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Merge branch 'ejh_rename_var_to_non_coord_var' of https://github.com/NetCDF-World-Domination-Council/netcdf-c into pr-aggregation.wif

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This commit is contained in:
Ward Fisher 2019-02-06 14:09:48 -07:00
commit 035b3030ef
4 changed files with 194 additions and 78 deletions
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9
include/hdf5internal.h
View File

@ -135,7 +135,14 @@ int nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_IN
extern hid_t NC4_image_init(NC_FILE_INFO_T* h5);
extern void NC4_image_finalize(void*);
/* These functions are internal to the libhdf5 directory. */
/* Create HDF5 dataset for dim without a coord var. */
extern int nc4_create_dim_wo_var(NC_DIM_INFO_T *dim);
/* Give a var a secret HDF5 name, for use when there is a dim of this
* name, but the var is not a coord var of that dim. */
extern int nc4_give_var_secret_name(NC_VAR_INFO_T *var);
/* Get the fill value for a var. */
int nc4_get_fill_value(NC_FILE_INFO_T *h5, NC_VAR_INFO_T *var, void **fillp);

68
libhdf5/hdf5var.c
View File

@ -220,6 +220,36 @@ nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
return NC_NOERR;
}
/**
* @internal Give a var a secret HDF5 name. This is needed when a var
* is defined with the same name as a dim, but it is not a coord var
* of that dim. In that case, the var uses a secret name inside the
* HDF5 file.
*
* @param var Pointer to var info.
* @param name Name to use for base of secret name.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EMAXNAME Name too long to fit secret prefix.
* @returns ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
give_var_secret_name(NC_VAR_INFO_T *var, const char *name)
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
return NC_EMAXNAME;
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(name) + 1) * sizeof(char))))
return NC_ENOMEM;
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, name);
return NC_NOERR;
}
/**
* @internal This is called when a new netCDF-4 variable is defined
* with nc_def_var().
@ -502,17 +532,8 @@ NC4_def_var(int ncid, const char *name, nc_type xtype,
* and this var has the same name. */
dim = (NC_DIM_INFO_T*)ncindexlookup(grp->dim,norm_name);
if (dim && (!var->ndims || dimidsp[0] != dim->hdr.id))
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
BAIL(NC_EMAXNAME);
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(norm_name) + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name);
}
if ((retval = give_var_secret_name(var, var->hdr.name)))
BAIL(retval);
/* If this is a coordinate var, it is marked as a HDF5 dimension
* scale. (We found dim above.) Otherwise, allocate space to
@ -1039,6 +1060,8 @@ NC4_rename_var(int ncid, int varid, const char *name)
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *other_dim;
int use_secret_name = 0;
int retval = NC_NOERR;
if (!name)
@ -1082,10 +1105,31 @@ NC4_rename_var(int ncid, int varid, const char *name)
(h5->cmode & NC_CLASSIC_MODEL))
return NC_ENOTINDEFINE;
/* Is there another dim with this name, for which this var will not
* be a coord var? If so, we have to create a dim without a
* variable for the old name. */
if ((other_dim = (NC_DIM_INFO_T *)ncindexlookup(grp->dim, name)) &&
strcmp(name, var->dim[0]->hdr.name))
{
/* Create a dim without var dataset for old dim. */
if ((retval = nc4_create_dim_wo_var(other_dim)))
return retval;
/* Give this var a secret HDF5 name so it can co-exist in file
* with dim wp var dataset. Base the secret name on the new var
* name. */
if ((retval = give_var_secret_name(var, name)))
return retval;
use_secret_name++;
}
/* Change the HDF5 file, if this var has already been created
there. */
if (var->created)
{
char *hdf5_name;
hdf5_name = use_secret_name ? var->hdf5_name: (char *)name;
/* Do we need to read var metadata? */
if (!var->meta_read)
if ((retval = nc4_get_var_meta(var)))
@ -1107,7 +1151,7 @@ NC4_rename_var(int ncid, int varid, const char *name)
}
LOG((3, "Moving dataset %s to %s", var->hdr.name, name));
if (H5Gmove(hdf5_grp->hdf_grpid, var->hdr.name, name) < 0)
if (H5Gmove(hdf5_grp->hdf_grpid, var->hdr.name, hdf5_name) < 0)
BAIL(NC_EHDFERR);
}

153
libhdf5/nc4hdf.c
View File

@ -1707,6 +1707,92 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
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);
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.
*
@ -1722,76 +1808,21 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
static int
write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
hid_t spaceid = -1, create_propid = -1;
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_DIM_INFO_T *hdf5_dim;
hsize_t *new_size = NULL;
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;
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_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)
{
hsize_t dims[1], max_dims[1], chunk_dims[1] = {1};
char dimscale_wo_var[NC_MAX_NAME];
LOG((4, "%s: creating dim %s", __func__, dim->hdr.name));
/* Sanity check */
assert(!dim->coord_var);
/* Create a property list. If this dimension scale is
* unlimited (i.e. it's an unlimited dimension), then set
* up chunking, with a chunksize of 1. */
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);
dims[0] = dim->len;
max_dims[0] = dim->len;
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);
}
if ((retval = nc4_create_dim_wo_var(dim)))
BAIL(retval);
/* Did we extend an unlimited dimension? */
if (dim->extended)
@ -1806,6 +1837,7 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
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;
@ -1821,6 +1853,7 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
}
if (H5Dset_extent(hdf5_v1->hdf_datasetid, new_size) < 0)
BAIL(NC_EHDFERR);
free(new_size);
}
}
@ -1833,12 +1866,6 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
BAIL(retval);
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (create_propid > 0 && H5Pclose(create_propid) < 0)
BAIL2(NC_EHDFERR);
if (new_size)
free(new_size);
return retval;
}

42
nc_test4/tst_rename2.c
View File

@ -34,6 +34,9 @@ See \ref copyright file for more info.
#define NDIM1 1
#define NDIM3 3
#define NUM_ENDDEF_SETTINGS 2
#define D1_NAME "d1"
#define D2_NAME "d2"
#define TMP_NAME "t1"
int
main(int argc, char **argv)
@ -166,7 +169,6 @@ main(int argc, char **argv)
/* Create file with dim and associated coordinate var. */
sprintf(file_name, "%s_sync.nc", TEST_NAME);
nc_set_log_level(4);
if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, DIM_NAME_END, DIM1_LEN, &dimid)) ERR;
if (nc_def_var(ncid, DIM_NAME_END, NC_INT, NDIM1, &dimid, &varid)) ERR;
@ -205,7 +207,7 @@ main(int argc, char **argv)
if (nc_def_var(ncid, VAR_NAME_START, NC_INT, NDIM1, &dimid, &varid)) ERR;
if (nc_close(ncid)) ERR;
nc_set_log_level(4);
/* nc_set_log_level(4); */
/* Open the file and rename the var. */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, DIM_NAME_START, &dimid)) ERR;
@ -235,5 +237,41 @@ main(int argc, char **argv)
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
fprintf(stderr,"*** test renaming non-coord var to same name as dim...");
{
int ncid, dimid1, dimid2, varid1, varid2;
int dimid_in, varid_in;
char file_name[NC_MAX_NAME + 1];
/* Create file with dim and associated coordinate var. */
sprintf(file_name, "%s_non_coord_to_dim.nc", TEST_NAME);
if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, D1_NAME, DIM1_LEN, &dimid1)) ERR;
if (nc_def_dim(ncid, D2_NAME, DIM1_LEN, &dimid2)) ERR;
if (nc_def_var(ncid, D1_NAME, NC_INT, NDIM1, &dimid1, &varid1)) ERR;
if (nc_def_var(ncid, D2_NAME, NC_INT, NDIM1, &dimid2, &varid2)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and rename the vars. */
/* nc_set_log_level(4); */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_rename_var(ncid, varid1, TMP_NAME)) ERR;
if (nc_rename_var(ncid, varid2, D1_NAME)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen file and check, */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, D1_NAME, &dimid_in)) ERR;
if (dimid_in != dimid1) ERR;
if (nc_inq_dimid(ncid, D2_NAME, &dimid_in)) ERR;
if (dimid_in != dimid2) ERR;
if (nc_inq_dimid(ncid, TMP_NAME, &dimid_in) != NC_EBADDIM) ERR;
if (nc_inq_varid(ncid, TMP_NAME, &varid_in)) ERR;
if (varid_in != varid1) ERR;
if (nc_inq_varid(ncid, D1_NAME, &varid_in)) ERR;
if (varid_in != varid2) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}