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hdf5/tools/h5repack/h5repack_copy.c
Quincey Koziol bb392083b2 [svn-r13297] Description: 
Add small 'h5mkgrp' tool to create groups in an HDF5 file from the command
line, allowing the group structure for a file to be created in a script.  This
tool closely follows the 'mkdir' command line tool in UNIX/Linux.

    Allow tool library applications to pass a FAPL to the h5tool_fopen() call,
giving some additional flexibility to tools which are adding objects to an
existing HDF5 file (like h5copy & h5mkgrp).

    Fix missing files in MANIFEST from previous checkin(s).

Tested on:
    Linux/32 2.6 (chicago)
    Linux/64 2.6 (chicago2)
2007-02-14 08:54:11 -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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5repack.h"
extern char *progname;
static int do_create_refs;
#define PER(A,B) { per = 0; \
if (A!=0) \
per = (double) fabs( (double)(B-A) / (double)A ); \
}
#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */
#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */
/* local functions */
static int do_hardlinks(hid_t fidout,trav_table_t *travt);
static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
static int do_copy_refobjs(hid_t fidin, hid_t fidout,trav_table_t *travt,pack_opt_t *options);
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 const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
/*-------------------------------------------------------------------------
* Function: print_dataset_info
*
* Purpose: print name, filters, percentage compression of a dataset
*
*-------------------------------------------------------------------------
*/
static void print_dataset_info(hid_t dcpl_id,
char *objname,
double per)
{
char strfilter[255];
#if defined (PRINT_DEBUG )
char temp[255];
#endif
int nfilters; /* number of filters */
unsigned filt_flags; /* filter flags */
H5Z_filter_t filtn; /* filter identification number */
unsigned cd_values[20]; /* filter client data values */
size_t cd_nelmts; /* filter client number of values */
char f_objname[256]; /* filter objname */
int i;
strcpy(strfilter,"\0");
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
return;
for ( i=0; i<nfilters; i++)
{
cd_nelmts = NELMTS(cd_values);
#ifdef H5_WANT_H5_V1_6_COMPAT
filtn = H5Pget_filter(dcpl_id,
(unsigned)i,
&filt_flags,
&cd_nelmts,
cd_values,
sizeof(f_objname),
f_objname);
#else
filtn = H5Pget_filter(dcpl_id,
(unsigned)i,
&filt_flags,
&cd_nelmts,
cd_values,
sizeof(f_objname),
f_objname,
NULL);
#endif /* H5_WANT_H5_V1_6_COMPAT */
switch (filtn)
{
default:
break;
case H5Z_FILTER_DEFLATE:
strcat(strfilter,"GZIP ");
#if defined (PRINT_DEBUG)
{
unsigned level=cd_values[0];
sprintf(temp,"(%d)",level);
strcat(strfilter,temp);
}
#endif
break;
case H5Z_FILTER_SZIP:
strcat(strfilter,"SZIP ");
#if defined (PRINT_DEBUG)
{
unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
unsigned ppb=cd_values[1];
sprintf(temp,"(%d,",ppb);
strcat(strfilter,temp);
if (options_mask & H5_SZIP_EC_OPTION_MASK)
strcpy(temp,"EC) ");
else if (options_mask & H5_SZIP_NN_OPTION_MASK)
strcpy(temp,"NN) ");
}
strcat(strfilter,temp);
#endif
break;
case H5Z_FILTER_SHUFFLE:
strcat(strfilter,"SHUF ");
break;
case H5Z_FILTER_FLETCHER32:
strcat(strfilter,"FLET ");
break;
case H5Z_FILTER_NBIT:
strcat(strfilter,"NBIT ");
break;
case H5Z_FILTER_SCALEOFFSET:
strcat(strfilter,"SCALEOFFSET ");
break;
} /* switch */
}/*i*/
if (strcmp(strfilter,"\0")==0)
printf(FORMAT_OBJ,"dset",objname );
else
{
char str[255], temp[20];
strcpy(str,"dset ");
strcat(str,strfilter);
sprintf(temp," (%.1f%%)",per);
strcat(str,temp);
printf(FORMAT_OBJ,str,objname);
}
}
/*-------------------------------------------------------------------------
* Function: copy_objects
*
* Purpose: duplicate all HDF5 objects in the file
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 23, 2003
*
*-------------------------------------------------------------------------
*/
int copy_objects(const char* fnamein,
const char* fnameout,
pack_opt_t *options)
{
hid_t fidin;
hid_t fidout=-1;
trav_table_t *travt=NULL;
/*-------------------------------------------------------------------------
* open the files
*-------------------------------------------------------------------------
*/
if ((fidin=h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))<0 ){
error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR );
goto out;
}
if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){
error_msg(progname, "<%s>: Could not create file\n", fnameout );
goto out;
}
if (options->verbose)
printf("Making file <%s>...\n",fnameout);
/* init table */
trav_table_init(&travt);
/* get the list of objects in the file */
if (h5trav_gettable(fidin,travt)<0)
goto out;
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if(do_copy_objects(fidin,fidout,travt,options)<0) {
error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
/*-------------------------------------------------------------------------
* do the copy of referenced objects in a second sweep if needed (references
* detected in the first traversal)
*-------------------------------------------------------------------------
*/
if (do_create_refs){
if(do_copy_refobjs(fidin,fidout,travt,options)<0) {
error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
}
/*-------------------------------------------------------------------------
* create hard links
*-------------------------------------------------------------------------
*/
if(do_hardlinks(fidout,travt)<0) {
error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
/* free table */
trav_table_free(travt);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
H5Fclose(fidin);
H5Fclose(fidout);
return 0;
/*-------------------------------------------------------------------------
* out
*-------------------------------------------------------------------------
*/
out:
H5E_BEGIN_TRY {
H5Fclose(fidin);
H5Fclose(fidout);
} H5E_END_TRY;
if (travt)
trav_table_free(travt);
return -1;
}
/*-------------------------------------------------------------------------
* Function: do_copy_objects
*
* Purpose: duplicate all HDF5 objects in the file
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 23, 2003
*
* Modifications:
*
* July 2004: Introduced the extra EC or NN option for SZIP
*
* December 2004: Added a check for H5Dcreate; if the dataset cannot be created
* with the requested filter, use the input one
*
* October 2006: Read/write using the file type by default.
* Read/write by hyperslabs for big datasets.
*
* November 2006: Use H5Ocopy in the copy of objects. The logic for using
* H5Ocopy or not is if the input DCPL has filters or non default layout or these are
* requested by the user then use read/write else use H5Ocopy.
* A detection is made for the cases where the recreation of references is needed
* in a second sweep of the file
*
*-------------------------------------------------------------------------
*/
int do_copy_objects(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in=-1; /* group ID */
hid_t grp_out=-1; /* 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 type_out=-1; /* named type ID */
hid_t dcpl_id=-1; /* dataset creation property list ID */
hid_t dcpl_out=-1; /* dataset creation property list ID */
hid_t f_space_id=-1; /* file space ID */
hid_t ftype_id=-1; /* file type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
hsize_t dsize_in; /* input dataset size before filter */
hsize_t dsize_out; /* output dataset size after filter */
int next; /* external files */
int apply_s; /* flag for apply filter to small dataset sizes */
int apply_f; /* flag for apply filter to return error on H5Dcreate */
double per; /* percent utilization of storage */
void *buf=NULL; /* buffer for raw data */
void *sm_buf=NULL; /* buffer for raw data */
unsigned i;
/*-------------------------------------------------------------------------
* copy the suppplied object list
*-------------------------------------------------------------------------
*/
if (options->verbose) {
printf("-----------------------------------------\n");
printf(" Type Filter (Ratio) Name\n");
printf("-----------------------------------------\n");
}
for ( i = 0; i < travt->nobjs; i++)
{
buf = NULL;
do_create_refs = 0;
switch ( travt->objs[i].type )
{
/*-------------------------------------------------------------------------
* H5G_GROUP
*-------------------------------------------------------------------------
*/
case H5G_GROUP:
if (options->verbose)
printf(FORMAT_OBJ,"group",travt->objs[i].name );
if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0)
goto error;
if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(grp_in,grp_out,options)<0)
goto error;
if (H5Gclose(grp_out)<0)
goto error;
if (H5Gclose(grp_in)<0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
/*-------------------------------------------------------------------------
* check if we should use H5Ocopy or not
* if there is a request for filters/layout, we read/write the object
* otherwise we do a copy using H5Ocopy
*-------------------------------------------------------------------------
*/
if (options->op_tbl->nelems
/* do we have input request for filter/chunk ? */
||
options->all_filter==1 || options->all_layout==1
)
{
int j;
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
goto error;
if ((f_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 ((dcpl_out = H5Pcopy (dcpl_id))<0)
goto error;
if ( (rank=H5Sget_simple_extent_ndims(f_space_id))<0)
goto error;
HDmemset(dims, 0, sizeof dims);
if ( H5Sget_simple_extent_dims(f_space_id,dims,NULL)<0)
goto error;
nelmts=1;
for (j=0; j<rank; j++)
nelmts*=dims[j];
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* check for external files
*-------------------------------------------------------------------------
*/
if ((next=H5Pget_external_count (dcpl_id))<0)
goto error;
if (next)
fprintf(stderr," <warning: %s has external files, ignoring read...>\n",
travt->objs[i].name );
/*-------------------------------------------------------------------------
* 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 (next==0 && h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
{
apply_s=1;
apply_f=1;
/*-------------------------------------------------------------------------
* references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
* in a second traversal of the output file
*-------------------------------------------------------------------------
*/
if (H5T_REFERENCE==H5Tget_class(wtype_id))
{
do_create_refs = 1;
}
else /* H5T_REFERENCE */
{
/* get the storage size of the input dataset */
dsize_in=H5Dget_storage_size(dset_in);
/* check for datasets too small */
if (nelmts*msize < options->threshold )
apply_s=0;
/* apply the filter */
if (apply_s){
if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options)<0)
goto error;
}
/*-------------------------------------------------------------------------
* create the output dataset;
* disable error checking in case the dataset cannot be created with the
* modified dcpl; in that case use the original instead
*-------------------------------------------------------------------------
*/
H5E_BEGIN_TRY {
dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out);
} H5E_END_TRY;
if (dset_out==FAIL)
{
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0)
goto error;
apply_f=0;
}
/*-------------------------------------------------------------------------
* read/write
*-------------------------------------------------------------------------
*/
if (nelmts)
{
size_t need = (size_t)(nelmts*msize); /* bytes needed */
if ( need < H5TOOLS_MALLOCSIZE )
buf = HDmalloc(need);
if (buf != NULL )
{
if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
}
else /* possibly not enough memory, read/write by hyperslabs */
{
size_t p_type_nbytes = msize; /*size of memory type */
hsize_t p_nelmts = nelmts; /*total selected elmts */
hsize_t elmtno; /*counter */
int carry; /*counter carry value */
unsigned int vl_data = 0; /*contains VL datatypes */
/* stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
hsize_t sm_nelmts; /*elements per stripmine*/
hid_t sm_space; /*stripmine data space */
/* hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
hsize_t hs_nelmts; /*elements in request */
hsize_t zero[8]; /*vector of zeros */
int k;
/* check if we have VL data in the dataset's datatype */
if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
vl_data = TRUE;
/*
* determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = p_type_nbytes;
for (k = rank; k > 0; --k) {
sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes);
sm_nbytes *= sm_size[k - 1];
assert(sm_nbytes > 0);
}
sm_buf = HDmalloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
/* the stripmine loop */
memset(hs_offset, 0, sizeof hs_offset);
memset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts)
{
/* calculate the hyperslab size */
if (rank > 0)
{
for (k = 0, hs_nelmts = 1; k < rank; k++)
{
hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
hs_nelmts *= hs_size[k];
}
if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0)
goto error;
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0)
goto error;
}
else
{
H5Sselect_all(f_space_id);
H5Sselect_all(sm_space);
hs_nelmts = 1;
} /* rank */
/* read/write */
if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0)
goto error;
if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0)
goto error;
/* reclaim any VL memory, if necessary */
if(vl_data)
H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
/* calculate the next hyperslab offset */
for (k = rank, carry = 1; k > 0 && carry; --k)
{
hs_offset[k - 1] += hs_size[k - 1];
if (hs_offset[k - 1] == dims[k - 1])
hs_offset[k - 1] = 0;
else
carry = 0;
} /* k */
} /* elmtno */
H5Sclose(sm_space);
/* free */
if (sm_buf!=NULL)
{
HDfree(sm_buf);
sm_buf=NULL;
}
} /* hyperslab read */
}/*nelmts*/
/*-------------------------------------------------------------------------
* amount of compression used
*-------------------------------------------------------------------------
*/
if (options->verbose)
{
if (apply_s && apply_f)
{
/* get the storage size of the input dataset */
dsize_out=H5Dget_storage_size(dset_out);
PER((hssize_t)dsize_in,(hssize_t)dsize_out);
print_dataset_info(dcpl_out,travt->objs[i].name,per*100.0);
}
else
print_dataset_info(dcpl_id,travt->objs[i].name,0.0);
}
if (apply_s==0 && options->verbose)
printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
travt->objs[i].name,
(int)options->threshold);
if (apply_f==0 && options->verbose)
printf(" <warning: could not apply the filter to %s>\n",
travt->objs[i].name);
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(dset_in,dset_out,options)<0)
goto error;
/*close */
if (H5Dclose(dset_out)<0)
goto error;
}/*H5T_REFERENCE*/
}/*h5tools_canreadf*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0)
goto error;
if (H5Tclose(wtype_id)<0)
goto error;
if (H5Pclose(dcpl_id)<0)
goto error;
if (H5Pclose(dcpl_out)<0)
goto error;
if (H5Sclose(f_space_id)<0)
goto error;
if (H5Dclose(dset_in)<0)
goto error;
}
/*-------------------------------------------------------------------------
* we do not have request for filter/chunking use H5Ocopy instead
*-------------------------------------------------------------------------
*/
else
{
hid_t pid;
/* create property to pass copy options */
if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
goto error;
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if (H5Ocopy(fidin, /* Source file or group identifier */
travt->objs[i].name, /* Name of the source object to be copied */
fidout, /* Destination file or group identifier */
travt->objs[i].name, /* Name of the destination object */
pid, /* Properties which apply to the copy */
H5P_DEFAULT)<0) /* Properties which apply to the new hard link */
goto error;
/* close property */
if (H5Pclose(pid)<0)
goto error;
} /* end do we have request for filter/chunking */
break;
/*-------------------------------------------------------------------------
* H5G_TYPE
*-------------------------------------------------------------------------
*/
case H5G_TYPE:
if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
goto error;
if ((type_out = H5Tcopy(type_in))<0)
goto error;
if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(type_in,type_out,options)<0)
goto error;
if (H5Tclose(type_in)<0)
goto error;
if (H5Tclose(type_out)<0)
goto error;
if (options->verbose)
printf(FORMAT_OBJ,"type",travt->objs[i].name );
break;
/*-------------------------------------------------------------------------
* H5G_LINK
* H5G_UDLINK
*
* Only handles external links; H5Lcopy will fail for other UD link types
* since we don't have creation or copy callbacks for them.
*-------------------------------------------------------------------------
*/
case H5G_LINK:
case H5G_UDLINK:
{
if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
if (options->verbose)
printf(FORMAT_OBJ,"link",travt->objs[i].name );
}
break;
default:
goto error;
} /* switch */
/* free */
if (buf!=NULL)
{
HDfree(buf);
buf=NULL;
}
} /* i */
/*-------------------------------------------------------------------------
* the root is a special case, we get an ID for the root group
* and copy its attributes using that ID
*-------------------------------------------------------------------------
*/
if ((grp_out = H5Gopen(fidout,"/"))<0)
goto error;
if ((grp_in = H5Gopen(fidin,"/"))<0)
goto error;
if (copy_attr(grp_in,grp_out,options)<0)
goto error;
if (H5Gclose(grp_out)<0)
goto error;
if (H5Gclose(grp_in)<0)
goto error;
return 0;
error:
H5E_BEGIN_TRY {
H5Gclose(grp_in);
H5Gclose(grp_out);
H5Pclose(dcpl_id);
H5Sclose(f_space_id);
H5Dclose(dset_in);
H5Dclose(dset_out);
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Tclose(type_in);
H5Tclose(type_out);
/* free */
if (buf!=NULL)
{
HDfree(buf);
buf=NULL;
}
if (sm_buf!=NULL)
{
HDfree(sm_buf);
sm_buf=NULL;
}
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: copy_attr
*
* Purpose: copy attributes located in LOC_IN, which is obtained either from
* loc_id = H5Gopen( fid, name);
* loc_id = H5Dopen( fid, name);
* loc_id = H5Topen( fid, name);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
int copy_attr(hid_t loc_in,
hid_t loc_out,
pack_opt_t *options
)
{
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 type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
void *buf=NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
int n, j;
unsigned u;
if ((n = H5Aget_num_attrs(loc_in))<0)
goto error;
for ( u = 0; u < (unsigned)n; u++)
{
/* set data buffer to NULL each iteration
we might not use it in the case of references
*/
buf=NULL;
/*-------------------------------------------------------------------------
* open
*-------------------------------------------------------------------------
*/
/* open attribute */
if ((attr_id = H5Aopen_idx(loc_in, u))<0)
goto error;
/* get name */
if (H5Aget_name( attr_id, 255, name )<0)
goto error;
/* get the file datatype */
if ((ftype_id = H5Aget_type( attr_id )) < 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;
nelmts=1;
for (j=0; j<rank; j++)
nelmts*=dims[j];
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
* this is done on a second sweep of the file that just copies
* the referenced objects
*-------------------------------------------------------------------------
*/
if ( ! H5Tequal(wtype_id, H5T_STD_REF_OBJ))
{
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,wtype_id,buf)<0)
goto error;
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
goto error;
if(H5Awrite(attr_out,wtype_id,buf)<0)
goto error;
/*close*/
if (H5Aclose(attr_out)<0)
goto error;
if (buf)
free(buf);
} /*H5T_STD_REF_OBJ*/
if (options->verbose)
printf(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0) goto error;
if (H5Tclose(wtype_id)<0) goto error;
if (H5Sclose(space_id)<0) goto error;
if (H5Aclose(attr_id)<0) goto error;
} /* u */
return 0;
error:
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
if (buf)
free(buf);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: do_hardlinks
*
* Purpose: duplicate hard links
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
*
*-------------------------------------------------------------------------
*/
static
int do_hardlinks(hid_t fidout,trav_table_t *travt)
{
unsigned int i, j;
for ( i = 0; i < travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
case H5G_GROUP:
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++)
{
if (H5Glink(fidout,
H5L_TYPE_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name)<0)
return -1;
}
}
break;
case H5G_DATASET:
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++){
if (H5Glink(fidout,
H5L_TYPE_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name)<0)
return -1;
}
}
break;
case H5G_TYPE:
case H5G_LINK:
case H5G_UDLINK:
/*nothing to do */
break;
default:
break;
}
}
return 0;
}
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
*
* Purpose: duplicate all referenced HDF5 objects in the file in a second traversal
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
*
*-------------------------------------------------------------------------
*/
static
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 type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
int next; /* external files */
unsigned i;
int j;
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for ( i = 0; i < travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
case H5G_GROUP:
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<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 (j=0; j<rank; j++)
nelmts*=dims[j];
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* check for external files
*-------------------------------------------------------------------------
*/
if ((next=H5Pget_external_count (dcpl_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 (next==0 && 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(wtype_id, H5T_STD_REF_OBJ))
{
H5G_obj_t obj_type;
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=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
goto error;
refbuf=HDmalloc((unsigned)nelmts*msize);
if ( refbuf==NULL){
error_msg(progname, "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(dset_in,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,-1)<0)
goto error;
if (options->verbose)
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
goto error;
if (nelmts) {
if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
goto error;
}
if (buf)
free(buf);
if (refbuf)
free(refbuf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
{
H5G_obj_t obj_type;
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=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
if ( refbuf==NULL){
error_msg(progname, "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(dset_in,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("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
goto error;
if (nelmts) {
if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
goto error;
}
if (buf)
free(buf);
if (refbuf)
free(refbuf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else
{
if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
goto error;
}
assert(dset_out!=FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
goto error;
if (H5Dclose(dset_out)<0)
goto error;
}/*can_read*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0)
goto error;
if (H5Tclose(wtype_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;
case H5G_TYPE:
case H5G_LINK:
case H5G_UDLINK:
/*nothing to do */
break;
default:
break;
}
}
/*-------------------------------------------------------------------------
* the root is a special case, we get an ID for the root group
* and copy its attributes using that ID
* it must be done last, because the attributes might contain references to
* objects in the object list
*-------------------------------------------------------------------------
*/
if ((grp_out = H5Gopen(fidout,"/"))<0)
goto error;
if ((grp_in = H5Gopen(fidin,"/"))<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;
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(wtype_id);
H5Tclose(type_in);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: copy_refs_attr
*
* Purpose: duplicate all referenced HDF5 objects located in attributes
* relative to LOC_IN, which is obtained either from
* loc_id = H5Gopen( fid, name);
* loc_id = H5Dopen( fid, name);
* loc_id = H5Topen( fid, name);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* 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 type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
int n, j;
unsigned u;
if ((n = H5Aget_num_attrs(loc_in))<0)
goto error;
for ( u = 0; u < (unsigned)n; u++)
{
/*-------------------------------------------------------------------------
* open
*-------------------------------------------------------------------------
*/
/* open attribute */
if ((attr_id = H5Aopen_idx(loc_in, u))<0)
goto error;
/* get name */
if (H5Aget_name( attr_id, 255, name )<0)
goto error;
/* get the file datatype */
if ((ftype_id = H5Aget_type( attr_id )) < 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<rank; j++)
nelmts*=dims[j];
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
{
H5G_obj_t obj_type;
hid_t refobj_id;
hobj_ref_t *refbuf=NULL;
unsigned k;
const char* refname;
hobj_ref_t *buf=NULL;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,wtype_id,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
goto error;
refbuf=HDmalloc((unsigned)nelmts*msize);
if ( refbuf==NULL){
error_msg(progname, "cannot allocate memory\n" );
goto error;
}
for ( k=0; k<nelmts; k++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
goto error;
} 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 */
if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if (options->verbose)
printf("object <%s> reference created to <%s>\n",name,refname);
}
close_obj(obj_type,refobj_id);
}/* k */
}/*nelmts*/
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
goto error;
if (nelmts) {
if(H5Awrite(attr_out,wtype_id,refbuf)<0)
goto error;
}
if (H5Aclose(attr_out)<0)
goto error;
if (refbuf)
free(refbuf);
if (buf)
free(buf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
{
H5G_obj_t obj_type;
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 k;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,wtype_id,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
if ( refbuf==NULL){
error_msg(progname, "cannot allocate memory\n" );
goto error;
}
for ( k=0; k<nelmts; k++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<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(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
goto error;
/* create the reference, we need the space_id */
if (H5Rcreate(&refbuf[k],fidout,refname,H5R_DATASET_REGION,region_id)<0)
goto error;
if (H5Sclose(region_id)<0)
goto error;
if (options->verbose)
printf("object <%s> region reference created to <%s>\n",name,refname);
}
close_obj(obj_type,refobj_id);
}/* k */
}/*nelmts */
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
goto error;
if (nelmts) {
if(H5Awrite(attr_out,wtype_id,refbuf)<0)
goto error;
}
if (H5Aclose(attr_out)<0)
goto error;
if (refbuf)
free(refbuf);
if (buf)
free(buf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0) goto error;
if (H5Tclose(wtype_id)<0) goto error;
if (H5Sclose(space_id)<0) goto error;
if (H5Aclose(attr_id)<0) goto error;
} /* u */
return 0;
error:
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: close_obj
*
* Purpose: Auxiliary function to close an object
*
*-------------------------------------------------------------------------
*/
static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
{
H5E_BEGIN_TRY
{
switch (obj_type)
{
case H5G_GROUP:
H5Gclose(obj_id);
break;
case H5G_DATASET:
H5Dclose(obj_id);
break;
case H5G_TYPE:
H5Tclose(obj_id);
break;
default:
break;
}
} H5E_END_TRY;
}
/*-------------------------------------------------------------------------
* Function: MapIdToName
*
* Purpose: map an object ID to a name
*
*-------------------------------------------------------------------------
*/
static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt)
{
hid_t id;
hid_t fid;
H5G_stat_t refstat; /* Stat for the refobj id */
H5G_stat_t objstat; /* Stat for objects in the file */
unsigned int i;
/* obtain information to identify the referenced object uniquely */
if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0)
return NULL;
/* obtains the file ID given an object ID. This ID must be closed */
if ((fid = H5Iget_file_id(refobj_id))<0)
{
return NULL;
}
/* linear search */
for ( i=0; i<travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
default:
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
if ((id = H5Dopen(fid,travt->objs[i].name))<0)
return NULL;
if(H5Gget_objinfo(id, ".", 0, &objstat) <0)
return NULL;
if (H5Dclose(id)<0)
return NULL;
if (!HDmemcmp(&refstat.fileno, &objstat.fileno, sizeof(refstat.fileno)) && !HDmemcmp(&refstat.objno, &objstat.objno, sizeof(refstat.objno)))
{
H5Fclose(fid);
return travt->objs[i].name;
}
break;
} /* switch */
} /* i */
if (H5Fclose(fid)<0)
return NULL;
return NULL;
}
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