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netcdf-c/libhdf5/nc4hdf.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 2018, University Corporation for Atmospheric
* Research. See the COPYRIGHT file for copying and redistribution
* conditions. */
/**
* @file
* @internal This file is part of netcdf-4, a netCDF-like interface
* for HDF5, or a HDF5 backend for netCDF, depending on your point of
* view.
*
* This file contains functions internal to the netcdf4 library. None of
* the functions in this file are exposed in the exetnal API. These
* functions handle the HDF interface.
*
* @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
*/
#include "config.h"
#include "netcdf.h"
#include "nc4internal.h"
#include "ncdispatch.h"
#include "ncfilter.h"
#include "hdf5internal.h"
#include "hdf5debug.h"
#include <math.h>
#ifdef HAVE_INTTYPES_H
#define __STDC_FORMAT_MACROS
#include <inttypes.h>
#endif
#define NC_HDF5_MAX_NAME 1024 /**< @internal Max size of HDF5 name. */
/**
* @internal Flag attributes in a linked list as dirty.
*
* @param attlist List of attributes, may be NULL.
*
* @return NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
flag_atts_dirty(NCindex *attlist) {
NC_ATT_INFO_T *att = NULL;
int i;
if(attlist == NULL) {
return NC_NOERR;
}
for(i=0;i<ncindexsize(attlist);i++) {
att = (NC_ATT_INFO_T*)ncindexith(attlist,i);
if(att == NULL) continue;
att->dirty = NC_TRUE;
}
return NC_NOERR;
}
/**
* @internal This function is needed to handle one special case: what
* if the user defines a dim, writes metadata, then goes back into
* define mode and adds a coordinate var for the already existing
* dim. In that case, I need to recreate the dim's dimension scale
* dataset, and then I need to go to every var in the file which uses
* that dimension, and attach the new dimension scale.
*
* @param grp Pointer to group info struct.
* @param dimid Dimension ID.
* @param dimscaleid HDF5 dimension scale ID.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
int
rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
{
NC_VAR_INFO_T *var;
NC_GRP_INFO_T *child_grp;
int d, i;
int retval;
assert(grp && grp->hdr.name && dimid >= 0 && dimscaleid >= 0);
LOG((3, "%s: grp->hdr.name %s", __func__, grp->hdr.name));
/* If there are any child groups, attach dimscale there, if needed. */
for (i = 0; i < ncindexsize(grp->children); i++)
{
child_grp = (NC_GRP_INFO_T*)ncindexith(grp->children, i);
assert(child_grp);
if ((retval = rec_reattach_scales(child_grp, dimid, dimscaleid)))
return retval;
}
/* Find any vars that use this dimension id. */
for (i = 0; i < ncindexsize(grp->vars); i++)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
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;
hdf5_var = (NC_HDF5_VAR_INFO_T*)var->format_var_info;
assert(hdf5_var != NULL);
for (d = 0; d < var->ndims; d++)
{
if (var->dimids[d] == dimid && !hdf5_var->dimscale)
{
LOG((2, "%s: attaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->hdr.name));
if (var->created)
{
if (H5DSattach_scale(hdf5_var->hdf_datasetid,
dimscaleid, d) < 0)
return NC_EHDFERR;
hdf5_var->dimscale_attached[d] = NC_TRUE;
}
}
}
}
return NC_NOERR;
}
/**
* @internal This function is needed to handle one special case: what
* if the user defines a dim, writes metadata, then goes back into
* define mode and adds a coordinate var for the already existing
* dim. In that case, I need to recreate the dim's dimension scale
* dataset, and then I need to go to every var in the file which uses
* that dimension, and attach the new dimension scale.
*
* @param grp Pointer to group info struct.
* @param dimid Dimension ID.
* @param dimscaleid HDF5 dimension scale ID.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
int
rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
{
NC_VAR_INFO_T *var;
NC_GRP_INFO_T *child_grp;
int d, i;
int retval;
assert(grp && grp->hdr.name && dimid >= 0 && dimscaleid >= 0);
LOG((3, "%s: grp->hdr.name %s", __func__, grp->hdr.name));
/* If there are any child groups, detach dimscale there, if needed. */
for(i=0;i<ncindexsize(grp->children);i++) {
child_grp = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if(child_grp == NULL) continue;
if ((retval = rec_detach_scales(child_grp, dimid, dimscaleid)))
return retval;
}
/* Find any vars that use this dimension id. */
for (i = 0; i < ncindexsize(grp->vars); i++)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
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;
for (d = 0; d < var->ndims; d++)
{
if (var->dimids[d] == dimid && !hdf5_var->dimscale)
{
LOG((2, "%s: detaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->hdr.name));
if (var->created)
{
if (hdf5_var->dimscale_attached && hdf5_var->dimscale_attached[d])
{
if (H5DSdetach_scale(hdf5_var->hdf_datasetid,
dimscaleid, d) < 0)
return NC_EHDFERR;
hdf5_var->dimscale_attached[d] = NC_FALSE;
}
}
}
}
}
return NC_NOERR;
}
/**
* @internal Open a HDF5 dataset and leave it open.
*
* @param grp Pointer to group info struct.
* @param varid Variable ID.
* @param dataset Pointer that gets the HDF5 dataset ID.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
int
nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset)
{
NC_VAR_INFO_T *var;
NC_HDF5_VAR_INFO_T *hdf5_var;
assert(grp && grp->format_grp_info && dataset);
/* Find the requested varid. */
if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
return NC_ENOTVAR;
assert(var && var->hdr.id == varid && var->format_var_info);
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Open this dataset if necessary. */
if (!hdf5_var->hdf_datasetid)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
if ((hdf5_var->hdf_datasetid = H5Dopen2(hdf5_grp->hdf_grpid,
var->hdr.name, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
}
*dataset = hdf5_var->hdf_datasetid;
return NC_NOERR;
}
/**
* @internal Given a netcdf type, return appropriate HDF typeid. (All
* hdf_typeid's returned from this routine must be H5Tclosed by the
* caller).
*
* @param h5 Pointer to HDF5 file info struct.
* @param xtype NetCDF type ID.
* @param hdf_typeid Pointer that gets the HDF5 type ID.
* @param endianness Desired endianness in HDF5 type.
*
* @return NC_NOERR No error.
* @return NC_ECHAR Conversions of NC_CHAR forbidden.
* @return NC_EVARMETA HDF5 returning error creating datatype.
* @return NC_EHDFERR HDF5 returning error.
* @return NC_EBADTYE Type not found.
* @author Ed Hartnett
*/
int
nc4_get_hdf_typeid(NC_FILE_INFO_T *h5, nc_type xtype,
hid_t *hdf_typeid, int endianness)
{
NC_TYPE_INFO_T *type;
hid_t typeid = 0;
int retval = NC_NOERR;
assert(hdf_typeid && h5);
*hdf_typeid = -1;
/* Determine an appropriate HDF5 datatype */
if (xtype == NC_NAT)
return NC_EBADTYPE;
else if (xtype == NC_CHAR || xtype == NC_STRING)
{
/* NC_CHAR & NC_STRING types create a new HDF5 datatype */
if (xtype == NC_CHAR)
{
if ((typeid = H5Tcopy(H5T_C_S1)) < 0)
return NC_EHDFERR;
if (H5Tset_strpad(typeid, H5T_STR_NULLTERM) < 0)
BAIL(NC_EVARMETA);
if(H5Tset_cset(typeid, H5T_CSET_ASCII) < 0)
BAIL(NC_EVARMETA);
/* Take ownership of the newly created HDF5 datatype */
*hdf_typeid = typeid;
typeid = 0;
}
else
{
if ((typeid = H5Tcopy(H5T_C_S1)) < 0)
return NC_EHDFERR;
if (H5Tset_size(typeid, H5T_VARIABLE) < 0)
BAIL(NC_EVARMETA);
if(H5Tset_cset(typeid, H5T_CSET_UTF8) < 0)
BAIL(NC_EVARMETA);
/* Take ownership of the newly created HDF5 datatype */
*hdf_typeid = typeid;
typeid = 0;
}
}
else
{
/* All other types use an existing HDF5 datatype */
switch (xtype)
{
case NC_BYTE: /* signed 1 byte integer */
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I8LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I8BE;
else
typeid = H5T_NATIVE_SCHAR;
break;
case NC_SHORT: /* signed 2 byte integer */
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I16LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I16BE;
else
typeid = H5T_NATIVE_SHORT;
break;
case NC_INT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I32LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I32BE;
else
typeid = H5T_NATIVE_INT;
break;
case NC_UBYTE:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U8LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U8BE;
else
typeid = H5T_NATIVE_UCHAR;
break;
case NC_USHORT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U16LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U16BE;
else
typeid = H5T_NATIVE_USHORT;
break;
case NC_UINT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U32LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U32BE;
else
typeid = H5T_NATIVE_UINT;
break;
case NC_INT64:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I64LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I64BE;
else
typeid = H5T_NATIVE_LLONG;
break;
case NC_UINT64:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U64LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U64BE;
else
typeid = H5T_NATIVE_ULLONG;
break;
case NC_FLOAT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_IEEE_F32LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_IEEE_F32BE;
else
typeid = H5T_NATIVE_FLOAT;
break;
case NC_DOUBLE:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_IEEE_F64LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_IEEE_F64BE;
else
typeid = H5T_NATIVE_DOUBLE;
break;
default:
/* Maybe this is a user defined type? */
if (nc4_find_type(h5, xtype, &type))
return NC_EBADTYPE;
if (!type)
return NC_EBADTYPE;
typeid = ((NC_HDF5_TYPE_INFO_T *)type->format_type_info)->hdf_typeid;
break;
}
assert(typeid);
/* Copy the HDF5 datatype, so the function operates uniformly */
if ((*hdf_typeid = H5Tcopy(typeid)) < 0)
return NC_EHDFERR;
typeid = 0;
}
assert(*hdf_typeid != -1);
exit:
if (typeid > 0 && H5Tclose(typeid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Write an attribute.
*
* @param grp Pointer to group info struct.
* @param varid Variable ID or NC_GLOBAL.
* @param att Pointer to attribute info struct.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_ENOTVAR Variable not found.
* @returns ::NC_EPERM Read-only file.
* @returns ::NC_EHDFERR HDF5 returned error.
* @returns ::NC_EATTMETA HDF5 returned error with attribute calls.
* @author Ed Hartnett
*/
static int
put_att_grpa(NC_GRP_INFO_T *grp, int varid, NC_ATT_INFO_T *att)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
hid_t datasetid = 0, locid;
hid_t attid = 0, spaceid = 0, file_typeid = 0;
hid_t existing_att_typeid = 0, existing_attid = 0, existing_spaceid = 0;
hsize_t dims[1]; /* netcdf attributes always 1-D. */
htri_t attr_exists;
void *data;
int phoney_data = 99;
int retval = NC_NOERR;
assert(att->hdr.name && grp && grp->format_grp_info);
LOG((3, "%s: varid %d att->hdr.id %d att->hdr.name %s att->nc_typeid %d "
"att->len %d", __func__, varid, att->hdr.id, att->hdr.name,
att->nc_typeid, att->len));
/* Get HDF5-specific group info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
/* If the file is read-only, return an error. */
if (grp->nc4_info->no_write)
BAIL(NC_EPERM);
/* Get the hid to attach the attribute to, or read it from. */
if (varid == NC_GLOBAL)
locid = hdf5_grp->hdf_grpid;
else
{
if ((retval = nc4_open_var_grp2(grp, varid, &datasetid)))
BAIL(retval);
locid = datasetid;
}
/* Get the length ready, and find the HDF type we'll be
* writing. */
dims[0] = att->len;
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, att->nc_typeid,
&file_typeid, 0)))
BAIL(retval);
/* Even if the length is zero, HDF5 won't let me write with a
* NULL pointer. So if the length of the att is zero, point to
* some phoney data (which won't be written anyway.)*/
if (!dims[0])
data = &phoney_data;
else if (att->data)
data = att->data;
else if (att->stdata)
data = att->stdata;
else
data = att->vldata;
/* NC_CHAR types require some extra work. The space ID is set to
* scalar, and the type is told how long the string is. If it's
* really zero length, set the size to 1. (The fact that it's
* really zero will be marked by the NULL dataspace, but HDF5
* doesn't allow me to set the size of the type to zero.)*/
if (att->nc_typeid == NC_CHAR)
{
size_t string_size = dims[0];
if (!string_size)
{
string_size = 1;
if ((spaceid = H5Screate(H5S_NULL)) < 0)
BAIL(NC_EATTMETA);
}
else
{
if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EATTMETA);
}
if (H5Tset_size(file_typeid, string_size) < 0)
BAIL(NC_EATTMETA);
if (H5Tset_strpad(file_typeid, H5T_STR_NULLTERM) < 0)
BAIL(NC_EATTMETA);
}
else
{
if (!att->len)
{
if ((spaceid = H5Screate(H5S_NULL)) < 0)
BAIL(NC_EATTMETA);
}
else
{
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0)
BAIL(NC_EATTMETA);
}
}
/* Does the att exists already? */
if ((attr_exists = H5Aexists(locid, att->hdr.name)) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
hssize_t npoints;
/* Open the attribute. */
if ((existing_attid = H5Aopen(locid, att->hdr.name, H5P_DEFAULT)) < 0)
BAIL(NC_EATTMETA);
/* Find the type of the existing attribute. */
if ((existing_att_typeid = H5Aget_type(existing_attid)) < 0)
BAIL(NC_EATTMETA);
/* How big is the attribute? */
if ((existing_spaceid = H5Aget_space(existing_attid)) < 0)
BAIL(NC_EATTMETA);
if ((npoints = H5Sget_simple_extent_npoints(existing_spaceid)) < 0)
BAIL(NC_EATTMETA);
/* For text attributes the size is specified in the datatype
and it is enough to compare types using H5Tequal(). */
if (!H5Tequal(file_typeid, existing_att_typeid) ||
(att->nc_typeid != NC_CHAR && npoints != att->len))
{
/* The attribute exists but we cannot re-use it. */
/* Delete the attribute. */
if (H5Adelete(locid, att->hdr.name) < 0)
BAIL(NC_EHDFERR);
/* Re-create the attribute with the type and length
reflecting the new value (or values). */
if ((attid = H5Acreate(locid, att->hdr.name, file_typeid, spaceid,
H5P_DEFAULT)) < 0)
BAIL(NC_EATTMETA);
/* Write the values, (even if length is zero). */
if (H5Awrite(attid, file_typeid, data) < 0)
BAIL(NC_EATTMETA);
}
else
{
/* The attribute exists and we can re-use it. */
/* Write the values, re-using the existing attribute. */
if (H5Awrite(existing_attid, file_typeid, data) < 0)
BAIL(NC_EATTMETA);
}
}
else
{
/* The attribute does not exist yet. */
/* Create the attribute. */
if ((attid = H5Acreate(locid, att->hdr.name, file_typeid, spaceid,
H5P_DEFAULT)) < 0)
BAIL(NC_EATTMETA);
/* Write the values, (even if length is zero). */
if (H5Awrite(attid, file_typeid, data) < 0)
BAIL(NC_EATTMETA);
}
exit:
if (file_typeid && H5Tclose(file_typeid))
BAIL2(NC_EHDFERR);
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
if (existing_att_typeid && H5Tclose(existing_att_typeid))
BAIL2(NC_EHDFERR);
if (existing_attid > 0 && H5Aclose(existing_attid) < 0)
BAIL2(NC_EHDFERR);
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (existing_spaceid > 0 && H5Sclose(existing_spaceid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Write all the dirty atts in an attlist.
*
* @param attlist Pointer to the list if attributes.
* @param varid Variable ID.
* @param grp Pointer to group info struct.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
static int
write_attlist(NCindex *attlist, int varid, NC_GRP_INFO_T *grp)
{
NC_ATT_INFO_T *att;
int retval;
int i;
for(i = 0; i < ncindexsize(attlist); i++)
{
att = (NC_ATT_INFO_T *)ncindexith(attlist, i);
assert(att);
if (att->dirty)
{
LOG((4, "%s: writing att %s to varid %d", __func__, att->hdr.name, varid));
if ((retval = put_att_grpa(grp, varid, att)))
return retval;
att->dirty = NC_FALSE;
att->created = NC_TRUE;
}
}
return NC_NOERR;
}
/**
* @internal HDF5 dimension scales cannot themselves have scales
* attached. This is a problem for multidimensional coordinate
* variables. So this function writes a special attribute for such a
* variable, which has the ids of all the dimensions for that
* coordinate variable.
*
* @param var Pointer to var info struct.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
static int
write_coord_dimids(NC_VAR_INFO_T *var)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
hsize_t coords_len[1];
hid_t c_spaceid = -1, c_attid = -1;
int retval = NC_NOERR;
assert(var && var->format_var_info);
/* Get HDF5-specific var info. */
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Set up space for attribute. */
coords_len[0] = var->ndims;
if ((c_spaceid = H5Screate_simple(1, coords_len, coords_len)) < 0)
BAIL(NC_EHDFERR);
/* Create the attribute. */
if ((c_attid = H5Acreate(hdf5_var->hdf_datasetid, COORDINATES,
H5T_NATIVE_INT, c_spaceid, H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
/* Write our attribute. */
if (H5Awrite(c_attid, H5T_NATIVE_INT, var->dimids) < 0)
BAIL(NC_EHDFERR);
exit:
if (c_spaceid >= 0 && H5Sclose(c_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (c_attid >= 0 && H5Aclose(c_attid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Write a special attribute for the netCDF-4 dimension ID.
*
* @param datasetid HDF5 datasset ID.
* @param dimid NetCDF dimension ID.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
static int
write_netcdf4_dimid(hid_t datasetid, int dimid)
{
hid_t dimid_spaceid = -1, dimid_attid = -1;
htri_t attr_exists;
int retval = NC_NOERR;
/* Create the space. */
if ((dimid_spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
/* Does the attribute already exist? If so, don't try to create it. */
if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
dimid_attid = H5Aopen_by_name(datasetid, ".", NC_DIMID_ATT_NAME,
H5P_DEFAULT, H5P_DEFAULT);
else
/* Create the attribute if needed. */
dimid_attid = H5Acreate(datasetid, NC_DIMID_ATT_NAME,
H5T_NATIVE_INT, dimid_spaceid, H5P_DEFAULT);
if (dimid_attid < 0)
BAIL(NC_EHDFERR);
/* Write it. */
LOG((4, "%s: writing secret dimid %d", __func__, dimid));
if (H5Awrite(dimid_attid, H5T_NATIVE_INT, &dimid) < 0)
BAIL(NC_EHDFERR);
exit:
/* Close stuff*/
if (dimid_spaceid >= 0 && H5Sclose(dimid_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (dimid_attid >= 0 && H5Aclose(dimid_attid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal This function creates the HDF5 dataset for a variable.
*
* @param grp Pointer to group info struct.
* @param var Pointer to variable info struct.
* @param write_dimid True to write dimid.
*
* @return ::NC_NOERR
* @returns NC_ECHAR Conversions of NC_CHAR forbidden.
* @returns NC_EVARMETA HDF5 returning error creating datatype.
* @returns NC_EHDFERR HDF5 returning error.
* @returns NC_EBADTYE Type not found.
* @author Ed Hartnett
*/
static int
var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, nc_bool_t write_dimid)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_VAR_INFO_T *hdf5_var;
hid_t plistid = 0, access_plistid = 0, typeid = 0, spaceid = 0;
hsize_t chunksize[H5S_MAX_RANK], dimsize[H5S_MAX_RANK], maxdimsize[H5S_MAX_RANK];
int d;
void *fillp = NULL;
NC_DIM_INFO_T *dim = NULL;
char *name_to_use;
int retval;
unsigned int* params = NULL;
assert(grp && grp->format_grp_info && var && var->format_var_info);
LOG((3, "%s:: name %s", __func__, var->hdr.name));
/* Get HDF5-specific group and var info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Scalar or not, we need a creation property list. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
BAIL(NC_EHDFERR);
if ((access_plistid = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
BAIL(NC_EHDFERR);
/* Turn off object tracking times in HDF5. */
if (H5Pset_obj_track_times(plistid, 0) < 0)
BAIL(NC_EHDFERR);
/* Find the HDF5 type of the dataset. */
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, var->type_info->hdr.id, &typeid,
var->type_info->endianness)))
BAIL(retval);
/* Figure out what fill value to set, if any. */
if (var->no_fill)
{
/* Required to truly turn HDF5 fill values off */
if (H5Pset_fill_time(plistid, H5D_FILL_TIME_NEVER) < 0)
BAIL(NC_EHDFERR);
}
else
{
if ((retval = nc4_get_fill_value(grp->nc4_info, var, &fillp)))
BAIL(retval);
/* If there is a fill value, set it. */
if (fillp)
{
if (var->type_info->nc_type_class == NC_STRING)
{
if (H5Pset_fill_value(plistid, typeid, fillp) < 0)
BAIL(NC_EHDFERR);
}
else
{
/* The fill value set in HDF5 must always be presented as
* a native type, even if the endianness for this dataset
* is non-native. HDF5 will translate the fill value to
* the target endiannesss. */
hid_t fill_typeid = 0;
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, var->type_info->hdr.id, &fill_typeid,
NC_ENDIAN_NATIVE)))
BAIL(retval);
if (H5Pset_fill_value(plistid, fill_typeid, fillp) < 0)
{
if (H5Tclose(fill_typeid) < 0)
BAIL(NC_EHDFERR);
BAIL(NC_EHDFERR);
}
if (H5Tclose(fill_typeid) < 0)
BAIL(NC_EHDFERR);
}
}
}
/* If the user wants to fletcher error correction, set that up now. */
/* Since it is a checksum of sorts, flatcher is always applied first */
if (var->fletcher32)
if (H5Pset_fletcher32(plistid) < 0)
BAIL(NC_EHDFERR);
/* If the user wants to shuffle the data, set that up now. */
if (var->shuffle) {
if (H5Pset_shuffle(plistid) < 0)
BAIL(NC_EHDFERR);
}
/* If the user wants to compress the data, using either zlib
* (a.k.a deflate) or szip, or another filter, set that up now.
* Szip and zip can be turned on
* either directly with nc_def_var_szip/deflate(), or using
* nc_def_var_filter(). If the user
* has specified a filter, it will be applied here. */
if(var->filters != NULL) {
int j;
for(j=0;j<nclistlength(var->filters);j++) {
NC_FILTERX_SPEC* fi = (NC_FILTERX_SPEC*)nclistget(var->filters,j);
unsigned int filterid;
size_t nparams;
if(!fi->active) {
nparams = fi->nparams;
/* Do the conversions */
if((retval = NC_cvtX2I_id(fi->filterid,&filterid))) BAIL(retval);
if((params = malloc(nparams*sizeof(unsigned int)))==NULL)
BAIL(NC_ENOMEM);
if((retval = NC_cvtX2I_params(nparams,(const char**)fi->params,params))) BAIL(retval);
if(filterid == H5Z_FILTER_DEFLATE) {/* Handle zip case here */
unsigned level;
if(nparams != 1)
BAIL(NC_EFILTER);
level = (int)params[0];
if(H5Pset_deflate(plistid, level) < 0)
BAIL(NC_EFILTER);
fi->active = 1;
} else if(filterid == H5Z_FILTER_SZIP) {/* Handle szip case here */
int options_mask;
int bits_per_pixel;
if(nparams != 2)
BAIL(NC_EFILTER);
options_mask = (int)params[0];
bits_per_pixel = (int)params[1];
if(H5Pset_szip(plistid, options_mask, bits_per_pixel) < 0)
BAIL(NC_EFILTER);
fi->active = 1;
} else {
herr_t code = H5Pset_filter(plistid, filterid, H5Z_FLAG_MANDATORY, nparams, params);
if(code < 0)
BAIL(NC_EFILTER);
fi->active = 1;
}
}
/* reclaim */
nullfree(params); params = NULL;
}
}
/* If ndims non-zero, get info for all dimensions. We look up the
dimids and get the len of each dimension. We need this to create
the space for the dataset. In netCDF a dimension length of zero
means an unlimited dimension. */
if (var->ndims)
{
int unlimdim = 0;
/* Check to see if any unlimited dimensions are used in this var. */
for (d = 0; d < var->ndims; d++) {
dim = var->dim[d];
assert(dim && dim->hdr.id == var->dimids[d]);
if (dim->unlimited)
unlimdim++;
}
/* If there are no unlimited dims, and no filters, and the user
* has not specified chunksizes, use contiguous variable for
* better performance. */
if (!var->shuffle && !var->fletcher32 && nclistlength(var->filters) == 0 &&
(var->chunksizes == NULL || !var->chunksizes[0]) && !unlimdim)
var->storage = NC_CONTIGUOUS;
/* Gather current & maximum dimension sizes, along with chunk
* sizes. */
for (d = 0; d < var->ndims; d++)
{
dim = var->dim[d];
assert(dim && dim->hdr.id == var->dimids[d]);
dimsize[d] = dim->unlimited ? NC_HDF5_UNLIMITED_DIMSIZE : dim->len;
maxdimsize[d] = dim->unlimited ? H5S_UNLIMITED : (hsize_t)dim->len;
if (var->storage == NC_CHUNKED)
{
if (var->chunksizes[d])
chunksize[d] = var->chunksizes[d];
else
{
size_t type_size;
if (var->type_info->nc_type_class == NC_STRING)
type_size = sizeof(char *);
else
type_size = var->type_info->size;
/* Unlimited dim always gets chunksize of 1. */
if (dim->unlimited)
chunksize[d] = 1;
else
chunksize[d] = pow((double)DEFAULT_CHUNK_SIZE/type_size,
1/(double)(var->ndims - unlimdim));
/* If the chunksize is greater than the dim
* length, make it the dim length. */
if (!dim->unlimited && chunksize[d] > dim->len)
chunksize[d] = dim->len;
/* Remember the computed chunksize */
var->chunksizes[d] = chunksize[d];
}
}
}
/* Create the dataspace. */
if ((spaceid = H5Screate_simple(var->ndims, dimsize, maxdimsize)) < 0)
BAIL(NC_EHDFERR);
}
else
{
if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
}
/* Set the var storage to contiguous, compact, or chunked. Don't
* try to set chunking for scalar vars, they will default to
* contiguous if not set to compact. */
if (var->storage == NC_CONTIGUOUS)
{
if (H5Pset_layout(plistid, H5D_CONTIGUOUS) < 0)
BAIL(NC_EHDFERR);
}
else if (var->storage == NC_COMPACT)
{
if (H5Pset_layout(plistid, H5D_COMPACT) < 0)
BAIL(NC_EHDFERR);
}
else if (var->ndims)
{
if (H5Pset_chunk(plistid, var->ndims, chunksize) < 0)
BAIL(NC_EHDFERR);
}
/* Turn on creation order tracking. */
if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Set per-var chunk cache, for chunked datasets. */
if (var->storage == NC_CHUNKED && var->chunk_cache_size)
if (H5Pset_chunk_cache(access_plistid, var->chunk_cache_nelems,
var->chunk_cache_size, var->chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
/* At long last, create the dataset. */
name_to_use = var->alt_name ? var->alt_name : var->hdr.name;
LOG((4, "%s: about to H5Dcreate2 dataset %s of type 0x%x", __func__,
name_to_use, typeid));
if ((hdf5_var->hdf_datasetid = H5Dcreate2(hdf5_grp->hdf_grpid, name_to_use, typeid,
spaceid, H5P_DEFAULT, plistid, access_plistid)) < 0)
BAIL(NC_EHDFERR);
var->created = NC_TRUE;
var->is_new_var = NC_FALSE;
/* Always write the hidden coordinates attribute, which lists the
* dimids of this var. When present, this speeds opens. When no
* present, dimscale matching is used. */
if (var->ndims > 1)
if ((retval = write_coord_dimids(var)))
BAIL(retval);
/* If this is a dimscale, mark it as such in the HDF5 file. Also
* find the dimension info and store the dataset id of the dimscale
* dataset. */
if (hdf5_var->dimscale)
{
if (H5DSset_scale(hdf5_var->hdf_datasetid, var->hdr.name) < 0)
BAIL(NC_EHDFERR);
/* If this is a multidimensional coordinate variable, write a
* coordinates attribute. */
/* if (var->ndims > 1) */
/* if ((retval = write_coord_dimids(var))) */
/* BAIL(retval); */
/* If desired, write the netCDF dimid. */
if (write_dimid)
if ((retval = write_netcdf4_dimid(hdf5_var->hdf_datasetid, var->dimids[0])))
BAIL(retval);
}
/* Write attributes for this var. */
if ((retval = write_attlist(var->att, var->hdr.id, grp)))
BAIL(retval);
var->attr_dirty = NC_FALSE;
exit:
nullfree(params);
if (typeid > 0 && H5Tclose(typeid) < 0)
BAIL2(NC_EHDFERR);
if (plistid > 0 && H5Pclose(plistid) < 0)
BAIL2(NC_EHDFERR);
if (access_plistid > 0 && H5Pclose(access_plistid) < 0)
BAIL2(NC_EHDFERR);
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (fillp)
{
if (var->type_info->nc_type_class == NC_VLEN)
nc_free_vlen((nc_vlen_t *)fillp);
else if (var->type_info->nc_type_class == NC_STRING && *(char **)fillp)
free(*(char **)fillp);
free(fillp);
}
return retval;
}
/**
* @internal Adjust the chunk cache of a var for better
* performance.
*
* @note For contiguous and compact storage vars, or when parallel I/O
* is in use, this function will do nothing and return ::NC_NOERR;
*
* @param grp Pointer to group info struct.
* @param var Pointer to var info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
size_t chunk_size_bytes = 1;
int d;
int retval;
/* Nothing to be done for contiguous or compact data. */
if (var->storage != NC_CHUNKED)
return NC_NOERR;
#ifdef USE_PARALLEL4
/* Don't set cache for files using parallel I/O. */
if (grp->nc4_info->parallel)
return NC_NOERR;
#endif
/* How many bytes in the chunk? */
for (d = 0; d < var->ndims; d++)
chunk_size_bytes *= var->chunksizes[d];
if (var->type_info->size)
chunk_size_bytes *= var->type_info->size;
else
chunk_size_bytes *= sizeof(char *);
/* If the chunk cache is too small, and the user has not changed
* the default value of the chunk cache size, then increase the
* size of the cache. */
if (var->chunk_cache_size == CHUNK_CACHE_SIZE)
if (chunk_size_bytes > var->chunk_cache_size)
{
var->chunk_cache_size = chunk_size_bytes * DEFAULT_CHUNKS_IN_CACHE;
if (var->chunk_cache_size > MAX_DEFAULT_CACHE_SIZE)
var->chunk_cache_size = MAX_DEFAULT_CACHE_SIZE;
if ((retval = nc4_reopen_dataset(grp, var)))
return retval;
}
return NC_NOERR;
}
/**
* @internal Create a HDF5 defined type from a NC_TYPE_INFO_T struct,
* and commit it to the file.
*
* @param grp Pointer to group info struct.
* @param type Pointer to type info struct.
*
* @return NC_NOERR No error.
* @return NC_EHDFERR HDF5 error.
* @return NC_ECHAR Conversions of NC_CHAR forbidden.
* @return NC_EVARMETA HDF5 returning error creating datatype.
* @return NC_EHDFERR HDF5 returning error.
* @return NC_EBADTYE Type not found.
* @author Ed Hartnett
*/
static int
commit_type(NC_GRP_INFO_T *grp, NC_TYPE_INFO_T *type)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_TYPE_INFO_T *hdf5_type;
hid_t base_hdf_typeid;
int retval;
assert(grp && grp->format_grp_info && type && type->format_type_info);
/* Get HDF5-specific group and type info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
hdf5_type = (NC_HDF5_TYPE_INFO_T *)type->format_type_info;
/* Did we already record this type? */
if (type->committed)
return NC_NOERR;
/* Is this a compound type? */
if (type->nc_type_class == NC_COMPOUND)
{
NC_FIELD_INFO_T *field;
hid_t hdf_base_typeid, hdf_typeid;
int i;
if ((hdf5_type->hdf_typeid = H5Tcreate(H5T_COMPOUND, type->size)) < 0)
return NC_EHDFERR;
LOG((4, "creating compound type %s hdf_typeid 0x%x", type->hdr.name,
hdf5_type->hdf_typeid));
for(i=0;i<nclistlength(type->u.c.field);i++)
{
field = (NC_FIELD_INFO_T *)nclistget(type->u.c.field, i);
assert(field);
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, field->nc_typeid,
&hdf_base_typeid, type->endianness)))
return retval;
/* If this is an array, create a special array type. */
if (field->ndims)
{
int d;
hsize_t dims[NC_MAX_VAR_DIMS];
for (d = 0; d < field->ndims; d++)
dims[d] = field->dim_size[d];
if ((hdf_typeid = H5Tarray_create(hdf_base_typeid, field->ndims,
dims, NULL)) < 0)
{
if (H5Tclose(hdf_base_typeid) < 0)
return NC_EHDFERR;
return NC_EHDFERR;
}
if (H5Tclose(hdf_base_typeid) < 0)
return NC_EHDFERR;
}
else
hdf_typeid = hdf_base_typeid;
LOG((4, "inserting field %s offset %d hdf_typeid 0x%x", field->hdr.name,
field->offset, hdf_typeid));
if (H5Tinsert(hdf5_type->hdf_typeid, field->hdr.name, field->offset,
hdf_typeid) < 0)
return NC_EHDFERR;
if (H5Tclose(hdf_typeid) < 0)
return NC_EHDFERR;
}
}
else if (type->nc_type_class == NC_VLEN)
{
/* Find the HDF typeid of the base type of this vlen. */
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, type->u.v.base_nc_typeid,
&base_hdf_typeid, type->endianness)))
return retval;
/* Create a vlen type. */
if ((hdf5_type->hdf_typeid = H5Tvlen_create(base_hdf_typeid)) < 0)
return NC_EHDFERR;
}
else if (type->nc_type_class == NC_OPAQUE)
{
/* Create the opaque type. */
if ((hdf5_type->hdf_typeid = H5Tcreate(H5T_OPAQUE, type->size)) < 0)
return NC_EHDFERR;
}
else if (type->nc_type_class == NC_ENUM)
{
NC_ENUM_MEMBER_INFO_T *enum_m;
int i;
if (nclistlength(type->u.e.enum_member) == 0)
return NC_EINVAL;
/* Find the HDF typeid of the base type of this enum. */
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, type->u.e.base_nc_typeid,
&base_hdf_typeid, type->endianness)))
return retval;
/* Create an enum type. */
if ((hdf5_type->hdf_typeid = H5Tenum_create(base_hdf_typeid)) < 0)
return NC_EHDFERR;
/* Add all the members to the HDF5 type. */
for(i=0;i<nclistlength(type->u.e.enum_member);i++) {
enum_m = (NC_ENUM_MEMBER_INFO_T*)nclistget(type->u.e.enum_member,i);
if (H5Tenum_insert(hdf5_type->hdf_typeid, enum_m->name, enum_m->value) < 0)
return NC_EHDFERR;
}
}
else
{
LOG((0, "Unknown class: %d", type->nc_type_class));
return NC_EBADTYPE;
}
/* Commit the type. */
if (H5Tcommit(hdf5_grp->hdf_grpid, type->hdr.name, hdf5_type->hdf_typeid) < 0)
return NC_EHDFERR;
type->committed = NC_TRUE;
LOG((4, "just committed type %s, HDF typeid: 0x%x", type->hdr.name,
hdf5_type->hdf_typeid));
/* Later we will always use the native typeid. In this case, it is
* a copy of the same type pointed to by hdf_typeid, but it's
* easier to maintain a copy. */
if ((hdf5_type->native_hdf_typeid = H5Tget_native_type(hdf5_type->hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/**
* @internal Write an attribute, with value 1, to indicate that strict
* NC3 rules apply to this file.
*
* @param hdf_grpid HDF5 group ID.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
static int
write_nc3_strict_att(hid_t hdf_grpid)
{
hid_t attid = 0, spaceid = 0;
int one = 1;
int retval = NC_NOERR;
htri_t attr_exists;
/* If the attribute already exists, call that a success and return
* NC_NOERR. */
if ((attr_exists = H5Aexists(hdf_grpid, NC3_STRICT_ATT_NAME)) < 0)
return NC_EHDFERR;
if (attr_exists)
return NC_NOERR;
/* Create the attribute to mark this as a file that needs to obey
* strict netcdf-3 rules. */
if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EFILEMETA);
if ((attid = H5Acreate(hdf_grpid, NC3_STRICT_ATT_NAME,
H5T_NATIVE_INT, spaceid, H5P_DEFAULT)) < 0)
BAIL(NC_EFILEMETA);
if (H5Awrite(attid, H5T_NATIVE_INT, &one) < 0)
BAIL(NC_EFILEMETA);
exit:
if (spaceid > 0 && (H5Sclose(spaceid) < 0))
BAIL2(NC_EFILEMETA);
if (attid > 0 && (H5Aclose(attid) < 0))
BAIL2(NC_EFILEMETA);
return retval;
}
/**
* @internal Create a HDF5 group that is not the root group. HDF5
* properties are set in the group to ensure that objects and
* attributes are kept in creation order, instead of alphebetical
* order (the HDF5 default).
*
* @param grp Pointer to group info struct.
*
* @return NC_NOERR No error.
* @return NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
static int
create_group(NC_GRP_INFO_T *grp)
{
NC_HDF5_GRP_INFO_T *hdf5_grp, *parent_hdf5_grp;
hid_t gcpl_id = -1;
int retval = NC_NOERR;;
assert(grp && grp->format_grp_info && grp->parent &&
grp->parent->format_grp_info);
/* Get HDF5 specific group info for group and parent. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
parent_hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->parent->format_grp_info;
assert(parent_hdf5_grp->hdf_grpid);
/* Create group, with link_creation_order set in the group
* creation property list. */
if ((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
BAIL(NC_EHDFERR);
/* Set track_times to be FALSE. */
if (H5Pset_obj_track_times(gcpl_id, 0) < 0)
BAIL(NC_EHDFERR);
/* Tell HDF5 to keep track of objects in creation order. */
if (H5Pset_link_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Tell HDF5 to keep track of attributes in creation order. */
if (H5Pset_attr_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Create the group. */
if ((hdf5_grp->hdf_grpid = H5Gcreate2(parent_hdf5_grp->hdf_grpid, grp->hdr.name,
H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
exit:
if (gcpl_id > -1 && H5Pclose(gcpl_id) < 0)
BAIL2(NC_EHDFERR);
if (retval)
if (hdf5_grp->hdf_grpid > 0 && H5Gclose(hdf5_grp->hdf_grpid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal After all the datasets of the file have been read, it's
* time to sort the wheat from the chaff. Which of the datasets are
* netCDF dimensions, and which are coordinate variables, and which
* are non-coordinate variables.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
attach_dimscales(NC_GRP_INFO_T *grp)
{
NC_VAR_INFO_T *var;
NC_HDF5_VAR_INFO_T *hdf5_var;
int d, v;
/* Attach dimension scales. */
for (v = 0; v < ncindexsize(grp->vars); v++)
{
/* Get pointer to var and HDF5-specific var info. */
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, v);
assert(var && var->format_var_info);
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Scales themselves do not attach. But I really wish they
* would. */
if (hdf5_var->dimscale)
continue;
/* Find the scale for each dimension, if any, and attach it. */
for (d = 0; d < var->ndims; d++)
{
/* Is there a dimscale for this dimension? */
if (hdf5_var->dimscale_attached)
{
if (!hdf5_var->dimscale_attached[d])
{
hid_t dsid; /* Dataset ID for dimension */
assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d] &&
var->dim[d]->format_dim_info);
LOG((2, "%s: attaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->hdr.name));
/* Find dataset ID for dimension */
if (var->dim[d]->coord_var)
dsid = ((NC_HDF5_VAR_INFO_T *)(var->dim[d]->coord_var->format_var_info))->hdf_datasetid;
else
dsid = ((NC_HDF5_DIM_INFO_T *)var->dim[d]->format_dim_info)->hdf_dimscaleid;
assert(dsid > 0);
/* Attach the scale. */
if (H5DSattach_scale(hdf5_var->hdf_datasetid, dsid, d) < 0)
return NC_EHDFERR;
hdf5_var->dimscale_attached[d] = NC_TRUE;
}
}
}
}
return NC_NOERR;
}
/**
* @internal Does a variable exist?
*
* @param grpid HDF5 group ID.
* @param name Name of variable.
* @param exists Pointer that gets 1 of the variable exists, 0 otherwise.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
var_exists(hid_t grpid, char *name, nc_bool_t *exists)
{
htri_t link_exists;
/* Reset the boolean */
*exists = NC_FALSE;
/* Check if the object name exists in the group */
if ((link_exists = H5Lexists(grpid, name, H5P_DEFAULT)) < 0)
return NC_EHDFERR;
if (link_exists)
{
H5G_stat_t statbuf;
/* Get info about the object */
if (H5Gget_objinfo(grpid, name, 1, &statbuf) < 0)
return NC_EHDFERR;
if (H5G_DATASET == statbuf.type)
*exists = NC_TRUE;
}
return NC_NOERR;
}
/**
* @internal Convert a coordinate variable HDF5 dataset into one that
* is not a coordinate variable. This happens during renaming of vars
* and dims. This function removes the HDF5 NAME and CLASS attributes
* associated with dimension scales, and also the NC_DIMID_ATT_NAME
* attribute which may be present, and, if it does, holds the dimid of
* the coordinate variable.
*
* @param hdf_datasetid The HDF5 dataset ID of the coordinate variable
* dataset.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
static int
remove_coord_atts(hid_t hdf_datasetid)
{
htri_t attr_exists;
/* If the variable dataset has an optional NC_DIMID_ATT_NAME
* attribute, delete it. */
if ((attr_exists = H5Aexists(hdf_datasetid, NC_DIMID_ATT_NAME)) < 0)
return NC_EHDFERR;
if (attr_exists)
{
if (H5Adelete(hdf_datasetid, NC_DIMID_ATT_NAME) < 0)
return NC_EHDFERR;
}
/* Remove the dimension scale 'CLASS' & 'NAME' attributes. */
if ((attr_exists = H5Aexists(hdf_datasetid,
HDF5_DIMSCALE_CLASS_ATT_NAME)) < 0)
return NC_EHDFERR;
if (attr_exists)
{
if (H5Adelete(hdf_datasetid, HDF5_DIMSCALE_CLASS_ATT_NAME) < 0)
return NC_EHDFERR;
}
if ((attr_exists = H5Aexists(hdf_datasetid,
HDF5_DIMSCALE_NAME_ATT_NAME)) < 0)
return NC_EHDFERR;
if (attr_exists)
{
if (H5Adelete(hdf_datasetid, HDF5_DIMSCALE_NAME_ATT_NAME) < 0)
return NC_EHDFERR;
}
return NC_NOERR;
}
/**
* @internal This function writes a variable. The principle difficulty
* comes from the possibility that this is a coordinate variable, and
* was already written to the file as a dimension-only dimscale. If
* this occurs, then it must be deleted and recreated.
*
* @param var Pointer to variable info struct.
* @param grp Pointer to group info struct.
* @param write_dimid
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett, Quincey Koziol
*/
static int
write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_VAR_INFO_T *hdf5_var;
nc_bool_t replace_existing_var = NC_FALSE;
int retval;
assert(var && var->format_var_info && grp && grp->format_grp_info);
LOG((4, "%s: writing var %s", __func__, var->hdr.name));
/* Get HDF5-specific group and var info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* If the variable has already been created & the fill value changed,
* indicate that the existing variable should be replaced. */
if (var->created && var->fill_val_changed)
{
replace_existing_var = NC_TRUE;
var->fill_val_changed = NC_FALSE;
/* If the variable is going to be replaced, we need to flag any
other attributes associated with the variable as 'dirty', or
else *only* the fill value attribute will be copied over and
the rest will be lost. See
https://github.com/Unidata/netcdf-c/issues/239 */
flag_atts_dirty(var->att);
}
/* Is this a coordinate var that has already been created in
* the HDF5 file as a dimscale dataset? Check for dims with the
* same name in this group. If there is one, check to see if
* this object exists in the HDF group. */
if (var->became_coord_var)
{
if ((NC_DIM_INFO_T *)ncindexlookup(grp->dim, var->hdr.name))
{
nc_bool_t exists;
if ((retval = var_exists(hdf5_grp->hdf_grpid, var->hdr.name, &exists)))
return retval;
if (exists)
{
/* Indicate that the variable already exists, and should
* be replaced. */
replace_existing_var = NC_TRUE;
flag_atts_dirty(var->att);
}
}
}
/* Check dims if the variable will be replaced, so that the
* dimensions will be de-attached and re-attached correctly. */
if (replace_existing_var)
{
NC_DIM_INFO_T *d1;
/* Is there a dim with this var's name? */
if ((d1 = (NC_DIM_INFO_T *)ncindexlookup(grp->dim, var->hdr.name)))
{
nc_bool_t exists;
assert(d1->format_dim_info && d1->hdr.name);
if ((retval = var_exists(hdf5_grp->hdf_grpid, var->hdr.name, &exists)))
return retval;
if (exists)
{
hid_t dsid;
/* Find dataset ID for dimension */
if (d1->coord_var)
dsid = ((NC_HDF5_VAR_INFO_T *)d1->coord_var->format_var_info)->hdf_datasetid;
else
dsid = ((NC_HDF5_DIM_INFO_T *)d1->format_dim_info)->hdf_dimscaleid;
assert(dsid > 0);
/* If we're replacing an existing dimscale dataset, go to
* every var in the file and detach this dimension scale,
* because we have to delete it. */
if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
var->dimids[0], dsid)))
return retval;
}
}
}
/* If this is not a dimension scale, remove any attached scales,
* and delete dimscale attributes from the var. */
if (var->was_coord_var && hdf5_var->dimscale_attached)
{
int d;
/* If the variable already exists in the file, Remove any dimension scale
* attributes from it, if they exist. */
if (var->created)
if ((retval = remove_coord_atts(hdf5_var->hdf_datasetid)))
return retval;
/* If this is a regular var, detach all its dim scales. */
for (d = 0; d < var->ndims; d++)
{
if (hdf5_var->dimscale_attached[d])
{
hid_t dsid; /* Dataset ID for dimension */
assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d] &&
var->dim[d]->format_dim_info);
/* Find dataset ID for dimension */
if (var->dim[d]->coord_var)
dsid = ((NC_HDF5_VAR_INFO_T *)var->dim[d]->coord_var->format_var_info)->hdf_datasetid;
else
dsid = ((NC_HDF5_DIM_INFO_T *)var->dim[d]->format_dim_info)->hdf_dimscaleid;
assert(dsid > 0);
/* Detach this dim scale. */
if (H5DSdetach_scale(hdf5_var->hdf_datasetid, dsid, d) < 0)
return NC_EHDFERR;
hdf5_var->dimscale_attached[d] = NC_FALSE;
}
}
}
/* Delete the HDF5 dataset that is to be replaced. */
if (replace_existing_var)
{
/* Free the HDF5 dataset id. */
if (hdf5_var->hdf_datasetid && H5Dclose(hdf5_var->hdf_datasetid) < 0)
return NC_EHDFERR;
hdf5_var->hdf_datasetid = 0;
/* Now delete the variable. */
if (H5Gunlink(hdf5_grp->hdf_grpid, var->hdr.name) < 0)
return NC_EDIMMETA;
}
/* Create the dataset. */
if (var->is_new_var || replace_existing_var)
{
if ((retval = var_create_dataset(grp, var, write_dimid)))
return retval;
}
else
{
if (write_dimid && var->ndims)
if ((retval = write_netcdf4_dimid(hdf5_var->hdf_datasetid,
var->dimids[0])))
return retval;
}
if (replace_existing_var)
{
/* If this is a dimension scale, reattach the scale everywhere it
* is used. (Recall that netCDF dimscales are always 1-D). */
if(hdf5_var->dimscale)
{
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], hdf5_var->hdf_datasetid)))
return retval;
}
/* If it's not a dimension scale, clear the dimscale attached flags,
* so the dimensions are re-attached. */
else
{
if (hdf5_var->dimscale_attached)
memset(hdf5_var->dimscale_attached, 0, sizeof(nc_bool_t) * var->ndims);
}
}
/* Clear coord. var state transition flags */
var->was_coord_var = NC_FALSE;
var->became_coord_var = NC_FALSE;
/* Now check the attributes for this var. */
if (var->attr_dirty)
{
/* Write attributes for this var. */
if ((retval = write_attlist(var->att, var->hdr.id, grp)))
return retval;
var->attr_dirty = NC_FALSE;
}
return NC_NOERR;
}
/**
* @internal Write a HDF5 dataset which is a dimension without a
* coordinate variable. This is a special 1-D dataset.
*
* @param dim Pointer to dim info struct.
* @param grp Pointer to group info struct.
* @param write_dimid
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EPERM Read-only file.
* @returns ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
int
nc4_create_dim_wo_var(NC_DIM_INFO_T *dim)
{
NC_HDF5_DIM_INFO_T *hdf5_dim;
NC_HDF5_GRP_INFO_T *hdf5_grp;
hid_t spaceid = -1, create_propid = -1;
hsize_t dims[1], max_dims[1], chunk_dims[1] = {1};
char dimscale_wo_var[NC_MAX_NAME];
int retval = NC_NOERR;
LOG((4, "%s: creating dim %s", __func__, dim->hdr.name));
/* Sanity check */
assert(!dim->coord_var);
/* Get HDF5-specific dim and group info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)dim->container->format_grp_info;
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
/* Create a property list. */
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
BAIL(NC_EHDFERR);
/* Turn off recording of times associated with this object. */
if (H5Pset_obj_track_times(create_propid, 0) < 0)
BAIL(NC_EHDFERR);
/* Set size of dataset to size of dimension. */
dims[0] = dim->len;
max_dims[0] = dim->len;
/* If this dimension scale is unlimited (i.e. it's an unlimited
* dimension), then set up chunking, with a chunksize of 1. */
if (dim->unlimited)
{
max_dims[0] = H5S_UNLIMITED;
if (H5Pset_chunk(create_propid, 1, chunk_dims) < 0)
BAIL(NC_EHDFERR);
}
/* Set up space. */
if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0)
BAIL(NC_EHDFERR);
/* Turn on creation-order tracking. */
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Create the dataset that will be the dimension scale. */
LOG((4, "%s: about to H5Dcreate1 a dimscale dataset %s", __func__,
dim->hdr.name));
if ((hdf5_dim->hdf_dimscaleid = H5Dcreate2(hdf5_grp->hdf_grpid, dim->hdr.name,
H5T_IEEE_F32BE, spaceid,
H5P_DEFAULT, create_propid,
H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
/* Indicate that this is a scale. Also indicate that not
* be shown to the user as a variable. It is hidden. It is
* a DIM WITHOUT A VARIABLE! */
sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, (int)dim->len);
if (H5DSset_scale(hdf5_dim->hdf_dimscaleid, dimscale_wo_var) < 0)
BAIL(NC_EHDFERR);
/* Since this dimension was created out of order, we cannot rely on
* it getting the correct dimid on file open. We must assign it
* explicitly. */
if ((retval = write_netcdf4_dimid(hdf5_dim->hdf_dimscaleid, dim->hdr.id)))
BAIL(retval);
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (create_propid > 0 && H5Pclose(create_propid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Write a dimension.
*
* @param dim Pointer to dim info struct.
* @param grp Pointer to group info struct.
* @param write_dimid
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EPERM Read-only file.
* @returns ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
NC_HDF5_DIM_INFO_T *hdf5_dim;
int retval = NC_NOERR;
assert(dim && dim->format_dim_info && grp && grp->format_grp_info);
/* Get HDF5-specific dim and group info. */
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
/* If there's no dimscale dataset for this dim, create one,
* and mark that it should be hidden from netCDF as a
* variable. (That is, it should appear as a dimension
* without an associated variable.) */
if (!hdf5_dim->hdf_dimscaleid)
if ((retval = nc4_create_dim_wo_var(dim)))
BAIL(retval);
/* Did we extend an unlimited dimension? */
if (dim->extended)
{
NC_VAR_INFO_T *v1 = NULL;
assert(dim->unlimited);
/* If this is a dimension with an associated coordinate var,
* then update the length of that coord var. */
v1 = dim->coord_var;
if (v1)
{
NC_HDF5_VAR_INFO_T *hdf5_v1;
hsize_t *new_size;
int d1;
hdf5_v1 = (NC_HDF5_VAR_INFO_T *)v1->format_var_info;
/* Extend the dimension scale dataset to reflect the new
* length of the dimension. */
if (!(new_size = malloc(v1->ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
for (d1 = 0; d1 < v1->ndims; d1++)
{
assert(v1->dim[d1] && v1->dim[d1]->hdr.id == v1->dimids[d1]);
new_size[d1] = v1->dim[d1]->len;
}
if (H5Dset_extent(hdf5_v1->hdf_datasetid, new_size) < 0)
BAIL(NC_EHDFERR);
free(new_size);
}
}
/* If desired, write the secret dimid. This will be used instead of
* the dimid that the dimension would otherwise receive based on
* creation order. This can be necessary when dims and their
* coordinate variables were created in different order. */
if (write_dimid && hdf5_dim->hdf_dimscaleid)
if ((retval = write_netcdf4_dimid(hdf5_dim->hdf_dimscaleid, dim->hdr.id)))
BAIL(retval);
exit:
return retval;
}
/**
* @internal Recursively write all the metadata in a group. Groups and
* types have all already been written. Propagate bad cooordinate
* order to subgroups, if detected.
*
* @param grp Pointer to group info struct.
* @param bad_coord_order 1 if there is a bad coordinate order.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
int
nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order)
{
NC_DIM_INFO_T *dim = NULL;
NC_VAR_INFO_T *var = NULL;
NC_GRP_INFO_T *child_grp = NULL;
int coord_varid = -1;
int var_index = 0;
int dim_index = 0;
int retval;
int i;
assert(grp && grp->hdr.name &&
((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid);
LOG((3, "%s: grp->hdr.name %s, bad_coord_order %d", __func__, grp->hdr.name,
bad_coord_order));
/* Write global attributes for this group. */
if ((retval = write_attlist(grp->att, NC_GLOBAL, grp)))
return retval;
/* Set the pointers to the beginning of the list of dims & vars in this
* group. */
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, dim_index);
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, var_index);
/* Because of HDF5 ordering the dims and vars have to be stored in
* this way to ensure that the dims and coordinate vars come out in
* the correct order. */
while (dim || var)
{
nc_bool_t found_coord, wrote_coord;
/* Write non-coord dims in order, stopping at the first one that
* has an associated coord var. */
for (found_coord = NC_FALSE; dim && !found_coord; )
{
if (!dim->coord_var)
{
if ((retval = write_dim(dim, grp, bad_coord_order)))
return retval;
}
else
{
coord_varid = dim->coord_var->hdr.id;
found_coord = NC_TRUE;
}
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, ++dim_index);
}
/* Write each var. When we get to the coord var we are waiting
* for (if any), then we break after writing it. */
for (wrote_coord = NC_FALSE; var && !wrote_coord; )
{
if ((retval = write_var(var, grp, bad_coord_order)))
return retval;
if (found_coord && var->hdr.id == coord_varid)
wrote_coord = NC_TRUE;
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, ++var_index);
}
} /* end while */
/* Attach dimscales to vars in this group. */
if ((retval = attach_dimscales(grp)))
return retval;
/* If there are any child groups, write their metadata. */
for (i = 0; i < ncindexsize(grp->children); i++)
{
child_grp = (NC_GRP_INFO_T *)ncindexith(grp->children, i);
assert(child_grp);
if ((retval = nc4_rec_write_metadata(child_grp, bad_coord_order)))
return retval;
}
return NC_NOERR;
}
/**
* @internal Recursively write all groups and types.
*
* @param grp Pointer to group info struct.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned an error.
* @author Ed Hartnett
*/
int
nc4_rec_write_groups_types(NC_GRP_INFO_T *grp)
{
NC_GRP_INFO_T *child_grp;
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_TYPE_INFO_T *type;
int retval;
int i;
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;
/* Create the group in the HDF5 file if it doesn't exist. */
if (!hdf5_grp->hdf_grpid)
if ((retval = create_group(grp)))
return retval;
/* If this is the root group of a file with strict NC3 rules, write
* an attribute. But don't leave the attribute open. */
if (!grp->parent && (grp->nc4_info->cmode & NC_CLASSIC_MODEL))
if ((retval = write_nc3_strict_att(hdf5_grp->hdf_grpid)))
return retval;
/* If there are any user-defined types, write them now. */
for(i=0;i<ncindexsize(grp->type);i++) {
type = (NC_TYPE_INFO_T *)ncindexith(grp->type, i);
assert(type);
if ((retval = commit_type(grp, type)))
return retval;
}
/* If there are any child groups, write their groups and types. */
for(i=0;i<ncindexsize(grp->children);i++) {
if((child_grp = (NC_GRP_INFO_T*)ncindexith(grp->children,i)) == NULL) continue;
if ((retval = nc4_rec_write_groups_types(child_grp)))
return retval;
}
return NC_NOERR;
}
/**
* @internal In our first pass through the data, we may have
* encountered variables before encountering their dimscales, so go
* through the vars in this file and make sure we've got a dimid for
* each.
*
* @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
*/
int
nc4_rec_match_dimscales(NC_GRP_INFO_T *grp)
{
NC_GRP_INFO_T *g;
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++)
{
g = (NC_GRP_INFO_T*)ncindexith(grp->children, i);
assert(g);
if ((retval = nc4_rec_match_dimscales(g)))
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 ndims;
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. */
/* This loop is very odd. Under normal circumstances, var->dimid[d] is zero
(from the initial calloc) which is a legitimate dimid. The code does not
distinquish this case from the dimscale case where the id might actually
be defined.
The original nc4_find_dim searched up the group tree looking for the given
dimid in one of the dim lists associated with each ancestor group.
I changed nc4_fnd_dim to use the dimid directly using h5->alldims.
However, here that is incorrect because it will find the dimid 0 always
(if any dimensions were defined). Except that when dimscale dimids have
been defined, one or more of the values in var->dimids will have a
legitimate value.
The solution I choose is to modify nc4_var_list_add to initialize dimids to
illegal values (-1). This is another example of the problems with dimscales.
*/
ndims = var->ndims;
for (d = 0; d < ndims; d++)
{
if (var->dim[d] == NULL) {
nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
}
/* assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d]); */
}
/* 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_bool_t finished = NC_FALSE;
LOG((5, "%s: var %s has dimscale info...", __func__, var->hdr.name));
/* 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 */
LOG((5, "%s: dimid for this dimscale is %d", __func__,
var->type_info->hdr.id));
} /* next var->dim */
}
/* No dimscales for this var! Invent phony dimensions. */
else
{
hid_t spaceid = 0;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int dataset_ndims;
/* Find the space information for this dimension. */
if ((spaceid = H5Dget_space(hdf5_var->hdf_datasetid)) < 0)
return NC_EHDFERR;
/* Get the len of each dim in the space. */
if (var->ndims)
{
if (!(h5dimlen = malloc(var->ndims * sizeof(hsize_t))))
return NC_ENOMEM;
if (!(h5dimlenmax = malloc(var->ndims * sizeof(hsize_t))))
{
free(h5dimlen);
return NC_ENOMEM;
}
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid, h5dimlen,
h5dimlenmax)) < 0) {
free(h5dimlenmax);
free(h5dimlen);
return NC_EHDFERR;
}
if (dataset_ndims != var->ndims) {
free(h5dimlenmax);
free(h5dimlen);
return NC_EHDFERR;
}
}
else
{
/* Make sure it's scalar. */
if (H5Sget_simple_extent_type(spaceid) != H5S_SCALAR)
return NC_EHDFERR;
}
/* Release the space object. */
if (H5Sclose(spaceid) < 0) {
free(h5dimlen);
free(h5dimlenmax);
return NC_EHDFERR;
}
/* 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;
/* Is there already a phony dimension of the correct size? */
for(match=-1,k=0;k<ncindexsize(grp->dim);k++) {
if((dim = (NC_DIM_INFO_T*)ncindexith(grp->dim,k)) == NULL) continue;
if ((dim->len == h5dimlen[d]) &&
((h5dimlenmax[d] == H5S_UNLIMITED && dim->unlimited) ||
(h5dimlenmax[d] != H5S_UNLIMITED && !dim->unlimited)))
{match = k; break;}
}
/* Didn't find a phony dim? Then create one. */
if (match < 0)
{
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));
if ((retval = nc4_dim_list_add(grp, phony_dim_name, h5dimlen[d], -1, &dim)))
{
free(h5dimlenmax);
free(h5dimlen);
return retval;
}
/* Create struct for HDF5-specific dim info. */
if (!(dim->format_dim_info = calloc(1, sizeof(NC_HDF5_DIM_INFO_T))))
return 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 */
/* Free the memory we malloced. */
free(h5dimlen);
free(h5dimlenmax);
}
}
}
return retval;
}
/**
* @internal Get the class of a type
*
* @param h5 Pointer to the HDF5 file info struct.
* @param xtype NetCDF type ID.
* @param type_class Pointer that gets class of type, NC_INT,
* NC_FLOAT, NC_CHAR, or NC_STRING, NC_ENUM, NC_VLEN, NC_COMPOUND, or
* NC_OPAQUE.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_get_typeclass(const NC_FILE_INFO_T *h5, nc_type xtype, int *type_class)
{
int retval = NC_NOERR;
LOG((4, "%s xtype: %d", __func__, xtype));
assert(type_class);
/* If this is an atomic type, the answer is easy. */
if (xtype <= NC_STRING)
{
switch (xtype)
{
case NC_BYTE:
case NC_UBYTE:
case NC_SHORT:
case NC_USHORT:
case NC_INT:
case NC_UINT:
case NC_INT64:
case NC_UINT64:
/* NC_INT is class used for all integral types */
*type_class = NC_INT;
break;
case NC_FLOAT:
case NC_DOUBLE:
/* NC_FLOAT is class used for all floating-point types */
*type_class = NC_FLOAT;
break;
case NC_CHAR:
*type_class = NC_CHAR;
break;
case NC_STRING:
*type_class = NC_STRING;
break;
default:
BAIL(NC_EBADTYPE);
}
}
else
{
NC_TYPE_INFO_T *type;
/* See if it's a used-defined type */
if ((retval = nc4_find_type(h5, xtype, &type)))
BAIL(retval);
if (!type)
BAIL(NC_EBADTYPE);
*type_class = type->nc_type_class;
}
exit:
return retval;
}
/**
* @internal Report information about an open HDF5 object. This is
* called on any still-open objects when a HDF5 file close is
* attempted.
*
* @param uselog If true, send output to LOG not stderr.
* @param id HDF5 ID of open object.
* @param type Type of HDF5 object, file, dataset, etc.
*
* @author Dennis Heimbigner
*/
void
reportobject(int uselog, hid_t id, unsigned int type)
{
char name[NC_HDF5_MAX_NAME];
ssize_t len;
const char* typename = NULL;
long long printid = (long long)id;
len = H5Iget_name(id, name, NC_HDF5_MAX_NAME);
if(len < 0) return;
name[len] = '\0';
switch (type) {
case H5F_OBJ_FILE: typename = "File"; break;
case H5F_OBJ_DATASET: typename = "Dataset"; break;
case H5F_OBJ_GROUP: typename = "Group"; break;
case H5F_OBJ_DATATYPE: typename = "Datatype"; break;
case H5F_OBJ_ATTR:
typename = "Attribute";
len = H5Aget_name(id, NC_HDF5_MAX_NAME, name);
if(len < 0) len = 0;
name[len] = '\0';
break;
default: typename = "<unknown>"; break;
}
#ifdef LOGGING
if(uselog) {
LOG((0,"Type = %s(%lld) name='%s'",typename,printid,name));
} else
#endif
{
fprintf(stderr,"Type = %s(%lld) name='%s'",typename,printid,name);
}
}
/**
* @internal
*
* @param uselog
* @param fid HDF5 ID.
* @param ntypes Number of types.
* @param otypes Pointer that gets number of open types.
*
* @author Dennis Heimbigner
*/
static void
reportopenobjectsT(int uselog, hid_t fid, int ntypes, unsigned int* otypes)
{
int t,i;
ssize_t ocount;
size_t maxobjs = -1;
hid_t* idlist = NULL;
/* Always report somehow */
#ifdef LOGGING
if(uselog)
LOG((0,"\nReport: open objects on %lld",(long long)fid));
else
#endif
fprintf(stdout,"\nReport: open objects on %lld\n",(long long)fid);
maxobjs = H5Fget_obj_count(fid,H5F_OBJ_ALL);
if(idlist != NULL) free(idlist);
idlist = (hid_t*)malloc(sizeof(hid_t)*maxobjs);
for(t=0;t<ntypes;t++) {
unsigned int ot = otypes[t];
ocount = H5Fget_obj_ids(fid,ot,maxobjs,idlist);
for(i=0;i<ocount;i++) {
hid_t o = idlist[i];
reportobject(uselog,o,ot);
}
}
if(idlist != NULL) free(idlist);
}
/**
* @internal Report open objects.
*
* @param uselog
* @param fid HDF5 file ID.
*
* @author Dennit Heimbigner
*/
void
reportopenobjects(int uselog, hid_t fid)
{
unsigned int OTYPES[5] = {H5F_OBJ_FILE, H5F_OBJ_DATASET, H5F_OBJ_GROUP,
H5F_OBJ_DATATYPE, H5F_OBJ_ATTR};
reportopenobjectsT(uselog, fid ,5, OTYPES);
}
/**
* @internal Report open objects given a pointer to NC_FILE_INFO_T object
*
* @param h5 file object
*
* @author Dennis Heimbigner
*/
void
showopenobjects5(NC_FILE_INFO_T* h5)
{
NC_HDF5_FILE_INFO_T *hdf5_info;
assert(h5 && h5->format_file_info);
hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
fprintf(stderr,"===== begin showopenobjects =====\n");
reportopenobjects(0,hdf5_info->hdfid);
fprintf(stderr,"===== end showopenobjects =====\n");
fflush(stderr);
}
/**
* @internal Report open objects given an ncid
* Defined to support user or gdb level call.
*
* @param ncid file id
*
* @author Dennis Heimbigner
*/
void
showopenobjects(int ncid)
{
NC_FILE_INFO_T* h5 = NULL;
/* Find our metadata for this file. */
if (nc4_find_nc_grp_h5(ncid, NULL, NULL, &h5) != NC_NOERR)
fprintf(stderr,"failed\n");
else
showopenobjects5(h5);
fflush(stderr);
}
/**
* @internal Get HDF5 library version.
*
* @param major Pointer that gets major version number.
* @param minor Pointer that gets minor version number.
* @param release Pointer that gets release version number.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned error.
* @author Dennis Heimbigner
*/
int
NC4_hdf5get_libversion(unsigned* major,unsigned* minor,unsigned* release)
{
if(H5get_libversion(major,minor,release) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/**
* @internal Get HDF5 superblock version.
*
* @param h5 Pointer to HDF5 file info struct.
* @param idp Pointer that gets superblock version.
*
* @returns NC_NOERR No error.
* @returns NC_EHDFERR HDF5 returned error.
* @author Dennis Heimbigner
*/
int
NC4_hdf5get_superblock(struct NC_FILE_INFO* h5, int* idp)
{
NC_HDF5_FILE_INFO_T *hdf5_info;
int stat = NC_NOERR;
unsigned super;
hid_t plist = -1;
assert(h5 && h5->format_file_info);
hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
if((plist = H5Fget_create_plist(hdf5_info->hdfid)) < 0)
{stat = NC_EHDFERR; goto done;}
if(H5Pget_version(plist, &super, NULL, NULL, NULL) < 0)
{stat = NC_EHDFERR; goto done;}
if(idp) *idp = (int)super;
done:
if(plist >= 0) H5Pclose(plist);
return stat;
}
static int NC4_strict_att_exists(NC_FILE_INFO_T*);
static int NC4_walk(hid_t, int*);
/**
* @internal Determine whether file is netCDF-4.
*
* We define a file as being from netcdf-4 if any of the following
* are true:
* 1. NCPROPS attribute exists in root group
* 2. NC3_STRICT_ATT_NAME exists in root group
* 3. any of NC_ATT_REFERENCE_LIST, NC_ATT_CLASS,
* NC_ATT_DIMENSION_LIST, NC_ATT_NAME,
* NC_ATT_COORDINATES, NC_DIMID_ATT_NAME
* exist anywhere in the file; note that this
* requires walking the file.
* @note WARNINGS:
* 1. False negatives are possible for a small subset of netcdf-4
* created files.
* 2. Deliberate falsification in the file can be used to cause
* a false positive.
*
* @param h5 Pointer to HDF5 file info struct.
*
* @returns NC_NOERR No error.
* @author Dennis Heimbigner.
*/
int
NC4_isnetcdf4(struct NC_FILE_INFO* h5)
{
int stat;
int isnc4 = 0;
int exists;
int count;
/* Look for NC3_STRICT_ATT_NAME */
exists = NC4_strict_att_exists(h5);
if(exists)
goto done;
/* attribute did not exist */
/* => last resort: walk the HDF5 file looking for markers */
count = 0;
stat = NC4_walk(((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid,
&count);
if(stat != NC_NOERR)
isnc4 = 0;
else /* Threshold is at least two matches */
isnc4 = (count >= 2);
done:
return isnc4;
}
/**
* @internal See if the NC3 strict attribute exists.
*
* @param h5 Pointer to HDF5 file info struct.
*
* @returns 1 if error || exists; 0 otherwise
* @author Dennis Heimbigner.
*/
static int
NC4_strict_att_exists(NC_FILE_INFO_T *h5)
{
hid_t grpid = -1;
htri_t attr_exists;
/* Get root group ID. */
grpid = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid;
/* See if the NC3_STRICT_ATT_NAME attribute exists */
if ((attr_exists = H5Aexists(grpid, NC3_STRICT_ATT_NAME)) < 0)
return 1;
return (attr_exists?1:0);
}
/**
* @internal Walk group struct.
*
* @param gid HDF5 ID of starting group.
* @param countp Pointer that gets count.
*
* @returns NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
NC4_walk(hid_t gid, int* countp)
{
int ncstat = NC_NOERR;
int i,j,na;
ssize_t len;
hsize_t nobj;
herr_t err;
int otype;
hid_t grpid, dsid;
char name[NC_HDF5_MAX_NAME];
/* walk group members of interest */
err = H5Gget_num_objs(gid, &nobj);
if(err < 0) return err;
for(i = 0; i < nobj; i++) {
/* Get name & kind of object in the group */
len = H5Gget_objname_by_idx(gid,(hsize_t)i,name,(size_t)NC_HDF5_MAX_NAME);
if(len < 0) return len;
otype = H5Gget_objtype_by_idx(gid,(size_t)i);
switch(otype) {
case H5G_GROUP:
grpid = H5Gopen(gid,name);
NC4_walk(grpid,countp);
H5Gclose(grpid);
break;
case H5G_DATASET: /* variables */
/* Check for phony_dim */
if(strcmp(name,"phony_dim")==0)
*countp = *countp + 1;
dsid = H5Dopen(gid,name);
na = H5Aget_num_attrs(dsid);
for(j = 0; j < na; j++) {
hid_t aid = H5Aopen_idx(dsid,(unsigned int) j);
if(aid >= 0) {
const NC_reservedatt* ra;
ssize_t len = H5Aget_name(aid, NC_HDF5_MAX_NAME, name);
if(len < 0) return len;
/* Is this a netcdf-4 marker attribute */
/* Is this a netcdf-4 marker attribute */
ra = NC_findreserved(name);
if(ra != NULL)
*countp = *countp + 1;
}
H5Aclose(aid);
}
H5Dclose(dsid);
break;
default:/* ignore */
break;
}
}
return ncstat;
}
int
NC4_hdf5_remove_filter(NC_VAR_INFO_T* var, const char* filterid)
{
int stat = NC_NOERR;
NC_HDF5_VAR_INFO_T *hdf5_var;
hid_t propid = -1;
herr_t herr = -1;
H5Z_filter_t hft;
unsigned int id;
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
if ((propid = H5Dget_create_plist(hdf5_var->hdf_datasetid)) < 0)
{stat = NC_EHDFERR; goto done;}
if((stat = NC_cvtX2I_id(filterid,&id))) goto done;
hft = id;
if((herr = H5Premove_filter(propid,hft)) < 0)
{stat = NC_EHDFERR; goto done;}
done:
return stat;
}
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