mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-11-21 03:13:42 +08:00
945 lines
28 KiB
C
945 lines
28 KiB
C
/* Copyright 2003-2018, University Corporation for Atmospheric
|
|
* Research. See COPYRIGHT file for copying and redistribution
|
|
* conditions. */
|
|
/**
|
|
* @file
|
|
* @internal This file handles HDF5 attributes.
|
|
*
|
|
* @author Ed Hartnett
|
|
*/
|
|
|
|
#include "config.h"
|
|
#include "hdf5internal.h"
|
|
|
|
/**
|
|
* @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
|
|
*/
|
|
static int
|
|
getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
|
|
NCindex **attlist)
|
|
{
|
|
NC_VAR_INFO_T* var;
|
|
int retval;
|
|
|
|
if (varid == NC_GLOBAL)
|
|
{
|
|
/* Do we need to read the atts? */
|
|
if (grp->atts_not_read)
|
|
if ((retval = nc4_read_atts(grp, NULL)))
|
|
return retval;
|
|
|
|
if (varp)
|
|
*varp = NULL;
|
|
*attlist = grp->att;
|
|
}
|
|
else
|
|
{
|
|
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_not_read)
|
|
if ((retval = nc4_read_atts(grp, 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 HDF5 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
|
|
nc4_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) {
|
|
char* propdata = NULL;
|
|
int stat = NC_NOERR;
|
|
int len;
|
|
if(h5->provenance->propattr.version == 0)
|
|
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;
|
|
stat = NC4_buildpropinfo(&h5->provenance->propattr, &propdata);
|
|
if(stat != NC_NOERR) return stat;
|
|
len = strlen(propdata);
|
|
if(lenp) *lenp = len;
|
|
if(data) strncpy((char*)data,propdata,len+1);
|
|
free(propdata);
|
|
} 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 = NC4_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 Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_rename_att(int ncid, int varid, const char *name, const char *newname)
|
|
{
|
|
NC *nc;
|
|
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];
|
|
hid_t datasetid = 0;
|
|
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_nc_grp_h5(ncid, &nc, &grp, &h5)))
|
|
return retval;
|
|
assert(h5 && grp && h5);
|
|
|
|
/* 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 = 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;
|
|
|
|
/* Delete the original attribute, if it exists in the HDF5 file. */
|
|
if (att->created)
|
|
{
|
|
if (varid == NC_GLOBAL)
|
|
{
|
|
if (H5Adelete(((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid,
|
|
att->hdr.name) < 0)
|
|
return NC_EHDFERR;
|
|
}
|
|
else
|
|
{
|
|
if ((retval = nc4_open_var_grp2(grp, varid, &datasetid)))
|
|
return retval;
|
|
if (H5Adelete(datasetid, att->hdr.name) < 0)
|
|
return NC_EHDFERR;
|
|
}
|
|
att->created = NC_FALSE;
|
|
}
|
|
|
|
/* 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->hdr.hashkey = NC_hashmapkey(att->hdr.name,strlen(att->hdr.name)); /* Fix hash key */
|
|
|
|
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 Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
NC4_HDF5_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;
|
|
hid_t locid = 0;
|
|
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 = NC4_redef(ncid)))
|
|
return retval;
|
|
}
|
|
|
|
/* Get either the global or a variable attribute list. */
|
|
if ((retval = getattlist(grp, varid, &var, &attlist)))
|
|
return retval;
|
|
|
|
/* Determine the location id in the HDF5 file. */
|
|
if (varid == NC_GLOBAL)
|
|
locid = ((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid;
|
|
else if (var->created)
|
|
locid = ((NC_HDF5_VAR_INFO_T *)(var->format_var_info))->hdf_datasetid;
|
|
|
|
/* Now find the attribute by name. */
|
|
if (!(att = (NC_ATT_INFO_T*)ncindexlookup(attlist, name)))
|
|
return NC_ENOTATT;
|
|
|
|
/* Delete it from the HDF5 file, if it's been created. */
|
|
if (att->created)
|
|
{
|
|
assert(locid);
|
|
if (H5Adelete(locid, att->hdr.name) < 0)
|
|
return NC_EATTMETA;
|
|
}
|
|
|
|
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 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/HDF5 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 Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_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 = 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 & DIMSCALEFLAG */
|
|
if (varid != NC_GLOBAL && (ra->flags & DIMSCALEFLAG))
|
|
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 = 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_ENOTINDEFINE;
|
|
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, &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 HDF5 specific att info. */
|
|
if (!(att->format_att_info = calloc(1, sizeof(NC_HDF5_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);
|
|
}
|
|
|
|
/* Determine the size of the fill value in bytes. */
|
|
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;
|
|
|
|
/* 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);
|
|
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 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);
|
|
|
|
/* 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))))
|
|
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/HDF5 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 Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
NC4_HDF5_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_nc_grp_h5(ncid, NULL, &grp, &h5)))
|
|
return ret;
|
|
assert(grp && h5);
|
|
|
|
return nc4_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 nc4_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 Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_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 = nc4_hdf5_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 nc4_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 Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_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 = nc4_hdf5_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 nc4_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 Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_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 = nc4_hdf5_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 Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_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 = nc4_hdf5_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 nc4_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);
|
|
}
|
|
|