&dst_root_loc, buf_dst, ref_count, cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "unable to expand reference")
break;
case H5R_BADTYPE:
case H5R_MAXTYPE:
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
break;
} /* end switch */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_copy_expand_ref() */