/* Copyright 2003-2018, University Corporation for Atmospheric * Research. See the COPYRIGHT file for copying and redistribution * conditions. */ /** * @file * @internal * Internal netcdf-4 functions. * * This file contains functions internal to the netcdf4 library. None of * the functions in this file are exposed in the exetnal API. These * functions all relate to the manipulation of netcdf-4's in-memory * buffer of metadata information, i.e. the linked list of NC * structs. * * @author Ed Hartnett, Dennis Heimbigner, Ward Fisher */ #include "config.h" #include "nc4internal.h" #include "nc.h" /* from libsrc */ #include "ncdispatch.h" /* from libdispatch */ #include "ncutf8.h" #include "H5DSpublic.h" /* These are the default chunk cache sizes for HDF5 files created or * opened with netCDF-4. */ extern size_t nc4_chunk_cache_size; extern size_t nc4_chunk_cache_nelems; extern float nc4_chunk_cache_preemption; #ifdef LOGGING /* This is the severity level of messages which will be logged. Use severity 0 for errors, 1 for important log messages, 2 for less important, etc. */ int nc_log_level = NC_TURN_OFF_LOGGING; #endif /* LOGGING */ /** * @internal Check and normalize and name. * * @param name Name to normalize. * @param norm_name The normalized name. * * @return ::NC_NOERR No error. * @return ::NC_EMAXNAME Name too long. * @return ::NC_EINVAL NULL given for name. * @author Dennis Heimbigner */ int nc4_check_name(const char *name, char *norm_name) { char *temp; int retval; /* Check for NULL. */ if (!name) return NC_EINVAL; assert(norm_name); /* Check for NULL. */ if (!name) return NC_EINVAL; /* Check the length. */ if (strlen(name) > NC_MAX_NAME) return NC_EMAXNAME; /* Make sure this is a valid netcdf name. This should be done * before the name is normalized, because it gives better error * codes for bad utf8 strings. */ if ((retval = NC_check_name(name))) return retval; /* Normalize the name. */ retval = nc_utf8_normalize((const unsigned char *)name,(unsigned char**)&temp); if(retval != NC_NOERR) return retval; if(strlen(temp) > NC_MAX_NAME) { free(temp); return NC_EMAXNAME; } strcpy(norm_name, temp); free(temp); return NC_NOERR; } /** * @internal Given an NC pointer, add the necessary stuff for a * netcdf-4 file. * * @param nc Pointer to file's NC struct. * @param path The file name of the new file. * @param mode The mode flag. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_nc4f_list_add(NC *nc, const char *path, int mode) { NC_HDF5_FILE_INFO_T *h5; assert(nc && !NC4_DATA(nc) && path); /* We need to malloc and initialize the substructure NC_HDF_FILE_INFO_T. */ if (!(h5 = calloc(1, sizeof(NC_HDF5_FILE_INFO_T)))) return NC_ENOMEM; NC4_DATA_SET(nc,h5); h5->controller = nc; /* Hang on to cmode, and note that we're in define mode. */ h5->cmode = mode | NC_INDEF; /* The next_typeid needs to be set beyond the end of our atomic * types. */ h5->next_typeid = NC_FIRSTUSERTYPEID; h5->alldims = nclistnew(); h5->alltypes = nclistnew(); h5->allgroups = nclistnew(); /* There's always at least one open group - the root * group. Allocate space for one group's worth of information. Set * its hdf id, name, and a pointer to it's file structure. */ return nc4_build_root_grp(h5); } /** * @internal Given an ncid, find the relevant group and return a * pointer to it, return an error of this is not a netcdf-4 file (or * if strict nc3 is turned on for this file.) * * @param ncid File and group ID. * @param grp Pointer that gets pointer to group info struct. * * @return ::NC_NOERR No error. * @return ::NC_ENOTNC4 Not a netCDF-4 file. * @return ::NC_ESTRICTNC3 Not allowed for classic model. * @author Ed Hartnett */ int nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp) { NC_HDF5_FILE_INFO_T* h5; NC *f = nc4_find_nc_file(ncid,&h5); if(f == NULL) return NC_EBADID; /* No netcdf-3 files allowed! */ if (!h5) return NC_ENOTNC4; assert(h5->root_grp); /* This function demands netcdf-4 files without strict nc3 * rules.*/ if (h5->cmode & NC_CLASSIC_MODEL) return NC_ESTRICTNC3; /* If we can't find it, the grp id part of ncid is bad. */ if (!(*grp = nc4_rec_find_grp(h5, (ncid & GRP_ID_MASK)))) return NC_EBADID; return NC_NOERR; } /** * @internal Given an ncid, find the relevant group and return a * pointer to it, also set a pointer to the nc4_info struct of the * related file. For netcdf-3 files, *h5 will be set to NULL. * * @param ncid File and group ID. * @param grpp Pointer that gets pointer to group info struct. * @param h5p Pointer to HDF5 file struct. * * @return ::NC_NOERR No error. * @return ::NC_EBADID Bad ncid. * @author Ed Hartnett */ int nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grpp, NC_HDF5_FILE_INFO_T **h5p) { NC_HDF5_FILE_INFO_T *h5; NC_GRP_INFO_T *grp; NC *f = nc4_find_nc_file(ncid,&h5); if(f == NULL) return NC_EBADID; if (h5) { assert(h5->root_grp); /* If we can't find it, the grp id part of ncid is bad. */ if (!(grp = nc4_rec_find_grp(h5, (ncid & GRP_ID_MASK)))) return NC_EBADID; h5 = (grp)->nc4_info; assert(h5); } else { h5 = NULL; grp = NULL; } if(h5p) *h5p = h5; if(grpp) *grpp = grp; return NC_NOERR; } /** * @internal Find info for this file and group, and set pointer to each. * * @param ncid File and group ID. * @param nc Pointer that gets a pointer to the file's NC struct. * @param grpp Pointer that gets a pointer to the group struct. * @param h5p Pointer that gets HDF5 file struct. * * @return ::NC_NOERR No error. * @return ::NC_EBADID Bad ncid. * @author Ed Hartnett */ int nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grpp, NC_HDF5_FILE_INFO_T **h5p) { NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T* h5; NC *f = nc4_find_nc_file(ncid,&h5); if(f == NULL) return NC_EBADID; if(nc) *nc = f; if (h5) { assert(h5->root_grp); /* If we can't find it, the grp id part of ncid is bad. */ if (!(grp = nc4_rec_find_grp(h5, (ncid & GRP_ID_MASK)))) return NC_EBADID; h5 = (grp)->nc4_info; assert(h5); } else { h5 = NULL; grp = NULL; } if(h5p) *h5p = h5; if(grpp) *grpp = grp; return NC_NOERR; } /** * @internal Use NC_HDF5_FILE_INFO_T->allgroups to locate a group id. * * @param h5 Pointer to file info * @param target_nc_grpid Group ID to be found. * * @return Pointer to group info struct, or NULL if not found. * @author Ed Hartnett */ NC_GRP_INFO_T * nc4_rec_find_grp(NC_HDF5_FILE_INFO_T *h5, int target_nc_grpid) { NC_GRP_INFO_T *g; assert(h5); /* Is this the group we are searching for? */ g = nclistget(h5->allgroups,target_nc_grpid); return g; } /** * @internal Given an ncid and varid, get pointers to the group and var * metadata. * * @param nc Pointer to file's NC struct. * @param ncid File ID. * @param varid Variable ID. * @param grp Pointer that gets pointer to group info. * @param var Pointer that gets pointer to var info. * * @return ::NC_NOERR No error. */ int nc4_find_g_var_nc(NC *nc, int ncid, int varid, NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var) { NC_HDF5_FILE_INFO_T* h5 = NC4_DATA(nc); /* Find the group info. */ assert(grp && var && h5 && h5->root_grp); *grp = nc4_rec_find_grp(h5, (ncid & GRP_ID_MASK)); /* It is possible for *grp to be NULL. If it is, return an error. */ if(*grp == NULL) return NC_EBADID; /* Find the var info. */ (*var) = (NC_VAR_INFO_T*)ncindexith((*grp)->vars,varid); if((*var) == NULL) return NC_ENOTVAR; return NC_NOERR; } /** * @internal Find a dim in a grp (or its parents). * * @param grp Pointer to group info struct. * @param dimid Dimension ID to find. * @param dim Pointer that gets pointer to dim info if found. * @param dim_grp Pointer that gets pointer to group info of group that contains dimension. * * @return ::NC_NOERR No error. * @return ::NC_EBADDIM Dimension not found. * @author Ed Hartnett */ int nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim, NC_GRP_INFO_T **dim_grp) { NC_GRP_INFO_T *g; int found = 0; NC_HDF5_FILE_INFO_T* h5 = grp->nc4_info; assert(h5 && grp && dim); /* Find the dim info. */ (*dim) = nclistget(h5->alldims,dimid); if((*dim) == NULL) return NC_EBADDIM; /* Redundant: Verify that this dim is in fact in the group or its parent */ for (found=0, g = grp; g ; g = g->parent) { if(g == (*dim)->container) {found = 1; break;} } /* If we didn't find it, return an error. */ assert(found); /* Give the caller the group the dimension is in. */ if (dim_grp) *dim_grp = (*dim)->container; return NC_NOERR; } /** * @internal Find a var (by name) in a grp. * * @param grp Pointer to group info. * @param name Name of var to find. * @param var Pointer that gets pointer to var info struct, if found. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_find_var(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var) { assert(grp && var && name); /* Find the var info. */ *var = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name); return NC_NOERR; } /** * @internal Locate netCDF type by name. * * @param start_grp Pointer to starting group info. * @param name Name of type to find. * * @return Pointer to type info, or NULL if not found. * @author Ed Hartnett */ NC_TYPE_INFO_T * nc4_rec_find_named_type(NC_GRP_INFO_T *start_grp, char *name) { NC_GRP_INFO_T *g; NC_TYPE_INFO_T *type, *res; int i; assert(start_grp); /* Does this group have the type we are searching for? */ type = (NC_TYPE_INFO_T*)ncindexlookup(start_grp->type,name); if(type != NULL) return type; /* Search subgroups. */ for(i=0;ichildren);i++) { g = (NC_GRP_INFO_T*)ncindexith(start_grp->children,i); if(g == NULL) continue; if ((res = nc4_rec_find_named_type(g, name))) return res; } /* Can't find it. Oh, woe is me! */ return NULL; } /** * @internal Recursively hunt for a netCDF type id. * Note using h5->alltypes, we no longer do recursion * * @param h5 the root file * @param target_nc_typeid NetCDF type ID to find. * * @return Pointer to type info, or NULL if not found. * @author Ed Hartnett */ NC_TYPE_INFO_T * nc4_rec_find_nc_type(NC_HDF5_FILE_INFO_T *h5, nc_type target_nc_typeid) { assert(h5); return nclistget(h5->alltypes, target_nc_typeid); } /** * @internal Use a netCDF typeid to find a type in a type_list. * * @param h5 Pointer to HDF5 file info struct. * @param typeid The netCDF type ID. * @param type Pointer to pointer to the list of type info structs. * * @return ::NC_NOERR No error. * @return ::NC_EINVAL Invalid input. * @author Ed Hartnett */ int nc4_find_type(const NC_HDF5_FILE_INFO_T *h5, nc_type typeid, NC_TYPE_INFO_T **type) { if (typeid < 0 || !type) return NC_EINVAL; *type = NULL; /* Atomic types don't have associated NC_TYPE_INFO_T struct, just * return NOERR. */ if (typeid <= NC_STRING) return NC_NOERR; /* Find the type. */ *type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes,typeid); if((*type) == NULL) return NC_EBADTYPID; return NC_NOERR; } /** * @internal Given a group, find an att. If name is provided, use that, * otherwise use the attnum. * * @param grp Pointer to group info struct. * @param varid Variable ID. * @param name Name to of attribute. * @param attnum Number of attribute. * @param att Pointer to pointer that gets attribute info struct. * * @return ::NC_NOERR No error. * @return ::NC_ENOTVAR Variable not found. * @return ::NC_ENOTATT Attribute not found. * @author Ed Hartnett */ int nc4_find_grp_att(NC_GRP_INFO_T *grp, int varid, const char *name, int attnum, NC_ATT_INFO_T **att) { NC_VAR_INFO_T *var; NCindex* attlist = NULL; assert(grp && grp->hdr.name); LOG((4, "nc4_find_grp_att: grp->name %s varid %d name %s attnum %d", grp->hdr.name, varid, name, attnum)); /* Get either the global or a variable attribute list. */ if (varid == NC_GLOBAL) attlist = grp->att; else { var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid); if (!var) return NC_ENOTVAR; attlist = var->att; assert(var->hdr.id == varid); } /* Now find the attribute by name or number. If a name is provided, * ignore the attnum. */ if(attlist) { NC_ATT_INFO_T* a; if(name != NULL) a = (NC_ATT_INFO_T*)ncindexlookup(attlist,name); else a = (NC_ATT_INFO_T*)ncindexith(attlist,attnum); if(a != NULL) { *att = a; return NC_NOERR; } } /* If we get here, we couldn't find the attribute. */ return NC_ENOTATT; } /** * @internal Given an ncid, varid, and name or attnum, find and return * pointer to NC_ATT_INFO_T metadata. * * @param ncid File and group ID. * @param varid Variable ID. * @param name Name to of attribute. * @param attnum Number of attribute. * @param att Pointer to pointer that gets attribute info struct. * * @return ::NC_NOERR No error. * @return ::NC_ENOTVAR Variable not found. * @return ::NC_ENOTATT Attribute not found. * @author Ed Hartnett */ int nc4_find_nc_att(int ncid, int varid, const char *name, int attnum, NC_ATT_INFO_T **att) { NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; int retval; LOG((4, "nc4_find_nc_att: ncid 0x%x varid %d name %s attnum %d", ncid, varid, name, attnum)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_grp_h5(ncid, &grp, &h5))) return retval; assert(grp && h5); return nc4_find_grp_att(grp,varid,name,attnum,att); } /** * @internal Given an id, walk the list and find the appropriate NC. * * @param ext_ncid File/group ID to find. * @param h5p Pointer to pointer that gets the HDF5 file info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett, Dennis Heimbigner */ NC* nc4_find_nc_file(int ext_ncid, NC_HDF5_FILE_INFO_T** h5p) { NC* nc; int stat; stat = NC_check_id(ext_ncid,&nc); if(stat != NC_NOERR) nc = NULL; if(nc) if(h5p) *h5p = (NC_HDF5_FILE_INFO_T*)nc->dispatchdata; return nc; } /** * @internal Add NC_OBJ to appropriate indices. * * @param index NCindex into which to insert obj * @param obj Pointer to object to add. * * @author Ed Hartnett, Dennis Heimbigner */ static void obj_list_add(NCindex* index, NC_OBJ* obj) { /* Insert object into the index */ // ncindexset(index,obj->id,obj); ncindexadd(index,obj); } /** * @internal Add NC_OBJ to allXXX lists in a file * * @param file Pointer to the containing file * @param obj Pointer to object to add. * * @author Dennis Heimbigner */ static void obj_track(NC_HDF5_FILE_INFO_T* file, NC_OBJ* obj) { NClist* list = NULL; /* record the object in the file */ switch (obj->sort) { case NCDIM: list = file->alldims; break; case NCTYP: list = file->alltypes; break; case NCGRP: list = file->allgroups; break; default: assert(NC_FALSE); } /* Insert at the appropriate point in the list */ nclistset(list,obj->id,obj); } /** * @internal Remove object from a list * * @param index NCindex from which to delete * @param obj Pointer to object to delete. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ static void obj_list_del(NCindex* index, NC_OBJ *obj) { ncindexidel(index,obj->id); } /** * @internal Create a new variable and insert int relevant lists * * @param grp the containing group * @param name the name for the new variable * @param ndims the rank of the new variable * @param var Pointer in which to return a pointer to the new var. * * @param var Pointer to pointer that gets variable info struct. * * @return ::NC_NOERR No error. * @return ::NC_ENOMEM Out of memory. * @author Ed Hartnett */ int nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims, NC_VAR_INFO_T **var) { NC_VAR_INFO_T *new_var = NULL; int retval = NC_NOERR; /* Allocate storage for new variable. */ if (!(new_var = calloc(1, sizeof(NC_VAR_INFO_T)))) BAIL(NC_ENOMEM); new_var->hdr.sort = NCVAR; /* These are the HDF5-1.8.4 defaults. */ new_var->chunk_cache_size = nc4_chunk_cache_size; new_var->chunk_cache_nelems = nc4_chunk_cache_nelems; new_var->chunk_cache_preemption = nc4_chunk_cache_preemption; /* Now fill in the values in the var info structure. */ new_var->hdr.id = ncindexsize(grp->vars); if (!(new_var->hdr.name = strdup(name))) BAIL(NC_ENOMEM); new_var->hdr.hashkey = NC_hashmapkey(new_var->hdr.name,strlen(new_var->hdr.name)); new_var->ndims = ndims; /* Allocate space for dimension information. */ if (ndims) { if (!(new_var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *)))) BAIL(NC_ENOMEM); if (!(new_var->dimids = calloc(ndims, sizeof(int)))) BAIL(NC_ENOMEM); /* Initialize dimids to illegal values (-1). See the comment in nc4hdf.c#nc4_rec_match_dimscales. */ memset(new_var->dimids, -1, ndims*sizeof(int)); } new_var->att = ncindexnew(0); /* Officially track it */ ncindexadd(grp->vars,(NC_OBJ*)new_var); /* Set the var pointer, if one was given */ if (var) *var = new_var; exit: if(retval != NC_NOERR) { nc4_var_list_del(grp,new_var); } return retval; } /** * @internal Add to the beginning of a dim list. * * @param grp container for the dim * @param name for the dim * @param len for the dim * @param assignedid override dimid if >= 0 * @param dim Pointer to pointer that gets the new dim info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_dim_list_add(NC_GRP_INFO_T* grp, const char* name, size_t len, int assignedid, NC_DIM_INFO_T **dim) { NC_DIM_INFO_T *new_dim = NULL; NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info; int retval = NC_NOERR; if (!(new_dim = calloc(1, sizeof(NC_DIM_INFO_T)))) BAIL(NC_ENOMEM); new_dim->hdr.sort = NCDIM; if(assignedid >= 0) new_dim->hdr.id = assignedid; else new_dim->hdr.id = h5->next_dimid++; /* Initialize the metadata for this dimension. */ if (!(new_dim->hdr.name = strdup(name))) BAIL(NC_ENOMEM); /* Create a hash of the name. */ new_dim->hdr.hashkey = NC_hashmapkey(new_dim->hdr.name,strlen(new_dim->hdr.name)); new_dim->len = len; if (len == NC_UNLIMITED) new_dim->unlimited = NC_TRUE; new_dim->container = grp; /* Add object to lists */ obj_list_add(grp->dim, (NC_OBJ*)new_dim); obj_track(h5,(NC_OBJ*)new_dim); /* Set the dim pointer, if one was given */ if (dim) *dim = new_dim; exit: if(retval != NC_NOERR) nc4_dim_free(new_dim); /* would not be in list yet*/ return retval; } /** * @internal Add to the end of an att list. * * @param list NCindex of att info structs. * @param name name of the new attribute * @param att Pointer to pointer that gets the new att info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_att_list_add(NCindex* list, const char* name, NC_ATT_INFO_T **att) { int retval = NC_NOERR; NC_ATT_INFO_T *new_att = NULL; LOG((3, "%s: name %s ", __func__, name)); if (!(new_att = calloc(1, sizeof(NC_ATT_INFO_T)))) return NC_ENOMEM; new_att->hdr.sort = NCATT; /* Fill in the information we know. */ new_att->hdr.id = ncindexsize(list); if (!(new_att->hdr.name = strdup(name))) BAIL(NC_ENOMEM); /* Create a hash of the name. */ new_att->hdr.hashkey = NC_hashmapkey(name, strlen(name)); /* Add object to list as specified by its number */ obj_list_add(list,(NC_OBJ*)new_att); /* Set the attribute pointer, if one was given */ if (att) *att = new_att; exit: if(retval) { nc4_att_list_del(list,new_att); } return retval; } /** * @internal Add to the end of a group list. Can't use 0 as a * new_nc_grpid - it's reserved for the root group. * * @param parent The parent group. * @param name Name of the group. * @param grp Pointer to pointer that gets new group info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_grp_list_add(NC_GRP_INFO_T * parent, char *name, NC_GRP_INFO_T **grp) { NC_GRP_INFO_T *new_grp; NC_HDF5_FILE_INFO_T* h5; NC* nc; h5 = parent->nc4_info; nc = h5->controller; LOG((3, "%s: name %s ", __func__, name)); /* Get the memory to store this groups info. */ if (!(new_grp = calloc(1, sizeof(NC_GRP_INFO_T)))) return NC_ENOMEM; new_grp->hdr.sort = NCGRP; /* Fill in this group's information. */ new_grp->hdr.id = h5->next_nc_grpid++; new_grp->parent = parent; if (!(new_grp->hdr.name = strdup(name))) { free(new_grp); return NC_ENOMEM; } new_grp->hdr.hashkey = NC_hashmapkey(new_grp->hdr.name,strlen(new_grp->hdr.name)); new_grp->nc4_info = NC4_DATA(nc); new_grp->children = ncindexnew(0); new_grp->dim = ncindexnew(0); new_grp->att = ncindexnew(0); new_grp->type = ncindexnew(0); new_grp->vars = ncindexnew(0); /* Add object to lists */ obj_list_add(parent->children, (NC_OBJ*)new_grp); obj_track(h5,(NC_OBJ*)new_grp); /* Set the group pointer, if one was given */ if (grp) *grp = new_grp; return NC_NOERR; } /** * @internal Build the root group with id 0. * * @param h5 root file * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_build_root_grp(NC_HDF5_FILE_INFO_T* h5) { NC_GRP_INFO_T *new_grp; NC* nc; assert(h5); nc = h5->controller; LOG((3, "%s: name %s ", __func__, NC_GROUP_NAME)); /* Get the memory to store this groups info. */ if (!(new_grp = calloc(1, sizeof(NC_GRP_INFO_T)))) return NC_ENOMEM; new_grp->hdr.sort = NCGRP; /* Fill in this group's information. */ new_grp->hdr.id = h5->next_nc_grpid++; /* should be 0 */ assert(new_grp->hdr.id == 0); new_grp->parent = NULL; if (!(new_grp->hdr.name = strdup(NC_GROUP_NAME))) { free(new_grp); return NC_ENOMEM; } new_grp->hdr.hashkey = NC_hashmapkey(new_grp->hdr.name,strlen(new_grp->hdr.name)); new_grp->nc4_info = NC4_DATA(nc); new_grp->children = ncindexnew(0); new_grp->dim = ncindexnew(0); new_grp->att = ncindexnew(0); new_grp->type = ncindexnew(0); new_grp->vars = ncindexnew(0); /* Add object to lists */ obj_track(h5,(NC_OBJ*)new_grp); /* Set the group pointer, if one was given */ h5->root_grp = new_grp; return NC_NOERR; } /** * @internal Names for groups, variables, and types must not be the * same. This function checks that a proposed name is not already in * use. Normalzation of UTF8 strings should happen before this * function is called. * * @param grp Pointer to group info struct. * @param name Name to check. * * @return ::NC_NOERR No error. * @return ::NC_ENAMEINUSE Name is in use. * @author Ed Hartnett */ int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *name) { NC_TYPE_INFO_T *type; NC_GRP_INFO_T *g; NC_VAR_INFO_T *var; /* Any types of this name? */ type = (NC_TYPE_INFO_T*)ncindexlookup(grp->type,name); if(type != NULL) return NC_ENAMEINUSE; /* Any child groups of this name? */ g = (NC_GRP_INFO_T*)ncindexlookup(grp->children,name); if(g != NULL) return NC_ENAMEINUSE; /* Any variables of this name? */ var = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name); if(var != NULL) return NC_ENAMEINUSE; return NC_NOERR; } /** * @internal Create a type, but do not add to various lists nor increment its ref count * * @param grp Pointer to group info struct. * @param size Size of type in bytes. * @param name Name of type. * @param assignedid if >= 0 then override the default type id * @param type Pointer that gets pointer to new type info * struct. Ignored if NULL. * * @return ::NC_NOERR No error. * @return ::NC_ENOMEM Out of memory. * @author Ed Hartnett, Ward Fisher */ int nc4_type_new(NC_GRP_INFO_T *grp, size_t size, const char *name, int assignedid, NC_TYPE_INFO_T **type) { NC_TYPE_INFO_T *new_type = NULL; /* Allocate memory for the type */ if (!(new_type = calloc(1, sizeof(NC_TYPE_INFO_T)))) return NC_ENOMEM; new_type->hdr.sort = NCTYP; /* Remember info about this type. */ new_type->hdr.id = assignedid; new_type->size = size; if (!(new_type->hdr.name = strdup(name))) { free(new_type); return NC_ENOMEM; } new_type->hdr.hashkey = NC_hashmapkey(name,strlen(name)); /* Return a pointer to the new type, if requested */ if (type) *type = new_type; return NC_NOERR; } /** * @internal Add to the end of a type list. * * @param grp Pointer to group info struct. * @param size Size of type in bytes. * @param name Name of type. * @param type Pointer that gets pointer to new type info * struct. Ignored if NULL. * * @return ::NC_NOERR No error. * @return ::NC_ENOMEM Out of memory. * @author Ed Hartnett */ int nc4_type_list_add(NC_GRP_INFO_T *grp, size_t size, const char *name, NC_TYPE_INFO_T **type) { int retval = NC_NOERR; NC_TYPE_INFO_T *new_type = NULL; retval = nc4_type_new(grp,size,name, grp->nc4_info->next_typeid,&new_type); if(retval) return retval; grp->nc4_info->next_typeid++; /* Increment the ref. count on the type */ new_type->rc++; /* Add object to lists */ obj_list_add(grp->type, (NC_OBJ*)new_type); obj_track(grp->nc4_info,(NC_OBJ*)new_type); /* Return a pointer to the new type, if requested */ if (type) *type = new_type; return NC_NOERR; } /** * @internal Add to the end of a compound field list. * * @param parent parent type * @param name Name of the field. * @param offset Offset in bytes. * @param field_hdf_typeid The HDF5 type ID of the field. * @param native_typeid The HDF5 native type ID of the field. * @param xtype The netCDF type of the field. * @param ndims The number of dimensions of the field. * @param dim_sizesp An array of dim sizes for the field. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_field_list_add(NC_TYPE_INFO_T *parent, const char *name, size_t offset, hid_t field_hdf_typeid, hid_t native_typeid, nc_type xtype, int ndims, const int *dim_sizesp) { NC_FIELD_INFO_T *field; /* Name has already been checked and UTF8 normalized. */ if (!name) return NC_EINVAL; /* Allocate storage for this field information. */ if (!(field = calloc(1, sizeof(NC_FIELD_INFO_T)))) return NC_ENOMEM; field->hdr.sort = NCFLD; /* Store the information about this field. */ if (!(field->hdr.name = strdup(name))) { free(field); return NC_ENOMEM; } field->hdr.hashkey = NC_hashmapkey(field->hdr.name,strlen(field->hdr.name)); field->hdf_typeid = field_hdf_typeid; field->native_hdf_typeid = native_typeid; field->nc_typeid = xtype; field->offset = offset; field->ndims = ndims; if (ndims) { int i; if (!(field->dim_size = malloc(ndims * sizeof(int)))) { free(field->hdr.name); free(field); return NC_ENOMEM; } for (i = 0; i < ndims; i++) field->dim_size[i] = dim_sizesp[i]; } /* Add object to lists */ field->hdr.id = nclistlength(parent->u.c.field); nclistpush(parent->u.c.field,field); return NC_NOERR; } /** * @internal Add a member to an enum type. * * @param parent Containing NC_TYPE_INFO_T object * @param size Size in bytes of new member. * @param name Name of the member. * @param value Value to associate with member. * * @return ::NC_NOERR No error. * @return ::NC_ENOMEM Out of memory. * @author Ed Hartnett */ int nc4_enum_member_add(NC_TYPE_INFO_T *parent, size_t size, const char *name, const void *value) { NC_ENUM_MEMBER_INFO_T *member; /* Name has already been checked. */ assert(name && size > 0 && value); LOG((4, "%s: size %d name %s", __func__, size, name)); /* Allocate storage for this field information. */ if (!(member = calloc(1, sizeof(NC_ENUM_MEMBER_INFO_T)))) return NC_ENOMEM; if (!(member->value = malloc(size))) { free(member); return NC_ENOMEM; } if (!(member->name = strdup(name))) { free(member->value); free(member); return NC_ENOMEM; } /* Store the value for this member. */ memcpy(member->value, value, size); /* Add object to list */ nclistpush(parent->u.e.enum_member,member); return NC_NOERR; } /** * @internal Free up a field * * @param field Pointer to field info of field to delete. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ static void field_free(NC_FIELD_INFO_T *field) { /* Free some stuff. */ if (field->hdr.name) free(field->hdr.name); if (field->dim_size) free(field->dim_size); /* Nc_Free the memory. */ free(field); } /** * @internal Free allocated space for type information. * * @param type Pointer to type info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_type_free(NC_TYPE_INFO_T *type) { int i; /* Decrement the ref. count on the type */ assert(type->rc); type->rc--; /* Release the type, if the ref. count drops to zero */ if (0 == type->rc) { /* Close any open user-defined HDF5 typeids. */ if (type->hdf_typeid && H5Tclose(type->hdf_typeid) < 0) return NC_EHDFERR; if (type->native_hdf_typeid && H5Tclose(type->native_hdf_typeid) < 0) return NC_EHDFERR; /* Free the name. */ if (type->hdr.name) free(type->hdr.name); /* Class-specific cleanup */ switch (type->nc_type_class) { case NC_COMPOUND: { NC_FIELD_INFO_T *field; /* Delete all the fields in this type (there will be some if its a * compound). */ for(i=0;iu.c.field);i++) { field = nclistget(type->u.c.field,i); field_free(field); } nclistfree(type->u.c.field); type->u.c.field = NULL; /* belt and suspenders */ } break; case NC_ENUM: { NC_ENUM_MEMBER_INFO_T *enum_member; /* Delete all the enum_members, if any. */ for(i=0;iu.e.enum_member);i++) { enum_member = nclistget(type->u.e.enum_member,i); free(enum_member->value); free(enum_member->name); free(enum_member); } nclistfree(type->u.e.enum_member); type->u.e.enum_member = NULL; /* belt and suspenders */ if (H5Tclose(type->u.e.base_hdf_typeid) < 0) return NC_EHDFERR; } break; case NC_VLEN: if (H5Tclose(type->u.v.base_hdf_typeid) < 0) return NC_EHDFERR; default: break; } /* Release the memory. */ free(type); } return NC_NOERR; } /** * @internal Delete a var, and free the memory. * * @param var Pointer to the var info struct of var to delete. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_var_free(NC_VAR_INFO_T *var) { NC_ATT_INFO_T *att; int ret = NC_NOERR; int i; if(var == NULL) return NC_NOERR; /* First delete all the attributes attached to this var. */ for(i=0;iatt);i++) { att = (NC_ATT_INFO_T*)ncindexith(var->att,i); if(att == NULL) continue; /* might be a gap */ if ((ret = nc4_att_free(att))) return ret; } ncindexfree(var->att); var->att = NULL; /* Free some things that may be allocated. */ if (var->chunksizes) {free(var->chunksizes);var->chunksizes = NULL;} if (var->hdf5_name) {free(var->hdf5_name); var->hdf5_name = NULL;} if (var->hdr.name) {free(var->hdr.name); var->hdr.name = NULL;} if (var->dimids) {free(var->dimids); var->dimids = NULL;} if (var->dim) {free(var->dim); var->dim = NULL;} /* Delete any fill value allocation. This must be done before the * type_info is freed. */ if (var->fill_value) { if (var->hdf_datasetid) { if (var->type_info) { if (var->type_info->nc_type_class == NC_VLEN) nc_free_vlen((nc_vlen_t *)var->fill_value); else if (var->type_info->nc_type_class == NC_STRING && *(char **)var->fill_value) free(*(char **)var->fill_value); } } free(var->fill_value); var->fill_value = NULL; } /* Release type information */ if (var->type_info) { int retval; if ((retval = nc4_type_free(var->type_info))) return retval; var->type_info = NULL; } /* Delete any HDF5 dimscale objid information. */ if (var->dimscale_hdf5_objids) free(var->dimscale_hdf5_objids); /* Delete information about the attachment status of dimscales. */ if (var->dimscale_attached) free(var->dimscale_attached); /* Release parameter information. */ if (var->params) free(var->params); /* Delete the var. */ free(var); return NC_NOERR; } /** * @internal Delete a var, and free the memory. * * @param grp the containing group * @param var Pointer to the var info struct of var to delete. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_var_list_del(NC_GRP_INFO_T* grp, NC_VAR_INFO_T *var) { int i; if(var == NULL) return NC_NOERR; /* Remove from lists */ if(grp) { i = ncindexfind(grp->vars,(NC_OBJ*)var); if(i >= 0) ncindexidel(grp->vars,i); } return nc4_var_free(var); } /** * @internal Free a dim * * @param dim Pointer to dim info struct of type to delete. * * @return ::NC_NOERR No error. * @author Ed Hartnett, Ward Fisher */ int nc4_dim_free(NC_DIM_INFO_T *dim) { /* Free memory allocated for names. */ if(dim) { if (dim->hdr.name) free(dim->hdr.name); free(dim); } return NC_NOERR; } /** * @internal Free a dim and unlist it * * @param grp Pointer to dim's containing group * @param dim Pointer to dim info struct of type to delete. * * @return ::NC_NOERR No error. * @author Dennis Heimbigner */ int nc4_dim_list_del(NC_GRP_INFO_T* grp, NC_DIM_INFO_T *dim) { if(grp && dim) { int pos = ncindexfind(grp->dim,(NC_OBJ*)dim); if(pos >= 0) ncindexidel(grp->dim,pos); } return nc4_dim_free(dim); } /** * @internal Recursively delete the data for a group (and everything * it contains) in our internal metadata store. * * @param grp Pointer to group info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_rec_grp_del(NC_GRP_INFO_T *grp) { NC_GRP_INFO_T *g; NC_VAR_INFO_T *var; NC_ATT_INFO_T *att; NC_DIM_INFO_T *dim; int retval; int i; assert(grp); LOG((3, "%s: grp->name %s", __func__, grp->hdr.name)); /* WARNING: for all these deletes, the nc4_xxx_del functions will modify the index, so we need to not assume any state about them. */ /* Recursively call this function for each child, if any, stopping * if there is an error. */ for(i=0;ichildren);i++) { g = (NC_GRP_INFO_T*)ncindexith(grp->children,i); if(g == NULL) continue; if ((retval = nc4_rec_grp_del(g))) return retval; } ncindexfree(grp->children); grp->children = NULL; /* Delete all the list contents for vars, dims, and atts, in this * group. */ for(i=0;iatt);i++) { att = (NC_ATT_INFO_T*)ncindexith(grp->att,i); if(att == NULL) continue; LOG((4, "%s: deleting att %s", __func__, att->hdr.name)); if ((retval = nc4_att_free(att))) /* free but leave in parent list */ return retval; } ncindexfree(grp->att); grp->att = NULL; /* Delete all vars. */ for(i=0;ivars);i++) { var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i); if(var == NULL) continue; LOG((4, "%s: deleting var %s", __func__, var->hdr.name)); /* Close HDF5 dataset associated with this var, unless it's a * scale. */ if (var->hdf_datasetid && H5Dclose(var->hdf_datasetid) < 0) return NC_EHDFERR; if ((retval = nc4_var_free(var))) /* free but leave in parent list */ return retval; } ncindexfree(grp->vars); grp->vars = NULL; /* Delete all dims. */ for(i=0;idim);i++) { dim = (NC_DIM_INFO_T*)ncindexith(grp->dim,i); if(dim == NULL) continue; LOG((4, "%s: deleting dim %s", __func__, dim->hdr.name)); /* If this is a dim without a coordinate variable, then close * the HDF5 DIM_WITHOUT_VARIABLE dataset associated with this * dim. */ if (dim->hdf_dimscaleid && H5Dclose(dim->hdf_dimscaleid) < 0) return NC_EHDFERR; if ((retval = nc4_dim_free(dim))) /* free but leave in parent list */ return retval; } ncindexfree(grp->dim); grp->dim = NULL; /* Delete all types. */ /* Is this code correct? I think it should do repeated passes over h5->alltypes using the ref count to decide what to delete */ for(i=0;itype);i++) { NC_TYPE_INFO_T* type = (NC_TYPE_INFO_T*)ncindexith(grp->type,i); if(type == NULL) continue; LOG((4, "%s: deleting type %s", __func__, type->hdr.name)); if ((retval = nc4_type_free(type))) /* free but leave in parent list */ return retval; } ncindexfree(grp->type); grp->type = NULL; /* Tell HDF5 we're closing this group. */ LOG((4, "%s: closing group %s", __func__, grp->hdr.name)); if (grp->hdf_grpid && H5Gclose(grp->hdf_grpid) < 0) return NC_EHDFERR; /* Free up this group */ /* Free the name. */ free(grp->hdr.name); free(grp); return NC_NOERR; } /** * @internal Remove a NC_ATT_INFO_T from an index. * This will nc_free the memory too. * * @param list Pointer to pointer of list. * @param att Pointer to attribute info struct. * * @return ::NC_NOERR No error. * @author Dennis Heimbigner */ int nc4_att_list_del(NCindex* list, NC_ATT_INFO_T *att) { assert(att != NULL); if(list != NULL) obj_list_del(list, (NC_OBJ *)att); return nc4_att_free(att); } /** * @internal Free memory of an attribute object * * @param att Pointer to attribute info struct. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc4_att_free(NC_ATT_INFO_T *att) { int i; LOG((3, "%s: name %s ", __func__, att->hdr.name)); /* Free memory that was malloced to hold data for this * attribute. */ if (att->data) free(att->data); /* Free the name. */ if (att->hdr.name) { free(att->hdr.name); att->hdr.name = NULL; } /* Close the HDF5 typeid. */ if (att->native_hdf_typeid && H5Tclose(att->native_hdf_typeid) < 0) return NC_EHDFERR; /* If this is a string array attribute, delete all members of the * string array, then delete the array of pointers to strings. (The * array was filled with pointers by HDF5 when the att was read, * and memory for each string was allocated by HDF5. That's why I * use free and not nc_free, because the netCDF library didn't * allocate the memory that is being freed.) */ if (att->stdata) { for (i = 0; i < att->len; i++) if(att->stdata[i]) free(att->stdata[i]); free(att->stdata); } /* If this att has vlen data, release it. */ if (att->vldata) { for (i = 0; i < att->len; i++) nc_free_vlen(&att->vldata[i]); free(att->vldata); } free(att); return NC_NOERR; } /** * @internal Normalize a UTF8 name. Put the result in norm_name, which * can be NC_MAX_NAME + 1 in size. This function makes sure the free() * gets called on the return from utf8proc_NFC, and also ensures that * the name is not too long. * * @param name Name to normalize. * @param norm_name The normalized name. * * @return ::NC_NOERR No error. * @return ::NC_EMAXNAME Name too long. * @author Dennis Heimbigner */ int nc4_normalize_name(const char *name, char *norm_name) { char *temp_name; int stat = nc_utf8_normalize((const unsigned char *)name,(unsigned char **)&temp_name); if(stat != NC_NOERR) return stat; if (strlen(temp_name) > NC_MAX_NAME) { free(temp_name); return NC_EMAXNAME; } strcpy(norm_name, temp_name); free(temp_name); return NC_NOERR; } /* Print out a bunch of info to stderr about the metadata for debugging purposes. */ #ifdef LOGGING /** * Use this to set the global log level. Set it to NC_TURN_OFF_LOGGING * (-1) to turn off all logging. Set it to 0 to show only errors, and * to higher numbers to show more and more logging details. * * @param new_level The new logging level. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int nc_set_log_level(int new_level) { if(!nc4_hdf5_initialized) nc4_hdf5_initialize(); /* /\* If the user wants to completely turn off logging, turn off HDF5 */ /* logging too. Now I truly can't think of what to do if this */ /* fails, so just ignore the return code. *\/ */ /* if (new_level == NC_TURN_OFF_LOGGING) */ /* { */ /* set_auto(NULL,NULL); */ /* LOG((1, "HDF5 error messages turned off!")); */ /* } */ /* /\* Do we need to turn HDF5 logging back on? *\/ */ /* if (new_level > NC_TURN_OFF_LOGGING && */ /* nc_log_level <= NC_TURN_OFF_LOGGING) */ /* { */ /* if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0) */ /* LOG((0, "H5Eset_auto failed!")); */ /* LOG((1, "HDF5 error messages turned on.")); */ /* } */ /* Now remember the new level. */ nc_log_level = new_level; LOG((4, "log_level changed to %d", nc_log_level)); return 0; } #define MAX_NESTS 10 /** * @internal Recursively print the metadata of a group. * * @param grp Pointer to group info struct. * @param tab_count Number of tabs. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ static int rec_print_metadata(NC_GRP_INFO_T *grp, int tab_count) { NC_GRP_INFO_T *g; NC_ATT_INFO_T *att; NC_VAR_INFO_T *var; NC_DIM_INFO_T *dim; NC_TYPE_INFO_T *type; NC_FIELD_INFO_T *field; char tabs[MAX_NESTS+1] = ""; char *dims_string = NULL; char temp_string[10]; int t, retval, d, i; /* Come up with a number of tabs relative to the group. */ for (t = 0; t < tab_count && t < MAX_NESTS; t++) tabs[t] = '\t'; tabs[t] = '\0'; LOG((2, "%s GROUP - %s nc_grpid: %d nvars: %d natts: %d", tabs, grp->hdr.name, grp->hdr.id, ncindexsize(grp->vars), ncindexsize(grp->att))); for(i=0;iatt);i++) { att = (NC_ATT_INFO_T*)ncindexith(grp->att,i); if(att == NULL) continue; LOG((2, "%s GROUP ATTRIBUTE - attnum: %d name: %s type: %d len: %d", tabs, att->hdr.id, att->hdr.name, att->nc_typeid, att->len)); } for(i=0;idim);i++) { dim = (NC_DIM_INFO_T*)ncindexith(grp->dim,i); if(dim == NULL) continue; LOG((2, "%s DIMENSION - dimid: %d name: %s len: %d unlimited: %d", tabs, dim->hdr.id, dim->hdr.name, dim->len, dim->unlimited)); } for(i=0;ivars);i++) { int j; var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i); if (var == NULL) continue; if(var->ndims > 0) { dims_string = (char*)malloc(sizeof(char)*(var->ndims*4)); strcpy(dims_string, ""); for (d = 0; d < var->ndims; d++) { sprintf(temp_string, " %d", var->dimids[d]); strcat(dims_string, temp_string); } } LOG((2, "%s VARIABLE - varid: %d name: %s type: %d ndims: %d dimscale: %d dimids:%s endianness: %d, hdf_typeid: %d", tabs, var->hdr.id, var->hdr.name, var->type_info->hdr.id, var->ndims, (int)var->dimscale, (dims_string ? dims_string : " -"),var->type_info->endianness, var->type_info->native_hdf_typeid)); for(j=0;jatt);j++) { att = (NC_ATT_INFO_T*)ncindexith(var->att,j); if(att == NULL) continue; LOG((2, "%s VAR ATTRIBUTE - attnum: %d name: %s type: %d len: %d", tabs, att->hdr.id, att->hdr.name, att->nc_typeid, att->len)); } if(dims_string) { free(dims_string); dims_string = NULL; } } for(i=0;itype);i++) { if((type = (NC_TYPE_INFO_T*)ncindexith(grp->type,i)) == NULL) continue; LOG((2, "%s TYPE - nc_typeid: %d hdf_typeid: 0x%x committed: %d " "name: %s num_fields: %d", tabs, type->hdr.id, type->hdf_typeid, type->size, (int)type->committed, type->hdr.name)); /* Is this a compound type? */ if (type->nc_type_class == NC_COMPOUND) { int j; LOG((3, "compound type")); for(j=0;ju.c.field);j++) { field = (NC_FIELD_INFO_T*)nclistget(type->u.c.field,j); LOG((4, "field %s offset %d nctype %d ndims %d", field->hdr.name, field->offset, field->nc_typeid, field->ndims)); } } else if (type->nc_type_class == NC_VLEN) { LOG((3, "VLEN type")); LOG((4, "base_nc_type: %d", type->u.v.base_nc_typeid)); } else if (type->nc_type_class == NC_OPAQUE) LOG((3, "Opaque type")); else if (type->nc_type_class == NC_ENUM) { LOG((3, "Enum type")); LOG((4, "base_nc_type: %d", type->u.e.base_nc_typeid)); } else { LOG((0, "Unknown class: %d", type->nc_type_class)); return NC_EBADTYPE; } } /* Call self for each child of this group. */ for(i=0;ichildren);i++) { if((g = (NC_GRP_INFO_T*)ncindexith(grp->children,i)) == NULL) continue; if ((retval = rec_print_metadata(g, tab_count + 1))) return retval; } return NC_NOERR; } /** * @internal Print out the internal metadata for a file. This is * useful to check that netCDF is working! Nonetheless, this function * will print nothing if logging is not set to at least two. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int log_metadata_nc(NC *nc) { NC_HDF5_FILE_INFO_T *h5 = NC4_DATA(nc); LOG((2, "*** NetCDF-4 Internal Metadata: int_ncid 0x%x ext_ncid 0x%x", nc->int_ncid, nc->ext_ncid)); if (!h5) { LOG((2, "This is a netCDF-3 file.")); return NC_NOERR; } LOG((2, "FILE - hdfid: 0x%x path: %s cmode: 0x%x parallel: %d redef: %d " "fill_mode: %d no_write: %d next_nc_grpid: %d", h5->hdfid, nc->path, h5->cmode, (int)h5->parallel, (int)h5->redef, h5->fill_mode, (int)h5->no_write, h5->next_nc_grpid)); if(nc_log_level >= 2) return rec_print_metadata(h5->root_grp, 0); return NC_NOERR; } #endif /*LOGGING */ /** * @internal Show the in-memory metadata for a netcdf file. * * @param ncid File and group ID. * * @return ::NC_NOERR No error. * @author Ed Hartnett */ int NC4_show_metadata(int ncid) { int retval = NC_NOERR; #ifdef LOGGING NC *nc; int old_log_level = nc_log_level; /* Find file metadata. */ if (!(nc = nc4_find_nc_file(ncid,NULL))) return NC_EBADID; /* Log level must be 2 to see metadata. */ nc_log_level = 2; retval = log_metadata_nc(nc); nc_log_level = old_log_level; #endif /*LOGGING*/ return retval; }