netcdf-c/libnczarr/zfilter.c

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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 2003-2018, University Corporation for Atmospheric
* Research. See the COPYRIGHT file for copying and redistribution
* conditions.
*/
/**
* @file @internal Internal functions for filters
*
* This file contains functions internal to the netcdf4 library. None of
* the functions in this file are exposed in the exetnal API. These
* functions all relate to the manipulation of netcdf-4 filters
*
* @author Dennis Heimbigner
*/
#include "config.h"
#include <stdlib.h>
#include "zincludes.h"
/* Mnemonic */
#define FILTERACTIVE 1
/* WARNING: GLOBAL VARIABLE */
#ifdef ENABLE_CLIENTSIDE_FILTERS
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
/* Define list of registered filters */
static NClist* NCZ_registeredfilters = NULL; /** List<NC_FILTER_CLIENT_ZARR*> */
/**************************************************/
/* Filter registration support */
static int
filterlookup(conbst char* id)
{
int i;
if(NCZ_registeredfilters == NULL)
NCZ_registeredfilters = nclistnew();
for(i=0;i<nclistlength(NCZ_registeredfilters);i++) {
NCX_FILTER_CLIENT* x = nclistget(NCZ_registeredfilters,i);
if(x != NULL && x->id == id) return i; /* return position */
}
return -1;
}
static void
reclaiminfo(NCX_FILTER_CLIENT* info)
{
nullfree(info);
}
static int
filterremove(int pos)
{
NCX_FILTER_CLIENT* info = NULL;
if(NCZ_registeredfilters == NULL)
return THROW(NC_EINVAL);
if(pos < 0 || pos >= nclistlength(NCZ_registeredfilters))
return THROW(NC_EINVAL);
info = nclistget(NCZ_registeredfilters,pos);
reclaiminfo(info);
nclistremove(NCZ_registeredfilters,pos);
return NC_NOERR;
}
static NCX_FILTER_CLIENT*
dupfilterinfo(NCX_FILTER_CLIENT* info)
{
NCX_FILTER_CLIENT* dup = NULL;
if(info == NULL) goto fail;
if((dup = calloc(1,sizeof(NCX_FILTER_CLIENT))) == NULL) goto fail;
*dup = *info;
return dup;
fail:
reclaiminfo(dup);
return NULL;
}
int
NCZ_global_filter_action(int op, unsigned int id, NC_FILTER_OBJ_HDF5* infop)
{
int stat = NC_NOERR;
H5Z_class2_t* h5filterinfo = NULL;
herr_t herr;
int pos = -1;
NCX_FILTER_CLIENT* dup = NULL;
NCX_FILTER_CLIENT* elem = NULL;
NCX_FILTER_CLIENT ncf;
switch (op) {
case NCFILTER_CLIENT_REG: /* Ignore id argument */
if(infop == NULL) {stat = NC_EINVAL; goto done;}
assert(NC_FILTER_FORMAT_HDF5 == infop->hdr.format);
assert(NC_FILTER_SORT_CLIENT == infop->sort);
elem = (NCX_FILTER_CLIENT*)&infop->u.client;
h5filterinfo = elem->info;
/* Another sanity check */
if(id != h5filterinfo->id)
{stat = NC_EINVAL; goto done;}
/* See if this filter is already defined */
if((pos = filterlookup(id)) >= 0)
{stat = NC_ENAMEINUSE; goto done;} /* Already defined */
if((herr = H5Zregister(h5filterinfo)) < 0)
{stat = NC_EFILTER; goto done;}
/* Save a copy of the passed in info */
ncf.id = id;
ncf.info = elem->info;
if((dup=dupfilterinfo(&ncf)) == NULL)
{stat = NC_ENOMEM; goto done;}
nclistpush(NCZ_registeredfilters,dup);
break;
case NCFILTER_CLIENT_UNREG:
if(id <= 0)
{stat = NC_EFILTER; goto done;}
/* See if this filter is already defined */
if((pos = filterlookup(id)) < 0)
{stat = NC_ENOFILTER; goto done;} /* Not defined */
if((herr = H5Zunregister(id)) < 0)
{stat = NC_EFILTER; goto done;}
if((stat=filterremove(pos))) goto done;
break;
case NCFILTER_CLIENT_INQ:
if(infop == NULL) goto done;
/* Look up the id in our local table */
if((pos = filterlookup(id)) < 0)
{stat = NC_ENOFILTER; goto done;} /* Not defined */
elem = (NCX_FILTER_CLIENT*)nclistget(NCZ_registeredfilters,pos);
if(elem == NULL) {stat = NC_EINTERNAL; goto done;}
if(infop != NULL) {
infop->u.client = *elem;
}
break;
default:
{stat = NC_EINTERNAL; goto done;}
}
done:
return THROW(stat);
}
#endif /*ENABLE_CLIENT_FILTERS*/
/**************************************************/
/**
* @internal Define filter settings. Called by nc_def_var_filter().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param id Filter ID
* @param nparams Number of parameters for filter.
* @param parms Filter parameters.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNCZ Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_EFILTER Filter error.
* @returns ::NC_EINVAL Invalid input
* @author Dennis Heimbigner
*/
int
NCZ_filter_actions(int ncid, int varid, int op, void* args)
{
int stat = NC_NOERR;
NC_GRP_INFO_T *grp = NULL;
NC_FILE_INFO_T *h5 = NULL;
NC_VAR_INFO_T *var = NULL;
NC_FILTERX_OBJ* obj = (NC_FILTERX_OBJ*)args;
NC_FILTERX_SPEC* spec = NULL;
char** xfilterids = NULL;
size_t nfilters = 0;
LOG((2, "%s: ncid 0x%x varid %d op=%d", __func__, ncid, varid, op));
if(args == NULL) return THROW(NC_EINVAL);
/* Find info for this file and group and var, and set pointer to each. */
if ((stat = nc4_find_grp_h5_var(ncid, varid, &h5, &grp, &var)))
return THROW(stat);
assert(h5 && var && var->hdr.id == varid);
nfilters = nclistlength(var->filters);
switch (op) {
case NCFILTER_DEF: {
if(obj->usort != NC_FILTER_UNION_SPEC) return THROW(NC_EFILTER);
/* If the dataset has already been created, then it is too
* late to set all the extra stuff. */
if (!(h5->flags & NC_INDEF)) {stat = THROW(NC_EINDEFINE); goto done;}
if (!var->ndims) goto done; /* For scalars, ignore */
if (var->created)
{stat = THROW(NC_ELATEDEF); goto done;}
/* Filter => chunking */
var->storage = NC_CHUNKED;
/* Determine default chunksizes for this variable unless already specified */
if(var->chunksizes && !var->chunksizes[0]) {
/* Should this throw error? */
if((stat = ncz_find_default_chunksizes2(grp, var)))
goto done;
}
spec = &obj->u.spec;
if((stat = NC4_filterx_add(var,!FILTERACTIVE,spec->filterid,spec->nparams,(const char**)spec->params)))
goto done;
} break;
case NCFILTER_FILTERIDS: {
if(obj->usort != NC_FILTER_UNION_IDS) return THROW(NC_EFILTER);
if((obj->u.ids.filterids = calloc(sizeof(char*),nfilters))==NULL)
{stat = NC_ENOMEM; goto done;}
obj->u.ids.nfilters = nfilters;
if(nfilters > 0) {
int k;
for(k=0;k<nfilters;k++) {
NC_FILTERX_SPEC* f = (NC_FILTERX_SPEC*)nclistget(var->filters,k);
if((obj->u.ids.filterids[k] = strdup(f->filterid)) == NULL)
{stat = NC_ENOMEM; goto done;}
}
}
} break;
case NCFILTER_INFO: {
int k,found;
if(obj->usort != NC_FILTER_UNION_SPEC) return THROW(NC_EFILTER);
for(found=0,k=0;k<nfilters;k++) {
NC_FILTERX_SPEC* f = (NC_FILTERX_SPEC*)nclistget(var->filters,k);
if(strcasecmp(f->filterid,obj->u.spec.filterid)==0) {
obj->u.spec.nparams = f->nparams;
obj->u.spec.active = f->active;
if((stat = NC_filterx_copy(f->nparams,(const char**)f->params,&obj->u.spec.params)))
goto done;
found = 1;
break;
}
}
if(!found) {stat = NC_ENOFILTER; goto done;}
} break;
case NCFILTER_REMOVE:
if (!(h5->flags & NC_INDEF)) return THROW(NC_EINDEFINE);
if(obj->usort != NC_FILTER_UNION_SPEC) return THROW(NC_EFILTER);
if((stat = NC4_filterx_lookup(var,obj->u.spec.filterid,&spec))) goto done;
if(spec && spec->active)
{stat = NC_EFILTER; goto done;}
if((stat = NC4_filterx_remove(var,obj->u.spec.filterid))) goto done;
break;
default:
{stat = NC_EINTERNAL; goto done;}
}
done:
NC_filterx_freestringvec(nfilters,xfilterids);
return THROW(stat);
}