mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-11-27 07:30:33 +08:00
fb40a72b45
re: Issue https://github.com/Unidata/netcdf-c/issues/2685 re: PR https://github.com/Unidata/netcdf-c/pull/2179 As noted in PR https://github.com/Unidata/netcdf-c/pull/2179, the old code did not allow for reclaiming instances of types, nor for properly copying them. That PR provided new functions capable of reclaiming/copying instances of arbitrary types. However, as noted by Issue https://github.com/Unidata/netcdf-c/issues/2685, using these most general functions resulted in a significant performance degradation, even for common cases. This PR attempts to mitigate the cost of using the general reclaim/copy functions in two ways. First, the previous functions operating at the top level by using ncid and typeid arguments. These functions were augmented with equivalent versions that used the netcdf-c library internal data structures to allow direct access to needed information. These new functions are used internally to the library. The second mitigation involves optimizing the internal functions by providing early tests for common cases. This avoids unnecessary recursive function calls. The overall result is a significant improvement in speed by a factor of roughly twenty -- your mileage may vary. These optimized functions are still not as fast as the original (more limited) functions, but they are getting close. Additional optimizations are possible. But the cost is a significant "uglification" of the code that I deemed a step too far, at least for now. ## Misc. Changes 1. Added a test case to check the proper reclamation/copy of complex types. 2. Found and fixed some places where nc_reclaim/copy should have been used. 3. Replaced, in the netcdf-c library, (almost all) occurrences of nc_reclaim_copy with calls to NC_reclaim/copy. This plus the optimizations is the primary speed-up mechanism. 4. In DAP4, the metadata is held in a substrate in-memory file; this required some changes so that the reclaim/copy code accessed that substrate dispatcher rather than the DAP4 dispatcher. 5. Re-factored and isolated the code that computes if a type is (transitively) variable-sized or not. 6. Clean up the reclamation code in ncgen; adding the use of nc_reclaim exposed some memory problems.
909 lines
28 KiB
C
909 lines
28 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 HDF5 attributes.
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*
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* @author Ed Hartnett
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*/
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#include "config.h"
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#include "hdf5internal.h"
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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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static int
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getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
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NCindex **attlist)
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{
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int retval;
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assert(grp && attlist);
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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 = nc4_read_atts(grp, NULL)))
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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 = nc4_read_atts(grp, 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 HDF5 file info struct.
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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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nc4_get_att_special(NC_FILE_INFO_T* h5, 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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/* Fail if asking for att id */
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if(attnump)
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return NC_EATTMETA;
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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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return NC_ENOTATT;
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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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return NC_ECHAR;
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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 = NC4_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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return NC_ERANGE;
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}
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}
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return NC_NOERR;
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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 Ed Hartnett
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*/
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int
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NC4_HDF5_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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hid_t datasetid = 0;
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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 = 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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/* Delete the original attribute, if it exists in the HDF5 file. */
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if (att->created)
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{
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if (varid == NC_GLOBAL)
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{
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if (H5Adelete(((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid,
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att->hdr.name) < 0)
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return NC_EHDFERR;
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}
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else
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{
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if ((retval = nc4_open_var_grp2(grp, varid, &datasetid)))
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return retval;
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if (H5Adelete(datasetid, att->hdr.name) < 0)
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return NC_EHDFERR;
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}
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att->created = NC_FALSE;
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}
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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 Ed Hartnett, Dennis Heimbigner
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*/
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int
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NC4_HDF5_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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hid_t locid = 0;
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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 = NC4_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 = getattlist(grp, varid, &var, &attlist)))
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return retval;
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/* Determine the location id in the HDF5 file. */
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if (varid == NC_GLOBAL)
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locid = ((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid;
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else if (var->created)
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locid = ((NC_HDF5_VAR_INFO_T *)(var->format_var_info))->hdf_datasetid;
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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(h5->controller,att->nc_typeid,att->data,att->len))) return retval;
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att->data = NULL;
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att->len = 0;
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/* Delete it from the HDF5 file, if it's been created. */
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if (att->created)
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{
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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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}
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deletedid = att->hdr.id;
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/* reclaim associated HDF5 info */
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if((retval=nc4_HDF5_close_att(att))) return retval;
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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 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/HDF5 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 Ed Hartnett, Dennis Heimbigner
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*/
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int
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nc4_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 ret;
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int ncid;
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void* copy = NULL;
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/* Save the old att data and length and old fillvalue in case we need to rollback on error */
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struct Save {
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size_t len;
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void* data;
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nc_type type; /* In case we change the type of the attribute */
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} attsave = {0,NULL,-1};
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struct Save fillsave = {0,NULL,-1};
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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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ncid = nc->ext_ncid | grp->hdr.id;
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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 = 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). */
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if((unsigned long) len > X_INT_MAX)
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return NC_EINVAL;
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/* Check name before LOG statement. */
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if (!name || strlen(name) > NC_MAX_NAME)
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return NC_EBADNAME;
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LOG((1, "%s: ncid 0x%x varid %d name %s file_type %d mem_type %d len %d",
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__func__,ncid, varid, name, file_type, mem_type, len));
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/* If len is not zero, then there must be some data. */
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if (len && !data)
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|
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|READONLYFLAG)))
|
|
return NC_ENAMEINUSE;
|
|
}
|
|
|
|
/* See if there is already an attribute with this name. */
|
|
att = (NC_ATT_INFO_T*)ncindexlookup(attlist,norm_name);
|
|
|
|
if (!att)
|
|
{
|
|
/* If this is a new att, require define mode. */
|
|
if (!(h5->flags & NC_INDEF))
|
|
{
|
|
if (h5->cmode & NC_CLASSIC_MODEL)
|
|
return NC_ENOTINDEFINE;
|
|
if ((retval = NC4_redef(ncid)))
|
|
BAIL(retval);
|
|
}
|
|
new_att = NC_TRUE;
|
|
}
|
|
else
|
|
{
|
|
/* For an existing att, if we're not in define mode, the len
|
|
must not be greater than the existing len for classic model. */
|
|
if (!(h5->flags & NC_INDEF) &&
|
|
len * nc4typelen(file_type) > (size_t)att->len * nc4typelen(att->nc_typeid))
|
|
{
|
|
if (h5->cmode & NC_CLASSIC_MODEL)
|
|
return NC_ENOTINDEFINE;
|
|
if ((retval = NC4_redef(ncid)))
|
|
BAIL(retval);
|
|
}
|
|
}
|
|
|
|
/* We must have two valid types to continue. */
|
|
if (file_type == NC_NAT || mem_type == NC_NAT)
|
|
return NC_EBADTYPE;
|
|
|
|
/* No character conversions are allowed. */
|
|
if (file_type != mem_type &&
|
|
(file_type == NC_CHAR || mem_type == NC_CHAR ||
|
|
file_type == NC_STRING || mem_type == NC_STRING))
|
|
return NC_ECHAR;
|
|
|
|
/* For classic mode file, only allow atts with classic types to be
|
|
* created. */
|
|
if (h5->cmode & NC_CLASSIC_MODEL && file_type > NC_DOUBLE)
|
|
return NC_ESTRICTNC3;
|
|
|
|
/* Add to the end of the attribute list, if this att doesn't
|
|
already exist. */
|
|
if (new_att)
|
|
{
|
|
LOG((3, "adding attribute %s to the list...", norm_name));
|
|
if ((ret = nc4_att_list_add(attlist, norm_name, &att)))
|
|
BAIL(ret);
|
|
|
|
/* Allocate storage for the HDF5 specific att info. */
|
|
if (!(att->format_att_info = calloc(1, sizeof(NC_HDF5_ATT_INFO_T))))
|
|
BAIL(NC_ENOMEM);
|
|
|
|
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_vlue pointer of the NC_VAR_INFO_T
|
|
* struct for this var. (But ignore a global _FillValue
|
|
* attribute).
|
|
* Since fill mismatch is no longer required, we need to convert the
|
|
* att's type to the vars's type as part of storing.
|
|
*/
|
|
if (!strcmp(att->hdr.name, _FillValue) && varid != NC_GLOBAL)
|
|
{
|
|
/* Fill value must have exactly one value */
|
|
if (len != 1)
|
|
BAIL(NC_EINVAL);
|
|
|
|
/* If we already wrote to the dataset, then return an error. */
|
|
if (var->written_to)
|
|
BAIL(NC_ELATEFILL);
|
|
|
|
/* Get the length of the variable's data type. */
|
|
if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id,
|
|
&type_size)))
|
|
BAIL(retval);
|
|
|
|
/* Fill value must be same type and have exactly one value */
|
|
if (att->nc_typeid != var->type_info->hdr.id)
|
|
return NC_EBADTYPE;
|
|
|
|
/* 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, 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;
|
|
}
|
|
|
|
/* 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)))
|
|
BAIL(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,file_type,data,len,copy)))
|
|
BAIL(retval);
|
|
} else
|
|
BAIL(NC_EURL);
|
|
/* Store it */
|
|
att->data = copy; copy = NULL;
|
|
}
|
|
}
|
|
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,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,fillsave.type,fillsave.data,fillsave.len);
|
|
fillsave.len = 0; fillsave.data = NULL;
|
|
}
|
|
|
|
exit:
|
|
if(copy)
|
|
(void)NC_reclaim_data_all(h5->controller,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,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,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/HDF5 file, converting
|
|
* data type if necessary.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name of attribute.
|
|
* @param file_type Type of the attribute data in file.
|
|
* @param len Number of elements in attribute array.
|
|
* @param data Attribute data.
|
|
* @param mem_type Type of data in memory.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EINVAL Invalid parameters.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @return ::NC_ENOTVAR Variable not found.
|
|
* @return ::NC_EBADNAME Name contains illegal characters.
|
|
* @return ::NC_ENAMEINUSE Name already in use.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
NC4_HDF5_put_att(int ncid, int varid, const char *name, nc_type file_type,
|
|
size_t len, const void *data, nc_type mem_type)
|
|
{
|
|
NC_FILE_INFO_T *h5;
|
|
NC_GRP_INFO_T *grp;
|
|
int ret;
|
|
|
|
/* Find info for this file, group, and h5 info. */
|
|
if ((ret = nc4_find_nc_grp_h5(ncid, NULL, &grp, &h5)))
|
|
return ret;
|
|
assert(grp && h5);
|
|
|
|
return nc4_put_att(grp, varid, name, file_type, len, data, mem_type, 0);
|
|
}
|
|
|
|
/**
|
|
* @internal Learn about an att. All the nc4 nc_inq_ functions just
|
|
* call nc4_get_att to get the metadata on an attribute.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name of attribute.
|
|
* @param xtypep Pointer that gets type of attribute.
|
|
* @param lenp Pointer that gets length of attribute data array.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_inq_att(int ncid, int varid, const char *name, nc_type *xtypep,
|
|
size_t *lenp)
|
|
{
|
|
NC_FILE_INFO_T *h5;
|
|
NC_GRP_INFO_T *grp;
|
|
NC_VAR_INFO_T *var = NULL;
|
|
char norm_name[NC_MAX_NAME + 1];
|
|
int retval;
|
|
|
|
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
|
|
|
|
/* Find the file, group, and var info, and do lazy att read if
|
|
* needed. */
|
|
if ((retval = nc4_hdf5_find_grp_var_att(ncid, varid, name, 0, 1, norm_name,
|
|
&h5, &grp, &var, NULL)))
|
|
return retval;
|
|
|
|
/* If this is one of the reserved atts, use nc_get_att_special. */
|
|
if (!var)
|
|
{
|
|
const NC_reservedatt *ra = NC_findreserved(norm_name);
|
|
if (ra && ra->flags & NAMEONLYFLAG)
|
|
return nc4_get_att_special(h5, norm_name, xtypep, NC_NAT, lenp, NULL,
|
|
NULL);
|
|
}
|
|
|
|
return nc4_get_att_ptrs(h5, grp, var, norm_name, xtypep, NC_NAT,
|
|
lenp, NULL, NULL);
|
|
}
|
|
|
|
/**
|
|
* @internal Learn an attnum, given a name.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name of attribute.
|
|
* @param attnump Pointer that gets the attribute index number.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_inq_attid(int ncid, int varid, const char *name, int *attnump)
|
|
{
|
|
NC_FILE_INFO_T *h5;
|
|
NC_GRP_INFO_T *grp;
|
|
NC_VAR_INFO_T *var = NULL;
|
|
char norm_name[NC_MAX_NAME + 1];
|
|
int retval;
|
|
|
|
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
|
|
|
|
/* Find the file, group, and var info, and do lazy att read if
|
|
* needed. */
|
|
if ((retval = nc4_hdf5_find_grp_var_att(ncid, varid, name, 0, 1, norm_name,
|
|
&h5, &grp, &var, NULL)))
|
|
return retval;
|
|
|
|
/* If this is one of the reserved atts, use nc_get_att_special. */
|
|
if (!var)
|
|
{
|
|
const NC_reservedatt *ra = NC_findreserved(norm_name);
|
|
if (ra && ra->flags & NAMEONLYFLAG)
|
|
return nc4_get_att_special(h5, norm_name, NULL, NC_NAT, NULL, attnump,
|
|
NULL);
|
|
}
|
|
|
|
return nc4_get_att_ptrs(h5, grp, var, norm_name, NULL, NC_NAT,
|
|
NULL, attnump, NULL);
|
|
}
|
|
|
|
/**
|
|
* @internal Given an attnum, find the att's name.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param attnum The index number of the attribute.
|
|
* @param name Pointer that gets name of attribute.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_inq_attname(int ncid, int varid, int attnum, char *name)
|
|
{
|
|
NC_ATT_INFO_T *att;
|
|
int retval;
|
|
|
|
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
|
|
|
|
/* Find the file, group, and var info, and do lazy att read if
|
|
* needed. */
|
|
if ((retval = nc4_hdf5_find_grp_var_att(ncid, varid, NULL, attnum, 0, NULL,
|
|
NULL, NULL, NULL, &att)))
|
|
return retval;
|
|
assert(att);
|
|
|
|
/* Get the name. */
|
|
if (name)
|
|
strcpy(name, att->hdr.name);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Get an attribute.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name of attribute.
|
|
* @param value Pointer that gets attribute data.
|
|
* @param memtype The type the data should be converted to as it is
|
|
* read.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_HDF5_get_att(int ncid, int varid, const char *name, void *value,
|
|
nc_type memtype)
|
|
{
|
|
NC_FILE_INFO_T *h5;
|
|
NC_GRP_INFO_T *grp;
|
|
NC_VAR_INFO_T *var = NULL;
|
|
char norm_name[NC_MAX_NAME + 1];
|
|
int retval;
|
|
|
|
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
|
|
|
|
/* Find the file, group, and var info, and do lazy att read if
|
|
* needed. */
|
|
if ((retval = nc4_hdf5_find_grp_var_att(ncid, varid, name, 0, 1, norm_name,
|
|
&h5, &grp, &var, NULL)))
|
|
return retval;
|
|
|
|
/* If this is one of the reserved atts, use nc_get_att_special. */
|
|
if (!var)
|
|
{
|
|
const NC_reservedatt *ra = NC_findreserved(norm_name);
|
|
if (ra && ra->flags & NAMEONLYFLAG)
|
|
return nc4_get_att_special(h5, norm_name, NULL, NC_NAT, NULL, NULL,
|
|
value);
|
|
}
|
|
|
|
return nc4_get_att_ptrs(h5, grp, var, norm_name, NULL, memtype,
|
|
NULL, NULL, value);
|
|
}
|