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netcdf-c/ncdump/utils.c
Dennis Heimbigner 735ae80928 merge master and fix conflicts
2018-12-12 11:47:54 -07:00

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/*********************************************************************
* Copyright 2018, University Corporation for Atmospheric Research
* See netcdf/README file for copying and redistribution conditions.
* $Id$
*********************************************************************/
#include "config.h"
#include <stdarg.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <netcdf.h>
#include <assert.h>
#include <ctype.h>
#include "utils.h"
#ifndef isascii
EXTERNL int isascii(int c);
#endif
/*
* Print error message to stderr and exit
*/
void
error(const char *fmt, ...)
{
va_list args ;
(void) fprintf(stderr,"%s: ", progname);
va_start(args, fmt) ;
(void) vfprintf(stderr,fmt,args) ;
va_end(args) ;
(void) fprintf(stderr, "\n") ;
(void) fflush(stderr); /* to ensure log files are current */
exit(EXIT_FAILURE);
}
void *
emalloc ( /* check return from malloc */
size_t size)
{
void *p;
p = (void *) malloc (size==0 ? 1 : size); /* malloc(0) not portable */
if (p == 0) {
error ("out of memory\n");
}
return p;
}
void *
ecalloc ( /* check return from calloc */
size_t size)
{
void *p;
p = (void *) calloc (1,(size==0 ? 1 : size)); /* calloc(0) not portable */
if (p == 0) {
error ("out of memory\n");
}
return p;
}
void *
erealloc (void* p0, /* check return from realloc */
size_t size)
{
void *p;
if(p0 == NULL)
return emalloc(size);
if(size == 0)
error("realloc with zero size");
p = (void *) realloc (p0,size); /* realloc(0) not portable */
if (p == 0) {
error ("out of memory\n");
}
return p;
}
void
check(int err, const char* file, const int line)
{
fprintf(stderr,"%s\n",nc_strerror(err));
fprintf(stderr,"Location: file %s; line %d\n", file,line);
fflush(stderr); fflush(stdout);
exit(1);
}
/*
* Returns malloced name with chars special to CDL escaped.
* Caller should free result when done with it.
*/
char*
escaped_name(const char* cp) {
char *ret; /* string returned */
char *sp;
assert(cp != NULL);
/* For some reason, and on some machines (e.g. tweety)
utf8 characters such as \343 are considered control character. */
/* if(*cp && (isspace(*cp) | iscntrl(*cp)))*/
if((*cp >= 0x01 && *cp <= 0x20) || (*cp == 0x7f))
{
error("name begins with space or control-character: %c",*cp);
}
ret = emalloc(4*strlen(cp) + 1); /* max if every char escaped */
sp = ret;
*sp = 0; /* empty name OK */
/* Special case: leading number allowed, but we must escape it for CDL */
if((*cp >= '0' && *cp <= '9'))
{
*sp++ = '\\';
}
for (; *cp; cp++) {
if (isascii((int)*cp)) {
if(iscntrl((int)*cp)) { /* render control chars as two hex digits, \%xx */
snprintf(sp, 4+1,"\\%%%.2x", *cp);
sp += 4;
} else {
switch (*cp) {
case ' ':
case '!':
case '"':
case '#':
case '$':
case '&':
case '\'':
case '(':
case ')':
case '*':
case ',':
case ':':
case ';':
case '<':
case '=':
case '>':
case '?':
case '[':
case ']':
case '\\':
case '^':
case '`':
case '{':
case '|':
case '}':
case '~':
*sp++ = '\\';
*sp++ = *cp;
break;
default: /* includes '/' */
*sp++ = *cp;
break;
}
}
} else { /* not ascii, assume just UTF-8 byte */
*sp++ = *cp;
}
}
*sp = 0;
return ret;
}
/*
* Print name with escapes for special characters
*/
void
print_name(const char* name) {
char *ename = escaped_name(name);
fputs(ename, stdout);
free(ename);
}
/* Convert a full path name to a group to the specific groupid. */
int
nc_inq_grpid2(int ncid, const char *grpname0, int *grpidp)
{
int ret = NC_NOERR;
char* grpname = NULL;
#ifdef USE_NETCDF4
char *sp = NULL;
#endif
grpname = strdup(grpname0);
if(grpname == NULL) {ret = NC_ENOMEM; goto done;}
#ifdef USE_NETCDF4
/* If '/' doesn't occur in name, just return id found by nc_inq_grpid() */
sp = strrchr(grpname, '/');
if(!sp) { /* No '/' in grpname, so return nc_inq_grpid() result */
ret = nc_inq_grp_ncid(ncid, grpname, grpidp);
goto done;
}
{ /* Parse group name out and get grpid using that */
char* p, *q;
int next;
p = grpname;
if(grpname[0] == '/') {
/* get ncid of the root group */
ncid = getrootid(ncid);
p++; /* skip leading '/' */
}
/* Walk down looking for each group in path in turn */
while(*p) {
q = strchr(p,'/');
if(q == NULL) q = p+strlen(p); /* point to trailing nul */
else *q++ = '\0';
/* Lookup this path segment wrt to current group */
if((ret=nc_inq_ncid(ncid,p,&next))) goto done;
/* move to next segment */
p = q;
ncid = next;
}
if(grpidp) *grpidp = ncid;
}
#else /* !USE_NETCDF4 */
/* Just return root */
if(grpidp) *grpidp = ncid;
#endif /* USE_NETCDF4 */
done:
if(grpname) free(grpname);
return ret;
}
/* Convert a full path name to a varid to the specific varid + grpid */
int
nc_inq_varid2(int ncid, const char *path0, int* varidp, int* grpidp)
{
int ret = NC_NOERR;
int grpid, varid;
char *v, *g, *prefix;
/* If '/' doesn't occur in name, just return id found by
* nc_inq_grpid()
*/
char* path = NULL;
path = strdup(path0);
if(path == NULL) {ret = NC_ENOMEM; goto done;}
/* Find the rightmost '/' and tag the start of the path */
g = strrchr(path,'/');
if(g == NULL) {
v = path;
prefix = "/"; /* make sure not free'd */
} else {
*g++ = '\0'; /* separate out the prefix */
prefix = path;
v = g;
}
/* convert the group prefix to a group id */
if((ret=nc_inq_grpid2(ncid,prefix,&grpid)))
goto done;
/* Lookup the var in the terminal group */
if((ret=nc_inq_varid(grpid,v,&varid)))
goto done;
if(grpidp)
*grpidp = grpid;
if(varidp)
*varidp = varid;
done:
if(path) free(path);
return ret;
}
/* Missing functionality that should be in nc_inq_dimid(), to get
* dimid from a full dimension path name that may include group
* names */
int
nc_inq_dimid2(int ncid, const char *dimname, int *dimidp) {
int ret = NC_NOERR;
/* If '/' doesn't occur in dimname, just return id found by
* nc_inq_dimid() */
char *sp = strrchr(dimname, '/');
if(!sp) { /* No '/' in dimname, so return nc_inq_dimid() result */
ret = nc_inq_dimid(ncid, dimname, dimidp);
}
#ifdef USE_NETCDF4
else { /* Parse group name out and get dimid using that */
size_t grp_namelen = sp - dimname;
char *grpname = emalloc(grp_namelen+1);
int grpid;
strncpy(grpname, dimname, grp_namelen+1);
grpname[grp_namelen] = '\0';
ret = nc_inq_grp_full_ncid(ncid, grpname, &grpid);
if(ret == NC_NOERR) {
ret = nc_inq_dimid(grpid, dimname, dimidp);
}
free(grpname);
}
#endif /* USE_NETCDF4 */
return ret;
}
/*
* return 1 if varid identifies a record variable
* else return 0
*/
int
isrecvar(int ncid, int varid)
{
int ndims;
int is_recvar = 0;
int *dimids;
NC_CHECK( nc_inq_varndims(ncid, varid, &ndims) );
#ifdef USE_NETCDF4
if (ndims > 0) {
int nunlimdims;
int *recdimids;
int dim, recdim;
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
NC_CHECK( nc_inq_unlimdims(ncid, &nunlimdims, NULL) );
recdimids = (int *) emalloc((nunlimdims + 1) * sizeof(int));
NC_CHECK( nc_inq_unlimdims(ncid, NULL, recdimids) );
for (dim = 0; dim < ndims && is_recvar == 0; dim++) {
for(recdim = 0; recdim < nunlimdims; recdim++) {
if(dimids[dim] == recdimids[recdim]) {
is_recvar = 1;
break;
}
}
}
free(dimids);
free(recdimids);
}
#else
if (ndims > 0) {
int recdimid;
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
NC_CHECK( nc_inq_unlimdim(ncid, &recdimid) );
if(dimids[0] == recdimid)
is_recvar = 1;
free(dimids);
}
#endif /* USE_NETCDF4 */
return is_recvar;
}
static idnode_t*
newidnode(void) {
idnode_t *newvp = (idnode_t*) emalloc(sizeof(idnode_t));
return newvp;
}
/*
* Get a new, empty variable list.
*/
idnode_t*
newidlist(void) {
idnode_t *vp = newidnode();
vp -> next = 0;
vp -> id = -1; /* bad id */
return vp;
}
void
idadd(idnode_t* vlist, int varid) {
idnode_t *newvp = newidnode();
newvp -> next = vlist -> next;
newvp -> id = varid;
vlist -> next = newvp;
}
/*
* return true if id is member of list that idlist points to.
*/
bool_t
idmember(const idnode_t* idlist, int id)
{
idnode_t *vp = idlist -> next;
for (; vp ; vp = vp->next)
if (vp->id == id)
return true;
return false;
}
/*
* Release a variable list.
*/
void
freeidlist(idnode_t *idlist)
{
while(idlist) {
idnode_t *vp = idlist->next;
free(idlist);
idlist = vp;
}
}
/*
* Return true if group identified by grpid is member of grpids, a list of groups.
* nlgrps is number of groups in the list.
*/
bool_t
group_wanted(int grpid, int nlgrps, const idnode_t* grpids)
{
/* If -g not specified, all groups are wanted */
if(nlgrps == 0) return true;
/* if -g specified, look for match in group id list */
return idmember(grpids, grpid);
}
/* Determine whether a group named formatting_specs.lgrps[igrp] exists
* in a netCDF file or group with id ncid. If so, return the count of
* how many matching groups were found, else return a count of 0. If
* the name begins with "/", it is interpreted as an absolute group
* name, in which case only 0 or 1 is returned. Otherwise, interpret
* it as a relative name, and the total number of occurrences within
* the file/group identified by ncid is returned.
*
* Also has side effect of updating the ngrpids and the associate
* grpids array that represent the group list specified by the -g
* option. TODO: put this in its own function instead.
*/
static size_t
nc_inq_grpname_count(int ncid, int igrp, char **lgrps, idnode_t *grpids) {
size_t count = 0;
#ifdef USE_NETCDF4
int numgrps;
int *ncids;
int g;
int grpid;
int status;
#endif
char *grpname = lgrps[igrp];
/* permit empty string to also designate root group */
if(grpname[0] == '\0' || NCSTREQ(grpname,"/")) {
count = 1;
idadd(grpids, ncid);
return count;
}
#ifdef USE_NETCDF4
/* Handle absolute group names */
if(grpname[0] == '/') {
int grpid;
status = nc_inq_grp_full_ncid(ncid, grpname, &grpid);
if(status == NC_NOERR) {
count = 1;
idadd(grpids, grpid);
} else if(status == NC_ENOGRP) {
count = 0;
} else {
error("when looking up group %s: %s ", grpname, nc_strerror(status));
}
return count;
}
/* look in this group */
status = nc_inq_grp_ncid(ncid, grpname, &grpid);
if (status == NC_NOERR) {
count++;
idadd(grpids, grpid);
}
/* if this group has subgroups, call recursively on each of them */
NC_CHECK( nc_inq_grps(ncid, &numgrps, NULL) );
if(numgrps > 0) {
/* Allocate memory to hold the list of group ids. */
ncids = emalloc(numgrps * sizeof(int));
/* Get the list of group ids. */
NC_CHECK( nc_inq_grps(ncid, NULL, ncids) );
/* Call this function recursively for each group. */
for (g = 0; g < numgrps; g++) {
count += nc_inq_grpname_count(ncids[g], igrp, lgrps, grpids);
}
free(ncids);
}
#endif /* USE_NETCDF4 */
return count;
}
/* Check if any group names specified with "-g grp1,...,grpn" are
* missing. Returns total number of matching groups if no missing
* groups detected, otherwise exits. */
int
grp_matches(int ncid, int nlgrps, char** lgrps, idnode_t *grpids) {
int ig;
size_t total = 0;
for (ig=0; ig < nlgrps; ig++) {
size_t count = nc_inq_grpname_count(ncid, ig, lgrps, grpids);
if(count == 0) {
error("%s: No such group", lgrps[ig]);
return 0;
}
total += count;
}
return total;
}
/* Returns 1 if string s1 ends with string s2, 0 otherwise. */
int
strendswith(const char *s1, const char *s2) {
size_t m1 = strlen(s1);
size_t m2 = strlen(s2);
if (m1 < m2)
return 0;
return (strcmp(s1 + (m1 - m2), s2) == 0);
}
/* Get varid of variable with name using nested group syntax
* "gp1/gp2/var" or "/gp1/gp2/var". In the former case, grpname of
* grp corresponding to grpid must end in "gp1/gp2". In the latter
* case, grpname for grpid must be exactly "/gp1/gp2". If variable
* named "var" is not in group grpid, returns NC_ENOTVAR, else sets
* varid and returns NC_NOERR. */
int
nc_inq_gvarid(int grpid, const char *varname, int *varidp) {
/* if varname has no "/" chars, then
return varidp from nc_inq_varid(grpid, varname, varidp)
if varname begins with "/"
else
get groupname corresponding to grpid
get vargroup = substring of varname up to last "/"
get relname = substring of varname after last "/"
if (varname starts with "/" and groupname == vargroup) ||
(groupname ends with vargroup)
return nc_inq_varid(grpid, relname, varidp)
else
return NC_ENOTVAR
*/
#ifdef USE_NETCDF4
char *vargroup;
char *relname;
char *groupname;
int status;
if (varname[0] == '\0')
return NC_ENOTVAR;
vargroup = strdup(varname);
if (vargroup == NULL)
return NC_ENOMEM;
relname = strrchr(vargroup, NC_GRP_DELIM);
if (relname != NULL) { /* name has a "/" in it */
size_t len; /* length of full group name for grpid */
*relname++ = '\0'; /* split vargroup string in two,
* vargroup and relname */
if ( (status = nc_inq_grpname_full(grpid, &len, NULL)) != NC_NOERR ) {
free(vargroup);
return status;
}
groupname = (char *)emalloc(len + 1);
if ( (status = nc_inq_grpname_full(grpid, &len, groupname)) == NC_NOERR ) {
if(varname[0] == NC_GRP_DELIM) {
if( strcmp(groupname, vargroup) == 0)
status = nc_inq_varid(grpid, relname, varidp);
else
status = NC_ENOTVAR;
} else {
if(strendswith(groupname, vargroup))
status = nc_inq_varid(grpid, relname, varidp);
else
status = NC_ENOTVAR;
}
}
free(vargroup);
free(groupname);
return status;
}
free(vargroup);
#endif /* USE_NETCDF4 */
return nc_inq_varid(grpid, varname, varidp);
}
/* Determine whether a variable named varname exists in any group in
an open netCDF file with id ncid. If so, return the count of how
many matching variables were found, else return a count of 0. The
variable name can be absolute such as "/foo" or "/GRP1/GRP1A/foo",
in which case there is only one group to look in, given by the path
from the root group. Alternatively, the variable name can be
relative, such as "foo" or "GRPA/GRPB/foo", in which case every
group is examined for a variable with that relative name. */
size_t
nc_inq_varname_count(int ncid, char *varname) {
/*
count = 0;
status = nc_inq_gvarid(ncid, varname, varid);
if (status == NC_NOERR)
count++;
for each subgroup gid {
count += nc_inq_varname_count(gid, varname);
}
return count;
*/
size_t count = 0;
int varid;
/* look in this group */
int status = nc_inq_gvarid(ncid, varname, &varid);
#ifdef USE_NETCDF4
int numgrps;
int *ncids;
int g;
#endif
if (status == NC_NOERR)
count++;
#ifdef USE_NETCDF4
/* if this group has subgroups, call recursively on each of them */
NC_CHECK( nc_inq_grps(ncid, &numgrps, NULL) );
/* Allocate memory to hold the list of group ids. */
ncids = emalloc((numgrps + 1) * sizeof(int));
/* Get the list of group ids. */
NC_CHECK( nc_inq_grps(ncid, NULL, ncids) );
/* Call this function for each group. */
for (g = 0; g < numgrps; g++) {
count += nc_inq_varname_count(ncids[g], varname);
}
free(ncids);
#endif /* USE_NETCDF4 */
return count;
}
/* Check if any variable names specified with "-v var1,...,varn" are
* missing. Returns 0 if no missing variables detected, otherwise
* exits. */
int
missing_vars(int ncid, int nlvars, char **lvars) {
int iv;
for (iv=0; iv < nlvars; iv++) {
if(nc_inq_varname_count(ncid, lvars[iv]) == 0) {
error("%s: No such variable", lvars[iv]);
}
}
return 0;
}
void
make_lvars(char *optarg, int *nlvarsp, char ***lvarsp)
{
char *cp = optarg;
int nvars = 1;
char ** cpp;
/* compute number of variable names in comma-delimited list */
*nlvarsp = 1;
while (*cp++)
if (*cp == ',')
nvars++;
*nlvarsp = nvars;
*lvarsp = (char **) emalloc(nvars * sizeof(char*));
cpp = *lvarsp;
/* copy variable names into list */
for (cp = strtok(optarg, ","); cp != NULL; cp = strtok((char *) NULL, ",")) {
*cpp = strdup(cp);
cpp++;
}
}
void
make_lgrps(char *optarg, int *nlgrps, char ***lgrpsp, idnode_t **grpidsp)
{
char *cp = optarg;
int ngrps = 1;
char ** cpp;
/* compute number of group names in comma-delimited list */
while (*cp++)
if (*cp == ',')
ngrps++;
*nlgrps = ngrps;
*lgrpsp = (char **) emalloc(ngrps * sizeof(char*));
cpp = *lgrpsp;
/* copy group names into list */
for (cp = strtok(optarg, ","); cp != NULL; cp = strtok((char *) NULL, ",")) {
*cpp = strdup(cp);
cpp++;
}
/* make empty list of grpids, to be filled in after input file opened */
*grpidsp = newidlist();
}
/* initialize and return a new empty stack of grpids */
static ncgiter_t *
gs_init() {
ncgiter_t *s = emalloc(sizeof(ncgiter_t));
s->ngrps = 0;
s->top = NULL;
return s;
}
/* free a stack and all its nodes */
static void
gs_free(ncgiter_t *s) {
grpnode_t *n0, *n1;
n0 = s->top;
while (n0) {
n1 = n0->next;
free(n0);
n0 = n1;
}
free(s);
}
/* test if a stack is empty */
static int
gs_empty(ncgiter_t *s)
{
return s->ngrps == 0;
}
/* push a grpid on stack */
static void
gs_push(ncgiter_t *s, int grpid)
{
grpnode_t *node = emalloc(sizeof(grpnode_t));
node->grpid = grpid;
node->next = gs_empty(s) ? NULL : s->top;
s->top = node;
s->ngrps++;
}
/* pop value off stack and return */
static int
gs_pop(ncgiter_t *s)
{
if (gs_empty(s)) {
return -1; /* underflow, stack is empty */
} else { /* pop a node */
grpnode_t *top = s->top;
int value = top->grpid;
s->top = top->next;
/* TODO: first call to free gets seg fault with libumem */
free(top);
s->ngrps--;
return value;
}
}
#ifdef UNUSED
/* Return top value on stack without popping stack. Defined for
* completeness but not used (here). */
static int
gs_top(ncgiter_t *s)
{
if (gs_empty(s)) {
return -1; /* underflow, stack is empty */
} else { /* get top value */
grpnode_t *top = s->top;
int value = top->grpid;
return value;
}
}
#endif
/* Like netCDF-4 function nc_inq_grps(), but can be called from
* netCDF-3 only code as well. Maybe this is what nc_inq_grps()
* should do if built without netCDF-4 data model support. */
static int
nc_inq_grps2(int ncid, int *numgrps, int *grpids)
{
int stat = NC_NOERR;
/* just check if ncid is valid id of open netCDF file */
NC_CHECK(nc_inq(ncid, NULL, NULL, NULL, NULL));
#ifdef USE_NETCDF4
NC_CHECK(nc_inq_grps(ncid, numgrps, grpids));
#else
*numgrps = 0;
#endif
return stat;
}
/* Initialize group iterator for start group and all its descendant
* groups. */
int
nc_get_giter(int grpid, /* start group id */
ncgiter_t **iterp /* returned opaque iteration state */
)
{
int stat = NC_NOERR;
stat = nc_inq(grpid, NULL, NULL, NULL, NULL); /* check if grpid is valid */
if(stat != NC_EBADGRPID && stat != NC_EBADID) {
*iterp = gs_init();
gs_push(*iterp, grpid);
}
return stat;
}
/*
* Get group id of next group. On first call gets start group id,
* subsequently returns other subgroup ids in preorder. Returns zero
* when no more groups left.
*/
int
nc_next_giter(ncgiter_t *iterp, int *grpidp) {
int stat = NC_NOERR;
int numgrps;
int *grpids;
int i;
if(gs_empty(iterp)) {
*grpidp = 0; /* not a group, signals iterator is done */
} else {
*grpidp = gs_pop(iterp);
NC_CHECK(nc_inq_grps2(*grpidp, &numgrps, NULL));
if(numgrps > 0) {
grpids = (int *)emalloc(sizeof(int) * numgrps);
NC_CHECK(nc_inq_grps2(*grpidp, &numgrps, grpids));
for(i = numgrps - 1; i >= 0; i--) { /* push ids on stack in reverse order */
gs_push(iterp, grpids[i]);
}
free(grpids);
}
}
return stat;
}
/*
* Release group iter.
*/
void
nc_free_giter(ncgiter_t *iterp)
{
gs_free(iterp);
}
/*
* Get total number of groups (including the top-level group and all
* descendant groups, recursively) and all descendant subgroup ids
* (including the input rootid of the start group) for a group and
* all its descendants, in preorder.
*
* If grpids or numgrps is NULL, it will be ignored. So typical use
* is to call with grpids NULL to get numgrps, allocate enough space
* for the group ids, then call again to get them.
*/
int
nc_inq_grps_full(int rootid, int *numgrps, int *grpids)
{
int stat = NC_NOERR;
ncgiter_t *giter; /* pointer to group iterator */
int grpid;
size_t count;
NC_CHECK(nc_get_giter(rootid, &giter));
count = 0;
NC_CHECK(nc_next_giter(giter, &grpid));
while(grpid != 0) {
if(grpids)
grpids[count] = grpid;
count++;
NC_CHECK(nc_next_giter(giter, &grpid));
}
if(numgrps)
*numgrps = count;
nc_free_giter(giter);
return stat;
}
int
getrootid(int grpid)
{
int current = grpid;
#ifdef USE_NETCDF4
int parent = current;
/* see if root id */
for(;;) {
int stat = nc_inq_grp_parent(current,&parent);
if(stat) break;
current = parent;
}
#endif
return current;
}
#if 0
static int
parseFQN(int ncid, const char* fqn0, VarID* idp)
{
int stat = NC_NOERR;
char* fqn;
VarID vid;
char* p;
char* q;
char* segment;
vid.grpid = ncid;
if(fqn0 == NULL || fqn0[1] != '/')
{stat = NC_EBADNAME; goto done;}
fqn = strdup(fqn0+1); /* skip leading '/'*/
p = fqn;
for(;;) {
int newgrp;
segment = p;
q = p;
while(*p != '\0' && *p != '/') {
if(*p == '\\') p++;
*q++ = *p++;
}
if(*p == '\0') break;
*p++ = '\0';
if((stat=nc_inq_grp_ncid(vid.grpid,segment,&newgrp))) goto done;
vid.grpid = newgrp;
}
/* Segment should point to the varname */
if((stat=nc_inq_varid(vid.grpid,segment,&vid.varid))) goto done;
done:
if(fqn) free(fqn);
if(stat == NC_NOERR && idp != NULL) *idp = vid;
return stat;
}
#endif
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