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2afbdbd18f
netcdf-c/libnczarr/zattr.c
Dennis Heimbigner 2afbdbd18f Add support for the XArray Zarr _ARRAY_DIMENSIONS attribute 
The XArray implementation that uses Zarr for storage
provides a mechanism to simulate named dimensions.
It does this by adding a per-variable attribute called
_ARRAY_DIMENSIONS. This attribute contains a list of names
to be matched against the shape values of the variable.
In effect a named dimension is created with the name
_ARRAY_DIMENSIONS(i) and length shape(i) for all i
in range 0..rank(variable).
Both read and write support is provided.

This XArray support is only invoked if the mode value
of "xarray" is defined. So for example, as in this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,xarray,s3
````
Note that the "xarray" mode flag also implies mode flag "zarr", so the above
is equivalent to this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,zarr,xarray,s3
````

The primary change to implement this was to unify the handling
of dimension references in libnczarr/zsync.

A test for this and other pure-zarr features was added as
nczarr_test/run_purezarr.sh

Other changes:
* Make sure distcheck leaves no files around.
* Change the special attribute flag DIMSCALEFLAG to HIDDENATTRFLAG
  to support the xarray attribute.
* Annotate the zmap implementations with feature flags such as
  WRITEONCE (for zip files).
2021-02-24 13:46:11 -07:00

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/* Copyright 2003-2018, University Corporation for Atmospheric
* Research. See COPYRIGHT file for copying and redistribution
* conditions. */
/**
* @file
* @internal This file handles ZARR attributes.
*
* @author Dennis Heimbigner, Ed Hartnett
*/
#include "zincludes.h"
#undef ADEBUG
/**
* @internal Get the attribute list for either a varid or NC_GLOBAL
*
* @param grp Group
* @param varid Variable ID | NC_BLOGAL
* @param varp Pointer that gets pointer to NC_VAR_INFO_T
* instance. Ignored if NULL.
* @param attlist Pointer that gets pointer to attribute list.
*
* @return NC_NOERR No error.
* @author Dennis Heimbigner, Ed Hartnett
* [Candidate for moving to libsrc4]
*/
int
ncz_getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp, NCindex **attlist)
{
int retval;
NC_FILE_INFO_T* file = grp->nc4_info;
NCZ_FILE_INFO_T* zinfo = file->format_file_info;
assert(grp && attlist && file && zinfo);
if (varid == NC_GLOBAL)
{
/* Do we need to read the atts? */
if (!grp->atts_read)
if ((retval = ncz_read_atts(file, (NC_OBJ*)grp)))
return retval;
if (varp)
*varp = NULL;
*attlist = grp->att;
}
else
{
NC_VAR_INFO_T *var;
if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* Do we need to read the atts? */
if (!var->atts_read)
if ((retval = ncz_read_atts(file, (NC_OBJ*)var)))
return retval;
if (varp)
*varp = var;
*attlist = var->att;
}
return NC_NOERR;
}
/**
* @internal Get one of three special attributes, NCPROPS,
* ISNETCDF4ATT, and SUPERBLOCKATT. These atts are not all really in
* the file, they are constructed on the fly.
*
* @param h5 Pointer to ZARR file info struct.
* @param name Name of attribute.
* @param filetypep Pointer that gets type of the attribute data in
* file.
* @param mem_type Type of attribute data in memory.
* @param lenp Pointer that gets length of attribute array.
* @param attnump Pointer that gets the attribute number.
* @param data Attribute data.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ERANGE Data conversion out of range.
* @author Dennis Heimbigner
*/
int
ncz_get_att_special(NC_FILE_INFO_T* h5, const char* name,
nc_type* filetypep, nc_type mem_type, size_t* lenp,
int* attnump, void* data)
{
/* Fail if asking for att id */
if(attnump)
return NC_EATTMETA;
if(strcmp(name,NCPROPS)==0) {
int len;
if(h5->provenance.ncproperties == NULL)
return NC_ENOTATT;
if(mem_type == NC_NAT) mem_type = NC_CHAR;
if(mem_type != NC_CHAR)
return NC_ECHAR;
if(filetypep) *filetypep = NC_CHAR;
len = strlen(h5->provenance.ncproperties);
if(lenp) *lenp = len;
if(data) strncpy((char*)data,h5->provenance.ncproperties,len+1);
} else if(strcmp(name,ISNETCDF4ATT)==0
|| strcmp(name,SUPERBLOCKATT)==0) {
unsigned long long iv = 0;
if(filetypep) *filetypep = NC_INT;
if(lenp) *lenp = 1;
if(strcmp(name,SUPERBLOCKATT)==0)
iv = (unsigned long long)h5->provenance.superblockversion;
else /* strcmp(name,ISNETCDF4ATT)==0 */
iv = NCZ_isnetcdf4(h5);
if(mem_type == NC_NAT) mem_type = NC_INT;
if(data)
switch (mem_type) {
case NC_BYTE: *((char*)data) = (char)iv; break;
case NC_SHORT: *((short*)data) = (short)iv; break;
case NC_INT: *((int*)data) = (int)iv; break;
case NC_UBYTE: *((unsigned char*)data) = (unsigned char)iv; break;
case NC_USHORT: *((unsigned short*)data) = (unsigned short)iv; break;
case NC_UINT: *((unsigned int*)data) = (unsigned int)iv; break;
case NC_INT64: *((long long*)data) = (long long)iv; break;
case NC_UINT64: *((unsigned long long*)data) = (unsigned long long)iv; break;
default:
return NC_ERANGE;
}
}
return NC_NOERR;
}
/**
* @internal I think all atts should be named the exact same thing, to
* avoid confusion!
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute.
* @param newname New name for attribute.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME New name too long.
* @return ::NC_EPERM File is read-only.
* @return ::NC_ENAMEINUSE New name already in use.
* @return ::NC_ENOTINDEFINE Classic model file not in define mode.
* @return ::NC_EHDFERR HDF error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EINTERNAL Could not rebuild list.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_rename_att(int ncid, int varid, const char *name, const char *newname)
{
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var = NULL;
NC_ATT_INFO_T *att;
NCindex *list;
char norm_newname[NC_MAX_NAME + 1], norm_name[NC_MAX_NAME + 1];
int retval = NC_NOERR;
if (!name || !newname)
return NC_EINVAL;
LOG((2, "nc_rename_att: ncid 0x%x varid %d name %s newname %s",
ncid, varid, name, newname));
/* If the new name is too long, that's an error. */
if (strlen(newname) > NC_MAX_NAME)
return NC_EMAXNAME;
/* Find info for this file, group, and h5 info. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(h5 && grp);
/* 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(newname, norm_newname)))
return retval;
/* Get the list of attributes. */
if ((retval = ncz_getattlist(grp, varid, &var, &list)))
return retval;
/* Is new name in use? */
att = (NC_ATT_INFO_T*)ncindexlookup(list,norm_newname);
if(att != NULL)
return NC_ENAMEINUSE;
/* Normalize name and find the attribute. */
if ((retval = nc4_normalize_name(name, norm_name)))
return retval;
att = (NC_ATT_INFO_T*)ncindexlookup(list,norm_name);
if (!att)
return NC_ENOTATT;
/* If we're not in define mode, new name must be of equal or
less size, if complying with strict NC3 rules. */
if (!(h5->flags & NC_INDEF) && strlen(norm_newname) > strlen(att->hdr.name) &&
(h5->cmode & NC_CLASSIC_MODEL))
return NC_ENOTINDEFINE;
/* Copy the new name into our metadata. */
if(att->hdr.name) free(att->hdr.name);
if (!(att->hdr.name = strdup(norm_newname)))
return NC_ENOMEM;
att->dirty = NC_TRUE;
/* Rehash the attribute list so that the new name is used */
if(!ncindexrebuild(list))
return NC_EINTERNAL;
/* Mark attributes on variable dirty, so they get written */
if(var)
var->attr_dirty = NC_TRUE;
return retval;
}
/**
* @internal Delete an att. Rub it out. Push the button on
* it. Liquidate it. Bump it off. Take it for a one-way
* ride. Terminate it.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute to delete.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTATT Attribute not found.
* @return ::NC_EINVAL No name provided.
* @return ::NC_EPERM File is read only.
* @return ::NC_ENOTINDEFINE Classic model not in define mode.
* @return ::NC_EINTERNAL Could not rebuild list.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_del_att(int ncid, int varid, const char *name)
{
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var;
NC_FILE_INFO_T *h5;
NC_ATT_INFO_T *att;
NCindex* attlist = NULL;
int i;
size_t deletedid;
int retval;
/* Name must be provided. */
if (!name)
return NC_EINVAL;
LOG((2, "nc_del_att: ncid 0x%x varid %d name %s", ncid, varid, name));
/* Find info for this file, group, and h5 info. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(h5 && grp);
/* If the file is read-only, return an error. */
if (h5->no_write)
return NC_EPERM;
/* If file is not in define mode, return error for classic model
* files, otherwise switch to define mode. */
if (!(h5->flags & NC_INDEF))
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_ENOTINDEFINE;
if ((retval = NCZ_redef(ncid)))
return retval;
}
/* Get either the global or a variable attribute list. */
if ((retval = ncz_getattlist(grp, varid, &var, &attlist)))
return retval;
#ifdef LOOK
/* Determine the location id in the ZARR file. */
if (varid == NC_GLOBAL)
locid = ((NCZ_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid;
else if (var->created)
locid = ((NCZ_VAR_INFO_T *)(var->format_var_info))->hdf_datasetid;
#endif
/* Now find the attribute by name. */
if (!(att = (NC_ATT_INFO_T*)ncindexlookup(attlist, name)))
return NC_ENOTATT;
/* Delete it from the ZARR file, if it's been created. */
if (att->created)
{
#ifdef LOOK
assert(locid);
if (H5Adelete(locid, att->hdr.name) < 0)
return NC_EATTMETA;
#endif
}
deletedid = att->hdr.id;
/* Remove this attribute in this list */
if ((retval = nc4_att_list_del(attlist, att)))
return retval;
/* Renumber all attributes with higher indices. */
for (i = 0; i < ncindexsize(attlist); i++)
{
NC_ATT_INFO_T *a;
if (!(a = (NC_ATT_INFO_T *)ncindexith(attlist, i)))
continue;
if (a->hdr.id > deletedid)
a->hdr.id--;
}
/* Rebuild the index. */
if (!ncindexrebuild(attlist))
return NC_EINTERNAL;
return NC_NOERR;
}
/**
* @internal This will return the length of a netcdf atomic data type
* in bytes.
*
* @param type A netcdf atomic type.
*
* @return Type size in bytes, or -1 if type not found.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
nc4typelen(nc_type type)
{
switch(type){
case NC_BYTE:
case NC_CHAR:
case NC_UBYTE:
return 1;
case NC_USHORT:
case NC_SHORT:
return 2;
case NC_FLOAT:
case NC_INT:
case NC_UINT:
return 4;
case NC_DOUBLE:
case NC_INT64:
case NC_UINT64:
return 8;
}
return -1;
}
/**
* @internal
* Write an attribute to a netCDF-4/NCZ file, converting
* data type if necessary.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute.
* @param file_type Type of the attribute data in file.
* @param len Number of elements in attribute array.
* @param data Attribute data.
* @param mem_type Type of data in memory.
* @param force write even if the attribute is special
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid parameters.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTVAR Variable not found.
* @return ::NC_EBADNAME Name contains illegal characters.
* @return ::NC_ENAMEINUSE Name already in use.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
ncz_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
size_t len, const void *data, nc_type mem_type, int force)
{
NC* nc;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var = NULL;
NCindex* attlist = NULL;
NC_ATT_INFO_T* att;
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 ret;
int ncid;
h5 = grp->nc4_info;
nc = h5->controller;
assert(nc && grp && h5);
ncid = nc->ext_ncid | grp->hdr.id;
/* Find att, if it exists. (Must check varid first or nc_test will
* break.) This also does lazy att reads if needed. */
if ((ret = ncz_getattlist(grp, varid, &var, &attlist)))
return ret;
/* The length needs to be positive (cast needed for braindead
systems with signed size_t). */
if((unsigned long) len > X_INT_MAX)
return NC_EINVAL;
/* Check name before LOG statement. */
if (!name || strlen(name) > NC_MAX_NAME)
return NC_EBADNAME;
LOG((1, "%s: ncid 0x%x varid %d name %s file_type %d mem_type %d len %d",
__func__,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;
/* 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;
/* Check that a reserved att name is not being used improperly */
const NC_reservedatt* ra = NC_findreserved(name);
if(ra != NULL && !force) {
/* case 1: grp=root, varid==NC_GLOBAL, flags & READONLYFLAG */
if (nc->ext_ncid == ncid && varid == NC_GLOBAL && grp->parent == NULL
&& (ra->flags & READONLYFLAG))
return NC_ENAMEINUSE;
/* case 2: grp=NA, varid!=NC_GLOBAL, flags & HIDDENATTRFLAG */
if (varid != NC_GLOBAL && (ra->flags & HIDDENATTRFLAG))
return NC_ENAMEINUSE;
}
/* See if there is already an attribute with this name. */
att = (NC_ATT_INFO_T*)ncindexlookup(attlist,norm_name);
if (!att)
{
/* If this is a new att, require define mode. */
if (!(h5->flags & NC_INDEF))
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_ENOTINDEFINE;
if ((retval = NCZ_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_ENOTINDEFINE;
if ((retval = NCZ_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, &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 ((ret = nc4_att_list_add(attlist, norm_name, &att)))
BAIL(ret);
/* Allocate storage for the ZARR specific att info. */
if (!(att->format_att_info = calloc(1, sizeof(NCZ_ATT_INFO_T))))
BAIL(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]); /* FIX: see warning of nc_free_vlen */
free(att->vldata);
att->vldata = NULL;
}
att->len = len;
/* 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->hdr.name, _FillValue) && varid != NC_GLOBAL)
{
int size;
/* Fill value must be same type and have exactly one value */
if (att->nc_typeid != var->type_info->hdr.id)
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;
/* Get the length of the veriable data type. */
if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id,
&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);
}
#ifdef LOOK
/* Determine the size of the fill value in bytes. */
if (var->type_info->nc_type_class == NC_VLEN)
size = sizeof(hvl_t);
else
#endif
if (var->type_info->nc_type_class == NC_STRING)
size = sizeof(char *);
else
size = type_size;
/* Allocate space for the fill value. */
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->hdr.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);
NC_TYPE_INFO_T* basetype;
size_t basetypesize = 0;
/* get the basetype and its size */
basetype = var->type_info;
if ((retval = nc4_get_typelen_mem(grp->nc4_info, basetype->hdr.id, &basetypesize)))
return retval;
/* shallow clone the content of the vlen; shallow because it has only a temporary existence */
fv_vlen->len = in_vlen->len;
if (!(fv_vlen->p = malloc(basetypesize * in_vlen->len)))
return NC_ENOMEM;
memcpy(fv_vlen->p, in_vlen->p, in_vlen->len * basetypesize);
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if (*(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);
#ifdef LOOK
if (type_class == NC_VLEN)
{
const hvl_t *vldata1;
NC_TYPE_INFO_T *vltype;
size_t base_typelen;
/* Get the type object for the attribute's type */
if ((retval = nc4_find_type(h5, file_type, &vltype)))
BAIL(retval);
/* Retrieve the size of the base type */
if ((retval = nc4_get_typelen_mem(h5, vltype->u.v.base_nc_typeid, &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;
/* Warning, this only works for cases described for nc_free_vlen() */
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
#endif
if (type_class == NC_STRING)
{
LOG((4, "copying array of NC_STRING"));
if (!(att->stdata = malloc(sizeof(char *) * att->len))) {
BAIL(NC_ENOMEM);
}
/* If we are overwriting an existing attribute,
specifically an NC_CHAR, we need to clean up
the pre-existing att->data. */
if (!new_att && att->data) {
free(att->data);
att->data = NULL;
}
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);
#ifdef ADEBUG
fprintf(stderr,"new attr: %s: len=%d alloc=%d\n",att->hdr.name,(int)att->len,(int)(att->len*type_size));
#endif
/* 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 if(mem_type == file_type) {
memcpy(att->data, data, len * type_size);
} else /* need to convert */
{
/* 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))))
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;
}
/**
* @internal Write an attribute to a netCDF-4/NCZ file, converting
* data type if necessary.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute.
* @param file_type Type of the attribute data in file.
* @param len Number of elements in attribute array.
* @param data Attribute data.
* @param mem_type Type of data in memory.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid parameters.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTVAR Variable not found.
* @return ::NC_EBADNAME Name contains illegal characters.
* @return ::NC_ENAMEINUSE Name already in use.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_put_att(int ncid, int varid, const char *name, nc_type file_type,
size_t len, const void *data, nc_type mem_type)
{
NC_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
int ret;
/* Find info for this file, group, and h5 info. */
if ((ret = nc4_find_grp_h5(ncid, &grp, &h5)))
return ret;
assert(grp && h5);
return ncz_put_att(grp, varid, name, file_type, len, data, mem_type, 0);
}
/**
* @internal Learn about an att. All the nc4 nc_inq_ functions just
* call ncz_get_att to get the metadata on an attribute.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute.
* @param xtypep Pointer that gets type of attribute.
* @param lenp Pointer that gets length of attribute data array.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_inq_att(int ncid, int varid, const char *name, nc_type *xtypep,
size_t *lenp)
{
NC_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var = NULL;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* Find the file, group, and var info, and do lazy att read if
* needed. */
if ((retval = ncz_find_grp_var_att(ncid, varid, name, 0, 1, norm_name,
&h5, &grp, &var, NULL)))
return retval;
/* If this is one of the reserved atts, use nc_get_att_special. */
if (!var)
{
const NC_reservedatt *ra = NC_findreserved(norm_name);
if (ra && ra->flags & NAMEONLYFLAG)
return ncz_get_att_special(h5, norm_name, xtypep, NC_NAT, lenp, NULL,
NULL);
}
return nc4_get_att_ptrs(h5, grp, var, norm_name, xtypep, NC_NAT,
lenp, NULL, NULL);
}
/**
* @internal Learn an attnum, given a name.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute.
* @param attnump Pointer that gets the attribute index number.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_inq_attid(int ncid, int varid, const char *name, int *attnump)
{
NC_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var = NULL;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* Find the file, group, and var info, and do lazy att read if
* needed. */
if ((retval = ncz_find_grp_var_att(ncid, varid, name, 0, 1, norm_name,
&h5, &grp, &var, NULL)))
return retval;
/* If this is one of the reserved atts, use nc_get_att_special. */
if (!var)
{
const NC_reservedatt *ra = NC_findreserved(norm_name);
if (ra && ra->flags & NAMEONLYFLAG)
return ncz_get_att_special(h5, norm_name, NULL, NC_NAT, NULL, attnump,
NULL);
}
return nc4_get_att_ptrs(h5, grp, var, norm_name, NULL, NC_NAT,
NULL, attnump, NULL);
}
/**
* @internal Given an attnum, find the att's name.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param attnum The index number of the attribute.
* @param name Pointer that gets name of attrribute.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_inq_attname(int ncid, int varid, int attnum, char *name)
{
NC_ATT_INFO_T *att;
int retval;
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* Find the file, group, and var info, and do lazy att read if
* needed. */
if ((retval = ncz_find_grp_var_att(ncid, varid, NULL, attnum, 0, NULL,
NULL, NULL, NULL, &att)))
return retval;
assert(att);
/* Get the name. */
if (name)
strcpy(name, att->hdr.name);
return NC_NOERR;
}
/**
* @internal Get an attribute.
*
* @param ncid File and group ID.
* @param varid Variable ID.
* @param name Name of attribute.
* @param value Pointer that gets attribute data.
* @param memtype The type the data should be converted to as it is
* read.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_get_att(int ncid, int varid, const char *name, void *value,
nc_type memtype)
{
NC_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var = NULL;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* Find the file, group, and var info, and do lazy att read if
* needed. */
if ((retval = ncz_find_grp_var_att(ncid, varid, name, 0, 1, norm_name,
&h5, &grp, &var, NULL)))
return retval;
/* If this is one of the reserved atts, use nc_get_att_special. */
if (!var)
{
const NC_reservedatt *ra = NC_findreserved(norm_name);
if (ra && ra->flags & NAMEONLYFLAG)
return ncz_get_att_special(h5, norm_name, NULL, NC_NAT, NULL, NULL,
value);
}
return nc4_get_att_ptrs(h5, grp, var, norm_name, NULL, memtype,
NULL, NULL, value);
}
#if 0
static int
ncz_del_attr(NC_FILE_INFO_T* file, NC_OBJ* container, const char* name)
{
int i,stat = NC_NOERR;
ZTRACE();
if(container->sort == NCGRP)
stat = ncz_getattlist((NC_GRP_INFO_T*)container,NC_GLOBAL,NULL,&attlist);
else
stat = ncz_getattlist((NC_VAR_INFO_T*)container,NC_GLOBAL,NULL,&attlist);
goto done;
/* Iterate over the attributes to locate the matching attribute */
for(i=0;i<nclistlength(jattrs->dict);i+=2) {
NCjson* key = nclistget(jattrs->dict,i);
assert(key->sort == NCJ_STRING);
if(strcmp(key->value,name)==0) {
/* Remove and reclaim */
NCjson* value = nclistget(jattrs->dict,i+1);
nclistremove(jattrs->dict,i);
nclistremove(jattrs->dict,i+1);
NCJreclaim(key);
NCJreclaim(value);
break;
}
}
/* Write the json back out */
if((stat = ncz_unload_jatts(zinfo, container, jattrs, jtypes)))
goto done;
done:
NCJreclaim(jattrs);
NCJreclaim(jtypes);
return stat;
}
#endif
/* If we do not have a _FillValue, then go ahead and create it */
int
ncz_create_fillvalue(NC_VAR_INFO_T* var)
{
int stat = NC_NOERR;
int i;
NC_ATT_INFO_T* fv = NULL;
/* Have the var's attributes been read? */
if(!var->atts_read) goto done; /* above my pay grade */
/* Is FillValue warranted? */
if(!var->no_fill && var->fill_value != NULL) {
/* Make sure _FillValue does not exist */
for(i=0;i<ncindexsize(var->att);i++) {
fv = (NC_ATT_INFO_T*)ncindexith(var->att,i);
if(strcmp(fv->hdr.name,_FillValue)==0) break;
fv = NULL;
}
if(fv == NULL) {
/* Create it */
if((stat = ncz_makeattr((NC_OBJ*)var,var->att,_FillValue,var->type_info->hdr.id,1,var->fill_value,&fv)))
goto done;
}
}
done:
return THROW(stat);
}
/* Create an attribute; This is an abbreviated form
of ncz_put_att above */
int
ncz_makeattr(NC_OBJ* container, NCindex* attlist, const char* name, nc_type typeid, size_t len, void* values, NC_ATT_INFO_T** attp)
{
int stat = NC_NOERR;
NC_ATT_INFO_T* att = NULL;
NCZ_ATT_INFO_T* zatt = NULL;
if((stat=nc4_att_list_add(attlist,name,&att)))
goto done;
if((zatt = calloc(1,sizeof(NCZ_ATT_INFO_T))) == NULL)
{stat = NC_ENOMEM; goto done;}
if(container->sort == NCGRP) {
zatt->common.file = ((NC_GRP_INFO_T*)container)->nc4_info;
} else if(container->sort == NCVAR) {
zatt->common.file = ((NC_VAR_INFO_T*)container)->container->nc4_info;
} else
abort();
att->container = container;
att->format_att_info = zatt;
/* Fill in the attribute's type and value */
att->nc_typeid = typeid;
att->len = len;
att->data = values;
att->dirty = NC_TRUE;
if(attp) {*attp = att; att = NULL;}
done:
if(stat) {
if(att) nc4_att_list_del(attlist,att);
nullfree(zatt);
}
return THROW(stat);
}
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