mirror of
https://github.com/Unidata/netcdf-c.git
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9380790ea8
re: The current netcdf-c release has some problems with the mingw platform on windows. Mostly they are path issues. Changes to support mingw+msys2: ------------------------------- * Enable option of looking into the windows registry to find the mingw root path. In aid of proper path handling. * Add mingw+msys as a specific platform in configure.ac and move testing of the platform to the front so it is available early. * Handle mingw X libncpoco (dynamic loader) properly even though mingw does not yet support it. * Handle mingw X plugins properly even though mingw does not yet support it. * Alias pwd='pwd -W' to better handle paths in shell scripts. * Plus a number of other minor compile irritations. * Disallow the use of multiple nc_open's on the same file for windows (and mingw) because windows does not seem to handle these properly. Not sure why we did not catch this earlier. * Add mountpoint info to dpathmgr.c to help support mingw. * Cleanup dpathmgr conversions. Known problems: --------------- * I have not been able to get shared libraries to work, so plugins/filters must be disabled. * There is some kind of problem with libcurl that I have not solved, so all uses of libcurl (currently DAP+Byterange) must be disabled. Misc. other fixes: ------------------ * Cleanup the relationship between ENABLE_PLUGINS and various other flags in CMakeLists.txt and configure.ac. * Re-arrange the TESTDIRS order in Makefile.am. * Add pseudo-breakpoint to nclog.[ch] for debugging. * Improve the documentation of the path manager code in ncpathmgr.h * Add better support for relative paths in dpathmgr.c * Default the mode args to NCfopen to include "b" (binary) for windows. * Add optional debugging output in various places. * Make sure that everything builds with plugins disabled. * Fix numerous (s)printf inconsistencies betweenb the format spec and the arguments.
1078 lines
33 KiB
C
1078 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 three special attributes, NCPROPS,
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* ISNETCDF4ATT, and SUPERBLOCKATT. These atts are not all really in
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* 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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/* 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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/* 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.
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* @return ::NC_ENAMEINUSE Name already in use.
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* @author Dennis Heimbigner, Ed Hartnett
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*/
|
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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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|
{
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NC* nc;
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NC_FILE_INFO_T *h5;
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NC_VAR_INFO_T *var = NULL;
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NCindex* attlist = NULL;
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NC_ATT_INFO_T* att;
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char norm_name[NC_MAX_NAME + 1];
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nc_bool_t new_att = NC_FALSE;
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int retval = NC_NOERR, range_error = 0;
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|
size_t type_size;
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int i;
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int ret;
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int ncid;
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|
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h5 = grp->nc4_info;
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nc = h5->controller;
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assert(nc && grp && h5);
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|
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ncid = nc->ext_ncid | grp->hdr.id;
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|
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/* Find att, if it exists. (Must check varid first or nc_test will
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* break.) This also does lazy att reads if needed. */
|
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if ((ret = ncz_getattlist(grp, varid, &var, &attlist)))
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return ret;
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|
|
/* The length needs to be positive (cast needed for braindead
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|
systems with signed size_t). */
|
|
if((unsigned long) len > X_INT_MAX)
|
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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;
|
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|
|
/* 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); var->fill_value = NULL;
|
|
}
|
|
|
|
#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),
|
|
NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
}
|
|
}
|
|
}
|
|
att->dirty = NC_TRUE;
|
|
att->created = NC_FALSE;
|
|
|
|
/* Mark attributes on variable dirty, so they get written */
|
|
if(var)
|
|
var->attr_dirty = NC_TRUE;
|
|
|
|
exit:
|
|
/* If there was an error return it, otherwise return any potential
|
|
range error value. If none, return NC_NOERR as usual.*/
|
|
if (retval)
|
|
return retval;
|
|
if (range_error)
|
|
return NC_ERANGE;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @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;
|
|
|
|
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 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;
|
|
NC_GRP_INFO_T* grp = (container->sort == NCGRP ? (NC_GRP_INFO_T*)container
|
|
: ((NC_VAR_INFO_T*)container)->container);
|
|
|
|
/* 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;}
|
|
memcpy(clone,values,clonesize);
|
|
|
|
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);
|
|
}
|
|
|