mirror of
https://github.com/Unidata/netcdf-c.git
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231ae96c4b
* re: https://github.com/Unidata/netcdf-c/pull/2278 * re: https://github.com/Unidata/netcdf-c/issues/2485 * re: https://github.com/Unidata/netcdf-c/issues/2474 This PR subsumes PR https://github.com/Unidata/netcdf-c/pull/2278. Actually is a bit an omnibus covering several issues. ## PR https://github.com/Unidata/netcdf-c/pull/2278 Add support for the Zarr string type. Zarr strings are restricted currently to be of fixed size. The primary issue to be addressed is to provide a way for user to specify the size of the fixed length strings. This is handled by providing the following new attributes special: 1. **_nczarr_default_maxstrlen** — This is an attribute of the root group. It specifies the default maximum string length for string types. If not specified, then it has the value of 64 characters. 2. **_nczarr_maxstrlen** — This is a per-variable attribute. It specifies the maximum string length for the string type associated with the variable. If not specified, then it is assigned the value of **_nczarr_default_maxstrlen**. This PR also requires some hacking to handle the existing netcdf-c NC_CHAR type, which does not exist in zarr. The goal was to choose numpy types for both the netcdf-c NC_STRING type and the netcdf-c NC_CHAR type such that if a pure zarr implementation read them, it would still work and an NC_CHAR type would be handled by zarr as a string of length 1. For writing variables and NCZarr attributes, the type mapping is as follows: * "|S1" for NC_CHAR. * ">S1" for NC_STRING && MAXSTRLEN==1 * ">Sn" for NC_STRING && MAXSTRLEN==n Note that it is a bit of a hack to use endianness, but it should be ok since for string/char, the endianness has no meaning. For reading attributes with pure zarr (i.e. with no nczarr atribute types defined), they will always be interpreted as of type NC_CHAR. ## Issue: https://github.com/Unidata/netcdf-c/issues/2474 This PR partly fixes this issue because it provided more comprehensive support for Zarr attributes that are JSON valued expressions. This PR still does not address the problem in that issue where the _ARRAY_DIMENSION attribute is incorrectly set. Than can only be fixed by the creator of the datasets. ## Issue: https://github.com/Unidata/netcdf-c/issues/2485 This PR also fixes the scalar failure shown in this issue. It generally cleans up scalar handling. It also adds a note to the documentation describing that NCZarr supports scalars while Zarr does not and also how scalar interoperability is achieved. ## Misc. Other Changes 1. Convert the nczarr special attributes and keys to be all lower case. So "_NCZARR_ATTR" now used "_nczarr_attr. Support back compatibility for the upper case names. 2. Cleanup my too-clever-by-half handling of scalars in libnczarr.
1059 lines
33 KiB
C
1059 lines
33 KiB
C
/* Copyright 2003-2018, University Corporation for Atmospheric
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* Research. See COPYRIGHT file for copying and redistribution
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* conditions. */
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/**
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* @file
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* @internal This file handles ZARR attributes.
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*
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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#include "zincludes.h"
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#include "zfilter.h"
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#undef ADEBUG
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/**
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* @internal Get the attribute list for either a varid or NC_GLOBAL
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*
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* @param grp Group
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* @param varid Variable ID | NC_BLOGAL
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* @param varp Pointer that gets pointer to NC_VAR_INFO_T
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* instance. Ignored if NULL.
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* @param attlist Pointer that gets pointer to attribute list.
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*
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* @return NC_NOERR No error.
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* @author Dennis Heimbigner, Ed Hartnett
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* [Candidate for moving to libsrc4]
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*/
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int
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ncz_getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp, NCindex **attlist)
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{
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int retval;
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NC_FILE_INFO_T* file = grp->nc4_info;
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NCZ_FILE_INFO_T* zinfo = file->format_file_info;
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assert(grp && attlist && file && zinfo);
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if (varid == NC_GLOBAL)
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{
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/* Do we need to read the atts? */
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if (!grp->atts_read)
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if ((retval = ncz_read_atts(file, (NC_OBJ*)grp)))
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return retval;
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if (varp)
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*varp = NULL;
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*attlist = grp->att;
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}
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else
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{
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NC_VAR_INFO_T *var;
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if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
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return NC_ENOTVAR;
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assert(var->hdr.id == varid);
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/* Do we need to read the atts? */
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if (!var->atts_read)
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if ((retval = ncz_read_atts(file, (NC_OBJ*)var)))
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return retval;
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if (varp)
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*varp = var;
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*attlist = var->att;
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}
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return NC_NOERR;
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}
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/**
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* @internal Get one of the special attributes:
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* See the reserved attribute table in libsrc4/nc4internal.c.
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* The special attributes are the ones marked with NAMEONLYFLAG.
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* For example: NCPROPS, ISNETCDF4ATT, and SUPERBLOCKATT, and CODECS.
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* These atts are not all really in the file, they are constructed on the fly.
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*
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* @param h5 Pointer to ZARR file info struct.
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* @param var Pointer to var info struct; NULL signals global.
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* @param name Name of attribute.
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* @param filetypep Pointer that gets type of the attribute data in
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* file.
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* @param mem_type Type of attribute data in memory.
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* @param lenp Pointer that gets length of attribute array.
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* @param attnump Pointer that gets the attribute number.
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* @param data Attribute data.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID Bad ncid.
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* @return ::NC_ERANGE Data conversion out of range.
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* @author Dennis Heimbigner
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*/
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int
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ncz_get_att_special(NC_FILE_INFO_T* h5, NC_VAR_INFO_T* var, const char* name,
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nc_type* filetypep, nc_type mem_type, size_t* lenp,
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int* attnump, void* data)
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{
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int stat = NC_NOERR;
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/* Fail if asking for att id */
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if(attnump)
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{stat = NC_EATTMETA; goto done;}
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/* Handle the per-var case(s) first */
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if(var != NULL) {
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#ifdef ENABLE_NCZARR_FILTERS
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if(strcmp(name,NC_ATT_CODECS)==0) {
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NClist* filters = (NClist*)var->filters;
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if(mem_type == NC_NAT) mem_type = NC_CHAR;
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if(mem_type != NC_CHAR)
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{stat = NC_ECHAR; goto done;}
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if(filetypep) *filetypep = NC_CHAR;
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if(lenp) *lenp = 0;
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if(filters == NULL) goto done;
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if((stat = NCZ_codec_attr(var,lenp,data))) goto done;
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}
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#endif
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goto done;
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}
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/* The global reserved attributes */
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if(strcmp(name,NCPROPS)==0) {
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int len;
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if(h5->provenance.ncproperties == NULL)
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{stat = NC_ENOTATT; goto done;}
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if(mem_type == NC_NAT) mem_type = NC_CHAR;
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if(mem_type != NC_CHAR)
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{stat = NC_ECHAR; goto done;}
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if(filetypep) *filetypep = NC_CHAR;
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len = strlen(h5->provenance.ncproperties);
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if(lenp) *lenp = len;
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if(data) strncpy((char*)data,h5->provenance.ncproperties,len+1);
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} else if(strcmp(name,ISNETCDF4ATT)==0
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|| strcmp(name,SUPERBLOCKATT)==0) {
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unsigned long long iv = 0;
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if(filetypep) *filetypep = NC_INT;
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if(lenp) *lenp = 1;
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if(strcmp(name,SUPERBLOCKATT)==0)
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iv = (unsigned long long)h5->provenance.superblockversion;
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else /* strcmp(name,ISNETCDF4ATT)==0 */
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iv = NCZ_isnetcdf4(h5);
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if(mem_type == NC_NAT) mem_type = NC_INT;
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if(data)
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switch (mem_type) {
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case NC_BYTE: *((char*)data) = (char)iv; break;
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case NC_SHORT: *((short*)data) = (short)iv; break;
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case NC_INT: *((int*)data) = (int)iv; break;
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case NC_UBYTE: *((unsigned char*)data) = (unsigned char)iv; break;
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case NC_USHORT: *((unsigned short*)data) = (unsigned short)iv; break;
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case NC_UINT: *((unsigned int*)data) = (unsigned int)iv; break;
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case NC_INT64: *((long long*)data) = (long long)iv; break;
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case NC_UINT64: *((unsigned long long*)data) = (unsigned long long)iv; break;
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default:
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{stat = NC_ERANGE; goto done;}
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}
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}
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done:
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return stat;
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}
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/**
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* @internal I think all atts should be named the exact same thing, to
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* avoid confusion!
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*
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* @param ncid File and group ID.
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* @param varid Variable ID.
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* @param name Name of attribute.
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* @param newname New name for attribute.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID Bad ncid.
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* @return ::NC_EMAXNAME New name too long.
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* @return ::NC_EPERM File is read-only.
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* @return ::NC_ENAMEINUSE New name already in use.
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* @return ::NC_ENOTINDEFINE Classic model file not in define mode.
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* @return ::NC_EHDFERR HDF error.
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* @return ::NC_ENOMEM Out of memory.
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* @return ::NC_EINTERNAL Could not rebuild list.
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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int
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NCZ_rename_att(int ncid, int varid, const char *name, const char *newname)
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{
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NC_GRP_INFO_T *grp;
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NC_FILE_INFO_T *h5;
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NC_VAR_INFO_T *var = NULL;
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NC_ATT_INFO_T *att;
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NCindex *list;
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char norm_newname[NC_MAX_NAME + 1], norm_name[NC_MAX_NAME + 1];
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int retval = NC_NOERR;
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if (!name || !newname)
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return NC_EINVAL;
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LOG((2, "nc_rename_att: ncid 0x%x varid %d name %s newname %s",
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ncid, varid, name, newname));
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/* If the new name is too long, that's an error. */
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if (strlen(newname) > NC_MAX_NAME)
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return NC_EMAXNAME;
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/* Find info for this file, group, and h5 info. */
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if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
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return retval;
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assert(h5 && grp);
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/* If the file is read-only, return an error. */
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if (h5->no_write)
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return NC_EPERM;
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/* Check and normalize the name. */
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if ((retval = nc4_check_name(newname, norm_newname)))
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return retval;
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/* Get the list of attributes. */
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if ((retval = ncz_getattlist(grp, varid, &var, &list)))
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return retval;
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/* Is new name in use? */
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att = (NC_ATT_INFO_T*)ncindexlookup(list,norm_newname);
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if(att != NULL)
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return NC_ENAMEINUSE;
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/* Normalize name and find the attribute. */
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if ((retval = nc4_normalize_name(name, norm_name)))
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return retval;
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att = (NC_ATT_INFO_T*)ncindexlookup(list,norm_name);
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if (!att)
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return NC_ENOTATT;
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/* If we're not in define mode, new name must be of equal or
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less size, if complying with strict NC3 rules. */
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if (!(h5->flags & NC_INDEF) && strlen(norm_newname) > strlen(att->hdr.name) &&
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(h5->cmode & NC_CLASSIC_MODEL))
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return NC_ENOTINDEFINE;
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/* Copy the new name into our metadata. */
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if(att->hdr.name) free(att->hdr.name);
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if (!(att->hdr.name = strdup(norm_newname)))
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return NC_ENOMEM;
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att->dirty = NC_TRUE;
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/* Rehash the attribute list so that the new name is used */
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if(!ncindexrebuild(list))
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return NC_EINTERNAL;
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/* Mark attributes on variable dirty, so they get written */
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if(var)
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var->attr_dirty = NC_TRUE;
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return retval;
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}
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/**
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* @internal Delete an att. Rub it out. Push the button on
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* it. Liquidate it. Bump it off. Take it for a one-way
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* ride. Terminate it.
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*
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* @param ncid File and group ID.
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* @param varid Variable ID.
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* @param name Name of attribute to delete.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID Bad ncid.
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* @return ::NC_ENOTATT Attribute not found.
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* @return ::NC_EINVAL No name provided.
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* @return ::NC_EPERM File is read only.
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* @return ::NC_ENOTINDEFINE Classic model not in define mode.
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* @return ::NC_EINTERNAL Could not rebuild list.
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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int
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NCZ_del_att(int ncid, int varid, const char *name)
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{
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NC_GRP_INFO_T *grp;
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NC_VAR_INFO_T *var;
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NC_FILE_INFO_T *h5;
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NC_ATT_INFO_T *att;
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NCindex* attlist = NULL;
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int i;
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size_t deletedid;
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int retval;
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/* Name must be provided. */
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if (!name)
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return NC_EINVAL;
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LOG((2, "nc_del_att: ncid 0x%x varid %d name %s", ncid, varid, name));
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/* Find info for this file, group, and h5 info. */
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if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
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return retval;
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assert(h5 && grp);
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/* If the file is read-only, return an error. */
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if (h5->no_write)
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return NC_EPERM;
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/* If file is not in define mode, return error for classic model
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* files, otherwise switch to define mode. */
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if (!(h5->flags & NC_INDEF))
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{
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if (h5->cmode & NC_CLASSIC_MODEL)
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return NC_ENOTINDEFINE;
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if ((retval = NCZ_redef(ncid)))
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return retval;
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}
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/* Get either the global or a variable attribute list. */
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if ((retval = ncz_getattlist(grp, varid, &var, &attlist)))
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return retval;
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#ifdef LOOK
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/* Determine the location id in the ZARR file. */
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if (varid == NC_GLOBAL)
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locid = ((NCZ_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid;
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else if (var->created)
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locid = ((NCZ_VAR_INFO_T *)(var->format_var_info))->hdf_datasetid;
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#endif
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/* Now find the attribute by name. */
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if (!(att = (NC_ATT_INFO_T*)ncindexlookup(attlist, name)))
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return NC_ENOTATT;
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/* Reclaim the content of the attribute */
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if(att->data) {
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if((retval = nc_reclaim_data_all(ncid,att->nc_typeid,att->data,att->len))) return retval;
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}
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att->data = NULL;
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att->len = 0;
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/* Delete it from the ZARR file, if it's been created. */
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if (att->created)
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{
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#ifdef LOOK
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assert(locid);
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if (H5Adelete(locid, att->hdr.name) < 0)
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return NC_EATTMETA;
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#endif
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}
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deletedid = att->hdr.id;
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/* reclaim associated NCZarr info */
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{
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NCZ_ATT_INFO_T* za = (NCZ_ATT_INFO_T*)att->format_att_info;
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nullfree(za);
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}
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/* Remove this attribute in this list */
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if ((retval = nc4_att_list_del(attlist, att)))
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return retval;
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/* Renumber all attributes with higher indices. */
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for (i = 0; i < ncindexsize(attlist); i++)
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{
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NC_ATT_INFO_T *a;
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if (!(a = (NC_ATT_INFO_T *)ncindexith(attlist, i)))
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continue;
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if (a->hdr.id > deletedid)
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a->hdr.id--;
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}
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/* Rebuild the index. */
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if (!ncindexrebuild(attlist))
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return NC_EINTERNAL;
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return NC_NOERR;
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}
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/**
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* @internal This will return the length of a netcdf atomic data type
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* in bytes.
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*
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* @param type A netcdf atomic type.
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*
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* @return Type size in bytes, or -1 if type not found.
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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static int
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nc4typelen(nc_type type)
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{
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switch(type){
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case NC_BYTE:
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case NC_CHAR:
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case NC_UBYTE:
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return 1;
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case NC_USHORT:
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case NC_SHORT:
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return 2;
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case NC_FLOAT:
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case NC_INT:
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case NC_UINT:
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return 4;
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case NC_DOUBLE:
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case NC_INT64:
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case NC_UINT64:
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return 8;
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}
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return -1;
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}
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/**
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* @internal
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* Write an attribute to a netCDF-4/NCZ file, converting
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* data type if necessary.
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*
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* @param ncid File and group ID.
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* @param varid Variable ID.
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* @param name Name of attribute.
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* @param file_type Type of the attribute data in file.
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* @param len Number of elements in attribute array.
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|
* @param data Attribute data.
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* @param mem_type Type of data in memory.
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* @param force write even if the attribute is special
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EINVAL Invalid parameters.
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* @return ::NC_EBADID Bad ncid.
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* @return ::NC_ENOTVAR Variable not found.
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|
* @return ::NC_EBADNAME Name contains illegal characters.
|
|
* @return ::NC_ENAMEINUSE Name already in use.
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* @author Dennis Heimbigner, Ed Hartnett
|
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*/
|
|
int
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ncz_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
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size_t len, const void *data, nc_type mem_type, int force)
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|
{
|
|
NC* nc;
|
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NC_FILE_INFO_T *h5 = NULL;
|
|
NC_VAR_INFO_T *var = NULL;
|
|
NCindex* attlist = NULL;
|
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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 ret;
|
|
int ncid;
|
|
void* copy = NULL;
|
|
/* Save the old att data and length and old fillvalue in case we need to rollback on error */
|
|
struct Save {
|
|
size_t len;
|
|
void* data;
|
|
nc_type type; /* In case we change the type of the attribute */
|
|
} attsave = {0,NULL,-1};
|
|
struct Save fillsave = {0,NULL,-1};
|
|
|
|
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;
|
|
|
|
/* 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);
|
|
|
|
if(varid == NC_GLOBAL)
|
|
att->container = (NC_OBJ*)grp;
|
|
else
|
|
att->container = (NC_OBJ*)var;
|
|
}
|
|
|
|
/* Now fill in the metadata. */
|
|
att->dirty = NC_TRUE;
|
|
|
|
/* When we reclaim existing data, make sure to use the right type */
|
|
if(new_att) attsave.type = file_type; else attsave.type = att->nc_typeid;
|
|
att->nc_typeid = file_type;
|
|
|
|
/* Get information about this (possibly new) type. */
|
|
if ((retval = nc4_get_typelen_mem(h5, file_type, &type_size)))
|
|
return retval;
|
|
|
|
if (att->data)
|
|
{
|
|
assert(attsave.data == NULL);
|
|
attsave.data = att->data;
|
|
attsave.len = att->len;
|
|
att->data = NULL;
|
|
}
|
|
|
|
/* If this is the _FillValue attribute, then we will also have to
|
|
* copy the value to the fill_value pointer of the NC_VAR_INFO_T
|
|
* struct for this var. (But ignore a global _FillValue
|
|
* attribute). Also kill the cache fillchunk as no longer valid */
|
|
if (!strcmp(att->hdr.name, _FillValue) && varid != NC_GLOBAL)
|
|
{
|
|
/* Fill value must have exactly one value */
|
|
if (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)
|
|
{
|
|
/* reclaim later */
|
|
fillsave.data = var->fill_value;
|
|
fillsave.type = var->type_info->hdr.id;
|
|
fillsave.len = 1;
|
|
var->fill_value = NULL;
|
|
}
|
|
|
|
/* Determine the size of the fill value in bytes. */
|
|
|
|
{
|
|
nc_type var_type = var->type_info->hdr.id;
|
|
size_t var_type_size = var->type_info->size;
|
|
/* The old code used the var's type as opposed to the att's type; normally same,
|
|
but not required. Now we need to convert from the att's type to the var's type.
|
|
Note that we use mem_type rather than file_type because our data is in the form
|
|
of the memory data. When we later capture the memory data for the actual
|
|
attribute, we will use file_type as the target of the conversion. */
|
|
if(mem_type != var_type && mem_type < NC_STRING && var_type < NC_STRING) {
|
|
/* Need to convert from memory data into copy buffer */
|
|
if((copy = malloc(len*var_type_size))==NULL) BAIL(NC_ENOMEM);
|
|
if ((retval = nc4_convert_type(data, copy, mem_type, var_type,
|
|
len, &range_error, NULL,
|
|
(h5->cmode & NC_CLASSIC_MODEL),
|
|
NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
} else { /* no conversion */
|
|
/* Still need a copy of the input data */
|
|
copy = NULL;
|
|
if((retval = nc_copy_data_all(h5->controller->ext_ncid, mem_type, data, 1, ©)))
|
|
BAIL(retval);
|
|
}
|
|
var->fill_value = copy;
|
|
copy = NULL;
|
|
}
|
|
|
|
/* 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;
|
|
/* Reclaim any existing fill_chunk */
|
|
if((retval = NCZ_reclaim_fill_chunk(((NCZ_VAR_INFO_T*)var->format_var_info)->cache))) BAIL(retval);
|
|
}
|
|
|
|
/* Copy the attribute data, if there is any. */
|
|
if (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);
|
|
{
|
|
/* Allocate top level of the copy */
|
|
if (!(copy = malloc(len * type_size)))
|
|
BAIL(NC_ENOMEM);
|
|
/* Special case conversion from memory to file type */
|
|
if(mem_type != file_type && mem_type < NC_STRING && file_type < NC_STRING) {
|
|
if ((retval = nc4_convert_type(data, copy, mem_type, file_type,
|
|
len, &range_error, NULL,
|
|
(h5->cmode & NC_CLASSIC_MODEL),
|
|
NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
} else if(mem_type == file_type) { /* General case: no conversion */
|
|
if((retval = nc_copy_data(h5->controller->ext_ncid,file_type,data,len,copy)))
|
|
BAIL(retval);
|
|
} else
|
|
BAIL(NC_EURL);
|
|
/* Store it */
|
|
att->data = copy; copy = NULL;
|
|
}
|
|
}
|
|
|
|
/* If this is a maxstrlen attribute, then we will also have to
|
|
* sync the value to NCZ_VAR_INFO_T or NCZ_FILE_INFO_T structure */
|
|
{
|
|
if(strcmp(att->hdr.name,NC_NCZARR_DEFAULT_MAXSTRLEN_ATTR)==0 && varid == NC_GLOBAL && len == 1) {
|
|
NCZ_FILE_INFO_T* zfile = (NCZ_FILE_INFO_T*)h5->format_file_info;
|
|
if((retval = nc4_convert_type(att->data, &zfile->default_maxstrlen, file_type, NC_INT,
|
|
len, &range_error, NULL, NC_CLASSIC_MODEL, NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
} else if(strcmp(att->hdr.name,NC_NCZARR_MAXSTRLEN_ATTR)==0 && varid != NC_GLOBAL && len == 1) {
|
|
NCZ_VAR_INFO_T* zvar = (NCZ_VAR_INFO_T*)var->format_var_info;
|
|
if((retval = nc4_convert_type(att->data, &zvar->maxstrlen, file_type, NC_INT,
|
|
len, &range_error, NULL, NC_CLASSIC_MODEL, NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
}
|
|
}
|
|
|
|
att->dirty = NC_TRUE;
|
|
att->created = NC_FALSE;
|
|
att->len = len;
|
|
|
|
/* Mark attributes on variable dirty, so they get written */
|
|
if(var)
|
|
var->attr_dirty = NC_TRUE;
|
|
/* Reclaim saved data */
|
|
if(attsave.data != NULL) {
|
|
assert(attsave.len > 0);
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,attsave.type,attsave.data,attsave.len);
|
|
attsave.len = 0; attsave.data = NULL;
|
|
}
|
|
if(fillsave.data != NULL) {
|
|
assert(fillsave.len > 0);
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,fillsave.type,fillsave.data,fillsave.len);
|
|
fillsave.len = 0; fillsave.data = NULL;
|
|
}
|
|
|
|
exit:
|
|
if(copy)
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,file_type,copy,len);
|
|
if(retval) {
|
|
/* Rollback */
|
|
if(attsave.data != NULL) {
|
|
assert(attsave.len > 0);
|
|
if(att->data)
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,attsave.type,att->data,att->len);
|
|
att->len = attsave.len; att->data = attsave.data;
|
|
}
|
|
if(fillsave.data != NULL) {
|
|
assert(fillsave.len > 0);
|
|
if(att->data)
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,fillsave.type,var->fill_value,1);
|
|
var->fill_value = fillsave.data;
|
|
}
|
|
}
|
|
/* If there was an error return it, otherwise return any potential
|
|
range error value. If none, return NC_NOERR as usual.*/
|
|
if (range_error)
|
|
return NC_ERANGE;
|
|
if (retval)
|
|
return retval;
|
|
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. */
|
|
{
|
|
const NC_reservedatt *ra = NC_findreserved(norm_name);
|
|
if (ra && ra->flags & NAMEONLYFLAG)
|
|
return ncz_get_att_special(h5, var, 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. */
|
|
{
|
|
const NC_reservedatt *ra = NC_findreserved(norm_name);
|
|
if (ra && ra->flags & NAMEONLYFLAG)
|
|
return ncz_get_att_special(h5, var, 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 = NC_NOERR;
|
|
|
|
ZTRACE(1,"ncid=%d varid=%d attnum=%d",ncid,varid,attnum);
|
|
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)))
|
|
goto done;
|
|
assert(att);
|
|
|
|
/* Get the name. */
|
|
if (name)
|
|
strcpy(name, att->hdr.name);
|
|
done:
|
|
return ZUNTRACEX(retval,"name=%s",(retval?"":name));
|
|
}
|
|
|
|
/**
|
|
* @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 global atts, use nc_get_att_special. */
|
|
{
|
|
const NC_reservedatt *ra = NC_findreserved(norm_name);
|
|
if (ra && ra->flags & NAMEONLYFLAG)
|
|
return ncz_get_att_special(h5, var, 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;
|
|
void* clone = NULL;
|
|
size_t typesize, clonesize;
|
|
int ncid;
|
|
NC* nc = NULL;
|
|
NC_GRP_INFO_T* grp = (container->sort == NCGRP ? (NC_GRP_INFO_T*)container
|
|
: ((NC_VAR_INFO_T*)container)->container);
|
|
|
|
nc = grp->nc4_info->controller;
|
|
ncid = nc->ext_ncid | grp->hdr.id;
|
|
|
|
/* Duplicate the values */
|
|
if ((stat = nc4_get_typelen_mem(grp->nc4_info, typeid, &typesize))) goto done;
|
|
clonesize = len*typesize;
|
|
if((clone = malloc(clonesize))==NULL) {stat = NC_ENOMEM; goto done;}
|
|
if((stat = nc_copy_data(ncid, typeid, values, len, clone))) goto done;
|
|
|
|
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 = clone; clone = NULL;
|
|
att->dirty = NC_TRUE;
|
|
if(attp) {*attp = att; att = NULL;}
|
|
|
|
done:
|
|
nullfree(clone);
|
|
if(stat) {
|
|
if(att) nc4_att_list_del(attlist,att);
|
|
nullfree(zatt);
|
|
}
|
|
return THROW(stat);
|
|
}
|
|
|