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hdf5/tools/h5repack/h5repack_refs.c
Quincey Koziol 33ea1ada24 [svn-r25496] Description: 
Merge 64-bit ID changes from branch to trunk.  (Plus a few minor cleanups
that aren't on the branch)

Tested on:
    Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
    (h5committested on branch already for a week)
2014-07-30 15:55:14 -05:00

882 lines
35 KiB
C
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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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5diff.h"
#include "h5tools.h"
/*-------------------------------------------------------------------------
* local functions
*-------------------------------------------------------------------------
*/
static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
trav_table_t *travt, hid_t fidout);
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt);
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
*
* Purpose: duplicate all referenced HDF5 objects in the file
* and create hard links
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
*
*-------------------------------------------------------------------------
*/
int do_copy_refobjs(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in = (-1); /* read group ID */
hid_t grp_out = (-1); /* write group ID */
hid_t dset_in = (-1); /* read dataset ID */
hid_t dset_out = (-1); /* write dataset ID */
hid_t type_in = (-1); /* named type ID */
hid_t dcpl_id = (-1); /* dataset creation property list ID */
hid_t space_id = (-1); /* space ID */
hid_t ftype_id = (-1); /* file data type ID */
hid_t mtype_id = (-1); /* memory data type ID */
size_t msize; /* memory size of memory type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes
copied */
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for(i = 0; i < travt->nobjs; i++) {
switch(travt->objs[i].type)
{
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_GROUP
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_GROUP:
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
goto error;
if(H5Gclose(grp_out) < 0)
goto error;
if(H5Gclose(grp_in) < 0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_DATASET
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_DATASET:
if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if((space_id = H5Dget_space(dset_in)) < 0)
goto error;
if((ftype_id = H5Dget_type(dset_in)) < 0)
goto error;
if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
goto error;
if((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
goto error;
if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
goto error;
nelmts = 1;
for(k = 0; k < rank; k++)
nelmts *= dims[k];
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
* are not registered in the current configuration
* 1) the external filters GZIP and SZIP might not be available
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
if(h5tools_canreadf(NULL, dcpl_id) == 1) {
/*-------------------------------------------------------------------------
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
dset_out = FAIL;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
hid_t refobj_id;
hobj_ref_t *refbuf = NULL; /* buffer for object references */
hobj_ref_t *buf = NULL;
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
printf("cannot read into memory\n" );
goto error;
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL){
printf("cannot allocate memory\n" );
goto error;
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur
* in the second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
/* create the reference, -1 parameter for objects */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
}
} /*refname*/
H5Oclose(refobj_id);
} /* u */
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
goto error;
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
/*------------------------------------------------------
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
goto error;
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf("cannot allocate memory\n");
goto error;
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur
* in the second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
hid_t region_id; /* region id of the referenced dataset */
if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
goto error;
/* create the reference, we need the space_id */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
goto error;
if(H5Sclose(region_id) < 0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
}
} /*refname*/
H5Oclose(refobj_id);
} /* u */
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
goto error;
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
/*-----------------------------------------------------
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else {
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
} /* end else */
HDassert(dset_out != FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
if(H5Dclose(dset_out) < 0)
goto error;
} /*can_read*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
goto error;
if(H5Tclose(mtype_id) < 0)
goto error;
if(H5Pclose(dcpl_id) < 0)
goto error;
if(H5Sclose(space_id) < 0)
goto error;
if(H5Dclose(dset_in) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_NAMED_DATATYPE
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if(H5Tclose(type_in) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_LINK
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_LINK:
/*nothing to do */
break;
case H5TRAV_TYPE_UNKNOWN:
case H5TRAV_TYPE_UDLINK:
goto error;
default:
break;
} /* end switch */
} /* end for */
/* Finalize (link) the stack of named datatypes (if any)
* This function is paired with copy_named_datatype() which is called
* in copy_attr(), so need to free.
*/
named_datatype_free(&named_dt_head, 0);
return 0;
error:
H5E_BEGIN_TRY {
H5Gclose(grp_in);
H5Gclose(grp_out);
H5Pclose(dcpl_id);
H5Sclose(space_id);
H5Dclose(dset_in);
H5Dclose(dset_out);
H5Tclose(ftype_id);
H5Tclose(mtype_id);
H5Tclose(type_in);
named_datatype_free(&named_dt_head, 0);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: copy_refs_attr
*
* Purpose: duplicate all referenced HDF5 located in attributes
* relative to LOC_IN, which is obtained either from
* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Modifier: xcao@hdfgroup.org, 9/12/2011
* Update values of references(object and region) for the following types:
* 1) References,
* 2) ARRAY of reference,
* 3) VLEN of references.
* 4) COMPOUND of references.
* This function does not handle references in other complicated structures,
* such as references in nested compound datatypes.
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
static int copy_refs_attr(hid_t loc_in,
hid_t loc_out,
pack_opt_t *options,
trav_table_t *travt,
hid_t fidout /* for saving references */
)
{
hid_t attr_id = -1; /* attr ID */
hid_t attr_out = -1; /* attr ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file data type ID */
hid_t mtype_id = -1; /* memory data type ID */
size_t msize; /* memory size of type */
hsize_t nelmts; /* number of elements in dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* Object info */
unsigned u, i, j;
int rank;
H5T_class_t type_class = -1;
hbool_t is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0;
void *refbuf = NULL;
void *buf = NULL;
const char* refname = NULL;
int *ref_comp_index = NULL;
size_t *ref_comp_size = NULL;
int ref_comp_field_n = 0;
if(H5Oget_info(loc_in, &oinfo) < 0)
goto error;
for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get the file datatype */
if((ftype_id = H5Aget_type(attr_id)) < 0)
goto error;
type_class = H5Tget_class(ftype_id);
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
is_ref = (type_class == H5T_REFERENCE);
if(type_class == H5T_VLEN ) {
hid_t base_type;
base_type = H5Tget_super(ftype_id);
is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
else if(type_class == H5T_ARRAY ) {
hid_t base_type;
base_type = H5Tget_super(ftype_id);
is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
else if(type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(ftype_id) ;
if (nmembers < 1)
goto error;
ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int));
ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size));
ref_comp_field_n = 0;
for (i=0; i<(unsigned)nmembers; i++) {
hid_t mtid = H5Tget_member_type( ftype_id, i );
if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
ref_comp_index[ref_comp_field_n] = i;
ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
ref_comp_field_n++;
}
H5Tclose(mtid);
}
/* if compound don't contain reference type member, free the above
* mallocs. Otherwise there can be memory leaks by the 'continue'
* statement below. */
if (!ref_comp_field_n) {
if (ref_comp_index) {
HDfree(ref_comp_index);
ref_comp_index = NULL;
}
if (ref_comp_size) {
HDfree(ref_comp_size);
ref_comp_size = NULL;
}
}
}
is_ref_comp = (ref_comp_field_n > 0);
if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) {
H5Tclose(mtype_id);
H5Tclose(ftype_id);
H5Aclose(attr_id);
continue;
}
/* get name */
if(H5Aget_name(attr_id, 255, name) < 0)
goto error;
/* get the dataspace handle */
if((space_id = H5Aget_space(attr_id)) < 0)
goto error;
/* get dimensions */
if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
goto error;
/*-------------------------------------------------------------------------
* elements
*-------------------------------------------------------------------------
*/
nelmts = 1;
for(j = 0; j < (unsigned)rank; j++)
nelmts *= dims[j];
if (is_ref_array) {
unsigned array_rank = 0;
hsize_t array_size = 1;
hsize_t array_dims[H5S_MAX_RANK];
hid_t base_type;
base_type = H5Tget_super(ftype_id);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
array_rank = H5Tget_array_ndims(mtype_id);
H5Tget_array_dims2(mtype_id, array_dims);
for(j = 0; j <array_rank; j++)
array_size *= array_dims[j];
nelmts *= array_size;
}
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if (nelmts>0) {
/* handle object references */
if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL) {
printf("cannot allocate memory\n");
goto error;
} /* end if */
for(i = 0; i < (unsigned)nelmts; i++) {
if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
continue;
if(options->verbose)
printf("object <%s> reference created to <%s>\n", name, refname);
} /* i */
} /* H5T_STD_REF_OBJ */
/* handle region references */
else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf( "cannot read into memory\n" );
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf( "cannot allocate memory\n" );
goto error;
} /* end if */
for(i = 0; i < (unsigned)nelmts; i++) {
if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
continue;
if(options->verbose)
printf("object <%s> region reference created to <%s>\n", name, refname);
}
} /* H5T_STD_REF_DSETREG */
else if (is_ref_vlen) {
/* handle VLEN of references */
buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
refbuf = buf; /* reuse the read buffer for write */
if(buf == NULL) {
printf( "cannot read into memory\n" );
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
if (H5R_OBJ_REF_BUF_SIZE==msize) {
hobj_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
} else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
hdset_reg_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
}
} /* else if (is_ref_vlen) */
else if (is_ref_comp) {
/* handle ref fields in a compound */
buf = HDmalloc((unsigned)(nelmts * msize));
refbuf = buf; /* reuse the read buffer for write */
if(buf == NULL)
{
printf( "cannot read into memory\n" );
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
for (i=0; i<(unsigned)nelmts; i++) {
for (j=0; j<(unsigned)ref_comp_field_n; j++) {
if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
hobj_ref_t ref_out;
if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* if */
else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
hdset_reg_ref_t ref_out;
if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* else if */
} /* j */
} /* i */
} /* else if (is_ref_comp) */
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
if (is_ref_vlen && buf)
H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
} /* if (nelmts) */
if (refbuf == buf)
refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
if(buf) {
HDfree(buf);
buf = NULL;
}
if(refbuf) {
HDfree(refbuf);
refbuf = NULL;
}
if (ref_comp_index) {
HDfree(ref_comp_index);
ref_comp_index = NULL;
}
if (ref_comp_size) {
HDfree(ref_comp_size);
ref_comp_size = NULL;
}
if(H5Aclose(attr_out) < 0)
goto error;
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
goto error;
if(H5Tclose(mtype_id) < 0)
goto error;
if(H5Sclose(space_id) < 0)
goto error;
if(H5Aclose(attr_id) < 0)
goto error;
} /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
return 0;
error:
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
if (ref_comp_index)
HDfree(ref_comp_index);
if (ref_comp_size)
HDfree(ref_comp_size);
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
H5Tclose(mtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: MapIdToName
*
* Purpose: map a ID from a reference to a dataset name
*
*-------------------------------------------------------------------------
*/
static const char*
MapIdToName(hid_t refobj_id, trav_table_t *travt)
{
unsigned int u;
const char* ret = NULL;
/* linear search */
for(u = 0; u < travt->nobjs; u++) {
if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET ||
travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP ||
travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) {
H5O_info_t ref_oinfo; /* Stat for the refobj id */
/* obtain information to identify the referenced object uniquely */
if(H5Oget_info(refobj_id, &ref_oinfo) < 0)
goto out;
if(ref_oinfo.addr == travt->objs[u].objno) {
ret = travt->objs[u].name;
goto out;
} /* end if */
} /* end if */
} /* u */
out:
return ret;
}
/*-------------------------------------------------------------------------
* Function: Update_Ref_value
*
* Purpose: Update a reference value
*
* Programmer: xcao@hdfgroup.org 9/12/2011
*
*-------------------------------------------------------------------------
*/
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt)
{
herr_t ret = -1;
const char* ref_obj_name;
hid_t space_id=-1, ref_obj_id=-1;
ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
if (ref_obj_id<0)
goto done;
ref_obj_name = MapIdToName(ref_obj_id, travt);
if (ref_obj_name == NULL)
goto done;
if (ref_type == H5R_DATASET_REGION) {
space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
if (space_id < 0)
goto done;
}
ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id);
if (ret < 0)
goto done;
ret = 0;
done:
H5E_BEGIN_TRY {
H5Sclose(space_id);
H5Oclose(ref_obj_id);
} H5E_END_TRY;
return ret;
}
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