netcdf-c/libsrc4/nc4internal.c

1611 lines
42 KiB
C

/* 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"
/* These hold the file caching settings for the library. */
size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE; /**< Default chunk cache size. */
size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /**< Default chunk cache number of elements. */
float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION; /**< Default 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.
* @return ::NC_ENOMEM Out of memory.
* @author Dennis Heimbigner
*/
int
nc4_check_name(const char *name, char *norm_name)
{
char *temp;
int retval;
assert(norm_name);
/* Check for NULL. */
if (!name)
return NC_EINVAL;
/* 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. */
if ((retval = nc_utf8_normalize((const unsigned char *)name,
(unsigned char **)&temp)))
return retval;
/* Check length of normalized name. */
if (strlen(temp) > NC_MAX_NAME)
{
free(temp);
return NC_EMAXNAME;
}
/* Copy the normalized name. */
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.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc4_nc4f_list_add(NC *nc, const char *path, int mode)
{
NC_FILE_INFO_T *h5;
int retval;
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_FILE_INFO_T))))
return NC_ENOMEM;
nc->dispatchdata = 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;
/* Initialize lists for dimensions, types, and groups. */
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. */
if ((retval = nc4_grp_list_add(h5, NULL, NC_GROUP_NAME, &h5->root_grp)))
return retval;
return NC_NOERR;
}
/**
* @internal Given an ncid, find the relevant group and return a
* pointer to it.
*
* @param ncid File and group ID.
* @param grp Pointer that gets pointer to group info struct. Ignored
* if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOTNC4 Not a netCDF-4 file.
* @author Ed Hartnett
*/
int
nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp)
{
return nc4_find_nc_grp_h5(ncid, NULL, grp, NULL);
}
/**
* @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.
*
* @param ncid File and group ID.
* @param grp Pointer that gets pointer to group info struct. Ignored
* if NULL.
* @param h5 Pointer that gets pointer to file info struct. Ignored if
* NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Ed Hartnett
*/
int
nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_FILE_INFO_T **h5)
{
return nc4_find_nc_grp_h5(ncid, NULL, grp, h5);
}
/**
* @internal Find info for this file and group, and set pointers.
*
* @param ncid File and group ID.
* @param nc Pointer that gets a pointer to the file's NC
* struct. Ignored if NULL.
* @param grp Pointer that gets a pointer to the group
* struct. Ignored if NULL.
* @param h5 Pointer that gets HDF5 file struct. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grp, NC_FILE_INFO_T **h5)
{
NC_GRP_INFO_T *my_grp = NULL;
NC_FILE_INFO_T *my_h5 = NULL;
NC *my_nc;
int retval;
/* Look up file metadata. */
if ((retval = NC_check_id(ncid, &my_nc)))
return retval;
my_h5 = my_nc->dispatchdata;
assert(my_h5 && my_h5->root_grp);
/* If we can't find it, the grp id part of ncid is bad. */
if (!(my_grp = nclistget(my_h5->allgroups, (ncid & GRP_ID_MASK))))
return NC_EBADID;
/* Return pointers to caller, if desired. */
if (nc)
*nc = my_nc;
if (h5)
*h5 = my_h5;
if (grp)
*grp = my_grp;
return NC_NOERR;
}
/**
* @internal Given an ncid and varid, get pointers to the group and var
* metadata.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param h5 Pointer that gets pointer to the NC_FILE_INFO_T struct
* for this file. Ignored if NULL.
* @param grp Pointer that gets pointer to group info. Ignored if
* NULL.
* @param var Pointer that gets pointer to var info. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5, NC_GRP_INFO_T **grp,
NC_VAR_INFO_T **var)
{
NC_FILE_INFO_T *my_h5;
NC_GRP_INFO_T *my_grp;
NC_VAR_INFO_T *my_var;
int retval;
/* Look up file and group metadata. */
if ((retval = nc4_find_grp_h5(ncid, &my_grp, &my_h5)))
return retval;
assert(my_grp && my_h5);
/* Find the var. */
if (!(my_var = (NC_VAR_INFO_T *)ncindexith(my_grp->vars, varid)))
return NC_ENOTVAR;
assert(my_var && my_var->hdr.id == varid);
/* Return pointers that caller wants. */
if (h5)
*h5 = my_h5;
if (grp)
*grp = my_grp;
if (var)
*var = my_var;
return NC_NOERR;
}
/**
* @internal Find a dim in the file.
*
* @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. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADDIM Dimension not found.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim,
NC_GRP_INFO_T **dim_grp)
{
assert(grp && grp->nc4_info && dim);
LOG((4, "%s: dimid %d", __func__, dimid));
/* Find the dim info. */
if (!((*dim) = nclistget(grp->nc4_info->alldims, dimid)))
return NC_EBADDIM;
/* 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, Dennis Heimbigner
*/
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;i<ncindexsize(start_grp->children);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 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_FILE_INFO_T *h5, nc_type typeid, NC_TYPE_INFO_T **type)
{
/* Check inputs. */
assert(h5);
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. */
if (!(*type = nclistget(h5->alltypes,typeid)))
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;
NC_ATT_INFO_T *my_att;
NCindex *attlist = NULL;
assert(grp && grp->hdr.name && att);
LOG((4, "%s: grp->name %s varid %d attnum %d", __func__, grp->hdr.name,
varid, 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(attlist);
/* Now find the attribute by name or number. If a name is provided,
* ignore the attnum. */
if (name)
my_att = (NC_ATT_INFO_T *)ncindexlookup(attlist, name);
else
my_att = (NC_ATT_INFO_T *)ncindexith(attlist, attnum);
if (!my_att)
return NC_ENOTATT;
*att = my_att;
return NC_NOERR;
}
/**
* @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;
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, NULL)))
return retval;
assert(grp);
return nc4_find_grp_att(grp, varid, name, attnum, att);
}
/**
* @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_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 Create a new variable and insert into relevant
* lists. Dimensionality info need not be known.
*
* @param grp the containing group
* @param name the name for 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_add2(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var)
{
NC_VAR_INFO_T *new_var;
/* Allocate storage for new variable. */
if (!(new_var = calloc(1, sizeof(NC_VAR_INFO_T))))
return NC_ENOMEM;
new_var->hdr.sort = NCVAR;
new_var->container = grp;
/* 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)))
return NC_ENOMEM;
new_var->hdr.hashkey = NC_hashmapkey(new_var->hdr.name,
strlen(new_var->hdr.name));
/* Create an indexed list for the attributes. */
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;
return NC_NOERR;
}
/**
* @internal Set the number of dims in an NC_VAR_INFO_T struct.
*
* @param var Pointer to the var.
* @param ndims Number of dimensions for this 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_set_ndims(NC_VAR_INFO_T *var, int ndims)
{
assert(var);
/* Remember the number of dimensions. */
var->ndims = ndims;
/* Allocate space for dimension information. */
if (ndims)
{
if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *))))
return NC_ENOMEM;
if (!(var->dimids = calloc(ndims, sizeof(int))))
return NC_ENOMEM;
/* Initialize dimids to illegal values (-1). See the comment
in nc4_rec_match_dimscales(). */
memset(var->dimids, -1, ndims * sizeof(int));
}
return NC_NOERR;
}
/**
* @internal Create a new variable and insert int relevant list.
*
* @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)
{
int retval;
if ((retval = nc4_var_list_add2(grp, name, var)))
return retval;
if ((retval = nc4_var_set_ndims(*var, ndims)))
return retval;
return NC_NOERR;
}
/**
* @internal Add a dimension to the dimension list for a group.
*
* @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.
* @return ::NC_ENOMEM Out of memory.
* @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;
assert(grp && name);
/* Allocate memory for dim metadata. */
if (!(new_dim = calloc(1, sizeof(NC_DIM_INFO_T))))
return NC_ENOMEM;
new_dim->hdr.sort = NCDIM;
/* Assign the dimension ID. */
if (assignedid >= 0)
new_dim->hdr.id = assignedid;
else
new_dim->hdr.id = grp->nc4_info->next_dimid++;
/* Remember the name and create a hash. */
if (!(new_dim->hdr.name = strdup(name)))
return NC_ENOMEM;
new_dim->hdr.hashkey = NC_hashmapkey(new_dim->hdr.name,
strlen(new_dim->hdr.name));
/* Is dimension unlimited? */
new_dim->len = len;
if (len == NC_UNLIMITED)
new_dim->unlimited = NC_TRUE;
/* Remember the containing group. */
new_dim->container = grp;
/* Add object to dimension list for this group. */
ncindexadd(grp->dim, (NC_OBJ *)new_dim);
obj_track(grp->nc4_info, (NC_OBJ *)new_dim);
/* Set the dim pointer, if one was given */
if (dim)
*dim = new_dim;
return NC_NOERR;
}
/**
* @internal Add to an attribute 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. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
int
nc4_att_list_add(NCindex *list, const char *name, NC_ATT_INFO_T **att)
{
NC_ATT_INFO_T *new_att;
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)))
return 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 */
ncindexadd(list, (NC_OBJ *)new_att);
/* Set the attribute pointer, if one was given */
if (att)
*att = new_att;
return NC_NOERR;
}
/**
* @internal Add a group to a group list.
*
* @param h5 Pointer to the file info.
* @param parent Pointer to the parent group. Will be NULL when adding
* the root group.
* @param name Name of the group.
* @param grp Pointer to pointer that gets new group info
* struct. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc4_grp_list_add(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *parent, char *name,
NC_GRP_INFO_T **grp)
{
NC_GRP_INFO_T *new_grp;
/* Check inputs. */
assert(h5 && name);
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;
/* Fill in this group's information. */
new_grp->hdr.sort = NCGRP;
new_grp->nc4_info = h5;
new_grp->parent = parent;
/* Assign the group ID. The root group will get id 0. */
new_grp->hdr.id = h5->next_nc_grpid++;
assert(parent || !new_grp->hdr.id);
/* Handle the group name. */
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));
/* Set up new indexed lists for stuff this group can contain. */
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 */
if (parent)
ncindexadd(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 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, Dennis Heimbigner
*/
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 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.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett, Ward Fisher
*/
int
nc4_type_new(size_t size, const char *name, int assignedid,
NC_TYPE_INFO_T **type)
{
NC_TYPE_INFO_T *new_type;
LOG((4, "%s: size %d name %s assignedid %d", __func__, size, name, assignedid));
/* Check inputs. */
assert(type);
/* 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. */
*type = new_type;
return NC_NOERR;
}
/**
* @internal Add to the 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.
*
* @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)
{
NC_TYPE_INFO_T *new_type;
int retval;
/* Check inputs. */
assert(grp && name && type);
LOG((4, "%s: size %d name %s", __func__, size, name));
/* Create the new TYPE_INFO struct. */
if ((retval = nc4_type_new(size, name, grp->nc4_info->next_typeid,
&new_type)))
return retval;
grp->nc4_info->next_typeid++;
/* Increment the ref. count on the type */
new_type->rc++;
/* Add object to lists */
ncindexadd(grp->type, (NC_OBJ *)new_type);
obj_track(grp->nc4_info,(NC_OBJ*)new_type);
/* Return a pointer to the new type. */
*type = new_type;
return NC_NOERR;
}
/**
* @internal Add to the compound field list.
*
* @param parent parent type
* @param name Name of the field.
* @param offset Offset in bytes.
* @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, Dennis Heimbigner
*/
int
nc4_field_list_add(NC_TYPE_INFO_T *parent, const char *name,
size_t offset, 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->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.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc4_type_free(NC_TYPE_INFO_T *type)
{
int i;
assert(type && type->rc && type->hdr.name);
/* Decrement the ref. count on the type */
type->rc--;
/* Release the type, if the ref. count drops to zero */
if (type->rc == 0)
{
LOG((4, "%s: deleting type %s", __func__, type->hdr.name));
/* Free the name. */
free(type->hdr.name);
/* Enums and compound types have lists of fields to clean up. */
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;i<nclistlength(type->u.c.field);i++) {
field = nclistget(type->u.c.field,i);
field_free(field);
}
nclistfree(type->u.c.field);
}
break;
case NC_ENUM:
{
NC_ENUM_MEMBER_INFO_T *enum_member;
/* Delete all the enum_members, if any. */
for(i=0;i<nclistlength(type->u.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);
}
break;
default:
break;
}
/* Release any HDF5-specific type info. */
if (type->format_type_info)
free(type->format_type_info);
/* Release the memory. */
free(type);
}
return NC_NOERR;
}
/**
* @internal Free memory of an attribute object
*
* @param att Pointer to attribute info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
att_free(NC_ATT_INFO_T *att)
{
int i;
assert(att);
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);
/* 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 any format-sepecific info. Some formats use this (ex. HDF5)
* and some don't (ex. HDF4). So it may be NULL. */
if (att->format_att_info)
free(att->format_att_info);
free(att);
return NC_NOERR;
}
/**
* @internal Delete a var, and free the memory. All HDF5 objects for
* the var must be closed before this is called.
*
* @param var Pointer to the var info struct of var to delete.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
var_free(NC_VAR_INFO_T *var)
{
int i;
int retval;
assert(var);
LOG((4, "%s: deleting var %s", __func__, var->hdr.name));
/* First delete all the attributes attached to this var. */
for (i = 0; i < ncindexsize(var->att); i++)
if ((retval = att_free((NC_ATT_INFO_T *)ncindexith(var->att, i))))
return retval;
ncindexfree(var->att);
/* Free some things that may be allocated. */
if (var->chunksizes)
free(var->chunksizes);
if (var->hdf5_name)
free(var->hdf5_name);
if (var->hdr.name)
free(var->hdr.name);
if (var->dimids)
free(var->dimids);
if (var->dim)
free(var->dim);
/* Delete any fill value allocation. */
if (var->fill_value)
free(var->fill_value);
/* Release type information */
if (var->type_info)
if ((retval = nc4_type_free(var->type_info)))
return retval;
/* 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 any format-specific info. */
if (var->format_var_info)
free(var->format_var_info);
/* Delete the var. */
free(var);
return NC_NOERR;
}
/**
* @internal Delete a var, and free the memory.
*
* @param grp Pointer to the strct for the containing group.
* @param var Pointer to the var info struct of var to delete.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc4_var_list_del(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
int i;
assert(var && grp);
/* Remove from lists */
i = ncindexfind(grp->vars, (NC_OBJ *)var);
if (i >= 0)
ncindexidel(grp->vars, i);
return 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
*/
static int
dim_free(NC_DIM_INFO_T *dim)
{
assert(dim);
LOG((4, "%s: deleting dim %s", __func__, dim->hdr.name));
/* Free memory allocated for names. */
if (dim->hdr.name)
free(dim->hdr.name);
/* Release any format-specific information. */
if (dim->format_dim_info)
free(dim->format_dim_info);
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 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, Dennis Heimbigner
*/
int
nc4_rec_grp_del(NC_GRP_INFO_T *grp)
{
int i;
int retval;
assert(grp);
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
/* Recursively call this function for each child, if any, stopping
* if there is an error. */
for (i = 0; i < ncindexsize(grp->children); i++)
if ((retval = nc4_rec_grp_del((NC_GRP_INFO_T *)ncindexith(grp->children,
i))))
return retval;
ncindexfree(grp->children);
/* Free attributes, but leave in parent list */
for (i = 0; i < ncindexsize(grp->att); i++)
if ((retval = att_free((NC_ATT_INFO_T *)ncindexith(grp->att, i))))
return retval;
ncindexfree(grp->att);
/* Delete all vars. */
for (i = 0; i < ncindexsize(grp->vars); i++)
if ((retval = var_free((NC_VAR_INFO_T *)ncindexith(grp->vars, i))))
return retval;
ncindexfree(grp->vars);
/* Delete all dims, and free the list of dims. */
for (i = 0; i < ncindexsize(grp->dim); i++)
if ((retval = dim_free((NC_DIM_INFO_T *)ncindexith(grp->dim, i))))
return retval;
ncindexfree(grp->dim);
/* Delete all types. */
for (i = 0; i < ncindexsize(grp->type); i++)
if ((retval = nc4_type_free((NC_TYPE_INFO_T *)ncindexith(grp->type, i))))
return retval;
ncindexfree(grp->type);
/* Free the name. */
free(grp->hdr.name);
/* Release any format-specific information about this group. */
if (grp->format_grp_info)
free(grp->format_grp_info);
/* Free up this group */
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 && list);
ncindexidel(list, ((NC_OBJ *)att)->id);
return att_free(att);
}
/**
* @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;
}
#ifdef ENABLE_SET_LOG_LEVEL
/**
* @internal 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. If logging is not enabled with --enable-logging at
* configure when building netCDF, this function will do nothing.
* Note that it is possible to set the log level using the environment
* variable named _NETCDF_LOG_LEVEL_ (e.g. _export NETCDF_LOG_LEVEL=4_).
*
* @param new_level The new logging level.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc_set_log_level(int new_level)
{
#ifdef LOGGING
/* Remember the new level. */
nc_log_level = new_level;
LOG((4, "log_level changed to %d", nc_log_level));
#endif /*LOGGING */
return 0;
}
#endif /* ENABLE_SET_LOG_LEVEL */
#ifdef LOGGING
#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, Dennis Heimbigner
*/
static int
rec_print_metadata(NC_GRP_INFO_T *grp, int tab_count)
{
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; i < ncindexsize(grp->att); i++)
{
att = (NC_ATT_INFO_T *)ncindexith(grp->att, i);
assert(att);
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; i < ncindexsize(grp->dim); i++)
{
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, i);
assert(dim);
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; i < ncindexsize(grp->vars); i++)
{
int j;
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
assert(var);
if (var->ndims > 0)
{
if (!(dims_string = malloc(sizeof(char) * var->ndims * 4)))
return NC_ENOMEM;
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 ndims: %d dimscale: %d dimids:%s",
tabs, var->hdr.id, var->hdr.name, var->ndims, (int)var->dimscale,
(dims_string ? dims_string : " -")));
for (j = 0; j < ncindexsize(var->att); j++)
{
att = (NC_ATT_INFO_T *)ncindexith(var->att, j);
assert(att);
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);
}
for (i = 0; i < ncindexsize(grp->type); i++)
{
type = (NC_TYPE_INFO_T*)ncindexith(grp->type, i);
assert(type);
LOG((2, "%s TYPE - nc_typeid: %d size: %d committed: %d name: %s",
tabs, type->hdr.id, 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; j < nclistlength(type->u.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; i < ncindexsize(grp->children); i++)
if ((retval = rec_print_metadata((NC_GRP_INFO_T *)ncindexith(grp->children, i),
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.
*
* @param Pointer to the file info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
log_metadata_nc(NC_FILE_INFO_T *h5)
{
LOG((2, "*** NetCDF-4 Internal Metadata: int_ncid 0x%x ext_ncid 0x%x",
h5->root_grp->nc4_info->controller->int_ncid,
h5->root_grp->nc4_info->controller->ext_ncid));
if (!h5)
{
LOG((2, "This is a netCDF-3 file."));
return NC_NOERR;
}
LOG((2, "FILE - path: %s cmode: 0x%x parallel: %d redef: %d "
"fill_mode: %d no_write: %d next_nc_grpid: %d", h5->root_grp->nc4_info->controller->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. This
* function does nothing unless netCDF was built with
* the configure option --enable-logging.
*
* @param ncid File and group ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Ed Hartnett
*/
int
NC4_show_metadata(int ncid)
{
int retval = NC_NOERR;
#ifdef LOGGING
NC_FILE_INFO_T *h5;
int old_log_level = nc_log_level;
/* Find file metadata. */
if ((retval = nc4_find_grp_h5(ncid, NULL, &h5)))
return retval;
/* Log level must be 2 to see metadata. */
nc_log_level = 2;
retval = log_metadata_nc(h5);
nc_log_level = old_log_level;
#endif /*LOGGING*/
return retval;
}