mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2024-12-27 08:01:04 +08:00
Code Issues Packages Projects Releases Wiki Activity
4d0187a483
hdf5/tools/lib/h5diff_attr.c
Albert Cheng 3dc1e6dd38 [svn-r25081] Bug HDFFV-8625, HDFFV-8639, HDFFV-8745: 
h5diff issues "unable to read attribute" error message when comparing two files

Description:
    h5diff did not handle attributes of variable length strings correctly. It created the wrong memory type if one but not both compared attributes are of the variable strings type. It ended in H5Aread() failure.

Solution:
    We decided to treat the case when one type is variable length string and the other is not as incomparable. That bypassed the above error.  We still need to figure out the proper way, if possible, to compare variable string with non-variable string types.

Tested: h5committested plus tested in Swallow (OS X 10.8).
2014-04-22 17:25:51 -05:00

589 lines
19 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 "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5diff.h"
#define ATTR_NAME_MAX 255
typedef struct table_attr_t {
char *name;
unsigned exist[2];
} match_attr_t;
typedef struct table_attrs_t {
size_t size;
size_t nattrs;
size_t nattrs_only1;
size_t nattrs_only2;
match_attr_t *attrs;
} table_attrs_t;
/*-------------------------------------------------------------------------
* Function: table_attrs_init
*
* Purpose: Initialize the table
*
* Parameter:
* - tbl [OUT]
*
* Programmer: Jonathan Kim
*
* Date: March 15, 2011
*------------------------------------------------------------------------*/
static void table_attrs_init(table_attrs_t **tbl)
{
table_attrs_t* table_attrs = (table_attrs_t*) HDmalloc(sizeof(table_attrs_t));
table_attrs->size = 0;
table_attrs->nattrs = 0;
table_attrs->nattrs_only1 = 0;
table_attrs->nattrs_only2 = 0;
table_attrs->attrs = NULL;
*tbl = table_attrs;
}
/*-------------------------------------------------------------------------
* Function: table_attrs_free
*
* Purpose: free given table
*
* Parameter:
* - table [IN]
*
* Programmer: Jonathan Kim
*
* Date: March 15, 2011
*------------------------------------------------------------------------*/
static void table_attrs_free( table_attrs_t *table )
{
unsigned int i;
if (table)
{
if(table->attrs)
{
for(i = 0; i < table->nattrs; i++)
{
if(table->attrs[i].name)
HDfree(table->attrs[i].name );
} /* end for */
HDfree(table->attrs);
table->attrs = NULL;
} /* end if */
HDfree(table);
table = NULL;
}
}
/*-------------------------------------------------------------------------
* Function: table_attr_mark_exist
*
* Purpose: mark given attribute name to table as sign of exsit
*
* Parameter:
* - exist [IN]
* - name [IN] : attribute name
* - table [OUT]
*
* Programmer: Jonathan Kim
*
* Date: March 15, 2011
*------------------------------------------------------------------------*/
static void table_attr_mark_exist(unsigned *exist, char *name, table_attrs_t *table)
{
size_t new_val;
if(table->nattrs == table->size) {
table->size = MAX(1, table->size * 2);
table->attrs = (match_attr_t *)HDrealloc(table->attrs, table->size * sizeof(match_attr_t));
} /* end if */
new_val = table->nattrs++;
table->attrs[new_val].exist[0] = exist[0];
table->attrs[new_val].exist[1] = exist[1];
table->attrs[new_val].name = (char *)HDstrdup(name);
}
/*-------------------------------------------------------------------------
* Function: build_match_list_attrs
*
* Purpose: get list of matching attribute name from obj1 and obj2
*
* Note:
* Find common attribute; the algorithm for search is referred from
* build_match_list() in h5diff.c .
*
* Parameter:
* table_out [OUT] : return the list
*
* Programmer: Jonathan Kim
*
* Date: March 15, 2011
*------------------------------------------------------------------------*/
static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t ** table_out, diff_opt_t *options)
{
H5O_info_t oinfo1, oinfo2; /* Object info */
hid_t attr1_id=-1; /* attr ID */
hid_t attr2_id=-1; /* attr ID */
size_t curr1 = 0;
size_t curr2 = 0;
unsigned infile[2];
char name1[ATTR_NAME_MAX];
char name2[ATTR_NAME_MAX];
int cmp;
unsigned i;
table_attrs_t *table_lp = NULL;
if(H5Oget_info(loc1_id, &oinfo1) < 0)
goto error;
if(H5Oget_info(loc2_id, &oinfo2) < 0)
goto error;
table_attrs_init( &table_lp );
/*--------------------------------------------------
* build the list
*/
while(curr1 < oinfo1.num_attrs && curr2 < oinfo2.num_attrs)
{
/*------------------
* open attribute1 */
if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr1_id, (size_t)ATTR_NAME_MAX, name1) < 0)
goto error;
/*------------------
* open attribute2 */
if((attr2_id = H5Aopen_by_idx(loc2_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr2_id, (size_t)ATTR_NAME_MAX, name2) < 0)
goto error;
/* criteria is string compare */
cmp = HDstrcmp(name1, name2);
if(cmp == 0)
{
infile[0] = 1;
infile[1] = 1;
table_attr_mark_exist(infile, name1, table_lp);
curr1++;
curr2++;
}
else if(cmp < 0)
{
infile[0] = 1;
infile[1] = 0;
table_attr_mark_exist(infile, name1, table_lp);
table_lp->nattrs_only1++;
curr1++;
}
else
{
infile[0] = 0;
infile[1] = 1;
table_attr_mark_exist(infile, name2, table_lp);
table_lp->nattrs_only2++;
curr2++;
}
/* close for next turn */
H5Aclose(attr1_id);
attr1_id = -1;
H5Aclose(attr2_id);
attr2_id = -1;
} /* end while */
/* list1 did not end */
infile[0] = 1;
infile[1] = 0;
while(curr1 < oinfo1.num_attrs)
{
/*------------------
* open attribute1 */
if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr1_id, (size_t)ATTR_NAME_MAX, name1) < 0)
goto error;
table_attr_mark_exist(infile, name1, table_lp);
table_lp->nattrs_only1++;
curr1++;
/* close for next turn */
H5Aclose(attr1_id);
attr1_id = -1;
}
/* list2 did not end */
infile[0] = 0;
infile[1] = 1;
while(curr2 < oinfo2.num_attrs)
{
/*------------------
* open attribute2 */
if((attr2_id = H5Aopen_by_idx(loc2_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr2_id, (size_t)ATTR_NAME_MAX, name2) < 0)
goto error;
table_attr_mark_exist(infile, name2, table_lp);
table_lp->nattrs_only2++;
curr2++;
/* close for next turn */
H5Aclose(attr2_id);
}
/*------------------------------------------------------
* print the list
*/
if(options->m_verbose_level == 2)
{
/* if '-v2' is detected */
parallel_print(" obj1 obj2\n");
parallel_print(" --------------------------------------\n");
for(i = 0; i < (unsigned int) table_lp->nattrs; i++)
{
char c1, c2;
c1 = (table_lp->attrs[i].exist[0]) ? 'x' : ' ';
c2 = (table_lp->attrs[i].exist[1]) ? 'x' : ' ';
parallel_print("%5c %6c %-15s\n", c1, c2, table_lp->attrs[i].name);
} /* end for */
}
if(options->m_verbose_level >= 1)
{
parallel_print("Attributes status: %d common, %d only in obj1, %d only in obj2\n", table_lp->nattrs - table_lp->nattrs_only1 - table_lp->nattrs_only2, table_lp->nattrs_only1, table_lp->nattrs_only2 );
}
*table_out = table_lp;
return 0;
error:
if (0 < attr1_id)
H5Aclose(attr1_id);
if (0 < attr2_id)
H5Aclose(attr2_id);
return -1;
}
/*-------------------------------------------------------------------------
* Function: diff_attr
*
* Purpose: compare attributes located in LOC1_ID and LOC2_ID, which are
* obtained either from
* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Dopen2(fid, name);
* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
*
* Return: number of differences found
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November, 03, 2003
*
* Modifications:
* March, 02, 2007: return the number of differences found
*
*-------------------------------------------------------------------------
*/
hsize_t diff_attr(hid_t loc1_id,
hid_t loc2_id,
const char *path1,
const char *path2,
diff_opt_t *options)
{
hid_t attr1_id=-1; /* attr ID */
hid_t attr2_id=-1; /* attr ID */
hid_t space1_id=-1; /* space ID */
hid_t space2_id=-1; /* space ID */
hid_t ftype1_id=-1; /* file data type ID */
hid_t ftype2_id=-1; /* file data type ID */
int vstrtype1=0; /* ftype1 is a variable string */
int vstrtype2=0; /* ftype2 is a variable string */
hid_t mtype1_id=-1; /* memory data type ID */
hid_t mtype2_id=-1; /* memory data type ID */
size_t msize1; /* memory size of memory type */
size_t msize2; /* memory size of memory type */
void *buf1=NULL; /* data buffer */
void *buf2=NULL; /* data buffer */
int buf1hasdata=0; /* buffer has data */
int buf2hasdata=0; /* buffer has data */
hsize_t nelmts1; /* number of elements in dataset */
int rank1; /* rank of dataset */
int rank2; /* rank of dataset */
hsize_t dims1[H5S_MAX_RANK];/* dimensions of dataset */
hsize_t dims2[H5S_MAX_RANK];/* dimensions of dataset */
char *name1;
char *name2;
char np1[512];
char np2[512];
unsigned u; /* Local index variable */
hsize_t nfound = 0;
hsize_t nfound_total = 0;
int j;
table_attrs_t * match_list_attrs = NULL;
if( build_match_list_attrs(loc1_id, loc2_id, &match_list_attrs, options) < 0)
goto error;
/* if detect any unique extra attr */
if(match_list_attrs->nattrs_only1 || match_list_attrs->nattrs_only2)
{
/* exit will be 1 */
options->contents = 0;
}
for(u = 0; u < (unsigned)match_list_attrs->nattrs; u++)
{
if( (match_list_attrs->attrs[u].exist[0]) && (match_list_attrs->attrs[u].exist[1]) )
{
name1 = name2 = match_list_attrs->attrs[u].name;
/*--------------
* attribute 1 */
if((attr1_id = H5Aopen(loc1_id, name1, H5P_DEFAULT)) < 0)
goto error;
/*--------------
* attribute 2 */
if((attr2_id = H5Aopen(loc2_id, name2, H5P_DEFAULT)) < 0)
goto error;
/* get the datatypes */
if((ftype1_id = H5Aget_type(attr1_id)) < 0)
goto error;
vstrtype1 = H5Tis_variable_str(ftype1_id);
if((ftype2_id = H5Aget_type(attr2_id)) < 0)
goto error;
vstrtype2 = H5Tis_variable_str(ftype2_id);
/* no compare if either one but not both are variable string type */
if (vstrtype1 != vstrtype2){
if ((options->m_verbose||options->m_list_not_cmp))
parallel_print("Not comparable: one of attribute <%s/%s> or <%s/%s> is of variable length type\n",
path1, name1, path2, name2);
options->not_cmp = 1;
return 0;
}
if((mtype1_id = h5tools_get_native_type(ftype1_id))<0)
goto error;
if((mtype2_id = h5tools_get_native_type(ftype2_id))<0)
goto error;
if((msize1 = H5Tget_size(mtype1_id))==0)
goto error;
if((msize2 = H5Tget_size(mtype2_id))==0)
goto error;
/* get the dataspace */
if((space1_id = H5Aget_space(attr1_id)) < 0)
goto error;
if((space2_id = H5Aget_space(attr2_id)) < 0)
goto error;
/* get dimensions */
if((rank1 = H5Sget_simple_extent_dims(space1_id, dims1, NULL)) < 0)
goto error;
if((rank2 = H5Sget_simple_extent_dims(space2_id, dims2, NULL)) < 0)
goto error;
/*----------------------------------------------------------------------
* check for comparable TYPE and SPACE
*----------------------------------------------------------------------
*/
/* pass dims1 and dims2 for maxdims as well since attribute's maxdims
* are always same */
if( diff_can_type(ftype1_id, ftype2_id, rank1, rank2, dims1, dims2,
dims1, dims2, name1, name2, options, 0) != 1 )
{
if(H5Tclose(ftype1_id) < 0)
goto error;
if(H5Tclose(ftype2_id) < 0)
goto error;
if(H5Sclose(space1_id) < 0)
goto error;
if(H5Sclose(space2_id) < 0)
goto error;
if(H5Aclose(attr1_id) < 0)
goto error;
if(H5Aclose(attr2_id) < 0)
goto error;
if(H5Tclose(mtype1_id) < 0)
goto error;
if(H5Tclose(mtype2_id) < 0)
goto error;
continue;
}
/*-----------------------------------------------------------------
* "upgrade" the smaller memory size
*------------------------------------------------------------------
*/
if (FAIL == match_up_memsize (ftype1_id, ftype2_id,
&mtype1_id, &mtype2_id,
&msize1, &msize2))
goto error;
/*---------------------------------------------------------------------
* read
*----------------------------------------------------------------------
*/
nelmts1 = 1;
for(j = 0; j < rank1; j++)
nelmts1 *= dims1[j];
buf1 = (void *)HDmalloc((size_t)(nelmts1 * msize1));
buf2 = (void *)HDmalloc((size_t)(nelmts1 * msize2));
if(buf1 == NULL || buf2 == NULL){
parallel_print( "cannot read into memory\n" );
goto error;
}
if(H5Aread(attr1_id,mtype1_id,buf1) < 0){
parallel_print("Failed reading attribute1 %s/%s\n", path1, name1);
goto error;
}else
buf1hasdata = 1;
if(H5Aread(attr2_id,mtype2_id,buf2) < 0){
parallel_print("Failed reading attribute2 %s/%s\n", path2, name2);
goto error;
}else
buf2hasdata = 1;
/* format output string */
HDsnprintf(np1, sizeof(np1), "%s of <%s>", name1, path1);
HDsnprintf(np2, sizeof(np1), "%s of <%s>", name2, path2);
/*---------------------------------------------------------------------
* array compare
*----------------------------------------------------------------------
*/
/* always print name */
/* verbose (-v) and report (-r) mode */
if(options->m_verbose || options->m_report) {
do_print_attrname("attribute", np1, np2);
nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
options, np1, np2, mtype1_id, attr1_id, attr2_id);
print_found(nfound);
}
/* quiet mode (-q), just count differences */
else if(options->m_quiet) {
nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
options, np1, np2, mtype1_id, attr1_id, attr2_id);
}
/* the rest (-c, none, ...) */
else {
nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
options, np1, np2, mtype1_id, attr1_id, attr2_id);
/* print info if compatible and difference found */
if(nfound) {
do_print_attrname("attribute", np1, np2);
print_found(nfound);
} /* end if */
} /* end else */
/*----------------------------------------------------------------------
* close
*----------------------------------------------------------------------
*/
/* Free buf1 and buf2, check both VLEN-data VLEN-string to reclaim any
* VLEN memory first */
if(TRUE == h5tools_detect_vlen(mtype1_id))
H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
HDfree(buf1);
buf1 = NULL;
if(TRUE == h5tools_detect_vlen(mtype2_id))
H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
HDfree(buf2);
buf2 = NULL;
if(H5Tclose(ftype1_id) < 0)
goto error;
if(H5Tclose(ftype2_id) < 0)
goto error;
if(H5Sclose(space1_id) < 0)
goto error;
if(H5Sclose(space2_id) < 0)
goto error;
if(H5Aclose(attr1_id) < 0)
goto error;
if(H5Aclose(attr2_id) < 0)
goto error;
if(H5Tclose(mtype1_id) < 0)
goto error;
if(H5Tclose(mtype2_id) < 0)
goto error;
nfound_total += nfound;
}
} /* u */
table_attrs_free(match_list_attrs);
return nfound_total;
error:
H5E_BEGIN_TRY {
if(buf1) {
if(buf1hasdata && TRUE == h5tools_detect_vlen(mtype1_id))
H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
HDfree(buf1);
} /* end if */
if(buf2) {
if(buf2hasdata && TRUE == h5tools_detect_vlen(mtype2_id))
H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
HDfree(buf2);
} /* end if */
table_attrs_free(match_list_attrs);
H5Tclose(ftype1_id);
H5Tclose(ftype2_id);
H5Tclose(mtype1_id);
H5Tclose(mtype2_id);
H5Sclose(space1_id);
H5Sclose(space2_id);
H5Aclose(attr1_id);
H5Aclose(attr2_id);
} H5E_END_TRY;
options->err_stat = 1;
return nfound_total;
}
Reference in New Issue View Git Blame Copy Permalink