netcdf-c/libnczarr/zdispatch.h

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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.
2020-06-29 08:02:47 +08:00
/* Copyright 2018-2018 University Corporation for Atmospheric
Research/Unidata. */
/**
* @file
* @internal Includes prototypes for libzarr dispatch functions.
*
* @author Dennis Heimbigner, Ed Hartnett
*/
#ifndef ZDISPATCH_H
#define ZDISPATCH_H
#include "zincludes.h"
#if defined(__cplusplus)
extern "C" {
#endif
EXTERNL int NCZ_create(const char *path, int cmode, size_t initialsz, int basepe, size_t *chunksizehintp, void* parameters, const NC_Dispatch*, int);
EXTERNL int NCZ_open(const char *path, int mode, int basepe, size_t *chunksizehintp, void* parameters, const NC_Dispatch*, int);
EXTERNL int NCZ_redef(int ncid);
EXTERNL int NCZ__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree, size_t r_align);
EXTERNL int NCZ_sync(int ncid);
EXTERNL int NCZ_abort(int ncid);
EXTERNL int NCZ_close(int ncid,void*);
EXTERNL int NCZ_set_fill(int ncid, int fillmode, int *old_modep);
EXTERNL int NCZ_set_base_pe(int ncid, int pe);
EXTERNL int NCZ_inq_base_pe(int ncid, int *pe);
EXTERNL int NCZ_inq_format(int ncid, int *formatp);
EXTERNL int NCZ_inq_format_extended(int ncid, int *formatp, int *modep);
EXTERNL int NCZ_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp);
EXTERNL int NCZ_inq_type(int, nc_type, char *, size_t *);
/* Begin _dim */
EXTERNL int NCZ_def_dim(int ncid, const char *name, size_t len, int *idp);
EXTERNL int NCZ_inq_dimid(int ncid, const char *name, int *idp);
EXTERNL int NCZ_inq_dim(int ncid, int dimid, char *name, size_t *lenp);
EXTERNL int NCZ_inq_unlimdim(int ncid, int *unlimdimidp);
EXTERNL int NCZ_rename_dim(int ncid, int dimid, const char *name);
/* End _dim */
/* Begin _att */
EXTERNL int NCZ_inq_att(int ncid, int varid, const char *name, nc_type *xtypep, size_t *lenp);
EXTERNL int NCZ_inq_attid(int ncid, int varid, const char *name, int *idp);
EXTERNL int NCZ_inq_attname(int ncid, int varid, int attnum, char *name);
EXTERNL int NCZ_rename_att(int ncid, int varid, const char *name, const char *newname);
EXTERNL int NCZ_del_att(int ncid, int varid, const char *name);
/* End _att */
/* Begin {put,get}_att */
EXTERNL int NCZ_get_att(int ncid, int varid, const char *name, void *value, nc_type);
EXTERNL int NCZ_put_att(int ncid, int varid, const char *name, nc_type file_type, size_t len, const void *data, nc_type mem_type);
/* End {put,get}_att */
/* Begin _var */
EXTERNL int NCZ_def_var(int ncid, const char *name, nc_type xtype, int ndims, const int *dimidsp, int *varidp);
EXTERNL int NCZ_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp, int *shufflep, int *deflatep, int *deflate_levelp, int *fletcher32p, int *contiguousp, size_t *chunksizesp, int *no_fill, void *fill_valuep, int *endiannessp, unsigned int* idp, size_t* nparamsp, unsigned int* params
);
EXTERNL int NCZ_inq_varid(int ncid, const char *name, int *varidp);
EXTERNL int NCZ_rename_var(int ncid, int varid, const char *name);
EXTERNL int NCZ_put_vara(int ncid, int varid, const size_t *start, const size_t *count, const void *value, nc_type);
EXTERNL int NCZ_get_vara(int ncid, int varid, const size_t *start, const size_t *count, void *value, nc_type);
extern int
NCZ_put_vars(int ncid, int varid, const size_t *start, const size_t *count, const ptrdiff_t* stride, const void *value, nc_type);
extern int
NCZ_get_vars(int ncid, int varid, const size_t *start, const size_t *count, const ptrdiff_t* stride, void *value, nc_type);
/* End _var */
/* netCDF4 API only */
EXTERNL int NCZ_inq_ncid(int, const char *, int *);
EXTERNL int NCZ_inq_grps(int, int *, int *);
EXTERNL int NCZ_inq_grpname(int, char *);
EXTERNL int NCZ_inq_grpname_full(int, size_t *, char *);
EXTERNL int NCZ_inq_grp_parent(int, int *);
EXTERNL int NCZ_inq_grp_full_ncid(int, const char *, int *);
EXTERNL int NCZ_inq_varids(int, int * nvars, int *);
EXTERNL int NCZ_inq_dimids(int, int * ndims, int *, int);
EXTERNL int NCZ_inq_typeids(int, int * ntypes, int *);
EXTERNL int NCZ_inq_type_equal(int, nc_type, int, nc_type, int *);
EXTERNL int NCZ_def_grp(int, const char *, int *);
EXTERNL int NCZ_rename_grp(int, const char *);
EXTERNL int NCZ_inq_user_type(int, nc_type, char *, size_t *, nc_type *, size_t *, int *);
EXTERNL int NCZ_def_compound(int, size_t, const char *, nc_type *);
EXTERNL int NCZ_insert_compound(int, nc_type, const char *, size_t, nc_type);
EXTERNL int NCZ_insert_array_compound(int, nc_type, const char *, size_t, nc_type, int, const int *);
EXTERNL int NCZ_inq_typeid(int, const char *, nc_type *);
EXTERNL int NCZ_inq_compound_field(int, nc_type, int, char *, size_t *, nc_type *, int *, int *);
EXTERNL int NCZ_inq_compound_fieldindex(int, nc_type, const char *, int *);
EXTERNL int NCZ_def_vlen(int, const char *, nc_type base_typeid, nc_type *);
EXTERNL int NCZ_put_vlen_element(int, int, void *, size_t, const void *);
EXTERNL int NCZ_get_vlen_element(int, int, const void *, size_t *, void *);
EXTERNL int NCZ_def_enum(int, nc_type, const char *, nc_type *);
EXTERNL int NCZ_insert_enum(int, nc_type, const char *, const void *);
EXTERNL int NCZ_inq_enum_member(int, nc_type, int, char *, void *);
EXTERNL int NCZ_inq_enum_ident(int, nc_type, long long, char *);
EXTERNL int NCZ_def_opaque(int, size_t, const char *, nc_type *);
EXTERNL int NCZ_def_var_deflate(int, int, int, int, int);
EXTERNL int NCZ_def_var_fletcher32(int, int, int);
EXTERNL int NCZ_def_var_chunking(int, int, int, const size_t *);
EXTERNL int NCZ_def_var_fill(int, int, int, const void *);
EXTERNL int NCZ_def_var_endian(int, int, int);
EXTERNL int NCZ_inq_unlimdims(int, int *, int *);
Mostly revert the filter code to reduce its complexity of use. re: https://github.com/Unidata/netcdf-c/issues/1836 Revert the internal filter code to simplify it. From the user's point of view, the only visible changes should be: 1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h 2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter. Internally,the dispatch table has been modified to get rid of the filter_actions entry and associated complex structures. It has been replaced with inq_var_filter_ids and inq_var_filter_info entries and the dispatch table version has been bumped to 3. Corresponding NOOP and NOTNC4 functions were added to libdispatch/dnotnc4.c. Also, the filter_action entries in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2, etc). This should only impact UDF users. In the process, it became clear that the form of the filters field in NC_VAR_INFO_T was format dependent, so I converted it to be of type void* and pushed its management into the various dispatch code bases. Specifically libhdf5 and libnczarr now manage the filters field in their own way. The auxilliary functions for parsing textual filter specifications were moved to netcdf_aux.h and were renamed to the following: * ncaux_h5filterspec_parse * ncaux_h5filterspec_parselist * ncaux_h5filterspec_free * ncaux_h5filter_fix8 Misc. Other Changes: 1. Document NUG/filters.md updated to reflect the changes above. 2. All the old data types (structs and enums) used by filter_actions actions were deleted. The exception is the NC_H5_Filterspec because it is needed by ncaux_h5filterspec_parselist. 3. Clientside filters were removed -- another enhancement for which no-one ever asked. 4. The ability to remove filters was itself removed. 5. Some functionality needed by nczarr was moved from libhdf5 to libsrc4 e.g. nc4_find_default_chunksizes 6. All the filterx code was removed 7. ncfilter.h and nc4filter.c no longer used Misc. Unrelated Changes: 1. The nczarr_test makefile clean was leaving some directories; so add clean-local to take care of them.
2020-09-28 02:43:46 +08:00
EXTERNL int NCZ_def_var_filter(int ncid, int varid, unsigned int filterid, size_t nparams, const unsigned int *params);
EXTERNL int NCZ_inq_var_filter_ids(int ncid, int varid, size_t* nfiltersp, unsigned int *filterids);
EXTERNL int NCZ_inq_var_filter_info(int ncid, int varid, unsigned int filterid, size_t* nparamsp, unsigned int *params);
EXTERNL int NCZ_def_var_quantize(int ncid, int varid, int quantize_mode, int nsd);
EXTERNL int NCZ_inq_var_quantize(int ncid, int varid, int *quantize_modep, int *nsdp);
/**************************************************/
/* Following functions wrap libsrc4 */
EXTERNL int NCZ_inq_type(int ncid, nc_type xtype, char *name, size_t *size);
EXTERNL int NCZ_inq_dimid(int ncid, const char *name, int *idp);
EXTERNL int NCZ_inq_unlimdim(int ncid, int *unlimdimidp);
EXTERNL int NCZ_inq_attname(int ncid, int varid, int attnum, char *name);
EXTERNL int NCZ_inq_varid(int ncid, const char* name, int *varidp);
EXTERNL int NCZ_inq_ncid(int ncid, const char* name, int* grpidp);
EXTERNL int NCZ_inq_grps(int ncid, int* n, int* ncids);
EXTERNL int NCZ_inq_grpname(int ncid, char* name);
EXTERNL int NCZ_inq_grpname_full(int ncid, size_t* lenp, char* fullname);
EXTERNL int NCZ_inq_grp_parent(int ncid, int* parentidp);
EXTERNL int NCZ_inq_grp_full_ncid(int ncid, const char* fullname, int* grpidp);
EXTERNL int NCZ_inq_varids(int ncid, int* nvars, int* varids);
EXTERNL int NCZ_inq_dimids(int ncid, int* ndims, int* dimids, int inclparents);
EXTERNL int NCZ_inq_typeids(int ncid, int* ntypes, int* typeids);
EXTERNL int NCZ_inq_user_type(int ncid, nc_type xtype, char* name, size_t* size, nc_type* basetid, size_t* nfields, int* classp);
/**************************************************/
Add filter support to NCZarr Filter support has three goals: 1. Use the existing HDF5 filter implementations, 2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr, 3. Allow filters to be used even when HDF5 is disabled Detailed usage directions are define in docs/filters.md. For now, the existing filter API is left in place. So filters are defined using ''nc_def_var_filter'' using the HDF5 style where the id and parameters are unsigned integers. This is a big change since filters affect many parts of the code. In the following, the terms "compressor" and "filter" and "codec" are generally used synonomously. ### Filter-Related Changes: * In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms. * Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h. * Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out. * Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h. * Add a number of new test to test the new nczarr filters. * Let ncgen parse _Codecs attribute, although it is ignored. ### Plugin directory changes: * Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file * Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip * Add a Codec defaulter (see docs/filters.md) for the big four filters. * Make plugins work with windows by properly adding __declspec declaration. ### Misc. Non-Filter Changes * Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5. * Improve support for caching * More fixes for path conversion code * Fix misc. memory leaks * Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath. * Add a number of new test to test the non-filter fixes. * Update the parsers * Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-03 07:04:26 +08:00
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.
2020-06-29 08:02:47 +08:00
#if defined(__cplusplus)
}
#endif
#endif /* ZDISPATCH_H */