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dde381add4e4bd4e03812ce8a5b678185d6296b7
hdf5/src/H5Ocopy.c
Quincey Koziol c227f4ffa5 [svn-r13499] Description: 
Avoid storing the # of attributes in the "attribute info" message
and regenerate it when the object is opened.

Tested on:
	FreeBSD/32 6.2 (duty)
2007-03-11 22:00:31 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*-------------------------------------------------------------------------
*
* Created: H5Ocopy.c
* Nov 6 2006
* Quincey Koziol <koziol@hdfgroup.org>
*
* Purpose: Object copying routines.
*
*-------------------------------------------------------------------------
*/
/****************/
/* Module Setup */
/****************/
#define H5O_PACKAGE /*suppress error about including H5Opkg */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free lists */
#include "H5Iprivate.h" /* IDs */
#include "H5HGprivate.h" /* Global Heaps */
#include "H5Lprivate.h" /* Links */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Package Typedefs */
/********************/
/********************/
/* Local Prototypes */
/********************/
static herr_t H5O_copy_free_addrmap_cb(void *item, void *key, void *op_data);
static herr_t H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
hid_t dxpl_id, H5O_copy_t *cpy_info);
static herr_t H5O_copy_header(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
hid_t dxpl_id, unsigned cpy_option);
static herr_t H5O_copy_obj(H5G_loc_t *src_loc, H5G_loc_t *dst_loc,
const char *dst_name, hid_t ocpypl_id, hid_t lcpl_id);
static herr_t H5O_copy_obj_by_ref(H5O_loc_t *src_oloc, hid_t dxpl_id,
H5O_loc_t *dst_oloc, H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info);
/*********************/
/* Package Variables */
/*********************/
/* Declare a free list to manage the H5O_addr_map_t struct */
H5FL_DEFINE(H5O_addr_map_t);
/*****************************/
/* Library Private Variables */
/*****************************/
/*******************/
/* Local Variables */
/*******************/
/*-------------------------------------------------------------------------
* Function: H5Ocopy
*
* Purpose: Copy an object (group or dataset) to destination location
* within a file or cross files. PLIST_ID is a property list
* which is used to pass user options and properties to the
* copy. The name, dst_name, must not already be taken by some
* other object in the destination group.
*
* H5Ocopy() will fail if the name of the destination object
* exists in the destination group. For example,
* H5Ocopy(fid_src, "/dset", fid_dst, "/dset", ...)
* will fail if "/dset" exists in the destination file
*
* OPTIONS THAT HAVE BEEN IMPLEMENTED.
* H5O_COPY_SHALLOW_HIERARCHY_FLAG
* If this flag is specified, only immediate members of
* the group are copied. Otherwise (default), it will
* recursively copy all objects below the group
* H5O_COPY_EXPAND_SOFT_LINK_FLAG
* If this flag is specified, it will copy the objects
* pointed by the soft links. Otherwise (default), it
* will copy the soft link as they are
* H5O_COPY_WITHOUT_ATTR_FLAG
* If this flag is specified, it will copy object without
* copying attributes. Otherwise (default), it will
* copy object along with all its attributes
* H5O_COPY_EXPAND_REFERENCE_FLAG
* 1) Copy object between two different files:
* When this flag is specified, it will copy objects that
* are pointed by the references and update the values of
* references in the destination file. Otherwise (default)
* the values of references in the destination will set to
* zero
* The current implementation does not handle references
* inside of other datatype structure. For example, if
* a member of compound datatype is reference, H5Ocopy()
* will copy that field as it is. It will not set the
* value to zero as default is used nor copy the object
* pointed by that field the flag is set
* 2) Copy object within the same file:
* This flag does not have any effect to the H5Ocopy().
* Datasets or attributes of references are copied as they
* are, i.e. values of references of the destination object
* are the same as the values of the source object
*
* OPTIONS THAT MAY APPLY TO COPY IN THE FUTURE.
* H5O_COPY_EXPAND_EXT_LINK_FLAG
* If this flag is specified, it will expand the external links
* into new objects, Otherwise (default), it will keep external
* links as they are (default)
*
* PROPERTIES THAT MAY APPLY TO COPY IN FUTURE
* Change data layout such as chunk size
* Add filter such as data compression.
* Add an attribute to the copied object(s) that say the date/time
* for the copy or other information about the source file.
*
* The intermediate group creation property should be passed in
* using the lcpl instead of the ocpypl.
*
* Usage: H5Ocopy(src_loc_id, src_name, dst_loc_id, dst_name, ocpypl_id, lcpl_id)
* hid_t src_loc_id IN: Source file or group identifier.
* const char *src_name IN: Name of the source object to be copied
* hid_t dst_loc_id IN: Destination file or group identifier
* const char *dst_name IN: Name of the destination object
* hid_t ocpypl_id IN: Properties which apply to the copy
* hid_t lcpl_id IN: Properties which apply to the new hard link
*
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* June 4, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id,
const char *dst_name, hid_t ocpypl_id, hid_t lcpl_id)
{
H5G_loc_t loc; /* Source group group location */
H5G_loc_t src_loc; /* Source object group location */
H5G_loc_t dst_loc; /* Destination group location */
/* for opening the destination object */
H5G_name_t src_path; /* Opened source object hier. path */
H5O_loc_t src_oloc; /* Opened source object object location */
hbool_t loc_found = FALSE; /* Location at 'name' found */
hbool_t obj_open = FALSE; /* Entry at 'name' found */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(H5Ocopy, FAIL)
H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name,
ocpypl_id, lcpl_id);
/* Check arguments */
if(H5G_loc(src_loc_id, &loc) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
if(H5G_loc(dst_loc_id, &dst_loc) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
if(!src_name || !*src_name)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no source name specified")
if(!dst_name || !*dst_name)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no destination name specified")
/* check if destination name already exists */
{
H5G_name_t tmp_path;
H5O_loc_t tmp_oloc;
H5G_loc_t tmp_loc;
/* Set up group location */
tmp_loc.oloc = &tmp_oloc;
tmp_loc.path = &tmp_path;
H5G_loc_reset(&tmp_loc);
/* Check if object already exists in destination */
if(H5G_loc_find(&dst_loc, dst_name, &tmp_loc, H5P_DEFAULT, H5AC_dxpl_id) >= 0) {
H5G_name_free(&tmp_path);
HGOTO_ERROR(H5E_SYM, H5E_EXISTS, FAIL, "destination object already exists")
} /* end if */
}
/* Set up opened group location to fill in */
src_loc.oloc = &src_oloc;
src_loc.path = &src_path;
H5G_loc_reset(&src_loc);
/* Find the source object to copy */
if(H5G_loc_find(&loc, src_name, &src_loc/*out*/, H5P_DEFAULT, H5AC_dxpl_id) < 0)
HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, FAIL, "source object not found")
loc_found = TRUE;
/* Open source object's object header */
if(H5O_open(&src_oloc) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTOPENOBJ, FAIL, "unable to open object")
obj_open = TRUE;
/* Get correct property lists */
if(H5P_DEFAULT == lcpl_id) {
if((lcpl_id = H5L_get_default_lcpl()) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "unable to get default lcpl")
} /* end if */
else
if(TRUE != H5P_isa_class(lcpl_id, H5P_LINK_CREATE))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not link creation property list")
/* Get object copy property list */
if(H5P_DEFAULT == ocpypl_id)
ocpypl_id = H5P_OBJECT_COPY_DEFAULT;
else
if(TRUE != H5P_isa_class(ocpypl_id, H5P_OBJECT_COPY))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not object copy property list")
/* Do the actual copying of the object */
if(H5O_copy_obj(&src_loc, &dst_loc, dst_name, ocpypl_id, lcpl_id) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
done:
if(loc_found) {
if(H5G_loc_free(&src_loc) < 0)
HDONE_ERROR(H5E_SYM, H5E_CANTRELEASE, FAIL, "can't free location")
}
if(obj_open)
H5O_close(&src_oloc);
FUNC_LEAVE_API(ret_value)
} /* end H5Ocopy() */
/*-------------------------------------------------------------------------
* Function: H5O_copy_header_real
*
* Purpose: Copy header object from one location to another using
* pre-copy, copy, and post-copy callbacks for each message
* type.
*
* The source header object is compressed into a single chunk
* (since we know how big it is) and any continuation messages
* are converted into NULL messages.
*
* By default, NULL messages are not copied.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* May 30, 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
hid_t dxpl_id, H5O_copy_t *cpy_info)
{
H5O_addr_map_t *addr_map = NULL; /* Address mapping of object copied */
H5O_t *oh_src = NULL; /* Object header for source object */
H5O_t *oh_dst = NULL; /* Object header for destination object */
unsigned mesgno = 0;
haddr_t addr_new = HADDR_UNDEF;
hbool_t *deleted = NULL; /* Array of flags indicating whether messages should be copied */
size_t null_msgs; /* Number of NULL messages found in each loop */
size_t orig_dst_msgs; /* Original # of messages in dest. object */
H5O_mesg_t *mesg_src; /* Message in source object header */
H5O_mesg_t *mesg_dst; /* Message in source object header */
const H5O_msg_class_t *copy_type; /* Type of message to use for copying */
const H5O_obj_class_t *obj_class = NULL; /* Type of object we are copying */
void *udata = NULL; /* User data for passing to message callbacks */
size_t dst_oh_size; /* Total size of the destination OH */
size_t dst_oh_null; /* Size of the null message to add to destination OH */
unsigned dst_oh_gap; /* Size of the gap in chunk #0 of destination OH */
uint8_t *current_pos; /* Current position in destination image */
size_t msghdr_size;
hbool_t shared; /* Whether copy_file callback created a shared message */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT(H5O_copy_header_real)
HDassert(oloc_src);
HDassert(oloc_src->file);
HDassert(H5F_addr_defined(oloc_src->addr));
HDassert(oloc_dst->file);
HDassert(cpy_info);
/* Get source object header */
if(NULL == (oh_src = (H5O_t *)H5AC_protect(oloc_src->file, dxpl_id, H5AC_OHDR, oloc_src->addr, NULL, NULL, H5AC_READ)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "unable to load object header")
/* Get pointer to object class for this object */
if(NULL == (obj_class = H5O_obj_class_real(oh_src)))
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to determine object type")
/* Retrieve user data for particular type of object to copy */
if(obj_class->get_copy_file_udata &&
(NULL == (udata = (obj_class->get_copy_file_udata)())))
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to retrieve copy user data")
/* Flush any dirty messages in source object header to update the header chunks */
if(H5O_flush_msgs(oloc_src->file, oh_src) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object header messages")
/* Allocate the destination object header and fill in header fields */
if(NULL == (oh_dst = H5FL_CALLOC(H5O_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Initialize header information */
oh_dst->version = oh_src->version;
oh_dst->flags = oh_src->flags;
oh_dst->skipped_mesg_size = oh_src->skipped_mesg_size;
oh_dst->link_msgs_seen = oh_src->link_msgs_seen;
oh_dst->attr_msgs_seen = oh_src->attr_msgs_seen;
oh_dst->sizeof_size = H5F_SIZEOF_SIZE(oloc_dst->file);
oh_dst->sizeof_addr = H5F_SIZEOF_ADDR(oloc_dst->file);
/* Copy time fields */
oh_dst->atime = oh_src->atime;
oh_dst->mtime = oh_src->mtime;
oh_dst->ctime = oh_src->ctime;
oh_dst->btime = oh_src->btime;
/* Copy attribute storage information */
oh_dst->max_compact = oh_src->max_compact;
oh_dst->min_dense = oh_src->min_dense;
/* Initialize size of chunk array. The destination always has only one
* chunk.
*/
oh_dst->alloc_nchunks = oh_dst->nchunks = 1;
/* Allocate memory for the chunk array */
if(NULL == (oh_dst->chunk = H5FL_SEQ_MALLOC(H5O_chunk_t, oh_dst->alloc_nchunks)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Allocate memory for "deleted" array. This array marks the message in
* the source that shouldn't be copied to the destination.
*/
if(NULL == (deleted = (hbool_t *)HDmalloc(sizeof(hbool_t) * oh_src->nmesgs)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
HDmemset(deleted, FALSE, sizeof(hbool_t) * oh_src->nmesgs);
/* "pre copy" pass over messages, to gather information for actual message copy operation
* (for messages which depend on information from other messages)
* Keep track of how many NULL or deleted messages we find (or create)
*/
null_msgs = 0;
for(mesgno = 0; mesgno < oh_src->nmesgs; mesgno++) {
/* Set up convenience variables */
mesg_src = &(oh_src->mesg[mesgno]);
/* Sanity check */
HDassert(!mesg_src->dirty); /* Should be cleared by earlier call to flush messages */
/* Get message class to operate on */
copy_type = mesg_src->type;
/* Check for continuation message; these are converted to NULL
* messages because the destination OH will have only one chunk
*/
if(H5O_CONT_ID == mesg_src->type->id || H5O_NULL_ID == mesg_src->type->id) {
deleted[mesgno] = TRUE;
++null_msgs;
copy_type = H5O_MSG_NULL;
} /* end if */
HDassert(copy_type);
if(copy_type->pre_copy_file) {
/* Decode the message if necessary. */
H5O_LOAD_NATIVE(oloc_src->file, dxpl_id, mesg_src, FAIL)
/* Perform "pre copy" operation on message */
if((copy_type->pre_copy_file)(oloc_src->file, mesg_src->native, &(deleted[mesgno]), cpy_info, udata) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to perform 'pre copy' operation on message")
/* Check if the message should be deleted in the destination */
if(deleted[mesgno])
/* Mark message as deleted */
++null_msgs;
} /* end if(copy_type->pre_copy_file) */
} /* end for */
/* Initialize size of message list. It may or may not include the NULL messages
* detected above.
*/
if(cpy_info->preserve_null)
oh_dst->alloc_nmesgs = oh_dst->nmesgs = oh_src->nmesgs;
else
oh_dst->alloc_nmesgs = oh_dst->nmesgs = (oh_src->nmesgs - null_msgs);
/* Allocate memory for destination message array */
if(oh_dst->alloc_nmesgs > 0)
if(NULL == (oh_dst->mesg = H5FL_SEQ_CALLOC(H5O_mesg_t, oh_dst->alloc_nmesgs)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* "copy" pass over messages, to perform main message copying */
null_msgs = 0;
for(mesgno = 0; mesgno < oh_dst->nmesgs; mesgno++) {
/* Skip any deleted or NULL messages in the source unless the
* preserve_null flag is set
*/
if(FALSE == cpy_info->preserve_null) {
while(deleted[mesgno + null_msgs]) {
++null_msgs;
HDassert(mesgno + null_msgs < oh_src->nmesgs);
} /* end while */
} /* end if */
/* Set up convenience variables */
mesg_src = &(oh_src->mesg[mesgno + null_msgs]);
mesg_dst = &(oh_dst->mesg[mesgno]);
/* Initialize non-zero components of destination message */
mesg_dst->crt_idx = mesg_src->crt_idx;
mesg_dst->flags = mesg_src->flags;
mesg_dst->raw_size = mesg_src->raw_size;
mesg_dst->type = mesg_src->type;
/* If we're preserving deleted messages, set their types to 'NULL'
* in the destination.
*/
if(cpy_info->preserve_null && deleted[mesgno]) {
mesg_dst->type = H5O_MSG_NULL;
mesg_dst->flags = 0;
mesg_dst->dirty = 1;
} /* end if */
/* Check for message class to operate on */
/* (Use destination message, in case the message has been removed (i.e
* converted to a nil message) in the destination -QAK)
*/
copy_type = mesg_dst->type;
HDassert(copy_type);
/* copy this message into destination file */
if(copy_type->copy_file) {
hbool_t recompute_size = FALSE; /* Whether to recompute the destination message's size */
/* Decode the message if necessary. */
H5O_LOAD_NATIVE(oloc_src->file, dxpl_id, mesg_src, FAIL)
/* Copy the source message */
if((mesg_dst->native = H5O_msg_copy_file(copy_type,
oloc_src->file, mesg_src->native, oloc_dst->file, dxpl_id,
&shared, cpy_info, udata)) == NULL)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object header message")
/* In being copied, the message may have become shared or stopped
* being shared. If its sharing status has changed, recalculate
* its size and set/unset its sharing flag.
*/
if(shared == TRUE && !(mesg_dst->flags & H5O_MSG_FLAG_SHARED)) {
/* Set shared flag */
mesg_dst->flags |= H5O_MSG_FLAG_SHARED;
/* Recompute shared message size (mesg_dst->native is really
* shared)
*/
recompute_size = TRUE;
} /* end if */
else if(shared == FALSE && (mesg_dst->flags & H5O_MSG_FLAG_SHARED)) {
/* Unset shared flag */
mesg_dst->flags &= ~H5O_MSG_FLAG_SHARED;
/* Recompute native message size (msg_dest->native is no longer
* shared)
*/
recompute_size = TRUE;
} /* end else */
if(recompute_size)
mesg_dst->raw_size = H5O_ALIGN_OH(oh_dst,
H5O_msg_raw_size(oloc_dst->file, mesg_dst->type->id, FALSE, mesg_dst->native));
/* Mark the message in the destination as dirty, so it'll get encoded when the object header is flushed */
mesg_dst->dirty = TRUE;
} /* end if (mesg_src->type->copy_file) */
} /* end of mesgno loop */
/* Allocate the destination header and copy any messages that didn't have
* copy callbacks. They get copied directly from the source image to the
* destination image.
*/
/* Calculate how big the destination object header will be on disk.
* This isn't necessarily the same size as the original.
*/
/* Compute space for messages. */
dst_oh_size = 0;
for(mesgno = 0; mesgno < oh_dst->nmesgs; mesgno++) {
dst_oh_size += H5O_SIZEOF_MSGHDR_OH(oh_dst);
dst_oh_size += oh_dst->mesg[mesgno].raw_size;
} /* end for */
/* Check if we need to determine correct value for chunk #0 size bits */
if(oh_dst->version > H5O_VERSION_1) {
/* Reset destination object header's "chunk 0 size" flags */
oh_dst->flags &= ~H5O_HDR_CHUNK0_SIZE;
/* Determine correct value for chunk #0 size bits */
if(dst_oh_size > 4294967295)
oh_dst->flags |= H5O_HDR_CHUNK0_8;
else if(dst_oh_size > 65535)
oh_dst->flags |= H5O_HDR_CHUNK0_4;
else if(dst_oh_size > 255)
oh_dst->flags |= H5O_HDR_CHUNK0_2;
} /* end if */
/* Check if the chunk's data portion is too small */
dst_oh_gap = dst_oh_null = 0;
if(dst_oh_size < H5O_MIN_SIZE) {
size_t delta = (H5O_MIN_SIZE - dst_oh_size); /* Delta in chunk size needed */
/* Sanity check */
HDassert((oh_dst->flags & H5O_HDR_CHUNK0_SIZE) == H5O_HDR_CHUNK0_1);
/* Determine whether to create gap or NULL message */
if(delta < H5O_SIZEOF_MSGHDR_OH(oh_dst))
dst_oh_gap = delta;
else
dst_oh_null = delta;
/* Increase destination object header size */
dst_oh_size += delta;
/* Sanity check */
HDassert(dst_oh_size <= 255);
} /* end if */
/* Add in destination's object header size now */
dst_oh_size += H5O_SIZEOF_HDR(oh_dst);
/* Allocate space for chunk in destination file */
if(HADDR_UNDEF == (oh_dst->chunk[0].addr = H5MF_alloc(oloc_dst->file, H5FD_MEM_OHDR, dxpl_id, (hsize_t)dst_oh_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "file allocation failed for object header")
addr_new = oh_dst->chunk[0].addr;
/* Create memory image for the new chunk */
if(NULL == (oh_dst->chunk[0].image = H5FL_BLK_MALLOC(chunk_image, dst_oh_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Set dest. chunk information */
oh_dst->chunk[0].dirty = TRUE;
oh_dst->chunk[0].size = dst_oh_size;
oh_dst->chunk[0].gap = dst_oh_gap;
/* Set up raw pointers and copy messages that didn't need special
* treatment. This has to happen after the destination header has been
* allocated.
*/
HDassert(H5O_SIZEOF_MSGHDR_OH(oh_src) == H5O_SIZEOF_MSGHDR_OH(oh_dst));
msghdr_size = H5O_SIZEOF_MSGHDR_OH(oh_src);
current_pos = oh_dst->chunk[0].image;
/* Write the magic number for versions > 1 and skip the rest of the
* header. This will be written when the header is flushed to disk.
*/
if(oh_dst->version > H5O_VERSION_1)
HDmemcpy(current_pos, H5O_HDR_MAGIC, (size_t)H5O_SIZEOF_MAGIC);
current_pos += H5O_SIZEOF_HDR(oh_dst) - H5O_SIZEOF_CHKSUM_OH(oh_dst);
/* Loop through destination messages, updating their "raw" info */
null_msgs = 0;
for(mesgno = 0; mesgno < oh_dst->nmesgs; mesgno++) {
/* Skip any deleted or NULL messages in the source unless the
* preserve_null flag is set.
*/
if(FALSE == cpy_info->preserve_null) {
while(deleted[mesgno + null_msgs]) {
++null_msgs;
HDassert(mesgno + null_msgs < oh_src->nmesgs);
} /* end while */
} /* end if */
/* Set up convenience variables */
mesg_src = &(oh_src->mesg[mesgno + null_msgs]);
mesg_dst = &(oh_dst->mesg[mesgno]);
/* Copy each message that wasn't dirtied above */
if(!mesg_dst->dirty)
/* Copy the message header plus the message's raw data. */
HDmemcpy(current_pos, mesg_src->raw - msghdr_size, msghdr_size + mesg_src->raw_size);
/* Set message's raw pointer to destination chunk's new "image" */
mesg_dst->raw = current_pos + msghdr_size;
/* Move to location where next message should go */
current_pos += mesg_dst->raw_size + msghdr_size;
} /* end for */
/* Save this in case more messages are added during NULL message checking */
orig_dst_msgs = oh_dst->nmesgs;
/* Check if we need to add a NULL message to this header */
if(dst_oh_null > 0) {
unsigned null_idx; /* Index of new NULL message */
/* Make sure we have enough space for new NULL message */
if(oh_dst->nmesgs + 1 > oh_dst->alloc_nmesgs)
if(H5O_alloc_msgs(oh_dst, (size_t)1) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate more space for messages")
/* Create null message for [rest of] space in new chunk */
/* (account for chunk's magic # & checksum) */
null_idx = oh_dst->nmesgs++;
oh_dst->mesg[null_idx].type = H5O_MSG_NULL;
oh_dst->mesg[null_idx].dirty = TRUE;
oh_dst->mesg[null_idx].native = NULL;
oh_dst->mesg[null_idx].raw = current_pos + msghdr_size;
oh_dst->mesg[null_idx].raw_size = dst_oh_null - msghdr_size;
oh_dst->mesg[null_idx].chunkno = 0;
} /* end if */
/* Make sure we filled the chunk, except for room at the end for a checksum */
HDassert(current_pos + dst_oh_gap + dst_oh_null + H5O_SIZEOF_CHKSUM_OH(oh_dst) == dst_oh_size + oh_dst->chunk[0].image);
/* Set the dest. object location to the first chunk address */
HDassert(H5F_addr_defined(addr_new));
oloc_dst->addr = addr_new;
/* Allocate space for the address mapping of the object copied */
if(NULL == (addr_map = H5FL_MALLOC(H5O_addr_map_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Insert the address mapping for the new object into the copied list */
/* (Do this here, because "post copy" possibly checks it) */
addr_map->src_addr = oloc_src->addr;
addr_map->dst_addr = oloc_dst->addr;
addr_map->is_locked = TRUE; /* We've locked the object currently */
addr_map->inc_ref_count = 0; /* Start with no additional ref counts to add */
if(H5SL_insert(cpy_info->map_list, addr_map, &(addr_map->src_addr)) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTINSERT, FAIL, "can't insert object into skip list")
/* "post copy" loop over messages, to fix up any messages which require a complete
* object header for destination object
*/
null_msgs = 0;
for(mesgno = 0; mesgno < orig_dst_msgs; mesgno++) {
/* Skip any deleted or NULL messages in the source unless the
* preserve_null flag is set
*/
if(FALSE == cpy_info->preserve_null) {
while(deleted[mesgno + null_msgs]) {
++null_msgs;
HDassert(mesgno + null_msgs < oh_src->nmesgs);
} /* end while */
} /* end if */
/* Set up convenience variables */
mesg_src = &(oh_src->mesg[mesgno + null_msgs]);
mesg_dst = &(oh_dst->mesg[mesgno]);
/* Check for message class to operate on */
/* (Use destination message, in case the message has been removed (i.e
* converted to a nil message) in the destination -QAK)
*/
copy_type = mesg_dst->type;
HDassert(copy_type);
if(copy_type->post_copy_file && mesg_src->native) {
/* Sanity check destination message */
HDassert(mesg_dst->type == mesg_src->type);
HDassert(mesg_dst->native);
/* Perform "post copy" operation on message */
if((copy_type->post_copy_file)(oloc_src, mesg_src->native, oloc_dst,
mesg_dst->native, dxpl_id, cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to perform 'post copy' operation on message")
} /* end if */
} /* end for */
/* Indicate that the destination address will no longer be locked */
addr_map->is_locked = FALSE;
/* Increment object header's reference count, if any descendents have created links to this object */
if(addr_map->inc_ref_count) {
H5_CHECK_OVERFLOW(addr_map->inc_ref_count, hsize_t, unsigned);
oh_dst->nlink += (unsigned)addr_map->inc_ref_count;
} /* end if */
/* Insert destination object header in cache */
if(H5AC_set(oloc_dst->file, dxpl_id, H5AC_OHDR, oloc_dst->addr, oh_dst, H5AC__DIRTIED_FLAG) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to cache object header")
done:
/* Free deleted array */
if(deleted)
HDfree(deleted);
/* Release pointer to source object header and its derived objects */
if(oh_src != NULL) {
/* Unprotect the source object header */
if(H5AC_unprotect(oloc_src->file, dxpl_id, H5AC_OHDR, oloc_src->addr, oh_src, H5AC__NO_FLAGS_SET) < 0)
HDONE_ERROR(H5E_OHDR, H5E_PROTECT, FAIL, "unable to release object header")
} /* end if */
/* Release pointer to destination object header */
if(ret_value < 0 && oh_dst) {
if(H5O_dest(oloc_dst->file, oh_dst) < 0)
HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to destroy object header data")
} /* end if */
/* Release user data for particular type of object to copy */
if(udata) {
HDassert(obj_class);
HDassert(obj_class->free_copy_file_udata);
(obj_class->free_copy_file_udata)(udata);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_copy_header_real() */
/*-------------------------------------------------------------------------
* Function: H5O_copy_header_map
*
* Purpose: Copy header object from one location to another, detecting
* already mapped objects, etc.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* November 1, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5O_copy_header_map(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
hid_t dxpl_id, H5O_copy_t *cpy_info, hbool_t inc_depth)
{
H5O_addr_map_t *addr_map; /* Address mapping of object copied */
hbool_t inc_link; /* Whether to increment the link count for the object */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5O_copy_header_map, FAIL)
/* Sanity check */
HDassert(oloc_src);
HDassert(oloc_dst);
HDassert(oloc_dst->file);
HDassert(cpy_info);
/* Look up the address of the object to copy in the skip list */
addr_map = (H5O_addr_map_t *)H5SL_search(cpy_info->map_list, &(oloc_src->addr));
/* Check if address is already in list of objects copied */
if(addr_map == NULL) {
/* Copy object for the first time */
/* Check for incrementing the depth of copy */
/* (Can't do this for all copies, since committed datatypes should always be copied) */
if(inc_depth)
cpy_info->curr_depth++;
/* Copy object referred to */
if(H5O_copy_header_real(oloc_src, oloc_dst, dxpl_id, cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
/* Check for incrementing the depth of copy */
if(inc_depth)
cpy_info->curr_depth--;
/* When an object is copied for the first time, increment it's link */
inc_link = TRUE;
/* indicate that a new object is created */
ret_value++;
} /* end if */
else {
/* Object has already been copied, set its address in destination file */
oloc_dst->addr = addr_map->dst_addr;
/* If the object is locked currently (because we are copying a group
* hierarchy and this is a link to a group higher in the hierarchy),
* increment it's deferred reference count instead of incrementing the
* reference count now.
*/
if(addr_map->is_locked) {
addr_map->inc_ref_count++;
inc_link = FALSE;
} /* end if */
else
inc_link = TRUE;
} /* end else */
/* Increment destination object's link count, if allowed */
if(inc_link)
if(H5O_link(oloc_dst, 1, dxpl_id) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to increment object link count")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_copy_header_map() */
/*--------------------------------------------------------------------------
NAME
H5O_copy_free_addrmap_cb
PURPOSE
Internal routine to free address maps from the skip list for copying objects
USAGE
herr_t H5O_copy_free_addrmap_cb(item, key, op_data)
void *item; IN/OUT: Pointer to addr
void *key; IN/OUT: (unused)
void *op_data; IN: (unused)
RETURNS
Returns zero on success, negative on failure.
DESCRIPTION
Releases the memory for the address.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5O_copy_free_addrmap_cb(void *item, void UNUSED *key, void UNUSED *op_data)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_copy_free_addrmap_cb)
HDassert(item);
/* Release the item */
H5FL_FREE(H5O_addr_map_t, item);
FUNC_LEAVE_NOAPI(0)
} /* H5O_copy_free_addrmap_cb() */
/*-------------------------------------------------------------------------
* Function: H5O_copy_header
*
* Purpose: copy header object from one location to another.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* May 30, 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_copy_header(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
hid_t dxpl_id, unsigned cpy_option)
{
H5O_copy_t cpy_info; /* Information for copying object */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT(H5O_copy_header)
HDassert(oloc_src);
HDassert(oloc_src->file);
HDassert(H5F_addr_defined(oloc_src->addr));
HDassert(oloc_dst->file);
/* Convert copy flags into copy struct */
HDmemset(&cpy_info, 0, sizeof(H5O_copy_t));
if((cpy_option & H5O_COPY_SHALLOW_HIERARCHY_FLAG) > 0) {
cpy_info.copy_shallow = TRUE;
cpy_info.max_depth = 1;
} /* end if */
else
cpy_info.max_depth = -1; /* Current default is for full, recursive hier. copy */
cpy_info.curr_depth = 0;
if((cpy_option & H5O_COPY_EXPAND_SOFT_LINK_FLAG) > 0)
cpy_info.expand_soft_link = TRUE;
if((cpy_option & H5O_COPY_EXPAND_EXT_LINK_FLAG) > 0)
cpy_info.expand_ext_link = TRUE;
if((cpy_option & H5O_COPY_EXPAND_REFERENCE_FLAG) > 0)
cpy_info.expand_ref = TRUE;
if((cpy_option & H5O_COPY_WITHOUT_ATTR_FLAG) > 0)
cpy_info.copy_without_attr = TRUE;
if((cpy_option & H5O_COPY_PRESERVE_NULL_FLAG) > 0)
cpy_info.preserve_null = TRUE;
/* Create a skip list to keep track of which objects are copied */
if((cpy_info.map_list = H5SL_create(H5SL_TYPE_HADDR, 0.5, (size_t)16)) == NULL)
HGOTO_ERROR(H5E_SLIST, H5E_CANTCREATE, FAIL, "cannot make skip list")
/* copy the object from the source file to the destination file */
if(H5O_copy_header_real(oloc_src, oloc_dst, dxpl_id, &cpy_info) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
done:
if(cpy_info.map_list)
H5SL_destroy(cpy_info.map_list, H5O_copy_free_addrmap_cb, NULL);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_copy_header() */
/*-------------------------------------------------------------------------
* Function: H5O_copy_obj
*
* Purpose: Copy an object to destination location
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* June 4, 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_copy_obj(H5G_loc_t *src_loc, H5G_loc_t *dst_loc, const char *dst_name,
hid_t ocpypl_id, hid_t lcpl_id)
{
H5P_genplist_t *ocpy_plist=NULL; /* Object copy property list created */
hid_t dxpl_id=H5AC_dxpl_id;
H5G_name_t new_path; /* Copied object group hier. path */
H5O_loc_t new_oloc; /* Copied object object location */
H5G_loc_t new_loc; /* Group location of object copied */
hbool_t entry_inserted=FALSE; /* Flag to indicate that the new entry was inserted into a group */
unsigned cpy_option = 0; /* Copy options */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5O_copy_obj, FAIL)
HDassert(src_loc);
HDassert(src_loc->oloc->file);
HDassert(dst_loc);
HDassert(dst_loc->oloc->file);
HDassert(dst_name);
/* Get the copy property list */
if(NULL == (ocpy_plist = (H5P_genplist_t *)H5I_object(ocpypl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list")
/* Retrieve the copy parameters */
if(H5P_get(ocpy_plist, H5O_CPY_OPTION_NAME, &cpy_option) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get object copy flag")
/* Set up copied object location to fill in */
new_loc.oloc = &new_oloc;
new_loc.path = &new_path;
H5G_loc_reset(&new_loc);
new_oloc.file = dst_loc->oloc->file;
/* Copy the object from the source file to the destination file */
if(H5O_copy_header(src_loc->oloc, &new_oloc, dxpl_id, cpy_option) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
/* Insert the new object in the destination file's group */
if(H5L_link(dst_loc, dst_name, &new_loc, lcpl_id, H5P_DEFAULT, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to insert link")
entry_inserted = TRUE;
done:
/* Free the ID to name buffers */
if(entry_inserted)
H5G_loc_free(&new_loc);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_copy_obj() */
/*-------------------------------------------------------------------------
* Function: H5O_copy_obj_by_ref
*
* Purpose: Copy the object pointed by _src_ref.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* Aug 7 2006
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_copy_obj_by_ref(H5O_loc_t *src_oloc, hid_t dxpl_id, H5O_loc_t *dst_oloc,
H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info)
{
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5O_copy_obj_by_ref, FAIL)
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, dxpl_id, cpy_info, FALSE)) < 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 */
sprintf(tmp_obj_name, "~obj_pointed_by_%llu", (unsigned long_long)dst_oloc->addr);
/* Create a link to the newly copied object */
if(H5L_link(dst_root_loc, tmp_obj_name, &new_loc, H5P_DEFAULT, H5P_DEFAULT, dxpl_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
*
* Purpose: Copy the object pointed by _src_ref.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* Aug 7 2006
*
*-------------------------------------------------------------------------
*/
herr_t
H5O_copy_expand_ref(H5F_t *file_src, void *_src_ref, hid_t dxpl_id,
H5F_t *file_dst, void *_dst_ref, size_t ref_count, H5R_type_t ref_type,
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 */
uint8_t *p; /* Pointer to OID to store */
size_t i; /* Local index variable */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5O_copy_expand_ref, FAIL)
/* Sanity checks */
HDassert(file_src);
HDassert(_src_ref);
HDassert(file_dst);
HDassert(_dst_ref);
HDassert(ref_count);
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")
/* Copy object references */
if(H5R_OBJECT == ref_type) {
hobj_ref_t *src_ref = (hobj_ref_t *)_src_ref;
hobj_ref_t *dst_ref = (hobj_ref_t *)_dst_ref;
/* Making equivalent references in the destination file */
for(i = 0; i < ref_count; i++) {
/* Set up for the object copy for the reference */
p = (uint8_t *)(&src_ref[i]);
H5F_addr_decode(src_oloc.file, (const uint8_t **)&p, &(src_oloc.addr));
dst_oloc.addr = HADDR_UNDEF;
/* Attempt to copy object from source to destination file */
if(H5O_copy_obj_by_ref(&src_oloc, dxpl_id, &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 */
p = (uint8_t *)(&dst_ref[i]);
H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
} /* end for */
} /* end if */
/* Copy region references */
else if(H5R_DATASET_REGION == ref_type) {
hdset_reg_ref_t *src_ref = (hdset_reg_ref_t *)_src_ref;
hdset_reg_ref_t *dst_ref = (hdset_reg_ref_t *)_dst_ref;
uint8_t *buf; /* Buffer to store serialized selection in */
H5HG_t hobjid; /* Heap object ID */
size_t buf_size; /* Length of object in heap */
/* Making equivalent references in the destination file */
for(i = 0; i < ref_count; i++) {
/* Get the heap ID for the dataset region */
p = (uint8_t *)(&src_ref[i]);
H5F_addr_decode(src_oloc.file, (const uint8_t **)&p, &(hobjid.addr));
INT32DECODE(p, hobjid.idx);
/* Get the dataset region from the heap (allocate inside routine) */
if((buf = (uint8_t *)H5HG_read(src_oloc.file, dxpl_id, &hobjid, NULL, &buf_size)) == NULL)
HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
/* Get the object oid for the dataset */
p = (uint8_t *)buf;
H5F_addr_decode(src_oloc.file, (const uint8_t **)&p, &(src_oloc.addr));
dst_oloc.addr = HADDR_UNDEF;
/* copy the object pointed by the ref to the destination */
if(H5O_copy_obj_by_ref(&src_oloc, dxpl_id, &dst_oloc, &dst_root_loc, cpy_info) < 0) {
H5MM_xfree(buf);
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
} /* end if */
/* Serialize object ID */
p = (uint8_t *)buf;
H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
/* Save the serialized buffer to the destination */
if(H5HG_insert(dst_oloc.file, dxpl_id, buf_size, buf, &hobjid) < 0) {
H5MM_xfree(buf);
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "Unable to write dataset region information")
} /* end if */
/* Set the dataset region reference info for the destination file */
p = (uint8_t *)(&dst_ref[i]);
H5F_addr_encode(dst_oloc.file, &p, hobjid.addr);
INT32ENCODE(p, hobjid.idx);
/* Free the buffer allocated in H5HG_read() */
H5MM_xfree(buf);
} /* end for */
} /* end if */
else
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_copy_expand_ref() */
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