2011-01-06 07:48:47 +08:00
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/*********************************************************************
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* Copyright 2011, University Corporation for Atmospheric Research
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* See netcdf/README file for copying and redistribution conditions.
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* $Id$
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*********************************************************************/
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#include "config.h"
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#include <stdarg.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <netcdf.h>
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#include <assert.h>
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#include <ctype.h>
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#include "utils.h"
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/*
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* Print error message to stderr and exit
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*/
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void
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error(const char *fmt, ...)
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{
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va_list args ;
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(void) fprintf(stderr,"%s: ", progname);
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va_start(args, fmt) ;
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(void) vfprintf(stderr,fmt,args) ;
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va_end(args) ;
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(void) fprintf(stderr, "\n") ;
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(void) fflush(stderr); /* to ensure log files are current */
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exit(EXIT_FAILURE);
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}
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void *
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emalloc ( /* check return from malloc */
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size_t size)
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{
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void *p;
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p = (void *) malloc (size==0 ? 1 : size); /* malloc(0) not portable */
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if (p == 0) {
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error ("out of memory\n");
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}
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return p;
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}
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2018-10-31 10:48:12 +08:00
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void *
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ecalloc ( /* check return from calloc */
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size_t size)
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{
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void *p;
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p = (void *) calloc (1,(size==0 ? 1 : size)); /* calloc(0) not portable */
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if (p == 0) {
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error ("out of memory\n");
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}
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return p;
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}
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void *
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erealloc (void* p0, /* check return from realloc */
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size_t size)
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{
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void *p;
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if(p0 == NULL)
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return emalloc(size);
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if(size == 0)
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error("realloc with zero size");
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p = (void *) realloc (p0,size); /* realloc(0) not portable */
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if (p == 0) {
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error ("out of memory\n");
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}
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return p;
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}
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2011-01-06 07:48:47 +08:00
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void
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check(int err, const char* file, const int line)
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{
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fprintf(stderr,"%s\n",nc_strerror(err));
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fprintf(stderr,"Location: file %s; line %d\n", file,line);
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fflush(stderr); fflush(stdout);
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exit(1);
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}
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/*
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* Returns malloced name with chars special to CDL escaped.
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* Caller should free result when done with it.
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*/
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char*
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escaped_name(const char* cp) {
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char *ret; /* string returned */
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char *sp;
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assert(cp != NULL);
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/* For some reason, and on some machines (e.g. tweety)
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utf8 characters such as \343 are considered control character. */
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/* if(*cp && (isspace(*cp) | iscntrl(*cp)))*/
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if((*cp >= 0x01 && *cp <= 0x20) || (*cp == 0x7f))
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{
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error("name begins with space or control-character: %c",*cp);
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}
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ret = emalloc(4*strlen(cp) + 1); /* max if every char escaped */
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sp = ret;
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*sp = 0; /* empty name OK */
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/* Special case: leading number allowed, but we must escape it for CDL */
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if((*cp >= '0' && *cp <= '9'))
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{
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*sp++ = '\\';
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}
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for (; *cp; cp++) {
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2014-03-09 11:41:30 +08:00
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if (isascii((int)*cp)) {
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if(iscntrl((int)*cp)) { /* render control chars as two hex digits, \%xx */
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2018-10-11 03:32:17 +08:00
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snprintf(sp, 4+1,"\\%%%.2x", *cp);
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2011-01-06 07:48:47 +08:00
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sp += 4;
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} else {
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switch (*cp) {
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case ' ':
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case '!':
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case '"':
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case '#':
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case '$':
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case '&':
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case '\'':
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case '(':
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case ')':
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case '*':
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case ',':
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case ':':
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case ';':
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case '<':
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case '=':
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case '>':
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case '?':
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case '[':
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case ']':
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case '\\':
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case '^':
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case '`':
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case '{':
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case '|':
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case '}':
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case '~':
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*sp++ = '\\';
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*sp++ = *cp;
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break;
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default: /* includes '/' */
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*sp++ = *cp;
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break;
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}
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}
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} else { /* not ascii, assume just UTF-8 byte */
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*sp++ = *cp;
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}
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}
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*sp = 0;
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return ret;
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}
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/*
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* Print name with escapes for special characters
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*/
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void
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print_name(const char* name) {
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char *ename = escaped_name(name);
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fputs(ename, stdout);
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free(ename);
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}
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2011-01-07 06:09:14 +08:00
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2018-07-27 10:16:02 +08:00
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/* Convert a full path name to a group to the specific groupid. */
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int
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nc_inq_grpid2(int ncid, const char *grpname0, int *grpidp)
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{
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int ret = NC_NOERR;
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char* grpname = NULL;
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#ifdef USE_NETCDF4
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char *sp = NULL;
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#endif
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grpname = strdup(grpname0);
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if(grpname == NULL) {ret = NC_ENOMEM; goto done;}
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#ifdef USE_NETCDF4
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/* If '/' doesn't occur in name, just return id found by nc_inq_grpid() */
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sp = strrchr(grpname, '/');
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if(!sp) { /* No '/' in grpname, so return nc_inq_grpid() result */
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ret = nc_inq_grp_ncid(ncid, grpname, grpidp);
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goto done;
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}
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{ /* Parse group name out and get grpid using that */
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char* p, *q;
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int next;
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p = grpname;
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if(grpname[0] == '/') {
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/* get ncid of the root group */
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ncid = getrootid(ncid);
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p++; /* skip leading '/' */
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}
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/* Walk down looking for each group in path in turn */
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while(*p) {
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q = strchr(p,'/');
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if(q == NULL) q = p+strlen(p); /* point to trailing nul */
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else *q++ = '\0';
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/* Lookup this path segment wrt to current group */
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if((ret=nc_inq_ncid(ncid,p,&next))) goto done;
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/* move to next segment */
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p = q;
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ncid = next;
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}
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if(grpidp) *grpidp = ncid;
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}
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#else /* !USE_NETCDF4 */
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/* Just return root */
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if(grpidp) *grpidp = ncid;
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#endif /* USE_NETCDF4 */
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done:
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if(grpname) free(grpname);
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return ret;
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}
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/* Convert a full path name to a varid to the specific varid + grpid */
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int
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nc_inq_varid2(int ncid, const char *path0, int* varidp, int* grpidp)
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{
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int ret = NC_NOERR;
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int grpid, varid;
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char *v, *g, *prefix;
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/* If '/' doesn't occur in name, just return id found by
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* nc_inq_grpid()
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*/
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char* path = NULL;
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path = strdup(path0);
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if(path == NULL) {ret = NC_ENOMEM; goto done;}
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/* Find the rightmost '/' and tag the start of the path */
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g = strrchr(path,'/');
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if(g == NULL) {
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v = path;
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prefix = "/"; /* make sure not free'd */
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} else {
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*g++ = '\0'; /* separate out the prefix */
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prefix = path;
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v = g;
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}
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/* convert the group prefix to a group id */
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if((ret=nc_inq_grpid2(ncid,prefix,&grpid)))
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goto done;
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/* Lookup the var in the terminal group */
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if((ret=nc_inq_varid(grpid,v,&varid)))
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goto done;
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if(grpidp)
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*grpidp = grpid;
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if(varidp)
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*varidp = varid;
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done:
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if(path) free(path);
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return ret;
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}
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2011-01-07 06:09:14 +08:00
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/* Missing functionality that should be in nc_inq_dimid(), to get
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* dimid from a full dimension path name that may include group
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* names */
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int
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nc_inq_dimid2(int ncid, const char *dimname, int *dimidp) {
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int ret = NC_NOERR;
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/* If '/' doesn't occur in dimname, just return id found by
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* nc_inq_dimid() */
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char *sp = strrchr(dimname, '/');
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if(!sp) { /* No '/' in dimname, so return nc_inq_dimid() result */
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ret = nc_inq_dimid(ncid, dimname, dimidp);
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}
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#ifdef USE_NETCDF4
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else { /* Parse group name out and get dimid using that */
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2014-03-31 23:56:39 +08:00
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size_t grp_namelen = sp - dimname;
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char *grpname = emalloc(grp_namelen+1);
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int grpid;
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strncpy(grpname, dimname, grp_namelen+1);
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grpname[grp_namelen] = '\0';
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ret = nc_inq_grp_full_ncid(ncid, grpname, &grpid);
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if(ret == NC_NOERR) {
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ret = nc_inq_dimid(grpid, dimname, dimidp);
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}
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free(grpname);
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2011-01-07 06:09:14 +08:00
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}
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#endif /* USE_NETCDF4 */
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return ret;
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}
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2012-03-09 03:48:57 +08:00
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/*
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* return 1 if varid identifies a record variable
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* else return 0
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*/
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int
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isrecvar(int ncid, int varid)
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{
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int ndims;
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int is_recvar = 0;
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int *dimids;
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NC_CHECK( nc_inq_varndims(ncid, varid, &ndims) );
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#ifdef USE_NETCDF4
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if (ndims > 0) {
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int nunlimdims;
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int *recdimids;
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int dim, recdim;
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dimids = (int *) emalloc((ndims + 1) * sizeof(int));
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NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
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NC_CHECK( nc_inq_unlimdims(ncid, &nunlimdims, NULL) );
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recdimids = (int *) emalloc((nunlimdims + 1) * sizeof(int));
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NC_CHECK( nc_inq_unlimdims(ncid, NULL, recdimids) );
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for (dim = 0; dim < ndims && is_recvar == 0; dim++) {
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for(recdim = 0; recdim < nunlimdims; recdim++) {
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if(dimids[dim] == recdimids[recdim]) {
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is_recvar = 1;
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break;
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}
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}
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}
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free(dimids);
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free(recdimids);
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}
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#else
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if (ndims > 0) {
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int recdimid;
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dimids = (int *) emalloc((ndims + 1) * sizeof(int));
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NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
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NC_CHECK( nc_inq_unlimdim(ncid, &recdimid) );
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if(dimids[0] == recdimid)
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is_recvar = 1;
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free(dimids);
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}
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#endif /* USE_NETCDF4 */
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return is_recvar;
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}
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|
2013-01-24 01:45:29 +08:00
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|
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static idnode_t*
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newidnode(void) {
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idnode_t *newvp = (idnode_t*) emalloc(sizeof(idnode_t));
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return newvp;
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}
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/*
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* Get a new, empty variable list.
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*/
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idnode_t*
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newidlist(void) {
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idnode_t *vp = newidnode();
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vp -> next = 0;
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vp -> id = -1; /* bad id */
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return vp;
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}
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void
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idadd(idnode_t* vlist, int varid) {
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idnode_t *newvp = newidnode();
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newvp -> next = vlist -> next;
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newvp -> id = varid;
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vlist -> next = newvp;
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}
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/*
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* return true if id is member of list that idlist points to.
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*/
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bool_t
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idmember(const idnode_t* idlist, int id)
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{
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idnode_t *vp = idlist -> next;
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|
|
|
|
|
|
|
for (; vp ; vp = vp->next)
|
|
|
|
if (vp->id == id)
|
|
|
|
return true;
|
|
|
|
return false;
|
|
|
|
}
|
|
|
|
|
Corrected "BAIL" macros to avoid infinite loop when logging is disabled and an
error occurs after an "exit:" label.
Corrected a dozen Coverity errors (mainly allocation issues, along with a few
other things):
711711, 711802, 711803, 711905, 970825, 996123, 996124, 1025787,
1047274, 1130013, 1130014, 1139538
Refactored internal fill-value code to correctly handle string types, and
especially to allow NULL pointers and null strings (ie. "") to be
distinguished. The code now avoids partially aliasing the two together
(which only happened on the 'write' side of things and wasn't reflected on
the 'read' side, adding to the previous confusion).
Probably still weak on handling fill-values of variable-length and compound
datatypes.
Refactored the recursive metadata reads a bit more, to process HDF5 named
datatypes and datasets immediately, avoiding chewing up memory for those
types of objects, etc.
Finished uncommenting and updating the nc_test4/tst_fills2.c code (as I'm
proceeding alphabetically through the nc_test4 code files).
2013-12-29 15:12:43 +08:00
|
|
|
/*
|
|
|
|
* Release a variable list.
|
|
|
|
*/
|
|
|
|
void
|
|
|
|
freeidlist(idnode_t *idlist)
|
|
|
|
{
|
|
|
|
while(idlist) {
|
|
|
|
idnode_t *vp = idlist->next;
|
|
|
|
free(idlist);
|
|
|
|
idlist = vp;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
|
2013-01-24 01:45:29 +08:00
|
|
|
/*
|
|
|
|
* 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 */
|
2018-05-12 22:55:51 +08:00
|
|
|
if(grpname[0] == '\0' || NCSTREQ(grpname,"/")) {
|
2013-01-24 01:45:29 +08:00
|
|
|
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;
|
|
|
|
}
|
2016-05-04 11:17:06 +08:00
|
|
|
|
|
|
|
int
|
|
|
|
getrootid(int grpid)
|
|
|
|
{
|
|
|
|
int current = grpid;
|
2016-08-08 23:24:19 +08:00
|
|
|
#ifdef USE_NETCDF4
|
2016-05-04 11:17:06 +08:00
|
|
|
int parent = current;
|
|
|
|
/* see if root id */
|
|
|
|
for(;;) {
|
|
|
|
int stat = nc_inq_grp_parent(current,&parent);
|
|
|
|
if(stat) break;
|
|
|
|
current = parent;
|
|
|
|
}
|
2016-08-08 23:24:19 +08:00
|
|
|
#endif
|
2016-05-04 11:17:06 +08:00
|
|
|
return current;
|
|
|
|
}
|
|
|
|
|
2018-07-27 10:16:02 +08:00
|
|
|
#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
|