mirror of
https://github.com/Unidata/netcdf-c.git
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8b9253fef2
re: https://github.com/Unidata/netcdf-c/issues/541 re: https://github.com/Unidata/netcdf-c/issues/1208 re: https://github.com/Unidata/netcdf-c/issues/2078 re: https://github.com/Unidata/netcdf-c/issues/2041 re: https://github.com/Unidata/netcdf-c/issues/2143 For a long time, there have been known problems with the management of complex types containing VLENs. This also involves the string type because it is stored as a VLEN of chars. This PR (mostly) fixes this problem. But note that it adds new functions to netcdf.h (see below) and this may require bumping the .so number. These new functions can be removed, if desired, in favor of functions in netcdf_aux.h, but netcdf.h seems the better place for them because they are intended as alternatives to the nc_free_vlen and nc_free_string functions already in netcdf.h. The term complex type refers to any type that directly or transitively references a VLEN type. So an array of VLENS, a compound with a VLEN field, and so on. In order to properly handle instances of these complex types, it is necessary to have function that can recursively walk instances of such types to perform various actions on them. The term "deep" is also used to mean recursive. At the moment, the two operations needed by the netcdf library are: * free'ing an instance of the complex type * copying an instance of the complex type. The current library does only shallow free and shallow copy of complex types. This means that only the top level is properly free'd or copied, but deep internal blocks in the instance are not touched. Note that the term "vector" will be used to mean a contiguous (in memory) sequence of instances of some type. Given an array with, say, dimensions 2 X 3 X 4, this will be stored in memory as a vector of length 2*3*4=24 instances. The use cases are primarily these. ## nc_get_vars Suppose one is reading a vector of instances using nc_get_vars (or nc_get_vara or nc_get_var, etc.). These functions will return the vector in the top-level memory provided. All interior blocks (form nested VLEN or strings) will have been dynamically allocated. After using this vector of instances, it is necessary to free (aka reclaim) the dynamically allocated memory, otherwise a memory leak occurs. So, the recursive reclaim function is used to walk the returned instance vector and do a deep reclaim of the data. Currently functions are defined in netcdf.h that are supposed to handle this: nc_free_vlen(), nc_free_vlens(), and nc_free_string(). Unfortunately, these functions only do a shallow free, so deeply nested instances are not properly handled by them. Note that internally, the provided data is immediately written so there is no need to copy it. But the caller may need to reclaim the data it passed into the function. ## nc_put_att Suppose one is writing a vector of instances as the data of an attribute using, say, nc_put_att. Internally, the incoming attribute data must be copied and stored so that changes/reclamation of the input data will not affect the attribute. Again, the code inside the netcdf library does only shallow copying rather than deep copy. As a result, one sees effects such as described in Github Issue https://github.com/Unidata/netcdf-c/issues/2143. Also, after defining the attribute, it may be necessary for the user to free the data that was provided as input to nc_put_att(). ## nc_get_att Suppose one is reading a vector of instances as the data of an attribute using, say, nc_get_att. Internally, the existing attribute data must be copied and returned to the caller, and the caller is responsible for reclaiming the returned data. Again, the code inside the netcdf library does only shallow copying rather than deep copy. So this can lead to memory leaks and errors because the deep data is shared between the library and the user. # Solution The solution is to build properly recursive reclaim and copy functions and use those as needed. These recursive functions are defined in libdispatch/dinstance.c and their signatures are defined in include/netcdf.h. For back compatibility, corresponding "ncaux_XXX" functions are defined in include/netcdf_aux.h. ```` int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy); int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp); ```` There are two variants. The first two, nc_reclaim_data() and nc_copy_data(), assume the top-level vector is managed by the caller. For reclaim, this is so the user can use, for example, a statically allocated vector. For copy, it assumes the user provides the space into which the copy is stored. The second two, nc_reclaim_data_all() and nc_copy_data_all(), allows the functions to manage the top-level. So for nc_reclaim_data_all, the top level is assumed to be dynamically allocated and will be free'd by nc_reclaim_data_all(). The nc_copy_data_all() function will allocate the top level and return a pointer to it to the user. The user can later pass that pointer to nc_reclaim_data_all() to reclaim the instance(s). # Internal Changes The netcdf-c library internals are changed to use the proper reclaim and copy functions. It turns out that the places where these functions are needed is quite pervasive in the netcdf-c library code. Using these functions also allows some simplification of the code since the stdata and vldata fields of NC_ATT_INFO are no longer needed. Currently this is commented out using the SEPDATA \#define macro. When any bugs are largely fixed, all this code will be removed. # Known Bugs 1. There is still one known failure that has not been solved. All the failures revolve around some variant of this .cdl file. The proximate cause of failure is the use of a VLEN FillValue. ```` netcdf x { types: float(*) row_of_floats ; dimensions: m = 5 ; variables: row_of_floats ragged_array(m) ; row_of_floats ragged_array:_FillValue = {-999} ; data: ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32}, {40, 41}, _ ; } ```` When a solution is found, I will either add it to this PR or post a new PR. # Related Changes * Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data. * Remove the --enable-unfixed-memory-leaks option. * Remove the NC_VLENS_NOTEST code that suppresses some vlen tests. * Document this change in docs/internal.md * Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh. * Mark types as fixed size or not (transitively) to optimize the reclaim and copy functions. # Misc. Changes * Make Doxygen process libdispatch/daux.c * Make sure the NC_ATT_INFO_T.container field is set.
1067 lines
34 KiB
C
1067 lines
34 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(ncid,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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}
|
|
return -1;
|
|
}
|
|
|
|
/**
|
|
* @internal
|
|
* Write an attribute to a netCDF-4/HDF5 file, converting
|
|
* data type if necessary.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name of attribute.
|
|
* @param file_type Type of the attribute data in file.
|
|
* @param len Number of elements in attribute array.
|
|
* @param data Attribute data.
|
|
* @param mem_type Type of data in memory.
|
|
* @param force write even if the attribute is special
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EINVAL Invalid parameters.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @return ::NC_ENOTVAR Variable not found.
|
|
* @return ::NC_EBADNAME Name contains illegal characters.
|
|
* @return ::NC_ENAMEINUSE Name already in use.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
|
|
size_t len, const void *data, nc_type mem_type, int force)
|
|
{
|
|
NC* nc;
|
|
NC_FILE_INFO_T *h5;
|
|
NC_VAR_INFO_T *var = NULL;
|
|
NCindex* attlist = NULL;
|
|
NC_ATT_INFO_T* att;
|
|
char norm_name[NC_MAX_NAME + 1];
|
|
nc_bool_t new_att = NC_FALSE;
|
|
int retval = NC_NOERR, range_error = 0;
|
|
size_t type_size;
|
|
int ret;
|
|
int ncid;
|
|
void* copy = NULL;
|
|
/* Save the old att data and length and old fillvalue in case we need to rollback on error */
|
|
struct Save {
|
|
size_t len;
|
|
void* data;
|
|
nc_type type; /* In case we change the type of the attribute */
|
|
} attsave = {0,NULL,-1};
|
|
struct Save fillsave = {0,NULL,-1};
|
|
|
|
h5 = grp->nc4_info;
|
|
nc = h5->controller;
|
|
assert(nc && grp && h5);
|
|
|
|
ncid = nc->ext_ncid | grp->hdr.id;
|
|
|
|
/* Find att, if it exists. (Must check varid first or nc_test will
|
|
* break.) This also does lazy att reads if needed. */
|
|
if ((ret = getattlist(grp, varid, &var, &attlist)))
|
|
return ret;
|
|
|
|
/* The length needs to be positive (cast needed for braindead
|
|
systems with signed size_t). */
|
|
if((unsigned long) len > X_INT_MAX)
|
|
return NC_EINVAL;
|
|
|
|
/* Check name before LOG statement. */
|
|
if (!name || strlen(name) > NC_MAX_NAME)
|
|
return NC_EBADNAME;
|
|
|
|
LOG((1, "%s: ncid 0x%x varid %d name %s file_type %d mem_type %d len %d",
|
|
__func__,ncid, varid, name, file_type, mem_type, len));
|
|
|
|
/* If len is not zero, then there must be some data. */
|
|
if (len && !data)
|
|
return NC_EINVAL;
|
|
|
|
/* If the file is read-only, return an error. */
|
|
if (h5->no_write)
|
|
return NC_EPERM;
|
|
|
|
/* Check and normalize the name. */
|
|
if ((retval = nc4_check_name(name, norm_name)))
|
|
return retval;
|
|
|
|
/* Check that a reserved att name is not being used improperly */
|
|
const NC_reservedatt* ra = NC_findreserved(name);
|
|
if(ra != NULL && !force) {
|
|
/* case 1: grp=root, varid==NC_GLOBAL, flags & READONLYFLAG */
|
|
if (nc->ext_ncid == ncid && varid == NC_GLOBAL && grp->parent == NULL
|
|
&& (ra->flags & READONLYFLAG))
|
|
return NC_ENAMEINUSE;
|
|
/* case 2: grp=NA, varid!=NC_GLOBAL, flags & HIDDENATTRFLAG */
|
|
if (varid != NC_GLOBAL && (ra->flags & (HIDDENATTRFLAG|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;
|
|
|
|
#ifdef SEPDATA
|
|
/* If this att has vlen or string data, release it before we lose the length value. */
|
|
if (att->stdata)
|
|
{
|
|
int i;
|
|
for (i = 0; i < att->len; i++)
|
|
if(att->stdata[i])
|
|
free(att->stdata[i]);
|
|
free(att->stdata);
|
|
att->stdata = NULL;
|
|
}
|
|
if (att->vldata)
|
|
{
|
|
int i;
|
|
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;
|
|
}
|
|
#else
|
|
if (att->data)
|
|
{
|
|
assert(attsave.data == NULL);
|
|
attsave.data = att->data;
|
|
attsave.len = att->len;
|
|
att->data = NULL;
|
|
}
|
|
#endif
|
|
|
|
/* 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)
|
|
{
|
|
#ifdef SEPDATA
|
|
if (var->type_info->nc_type_class == NC_VLEN)
|
|
{
|
|
if ((retval = nc_free_vlen(var->fill_value)))
|
|
BAIL(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);
|
|
#else
|
|
/* reclaim later */
|
|
fillsave.data = var->fill_value;
|
|
fillsave.type = var->type_info->hdr.id;
|
|
fillsave.len = 1;
|
|
#endif
|
|
var->fill_value = NULL;
|
|
}
|
|
|
|
/* Determine the size of the fill value in bytes. */
|
|
#ifdef SEPDATA
|
|
if (var->type_info->nc_type_class == NC_VLEN)
|
|
size = sizeof(hvl_t);
|
|
else if (var->type_info->nc_type_class == NC_STRING)
|
|
size = sizeof(char *);
|
|
else
|
|
size = type_size;
|
|
#endif
|
|
|
|
#ifdef SEPDATA
|
|
/* Allocate space for the fill value. */
|
|
if (!(var->fill_value = calloc(1, size)))
|
|
BAIL(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)))
|
|
BAIL(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)))
|
|
BAIL(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)))
|
|
BAIL(NC_ENOMEM);
|
|
strcpy(*(char **)var->fill_value, *(char **)data);
|
|
}
|
|
else
|
|
*(char **)var->fill_value = NULL;
|
|
}
|
|
else
|
|
memcpy(var->fill_value, data, type_size);
|
|
#else
|
|
{
|
|
nc_type var_type = var->type_info->hdr.id;
|
|
size_t var_type_size = var->type_info->size;
|
|
/* The old code used the var's type as opposed to the att's type; normally same,
|
|
but not required. Now we need to convert from the att's type to the var's type.
|
|
Note that we use mem_type rather than file_type because our data is in the form
|
|
of the memory data. When we later capture the memory data for the actual
|
|
attribute, we will use file_type as the target of the conversion. */
|
|
if(mem_type != var_type && mem_type < NC_STRING && var_type < NC_STRING) {
|
|
/* Need to convert from memory data into copy buffer */
|
|
if((copy = malloc(len*var_type_size))==NULL) BAIL(NC_ENOMEM);
|
|
if ((retval = nc4_convert_type(data, copy, mem_type, var_type,
|
|
len, &range_error, NULL,
|
|
(h5->cmode & NC_CLASSIC_MODEL),
|
|
NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
} else { /* no conversion */
|
|
/* Still need a copy of the input data */
|
|
copy = NULL;
|
|
if((retval = nc_copy_data_all(h5->controller->ext_ncid, mem_type, data, 1, ©)))
|
|
BAIL(retval);
|
|
}
|
|
var->fill_value = copy;
|
|
copy = NULL;
|
|
}
|
|
#endif
|
|
/* 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);
|
|
#ifdef SEPDATA
|
|
if (type_class == NC_VLEN)
|
|
{
|
|
const hvl_t *vldata1;
|
|
NC_TYPE_INFO_T *vltype;
|
|
size_t base_typelen;
|
|
|
|
/* Get the type object for the attribute's type */
|
|
if ((retval = nc4_find_type(h5, file_type, &vltype)))
|
|
BAIL(retval);
|
|
|
|
/* Retrieve the size of the base type */
|
|
if ((retval = nc4_get_typelen_mem(h5, vltype->u.v.base_nc_typeid, &base_typelen)))
|
|
BAIL(retval);
|
|
|
|
vldata1 = data;
|
|
if (!(att->vldata = (nc_vlen_t*)malloc(att->len * sizeof(hvl_t))))
|
|
BAIL(NC_ENOMEM);
|
|
for (i = 0; i < att->len; i++)
|
|
{
|
|
att->vldata[i].len = vldata1[i].len;
|
|
/* Warning, this only works for cases described for nc_free_vlen() */
|
|
if (!(att->vldata[i].p = malloc(base_typelen * att->vldata[i].len)))
|
|
BAIL(NC_ENOMEM);
|
|
memcpy(att->vldata[i].p, vldata1[i].p, base_typelen * att->vldata[i].len);
|
|
}
|
|
}
|
|
else if (type_class == NC_STRING)
|
|
{
|
|
LOG((4, "copying array of NC_STRING"));
|
|
if (!(att->stdata = malloc(sizeof(char *) * att->len))) {
|
|
BAIL(NC_ENOMEM);
|
|
}
|
|
|
|
/* If we are overwriting an existing attribute,
|
|
specifically an NC_CHAR, we need to clean up
|
|
the pre-existing att->data. */
|
|
if (!new_att && att->data) {
|
|
|
|
free(att->data);
|
|
att->data = NULL;
|
|
}
|
|
|
|
for (i = 0; i < att->len; i++)
|
|
{
|
|
if(NULL != ((char **)data)[i]) {
|
|
LOG((5, "copying string %d of size %d", i, strlen(((char **)data)[i]) + 1));
|
|
if (!(att->stdata[i] = strdup(((char **)data)[i])))
|
|
BAIL(NC_ENOMEM);
|
|
}
|
|
else
|
|
att->stdata[i] = ((char **)data)[i];
|
|
}
|
|
}
|
|
else
|
|
{
|
|
/* [Re]allocate memory for the attribute data */
|
|
if (!new_att)
|
|
free (att->data);
|
|
if (!(att->data = malloc(att->len * type_size)))
|
|
BAIL(NC_ENOMEM);
|
|
|
|
/* Just copy the data, for non-atomic types */
|
|
if (type_class == NC_OPAQUE || type_class == NC_COMPOUND || type_class == NC_ENUM)
|
|
memcpy(att->data, data, len * type_size);
|
|
else
|
|
{
|
|
/* Data types are like religions, in that one can convert. */
|
|
if ((retval = nc4_convert_type(data, att->data, mem_type, file_type,
|
|
len, &range_error, NULL,
|
|
(h5->cmode & NC_CLASSIC_MODEL),
|
|
NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
}
|
|
}
|
|
#else
|
|
{
|
|
/* Allocate top level of the copy */
|
|
if (!(copy = malloc(len * type_size)))
|
|
BAIL(NC_ENOMEM);
|
|
/* Special case conversion from memory to file type */
|
|
if(mem_type != file_type && mem_type < NC_STRING && file_type < NC_STRING) {
|
|
if ((retval = nc4_convert_type(data, copy, mem_type, file_type,
|
|
len, &range_error, NULL,
|
|
(h5->cmode & NC_CLASSIC_MODEL),
|
|
NC_NOQUANTIZE, 0)))
|
|
BAIL(retval);
|
|
} else if(mem_type == file_type) { /* General case: no conversion */
|
|
if((retval = nc_copy_data(h5->controller->ext_ncid,file_type,data,len,copy)))
|
|
BAIL(retval);
|
|
} else
|
|
BAIL(NC_EURL);
|
|
/* Store it */
|
|
att->data = copy; copy = NULL;
|
|
}
|
|
#endif
|
|
}
|
|
att->dirty = NC_TRUE;
|
|
att->created = NC_FALSE;
|
|
att->len = len;
|
|
|
|
/* Mark attributes on variable dirty, so they get written */
|
|
if(var)
|
|
var->attr_dirty = NC_TRUE;
|
|
/* Reclaim saved data */
|
|
if(attsave.data != NULL) {
|
|
assert(attsave.len > 0);
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,attsave.type,attsave.data,attsave.len);
|
|
attsave.len = 0; attsave.data = NULL;
|
|
}
|
|
if(fillsave.data != NULL) {
|
|
assert(fillsave.len > 0);
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,fillsave.type,fillsave.data,fillsave.len);
|
|
fillsave.len = 0; fillsave.data = NULL;
|
|
}
|
|
|
|
exit:
|
|
if(copy)
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,file_type,copy,len);
|
|
if(retval) {
|
|
/* Rollback */
|
|
if(attsave.data != NULL) {
|
|
assert(attsave.len > 0);
|
|
if(att->data)
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,attsave.type,att->data,att->len);
|
|
att->len = attsave.len; att->data = attsave.data;
|
|
}
|
|
if(fillsave.data != NULL) {
|
|
assert(fillsave.len > 0);
|
|
if(att->data)
|
|
(void)nc_reclaim_data_all(h5->controller->ext_ncid,fillsave.type,var->fill_value,1);
|
|
var->fill_value = fillsave.data;
|
|
}
|
|
}
|
|
/* If there was an error return it, otherwise return any potential
|
|
range error value. If none, return NC_NOERR as usual.*/
|
|
if (range_error)
|
|
return NC_ERANGE;
|
|
if (retval)
|
|
return retval;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Write an attribute to a netCDF-4/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);
|
|
}
|