/* Copyright 2003-2018, University Corporation for Atmospheric * Research. See COPYRIGHT file for copying and redistribution * conditions. */ /** * @file * @internal This file handles HDF5 attributes. * * @author Ed Hartnett */ #include "config.h" #include "hdf5internal.h" /** * @internal Get the attribute list for either a varid or NC_GLOBAL * * @param grp Group * @param varid Variable ID | NC_BLOGAL * @param varp Pointer that gets pointer to NC_VAR_INFO_T * instance. Ignored if NULL. * @param attlist Pointer that gets pointer to attribute list. * * @return NC_NOERR No error. * @author Dennis Heimbigner, Ed Hartnett */ static int getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp, NCindex **attlist) { NC_VAR_INFO_T* var; int retval; if (varid == NC_GLOBAL) { /* Do we need to read the atts? */ if (grp->atts_not_read) if ((retval = nc4_read_atts(grp, NULL))) return retval; if (varp) *varp = NULL; *attlist = grp->att; } else { if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid))) return NC_ENOTVAR; assert(var->hdr.id == varid); /* Do we need to read the atts? */ if (var->atts_not_read) if ((retval = nc4_read_atts(grp, var))) return retval; if (varp) *varp = var; *attlist = var->att; } return NC_NOERR; } /** * @internal I think all atts should be named the exact same thing, to * avoid confusion! * * @param ncid File and group ID. * @param varid Variable ID. * @param name Name of attribute. * @param newname New name for attribute. * * @return ::NC_NOERR No error. * @return ::NC_EBADID Bad ncid. * @return ::NC_EMAXNAME New name too long. * @return ::NC_EPERM File is read-only. * @return ::NC_ENAMEINUSE New name already in use. * @return ::NC_ENOTINDEFINE Classic model file not in define mode. * @return ::NC_EHDFERR HDF error. * @return ::NC_ENOMEM Out of memory. * @return ::NC_EINTERNAL Could not rebuild list. * @author Ed Hartnett */ int NC4_rename_att(int ncid, int varid, const char *name, const char *newname) { NC *nc; NC_GRP_INFO_T *grp; NC_FILE_INFO_T *h5; NC_VAR_INFO_T *var = NULL; NC_ATT_INFO_T *att; NCindex *list; char norm_newname[NC_MAX_NAME + 1], norm_name[NC_MAX_NAME + 1]; hid_t datasetid = 0; int retval = NC_NOERR; if (!name || !newname) return NC_EINVAL; LOG((2, "nc_rename_att: ncid 0x%x varid %d name %s newname %s", ncid, varid, name, newname)); /* If the new name is too long, that's an error. */ if (strlen(newname) > NC_MAX_NAME) return NC_EMAXNAME; /* Find info for this file, group, and h5 info. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; assert(h5 && grp && h5); /* If the file is read-only, return an error. */ if (h5->no_write) return NC_EPERM; /* Check and normalize the name. */ if ((retval = nc4_check_name(newname, norm_newname))) return retval; /* Get the list of attributes. */ if ((retval = getattlist(grp, varid, &var, &list))) return retval; /* Is new name in use? */ att = (NC_ATT_INFO_T*)ncindexlookup(list,norm_newname); if(att != NULL) return NC_ENAMEINUSE; /* Normalize name and find the attribute. */ if ((retval = nc4_normalize_name(name, norm_name))) return retval; att = (NC_ATT_INFO_T*)ncindexlookup(list,norm_name); if (!att) return NC_ENOTATT; /* If we're not in define mode, new name must be of equal or less size, if complying with strict NC3 rules. */ if (!(h5->flags & NC_INDEF) && strlen(norm_newname) > strlen(att->hdr.name) && (h5->cmode & NC_CLASSIC_MODEL)) return NC_ENOTINDEFINE; /* Delete the original attribute, if it exists in the HDF5 file. */ if (att->created) { if (varid == NC_GLOBAL) { if (H5Adelete(grp->hdf_grpid, att->hdr.name) < 0) return NC_EHDFERR; } else { if ((retval = nc4_open_var_grp2(grp, varid, &datasetid))) return retval; if (H5Adelete(datasetid, att->hdr.name) < 0) return NC_EHDFERR; } att->created = NC_FALSE; } /* Copy the new name into our metadata. */ if(att->hdr.name) free(att->hdr.name); if (!(att->hdr.name = strdup(norm_newname))) return NC_ENOMEM; att->hdr.hashkey = NC_hashmapkey(att->hdr.name,strlen(att->hdr.name)); /* Fix hash key */ att->dirty = NC_TRUE; /* Rehash the attribute list so that the new name is used */ if(!ncindexrebuild(list)) return NC_EINTERNAL; /* Mark attributes on variable dirty, so they get written */ if(var) var->attr_dirty = NC_TRUE; return retval; } /** * @internal Delete an att. Rub it out. Push the button on * it. Liquidate it. Bump it off. Take it for a one-way * ride. Terminate it. * * @param ncid File and group ID. * @param varid Variable ID. * @param name Name of attribute to delete. * * @return ::NC_NOERR No error. * @return ::NC_EBADID Bad ncid. * @return ::NC_ENOTATT Attribute not found. * @return ::NC_EINVAL No name provided. * @return ::NC_EPERM File is read only. * @return ::NC_ENOTINDEFINE Classic model not in define mode. * @return ::NC_EINTERNAL Could not rebuild list. * @author Ed Hartnett, Dennis Heimbigner */ int NC4_del_att(int ncid, int varid, const char *name) { NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; NC_FILE_INFO_T *h5; NC_ATT_INFO_T *att; NCindex* attlist = NULL; hid_t locid = 0; int i; size_t deletedid; int retval; /* Name must be provided. */ if (!name) return NC_EINVAL; LOG((2, "nc_del_att: ncid 0x%x varid %d name %s", ncid, varid, name)); /* Find info for this file, group, and h5 info. */ if ((retval = nc4_find_grp_h5(ncid, &grp, &h5))) return retval; assert(h5 && grp); /* If the file is read-only, return an error. */ if (h5->no_write) return NC_EPERM; /* If file is not in define mode, return error for classic model * files, otherwise switch to define mode. */ if (!(h5->flags & NC_INDEF)) { if (h5->cmode & NC_CLASSIC_MODEL) return NC_ENOTINDEFINE; if ((retval = NC4_redef(ncid))) return retval; } /* Get either the global or a variable attribute list. */ if ((retval = getattlist(grp, varid, &var, &attlist))) return retval; /* Determine the location id in the HDF5 file. */ if (varid == NC_GLOBAL) locid = grp->hdf_grpid; else if (var->created) locid = var->hdf_datasetid; /* Now find the attribute by name. */ if (!(att = (NC_ATT_INFO_T*)ncindexlookup(attlist, name))) return NC_ENOTATT; /* Delete it from the HDF5 file, if it's been created. */ if (att->created) { assert(locid); if (H5Adelete(locid, att->hdr.name) < 0) return NC_EATTMETA; } deletedid = att->hdr.id; /* Remove this attribute in this list */ if ((retval = nc4_att_list_del(attlist, att))) return retval; /* Renumber all attributes with higher indices. */ for (i = 0; i < ncindexsize(attlist); i++) { NC_ATT_INFO_T *a; if (!(a = (NC_ATT_INFO_T *)ncindexith(attlist, i))) continue; if (a->hdr.id > deletedid) a->hdr.id--; } /* Rebuild the index. */ if (!ncindexrebuild(attlist)) return NC_EINTERNAL; return NC_NOERR; } /** * @internal This will return the length of a netcdf atomic data type * in bytes. * * @param type A netcdf atomic type. * * @return Type size in bytes, or -1 if type not found. * @author Ed Hartnett */ static int nc4typelen(nc_type type) { switch(type){ case NC_BYTE: case NC_CHAR: case NC_UBYTE: return 1; case NC_USHORT: case NC_SHORT: return 2; case NC_FLOAT: case NC_INT: case NC_UINT: return 4; case NC_DOUBLE: case NC_INT64: case NC_UINT64: return 8; } return -1; } /** * @internal Write an attribute to a netCDF-4/HDF5 file, converting * data type if necessary. * * @param ncid File and group ID. * @param varid Variable ID. * @param name Name of attribute. * @param file_type Type of the attribute data in file. * @param len Number of elements in attribute array. * @param data Attribute data. * @param mem_type Type of data in memory. * * @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(int ncid, int varid, const char *name, nc_type file_type, size_t len, const void *data, nc_type mem_type) { NC *nc; NC_GRP_INFO_T *grp; NC_FILE_INFO_T *h5; NC_VAR_INFO_T *var = NULL; NCindex* attlist = NULL; NC_ATT_INFO_T* att; char norm_name[NC_MAX_NAME + 1]; nc_bool_t new_att = NC_FALSE; int retval = NC_NOERR, range_error = 0; size_t type_size; int i; int ret; /* Find info for this file, group, and h5 info. */ if ((ret = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return ret; assert(nc && grp && h5); /* Find att, if it exists. (Must check varid first or nc_test will * break.) */ 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) { /* case 1: grp=root, varid==NC_GLOBAL, flags & READONLYFLAG */ if (nc->ext_ncid == ncid && varid == NC_GLOBAL && grp->parent == NULL && (ra->flags & READONLYFLAG)) return NC_ENAMEINUSE; /* case 2: grp=NA, varid!=NC_GLOBAL, flags & DIMSCALEFLAG */ if (varid != NC_GLOBAL && (ra->flags & DIMSCALEFLAG)) return NC_ENAMEINUSE; } /* See if there is already an attribute with this name. */ att = (NC_ATT_INFO_T*)ncindexlookup(attlist,norm_name); 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 (!att) { /* If this is a new att, require define mode. */ if (!(h5->flags & NC_INDEF)) { if (h5->cmode & NC_CLASSIC_MODEL) return NC_EINDEFINE; 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_EINDEFINE; if ((retval = NC4_redef(ncid))) BAIL(retval); } } /* We must have two valid types to continue. */ if (file_type == NC_NAT || mem_type == NC_NAT) return NC_EBADTYPE; /* Get information about this type. */ if ((retval = nc4_get_typelen_mem(h5, file_type, &type_size))) return retval; /* No character conversions are allowed. */ if (file_type != mem_type && (file_type == NC_CHAR || mem_type == NC_CHAR || file_type == NC_STRING || mem_type == NC_STRING)) return NC_ECHAR; /* For classic mode file, only allow atts with classic types to be * created. */ if (h5->cmode & NC_CLASSIC_MODEL && file_type > NC_DOUBLE) return NC_ESTRICTNC3; /* Add to the end of the attribute list, if this att doesn't already exist. */ if (new_att) { LOG((3, "adding attribute %s to the list...", norm_name)); if ((ret = nc4_att_list_add(attlist, norm_name, &att))) BAIL (ret); } /* Now fill in the metadata. */ att->dirty = NC_TRUE; att->nc_typeid = file_type; /* If this att has vlen or string data, release it before we lose the length value. */ if (att->stdata) { for (i = 0; i < att->len; i++) if(att->stdata[i]) free(att->stdata[i]); free(att->stdata); att->stdata = NULL; } if (att->vldata) { for (i = 0; i < att->len; i++) nc_free_vlen(&att->vldata[i]); free(att->vldata); att->vldata = NULL; } att->len = len; /* If this is the _FillValue attribute, then we will also have to * copy the value to the fill_vlue pointer of the NC_VAR_INFO_T * struct for this var. (But ignore a global _FillValue * attribute). */ if (!strcmp(att->hdr.name, _FillValue) && varid != NC_GLOBAL) { int size; /* Fill value must be same type and have exactly one value */ if (att->nc_typeid != var->type_info->hdr.id) return NC_EBADTYPE; if (att->len != 1) return NC_EINVAL; /* If we already wrote to the dataset, then return an error. */ if (var->written_to) return NC_ELATEFILL; /* Get the length of the veriable data type. */ if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id, &type_size))) return retval; /* Already set a fill value? Now I'll have to free the old * one. Make up your damn mind, would you? */ if (var->fill_value) { if (var->type_info->nc_type_class == NC_VLEN) { if ((retval = nc_free_vlen(var->fill_value))) return retval; } else if (var->type_info->nc_type_class == NC_STRING) { if (*(char **)var->fill_value) free(*(char **)var->fill_value); } free(var->fill_value); } /* Determine the size of the fill value in bytes. */ if (var->type_info->nc_type_class == NC_VLEN) size = sizeof(hvl_t); else if (var->type_info->nc_type_class == NC_STRING) size = sizeof(char *); else size = type_size; /* Allocate space for the fill value. */ if (!(var->fill_value = calloc(1, size))) return NC_ENOMEM; /* Copy the fill_value. */ LOG((4, "Copying fill value into metadata for variable %s", var->hdr.name)); if (var->type_info->nc_type_class == NC_VLEN) { nc_vlen_t *in_vlen = (nc_vlen_t *)data, *fv_vlen = (nc_vlen_t *)(var->fill_value); fv_vlen->len = in_vlen->len; if (!(fv_vlen->p = malloc(size * in_vlen->len))) return NC_ENOMEM; memcpy(fv_vlen->p, in_vlen->p, in_vlen->len * size); } else if (var->type_info->nc_type_class == NC_STRING) { if (*(char **)data) { if (!(*(char **)(var->fill_value) = malloc(strlen(*(char **)data) + 1))) return NC_ENOMEM; strcpy(*(char **)var->fill_value, *(char **)data); } else *(char **)var->fill_value = NULL; } else memcpy(var->fill_value, data, type_size); /* Indicate that the fill value was changed, if the variable has already * been created in the file, so the dataset gets deleted and re-created. */ if (var->created) var->fill_val_changed = NC_TRUE; } /* Copy the attribute data, if there is any. VLENs and string * arrays have to be handled specially. */ if (att->len) { nc_type type_class; /* Class of attribute's type */ /* Get class for this type. */ if ((retval = nc4_get_typeclass(h5, file_type, &type_class))) return retval; assert(data); if (type_class == NC_VLEN) { const hvl_t *vldata1; NC_TYPE_INFO_T *type; size_t base_typelen; /* Get the type object for the attribute's type */ if ((retval = nc4_find_type(h5, file_type, &type))) BAIL(retval); /* Retrieve the size of the base type */ if ((retval = nc4_get_typelen_mem(h5, type->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; if (!(att->vldata[i].p = malloc(base_typelen * att->vldata[i].len))) BAIL(NC_ENOMEM); memcpy(att->vldata[i].p, vldata1[i].p, base_typelen * att->vldata[i].len); } } else if (type_class == NC_STRING) { LOG((4, "copying array of NC_STRING")); if (!(att->stdata = malloc(sizeof(char *) * att->len))) { BAIL(NC_ENOMEM); } /* If we are overwriting an existing attribute, specifically an NC_CHAR, we need to clean up the pre-existing att->data. */ if (!new_att && att->data) { free(att->data); att->data = NULL; } for (i = 0; i < att->len; i++) { if(NULL != ((char **)data)[i]) { LOG((5, "copying string %d of size %d", i, strlen(((char **)data)[i]) + 1)); if (!(att->stdata[i] = strdup(((char **)data)[i]))) BAIL(NC_ENOMEM); } else att->stdata[i] = ((char **)data)[i]; } } else { /* [Re]allocate memory for the attribute data */ if (!new_att) free (att->data); if (!(att->data = malloc(att->len * type_size))) BAIL(NC_ENOMEM); /* Just copy the data, for non-atomic types */ if (type_class == NC_OPAQUE || type_class == NC_COMPOUND || type_class == NC_ENUM) memcpy(att->data, data, len * type_size); else { /* Data types are like religions, in that one can convert. */ if ((retval = nc4_convert_type(data, att->data, mem_type, file_type, len, &range_error, NULL, (h5->cmode & NC_CLASSIC_MODEL)))) BAIL(retval); } } } att->dirty = NC_TRUE; att->created = NC_FALSE; /* Mark attributes on variable dirty, so they get written */ if(var) var->attr_dirty = NC_TRUE; exit: /* If there was an error return it, otherwise return any potential range error value. If none, return NC_NOERR as usual.*/ if (retval) return retval; if (range_error) return NC_ERANGE; return NC_NOERR; }