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netcdf-c/libhdf5/hdf5open.c
Dennis Heimbigner 59e04ae071 This PR adds EXPERIMENTAL support for accessing data in the 
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".

The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.

More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).

WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:

Platform | Build System | S3 support
------------------------------------
Linux+gcc      | Automake     | yes
Linux+gcc      | CMake        | yes
Visual Studio  | CMake        | no

Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future.  Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.

In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*.  The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
   and the version bumped.
4. An overly complex set of structs was created to support funnelling
   all of the filterx operations thru a single dispatch
   "filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
   to nczarr.

Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
   -- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
   support zarr and to regularize the structure of the fragments
   section of a URL.

Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
   e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
   * Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
   and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.

Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-28 18:02:47 -06:00

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/* Copyright 2003-2018, University Corporation for Atmospheric
* Research. See COPYRIGHT file for copying and redistribution
* conditions. */
/**
* @file
* @internal This file contains functions that are used in file
* opens.
*
* @author Ed Hartnett
*/
#include "config.h"
#include "hdf5internal.h"
#include "ncrc.h"
#include "ncmodel.h"
#include "ncfilter.h"
#ifdef ENABLE_BYTERANGE
#include "H5FDhttp.h"
#endif
/*Nemonic */
#define FILTERACTIVE 1
#define NUM_TYPES 12 /**< Number of netCDF atomic types. */
#define CD_NELEMS_ZLIB 1 /**< Number of parameters needed for ZLIB filter. */
/** @internal Native HDF5 constants for atomic types. For performance,
* fill this array only the first time, and keep it in global memory
* for each further use. */
static hid_t h5_native_type_constant_g[NUM_TYPES];
/** @internal NetCDF atomic type names. */
static const char nc_type_name_g[NUM_TYPES][NC_MAX_NAME + 1] = {"char", "byte", "short",
"int", "float", "double", "ubyte",
"ushort", "uint", "int64",
"uint64", "string"};
/** @internal NetCDF atomic types. */
static const nc_type nc_type_constant_g[NUM_TYPES] = {NC_CHAR, NC_BYTE, NC_SHORT,
NC_INT, NC_FLOAT, NC_DOUBLE, NC_UBYTE,
NC_USHORT, NC_UINT, NC_INT64,
NC_UINT64, NC_STRING};
/** @internal NetCDF atomic type sizes. */
static const int nc_type_size_g[NUM_TYPES] = {sizeof(char), sizeof(char), sizeof(short),
sizeof(int), sizeof(float), sizeof(double), sizeof(unsigned char),
sizeof(unsigned short), sizeof(unsigned int), sizeof(long long),
sizeof(unsigned long long), sizeof(char *)};
/** @internal These flags may not be set for open mode. */
static const int ILLEGAL_OPEN_FLAGS = (NC_MMAP);
/* From libsrc4, these are the netcdf-4 cache sizes. */
extern size_t nc4_chunk_cache_size;
extern size_t nc4_chunk_cache_nelems;
extern float nc4_chunk_cache_preemption;
/* From nc4mem.c */
extern int NC4_open_image_file(NC_FILE_INFO_T* h5);
/* Defined later in this file. */
static int rec_read_metadata(NC_GRP_INFO_T *grp);
/**
* @internal Struct to track HDF5 object info, for
* rec_read_metadata(). We get this info for every object in the
* HDF5 file when we H5Literate() over the file. */
typedef struct hdf5_obj_info
{
hid_t oid; /* HDF5 object ID */
char oname[NC_MAX_NAME + 1]; /* Name of object */
#if H5_VERSION_GE(1,12,0)
H5O_info2_t statbuf;
#else
H5G_stat_t statbuf; /* Information about the object */
#endif
struct hdf5_obj_info *next; /* Pointer to next node in list */
} hdf5_obj_info_t;
/**
* @internal User data struct for call to H5Literate() in
* rec_read_metadata(). When iterating through the objects in a
* group, if we find child groups, we save their hdf5_obj_info_t
* object in a list. Then we processes them after completely
* processing the parent group. */
typedef struct user_data
{
NClist *grps; /* NClist<hdf5_obj_info_t*> */
NC_GRP_INFO_T *grp; /* Pointer to parent group */
} user_data_t;
/* Custom iteration callback data */
typedef struct {
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var;
} att_iter_info;
/**
* @internal Given an HDF5 type, set a pointer to netcdf type_info
* struct, either an existing one (for user-defined types) or a newly
* created one.
*
* @param h5 Pointer to HDF5 file info struct.
* @param datasetid HDF5 dataset ID.
* @param type_info Pointer to pointer that gets type info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EBADTYPID Type not found.
* @author Ed Hartnett
*/
static int
get_type_info2(NC_FILE_INFO_T *h5, hid_t datasetid, NC_TYPE_INFO_T **type_info)
{
NC_HDF5_TYPE_INFO_T *hdf5_type;
htri_t is_str, equal = 0;
H5T_class_t class;
hid_t native_typeid, hdf_typeid;
H5T_order_t order;
int t;
assert(h5 && type_info);
/* Because these N5T_NATIVE_* constants are actually function calls
* (!) in H5Tpublic.h, I can't initialize this array in the usual
* way, because at least some C compilers (like Irix) complain
* about calling functions when defining constants. So I have to do
* it like this. Note that there's no native types for char or
* string. Those are handled later. */
if (!h5_native_type_constant_g[1])
{
h5_native_type_constant_g[1] = H5T_NATIVE_SCHAR;
h5_native_type_constant_g[2] = H5T_NATIVE_SHORT;
h5_native_type_constant_g[3] = H5T_NATIVE_INT;
h5_native_type_constant_g[4] = H5T_NATIVE_FLOAT;
h5_native_type_constant_g[5] = H5T_NATIVE_DOUBLE;
h5_native_type_constant_g[6] = H5T_NATIVE_UCHAR;
h5_native_type_constant_g[7] = H5T_NATIVE_USHORT;
h5_native_type_constant_g[8] = H5T_NATIVE_UINT;
h5_native_type_constant_g[9] = H5T_NATIVE_LLONG;
h5_native_type_constant_g[10] = H5T_NATIVE_ULLONG;
}
/* Get the HDF5 typeid - we'll need it later. */
if ((hdf_typeid = H5Dget_type(datasetid)) < 0)
return NC_EHDFERR;
/* Get the native typeid. Will be equivalent to hdf_typeid when
* creating but not necessarily when reading, a variable. */
if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* Is this type an integer, string, compound, or what? */
if ((class = H5Tget_class(native_typeid)) < 0)
return NC_EHDFERR;
/* Is this an atomic type? */
if (class == H5T_STRING || class == H5T_INTEGER || class == H5T_FLOAT)
{
/* Allocate a phony NC_TYPE_INFO_T struct to hold type info. */
if (!(*type_info = calloc(1, sizeof(NC_TYPE_INFO_T))))
return NC_ENOMEM;
/* Allocate storage for HDF5-specific type info. */
if (!(hdf5_type = calloc(1, sizeof(NC_HDF5_TYPE_INFO_T))))
return NC_ENOMEM;
(*type_info)->format_type_info = hdf5_type;
/* H5Tequal doesn't work with H5T_C_S1 for some reason. But
* H5Tget_class will return H5T_STRING if this is a string. */
if (class == H5T_STRING)
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
/* Make sure fixed-len strings will work like variable-len
* strings */
if (is_str || H5Tget_size(hdf_typeid) > 1)
{
/* Set a class for the type */
t = NUM_TYPES - 1;
(*type_info)->nc_type_class = NC_STRING;
}
else
{
/* Set a class for the type */
t = 0;
(*type_info)->nc_type_class = NC_CHAR;
}
}
else
{
for (t = 1; t < NUM_TYPES - 1; t++)
{
if ((equal = H5Tequal(native_typeid,
h5_native_type_constant_g[t])) < 0)
return NC_EHDFERR;
if (equal)
break;
}
/* Find out about endianness. As of HDF 1.8.6, this works
* with all data types Not just H5T_INTEGER. See
* https://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetOrder */
if ((order = H5Tget_order(hdf_typeid)) < 0)
return NC_EHDFERR;
if (order == H5T_ORDER_LE)
(*type_info)->endianness = NC_ENDIAN_LITTLE;
else if (order == H5T_ORDER_BE)
(*type_info)->endianness = NC_ENDIAN_BIG;
else
return NC_EBADTYPE;
if (class == H5T_INTEGER)
(*type_info)->nc_type_class = NC_INT;
else
(*type_info)->nc_type_class = NC_FLOAT;
}
(*type_info)->hdr.id = nc_type_constant_g[t];
(*type_info)->size = nc_type_size_g[t];
if (!((*type_info)->hdr.name = strdup(nc_type_name_g[t])))
return NC_ENOMEM;
hdf5_type->hdf_typeid = hdf_typeid;
hdf5_type->native_hdf_typeid = native_typeid;
return NC_NOERR;
}
else
{
NC_TYPE_INFO_T *type;
/* This is a user-defined type. */
if((type = nc4_rec_find_hdf_type(h5, native_typeid)))
*type_info = type;
/* The type entry in the array of user-defined types already has
* an open data typeid (and native typeid), so close the ones we
* opened above. */
if (H5Tclose(native_typeid) < 0)
return NC_EHDFERR;
if (H5Tclose(hdf_typeid) < 0)
return NC_EHDFERR;
if (type)
return NC_NOERR;
}
return NC_EBADTYPID;
}
/**
* @internal This function reads the coordinates attribute used for
* multi-dimensional coordinates. It then sets var->dimids[], and
* attempts to find a pointer to the dims and sets var->dim[] as well.
*
* @param grp Group info pointer.
* @param var Var info pointer.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOTATT Attribute does not exist.
* @return ::NC_EATTMETA Attribute metadata error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
static int
read_coord_dimids(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
hid_t coord_att_typeid = -1, coord_attid = -1, spaceid = -1;
hssize_t npoints;
htri_t attr_exists;
int d;
int retval = NC_NOERR;
assert(grp && var && var->format_var_info);
LOG((3, "%s: var->hdr.name %s", __func__, var->hdr.name));
/* Have we already read the coordinates hidden att for this var? */
if (var->coords_read)
return NC_NOERR;
/* Get HDF5-sepecific var info. */
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Does the COORDINATES att exist? */
if ((attr_exists = H5Aexists(hdf5_var->hdf_datasetid, COORDINATES)) < 0)
return NC_EHDFERR;
if (!attr_exists)
return NC_ENOTATT;
/* There is a hidden attribute telling us the ids of the
* dimensions that apply to this multi-dimensional coordinate
* variable. Read it. */
if ((coord_attid = H5Aopen_name(hdf5_var->hdf_datasetid, COORDINATES)) < 0)
BAIL(NC_EATTMETA);
if ((coord_att_typeid = H5Aget_type(coord_attid)) < 0)
BAIL(NC_EATTMETA);
/* How many dimensions are there? */
if ((spaceid = H5Aget_space(coord_attid)) < 0)
BAIL(NC_EATTMETA);
if ((npoints = H5Sget_simple_extent_npoints(spaceid)) < 0)
BAIL(NC_EATTMETA);
/* Check that the number of points is the same as the number of
* dimensions for the variable. */
if (npoints != var->ndims)
BAIL(NC_EATTMETA);
/* Read the dimids for this var. */
if (H5Aread(coord_attid, coord_att_typeid, var->dimids) < 0)
BAIL(NC_EATTMETA);
LOG((4, "read dimids for this var"));
/* Update var->dim field based on the var->dimids. Ok if does not
* find a dim at this time, but if found set it. */
for (d = 0; d < var->ndims; d++)
nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
/* Remember that we have read the coordinates hidden attribute. */
var->coords_read = NC_TRUE;
exit:
if (spaceid >= 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (coord_att_typeid >= 0 && H5Tclose(coord_att_typeid) < 0)
BAIL2(NC_EHDFERR);
if (coord_attid >= 0 && H5Aclose(coord_attid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal This function is called when reading a file's metadata
* for each dimension scale attached to a variable.
*
* @param did HDF5 ID for dimscale.
* @param dim
* @param dsid
* @param dimscale_hdf5_objids
*
* @return 0 for success, -1 for error.
* @author Ed Hartnett
*/
static herr_t
dimscale_visitor(hid_t did, unsigned dim, hid_t dsid,
void *dimscale_hdf5_objids)
{
LOG((4, "%s", __func__));
/* Get more info on the dimscale object.*/
#if H5_VERSION_GE(1,12,0)
H5O_info2_t statbuf;
if (H5Oget_info3(dsid, &statbuf, H5O_INFO_BASIC) < 0)
return -1;
/* Pass this information back to caller. */
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno = statbuf.fileno;
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).token = statbuf.token;
#else
H5G_stat_t statbuf;
if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0)
return -1;
/* Pass this information back to caller. */
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[0] = statbuf.fileno[0];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[1] = statbuf.fileno[1];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[0] = statbuf.objno[0];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[1] = statbuf.objno[1];
#endif
return 0;
}
/**
* @internal For files without any netCDF-4 dimensions defined, create
* phony dimension to match the available datasets. Each new dimension
* of a new size gets a phony dimension. However, if a var has more
* than one dimension defined, and they are the same size, they each
* get their own phony dimension (starting in netcdf-c-4.7.3).
*
* @param grp Pointer to the group info.
* @param hdf_datasetid HDF5 datsetid for the var's dataset.
* @param var Pointer to the var info.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @returns NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
create_phony_dims(NC_GRP_INFO_T *grp, hid_t hdf_datasetid, NC_VAR_INFO_T *var)
{
NC_DIM_INFO_T *dim;
hid_t spaceid = 0;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int dataset_ndims;
int d;
int retval = NC_NOERR;
/* Find the space information for this dimension. */
if ((spaceid = H5Dget_space(hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
/* Get the len of each dim in the space. */
if (var->ndims)
{
/* Allocate storage for dim lens and max lens for this var. */
if (!(h5dimlen = malloc(var->ndims * sizeof(hsize_t))))
return NC_ENOMEM;
if (!(h5dimlenmax = malloc(var->ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
/* Get ndims, also len and mac len of all dims. */
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid, h5dimlen,
h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
assert(dataset_ndims == var->ndims);
}
else
{
/* Make sure it's scalar. */
assert(H5Sget_simple_extent_type(spaceid) == H5S_SCALAR);
}
/* Create a phony dimension for each dimension in the dataset,
* unless there already is one the correct size. */
for (d = 0; d < var->ndims; d++)
{
int k;
int match = 0;
/* Is there already a phony dimension of the correct size? */
for (k = 0; k < ncindexsize(grp->dim); k++)
{
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, k);
assert(dim);
if ((dim->len == h5dimlen[d]) &&
((h5dimlenmax[d] == H5S_UNLIMITED && dim->unlimited) ||
(h5dimlenmax[d] != H5S_UNLIMITED && !dim->unlimited)))
{
int k1;
/* We found a match! */
match++;
/* If this phony dimension has already in use for this
* var, we should not use it again. */
for (k1 = 0; k1 < d; k1++)
if (var->dimids[k1] == dim->hdr.id)
match = 0;
if (match)
break;
}
}
/* Didn't find a phony dim? Then create one. */
if (!match)
{
char phony_dim_name[NC_MAX_NAME + 1];
sprintf(phony_dim_name, "phony_dim_%d", grp->nc4_info->next_dimid);
LOG((3, "%s: creating phony dim for var %s", __func__, var->hdr.name));
/* Add phony dim to metadata list. */
if ((retval = nc4_dim_list_add(grp, phony_dim_name, h5dimlen[d], -1, &dim)))
BAIL(retval);
/* Create struct for HDF5-specific dim info. */
if (!(dim->format_dim_info = calloc(1, sizeof(NC_HDF5_DIM_INFO_T))))
BAIL(NC_ENOMEM);
if (h5dimlenmax[d] == H5S_UNLIMITED)
dim->unlimited = NC_TRUE;
}
/* The variable must remember the dimid. */
var->dimids[d] = dim->hdr.id;
var->dim[d] = dim;
} /* next dim */
exit:
/* Free resources. */
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (h5dimlenmax)
free(h5dimlenmax);
if (h5dimlen)
free(h5dimlen);
return retval;
}
/**
* @internal Iterate through the vars in this file and make sure we've
* got a dimid and a pointer to a dim for each dimension. This may
* already have been done using the COORDINATES hidden attribute, in
* which case this function will not have to do anything. This is
* desirable because recurdively matching the dimscales (when
* necessary) is very much the slowest part of opening a file.
*
* @param grp Pointer to group info struct.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @returns NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
rec_match_dimscales(NC_GRP_INFO_T *grp)
{
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
int retval = NC_NOERR;
int i;
assert(grp && grp->hdr.name);
LOG((4, "%s: grp->hdr.name %s", __func__, grp->hdr.name));
/* Perform var dimscale match for child groups. */
for (i = 0; i < ncindexsize(grp->children); i++)
if ((retval = rec_match_dimscales((NC_GRP_INFO_T *)ncindexith(grp->children, i))))
return retval;
/* Check all the vars in this group. If they have dimscale info,
* try and find a dimension for them. */
for (i = 0; i < ncindexsize(grp->vars); i++)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
int d;
/* Get pointer to var and to the HDF5-specific var info. */
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
assert(var && var->format_var_info);
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Check all vars and see if dim[i] != NULL if dimids[i]
* valid. Recall that dimids were initialized to -1. */
for (d = 0; d < var->ndims; d++)
{
if (!var->dim[d])
nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
}
/* Skip dimension scale variables */
if (hdf5_var->dimscale)
continue;
/* If we have already read hidden coordinates att, then we don't
* have to match dimscales for this var. */
if (var->coords_read)
continue;
/* Skip dimension scale variables */
if (!hdf5_var->dimscale)
{
int d;
int j;
/* Are there dimscales for this variable? */
if (hdf5_var->dimscale_hdf5_objids)
{
for (d = 0; d < var->ndims; d++)
{
NC_GRP_INFO_T *g;
nc_bool_t finished = NC_FALSE;
LOG((5, "%s: var %s has dimscale info...", __func__, var->hdr.name));
/* If we already have the dimension, we don't need to
* match the dimscales. This is better because matching
* the dimscales is slow. */
if (var->dim[d])
continue;
/* Now we have to try to match dimscales. Check this
* and parent groups. */
for (g = grp; g && !finished; g = g->parent)
{
/* Check all dims in this group. */
for (j = 0; j < ncindexsize(g->dim); j++)
{
/* Get the HDF5 specific dim info. */
NC_HDF5_DIM_INFO_T *hdf5_dim;
dim = (NC_DIM_INFO_T *)ncindexith(g->dim, j);
assert(dim && dim->format_dim_info);
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
/* Check for exact match of fileno/objid arrays
* to find identical objects in HDF5 file. */
#if H5_VERSION_GE(1,12,0)
int token_cmp;
if (H5Otoken_cmp(hdf5_var->hdf_datasetid,
&hdf5_var->dimscale_hdf5_objids[d].token,
&hdf5_dim->hdf5_objid.token, &token_cmp) < 0)
return NC_EHDFERR;
if (hdf5_var->dimscale_hdf5_objids[d].fileno == hdf5_dim->hdf5_objid.fileno &&
token_cmp == 0)
#else
if (hdf5_var->dimscale_hdf5_objids[d].fileno[0] == hdf5_dim->hdf5_objid.fileno[0] &&
hdf5_var->dimscale_hdf5_objids[d].objno[0] == hdf5_dim->hdf5_objid.objno[0] &&
hdf5_var->dimscale_hdf5_objids[d].fileno[1] == hdf5_dim->hdf5_objid.fileno[1] &&
hdf5_var->dimscale_hdf5_objids[d].objno[1] == hdf5_dim->hdf5_objid.objno[1])
#endif
{
LOG((4, "%s: for dimension %d, found dim %s", __func__,
d, dim->hdr.name));
var->dimids[d] = dim->hdr.id;
var->dim[d] = dim;
finished = NC_TRUE;
break;
}
} /* next dim */
} /* next grp */
} /* next var->dim */
}
else
{
/* No dimscales for this var! Invent phony dimensions. */
if ((retval = create_phony_dims(grp, hdf5_var->hdf_datasetid, var)))
return retval;
}
}
}
return retval;
}
/**
* @internal Check for the attribute that indicates that netcdf
* classic model is in use.
*
* @param root_grp pointer to the group info for the root group of the
* @param is_classic store 1 if this is a classic file.
* file.
*
* @return NC_NOERR No error.
* @author Ed Hartnett
*/
static int
check_for_classic_model(NC_GRP_INFO_T *root_grp, int *is_classic)
{
htri_t attr_exists;
hid_t grpid;
/* Check inputs. */
assert(root_grp && root_grp->format_grp_info && !root_grp->parent
&& is_classic);
/* Get the HDF5 group id. */
grpid = ((NC_HDF5_GRP_INFO_T *)(root_grp->format_grp_info))->hdf_grpid;
/* If this attribute exists in the root group, then classic model
* is in effect. */
if ((attr_exists = H5Aexists(grpid, NC3_STRICT_ATT_NAME)) < 0)
return NC_EHDFERR;
*is_classic = attr_exists ? 1 : 0;
return NC_NOERR;
}
/**
* @internal Open a netcdf-4 file. Things have already been kicked off
* in ncfunc.c in nc_open, but here the netCDF-4 part of opening a
* file is handled.
*
* @param path The file name of the new file.
* @param mode The open mode flag.
* @param parameters File parameters.
* @param ncid The ncid that has been assigned to this file.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EINTERNAL Internal list error.
* @return ::NC_EHDFERR HDF error.
* @return ::NC_EMPI MPI error for parallel.
* @return ::NC_EPARINIT Parallel I/O initialization error.
* @return ::NC_EINMEMMORY Memory file error.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
nc4_open_file(const char *path, int mode, void* parameters, int ncid)
{
NC_FILE_INFO_T *nc4_info = NULL;
NC_HDF5_FILE_INFO_T *h5 = NULL;
NC *nc;
hid_t fapl_id = H5P_DEFAULT;
unsigned flags;
int is_classic;
#ifdef USE_PARALLEL4
NC_MPI_INFO *mpiinfo = NULL;
int comm_duped = 0; /* Whether the MPI Communicator was duplicated */
int info_duped = 0; /* Whether the MPI Info object was duplicated */
#endif
int retval;
LOG((3, "%s: path %s mode %d", __func__, path, mode));
assert(path);
/* Find pointer to NC. */
if ((retval = NC_check_id(ncid, &nc)))
return retval;
assert(nc);
/* Determine the HDF5 open flag to use. */
flags = (mode & NC_WRITE) ? H5F_ACC_RDWR : H5F_ACC_RDONLY;
/* Add necessary structs to hold netcdf-4 file data. */
if ((retval = nc4_nc4f_list_add(nc, path, mode)))
BAIL(retval);
nc4_info = (NC_FILE_INFO_T *)nc->dispatchdata;
assert(nc4_info && nc4_info->root_grp);
/* Add struct to hold HDF5-specific file metadata. */
if (!(nc4_info->format_file_info = calloc(1, sizeof(NC_HDF5_FILE_INFO_T))))
BAIL(NC_ENOMEM);
/* Add struct to hold HDF5-specific group info. */
if (!(nc4_info->root_grp->format_grp_info = calloc(1, sizeof(NC_HDF5_GRP_INFO_T))))
BAIL(NC_ENOMEM);
h5 = (NC_HDF5_FILE_INFO_T*)nc4_info->format_file_info;
#ifdef ENABLE_BYTERANGE
/* See if we want the byte range protocol */
if(NC_testmode(path,"bytes")) {
h5->http.iosp = 1;
/* Kill off any conflicting modes flags */
mode &= ~(NC_WRITE|NC_DISKLESS|NC_PERSIST|NC_INMEMORY);
parameters = NULL; /* kill off parallel */
} else
h5->http.iosp = 0;
#endif /*ENABLE_BYTERANGE*/
nc4_info->mem.inmemory = ((mode & NC_INMEMORY) == NC_INMEMORY);
nc4_info->mem.diskless = ((mode & NC_DISKLESS) == NC_DISKLESS);
nc4_info->mem.persist = ((mode & NC_PERSIST) == NC_PERSIST);
/* Does the mode specify that this file is read-only? */
if ((mode & NC_WRITE) == 0)
nc4_info->no_write = NC_TRUE;
if(nc4_info->mem.inmemory && nc4_info->mem.diskless)
BAIL(NC_EINTERNAL);
#ifdef USE_PARALLEL4
mpiinfo = (NC_MPI_INFO *)parameters; /* assume, may be changed if inmemory is true */
#endif /* !USE_PARALLEL4 */
/* Need this access plist to control how HDF5 handles open objects
* on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to
* fail if there are any open objects in the file). */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI) < 0)
BAIL(NC_EHDFERR);
#ifdef USE_PARALLEL4
if (!(mode & (NC_INMEMORY | NC_DISKLESS)) && mpiinfo != NULL) {
/* If this is a parallel file create, set up the file creation
* property list. */
nc4_info->parallel = NC_TRUE;
LOG((4, "opening parallel file with MPI/IO"));
if (H5Pset_fapl_mpio(fapl_id, mpiinfo->comm, mpiinfo->info) < 0)
BAIL(NC_EPARINIT);
/* Keep copies of the MPI Comm & Info objects */
if (MPI_Comm_dup(mpiinfo->comm, &nc4_info->comm) != MPI_SUCCESS)
BAIL(NC_EMPI);
comm_duped++;
if (mpiinfo->info != MPI_INFO_NULL)
{
if (MPI_Info_dup(mpiinfo->info, &nc4_info->info) != MPI_SUCCESS)
BAIL(NC_EMPI);
info_duped++;
}
else
{
/* No dup, just copy it. */
nc4_info->info = mpiinfo->info;
}
}
#ifdef HDF5_HAS_COLL_METADATA_OPS
/* If collective metadata operations are available in HDF5, turn
* them on. */
if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0)
BAIL(NC_EPARINIT);
#endif /* HDF5_HAS_COLL_METADATA_OPS */
#endif /* USE_PARALLEL4 */
/* Only set cache for non-parallel opens. */
if (!nc4_info->parallel)
{
if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
nc4_chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
LOG((4, "%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
__func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems,
nc4_chunk_cache_preemption));
}
/* Process NC_INMEMORY */
if(nc4_info->mem.inmemory) {
NC_memio* memio;
/* validate */
if(parameters == NULL)
BAIL(NC_EINMEMORY);
memio = (NC_memio*)parameters;
if(memio->memory == NULL || memio->size == 0)
BAIL(NC_EINMEMORY);
/* initialize h5->mem */
nc4_info->mem.memio = *memio;
/* Is the incoming memory locked? */
nc4_info->mem.locked = (nc4_info->mem.memio.flags & NC_MEMIO_LOCKED) == NC_MEMIO_LOCKED;
/* As a safeguard, if not locked and not read-only,
then we must take control of the incoming memory */
if(!nc4_info->mem.locked && !nc4_info->no_write) {
memio->memory = NULL; /* take control */
memio->size = 0;
}
retval = NC4_open_image_file(nc4_info);
if(retval)
BAIL(NC_EHDFERR);
}
else
if(nc4_info->mem.diskless) { /* Process NC_DISKLESS */
size_t min_incr = 65536; /* Minimum buffer increment */
/* Configure FAPL to use the core file driver */
if (H5Pset_fapl_core(fapl_id, min_incr, (nc4_info->mem.persist?1:0)) < 0)
BAIL(NC_EHDFERR);
/* Open the HDF5 file. */
if ((h5->hdfid = H5Fopen(path, flags, fapl_id)) < 0)
BAIL(NC_EHDFERR);
}
#ifdef ENABLE_BYTERANGE
else
if(h5->http.iosp) { /* Arrange to use the byte-range driver */
/* Configure FAPL to use the byte-range file driver */
if (H5Pset_fapl_http(fapl_id) < 0)
BAIL(NC_EHDFERR);
/* Open the HDF5 file. */
if ((h5->hdfid = H5Fopen(path, flags, fapl_id)) < 0)
BAIL(NC_EHDFERR);
}
#endif
else
{
/* Open the HDF5 file. */
if ((h5->hdfid = H5Fopen(path, flags, fapl_id)) < 0)
BAIL(NC_EHDFERR);
}
/* Now read in all the metadata. Some types and dimscale
* information may be difficult to resolve here, if, for example, a
* dataset of user-defined type is encountered before the
* definition of that type. */
if ((retval = rec_read_metadata(nc4_info->root_grp)))
BAIL(retval);
/* Check for classic model attribute. */
if ((retval = check_for_classic_model(nc4_info->root_grp, &is_classic)))
BAIL(retval);
if (is_classic)
nc4_info->cmode |= NC_CLASSIC_MODEL;
/* Set the provenance info for this file */
if ((retval = NC4_read_provenance(nc4_info)))
BAIL(retval);
/* Now figure out which netCDF dims are indicated by the dimscale
* information. */
if ((retval = rec_match_dimscales(nc4_info->root_grp)))
BAIL(retval);
#ifdef LOGGING
/* This will print out the names, types, lens, etc of the vars and
atts in the file, if the logging level is 2 or greater. */
log_metadata_nc(nc4_info);
#endif
/* Close the property list. */
if (H5Pclose(fapl_id) < 0)
BAIL(NC_EHDFERR);
return NC_NOERR;
exit:
#ifdef USE_PARALLEL4
if (comm_duped) MPI_Comm_free(&nc4_info->comm);
if (info_duped) MPI_Info_free(&nc4_info->info);
#endif
if (fapl_id > 0 && fapl_id != H5P_DEFAULT)
H5Pclose(fapl_id);
if (nc4_info)
nc4_close_hdf5_file(nc4_info, 1, 0); /* treat like abort*/
return retval;
}
/**
* @internal Open a netCDF-4 file.
*
* @param path The file name of the new file.
* @param mode The open mode flag.
* @param basepe Ignored by this function.
* @param chunksizehintp Ignored by this function.
* @param parameters pointer to struct holding extra data (e.g. for parallel I/O)
* layer. Ignored if NULL.
* @param dispatch Pointer to the dispatch table for this file.
* @param nc_file Pointer to an instance of NC.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid inputs.
* @author Ed Hartnett
*/
int
NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
void *parameters, const NC_Dispatch *dispatch, int ncid)
{
assert(path && dispatch);
LOG((1, "%s: path %s mode %d params %x",
__func__, path, mode, parameters));
/* Check the mode for validity */
if (mode & ILLEGAL_OPEN_FLAGS)
return NC_EINVAL;
if((mode & NC_DISKLESS) && (mode & NC_INMEMORY))
return NC_EINVAL;
/* If this is our first file, initialize HDF5. */
if (!nc4_hdf5_initialized)
nc4_hdf5_initialize();
#ifdef LOGGING
/* If nc logging level has changed, see if we need to turn on
* HDF5's error messages. */
hdf5_set_log_level();
#endif /* LOGGING */
/* Open the file. */
return nc4_open_file(path, mode, parameters, ncid);
}
/**
* @internal Find out what filters are applied to this HDF5 dataset,
* fletcher32, deflate, and/or shuffle. All other filters are
* captured.
*
* @param propid ID of HDF5 var creation properties list.
* @param var Pointer to NC_VAR_INFO_T for this variable.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int get_filter_info(hid_t propid, NC_VAR_INFO_T *var)
{
H5Z_filter_t filter;
int num_filters;
unsigned int* cd_values = NULL;
size_t cd_nelems;
int f;
int stat = NC_NOERR;
NC_FILTERX_SPEC* spec = NULL;
assert(var);
if ((num_filters = H5Pget_nfilters(propid)) < 0)
{stat = NC_EHDFERR; goto done;}
for (f = 0; f < num_filters; f++)
{
cd_nelems = 0;
if ((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems, NULL, 0, NULL, NULL)) < 0)
{stat = NC_EHDFERR; goto done;}
if((cd_values = calloc(sizeof(unsigned int),cd_nelems))==NULL)
{stat = NC_EHDFERR; goto done;}
if ((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems, cd_values, 0, NULL, NULL)) < 0)
{stat = NC_EHDFERR; goto done;}
switch (filter)
{
case H5Z_FILTER_SHUFFLE:
var->shuffle = NC_TRUE;
break;
case H5Z_FILTER_FLETCHER32:
var->fletcher32 = NC_TRUE;
break;
case H5Z_FILTER_DEFLATE:
if (cd_nelems != CD_NELEMS_ZLIB ||
cd_values[0] > NC_MAX_DEFLATE_LEVEL)
{stat = NC_EHDFERR; goto done;}
if((stat = NC4_hdf5_addfilter(var,FILTERACTIVE,filter,cd_nelems,cd_values)))
goto done;
break;
case H5Z_FILTER_SZIP: {
/* Szip is tricky because the filter code expands the set of parameters from 2 to 4
and changes some of the parameter values; try to compensate */
if(cd_nelems == 0) {
if((stat = NC4_hdf5_addfilter(var,FILTERACTIVE,filter,0,NULL)))
goto done;
} else {
/* fix up the parameters and the #params */
if(cd_nelems != 4)
{stat = NC_EHDFERR; goto done;}
cd_nelems = 2; /* ignore last two */
/* Fix up changed params */
cd_values[0] &= (H5_SZIP_ALL_MASKS);
/* Save info */
stat = NC4_hdf5_addfilter(var,FILTERACTIVE,filter,cd_nelems,cd_values);
if(stat) goto done;
}
} break;
default:
if(cd_nelems == 0) {
if((stat = NC4_hdf5_addfilter(var,FILTERACTIVE,filter,0,NULL))) goto done;
} else {
stat = NC4_hdf5_addfilter(var,FILTERACTIVE,filter,cd_nelems,cd_values);
if(stat) goto done;
}
break;
}
nullfree(cd_values); cd_values = NULL;
}
done:
nullfree(cd_values);
NC4_filterx_free(spec);
return stat;
}
/**
* @internal Learn if there is a fill value defined for a variable,
* and, if so, its value.
*
* @param propid ID of HDF5 var creation properties list.
* @param var Pointer to NC_VAR_INFO_T for this variable.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int get_fill_info(hid_t propid, NC_VAR_INFO_T *var)
{
H5D_fill_value_t fill_status;
/* Is there a fill value associated with this dataset? */
if (H5Pfill_value_defined(propid, &fill_status) < 0)
return NC_EHDFERR;
/* Get the fill value, if there is one defined. */
if (fill_status == H5D_FILL_VALUE_USER_DEFINED)
{
/* Allocate space to hold the fill value. */
if (!var->fill_value)
{
if (var->type_info->nc_type_class == NC_VLEN)
{
if (!(var->fill_value = malloc(sizeof(nc_vlen_t))))
return NC_ENOMEM;
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if (!(var->fill_value = malloc(sizeof(char *))))
return NC_ENOMEM;
}
else
{
assert(var->type_info->size);
if (!(var->fill_value = malloc(var->type_info->size)))
return NC_ENOMEM;
}
}
/* Get the fill value from the HDF5 property lust. */
if (H5Pget_fill_value(propid, ((NC_HDF5_TYPE_INFO_T *)var->type_info->format_type_info)->native_hdf_typeid,
var->fill_value) < 0)
return NC_EHDFERR;
}
else
var->no_fill = NC_TRUE;
return NC_NOERR;
}
/**
* @internal Learn the storage and (if chunked) chunksizes of a var.
*
* @param propid ID of HDF5 var creation properties list.
* @param var Pointer to NC_VAR_INFO_T for this variable.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
get_chunking_info(hid_t propid, NC_VAR_INFO_T *var)
{
H5D_layout_t layout;
hsize_t chunksize[H5S_MAX_RANK] = {0};
int d;
/* Get the chunking info the var. */
if ((layout = H5Pget_layout(propid)) < -1)
return NC_EHDFERR;
/* Remember the layout and, if chunked, the chunksizes. */
if (layout == H5D_CHUNKED)
{
var->storage = NC_CHUNKED;
if (H5Pget_chunk(propid, H5S_MAX_RANK, chunksize) < 0)
return NC_EHDFERR;
if (!(var->chunksizes = malloc(var->ndims * sizeof(size_t))))
return NC_ENOMEM;
for (d = 0; d < var->ndims; d++)
var->chunksizes[d] = chunksize[d];
}
else if (layout == H5D_CONTIGUOUS)
{
var->storage = NC_CONTIGUOUS;
}
else if (layout == H5D_COMPACT)
{
var->storage = NC_COMPACT;
}
return NC_NOERR;
}
/**
* @internal This function gets info about the dimscales attached to a
* dataset. The info is used later for dimscale matching.
*
* @param var Pointer to var info struct.
* @param hdf5_var Pointer to HDF5 var info struct.
* @param ndims Number of dims for this var.
* @param datasetid HDF5 datasetid.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EVARMETA Error with var metadata.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
get_attached_info(NC_VAR_INFO_T *var, NC_HDF5_VAR_INFO_T *hdf5_var, int ndims,
hid_t datasetid)
{
int d;
int num_scales = 0;
LOG((4, "%s ndims %d datasetid %ld", __func__, ndims, datasetid));
/* Find out how many scales are attached to this
* dataset. H5DSget_num_scales returns an error if there are no
* scales, so convert a negative return value to zero. */
num_scales = H5DSget_num_scales(datasetid, 0);
if (num_scales < 0)
num_scales = 0;
LOG((4, "num_scales %d", num_scales));
/* If an enddef has already been called, the dimscales will already
* be taken care of. */
if (num_scales && ndims && !hdf5_var->dimscale_attached)
{
/* Allocate space to remember whether the dimscale has been
* attached for each dimension, and the HDF5 object IDs of the
* scale(s). */
assert(!hdf5_var->dimscale_hdf5_objids);
if (!(hdf5_var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
return NC_ENOMEM;
if (!(hdf5_var->dimscale_hdf5_objids = malloc(ndims *
sizeof(struct hdf5_objid))))
return NC_ENOMEM;
/* Store id information allowing us to match hdf5 dimscales to
* netcdf dimensions. */
for (d = 0; d < var->ndims; d++)
{
LOG((4, "about to iterate scales for dim %d", d));
if (H5DSiterate_scales(hdf5_var->hdf_datasetid, d, NULL, dimscale_visitor,
&(hdf5_var->dimscale_hdf5_objids[d])) < 0)
return NC_EHDFERR;
hdf5_var->dimscale_attached[d] = NC_TRUE;
LOG((4, "dimscale attached"));
}
}
return NC_NOERR;
}
/**
* @internal This function reads scale info for vars, whether they
* are scales or not.
*
* @param grp Pointer to group info struct.
* @param dim Pointer to dim info struct if this is a scale, NULL
* otherwise.
* @param var Pointer to var info struct.
* @param hdf5_var Pointer to HDF5 var info struct.
* @param ndims Number of dims for this var.
* @param datasetid HDF5 datasetid.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EVARMETA Error with var metadata.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
get_scale_info(NC_GRP_INFO_T *grp, NC_DIM_INFO_T *dim, NC_VAR_INFO_T *var,
NC_HDF5_VAR_INFO_T *hdf5_var, int ndims, hid_t datasetid)
{
int retval;
/* If it's a scale, mark it as such. */
if (dim)
{
assert(ndims);
hdf5_var->dimscale = NC_TRUE;
/* If this is a multi-dimensional coordinate var, then the
* dimids must be stored in the hidden coordinates attribute. */
if (var->ndims > 1)
{
if ((retval = read_coord_dimids(grp, var)))
return retval;
}
else
{
/* This is a 1-dimensional coordinate var. */
assert(!strcmp(var->hdr.name, dim->hdr.name));
var->dimids[0] = dim->hdr.id;
var->dim[0] = dim;
}
dim->coord_var = var;
}
else /* Not a scale. */
{
if (!var->coords_read)
if ((retval = get_attached_info(var, hdf5_var, ndims, datasetid)))
return retval;
}
return NC_NOERR;
}
/**
* @internal Get the metadata for a variable.
*
* @param var Pointer to var info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EVARMETA Error with var metadata.
* @author Ed Hartnett
*/
int
nc4_get_var_meta(NC_VAR_INFO_T *var)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
hid_t access_pid = 0;
hid_t propid = 0;
double rdcc_w0;
int retval = NC_NOERR;
assert(var && var->format_var_info);
LOG((3, "%s: var %s", __func__, var->hdr.name));
/* Have we already read the var metadata? */
if (var->meta_read)
return NC_NOERR;
/* Get pointer to the HDF5-specific var info struct. */
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Get the current chunk cache settings. */
if ((access_pid = H5Dget_access_plist(hdf5_var->hdf_datasetid)) < 0)
BAIL(NC_EVARMETA);
/* Learn about current chunk cache settings. */
if ((H5Pget_chunk_cache(access_pid, &(var->chunk_cache_nelems),
&(var->chunk_cache_size), &rdcc_w0)) < 0)
BAIL(NC_EHDFERR);
var->chunk_cache_preemption = rdcc_w0;
/* Get the dataset creation properties. */
if ((propid = H5Dget_create_plist(hdf5_var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
/* Get var chunking info. */
if ((retval = get_chunking_info(propid, var)))
BAIL(retval);
/* Get filter info for a var. */
if ((retval = get_filter_info(propid, var)))
BAIL(retval);
/* Get fill value, if defined. */
if ((retval = get_fill_info(propid, var)))
BAIL(retval);
/* Is this a deflated variable with a chunksize greater than the
* current cache size? */
if ((retval = nc4_adjust_var_cache(var->container, var)))
BAIL(retval);
if (var->coords_read && !hdf5_var->dimscale)
if ((retval = get_attached_info(var, hdf5_var, var->ndims, hdf5_var->hdf_datasetid)))
return retval;
/* Remember that we have read the metadata for this var. */
var->meta_read = NC_TRUE;
exit:
if (access_pid && H5Pclose(access_pid) < 0)
BAIL2(NC_EHDFERR);
if (propid > 0 && H5Pclose(propid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal This function is called by read_dataset(), (which is
* called by rec_read_metadata()) when a netCDF variable is found in
* the file. This function reads in all the metadata about the
* var. Attributes are not read until the user asks for information
* about one of them.
*
* @param grp Pointer to group info struct.
* @param datasetid HDF5 dataset ID.
* @param obj_name Name of the HDF5 object to read.
* @param ndims Number of dimensions.
* @param dim If non-NULL, then this var is a coordinate var for a
* dimension, and this points to the info for that dimension.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EVARMETA Error with var metadata.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
size_t ndims, NC_DIM_INFO_T *dim)
{
NC_VAR_INFO_T *var = NULL;
NC_HDF5_VAR_INFO_T *hdf5_var;
int incr_id_rc = 0; /* Whether dataset ID's ref count has been incremented */
char *finalname = NULL;
int retval = NC_NOERR;
assert(obj_name && grp);
LOG((4, "%s: obj_name %s", __func__, obj_name));
/* Check for a weird case: a non-coordinate variable that has the
* same name as a dimension. It's legal in netcdf, and requires
* that the HDF5 dataset name be changed. */
if (strlen(obj_name) > strlen(NON_COORD_PREPEND) &&
!strncmp(obj_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)))
{
/* Allocate space for the name. */
if (!(finalname = malloc(((strlen(obj_name) -
strlen(NON_COORD_PREPEND))+ 1) * sizeof(char))))
BAIL(NC_ENOMEM);
strcpy(finalname, &obj_name[strlen(NON_COORD_PREPEND)]);
} else
finalname = strdup(obj_name);
/* Add a variable to the end of the group's var list. */
if ((retval = nc4_var_list_add(grp, finalname, ndims, &var)))
BAIL(retval);
/* Add storage for HDF5-specific var info. */
if (!(var->format_var_info = calloc(1, sizeof(NC_HDF5_VAR_INFO_T))))
BAIL(NC_ENOMEM);
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Fill in what we already know. */
hdf5_var->hdf_datasetid = datasetid;
H5Iinc_ref(hdf5_var->hdf_datasetid); /* Increment number of objects using ID */
incr_id_rc++; /* Indicate that we've incremented the ref. count (for errors) */
var->created = NC_TRUE;
var->atts_read = 0;
/* Try and read the dimids from the COORDINATES attribute. If it's
* not present, we will have to do dimsscale matching to locate the
* dims for this var. */
retval = read_coord_dimids(grp, var);
if (retval && retval != NC_ENOTATT)
BAIL(retval);
retval = NC_NOERR;
/* Handle scale info. */
if ((retval = get_scale_info(grp, dim, var, hdf5_var, ndims, datasetid)))
BAIL(retval);
/* Learn all about the type of this variable. This will fail for
* HDF5 reference types, and then the var we just created will be
* deleted, thus ignoring HDF5 reference type objects. */
if ((retval = get_type_info2(var->container->nc4_info, hdf5_var->hdf_datasetid,
&var->type_info)))
BAIL(retval);
/* Indicate that the variable has a pointer to the type */
var->type_info->rc++;
/* Transfer endianness */
var->endianness = var->type_info->endianness;
exit:
if (finalname)
free(finalname);
if (retval)
{
/* If there was an error, decrement the dataset ref counter, and
* delete the var info struct we just created. */
if (incr_id_rc && H5Idec_ref(datasetid) < 0)
BAIL2(NC_EHDFERR);
if(var && var->format_var_info)
free(var->format_var_info);
if (var)
nc4_var_list_del(grp, var);
}
return retval;
}
/**
* @internal Given an HDF5 type, set a pointer to netcdf type.
*
* @param h5 Pointer to HDF5 file info struct.
* @param native_typeid HDF5 type ID.
* @param xtype Pointer that gets netCDF type.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EBADTYPID Type not found.
* @author Ed Hartnett
*/
static int
get_netcdf_type(NC_FILE_INFO_T *h5, hid_t native_typeid,
nc_type *xtype)
{
NC_TYPE_INFO_T *type;
H5T_class_t class;
htri_t is_str, equal = 0;
assert(h5 && xtype);
if ((class = H5Tget_class(native_typeid)) < 0)
return NC_EHDFERR;
/* H5Tequal doesn't work with H5T_C_S1 for some reason. But
* H5Tget_class will return H5T_STRING if this is a string. */
if (class == H5T_STRING)
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
if (is_str)
*xtype = NC_STRING;
else
*xtype = NC_CHAR;
return NC_NOERR;
}
else if (class == H5T_INTEGER || class == H5T_FLOAT)
{
/* For integers and floats, we don't have to worry about
* endianness if we compare native types. */
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SCHAR)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_BYTE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SHORT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_SHORT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_INT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_INT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_FLOAT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_FLOAT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_DOUBLE)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_DOUBLE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UCHAR)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UBYTE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_USHORT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_USHORT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UINT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UINT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_LLONG)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_INT64;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_ULLONG)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UINT64;
return NC_NOERR;
}
}
/* Maybe we already know about this type. */
if (!equal)
if((type = nc4_rec_find_hdf_type(h5, native_typeid)))
{
*xtype = type->hdr.id;
return NC_NOERR;
}
*xtype = NC_NAT;
return NC_EBADTYPID;
}
/**
* @internal Read an attribute. This is called by
* att_read_callbk().
*
* @param grp Pointer to group info struct.
* @param attid Attribute ID.
* @param att Pointer that gets att info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EATTMETA Att metadata error.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
{
NC_HDF5_ATT_INFO_T *hdf5_att;
hid_t spaceid = 0, file_typeid = 0;
hsize_t dims[1] = {0}; /* netcdf attributes always 1-D. */
size_t type_size;
int att_ndims;
hssize_t att_npoints;
H5T_class_t att_class;
int fixed_len_string = 0;
size_t fixed_size = 0;
int retval = NC_NOERR;
assert(att && att->hdr.name && att->format_att_info);
LOG((5, "%s: att->hdr.id %d att->hdr.name %s att->nc_typeid %d att->len %d",
__func__, att->hdr.id, att->hdr.name, (int)att->nc_typeid, att->len));
/* Get HDF5-sepecific info struct for this attribute. */
hdf5_att = (NC_HDF5_ATT_INFO_T *)att->format_att_info;
/* Get type of attribute in file. */
if ((file_typeid = H5Aget_type(attid)) < 0)
return NC_EATTMETA;
if ((hdf5_att->native_hdf_typeid = H5Tget_native_type(file_typeid,
H5T_DIR_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if ((att_class = H5Tget_class(hdf5_att->native_hdf_typeid)) < 0)
BAIL(NC_EATTMETA);
if (att_class == H5T_STRING &&
!H5Tis_variable_str(hdf5_att->native_hdf_typeid))
{
fixed_len_string++;
if (!(fixed_size = H5Tget_size(hdf5_att->native_hdf_typeid)))
BAIL(NC_EATTMETA);
}
if ((retval = get_netcdf_type(grp->nc4_info, hdf5_att->native_hdf_typeid,
&(att->nc_typeid))))
BAIL(retval);
/* Get len. */
if ((spaceid = H5Aget_space(attid)) < 0)
BAIL(NC_EATTMETA);
if ((att_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EATTMETA);
if ((att_npoints = H5Sget_simple_extent_npoints(spaceid)) < 0)
BAIL(NC_EATTMETA);
/* If both att_ndims and att_npoints are zero, then this is a
* zero length att. */
if (att_ndims == 0 && att_npoints == 0)
dims[0] = 0;
else if (att->nc_typeid == NC_STRING)
dims[0] = att_npoints;
else if (att->nc_typeid == NC_CHAR)
{
/* NC_CHAR attributes are written as a scalar in HDF5, of type
* H5T_C_S1, of variable length. */
if (att_ndims == 0)
{
if (!(dims[0] = H5Tget_size(file_typeid)))
BAIL(NC_EATTMETA);
}
else
{
/* This is really a string type! */
att->nc_typeid = NC_STRING;
dims[0] = att_npoints;
}
}
else
{
H5S_class_t space_class;
/* All netcdf attributes are scalar or 1-D only. */
if (att_ndims > 1)
BAIL(NC_EATTMETA);
/* Check class of HDF5 dataspace */
if ((space_class = H5Sget_simple_extent_type(spaceid)) < 0)
BAIL(NC_EATTMETA);
/* Check for NULL HDF5 dataspace class (should be weeded out
* earlier) */
if (H5S_NULL == space_class)
BAIL(NC_EATTMETA);
/* check for SCALAR HDF5 dataspace class */
if (H5S_SCALAR == space_class)
dims[0] = 1;
else /* Must be "simple" dataspace */
{
/* Read the size of this attribute. */
if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0)
BAIL(NC_EATTMETA);
}
}
/* Tell the user what the length if this attribute is. */
att->len = dims[0];
/* Allocate some memory if the len is not zero, and read the
attribute. */
if (dims[0])
{
if ((retval = nc4_get_typelen_mem(grp->nc4_info, att->nc_typeid,
&type_size)))
return retval;
if (att_class == H5T_VLEN)
{
if (!(att->vldata = malloc((unsigned int)(att->len * sizeof(hvl_t)))))
BAIL(NC_ENOMEM);
if (H5Aread(attid, hdf5_att->native_hdf_typeid, att->vldata) < 0)
BAIL(NC_EATTMETA);
}
else if (att->nc_typeid == NC_STRING)
{
if (!(att->stdata = calloc(att->len, sizeof(char *))))
BAIL(NC_ENOMEM);
/* For a fixed length HDF5 string, the read requires
* contiguous memory. Meanwhile, the netCDF API requires that
* nc_free_string be called on string arrays, which would not
* work if one contiguous memory block were used. So here I
* convert the contiguous block of strings into an array of
* malloced strings (each string with its own malloc). Then I
* copy the data and free the contiguous memory. This
* involves copying the data, which is bad, but this only
* occurs for fixed length string attributes, and presumably
* these are small. (And netCDF-4 does not create them - it
* always uses variable length strings. */
if (fixed_len_string)
{
int i;
char *contig_buf, *cur;
/* Alloc space for the contiguous memory read. */
if (!(contig_buf = malloc(att->len * fixed_size * sizeof(char))))
BAIL(NC_ENOMEM);
/* Read the fixed-len strings as one big block. */
if (H5Aread(attid, hdf5_att->native_hdf_typeid, contig_buf) < 0) {
free(contig_buf);
BAIL(NC_EATTMETA);
}
/* Copy strings, one at a time, into their new home. Alloc
space for each string. The user will later free this
space with nc_free_string. */
cur = contig_buf;
for (i = 0; i < att->len; i++)
{
if (!(att->stdata[i] = malloc(fixed_size))) {
free(contig_buf);
BAIL(NC_ENOMEM);
}
strncpy(att->stdata[i], cur, fixed_size);
cur += fixed_size;
}
/* Free contiguous memory buffer. */
free(contig_buf);
}
else
{
/* Read variable-length string atts. */
if (H5Aread(attid, hdf5_att->native_hdf_typeid, att->stdata) < 0)
BAIL(NC_EATTMETA);
}
}
else
{
if (!(att->data = malloc((unsigned int)(att->len * type_size))))
BAIL(NC_ENOMEM);
if (H5Aread(attid, hdf5_att->native_hdf_typeid, att->data) < 0)
BAIL(NC_EATTMETA);
}
}
if (H5Tclose(file_typeid) < 0)
BAIL(NC_EHDFERR);
if (H5Sclose(spaceid) < 0)
return NC_EHDFERR;
return NC_NOERR;
exit:
if (H5Tclose(file_typeid) < 0)
BAIL2(NC_EHDFERR);
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Wrap HDF5 allocated memory free operations
*
* @param memory Pointer to memory to be freed.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static void
hdf5free(void* memory)
{
#ifndef JNA
/* On Windows using the microsoft runtime, it is an error
for one library to free memory allocated by a different library.*/
#ifdef HAVE_H5FREE_MEMORY
if(memory != NULL) H5free_memory(memory);
#else
#ifndef _MSC_VER
if(memory != NULL) free(memory);
#endif
#endif
#endif
}
/**
* @internal Read information about a user defined type from the HDF5
* file, and stash it in the group's list of types.
*
* @param grp Pointer to group info struct.
* @param hdf_typeid HDF5 type ID.
* @param type_name Pointer that gets the type name.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EBADTYPID Type not found.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
{
NC_TYPE_INFO_T *type;
NC_HDF5_TYPE_INFO_T *hdf5_type;
H5T_class_t class;
hid_t native_typeid;
size_t type_size;
int nmembers;
int retval;
assert(grp && type_name);
LOG((4, "%s: type_name %s grp->hdr.name %s", __func__, type_name,
grp->hdr.name));
/* What is the native type for this platform? */
if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* What is the size of this type on this platform. */
if (!(type_size = H5Tget_size(native_typeid)))
return NC_EHDFERR;
LOG((5, "type_size %d", type_size));
/* Add to the list for this new type, and get a local pointer to it. */
if ((retval = nc4_type_list_add(grp, type_size, type_name, &type)))
return retval;
/* Allocate storage for HDF5-specific type info. */
if (!(hdf5_type = calloc(1, sizeof(NC_HDF5_TYPE_INFO_T))))
return NC_ENOMEM;
type->format_type_info = hdf5_type;
/* Remember HDF5-specific type info. */
hdf5_type->hdf_typeid = hdf_typeid;
hdf5_type->native_hdf_typeid = native_typeid;
/* Remember we have committed this type. */
type->committed = NC_TRUE;
/* Increment number of objects using ID. */
if (H5Iinc_ref(hdf5_type->hdf_typeid) < 0)
return NC_EHDFERR;
/* What is the class of this type, compound, vlen, etc. */
if ((class = H5Tget_class(hdf_typeid)) < 0)
return NC_EHDFERR;
switch (class)
{
case H5T_STRING:
type->nc_type_class = NC_STRING;
break;
case H5T_COMPOUND:
{
int nmembers;
unsigned int m;
char* member_name = NULL;
#ifdef JNA
char jna[1001];
#endif
type->nc_type_class = NC_COMPOUND;
if ((nmembers = H5Tget_nmembers(hdf_typeid)) < 0)
return NC_EHDFERR;
LOG((5, "compound type has %d members", nmembers));
type->u.c.field = nclistnew();
nclistsetalloc(type->u.c.field,nmembers);
for (m = 0; m < nmembers; m++)
{
hid_t member_hdf_typeid;
hid_t member_native_typeid;
size_t member_offset;
H5T_class_t mem_class;
nc_type member_xtype;
/* Get the typeid and native typeid of this member of the
* compound type. */
if ((member_hdf_typeid = H5Tget_member_type(native_typeid, m)) < 0)
return NC_EHDFERR;
if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* Get the name of the member.*/
member_name = H5Tget_member_name(native_typeid, m);
if (!member_name || strlen(member_name) > NC_MAX_NAME) {
retval = NC_EBADNAME;
break;
}
#ifdef JNA
else {
strncpy(jna,member_name,1000);
member_name = jna;
}
#endif
/* Offset in bytes on *this* platform. */
member_offset = H5Tget_member_offset(native_typeid, m);
/* Get dimensional data if this member is an array of something. */
if ((mem_class = H5Tget_class(member_hdf_typeid)) < 0)
return NC_EHDFERR;
if (mem_class == H5T_ARRAY)
{
int ndims, dim_size[NC_MAX_VAR_DIMS];
hsize_t dims[NC_MAX_VAR_DIMS];
int d;
if ((ndims = H5Tget_array_ndims(member_hdf_typeid)) < 0)
return NC_EHDFERR;
if (H5Tget_array_dims(member_hdf_typeid, dims, NULL) != ndims)
return NC_EHDFERR;
for (d = 0; d < ndims; d++)
dim_size[d] = dims[d];
/* What is the netCDF typeid of this member? */
if ((retval = get_netcdf_type(grp->nc4_info, H5Tget_super(member_hdf_typeid),
&member_xtype)))
return retval;
/* Add this member to our list of fields in this compound type. */
if ((retval = nc4_field_list_add(type, member_name, member_offset,
member_xtype, ndims, dim_size)))
return retval;
}
else
{
/* What is the netCDF typeid of this member? */
if ((retval = get_netcdf_type(grp->nc4_info, member_native_typeid,
&member_xtype)))
return retval;
/* Add this member to our list of fields in this compound type. */
if ((retval = nc4_field_list_add(type, member_name, member_offset,
member_xtype, 0, NULL)))
return retval;
}
hdf5free(member_name);
}
}
break;
case H5T_VLEN:
{
htri_t ret;
/* For conveninence we allow user to pass vlens of strings
* with null terminated strings. This means strings are
* treated slightly differently by the API, although they are
* really just VLENs of characters. */
if ((ret = H5Tis_variable_str(hdf_typeid)) < 0)
return NC_EHDFERR;
if (ret)
type->nc_type_class = NC_STRING;
else
{
hid_t base_hdf_typeid;
nc_type base_nc_type = NC_NAT;
type->nc_type_class = NC_VLEN;
/* Find the base type of this vlen (i.e. what is this a
* vlen of?) */
if (!(base_hdf_typeid = H5Tget_super(native_typeid)))
return NC_EHDFERR;
/* What size is this type? */
if (!(type_size = H5Tget_size(base_hdf_typeid)))
return NC_EHDFERR;
/* What is the netcdf corresponding type. */
if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
&base_nc_type)))
return retval;
LOG((5, "base_hdf_typeid 0x%x type_size %d base_nc_type %d",
base_hdf_typeid, type_size, base_nc_type));
/* Remember the base type for this vlen. */
type->u.v.base_nc_typeid = base_nc_type;
}
}
break;
case H5T_OPAQUE:
type->nc_type_class = NC_OPAQUE;
break;
case H5T_ENUM:
{
hid_t base_hdf_typeid;
nc_type base_nc_type = NC_NAT;
void *value;
int i;
char *member_name = NULL;
#ifdef JNA
char jna[1001];
#endif
type->nc_type_class = NC_ENUM;
/* Find the base type of this enum (i.e. what is this a
* enum of?) */
if (!(base_hdf_typeid = H5Tget_super(hdf_typeid)))
return NC_EHDFERR;
/* What size is this type? */
if (!(type_size = H5Tget_size(base_hdf_typeid)))
return NC_EHDFERR;
/* What is the netcdf corresponding type. */
if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
&base_nc_type)))
return retval;
LOG((5, "base_hdf_typeid 0x%x type_size %d base_nc_type %d",
base_hdf_typeid, type_size, base_nc_type));
/* Remember the base type for this enum. */
type->u.e.base_nc_typeid = base_nc_type;
/* Find out how many member are in the enum. */
if ((nmembers = H5Tget_nmembers(hdf_typeid)) < 0)
return NC_EHDFERR;
type->u.e.enum_member = nclistnew();
nclistsetalloc(type->u.e.enum_member,nmembers);
/* Allocate space for one value. */
if (!(value = calloc(1, type_size)))
return NC_ENOMEM;
/* Read each name and value defined in the enum. */
for (i = 0; i < nmembers; i++)
{
/* Get the name and value from HDF5. */
if (!(member_name = H5Tget_member_name(hdf_typeid, i)))
return NC_EHDFERR;
#ifdef JNA
strncpy(jna,member_name,1000);
member_name = jna;
#endif
if (strlen(member_name) > NC_MAX_NAME)
return NC_EBADNAME;
if (H5Tget_member_value(hdf_typeid, i, value) < 0)
return NC_EHDFERR;
/* Insert new field into this type's list of fields. */
if ((retval = nc4_enum_member_add(type, type->size,
member_name, value)))
return retval;
hdf5free(member_name);
}
free(value);
}
break;
default:
LOG((0, "unknown class"));
return NC_EBADCLASS;
}
return retval;
}
/**
* @internal Callback function for reading attributes. This is used
* for both global and variable attributes.
*
* @param loc_id HDF5 attribute ID.
* @param att_name Name of the attrigute.
* @param ainfo HDF5 info struct for attribute.
* @param att_data Pointer to an att_iter_info struct, which contains
* pointers to the NC_GRP_INFO_T and (for variable attributes) the
* NC_VAR_INFO_T. For global atts the var pointer is NULL.
*
* @return ::NC_NOERR No error. Iteration continues.
* @return ::-1 Error. Stop iteration.
* @author Ed Hartnett
*/
static herr_t
att_read_callbk(hid_t loc_id, const char *att_name, const H5A_info_t *ainfo,
void *att_data)
{
hid_t attid = 0;
NC_ATT_INFO_T *att;
NCindex *list;
att_iter_info *att_info = (att_iter_info *)att_data;
int retval = NC_NOERR;
/* Determine what list is being added to. */
list = att_info->var ? att_info->var->att : att_info->grp->att;
/* This may be an attribute telling us that strict netcdf-3 rules
* are in effect. If so, we will make note of the fact, but not add
* this attribute to the metadata. It's not a user attribute, but
* an internal netcdf-4 one. */
if (!strcmp(att_name, NC3_STRICT_ATT_NAME))
{
/* Only relevant for groups, not vars. */
if (!att_info->var)
att_info->grp->nc4_info->cmode |= NC_CLASSIC_MODEL;
return NC_NOERR;
}
/* Should we ignore this attribute? */
if (NC_findreserved(att_name))
return NC_NOERR;
/* Add to the end of the list of atts for this var. */
if ((retval = nc4_att_list_add(list, att_name, &att)))
BAIL(-1);
/* Allocate storage for the HDF5 specific att info. */
if (!(att->format_att_info = calloc(1, sizeof(NC_HDF5_ATT_INFO_T))))
BAIL(-1);
/* Open the att by name. */
if ((attid = H5Aopen(loc_id, att_name, H5P_DEFAULT)) < 0)
BAIL(-1);
LOG((4, "%s:: att_name %s", __func__, att_name));
/* Read the rest of the info about the att,
* including its values. */
if ((retval = read_hdf5_att(att_info->grp, attid, att)))
BAIL(retval);
if (att)
att->created = NC_TRUE;
exit:
if (retval == NC_EBADTYPID)
{
/* NC_EBADTYPID will be normally converted to NC_NOERR so that
the parent iterator does not fail. */
/* Free up the format_att_info */
if((retval=nc4_HDF5_close_att(att))) return retval;
retval = nc4_att_list_del(list, att);
att = NULL;
}
if (attid > 0 && H5Aclose(attid) < 0)
retval = -1;
/* Since this is a HDF5 iterator callback, return -1 for any error
* to stop iteration. */
if (retval)
retval = -1;
return retval;
}
/**
* @internal This function reads all the attributes of a variable or
* the global attributes of a group.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info. NULL for global att reads.
*
* @return ::NC_NOERR No error.
* @return ::NC_EATTMETA Some error occurred reading attributes.
* @author Ed Hartnett
*/
int
nc4_read_atts(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
att_iter_info att_info; /* Custom iteration information */
hid_t locid; /* HDF5 location to read atts from. */
/* Check inputs. */
assert(grp);
/* Assign var and grp in struct. (var may be NULL). */
att_info.var = var;
att_info.grp = grp;
/* Determine where to read from in the HDF5 file. */
locid = var ? ((NC_HDF5_VAR_INFO_T *)(var->format_var_info))->hdf_datasetid :
((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid;
/* Now read all the attributes at this location, ignoring special
* netCDF hidden attributes. */
if ((H5Aiterate2(locid, H5_INDEX_CRT_ORDER, H5_ITER_INC, NULL,
att_read_callbk, &att_info)) < 0)
return NC_EATTMETA;
/* Remember that we have read the atts for this var or group. */
if (var)
var->atts_read = 1;
else
grp->atts_read = 1;
return NC_NOERR;
}
/**
* @internal This function is called by read_dataset() when a
* dimension scale dataset is encountered. It reads in the dimension
* data (creating a new NC_DIM_INFO_T object), and also checks to see
* if this is a dimension without a variable - that is, a coordinate
* dimension which does not have any coordinate data.
*
* @param grp Pointer to group info struct.
* @param datasetid The HDF5 dataset ID.
* @param obj_name The HDF5 object name.
* @param statbuf HDF5 status buffer.
* @param scale_size Size of dimension scale.
* @param max_scale_size Maximum size of dim scale.
* @param dim Pointer to pointer that gets new dim info struct.
*
* @returns ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
* [Candidate for libsrc4]
*/
static int
read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
#if H5_VERSION_GE(1,12,0)
const H5O_info2_t *statbuf,
#else
const H5G_stat_t *statbuf,
#endif
hsize_t scale_size,
hsize_t max_scale_size, NC_DIM_INFO_T **dim)
{
NC_DIM_INFO_T *new_dim; /* Dimension added to group */
NC_HDF5_DIM_INFO_T *new_hdf5_dim; /* HDF5-specific dim info. */
char dimscale_name_att[NC_MAX_NAME + 1] = ""; /* Dimscale name, for checking if dim without var */
htri_t attr_exists = -1; /* Flag indicating hidden attribute exists */
hid_t attid = -1; /* ID of hidden attribute (to store dim ID) */
int dimscale_created = 0; /* Remember if a dimension was created (for error recovery) */
short initial_next_dimid = grp->nc4_info->next_dimid;/* Retain for error recovery */
size_t len = 0;
int too_long = NC_FALSE;
int assigned_id = -1;
int retval = NC_NOERR;
assert(grp && dim);
/* Does this dataset have a hidden attribute that tells us its
* dimid? If so, read it. */
if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
if ((attid = H5Aopen_name(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (H5Aread(attid, H5T_NATIVE_INT, &assigned_id) < 0)
BAIL(NC_EHDFERR);
/* Check if scale's dimid should impact the group's next dimid */
if (assigned_id >= grp->nc4_info->next_dimid)
grp->nc4_info->next_dimid = assigned_id + 1;
}
/* Get dim size. On machines with a size_t of less than 8 bytes, it
* is possible for a dimension to be too long. */
if (SIZEOF_SIZE_T < 8 && scale_size > NC_MAX_UINT)
{
len = NC_MAX_UINT;
too_long = NC_TRUE;
}
else
len = scale_size;
/* Create the dimension for this scale. */
if ((retval = nc4_dim_list_add(grp, obj_name, len, assigned_id, &new_dim)))
BAIL(retval);
new_dim->too_long = too_long;
/* Create struct for HDF5-specific dim info. */
if (!(new_dim->format_dim_info = calloc(1, sizeof(NC_HDF5_DIM_INFO_T))))
BAIL(NC_ENOMEM);
new_hdf5_dim = (NC_HDF5_DIM_INFO_T *)new_dim->format_dim_info;
dimscale_created++;
/* Remember these 4 (or 2 for HDF5 1.12) values to uniquely identify this dataset in the
* HDF5 file. */
#if H5_VERSION_GE(1,12,0)
new_hdf5_dim->hdf5_objid.fileno = statbuf->fileno;
new_hdf5_dim->hdf5_objid.token = statbuf->token;
#else
new_hdf5_dim->hdf5_objid.fileno[0] = statbuf->fileno[0];
new_hdf5_dim->hdf5_objid.fileno[1] = statbuf->fileno[1];
new_hdf5_dim->hdf5_objid.objno[0] = statbuf->objno[0];
new_hdf5_dim->hdf5_objid.objno[1] = statbuf->objno[1];
#endif
/* If the dimscale has an unlimited dimension, then this dimension
* is unlimited. */
if (max_scale_size == H5S_UNLIMITED)
new_dim->unlimited = NC_TRUE;
/* If the scale name is set to DIM_WITHOUT_VARIABLE, then this is a
* dimension, but not a variable. (If get_scale_name returns an
* error, just move on, there's no NAME.) */
if (H5DSget_scale_name(datasetid, dimscale_name_att, NC_MAX_NAME) >= 0)
{
if (!strncmp(dimscale_name_att, DIM_WITHOUT_VARIABLE,
strlen(DIM_WITHOUT_VARIABLE)))
{
if (new_dim->unlimited)
{
size_t len = 0, *lenp = &len;
/* Find actual length by checking all datasets that use
* this dim. */
if ((retval = nc4_find_dim_len(grp, new_dim->hdr.id, &lenp)))
BAIL(retval);
new_dim->len = *lenp;
}
/* Hold open the dataset, since the dimension doesn't have a
* coordinate variable */
new_hdf5_dim->hdf_dimscaleid = datasetid;
H5Iinc_ref(new_hdf5_dim->hdf_dimscaleid); /* Increment number of objects using ID */
}
}
/* Set the dimension created. */
*dim = new_dim;
exit:
/* Close the hidden attribute, if it was opened. */
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
/* On error, undo any dimscale creation */
if (retval && dimscale_created)
{
/* free the dimension */
if ((retval = nc4_dim_list_del(grp, new_dim)))
BAIL2(retval);
/* Reset the group's information */
grp->nc4_info->next_dimid = initial_next_dimid;
}
return retval;
}
/**
* @internal Read a HDF5 dataset. This function is called when
* read_hdf5_obj() encounters an HDF5 dataset when opening a file.
*
* @param grp Pointer to group info struct.
* @param datasetid HDF5 dataset ID.
* @param obj_name Object name.
* @param statbuf HDF5 status buffer.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
read_dataset(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
#if H5_VERSION_GE(1,12,0)
const H5O_info2_t *statbuf
#else
const H5G_stat_t *statbuf
#endif
)
{
NC_DIM_INFO_T *dim = NULL; /* Dimension created for scales */
NC_HDF5_DIM_INFO_T *hdf5_dim;
hid_t spaceid = 0;
int ndims;
htri_t is_scale;
int retval = NC_NOERR;
/* Get the dimension information for this dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0)
BAIL(NC_EHDFERR);
if (is_scale)
{
hsize_t dims[H5S_MAX_RANK];
hsize_t max_dims[H5S_MAX_RANK];
/* Query the scale's size & max. size */
if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0)
BAIL(NC_EHDFERR);
/* Read the scale information. */
if ((retval = read_scale(grp, datasetid, obj_name, statbuf, dims[0],
max_dims[0], &dim)))
BAIL(retval);
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
}
/* Add a var to the linked list, and get its metadata,
* unless this is one of those funny dimscales that are a
* dimension in netCDF but not a variable. (Spooky!) */
if (!dim || (dim && !hdf5_dim->hdf_dimscaleid))
if ((retval = read_var(grp, datasetid, obj_name, ndims, dim)))
BAIL(retval);
exit:
if (spaceid && H5Sclose(spaceid) <0)
BAIL2(retval);
return retval;
}
/**
* @internal Add HDF5 object info for a group to a list for later
* processing. We do this when we encounter groups, so that the parent
* group can be fully processed before the child groups.
*
* @param udata Pointer to the user data, in this case a
* user_data_t.
* @param oinfo The HDF5 object info.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
oinfo_list_add(user_data_t *udata, const hdf5_obj_info_t *oinfo)
{
hdf5_obj_info_t *new_oinfo; /* Pointer to info for object */
/* Allocate memory for the object's info. */
if (!(new_oinfo = calloc(1, sizeof(hdf5_obj_info_t))))
return NC_ENOMEM;
/* Make a copy of the object's info. */
memcpy(new_oinfo, oinfo, sizeof(hdf5_obj_info_t));
/* Add it to the list for future processing. */
nclistpush(udata->grps, new_oinfo);
return NC_NOERR;
}
/**
* @internal Callback function called by H5Literate() for every HDF5
* object in the file.
*
* @note This function is called by HDF5 so does not return a netCDF
* error code.
*
* @param grpid HDF5 group ID.
* @param name Name of object.
* @param info Info struct for object.
* @param _op_data Pointer to user data, a user_data_t. It will
* contain a pointer to the current group and a list of
* hdf5_obj_info_t. Any child groups will get their hdf5_obj_info
* added to this list.
*
* @return H5_ITER_CONT No error, continue iteration.
* @return H5_ITER_ERROR HDF5 error, stop iteration.
* @author Ed Hartnett
*/
static int
read_hdf5_obj(hid_t grpid, const char *name, const H5L_info_t *info,
void *_op_data)
{
/* Pointer to user data for callback */
user_data_t *udata = (user_data_t *)_op_data;
hdf5_obj_info_t oinfo; /* Pointer to info for object */
int retval = H5_ITER_CONT;
/* Open this critter. */
if ((oinfo.oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0)
BAIL(H5_ITER_ERROR);
/* Get info about the object.*/
#if H5_VERSION_GE(1,12,0)
if (H5Oget_info3(oinfo.oid, &oinfo.statbuf, H5O_INFO_BASIC) < 0)
BAIL(H5_ITER_ERROR);
#else
if (H5Gget_objinfo(oinfo.oid, ".", 1, &oinfo.statbuf) < 0)
BAIL(H5_ITER_ERROR);
#endif
strncpy(oinfo.oname, name, NC_MAX_NAME);
/* Add object to list, for later */
switch(oinfo.statbuf.type)
{
case H5G_GROUP:
LOG((3, "found group %s", oinfo.oname));
/* Defer descending into child group immediately, so that the
* types in the current group can be processed and be ready for
* use by vars in the child group(s). */
if (oinfo_list_add(udata, &oinfo))
BAIL(H5_ITER_ERROR);
break;
case H5G_DATASET:
LOG((3, "found dataset %s", oinfo.oname));
/* Learn all about this dataset, which may be a dimscale
* (i.e. dimension metadata), or real data. */
if ((retval = read_dataset(udata->grp, oinfo.oid, oinfo.oname,
&oinfo.statbuf)))
{
/* Allow NC_EBADTYPID to transparently skip over datasets
* which have a datatype that netCDF-4 doesn't understand
* (currently), but break out of iteration for other
* errors. */
if (retval != NC_EBADTYPID)
BAIL(H5_ITER_ERROR);
else
retval = H5_ITER_CONT;
}
/* Close the object */
if (H5Oclose(oinfo.oid) < 0)
BAIL(H5_ITER_ERROR);
break;
case H5G_TYPE:
LOG((3, "found datatype %s", oinfo.oname));
/* Process the named datatype */
if (read_type(udata->grp, oinfo.oid, oinfo.oname))
BAIL(H5_ITER_ERROR);
/* Close the object */
if (H5Oclose(oinfo.oid) < 0)
BAIL(H5_ITER_ERROR);
break;
default:
LOG((0, "Unknown object class %d in %s!", oinfo.statbuf.type, __func__));
BAIL(H5_ITER_ERROR);
}
exit:
if (retval)
{
if (oinfo.oid > 0 && H5Oclose(oinfo.oid) < 0)
BAIL2(H5_ITER_ERROR);
}
return (retval);
}
/**
* @internal This is the main function to recursively read all the
* metadata for the file. The links in the 'grp' are iterated over and
* added to the file's metadata information. Note that child groups
* are not immediately processed, but are deferred until all the other
* links in the group are handled (so that vars in the child groups
* are guaranteed to have types that they use in a parent group in
* place).
*
* @param grp Pointer to a group.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_ECANTWRITE File must be opened read-only.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
rec_read_metadata(NC_GRP_INFO_T *grp)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
user_data_t udata; /* User data for iteration */
hdf5_obj_info_t *oinfo; /* Pointer to info for object */
hsize_t idx = 0;
hid_t pid = -1;
unsigned crt_order_flags = 0;
H5_index_t iter_index;
int i, retval = NC_NOERR;
assert(grp && grp->hdr.name && grp->format_grp_info);
LOG((3, "%s: grp->hdr.name %s", __func__, grp->hdr.name));
/* Get HDF5-specific group info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
/* Set user data for iteration over any child groups. */
udata.grp = grp;
udata.grps = nclistnew();
/* Open this HDF5 group and retain its grpid. It will remain open
* with HDF5 until this file is nc_closed. */
if (!hdf5_grp->hdf_grpid)
{
if (grp->parent)
{
/* This is a child group. */
NC_HDF5_GRP_INFO_T *parent_hdf5_grp;
parent_hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->parent->format_grp_info;
if ((hdf5_grp->hdf_grpid = H5Gopen2(parent_hdf5_grp->hdf_grpid,
grp->hdr.name, H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
}
else
{
/* This is the root group. */
NC_HDF5_FILE_INFO_T *hdf5_info;
hdf5_info = (NC_HDF5_FILE_INFO_T *)grp->nc4_info->format_file_info;
if ((hdf5_grp->hdf_grpid = H5Gopen2(hdf5_info->hdfid, "/",
H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
}
}
assert(hdf5_grp->hdf_grpid > 0);
/* Get the group creation flags, to check for creation ordering. */
if ((pid = H5Gget_create_plist(hdf5_grp->hdf_grpid)) < 0)
BAIL(NC_EHDFERR);
if (H5Pget_link_creation_order(pid, &crt_order_flags) < 0)
BAIL(NC_EHDFERR);
/* Set the iteration index to use. */
if (crt_order_flags & H5P_CRT_ORDER_TRACKED)
iter_index = H5_INDEX_CRT_ORDER;
else
{
NC_FILE_INFO_T *h5 = grp->nc4_info;
/* Without creation ordering, file must be read-only. */
if (!h5->no_write)
BAIL(NC_ECANTWRITE);
iter_index = H5_INDEX_NAME;
}
/* Iterate over links in this group, building lists for the types,
* datasets and groups encountered. A pointer to udata will be
* passed as a parameter to the callback function
* read_hdf5_obj(). (I have also tried H5Oiterate(), but it is much
* slower iterating over the same file - Ed.) */
if (H5Literate(hdf5_grp->hdf_grpid, iter_index, H5_ITER_INC, &idx,
read_hdf5_obj, (void *)&udata) < 0)
BAIL(NC_EHDFERR);
/* Process the child groups found. (Deferred until now, so that the
* types in the current group get processed and are available for
* vars in the child group(s).) */
for (i = 0; i < nclistlength(udata.grps); i++)
{
NC_GRP_INFO_T *child_grp;
oinfo = (hdf5_obj_info_t*)nclistget(udata.grps, i);
/* Add group to file's hierarchy. */
if ((retval = nc4_grp_list_add(grp->nc4_info, grp, oinfo->oname,
&child_grp)))
BAIL(retval);
/* Allocate storage for HDF5-specific group info. */
if (!(child_grp->format_grp_info = calloc(1, sizeof(NC_HDF5_GRP_INFO_T))))
return NC_ENOMEM;
/* Recursively read the child group's metadata. */
if ((retval = rec_read_metadata(child_grp)))
BAIL(retval);
}
/* When reading existing file, mark all variables as written. */
for (i = 0; i < ncindexsize(grp->vars); i++)
((NC_VAR_INFO_T *)ncindexith(grp->vars, i))->written_to = NC_TRUE;
exit:
if (pid > 0 && H5Pclose(pid) < 0)
BAIL2(NC_EHDFERR);
/* Clean up list of child groups. */
for (i = 0; i < nclistlength(udata.grps); i++)
{
oinfo = (hdf5_obj_info_t *)nclistget(udata.grps, i);
/* Close the open HDF5 object. */
if (H5Oclose(oinfo->oid) < 0)
BAIL2(NC_EHDFERR);
free(oinfo);
}
nclistfree(udata.grps);
return retval;
}
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