/* Given an ncid and varid, get pointers to the group and var
* metadata. */
int
nc4_find_g_var_nc(NC_FILE_INFO_T *nc, int ncid, int varid,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var)
{
/* Find the group info. */
assert(grp && var && nc && nc->nc4_info && nc->nc4_info->root_grp);
*grp = nc4_rec_find_grp(nc->nc4_info->root_grp, (ncid & GRP_ID_MASK));
/* Find the var info. */
for ((*var) = (*grp)->var; (*var); (*var) = (*var)->next)
if ((*var)->varid == varid)
break;
if (!(*var))
return NC_ENOTVAR;
return NC_NOERR;
}
/* Given an ncid, find the relevant group and return a pointer to it,
* also set a pointer to the nc4_info struct of the related file. For
* netcdf-3 files, *h5 will be set to NULL. */
int
nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_HDF5_FILE_INFO_T **h5)
{
NC_FILE_INFO_T *f = nc4_find_nc_file(ncid);
if(f == NULL) return NC_EBADID;
if (f->nc4_info) {
assert(f->nc4_info->root_grp);
/* If we can't find it, the grp id part of ncid is bad. */
if (!(*grp = nc4_rec_find_grp(f->nc4_info->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADID;
*h5 = (*grp)->file->nc4_info;
assert(*h5);
} else {
*h5 = NULL;
*grp = NULL;
}
return NC_NOERR;
}
int
nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp)
{
NC_FILE_INFO_T *f = nc4_find_nc_file(ncid);
if(f == NULL) return NC_EBADID;
/* No netcdf-3 files allowed! */
if (!f->nc4_info) return NC_ENOTNC4;
assert(f->nc4_info->root_grp);
/* This function demands netcdf-4 files without strict nc3
* rules.*/
if (f->nc4_info->cmode & NC_CLASSIC_MODEL) return NC_ESTRICTNC3;
/* If we can't find it, the grp id part of ncid is bad. */
if (!(*grp = nc4_rec_find_grp(f->nc4_info->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADID;
return NC_NOERR;
}
/* Recursively hunt for a group id. */
NC_GRP_INFO_T *
nc4_rec_find_grp(NC_GRP_INFO_T *start_grp, int target_nc_grpid)
{
NC_GRP_INFO_T *g, *res;
assert(start_grp);
/* Is this the group we are searching for? */
if (start_grp->nc_grpid == target_nc_grpid)
return start_grp;
/* Shake down the kids. */
if (start_grp->children)
for (g = start_grp->children; g; g = g->l.next)
if ((res = nc4_rec_find_grp(g, target_nc_grpid)))
return res;
/* Can't find it. Fate, why do you mock me? */
return NULL;
}
/* Given an ncid, find the relevant group and return a pointer to it,
* also set a pointer to the nc4_info struct of the related file. For
* netcdf-3 files, *h5 will be set to NULL. */
int
nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grpp, NC_HDF5_FILE_INFO_T **h5p)
{
NC_HDF5_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC *f = nc4_find_nc_file(ncid,&h5);
if(f == NULL) return NC_EBADID;
if (h5) {
assert(h5->root_grp);
/* If we can't find it, the grp id part of ncid is bad. */
if (!(grp = nc4_rec_find_grp(h5->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADID;
h5 = (grp)->nc4_info;
assert(h5);
} else {
h5 = NULL;
grp = NULL;
}
if(h5p) *h5p = h5;
if(grpp) *grpp = grp;
return NC_NOERR;
}
int
nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grpp,
NC_HDF5_FILE_INFO_T **h5p)
{
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T* h5;
NC *f = nc4_find_nc_file(ncid,&h5);
if(f == NULL) return NC_EBADID;
*nc = f;
#if 0 /* I do not understand this code at all */
#if 0 /*def USE_PNETCDF*/
if (h5->pnetcdf_file) {
*h5p = NULL;
*grpp = NULL;
return NC_NOERR;
}
#endif
#endif
if (h5) {
assert(h5->root_grp);
/* If we can't find it, the grp id part of ncid is bad. */
if (!(grp = nc4_rec_find_grp(h5->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADID;
h5 = (grp)->nc4_info;
assert(h5);
} else {
h5 = NULL;
grp = NULL;
}
if(h5p) *h5p = h5;
if(grpp) *grpp = grp;
return NC_NOERR;
}
/* Given an ncid and varid, get pointers to the group and var
* metadata. */
int
nc4_find_g_var_nc(NC *nc, int ncid, int varid,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var)
{
NC_HDF5_FILE_INFO_T* h5 = NC4_DATA(nc);
/* Find the group info. */
assert(grp && var && h5 && h5->root_grp);
*grp = nc4_rec_find_grp(h5->root_grp, (ncid & GRP_ID_MASK));
/* It is possible for *grp to be NULL. If it is,
return an error. */
if(*grp == NULL)
return NC_ENOTVAR;
/* Find the var info. */
for ((*var) = (*grp)->var; (*var); (*var) = (*var)->l.next)
if ((*var)->varid == varid)
break;
if (!(*var))
return NC_ENOTVAR;
return NC_NOERR;
}
/* Get or put attribute metadata from our linked list of file
info. Always locate the attribute by name, never by attnum.
The mem_type is ignored if data=NULL. */
int
nc4_get_att(int ncid, NC *nc, int varid, const char *name,
nc_type *xtype, nc_type mem_type, size_t *lenp,
int *attnum, int is_long, void *data)
{
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_ATT_INFO_T *att = NULL;
int my_attnum = -1;
int need_to_convert = 0;
int range_error = NC_NOERR;
void *bufr = NULL;
size_t type_size;
char norm_name[NC_MAX_NAME + 1];
int i;
int retval = NC_NOERR;
if (attnum)
my_attnum = *attnum;
assert(nc && NC4_DATA(nc));
LOG((3, "%s: ncid 0x%x varid %d name %s attnum %d mem_type %d",
__func__, ncid, varid, name, my_attnum, mem_type));
/* Find info for this file and group, and set pointer to each. */
h5 = NC4_DATA(nc);
if (!(grp = nc4_rec_find_grp(h5->root_grp, (ncid & GRP_ID_MASK))))
BAIL(NC_EBADGRPID);
/* Normalize name. */
if ((retval = nc4_normalize_name(name, norm_name)))
BAIL(retval);
/* Find the attribute, if it exists. If we don't find it, we are
major failures. */
if ((retval = nc4_find_grp_att(grp, varid, norm_name, my_attnum, &att)))
BAIL(retval);
/* If mem_type is NC_NAT, it means we want to use the attribute's
* file type as the mem type as well. */
if (mem_type == NC_NAT)
mem_type = att->nc_typeid;
/* If the attribute is NC_CHAR, and the mem_type isn't, or vice
* versa, that's a freakish attempt to convert text to
* numbers. Some pervert out there is trying to pull a fast one!
* Send him an NC_ECHAR error...*/
if (data && att->len &&
((att->nc_typeid == NC_CHAR && mem_type != NC_CHAR) ||
(att->nc_typeid != NC_CHAR && mem_type == NC_CHAR)))
BAIL(NC_ECHAR); /* take that, you freak! */
/* Copy the info. */
if (lenp)
*lenp = att->len;
if (xtype)
*xtype = att->nc_typeid;
if (attnum)
*attnum = att->attnum;
/* Zero len attributes are easy to read! */
if (!att->len)
BAIL(NC_NOERR);
/* Later on, we will need to know the size of this type. */
if ((retval = nc4_get_typelen_mem(h5, mem_type, is_long, &type_size)))
BAIL(retval);
/* We may have to convert data. Treat NC_CHAR the same as
* NC_UBYTE. If the mem_type is NAT, don't try any conversion - use
* the attribute's type. */
if (data && att->len && mem_type != att->nc_typeid &&
mem_type != NC_NAT &&
!(mem_type == NC_CHAR &&
(att->nc_typeid == NC_UBYTE || att->nc_typeid == NC_BYTE)))
{
if (!(bufr = malloc((size_t)(att->len * type_size))))
BAIL(NC_ENOMEM);
need_to_convert++;
if ((retval = nc4_convert_type(att->data, bufr, att->nc_typeid,
mem_type, (size_t)att->len, &range_error,
NULL, (h5->cmode & NC_CLASSIC_MODEL), 0, is_long)))
BAIL(retval);
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
if ((h5->cmode & NC_CLASSIC_MODEL) &&
(att->nc_typeid == NC_UBYTE || att->nc_typeid == NC_BYTE) &&
(mem_type == NC_UBYTE || mem_type == NC_BYTE) &&
range_error)
range_error = 0;
}
else
{
bufr = att->data;
}
/* If the caller wants data, copy it for him. If he hasn't
allocated enough memory for it, he will burn in segmentation
fault hell, writhing with the agony of undiscovered memory
bugs! */
if (data)
{
if (att->vldata)
{
size_t base_typelen;
hvl_t *vldest = data;
NC_TYPE_INFO_T *type;
/* Get the type object for the attribute's type */
if ((retval = nc4_find_type(h5, att->nc_typeid, &type)))
BAIL(retval);
/* Retrieve the size of the base type */
if ((retval = nc4_get_typelen_mem(h5, type->u.v.base_nc_typeid, 0, &base_typelen)))
BAIL(retval);
for (i = 0; i < att->len; i++)
{
vldest[i].len = att->vldata[i].len;
if (!(vldest[i].p = malloc(vldest[i].len * base_typelen)))
BAIL(NC_ENOMEM);
memcpy(vldest[i].p, att->vldata[i].p, vldest[i].len * base_typelen);
}
}
else if (att->stdata)
{
for (i = 0; i < att->len; i++)
{
/* Check for NULL pointer for string (valid in HDF5) */
if(att->stdata[i])
{
if (!(((char **)data)[i] = strdup(att->stdata[i])))
BAIL(NC_ENOMEM);
}
else
((char **)data)[i] = att->stdata[i];
}
}
else
{
/* For long types, we need to handle this special... */
if (is_long && att->nc_typeid == NC_INT)
{
long *lp = data;
int *ip = bufr;
for (i = 0; i < att->len; i++)
*lp++ = *ip++;
}
else
memcpy(data, bufr, (size_t)(att->len * type_size));
}
}
exit:
if (need_to_convert)
free(bufr);
if (range_error)
retval = NC_ERANGE;
return retval;
}
/* Put attribute metadata into our global metadata. */
static int
nc4_put_att(int ncid, NC *nc, int varid, const char *name,
nc_type file_type, nc_type mem_type, size_t len, int is_long,
const void *data)
{
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var = NULL;
NC_ATT_INFO_T *att, **attlist = NULL;
char norm_name[NC_MAX_NAME + 1];
nc_bool_t new_att = NC_FALSE;
int retval = NC_NOERR, range_error = 0;
size_t type_size;
int i;
int res;
if (!name)
return NC_EBADNAME;
assert(nc && NC4_DATA(nc));
LOG((1, "nc4_put_att: ncid 0x%x varid %d name %s "
"file_type %d mem_type %d len %d", ncid, varid,
name, file_type, mem_type, len));
/* If len is not zero, then there must be some data. */
if (len && !data)
return NC_EINVAL;
/* Find info for this file and group, and set pointer to each. */
h5 = NC4_DATA(nc);
if (!(grp = nc4_rec_find_grp(h5->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADGRPID;
/* If the file is read-only, return an error. */
if (h5->no_write)
return NC_EPERM;
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
/* Find att, if it exists. */
if (varid == NC_GLOBAL)
attlist = &grp->att;
else
{
for (var = grp->var; var; var = var->l.next)
if (var->varid == varid)
{
attlist = &var->att;
break;
}
if (!var)
return NC_ENOTVAR;
}
for (att = *attlist; att; att = att->l.next)
if (!strcmp(att->name, norm_name))
break;
if (!att)
{
/* If this is a new att, require define mode. */
if (!(h5->flags & NC_INDEF))
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_EINDEFINE;
if ((retval = NC4_redef(ncid)))
BAIL(retval);
}
new_att = NC_TRUE;
}
else
{
/* For an existing att, if we're not in define mode, the len
must not be greater than the existing len for classic model. */
if (!(h5->flags & NC_INDEF) &&
len * nc4typelen(file_type) > (size_t)att->len * nc4typelen(att->nc_typeid))
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_EINDEFINE;
if ((retval = NC4_redef(ncid)))
BAIL(retval);
}
}
/* We must have two valid types to continue. */
if (file_type == NC_NAT || mem_type == NC_NAT)
return NC_EBADTYPE;
/* Get information about this type. */
if ((retval = nc4_get_typelen_mem(h5, file_type, is_long, &type_size)))
return retval;
/* No character conversions are allowed. */
if (file_type != mem_type &&
(file_type == NC_CHAR || mem_type == NC_CHAR ||
file_type == NC_STRING || mem_type == NC_STRING))
return NC_ECHAR;
/* For classic mode file, only allow atts with classic types to be
* created. */
if (h5->cmode & NC_CLASSIC_MODEL && file_type > NC_DOUBLE)
return NC_ESTRICTNC3;
/* Add to the end of the attribute list, if this att doesn't
already exist. */
if (new_att)
{
LOG((3, "adding attribute %s to the list...", norm_name));
if ((res = nc4_att_list_add(attlist, &att)))
BAIL (res);
if (!(att->name = strdup(norm_name)))
return NC_ENOMEM;
}
/* Now fill in the metadata. */
att->dirty = NC_TRUE;
att->nc_typeid = file_type;
/* If this att has vlen or string data, release it before we lose the length value. */
if (att->stdata)
{
for (i = 0; i < att->len; i++)
if(att->stdata[i])
free(att->stdata[i]);
free(att->stdata);
att->stdata = NULL;
}
if (att->vldata)
{
for (i = 0; i < att->len; i++)
nc_free_vlen(&att->vldata[i]);
free(att->vldata);
att->vldata = NULL;
}
att->len = len;
if (att->l.prev)
att->attnum = ((NC_ATT_INFO_T *)att->l.prev)->attnum + 1;
else
att->attnum = 0;
/* If this is the _FillValue attribute, then we will also have to
* copy the value to the fill_vlue pointer of the NC_VAR_INFO_T
* struct for this var. (But ignore a global _FillValue
* attribute). */
if (!strcmp(att->name, _FillValue) && varid != NC_GLOBAL)
{
NC_ATT_INFO_T *varatt;
int size;
/* Fill value must be same type and have exactly one value */
if (att->nc_typeid != var->type_info->nc_typeid)
return NC_EBADTYPE;
if (att->len != 1)
return NC_EINVAL;
/* If we already wrote to the dataset, then return an error. */
if (var->written_to)
return NC_ELATEFILL;
/* If fill value hasn't been set, allocate space. Of course,
* vlens have to be different... */
if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->nc_typeid, 0,
&type_size)))
return retval;
/* Already set a fill value? Now I'll have to free the old
* one. Make up your damn mind, would you? */
if (var->fill_value)
{
if (var->type_info->nc_type_class == NC_VLEN)
{
if ((retval = nc_free_vlen(var->fill_value)))
return retval;
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if (*(char **)var->fill_value)
free(*(char **)var->fill_value);
}
free(var->fill_value);
}
/* Allocate space for the fill value. */
if (var->type_info->nc_type_class == NC_VLEN)
size = sizeof(hvl_t);
else if (var->type_info->nc_type_class == NC_STRING)
size = sizeof(char *);
else
size = type_size;
if (!(var->fill_value = calloc(1, size)))
return NC_ENOMEM;
/* Copy the fill_value. */
LOG((4, "Copying fill value into metadata for variable %s", var->name));
if (var->type_info->nc_type_class == NC_VLEN)
{
nc_vlen_t *in_vlen = (nc_vlen_t *)data, *fv_vlen = (nc_vlen_t *)(var->fill_value);
fv_vlen->len = in_vlen->len;
if (!(fv_vlen->p = malloc(size * in_vlen->len)))
return NC_ENOMEM;
memcpy(fv_vlen->p, in_vlen->p, in_vlen->len * size);
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if(NULL != (*(char **)data))
{
if (!(*(char **)(var->fill_value) = malloc(strlen(*(char **)data) + 1)))
return NC_ENOMEM;
strcpy(*(char **)var->fill_value, *(char **)data);
}
else
*(char **)var->fill_value = NULL;
}
else
memcpy(var->fill_value, data, type_size);
/* Indicate that the fill value was changed, if the variable has already
* been created in the file, so the dataset gets deleted and re-created. */
if (var->created)
var->fill_val_changed = NC_TRUE;
}
/* Copy the attribute data, if there is any. VLENs and string
* arrays have to be handled specially. */
if(att->len)
{
nc_type type_class; /* Class of attribute's type */
/* Get class for this type. */
if ((retval = nc4_get_typeclass(h5, file_type, &type_class)))
return retval;
assert(data);
if (type_class == NC_VLEN)
{
const hvl_t *vldata1;
NC_TYPE_INFO_T *type;
size_t base_typelen;
/* Get the type object for the attribute's type */
if ((retval = nc4_find_type(h5, file_type, &type)))
BAIL(retval);
/* Retrieve the size of the base type */
if ((retval = nc4_get_typelen_mem(h5, type->u.v.base_nc_typeid, 0, &base_typelen)))
BAIL(retval);
vldata1 = data;
if (!(att->vldata = (nc_vlen_t*)malloc(att->len * sizeof(hvl_t))))
BAIL(NC_ENOMEM);
for (i = 0; i < att->len; i++)
{
att->vldata[i].len = vldata1[i].len;
if (!(att->vldata[i].p = malloc(base_typelen * att->vldata[i].len)))
BAIL(NC_ENOMEM);
memcpy(att->vldata[i].p, vldata1[i].p, base_typelen * att->vldata[i].len);
}
}
else if (type_class == NC_STRING)
{
LOG((4, "copying array of NC_STRING"));
if (!(att->stdata = malloc(sizeof(char *) * att->len)))
BAIL(NC_ENOMEM);
for (i = 0; i < att->len; i++)
{
if(NULL != ((char **)data)[i]) {
LOG((5, "copying string %d of size %d", i, strlen(((char **)data)[i]) + 1));
if (!(att->stdata[i] = strdup(((char **)data)[i])))
BAIL(NC_ENOMEM);
}
else
att->stdata[i] = ((char **)data)[i];
}
}
else
{
/* [Re]allocate memory for the attribute data */
if (!new_att)
free (att->data);
if (!(att->data = malloc(att->len * type_size)))
BAIL(NC_ENOMEM);
/* Just copy the data, for non-atomic types */
if (type_class == NC_OPAQUE || type_class == NC_COMPOUND || type_class == NC_ENUM)
memcpy(att->data, data, len * type_size);
else
{
/* Data types are like religions, in that one can convert. */
if ((retval = nc4_convert_type(data, att->data, mem_type, file_type,
len, &range_error, NULL,
(h5->cmode & NC_CLASSIC_MODEL), is_long, 0)))
BAIL(retval);
}
}
}
att->dirty = NC_TRUE;
att->created = NC_FALSE;
/* Mark attributes on variable dirty, so they get written */
if(var)
var->attr_dirty = NC_TRUE;
exit:
/* If there was an error return it, otherwise return any potential
range error value. If none, return NC_NOERR as usual.*/
if (retval)
return retval;
if (range_error)
return NC_ERANGE;
return NC_NOERR;
}
