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f0f0f39950
# Description
Remove various obsolete build options. Also do some code movement.
## Specific Changes
* The remotetest server is sometimes unstable, so provide a mechanism
to force disabling calls to remotetest.unidata.ucar.edu.
This is enabled by adding a repository variable named
REMOTETESTDOWN with the value "yes".
* Fix CMakeLists.txt to use the uname command as an alternate
to using the hostname command (which does not work under cygwin).
* Remove the JNA stuff as obsolete
* Remove the ENABLE_CLIENTSIDE_FILTERS options since it has been
disabled for a while.
* Fix bad option flag in some github action .yml files: change --disable-xml2 to --disable-libxml2
* Collect globalstate definitions into nc4internal.h
* Remove ENABLE_NCZARR_FILTERS_TESTING option as obsolete and replace
with ENABLE_NCZARR_FILTERS
* Move some dispatcher independent functions from libsrc4/nc4internal.c to libdispatch/ddispatch.c
* As a long term goal, and because it is now the case that --enable-nczarr
=> USE_NETCDF4, make the external options --enable-netcdf-4 and
--enable-netcdf4 obsolete in favor of --enable-hdf5
We will do the following for one more release cycle.
1. Make --enable-netcdf-4 be an alias for --enable-netcdf4.
2. Make --enable-netcdf4 an alias for --enable-hdf5.
3. Internally, convert most uses of USE_NETCDF_4 ad USE_NETCDF4 to USE_HDF5
After the next release, --enable-netcdf-4 and --enable-netcdf4 will
be removed.
229 lines
8.4 KiB
C
229 lines
8.4 KiB
C
/* Copyright 2018-2022 University Corporation for Atmospheric
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Research/Unidata. */
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/**
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* @file This header file contains macros, types, and prototypes for
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* the HDF5 code in libhdf5. This header should not be included in
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* code outside libhdf5.
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*
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* @author Ed Hartnett
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*/
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#ifndef _HDF5INTERNAL_
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#define _HDF5INTERNAL_
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#include "config.h"
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#include <hdf5.h>
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#include <hdf5_hl.h>
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#include "nc4internal.h"
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#include "ncdimscale.h"
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#include "nc4dispatch.h"
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#include "hdf5dispatch.h"
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#include "netcdf_filter.h"
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#define NC_MAX_HDF5_NAME (NC_MAX_NAME + 10)
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/* These have to do with creating chunked datasets in HDF5. */
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#define NC_HDF5_UNLIMITED_DIMSIZE (0)
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#define NC_HDF5_CHUNKSIZE_FACTOR (10)
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#define NC_HDF5_MIN_CHUNK_SIZE (2)
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#define NC_EMPTY_SCALE "NC_EMPTY_SCALE"
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/* This is an attribute I had to add to handle multidimensional
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* coordinate variables. See nc4internal.h:NC_ATT_COORDINATES.
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* in nc4internal.h.
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*/
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#define COORDINATES NC_ATT_COORDINATES
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#define COORDINATES_LEN (NC_MAX_NAME * 5)
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/* This is used when the user defines a non-coordinate variable with
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* same name as a dimension. */
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#define NON_COORD_PREPEND "_nc4_non_coord_"
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/* An attribute in the HDF5 root group of this name means that the
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* file must follow strict netCDF classic format rules. */
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#define NC3_STRICT_ATT_NAME NC_ATT_NC3_STRICT_NAME
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/* If this attribute is present on a dimscale variable, use the value
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* as the netCDF dimid. */
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#define NC_DIMID_ATT_NAME NC_ATT_DIMID_NAME /*See nc4internal.h*/
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/** This is the name of the class HDF5 dimension scale attribute. */
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#define HDF5_DIMSCALE_CLASS_ATT_NAME NC_ATT_CLASS /*See nc4internal.h*/
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/** This is the name of the name HDF5 dimension scale attribute. */
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#define HDF5_DIMSCALE_NAME_ATT_NAME NC_ATT_NAME
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/* forward */
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struct NCauth;
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/** Struct to hold HDF5-specific info for the file. */
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typedef struct NC_HDF5_FILE_INFO {
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hid_t hdfid;
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unsigned transientid; /* counter for transient ids */
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NCURI* uri; /* Parse of the incoming path, if url */
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#if defined(NETCDF_ENABLE_BYTERANGE)
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int byterange;
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#endif
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#ifdef NETCDF_ENABLE_S3
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struct NCauth* auth;
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#endif
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} NC_HDF5_FILE_INFO_T;
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/* This is a struct to handle the dim metadata. */
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typedef struct NC_HDF5_DIM_INFO
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{
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hid_t hdf_dimscaleid; /* Non-zero if a DIM_WITHOUT_VARIABLE dataset is in use (no coord var). */
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HDF5_OBJID_T hdf5_objid;
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} NC_HDF5_DIM_INFO_T;
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/** Strut to hold HDF5-specific info for attributes. */
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typedef struct NC_HDF5_ATT_INFO
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{
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hid_t native_hdf_typeid; /* Native HDF5 datatype for attribute's data */
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} NC_HDF5_ATT_INFO_T;
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/* Struct to hold HDF5-specific info for a group. */
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typedef struct NC_HDF5_GRP_INFO
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{
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hid_t hdf_grpid;
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} NC_HDF5_GRP_INFO_T;
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/* Struct to hold HDF5-specific info for a variable. */
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typedef struct NC_HDF5_VAR_INFO
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{
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hid_t hdf_datasetid;
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HDF5_OBJID_T *dimscale_hdf5_objids;
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nc_bool_t dimscale; /**< True if var is a dimscale. */
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nc_bool_t *dimscale_attached; /**< Array of flags that are true if dimscale is attached for that dim index. */
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int flags;
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# define NC_HDF5_VAR_FILTER_MISSING 1 /* if any filter is missing */
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} NC_HDF5_VAR_INFO_T;
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/* Struct to hold HDF5-specific info for a field. */
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typedef struct NC_HDF5_FIELD_INFO
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{
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hid_t hdf_typeid;
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hid_t native_hdf_typeid;
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} NC_HDF5_FIELD_INFO_T;
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/* Struct to hold HDF5-specific info for a type. */
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typedef struct NC_HDF5_TYPE_INFO
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{
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hid_t hdf_typeid;
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hid_t native_hdf_typeid;
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} NC_HDF5_TYPE_INFO_T;
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/* Logging and debugging. */
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void reportopenobjects(int log, hid_t);
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int hdf5_set_log_level();
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void nc_log_hdf5(void);
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/* These functions deal with HDF5 dimension scales. */
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int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
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int rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
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int delete_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim);
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/* Write metadata. */
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int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order);
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int nc4_rec_write_groups_types(NC_GRP_INFO_T *grp);
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/* Adjust the cache. */
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int nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T * var);
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/* Open a HDF5 dataset. */
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int nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset);
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/* Find types. */
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NC_TYPE_INFO_T *nc4_rec_find_hdf_type(NC_FILE_INFO_T* h5,
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hid_t target_hdf_typeid);
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int nc4_get_hdf_typeid(NC_FILE_INFO_T *h5, nc_type xtype,
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hid_t *hdf_typeid, int endianness);
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/* Enddef and closing files. */
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int nc4_close_hdf5_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio);
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int nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp);
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int nc4_enddef_netcdf4_file(NC_FILE_INFO_T *h5);
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int nc4_HDF5_close_type(NC_TYPE_INFO_T* type);
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/* Break & reform coordinate variables */
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int nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim);
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int nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim);
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/* In-memory functions */
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extern hid_t NC4_image_init(NC_FILE_INFO_T* h5);
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extern void NC4_image_finalize(void*);
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/* Create HDF5 dataset for dim without a coord var. */
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extern int nc4_create_dim_wo_var(NC_DIM_INFO_T *dim);
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/* Give a var a secret HDF5 name, for use when there is a dim of this
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* name, but the var is not a coord var of that dim. */
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extern int nc4_give_var_secret_name(NC_VAR_INFO_T *var);
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/* Find file, group, var, and att info, doing lazy reads if needed. */
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int nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
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int use_name, char *norm_name, NC_FILE_INFO_T **h5,
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NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var,
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NC_ATT_INFO_T **att);
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/* Find var, doing lazy var metadata read if needed. */
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int nc4_hdf5_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5,
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NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var);
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int nc4_HDF5_close_att(NC_ATT_INFO_T *att);
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/* Perform lazy read of the rest of the metadata for a var. */
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int nc4_get_var_meta(NC_VAR_INFO_T *var);
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/* Get the file chunk cache settings from HDF5. */
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int nc4_hdf5_get_chunk_cache(int ncid, size_t *sizep, size_t *nelemsp,
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float *preemptionp);
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/* Filter Dispatch Entries */
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int NC4_hdf5_def_var_filter(int ncid, int varid, unsigned int filterid, size_t nparams, const unsigned int *params);
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int NC4_hdf5_inq_var_filter_ids(int ncid, int varid, size_t* nfiltersp, unsigned int *filterids);
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int NC4_hdf5_inq_var_filter_info(int ncid, int varid, unsigned int filterid, size_t* nparamsp, unsigned int *params);
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int NC4_hdf5_inq_filter_avail(int ncid, unsigned id);
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/* Filterlist management */
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/* The NC_VAR_INFO_T->filters field is an NClist of this struct */
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struct NC_HDF5_Filter {
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int flags; /**< Flags describing state of this filter. */
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# define NC_HDF5_FILTER_MISSING 1 /* Filter implementation is not accessible */
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unsigned int filterid; /**< ID for arbitrary filter. */
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size_t nparams; /**< nparams for arbitrary filter. */
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unsigned int* params; /**< Params for arbitrary filter. */
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};
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int NC4_hdf5_filter_initialize(void);
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int NC4_hdf5_filter_finalize(void);
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int NC4_hdf5_filter_remove(NC_VAR_INFO_T* var, unsigned int id);
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int NC4_hdf5_filter_lookup(NC_VAR_INFO_T* var, unsigned int id, struct NC_HDF5_Filter** fi);
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int NC4_hdf5_addfilter(NC_VAR_INFO_T* var, unsigned int id, size_t nparams, const unsigned int* params, int flags);
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int NC4_hdf5_filter_freelist(NC_VAR_INFO_T* var);
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int NC4_hdf5_find_missing_filter(NC_VAR_INFO_T* var, unsigned int* idp);
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/* Add an attribute to the attribute list. */
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int nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
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size_t len, const void *data, nc_type mem_type, int force);
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/* Support functions for provenance info (defined in nc4hdf.c) */
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extern int NC4_hdf5get_libversion(unsigned*,unsigned*,unsigned*);/*libsrc4/nc4hdf.c*/
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extern int NC4_hdf5get_superblock(struct NC_FILE_INFO*, int*);/*libsrc4/nc4hdf.c*/
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extern int NC4_isnetcdf4(struct NC_FILE_INFO*); /*libsrc4/nc4hdf.c*/
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extern int nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
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EXTERNL hid_t nc4_H5Fopen(const char *filename, unsigned flags, hid_t fapl_id);
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EXTERNL hid_t nc4_H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id);
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int hdf5set_format_compatibility(hid_t fapl_id);
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/* HDF5 initialization/finalization */
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extern int nc4_hdf5_initialized;
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extern void nc4_hdf5_initialize(void);
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extern void nc4_hdf5_finalize(void);
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#endif /* _HDF5INTERNAL_ */
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