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hdf5/tools/h5repack/h5repack_refs.c
Jonathan Kim 23a80ac554 [svn-r20103] Purpose: 
Change to use HDxxx macros.

Description:
    Originally this started for fixing incorrect pointer usage. But that got
    fixed through coverity merge. So this is mainly changing to use HDxxx 
    macros and clean up some related code.
     
Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2011-02-14 17:20:32 -05:00

733 lines
31 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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);
/*-------------------------------------------------------------------------
* 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 = 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(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 = 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(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 */
assert(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
*
* 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 */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* Object info */
int j;
unsigned u;
if(H5Oget_info(loc_in, &oinfo) < 0)
goto error;
for(u = 0; u < (unsigned)oinfo.num_attrs; u++)
{
/*-------------------------------------------------------------------------
* open
*-------------------------------------------------------------------------
*/
/* 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 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((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* 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;
unsigned k;
const char* refname;
hobj_ref_t *buf = NULL;
/*-------------------------------------------------------------------------
* read input 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(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(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);
}
H5Oclose(refobj_id);
} /* k */
} /*nelmts*/
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
if(H5Aclose(attr_out) < 0)
goto error;
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
}/*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 k;
/*-------------------------------------------------------------------------
* 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(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(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);
} /* end if */
H5Oclose(refobj_id);
} /* k */
} /*nelmts */
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
{
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
}
if(H5Aclose(attr_out) < 0)
goto error;
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* 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;
} /* u */
return 0;
error:
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 == H5O_TYPE_DATASET ||
travt->objs[u].type == H5O_TYPE_GROUP ||
travt->objs[u].type == 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;
}
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