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a4069db8f4
hdf5/tools/lib/h5trav.c
Quincey Koziol a4069db8f4 [svn-r14131] Description: 
Move H5Giterate() and H5G_iterate_t to deprecated symbols section,
replacing them with H5Literate and H5L_iterate_t respectively.

Tested on:
	FreeBSD/32 6.2 (duty)
	FreeBSD/64 6.2 (liberty)
	Linux/32 2.6 (kagiso)
	Linux/64 2.6 (smirom)
	AIX/32 5.3 (copper)
	Solaris/32 5.10 (linew)
	Mac OS X/32 10.4.10 (amazon)
2007-08-30 15:03:37 -05:00

951 lines
24 KiB
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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 "h5trav.h"
#include "H5private.h"
/*-------------------------------------------------------------------------
* local functions
*-------------------------------------------------------------------------
*/
static int traverse( hid_t loc_id,
const char *group_name,
trav_table_t *table,
trav_info_t *info,
int *idx,
int print);
static hssize_t get_nnames( hid_t loc_id,
const char *group_name );
static herr_t get_name_type( hid_t loc_id,
const char *group_name,
int idx,
char **name,
H5G_obj_t *type );
/*-------------------------------------------------------------------------
* "h5trav info" public functions. used in h5diff
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: h5trav_getinfo
*
* Purpose: get an array of "trav_info_t" , containing the name and type of
* objects in the file
*
* Return: number of object names in file
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 6, 2002
*
*-------------------------------------------------------------------------
*/
int h5trav_getinfo(hid_t file_id,
trav_info_t *info,
int print )
{
trav_table_t *table=NULL;
int nnames=0;
/* init table */
trav_table_init( &table );
/* iterate starting on the root group */
if (( nnames = traverse( file_id, "/", table, info, &nnames, print )) < 0 )
return -1;
/* free table */
trav_table_free( table );
return nnames;
}
/*-------------------------------------------------------------------------
* Function: h5trav_getindex
*
* Purpose: get index of OBJ in list
*
* Return: index, -1 if not found
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: May 9, 2003
*
*-------------------------------------------------------------------------
*/
int h5trav_getindex( const char *obj, int nobjs, trav_info_t *info )
{
char *pdest;
int result;
int i;
for ( i = 0; i < nobjs; i++)
{
if ( strcmp(obj,info[i].name)==0 )
return i;
pdest = strstr( info[i].name, obj );
result = (int)(pdest - info[i].name);
/* found at position 1, meaning without '/' */
if( pdest != NULL && result==1 )
return i;
}
return -1;
}
/*-------------------------------------------------------------------------
* Function: h5trav_freeinfo
*
* Purpose: free info memory
*
*-------------------------------------------------------------------------
*/
void h5trav_freeinfo( trav_info_t *info, int nobjs )
{
int i;
if ( info )
{
for ( i = 0; i < nobjs; i++)
{
if (info[i].name)
HDfree( info[i].name );
}
HDfree(info);
}
}
/*-------------------------------------------------------------------------
* Function: h5trav_printinfo
*
* Purpose: print list of names in file
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: May 9, 2003
*
*-------------------------------------------------------------------------
*/
void h5trav_printinfo(int nobjs, trav_info_t *travi)
{
int i;
for ( i = 0; i < nobjs; i++)
{
switch ( travi[i].type )
{
case H5G_GROUP:
printf(" %-10s %s\n", "group", travi[i].name );
break;
case H5G_DATASET:
printf(" %-10s %s\n", "dataset", travi[i].name );
break;
case H5G_TYPE:
printf(" %-10s %s\n", "datatype", travi[i].name );
break;
case H5G_LINK:
printf(" %-10s %s\n", "link", travi[i].name );
break;
case H5G_UDLINK:
printf(" %-10s %s\n", "User defined link", travi[i].name );
break;
default:
printf(" %-10s %s\n", "User defined object", travi[i].name );
break;
}
}
}
/*-------------------------------------------------------------------------
* "h5trav table" public functions. used in h5repack
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: h5trav_getindext
*
* Purpose: get index of NAME in list
*
* Return: index, -1 if not found
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 18, 2003
*
*-------------------------------------------------------------------------
*/
int h5trav_getindext(const char *name, trav_table_t *table)
{
char *pdest;
int result;
unsigned int i, j;
for ( i = 0; i < table->nobjs; i++)
{
if ( strcmp(name,table->objs[i].name)==0 )
return i;
pdest = strstr( table->objs[i].name, name );
result = (int)(pdest - table->objs[i].name);
/* found at position 1, meaning without '/' */
if( pdest != NULL && result==1 && strlen(table->objs[i].name)-1==strlen(name))
return i;
/* search also in the list of links */
if (table->objs[i].nlinks)
{
for ( j=0; j<table->objs[i].nlinks; j++)
{
if ( strcmp(name,table->objs[i].links[j].new_name)==0 )
return i;
pdest = strstr( table->objs[i].links[j].new_name, name );
result = (int)(pdest - table->objs[i].links[j].new_name);
/* found at position 1, meaning without '/' */
if( pdest != NULL && result==1 )
return i;
}
}
}
return -1;
}
/*-------------------------------------------------------------------------
* Function: h5trav_gettable
*
* Purpose: get the trav_table_t struct
*
* Return: 0, -1 on error
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 17, 2003
*
*-------------------------------------------------------------------------
*/
int h5trav_gettable(hid_t fid, trav_table_t *travt)
{
int nnames=0;
/* iterate starting on the root group */
if (( nnames = traverse(fid,"/",travt,NULL,&nnames,0))<0)
return -1;
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5trav_printtable
*
* Purpose: print list of objects in file
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: May 9, 2003
*
*-------------------------------------------------------------------------
*/
void h5trav_printtable(trav_table_t *table)
{
unsigned int i, j;
for ( i = 0; i < table->nobjs; i++)
{
switch ( table->objs[i].type )
{
case H5G_GROUP:
printf(" %-10s %s\n", "group", table->objs[i].name );
break;
case H5G_DATASET:
printf(" %-10s %s\n", "dataset", table->objs[i].name );
break;
case H5G_TYPE:
printf(" %-10s %s\n", "datatype", table->objs[i].name );
break;
case H5G_LINK:
printf(" %-10s %s\n", "link", table->objs[i].name );
break;
default:
printf(" %-10s %s\n", "User defined object", table->objs[i].name );
break;
}
if (table->objs[i].nlinks)
{
for ( j=0; j<table->objs[i].nlinks; j++)
{
printf(" %-10s %s\n", " hardlink", table->objs[i].links[j].new_name );
}
}
}
}
/*-------------------------------------------------------------------------
* Function: get_nnames
*
* Purpose: Counts the number of names in the group GROUP_NAME
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October 10, 2002
*
* Return:
* Success: The return value of the first operator that
* returns non-zero, or zero if all members were
* processed with no operator returning non-zero.
*
* Failure: Negative if something goes wrong within the
* library, or the negative value returned by one
* of the operators.
*
*-------------------------------------------------------------------------
*/
static hssize_t get_nnames( hid_t loc_id, const char *group_name )
{
hid_t gid;
hsize_t nobjs = 0;
/* Open the group */
if((gid = H5Gopen2(loc_id, group_name, H5P_DEFAULT)) < 0)
return(-1);
/* Retrieve the number of objects in it */
if(H5Gget_num_objs(gid, &nobjs) < 0)
return(-1);
/* Close the group */
if(H5Gclose(gid) < 0)
return(-1);
return((hssize_t)nobjs);
}
/*-------------------------------------------------------------------------
* Function: opget_info
*
* Purpose: operator function
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October 10, 2002
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
opget_info(hid_t loc_id, const char *name, const H5L_info_t *linfo, void *op_data)
{
H5G_stat_t statbuf;
if(H5Gget_objinfo(loc_id, name, FALSE, &statbuf) < 0)
return -1;
((trav_info_t *)op_data)->type = statbuf.type;
((trav_info_t *)op_data)->name = (char *)HDstrdup(name);
/* Define 1 for return. This will cause the iterator to stop */
return 1;
}
/*-------------------------------------------------------------------------
* Function: get_name_type
*
* Purpose:
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October 10, 2002
*
* Return:
* Success: The return value of the first operator that
* returns non-zero, or zero if all members were
* processed with no operator returning non-zero.
*
* Failure: Negative if something goes wrong within the
* library, or the negative value returned by one
* of the operators.
*
*-------------------------------------------------------------------------
*/
static herr_t get_name_type( hid_t loc_id,
const char *group_name,
int _idx,
char **name,
H5G_obj_t *type )
{
trav_info_t info;
hsize_t idx = (hsize_t)_idx;
if(H5Literate(loc_id, group_name, H5_INDEX_NAME, H5_ITER_INC, &idx, opget_info, (void *)&info, H5P_DEFAULT) < 0)
return -1;
*name = info.name;
*type = info.type;
return 0;
}
/*-------------------------------------------------------------------------
* Function: traverse
*
* Purpose: recursive function that searches HDF5 objects in LOC_ID
*
* Return: number of objects found in LOC_ID
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 4, 2002
*
*-------------------------------------------------------------------------
*/
static int traverse( hid_t loc_id,
const char *group_name,
trav_table_t *table,
trav_info_t *info,
int *idx,
int print)
{
haddr_t objno; /* Compact form of object's location */
char *name=NULL;
H5G_obj_t type;
int n_names;
char *path=NULL;
H5G_stat_t statbuf;
int inserted_objs=0;
int i, j;
/* get the number of names */
if (( n_names = (int)get_nnames( loc_id, group_name )) < 0 )
return -1;
for ( i = 0; i < n_names; i++)
{
if (get_name_type( loc_id, group_name, i, &name, &type ) < 0 )
return -1;
/* allocate path buffer */
path = (char*) HDmalloc(HDstrlen(group_name) + HDstrlen(name) + 2);
/* initialize path */
HDstrcpy( path, group_name );
if ( HDstrcmp(group_name, "/") != 0 )
HDstrcat( path, "/" );
HDstrcat( path, name );
/* disable error reporting */
H5E_BEGIN_TRY {
/* get info */
H5Gget_objinfo( loc_id, path, FALSE, &statbuf);
} H5E_END_TRY;
objno = (haddr_t)statbuf.objno[0] | ((haddr_t)statbuf.objno[1] << (8 * sizeof(long)));
/* add to array */
if ( info )
{
info[*idx].name = (char *)HDstrdup(path);
info[*idx].type = type;
(*idx)++;
}
switch ( type )
{
/*-------------------------------------------------------------------------
* H5G_GROUP
*-------------------------------------------------------------------------
*/
case H5G_GROUP:
/* increment */
inserted_objs++;
/* nlink is number of hard links to object */
if (statbuf.nlink > 0 && trav_table_search(objno, table ) == -1)
{
/* add object to table */
trav_table_add(objno, path, H5G_GROUP, table );
/* print it */
if (print)
printf(" %-10s %s\n", "group", path );
/* recurse with the absolute name */
inserted_objs += traverse( loc_id, path, table, info, idx, print );
}
/* search table
group with more than one link to it */
if (statbuf.nlink > 1)
{
if ((j = trav_table_search(objno, table )) < 0 )
return -1;
trav_table_addlink(table,j,path);
if ( table->objs[j].displayed == 0 )
{
table->objs[j].displayed = 1;
}
else
{
/* print it */
if (print)
printf(" %-10s %s %s %s\n", "group", path, "->", table->objs[j].name );
}
}
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
/* increment */
inserted_objs++;
/* nlink is number of hard links to object */
if (statbuf.nlink > 0 && trav_table_search(objno, table ) == -1)
{
/* add object to table */
trav_table_add(objno, path, H5G_DATASET, table );
/* print it */
if (print)
printf(" %-10s %s\n", "dataset", path );
}
/* search table
dataset with more than one link to it */
if (statbuf.nlink > 1)
{
if ((j = trav_table_search(objno, table )) < 0 )
return -1;
trav_table_addlink(table,j,path);
if ( table->objs[j].displayed == 0 )
{
table->objs[j].displayed = 1;
}
else
{
/* print it */
if (print)
printf(" %-10s %s %s %s\n", "dataset", path, "->", table->objs[j].name );
} /* displayed==1 */
} /* nlink>1 */
break;
/*-------------------------------------------------------------------------
* H5G_TYPE
*-------------------------------------------------------------------------
*/
case H5G_TYPE:
/* increment */
inserted_objs++;
/* nlink is number of hard links to object */
if (statbuf.nlink > 0 && trav_table_search(objno, table ) == -1)
{
/* add object to table */
trav_table_add(objno, path, H5G_TYPE, table );
/* print it */
if (print)
printf(" %-10s %s\n", "datatype", path );
}
break;
/*-------------------------------------------------------------------------
* H5G_LINK
*-------------------------------------------------------------------------
*/
case H5G_LINK:
/* increment */
inserted_objs++;
/* add object to table */
trav_table_add(HADDR_UNDEF, path, H5G_LINK, table);
if(statbuf.linklen > 0) {
char *targbuf;
targbuf = HDmalloc(statbuf.linklen);
assert(targbuf);
H5Lget_val(loc_id, path, targbuf, statbuf.linklen, H5P_DEFAULT);
if(print)
printf(" %-10s %s -> %s\n", "link", path, targbuf);
free(targbuf);
}
else {
if(print)
printf(" %-10s %s ->\n", "link", path);
}
break;
/*-------------------------------------------------------------------------
* H5G_UDLINK
*-------------------------------------------------------------------------
*/
case H5G_UDLINK:
{
H5L_info_t linkbuf;
/* increment */
inserted_objs++;
/* add object to table */
trav_table_add(HADDR_UNDEF, path, H5G_UDLINK, table );
/* Get type of link */
H5E_BEGIN_TRY {
/* get link class info */
H5Lget_info( loc_id, path, &linkbuf, H5P_DEFAULT);
} H5E_END_TRY;
if(linkbuf.type == H5L_TYPE_EXTERNAL) {
if(statbuf.linklen > 0) {
char *targbuf;
const char *filename;
const char *objname;
targbuf = HDmalloc(statbuf.linklen);
assert(targbuf);
H5Lget_val(loc_id, path, targbuf, statbuf.linklen, H5P_DEFAULT);
H5Lunpack_elink_val(targbuf, statbuf.linklen, NULL, &filename, &objname);
if(print)
printf(" %-10s %s -> %s %s\n", "ext link", path, filename, objname);
free(targbuf);
} /* end if */
else {
if(print)
printf(" %-10s %s ->\n", "udlink", path);
} /* end else */
} /* end if */
else { /* Unknown user-defined type */
if(print)
printf(" %-10s %s ->\n", "UD link type", path);
} /* end else */
}
break;
default:
HDfprintf(stderr, "traverse: Unknown object %d!\n", type);
return (-1);
break;
}
/*-------------------------------------------------------------------------
* end switch
*-------------------------------------------------------------------------
*/
if ( name )
HDfree( name );
if ( path )
HDfree( path );
} /* i */
return inserted_objs;
}
/*-------------------------------------------------------------------------
* Function: trav_table_search
*
* Purpose: Search in the table for OBJNO
*
* Return: index of object in table
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 4, 2002
*
*-------------------------------------------------------------------------
*/
int trav_table_search(haddr_t objno, trav_table_t *table )
{
unsigned int i;
for (i = 0; i < table->nobjs; i++)
if (table->objs[i].objno == objno)
return i;
return -1;
}
/*-------------------------------------------------------------------------
* Function: trav_table_add
*
* Purpose: Add OBJNO, NAME and TYPE of object to table
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 4, 2002
*
*-------------------------------------------------------------------------
*/
void trav_table_add(haddr_t objno,
char *name,
H5G_obj_t type,
trav_table_t *table)
{
unsigned int i;
if (table->nobjs == table->size) {
table->size *= 2;
table->objs =
(trav_obj_t*)HDrealloc(table->objs, table->size * sizeof(trav_obj_t));
for (i = table->nobjs; i < table->size; i++) {
table->objs[i].objno = 0;
table->objs[i].flags[0] = table->objs[i].flags[1] = 0;
table->objs[i].displayed = 0;
table->objs[i].type = H5G_UNKNOWN;
table->objs[i].name = NULL;
table->objs[i].links = NULL;
table->objs[i].nlinks = 0;
table->objs[i].sizelinks = 0;
}
}
i = table->nobjs++;
table->objs[i].objno = objno;
table->objs[i].flags[0] = table->objs[i].flags[1] = 0;
HDfree(table->objs[i].name);
table->objs[i].name = (char *)HDstrdup(name);
table->objs[i].type = type;
table->objs[i].links = NULL;
table->objs[i].nlinks = 0;
}
/*-------------------------------------------------------------------------
* Function: trav_table_addflags
*
* Purpose: Add FLAGS, NAME and TYPE of object to table
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 4, 2002
*
*-------------------------------------------------------------------------
*/
void trav_table_addflags(unsigned *flags,
char *name,
H5G_obj_t type,
trav_table_t *table)
{
unsigned int i;
if (table->nobjs == table->size) {
table->size *= 2;
table->objs =
(trav_obj_t*)HDrealloc(table->objs, table->size * sizeof(trav_obj_t));
for (i = table->nobjs; i < table->size; i++) {
table->objs[i].objno = 0;
table->objs[i].flags[0] = table->objs[i].flags[1] = 0;
table->objs[i].displayed = 0;
table->objs[i].type = H5G_UNKNOWN;
table->objs[i].name = NULL;
table->objs[i].links = NULL;
table->objs[i].nlinks = 0;
table->objs[i].sizelinks = 0;
}
}
i = table->nobjs++;
table->objs[i].objno = 0;
table->objs[i].flags[0] = flags[0];
table->objs[i].flags[1] = flags[1];
HDfree(table->objs[i].name);
table->objs[i].name = (char *)HDstrdup(name);
table->objs[i].type = type;
table->objs[i].links = NULL;
table->objs[i].nlinks = 0;
}
/*-------------------------------------------------------------------------
* Function: trav_table_init
*
* Purpose: Initialize the table
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 4, 2002
*
*-------------------------------------------------------------------------
*/
void trav_table_init( trav_table_t **tbl )
{
unsigned int i;
trav_table_t* table = (trav_table_t*) HDmalloc(sizeof(trav_table_t));
table->size = 20;
table->nobjs = 0;
table->objs =
(trav_obj_t*)HDmalloc(table->size * sizeof(trav_obj_t));
for (i = 0; i < table->size; i++) {
table->objs[i].objno = 0;
table->objs[i].flags[0] = table->objs[i].flags[1] = 0;
table->objs[i].displayed = 0;
table->objs[i].type = H5G_UNKNOWN;
table->objs[i].name = NULL;
table->objs[i].links = NULL;
table->objs[i].nlinks = 0;
table->objs[i].sizelinks = 0;
}
*tbl = table;
}
/*-------------------------------------------------------------------------
* Function: trav_table_free
*
* Purpose: free table memory
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 4, 2002
*
*-------------------------------------------------------------------------
*/
void trav_table_free( trav_table_t *table )
{
unsigned int i, j;
for ( i = 0; i < table->nobjs; i++)
{
HDfree( table->objs[i].name );
if (table->objs[i].nlinks)
{
for ( j=0; j<table->objs[i].nlinks; j++)
HDfree( table->objs[i].links[j].new_name );
HDfree(table->objs[i].links);
}
}
HDfree(table->objs);
HDfree(table);
}
/*-------------------------------------------------------------------------
* Function: trav_table_addlink
*
* Purpose: Add a hardlink name to the object
*
* Return: void
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 17, 2003
*
*-------------------------------------------------------------------------
*/
void trav_table_addlink(trav_table_t *table,
int j /* the object index */,
char *path )
{
unsigned int k;
/* already inserted */
if (strcmp(table->objs[j].name,path)==0)
return;
/* allocate space if necessary */
if (table->objs[j].nlinks == (unsigned)table->objs[j].sizelinks) {
table->objs[j].sizelinks += 2;
table->objs[j].links =
(trav_link_t*)HDrealloc(table->objs[j].links,
table->objs[j].sizelinks * sizeof(trav_link_t));
}
/* insert it */
k=table->objs[j].nlinks++;
table->objs[j].links[k].new_name = (char*)HDstrdup(path);
}
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