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netcdf-c/libnczarr/zsync.c
Dennis Heimbigner 1552d894a2 Cleanup a number of issues. 
re: Issue https://github.com/Unidata/netcdf-c/issues/2748

This PR fixes a number of issues and bugs.

## s3cleanup fixes
* Delete extraneous s3cleanup.sh related files.
* Remove duplicate s3cleanup.uids entries.

## Support the Google S3 API
* Add code to recognize "storage.gooleapis.com"
* Add extra code to track the kind of server being accessed: unknown, Amazon, Google.
* Add a new mode flag "gs3" (analog to "s3") to support this api.
* Modify the S3 URL code to support this case.
* Modify the listobjects result parsing because Google returns some non-standard XML elements.
* Change signature and calls for NC_s3urlrebuild.

## Handle corrupt Zarr files where shape is empty for a variable.
Modify behavior when a variable's "shape" dictionary entry.
Previously it returned an error, but now it suppresses such a variable.
This change makes it possible to read non-corrupt data from the file.
Also added a test case.

## Misc. Other Changes
* Fix the nclog level handling to suppress output by default.
* Fix de-duplicates code in ncuri.c
* Restore testing of iridl.ldeo.columbia.edu.
* Fix bug in define_vars() which did not always do a proper reclaim between variables.
2023-10-08 11:22:52 -06:00

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/*********************************************************************
* Copyright 1993, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
#include "zincludes.h"
#include "zfilter.h"
#ifndef nulldup
#define nulldup(x) ((x)?strdup(x):(x))
#endif
#undef FILLONCLOSE
/*mnemonics*/
#define DICTOPEN '{'
#define DICTCLOSE '}'
/* Forward */
static int ncz_collect_dims(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NCjson** jdimsp);
static int ncz_sync_var(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int isclose);
static int load_jatts(NCZMAP* map, NC_OBJ* container, int nczarrv1, NCjson** jattrsp, NClist** atypes);
static int zconvert(NCjson* src, nc_type typeid, size_t typelen, int* countp, NCbytes* dst);
static int computeattrinfo(const char* name, NClist* atypes, nc_type typehint, int purezarr, NCjson* values,
nc_type* typeidp, size_t* typelenp, size_t* lenp, void** datap);
static int parse_group_content(NCjson* jcontent, NClist* dimdefs, NClist* varnames, NClist* subgrps);
static int parse_group_content_pure(NCZ_FILE_INFO_T* zinfo, NC_GRP_INFO_T* grp, NClist* varnames, NClist* subgrps);
static int define_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp);
static int define_dims(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* diminfo);
static int define_vars(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* varnames);
static int define_subgrps(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* subgrpnames);
static int searchvars(NCZ_FILE_INFO_T*, NC_GRP_INFO_T*, NClist*);
static int searchsubgrps(NCZ_FILE_INFO_T*, NC_GRP_INFO_T*, NClist*);
static int locategroup(NC_FILE_INFO_T* file, size_t nsegs, NClist* segments, NC_GRP_INFO_T** grpp);
static int createdim(NC_FILE_INFO_T* file, const char* name, size64_t dimlen, NC_DIM_INFO_T** dimp);
static int parsedimrefs(NC_FILE_INFO_T*, NClist* dimnames, size64_t* shape, NC_DIM_INFO_T** dims, int create);
static int decodeints(NCjson* jshape, size64_t* shapes);
static int computeattrdata(nc_type typehint, nc_type* typeidp, NCjson* values, size_t* typelenp, size_t* lenp, void** datap);
static int computedimrefs(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int purezarr, int xarray, int ndims, NClist* dimnames, size64_t* shapes, NC_DIM_INFO_T** dims);
static int json_convention_read(NCjson* jdict, NCjson** jtextp);
static int jtypes2atypes(NCjson* jtypes, NClist* atypes);
static int ncz_validate(NC_FILE_INFO_T* file);
/**************************************************/
/**************************************************/
/* Synchronize functions to make map and memory
be consistent. There are two sets of functions,
1) _sync_ - push memory to map (optionally create target)
2) _read_ - pull map data into memory
These functions are generally non-recursive. It is assumed
that the recursion occurs in the caller's code.
*/
/**
* @internal Synchronize file metadata from memory to map.
*
* @param file Pointer to file info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
ncz_sync_file(NC_FILE_INFO_T* file, int isclose)
{
int stat = NC_NOERR;
NCjson* json = NULL;
NC_UNUSED(isclose);
LOG((3, "%s: file: %s", __func__, file->controller->path));
ZTRACE(3,"file=%s isclose=%d",file->controller->path,isclose);
/* Write out root group recursively */
if((stat = ncz_sync_grp(file, file->root_grp, isclose)))
goto done;
done:
NCJreclaim(json);
return ZUNTRACE(stat);
}
/**
* @internal Synchronize dimension data from memory to map.
*
* @param grp Pointer to grp struct containing the dims.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
ncz_collect_dims(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NCjson** jdimsp)
{
int i, stat=NC_NOERR;
NCjson* jdims = NULL;
NCjson* jdimsize = NULL;
NCjson* jdimargs = NULL;
LOG((3, "%s: ", __func__));
ZTRACE(3,"file=%s grp=%s",file->controller->path,grp->hdr.name);
NCJnew(NCJ_DICT,&jdims);
for(i=0; i<ncindexsize(grp->dim); i++) {
NC_DIM_INFO_T* dim = (NC_DIM_INFO_T*)ncindexith(grp->dim,i);
char slen[128];
snprintf(slen,sizeof(slen),"%llu",(unsigned long long)dim->len);
if((stat = NCJnewstring(NCJ_INT,slen,&jdimsize))) goto done;
/* If dim is not unlimited, then write in the old format to provide
maximum back compatibility.
*/
if(dim->unlimited) {
NCJnew(NCJ_DICT,&jdimargs);
if((stat = NCJaddstring(jdimargs,NCJ_STRING,"size"))) goto done;
if((stat = NCJappend(jdimargs,jdimsize))) goto done;
jdimsize = NULL;
if((stat = NCJaddstring(jdimargs,NCJ_STRING,"unlimited"))) goto done;
if((stat = NCJaddstring(jdimargs,NCJ_INT,"1"))) goto done;
} else { /* !dim->unlimited */
jdimargs = jdimsize;
jdimsize = NULL;
}
if((stat = NCJaddstring(jdims,NCJ_STRING,dim->hdr.name))) goto done;
if((stat = NCJappend(jdims,jdimargs))) goto done;
}
if(jdimsp) {*jdimsp = jdims; jdims = NULL;}
done:
NCJreclaim(jdims);
return ZUNTRACE(THROW(stat));
}
/**
* @internal Recursively synchronize group from memory to map.
*
* @param file Pointer to file struct
* @param grp Pointer to grp struct
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
ncz_sync_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, int isclose)
{
int i,stat = NC_NOERR;
NCZ_FILE_INFO_T* zinfo = NULL;
char version[1024];
int purezarr = 0;
NCZMAP* map = NULL;
char* fullpath = NULL;
char* key = NULL;
NCjson* json = NULL;
NCjson* jgroup = NULL;
NCjson* jdims = NULL;
NCjson* jvars = NULL;
NCjson* jsubgrps = NULL;
NCjson* jsuper = NULL;
NCjson* jtmp = NULL;
LOG((3, "%s: dims: %s", __func__, key));
ZTRACE(3,"file=%s grp=%s isclose=%d",file->controller->path,grp->hdr.name,isclose);
zinfo = file->format_file_info;
map = zinfo->map;
purezarr = (zinfo->controls.flags & FLAG_PUREZARR)?1:0;
/* Construct grp key */
if((stat = NCZ_grpkey(grp,&fullpath)))
goto done;
if(!purezarr) {
/* Create dimensions dict */
if((stat = ncz_collect_dims(file,grp,&jdims))) goto done;
/* Create vars list */
if((stat = NCJnew(NCJ_ARRAY,&jvars)))
goto done;
for(i=0; i<ncindexsize(grp->vars); i++) {
NC_VAR_INFO_T* var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
if((stat = NCJaddstring(jvars,NCJ_STRING,var->hdr.name))) goto done;
}
/* Create subgroups list */
if((stat = NCJnew(NCJ_ARRAY,&jsubgrps)))
goto done;
for(i=0; i<ncindexsize(grp->children); i++) {
NC_GRP_INFO_T* g = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if((stat = NCJaddstring(jsubgrps,NCJ_STRING,g->hdr.name))) goto done;
}
/* Create the "_nczarr_group" dict */
if((stat = NCJnew(NCJ_DICT,&json)))
goto done;
/* Insert the various dicts and arrays */
if((stat = NCJinsert(json,"dims",jdims))) goto done;
jdims = NULL; /* avoid memory problems */
if((stat = NCJinsert(json,"vars",jvars))) goto done;
jvars = NULL; /* avoid memory problems */
if((stat = NCJinsert(json,"groups",jsubgrps))) goto done;
jsubgrps = NULL; /* avoid memory problems */
}
/* build ZGROUP contents */
if((stat = NCJnew(NCJ_DICT,&jgroup)))
goto done;
snprintf(version,sizeof(version),"%d",zinfo->zarr.zarr_version);
if((stat = NCJaddstring(jgroup,NCJ_STRING,"zarr_format"))) goto done;
if((stat = NCJaddstring(jgroup,NCJ_INT,version))) goto done;
if(!purezarr && grp->parent == NULL) { /* Root group */
snprintf(version,sizeof(version),"%lu.%lu.%lu",
zinfo->zarr.nczarr_version.major,
zinfo->zarr.nczarr_version.minor,
zinfo->zarr.nczarr_version.release);
if((stat = NCJnew(NCJ_DICT,&jsuper))) goto done;
if((stat-NCJnewstring(NCJ_STRING,version,&jtmp))) goto done;
if((stat = NCJinsert(jsuper,"version",jtmp))) goto done;
jtmp = NULL;
if((stat = NCJinsert(jgroup,NCZ_V2_SUPERBLOCK,jsuper))) goto done;
jsuper = NULL;
}
if(!purezarr) {
/* Insert the "_NCZARR_GROUP" dict */
if((stat = NCJinsert(jgroup,NCZ_V2_GROUP,json))) goto done;
json = NULL;
}
/* build ZGROUP path */
if((stat = nczm_concat(fullpath,ZGROUP,&key)))
goto done;
/* Write to map */
if((stat=NCZ_uploadjson(map,key,jgroup)))
goto done;
nullfree(key); key = NULL;
/* Build the .zattrs object */
assert(grp->att);
if((stat = ncz_sync_atts(file,(NC_OBJ*)grp, grp->att, isclose)))
goto done;
/* Now synchronize all the variables */
for(i=0; i<ncindexsize(grp->vars); i++) {
NC_VAR_INFO_T* var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
if((stat = ncz_sync_var(file,var,isclose))) goto done;
}
/* Now recurse to synchronize all the subgrps */
for(i=0; i<ncindexsize(grp->children); i++) {
NC_GRP_INFO_T* g = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if((stat = ncz_sync_grp(file,g,isclose))) goto done;
}
done:
NCJreclaim(jtmp);
NCJreclaim(jsuper);
NCJreclaim(json);
NCJreclaim(jgroup);
NCJreclaim(jdims);
NCJreclaim(jvars);
NCJreclaim(jsubgrps);
nullfree(fullpath);
nullfree(key);
return ZUNTRACE(THROW(stat));
}
/**
* @internal Synchronize variable meta data from memory to map.
*
* @param file Pointer to file struct
* @param var Pointer to var struct
* @param isclose If this called as part of nc_close() as opposed to nc_enddef().
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
ncz_sync_var_meta(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int isclose)
{
int i,stat = NC_NOERR;
NCZ_FILE_INFO_T* zinfo = NULL;
char number[1024];
NCZMAP* map = NULL;
char* fullpath = NULL;
char* key = NULL;
char* dimpath = NULL;
NClist* dimrefs = NULL;
NCjson* jvar = NULL;
NCjson* jncvar = NULL;
NCjson* jdimrefs = NULL;
NCjson* jtmp = NULL;
NCjson* jfill = NULL;
char* dtypename = NULL;
int purezarr = 0;
size64_t shape[NC_MAX_VAR_DIMS];
NCZ_VAR_INFO_T* zvar = var->format_var_info;
#ifdef ENABLE_NCZARR_FILTERS
NClist* filterchain = NULL;
NCjson* jfilter = NULL;
#endif
ZTRACE(3,"file=%s var=%s isclose=%d",file->controller->path,var->hdr.name,isclose);
zinfo = file->format_file_info;
map = zinfo->map;
purezarr = (zinfo->controls.flags & FLAG_PUREZARR)?1:0;
/* Make sure that everything is established */
/* ensure the fill value */
if((stat = NCZ_ensure_fill_value(var))) goto done; /* ensure var->fill_value is set */
assert(var->no_fill || var->fill_value != NULL);
/* ensure the chunk cache */
if((stat = NCZ_adjust_var_cache(var))) goto done;
/* rebuild the fill chunk */
if((stat = NCZ_ensure_fill_chunk(zvar->cache))) goto done;
#ifdef ENABLE_NCZARR_FILTERS
/* Build the filter working parameters for any filters */
if((stat = NCZ_filter_setup(var))) goto done;
#endif
/* Construct var path */
if((stat = NCZ_varkey(var,&fullpath)))
goto done;
/* Create the zarray json object */
if((stat = NCJnew(NCJ_DICT,&jvar)))
goto done;
/* zarr_format key */
snprintf(number,sizeof(number),"%d",zinfo->zarr.zarr_version);
if((stat = NCJaddstring(jvar,NCJ_STRING,"zarr_format"))) goto done;
if((stat = NCJaddstring(jvar,NCJ_INT,number))) goto done;
/* Collect the shape vector */
for(i=0;i<var->ndims;i++) {
NC_DIM_INFO_T* dim = var->dim[i];
shape[i] = dim->len;
}
/* but might be scalar */
if(var->ndims == 0)
shape[0] = 1;
/* shape key */
/* Integer list defining the length of each dimension of the array.*/
/* Create the list */
if((stat = NCJnew(NCJ_ARRAY,&jtmp))) goto done;
if(zvar->scalar) {
NCJaddstring(jtmp,NCJ_INT,"1");
} else for(i=0;i<var->ndims;i++) {
snprintf(number,sizeof(number),"%llu",shape[i]);
NCJaddstring(jtmp,NCJ_INT,number);
}
if((stat = NCJinsert(jvar,"shape",jtmp))) goto done;
jtmp = NULL;
/* dtype key */
/* A string or list defining a valid data type for the array. */
if((stat = NCJaddstring(jvar,NCJ_STRING,"dtype"))) goto done;
{ /* Add the type name */
int endianness = var->type_info->endianness;
int atomictype = var->type_info->hdr.id;
assert(atomictype > 0 && atomictype <= NC_MAX_ATOMIC_TYPE);
if((stat = ncz_nctype2dtype(atomictype,endianness,purezarr,NCZ_get_maxstrlen((NC_OBJ*)var),&dtypename))) goto done;
if((stat = NCJaddstring(jvar,NCJ_STRING,dtypename))) goto done;
nullfree(dtypename); dtypename = NULL;
}
/* chunks key */
/* The zarr format does not support the concept
of contiguous (or compact), so it will never appear in the read case.
*/
/* list of chunk sizes */
if((stat = NCJaddstring(jvar,NCJ_STRING,"chunks"))) goto done;
/* Create the list */
if((stat = NCJnew(NCJ_ARRAY,&jtmp))) goto done;
if(zvar->scalar) {
NCJaddstring(jtmp,NCJ_INT,"1"); /* one chunk of size 1 */
} else for(i=0;i<var->ndims;i++) {
size64_t len = var->chunksizes[i];
snprintf(number,sizeof(number),"%lld",len);
NCJaddstring(jtmp,NCJ_INT,number);
}
if((stat = NCJappend(jvar,jtmp))) goto done;
jtmp = NULL;
/* fill_value key */
if(var->no_fill) {
if((stat=NCJnew(NCJ_NULL,&jfill))) goto done;
} else {/*!var->no_fill*/
int atomictype = var->type_info->hdr.id;
if(var->fill_value == NULL) {
if((stat = NCZ_ensure_fill_value(var))) goto done;
}
/* Convert var->fill_value to a string */
if((stat = NCZ_stringconvert(atomictype,1,var->fill_value,&jfill))) goto done;
assert(jfill->sort != NCJ_ARRAY);
}
if((stat = NCJinsert(jvar,"fill_value",jfill))) goto done;
jfill = NULL;
/* order key */
if((stat = NCJaddstring(jvar,NCJ_STRING,"order"))) goto done;
/* "C" means row-major order, i.e., the last dimension varies fastest;
"F" means column-major order, i.e., the first dimension varies fastest.*/
/* Default to C for now */
if((stat = NCJaddstring(jvar,NCJ_STRING,"C"))) goto done;
/* Compressor and Filters */
/* compressor key */
/* From V2 Spec: A JSON object identifying the primary compression codec and providing
configuration parameters, or ``null`` if no compressor is to be used. */
if((stat = NCJaddstring(jvar,NCJ_STRING,"compressor"))) goto done;
#ifdef ENABLE_NCZARR_FILTERS
filterchain = (NClist*)var->filters;
if(nclistlength(filterchain) > 0) {
struct NCZ_Filter* filter = (struct NCZ_Filter*)nclistget(filterchain,nclistlength(filterchain)-1);
/* encode up the compressor */
if((stat = NCZ_filter_jsonize(file,var,filter,&jtmp))) goto done;
} else
#endif
{ /* no filters at all */
/* Default to null */
if((stat = NCJnew(NCJ_NULL,&jtmp))) goto done;
}
if(jtmp && (stat = NCJappend(jvar,jtmp))) goto done;
jtmp = NULL;
/* filters key */
/* From V2 Spec: A list of JSON objects providing codec configurations,
or null if no filters are to be applied. Each codec configuration
object MUST contain a "id" key identifying the codec to be used. */
/* A list of JSON objects providing codec configurations, or ``null``
if no filters are to be applied. */
if((stat = NCJaddstring(jvar,NCJ_STRING,"filters"))) goto done;
#ifdef ENABLE_NCZARR_FILTERS
if(nclistlength(filterchain) > 1) {
int k;
/* jtmp holds the array of filters */
if((stat = NCJnew(NCJ_ARRAY,&jtmp))) goto done;
for(k=0;k<nclistlength(filterchain)-1;k++) {
struct NCZ_Filter* filter = (struct NCZ_Filter*)nclistget(filterchain,k);
/* encode up the filter as a string */
if((stat = NCZ_filter_jsonize(file,var,filter,&jfilter))) goto done;
if((stat = NCJappend(jtmp,jfilter))) goto done;
}
} else
#endif
{ /* no filters at all */
if((stat = NCJnew(NCJ_NULL,&jtmp))) goto done;
}
if((stat = NCJappend(jvar,jtmp))) goto done;
jtmp = NULL;
/* dimension_separator key */
/* Single char defining the separator in chunk keys */
if(zvar->dimension_separator != DFALT_DIM_SEPARATOR) {
char sep[2];
sep[0] = zvar->dimension_separator;/* make separator a string*/
sep[1] = '\0';
if((stat = NCJnewstring(NCJ_STRING,sep,&jtmp))) goto done;
if((stat = NCJinsert(jvar,"dimension_separator",jtmp))) goto done;
jtmp = NULL;
}
/* Capture dimref names as FQNs */
if(var->ndims > 0) {
if((dimrefs = nclistnew())==NULL) {stat = NC_ENOMEM; goto done;}
for(i=0;i<var->ndims;i++) {
NC_DIM_INFO_T* dim = var->dim[i];
if((stat = NCZ_dimkey(dim,&dimpath))) goto done;
nclistpush(dimrefs,dimpath);
dimpath = NULL;
}
}
/* Build the NCZ_V2_ARRAY object */
{
/* Create the dimrefs json object */
if((stat = NCJnew(NCJ_ARRAY,&jdimrefs)))
goto done;
for(i=0;i<nclistlength(dimrefs);i++) {
const char* dim = nclistget(dimrefs,i);
NCJaddstring(jdimrefs,NCJ_STRING,dim);
}
if((stat = NCJnew(NCJ_DICT,&jncvar)))
goto done;
/* Insert dimrefs */
if((stat = NCJinsert(jncvar,"dimrefs",jdimrefs)))
goto done;
jdimrefs = NULL; /* Avoid memory problems */
/* Add the _Storage flag */
/* Record if this is a scalar */
if(var->ndims == 0) {
if((stat = NCJnewstring(NCJ_INT,"1",&jtmp)))goto done;
if((stat = NCJinsert(jncvar,"scalar",jtmp))) goto done;
jtmp = NULL;
}
/* everything looks like it is chunked */
if((stat = NCJnewstring(NCJ_STRING,"chunked",&jtmp)))goto done;
if((stat = NCJinsert(jncvar,"storage",jtmp))) goto done;
jtmp = NULL;
if(!(zinfo->controls.flags & FLAG_PUREZARR)) {
if((stat = NCJinsert(jvar,NCZ_V2_ARRAY,jncvar))) goto done;
jncvar = NULL;
}
}
/* build .zarray path */
if((stat = nczm_concat(fullpath,ZARRAY,&key)))
goto done;
/* Write to map */
if((stat=NCZ_uploadjson(map,key,jvar)))
goto done;
nullfree(key); key = NULL;
var->created = 1;
/* Build .zattrs object */
assert(var->att);
if((stat = ncz_sync_atts(file,(NC_OBJ*)var, var->att, isclose)))
goto done;
done:
nclistfreeall(dimrefs);
nullfree(fullpath);
nullfree(key);
nullfree(dtypename);
nullfree(dimpath);
NCJreclaim(jvar);
NCJreclaim(jncvar);
NCJreclaim(jtmp);
NCJreclaim(jfill);
return ZUNTRACE(THROW(stat));
}
/**
* @internal Synchronize variable meta data and data from memory to map.
*
* @param file Pointer to file struct
* @param var Pointer to var struct
* @param isclose If this called as part of nc_close() as opposed to nc_enddef().
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
ncz_sync_var(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int isclose)
{
int stat = NC_NOERR;
NCZ_VAR_INFO_T* zvar = var->format_var_info;
ZTRACE(3,"file=%s var=%s isclose=%d",file->controller->path,var->hdr.name,isclose);
if(isclose) {
if((stat = ncz_sync_var_meta(file,var,isclose))) goto done;
}
/* flush only chunks that have been written */
if(zvar->cache) {
if((stat = NCZ_flush_chunk_cache(zvar->cache)))
goto done;
}
done:
return ZUNTRACE(THROW(stat));
}
/*
Flush all chunks to disk. Create any that are missing
and fill as needed.
*/
int
ncz_write_var(NC_VAR_INFO_T* var)
{
int stat = NC_NOERR;
NCZ_VAR_INFO_T* zvar = (NCZ_VAR_INFO_T*)var->format_var_info;
ZTRACE(3,"var=%s",var->hdr.name);
/* Flush the cache */
if(zvar->cache) {
if((stat = NCZ_flush_chunk_cache(zvar->cache))) goto done;
}
#ifdef FILLONCLOSE
/* If fill is enabled, then create missing chunks */
if(!var->no_fill) {
int i;
NCZOdometer* chunkodom = NULL;
NC_FILE_INFO_T* file = var->container->nc4_info;
NCZ_FILE_INFO_T* zfile = (NCZ_FILE_INFO_T*)file->format_file_info;
NCZMAP* map = zfile->map;
size64_t start[NC_MAX_VAR_DIMS];
size64_t stop[NC_MAX_VAR_DIMS];
size64_t stride[NC_MAX_VAR_DIMS];
char* key = NULL;
if(var->ndims == 0) { /* scalar */
start[i] = 0;
stop[i] = 1;
stride[i] = 1;
} else {
for(i=0;i<var->ndims;i++) {
size64_t nchunks = ceildiv(var->dim[i]->len,var->chunksizes[i]);
start[i] = 0;
stop[i] = nchunks;
stride[i] = 1;
}
}
{
if(zvar->scalar) {
if((chunkodom = nczodom_new(1,start,stop,stride,stop))==NULL)
} else {
/* Iterate over all the chunks to create missing ones */
if((chunkodom = nczodom_new(var->ndims,start,stop,stride,stop))==NULL)
{stat = NC_ENOMEM; goto done;}
}
for(;nczodom_more(chunkodom);nczodom_next(chunkodom)) {
size64_t* indices = nczodom_indices(chunkodom);
/* Convert to key */
if((stat = NCZ_buildchunkpath(zvar->cache,indices,&key))) goto done;
switch (stat = nczmap_exists(map,key)) {
case NC_NOERR: goto next; /* already exists */
case NC_EEMPTY: break; /* does not exist, create it with fill */
default: goto done; /* some other error */
}
/* If we reach here, then chunk does not exist, create it with fill */
assert(zvar->cache->fillchunk != NULL);
if((stat=nczmap_write(map,key,0,zvar->cache->chunksize,zvar->cache->fillchunk))) goto done;
next:
nullfree(key);
key = NULL;
}
}
nczodom_free(chunkodom);
nullfree(key);
}
#endif /*FILLONCLOSE*/
done:
return ZUNTRACE(THROW(stat));
}
/**
* @internal Synchronize attribute data from memory to map.
*
* @param container Pointer to grp|var struct containing the attributes
* @param key the name of the map entry
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
ncz_sync_atts(NC_FILE_INFO_T* file, NC_OBJ* container, NCindex* attlist, int isclose)
{
int i,stat = NC_NOERR;
NCZ_FILE_INFO_T* zinfo = NULL;
NCjson* jatts = NULL;
NCjson* jtypes = NULL;
NCjson* jtype = NULL;
NCjson* jdimrefs = NULL;
NCjson* jdict = NULL;
NCjson* jint = NULL;
NCjson* jdata = NULL;
NCZMAP* map = NULL;
char* fullpath = NULL;
char* key = NULL;
char* content = NULL;
char* dimpath = NULL;
int isxarray = 0;
int inrootgroup = 0;
NC_VAR_INFO_T* var = NULL;
NC_GRP_INFO_T* grp = NULL;
char* tname = NULL;
int purezarr = 0;
int endianness = (NC_isLittleEndian()?NC_ENDIAN_LITTLE:NC_ENDIAN_BIG);
LOG((3, "%s", __func__));
ZTRACE(3,"file=%s container=%s |attlist|=%u",file->controller->path,container->name,(unsigned)ncindexsize(attlist));
if(container->sort == NCVAR) {
var = (NC_VAR_INFO_T*)container;
if(var->container && var->container->parent == NULL)
inrootgroup = 1;
} else if(container->sort == NCGRP) {
grp = (NC_GRP_INFO_T*)container;
}
zinfo = file->format_file_info;
map = zinfo->map;
purezarr = (zinfo->controls.flags & FLAG_PUREZARR)?1:0;
if(zinfo->controls.flags & FLAG_XARRAYDIMS) isxarray = 1;
/* Create the attribute dictionary */
if((stat = NCJnew(NCJ_DICT,&jatts))) goto done;
if(ncindexsize(attlist) > 0) {
/* Create the jncattr.types object */
if((stat = NCJnew(NCJ_DICT,&jtypes)))
goto done;
/* Walk all the attributes convert to json and collect the dtype */
for(i=0;i<ncindexsize(attlist);i++) {
NC_ATT_INFO_T* a = (NC_ATT_INFO_T*)ncindexith(attlist,i);
size_t typesize = 0;
#if 0
const NC_reservedatt* ra = NC_findreserved(a->hdr.name);
/* If reserved and hidden, then ignore */
if(ra && (ra->flags & HIDDENATTRFLAG)) continue;
#endif
if(a->nc_typeid > NC_MAX_ATOMIC_TYPE)
{stat = (THROW(NC_ENCZARR)); goto done;}
if(a->nc_typeid == NC_STRING)
typesize = NCZ_get_maxstrlen(container);
else
{if((stat = NC4_inq_atomic_type(a->nc_typeid,NULL,&typesize))) goto done;}
/* Convert to storable json */
if((stat = NCZ_stringconvert(a->nc_typeid,a->len,a->data,&jdata))) goto done;
if((stat = NCJinsert(jatts,a->hdr.name,jdata))) goto done;
jdata = NULL;
/* Collect the corresponding dtype */
{
if((stat = ncz_nctype2dtype(a->nc_typeid,endianness,purezarr,typesize,&tname))) goto done;
if((stat = NCJnewstring(NCJ_STRING,tname,&jtype))) goto done;
nullfree(tname); tname = NULL;
if((stat = NCJinsert(jtypes,a->hdr.name,jtype))) goto done; /* add {name: type} */
jtype = NULL;
}
}
}
/* Construct container path */
if(container->sort == NCGRP)
stat = NCZ_grpkey(grp,&fullpath);
else
stat = NCZ_varkey(var,&fullpath);
if(stat)
goto done;
if(container->sort == NCVAR) {
if(inrootgroup && isxarray) {
int dimsinroot = 1;
/* Insert the XARRAY _ARRAY_ATTRIBUTE attribute */
if((stat = NCJnew(NCJ_ARRAY,&jdimrefs)))
goto done;
/* Fake the scalar case */
if(var->ndims == 0) {
NCJaddstring(jdimrefs,NCJ_STRING,XARRAYSCALAR);
} else /* Walk the dimensions and capture the names */
for(i=0;i<var->ndims;i++) {
NC_DIM_INFO_T* dim = var->dim[i];
/* Verify that the dimension is in the root group */
if(dim->container && dim->container->parent != NULL) {
dimsinroot = 0; /* dimension is not in root */
break;
}
}
if(dimsinroot) {
/* Walk the dimensions and capture the names */
for(i=0;i<var->ndims;i++) {
char* dimname;
NC_DIM_INFO_T* dim = var->dim[i];
dimname = strdup(dim->hdr.name);
if(dimname == NULL) {stat = NC_ENOMEM; goto done;}
NCJaddstring(jdimrefs,NCJ_STRING,dimname);
nullfree(dimname); dimname = NULL;
}
/* Add the _ARRAY_DIMENSIONS attribute */
if((stat = NCJinsert(jatts,NC_XARRAY_DIMS,jdimrefs))) goto done;
jdimrefs = NULL;
}
}
}
/* Add Quantize Attribute */
if(container->sort == NCVAR && var && var->quantize_mode > 0) {
char mode[64];
snprintf(mode,sizeof(mode),"%d",var->nsd);
if((stat = NCJnewstring(NCJ_INT,mode,&jint)))
goto done;
/* Insert the quantize attribute */
switch (var->quantize_mode) {
case NC_QUANTIZE_BITGROOM:
if((stat = NCJinsert(jatts,NC_QUANTIZE_BITGROOM_ATT_NAME,jint))) goto done;
jint = NULL;
break;
case NC_QUANTIZE_GRANULARBR:
if((stat = NCJinsert(jatts,NC_QUANTIZE_GRANULARBR_ATT_NAME,jint))) goto done;
jint = NULL;
break;
case NC_QUANTIZE_BITROUND:
if((stat = NCJinsert(jatts,NC_QUANTIZE_BITROUND_ATT_NAME,jint))) goto done;
jint = NULL;
break;
default: break;
}
}
if(NCJlength(jatts) > 0) {
if(!(zinfo->controls.flags & FLAG_PUREZARR)) {
/* Insert the _NCZARR_ATTR attribute */
if((stat = NCJnew(NCJ_DICT,&jdict)))
goto done;
if(jtypes != NULL)
{if((stat = NCJinsert(jdict,"types",jtypes))) goto done;}
jtypes = NULL;
if(jdict != NULL)
{if((stat = NCJinsert(jatts,NCZ_V2_ATTR,jdict))) goto done;}
jdict = NULL;
}
/* write .zattrs path */
if((stat = nczm_concat(fullpath,ZATTRS,&key)))
goto done;
/* Write to map */
if((stat=NCZ_uploadjson(map,key,jatts)))
goto done;
nullfree(key); key = NULL;
}
done:
nullfree(fullpath);
nullfree(key);
nullfree(content);
nullfree(dimpath);
nullfree(tname);
NCJreclaim(jatts);
NCJreclaim(jtypes);
NCJreclaim(jtype);
NCJreclaim(jdimrefs);
NCJreclaim(jdict);
NCJreclaim(jint);
NCJreclaim(jdata);
return ZUNTRACE(THROW(stat));
}
/**************************************************/
/**
@internal Extract attributes from a group or var and return
the corresponding NCjson dict.
@param map - [in] the map object for storage
@param container - [in] the containing object
@param jattrsp - [out] the json for .zattrs
@param jtypesp - [out] the json for .ztypes
@return NC_NOERR
@author Dennis Heimbigner
*/
static int
load_jatts(NCZMAP* map, NC_OBJ* container, int nczarrv1, NCjson** jattrsp, NClist** atypesp)
{
int stat = NC_NOERR;
char* fullpath = NULL;
char* key = NULL;
NCjson* jnczarr = NULL;
NCjson* jattrs = NULL;
NCjson* jncattr = NULL;
NClist* atypes = NULL; /* envv list */
ZTRACE(3,"map=%p container=%s nczarrv1=%d",map,container->name,nczarrv1);
/* alway return (possibly empty) list of types */
atypes = nclistnew();
if(container->sort == NCGRP) {
NC_GRP_INFO_T* grp = (NC_GRP_INFO_T*)container;
/* Get grp's fullpath name */
if((stat = NCZ_grpkey(grp,&fullpath)))
goto done;
} else {
NC_VAR_INFO_T* var = (NC_VAR_INFO_T*)container;
/* Get var's fullpath name */
if((stat = NCZ_varkey(var,&fullpath)))
goto done;
}
/* Construct the path to the .zattrs object */
if((stat = nczm_concat(fullpath,ZATTRS,&key)))
goto done;
/* Download the .zattrs object: may not exist if not NCZarr V1 */
switch ((stat=NCZ_downloadjson(map,key,&jattrs))) {
case NC_NOERR: break;
case NC_EEMPTY: stat = NC_NOERR; break; /* did not exist */
default: goto done; /* failure */
}
nullfree(key); key = NULL;
if(jattrs != NULL) {
if(nczarrv1) {
/* Construct the path to the NCZATTRS object */
if((stat = nczm_concat(fullpath,NCZATTRS,&key))) goto done;
/* Download the NCZATTRS object: may not exist if pure zarr or using deprecated name */
stat=NCZ_downloadjson(map,key,&jncattr);
if(stat == NC_EEMPTY) {
/* try deprecated name */
nullfree(key); key = NULL;
if((stat = nczm_concat(fullpath,NCZATTRDEP,&key))) goto done;
stat=NCZ_downloadjson(map,key,&jncattr);
}
} else {/* Get _nczarr_attrs from .zattrs */
stat = NCJdictget(jattrs,NCZ_V2_ATTR,&jncattr);
if(!stat && jncattr == NULL)
{stat = NCJdictget(jattrs,NCZ_V2_ATTR_UC,&jncattr);}
}
nullfree(key); key = NULL;
switch (stat) {
case NC_NOERR: break;
case NC_EEMPTY: stat = NC_NOERR; jncattr = NULL; break;
default: goto done; /* failure */
}
if(jncattr != NULL) {
NCjson* jtypes = NULL;
/* jncattr attribute should be a dict */
if(NCJsort(jncattr) != NCJ_DICT) {stat = (THROW(NC_ENCZARR)); goto done;}
/* Extract "types; may not exist if only hidden attributes are defined */
if((stat = NCJdictget(jncattr,"types",&jtypes))) goto done;
if(jtypes != NULL) {
if(NCJsort(jtypes) != NCJ_DICT) {stat = (THROW(NC_ENCZARR)); goto done;}
/* Convert to an envv list */
if((stat = jtypes2atypes(jtypes,atypes))) goto done;
}
}
}
if(jattrsp) {*jattrsp = jattrs; jattrs = NULL;}
if(atypesp) {*atypesp = atypes; atypes = NULL;}
done:
if(nczarrv1)
NCJreclaim(jncattr);
if(stat) {
NCJreclaim(jnczarr);
nclistfreeall(atypes);
}
nullfree(fullpath);
nullfree(key);
return ZUNTRACE(THROW(stat));
}
/* Convert a JSON singleton or array of strings to a single string */
static int
zcharify(NCjson* src, NCbytes* buf)
{
int i, stat = NC_NOERR;
struct NCJconst jstr = NCJconst_empty;
if(NCJsort(src) != NCJ_ARRAY) { /* singleton */
if((stat = NCJcvt(src, NCJ_STRING, &jstr))) goto done;
ncbytescat(buf,jstr.sval);
} else for(i=0;i<NCJlength(src);i++) {
NCjson* value = NCJith(src,i);
if((stat = NCJcvt(value, NCJ_STRING, &jstr))) goto done;
ncbytescat(buf,jstr.sval);
nullfree(jstr.sval);jstr.sval = NULL;
}
done:
nullfree(jstr.sval);
return stat;
}
/* Convert a json value to actual data values of an attribute. */
static int
zconvert(NCjson* src, nc_type typeid, size_t typelen, int* countp, NCbytes* dst)
{
int stat = NC_NOERR;
int i;
int count = 0;
ZTRACE(3,"src=%s typeid=%d typelen=%u",NCJtotext(src),typeid,typelen);
/* 3 cases:
(1) singleton atomic value
(2) array of atomic values
(3) other JSON expression
*/
switch (NCJsort(src)) {
case NCJ_INT: case NCJ_DOUBLE: case NCJ_BOOLEAN: /* case 1 */
count = 1;
if((stat = NCZ_convert1(src, typeid, dst)))
goto done;
break;
case NCJ_ARRAY:
if(typeid == NC_CHAR) {
if((stat = zcharify(src,dst))) goto done;
count = ncbyteslength(dst);
} else {
count = NCJlength(src);
for(i=0;i<count;i++) {
NCjson* value = NCJith(src,i);
if((stat = NCZ_convert1(value, typeid, dst))) goto done;
}
}
break;
case NCJ_STRING:
if(typeid == NC_CHAR) {
if((stat = zcharify(src,dst))) goto done;
count = ncbyteslength(dst);
/* Special case for "" */
if(count == 0) {
ncbytesappend(dst,'\0');
count = 1;
}
} else {
if((stat = NCZ_convert1(src, typeid, dst))) goto done;
count = 1;
}
break;
default: stat = (THROW(NC_ENCZARR)); goto done;
}
if(countp) *countp = count;
done:
return ZUNTRACE(THROW(stat));
}
/*
Extract type and data for an attribute
*/
static int
computeattrinfo(const char* name, NClist* atypes, nc_type typehint, int purezarr, NCjson* values,
nc_type* typeidp, size_t* typelenp, size_t* lenp, void** datap)
{
int stat = NC_NOERR;
int i;
size_t len, typelen;
void* data = NULL;
nc_type typeid;
ZTRACE(3,"name=%s |atypes|=%u typehint=%d purezarr=%d values=|%s|",name,nclistlength(atypes),typehint,purezarr,NCJtotext(values));
/* Get type info for the given att */
typeid = NC_NAT;
for(i=0;i<nclistlength(atypes);i+=2) {
const char* aname = nclistget(atypes,i);
if(strcmp(aname,name)==0) {
const char* atype = nclistget(atypes,i+1);
if((stat = ncz_dtype2nctype(atype,typehint,purezarr,&typeid,NULL,NULL))) goto done;
// if((stat = ncz_nctypedecode(atype,&typeid))) goto done;
break;
}
}
if(typeid > NC_MAX_ATOMIC_TYPE)
{stat = NC_EINTERNAL; goto done;}
/* Use the hint if given one */
if(typeid == NC_NAT)
typeid = typehint;
if((stat = computeattrdata(typehint, &typeid, values, &typelen, &len, &data))) goto done;
if(typeidp) *typeidp = typeid;
if(lenp) *lenp = len;
if(typelenp) *typelenp = typelen;
if(datap) {*datap = data; data = NULL;}
done:
nullfree(data);
return ZUNTRACEX(THROW(stat),"typeid=%d typelen=%d len=%u",*typeidp,*typelenp,*lenp);
}
/*
Extract data for an attribute
*/
static int
computeattrdata(nc_type typehint, nc_type* typeidp, NCjson* values, size_t* typelenp, size_t* countp, void** datap)
{
int stat = NC_NOERR;
NCbytes* buf = ncbytesnew();
size_t typelen;
nc_type typeid = NC_NAT;
NCjson* jtext = NULL;
int reclaimvalues = 0;
int isjson = 0; /* 1 => attribute value is neither scalar nor array of scalars */
int count = 0; /* no. of attribute values */
ZTRACE(3,"typehint=%d typeid=%d values=|%s|",typehint,*typeidp,NCJtotext(values));
/* Get assumed type */
if(typeidp) typeid = *typeidp;
if(typeid == NC_NAT && !isjson) {
if((stat = NCZ_inferattrtype(values,typehint, &typeid))) goto done;
}
/* See if this is a simple vector (or scalar) of atomic types */
isjson = NCZ_iscomplexjson(values,typeid);
if(isjson) {
/* Apply the JSON attribute convention and convert to JSON string */
typeid = NC_CHAR;
if((stat = json_convention_read(values,&jtext))) goto done;
values = jtext; jtext = NULL;
reclaimvalues = 1;
}
if((stat = NC4_inq_atomic_type(typeid, NULL, &typelen)))
goto done;
/* Convert the JSON attribute values to the actual netcdf attribute bytes */
if((stat = zconvert(values,typeid,typelen,&count,buf))) goto done;
if(typelenp) *typelenp = typelen;
if(typeidp) *typeidp = typeid; /* return possibly inferred type */
if(countp) *countp = count;
if(datap) *datap = ncbytesextract(buf);
done:
ncbytesfree(buf);
if(reclaimvalues) NCJreclaim(values); /* we created it */
return ZUNTRACEX(THROW(stat),"typelen=%d count=%u",(typelenp?*typelenp:0),(countp?*countp:-1));
}
/**
* @internal Read file data from map to memory.
*
* @param file Pointer to file info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
ncz_read_file(NC_FILE_INFO_T* file)
{
int stat = NC_NOERR;
NCjson* json = NULL;
LOG((3, "%s: file: %s", __func__, file->controller->path));
ZTRACE(3,"file=%s",file->controller->path);
/* _nczarr should already have been read in ncz_open_dataset */
/* Now load the groups starting with root */
if((stat = define_grp(file,file->root_grp)))
goto done;
done:
NCJreclaim(json);
return ZUNTRACE(THROW(stat));
}
/**
* @internal Read group data from map to memory
*
* @param file Pointer to file struct
* @param grp Pointer to grp struct
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
define_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp)
{
int stat = NC_NOERR;
NCZ_FILE_INFO_T* zinfo = NULL;
NCZMAP* map = NULL;
char* fullpath = NULL;
char* key = NULL;
NCjson* json = NULL;
NCjson* jgroup = NULL;
NCjson* jdict = NULL;
NClist* dimdefs = nclistnew();
NClist* varnames = nclistnew();
NClist* subgrps = nclistnew();
int purezarr = 0;
int v1 = 0;
LOG((3, "%s: dims: %s", __func__, key));
ZTRACE(3,"file=%s grp=%s",file->controller->path,grp->hdr.name);
zinfo = file->format_file_info;
map = zinfo->map;
/* Construct grp path */
if((stat = NCZ_grpkey(grp,&fullpath)))
goto done;
if(zinfo->controls.flags & FLAG_PUREZARR) {
if((stat = parse_group_content_pure(zinfo,grp,varnames,subgrps)))
goto done;
purezarr = 1;
} else { /*!purezarr*/
if(zinfo->controls.flags & FLAG_NCZARR_V1) {
/* build NCZGROUP path */
if((stat = nczm_concat(fullpath,NCZGROUP,&key)))
goto done;
/* Read */
jdict = NULL;
stat=NCZ_downloadjson(map,key,&jdict);
v1 = 1;
} else {
/* build ZGROUP path */
if((stat = nczm_concat(fullpath,ZGROUP,&key)))
goto done;
/* Read */
switch (stat=NCZ_downloadjson(map,key,&jgroup)) {
case NC_NOERR: /* Extract the NCZ_V2_GROUP dict */
if((stat = NCJdictget(jgroup,NCZ_V2_GROUP,&jdict))) goto done;
if(!stat && jdict == NULL)
{if((stat = NCJdictget(jgroup,NCZ_V2_GROUP_UC,&jdict))) goto done;}
break;
case NC_EEMPTY: /* does not exist, use search */
if((stat = parse_group_content_pure(zinfo,grp,varnames,subgrps)))
goto done;
purezarr = 1;
break;
default: goto done;
}
}
nullfree(key); key = NULL;
if(jdict) {
/* Pull out lists about group content */
if((stat = parse_group_content(jdict,dimdefs,varnames,subgrps)))
goto done;
}
}
if(!purezarr) {
/* Define dimensions */
if((stat = define_dims(file,grp,dimdefs))) goto done;
}
/* Define vars taking xarray into account */
if((stat = define_vars(file,grp,varnames))) goto done;
/* Define sub-groups */
if((stat = define_subgrps(file,grp,subgrps))) goto done;
done:
if(v1) NCJreclaim(jdict);
NCJreclaim(json);
NCJreclaim(jgroup);
nclistfreeall(dimdefs);
nclistfreeall(varnames);
nclistfreeall(subgrps);
nullfree(fullpath);
nullfree(key);
return ZUNTRACE(THROW(stat));
}
/**
@internal Read attributes from a group or var and create a list
of annotated NC_ATT_INFO_T* objects. This will process
_NCProperties attribute specially.
@param zfile - [in] the containing file (annotation)
@param container - [in] the containing object
@return NC_NOERR
@author Dennis Heimbigner
*/
int
ncz_read_atts(NC_FILE_INFO_T* file, NC_OBJ* container)
{
int stat = NC_NOERR;
int i;
char* fullpath = NULL;
char* key = NULL;
NCZ_FILE_INFO_T* zinfo = NULL;
NC_VAR_INFO_T* var = NULL;
NCZ_VAR_INFO_T* zvar = NULL;
NC_GRP_INFO_T* grp = NULL;
NCZMAP* map = NULL;
NC_ATT_INFO_T* att = NULL;
NCindex* attlist = NULL;
NCjson* jattrs = NULL;
NClist* atypes = NULL;
nc_type typeid;
size_t len, typelen;
void* data = NULL;
NC_ATT_INFO_T* fillvalueatt = NULL;
nc_type typehint = NC_NAT;
int purezarr;
ZTRACE(3,"file=%s container=%s",file->controller->path,container->name);
zinfo = file->format_file_info;
map = zinfo->map;
purezarr = (zinfo->controls.flags & FLAG_PUREZARR)?1:0;
if(container->sort == NCGRP) {
grp = ((NC_GRP_INFO_T*)container);
attlist = grp->att;
} else {
var = ((NC_VAR_INFO_T*)container);
zvar = (NCZ_VAR_INFO_T*)(var->format_var_info);
attlist = var->att;
}
switch ((stat = load_jatts(map, container, (zinfo->controls.flags & FLAG_NCZARR_V1), &jattrs, &atypes))) {
case NC_NOERR: break;
case NC_EEMPTY: /* container has no attributes */
stat = NC_NOERR;
break;
default: goto done; /* true error */
}
if(jattrs != NULL) {
/* Iterate over the attributes to create the in-memory attributes */
/* Watch for special cases: _FillValue and _ARRAY_DIMENSIONS (xarray), etc. */
for(i=0;i<NCJlength(jattrs);i+=2) {
NCjson* key = NCJith(jattrs,i);
NCjson* value = NCJith(jattrs,i+1);
const NC_reservedatt* ra = NULL;
int isfillvalue = 0;
int isdfaltmaxstrlen = 0;
int ismaxstrlen = 0;
const char* aname = NCJstring(key);
/* See if this is a notable attribute */
if(var != NULL && strcmp(aname,NC_ATT_FILLVALUE)==0) isfillvalue = 1;
if(grp != NULL && grp->parent == NULL && strcmp(aname,NC_NCZARR_DEFAULT_MAXSTRLEN_ATTR)==0)
isdfaltmaxstrlen = 1;
if(var != NULL && strcmp(aname,NC_NCZARR_MAXSTRLEN_ATTR)==0)
ismaxstrlen = 1;
/* See if this is reserved attribute */
ra = NC_findreserved(aname);
if(ra != NULL) {
/* case 1: name = _NCProperties, grp=root, varid==NC_GLOBAL */
if(strcmp(aname,NCPROPS)==0 && grp != NULL && file->root_grp == grp) {
/* Setup provenance */
if(NCJsort(value) != NCJ_STRING)
{stat = (THROW(NC_ENCZARR)); goto done;} /*malformed*/
if((stat = NCZ_read_provenance(file,aname,NCJstring(value))))
goto done;
}
/* case 2: name = _ARRAY_DIMENSIONS, sort==NCVAR, flags & HIDDENATTRFLAG */
if(strcmp(aname,NC_XARRAY_DIMS)==0 && var != NULL && (ra->flags & HIDDENATTRFLAG)) {
/* store for later */
int i;
assert(NCJsort(value) == NCJ_ARRAY);
if((zvar->xarray = nclistnew())==NULL)
{stat = NC_ENOMEM; goto done;}
for(i=0;i<NCJlength(value);i++) {
const NCjson* k = NCJith(value,i);
assert(k != NULL && NCJsort(k) == NCJ_STRING);
nclistpush(zvar->xarray,strdup(NCJstring(k)));
}
}
/* case other: if attribute is hidden */
if(ra->flags & HIDDENATTRFLAG) continue; /* ignore it */
}
typehint = NC_NAT;
if(isfillvalue)
typehint = var->type_info->hdr.id ; /* if unknown use the var's type for _FillValue */
/* Create the attribute */
/* Collect the attribute's type and value */
if((stat = computeattrinfo(aname,atypes,typehint,purezarr,value,
&typeid,&typelen,&len,&data)))
goto done;
if((stat = ncz_makeattr(container,attlist,aname,typeid,len,data,&att)))
goto done;
/* No longer need this copy of the data */
if((stat = NC_reclaim_data_all(file->controller,att->nc_typeid,data,len))) goto done;
data = NULL;
if(isfillvalue)
fillvalueatt = att;
if(ismaxstrlen && att->nc_typeid == NC_INT)
zvar->maxstrlen = ((int*)att->data)[0];
if(isdfaltmaxstrlen && att->nc_typeid == NC_INT)
zinfo->default_maxstrlen = ((int*)att->data)[0];
}
}
/* If we have not read a _FillValue, then go ahead and create it */
if(fillvalueatt == NULL && container->sort == NCVAR) {
if((stat = ncz_create_fillvalue((NC_VAR_INFO_T*)container)))
goto done;
}
/* Remember that we have read the atts for this var or group. */
if(container->sort == NCVAR)
((NC_VAR_INFO_T*)container)->atts_read = 1;
else
((NC_GRP_INFO_T*)container)->atts_read = 1;
done:
if(data != NULL)
stat = NC_reclaim_data(file->controller,att->nc_typeid,data,len);
NCJreclaim(jattrs);
nclistfreeall(atypes);
nullfree(fullpath);
nullfree(key);
return ZUNTRACE(THROW(stat));
}
/**
* @internal Materialize dimensions into memory
*
* @param file Pointer to file info struct.
* @param grp Pointer to grp info struct.
* @param diminfo List of (name,length,isunlimited) triples
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
define_dims(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* diminfo)
{
int i,stat = NC_NOERR;
ZTRACE(3,"file=%s grp=%s |diminfo|=%u",file->controller->path,grp->hdr.name,nclistlength(diminfo));
/* Reify each dim in turn */
for(i = 0; i < nclistlength(diminfo); i+=3) {
NC_DIM_INFO_T* dim = NULL;
size64_t len = 0;
long long isunlim = 0;
const char* name = nclistget(diminfo,i);
const char* slen = nclistget(diminfo,i+1);
const char* sisunlimited = nclistget(diminfo,i+2);
/* Create the NC_DIM_INFO_T object */
sscanf(slen,"%lld",&len); /* Get length */
if(sisunlimited != NULL)
sscanf(sisunlimited,"%lld",&isunlim); /* Get unlimited flag */
else
isunlim = 0;
if((stat = nc4_dim_list_add(grp, name, (size_t)len, -1, &dim)))
goto done;
dim->unlimited = (isunlim ? 1 : 0);
if((dim->format_dim_info = calloc(1,sizeof(NCZ_DIM_INFO_T))) == NULL)
{stat = NC_ENOMEM; goto done;}
((NCZ_DIM_INFO_T*)dim->format_dim_info)->common.file = file;
}
done:
return ZUNTRACE(THROW(stat));
}
/**
* @internal Materialize vars into memory;
* Take xarray and purezarr into account.
*
* @param file Pointer to file info struct.
* @param grp Pointer to grp info struct.
* @param varnames List of names of variables in this group
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
define_vars(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* varnames)
{
int stat = NC_NOERR;
int i,j;
NCZ_FILE_INFO_T* zinfo = NULL;
NCZMAP* map = NULL;
int purezarr = 0;
int xarray = 0;
int formatv1 = 0;
ZTRACE(3,"file=%s grp=%s |varnames|=%u",file->controller->path,grp->hdr.name,nclistlength(varnames));
zinfo = file->format_file_info;
map = zinfo->map;
if(zinfo->controls.flags & FLAG_PUREZARR) purezarr = 1;
if(zinfo->controls.flags & FLAG_NCZARR_V1) formatv1 = 1;
if(zinfo->controls.flags & FLAG_XARRAYDIMS) {xarray = 1;}
/* Load each var in turn */
for(i = 0; i < nclistlength(varnames); i++) {
/* per-variable info */
NC_VAR_INFO_T* var = NULL;
NCZ_VAR_INFO_T* zvar = NULL;
NCjson* jvar = NULL;
NCjson* jncvar = NULL;
NCjson* jdimrefs = NULL;
NCjson* jvalue = NULL;
char* varpath = NULL;
char* key = NULL;
const char* varname = NULL;
size64_t* shapes = NULL;
NClist* dimnames = NULL;
int varsized = 0;
int suppress = 0; /* Abort processing of this variable */
nc_type vtype = NC_NAT;
int vtypelen = 0;
int rank = 0;
int zarr_rank = 0; /* Need to watch out for scalars */
#ifdef ENABLE_NCZARR_FILTERS
NCjson* jfilter = NULL;
int chainindex = 0;
#endif
dimnames = nclistnew();
varname = nclistget(varnames,i);
if((stat = nc4_var_list_add2(grp, varname, &var)))
goto done;
/* And its annotation */
if((zvar = calloc(1,sizeof(NCZ_VAR_INFO_T)))==NULL)
{stat = NC_ENOMEM; goto done;}
var->format_var_info = zvar;
zvar->common.file = file;
/* pretend it was created */
var->created = 1;
/* Indicate we do not have quantizer yet */
var->quantize_mode = -1;
/* Construct var path */
if((stat = NCZ_varkey(var,&varpath)))
goto done;
/* Construct the path to the zarray object */
if((stat = nczm_concat(varpath,ZARRAY,&key)))
goto done;
/* Download the zarray object */
if((stat=NCZ_readdict(map,key,&jvar)))
goto done;
nullfree(key); key = NULL;
assert(NCJsort(jvar) == NCJ_DICT);
/* Extract the .zarray info from jvar */
/* Verify the format */
{
int version;
if((stat = NCJdictget(jvar,"zarr_format",&jvalue))) goto done;
sscanf(NCJstring(jvalue),"%d",&version);
if(version != zinfo->zarr.zarr_version)
{stat = (THROW(NC_ENCZARR)); goto done;}
}
/* Set the type and endianness of the variable */
{
int endianness;
if((stat = NCJdictget(jvar,"dtype",&jvalue))) goto done;
/* Convert dtype to nc_type + endianness */
if((stat = ncz_dtype2nctype(NCJstring(jvalue),NC_NAT,purezarr,&vtype,&endianness,&vtypelen)))
goto done;
if(vtype > NC_NAT && vtype <= NC_MAX_ATOMIC_TYPE) {
/* Locate the NC_TYPE_INFO_T object */
if((stat = ncz_gettype(file,grp,vtype,&var->type_info)))
goto done;
} else {stat = NC_EBADTYPE; goto done;}
#if 0 /* leave native in place */
if(endianness == NC_ENDIAN_NATIVE)
endianness = zinfo->native_endianness;
if(endianness == NC_ENDIAN_NATIVE)
endianness = (NCZ_isLittleEndian()?NC_ENDIAN_LITTLE:NC_ENDIAN_BIG);
if(endianness == NC_ENDIAN_LITTLE || endianness == NC_ENDIAN_BIG) {
var->endianness = endianness;
} else {stat = NC_EBADTYPE; goto done;}
#else
var->endianness = endianness;
#endif
var->type_info->endianness = var->endianness; /* Propagate */
if(vtype == NC_STRING) {
zvar->maxstrlen = vtypelen;
vtypelen = sizeof(char*); /* in-memory len */
if(zvar->maxstrlen <= 0) zvar->maxstrlen = NCZ_get_maxstrlen((NC_OBJ*)var);
}
}
if(!purezarr) {
/* Extract the _NCZARR_ARRAY values */
/* Do this first so we know about storage esp. scalar */
if(formatv1) {
/* Construct the path to the zarray object */
if((stat = nczm_concat(varpath,NCZARRAY,&key)))
goto done;
/* Download the nczarray object */
if((stat=NCZ_readdict(map,key,&jncvar)))
goto done;
nullfree(key); key = NULL;
} else {/* format v2 */
/* Extract the NCZ_V2_ARRAY dict */
if((stat = NCJdictget(jvar,NCZ_V2_ARRAY,&jncvar))) goto done;
if(!stat && jncvar == NULL)
{if((stat = NCJdictget(jvar,NCZ_V2_ARRAY_UC,&jncvar))) goto done;}
}
if(jncvar == NULL) {stat = NC_ENCZARR; goto done;}
assert((NCJsort(jncvar) == NCJ_DICT));
/* Extract scalar flag */
if((stat = NCJdictget(jncvar,"scalar",&jvalue)))
goto done;
if(jvalue != NULL) {
var->storage = NC_CHUNKED;
zvar->scalar = 1;
}
/* Extract storage flag */
if((stat = NCJdictget(jncvar,"storage",&jvalue)))
goto done;
if(jvalue != NULL) {
var->storage = NC_CHUNKED;
}
/* Extract dimrefs list */
switch ((stat = NCJdictget(jncvar,"dimrefs",&jdimrefs))) {
case NC_NOERR: /* Extract the dimref names */
assert((NCJsort(jdimrefs) == NCJ_ARRAY));
if(zvar->scalar) {
assert(NCJlength(jdimrefs) == 0);
} else {
rank = NCJlength(jdimrefs);
for(j=0;j<rank;j++) {
const NCjson* dimpath = NCJith(jdimrefs,j);
assert(NCJsort(dimpath) == NCJ_STRING);
nclistpush(dimnames,strdup(NCJstring(dimpath)));
}
}
jdimrefs = NULL; /* avoid double free */
break;
case NC_EEMPTY: /* will simulate it from the shape of the variable */
stat = NC_NOERR;
break;
default: goto done;
}
jdimrefs = NULL;
}
/* Capture dimension_separator (must precede chunk cache creation) */
{
NCglobalstate* ngs = NC_getglobalstate();
assert(ngs != NULL);
zvar->dimension_separator = 0;
if((stat = NCJdictget(jvar,"dimension_separator",&jvalue))) goto done;
if(jvalue != NULL) {
/* Verify its value */
if(NCJsort(jvalue) == NCJ_STRING && NCJstring(jvalue) != NULL && strlen(NCJstring(jvalue)) == 1)
zvar->dimension_separator = NCJstring(jvalue)[0];
}
/* If value is invalid, then use global default */
if(!islegaldimsep(zvar->dimension_separator))
zvar->dimension_separator = ngs->zarr.dimension_separator; /* use global value */
assert(islegaldimsep(zvar->dimension_separator)); /* we are hosed */
}
/* fill_value; must precede calls to adjust cache */
{
if((stat = NCJdictget(jvar,"fill_value",&jvalue))) goto done;
if(jvalue == NULL || NCJsort(jvalue) == NCJ_NULL)
var->no_fill = 1;
else {
size_t fvlen;
nc_type atypeid = vtype;
var->no_fill = 0;
if((stat = computeattrdata(var->type_info->hdr.id, &atypeid, jvalue, NULL, &fvlen, &var->fill_value)))
goto done;
assert(atypeid == vtype);
/* Note that we do not create the _FillValue
attribute here to avoid having to read all
the attributes and thus foiling lazy read.*/
}
}
/* shape */
{
if((stat = NCJdictget(jvar,"shape",&jvalue))) goto done;
if(NCJsort(jvalue) != NCJ_ARRAY) {stat = (THROW(NC_ENCZARR)); goto done;}
/* Process the rank */
zarr_rank = NCJlength(jvalue);
if(zarr_rank == 0) {
/* suppress variable */
ZLOG(NCLOGWARN,"Empty shape for variable %s suppressed",var->hdr.name);
suppress = 1;
goto suppressvar;
}
if(zvar->scalar) {
rank = 0;
zarr_rank = 1; /* Zarr does not support scalars */
} else
rank = (zarr_rank = NCJlength(jvalue));
if(zarr_rank > 0) {
/* Save the rank of the variable */
if((stat = nc4_var_set_ndims(var, rank))) goto done;
/* extract the shapes */
if((shapes = (size64_t*)malloc(sizeof(size64_t)*zarr_rank)) == NULL)
{stat = (THROW(NC_ENOMEM)); goto done;}
if((stat = decodeints(jvalue, shapes))) goto done;
}
}
/* chunks */
{
size64_t chunks[NC_MAX_VAR_DIMS];
if((stat = NCJdictget(jvar,"chunks",&jvalue))) goto done;
if(jvalue != NULL && NCJsort(jvalue) != NCJ_ARRAY)
{stat = (THROW(NC_ENCZARR)); goto done;}
/* Verify the rank */
if(zvar->scalar || zarr_rank == 0) {
if(var->ndims != 0)
{stat = (THROW(NC_ENCZARR)); goto done;}
zvar->chunkproduct = 1;
zvar->chunksize = zvar->chunkproduct * var->type_info->size;
/* Create the cache */
if((stat = NCZ_create_chunk_cache(var,var->type_info->size*zvar->chunkproduct,zvar->dimension_separator,&zvar->cache)))
goto done;
} else {/* !zvar->scalar */
if(zarr_rank == 0) {stat = NC_ENCZARR; goto done;}
var->storage = NC_CHUNKED;
if(var->ndims != rank)
{stat = (THROW(NC_ENCZARR)); goto done;}
if((var->chunksizes = malloc(sizeof(size_t)*zarr_rank)) == NULL)
{stat = NC_ENOMEM; goto done;}
if((stat = decodeints(jvalue, chunks))) goto done;
/* validate the chunk sizes */
zvar->chunkproduct = 1;
for(j=0;j<rank;j++) {
if(chunks[j] == 0)
{stat = (THROW(NC_ENCZARR)); goto done;}
var->chunksizes[j] = (size_t)chunks[j];
zvar->chunkproduct *= chunks[j];
}
zvar->chunksize = zvar->chunkproduct * var->type_info->size;
/* Create the cache */
if((stat = NCZ_create_chunk_cache(var,var->type_info->size*zvar->chunkproduct,zvar->dimension_separator,&zvar->cache)))
goto done;
}
if((stat = NCZ_adjust_var_cache(var))) goto done;
}
/* Capture row vs column major; currently, column major not used*/
{
if((stat = NCJdictget(jvar,"order",&jvalue))) goto done;
if(strcmp(NCJstring(jvalue),"C")==1)
((NCZ_VAR_INFO_T*)var->format_var_info)->order = 1;
else ((NCZ_VAR_INFO_T*)var->format_var_info)->order = 0;
}
/* filters key */
/* From V2 Spec: A list of JSON objects providing codec configurations,
or null if no filters are to be applied. Each codec configuration
object MUST contain a "id" key identifying the codec to be used. */
/* Do filters key before compressor key so final filter chain is in correct order */
{
#ifdef ENABLE_NCZARR_FILTERS
if(var->filters == NULL) var->filters = (void*)nclistnew();
if(zvar->incompletefilters == NULL) zvar->incompletefilters = (void*)nclistnew();
chainindex = 0; /* track location of filter in the chain */
if((stat = NCZ_filter_initialize())) goto done;
if((stat = NCJdictget(jvar,"filters",&jvalue))) goto done;
if(jvalue != NULL && NCJsort(jvalue) != NCJ_NULL) {
int k;
if(NCJsort(jvalue) != NCJ_ARRAY) {stat = NC_EFILTER; goto done;}
for(k=0;;k++) {
jfilter = NULL;
jfilter = NCJith(jvalue,k);
if(jfilter == NULL) break; /* done */
if(NCJsort(jfilter) != NCJ_DICT) {stat = NC_EFILTER; goto done;}
if((stat = NCZ_filter_build(file,var,jfilter,chainindex++))) goto done;
}
}
#endif
}
/* compressor key */
/* From V2 Spec: A JSON object identifying the primary compression codec and providing
configuration parameters, or ``null`` if no compressor is to be used. */
#ifdef ENABLE_NCZARR_FILTERS
{
if(var->filters == NULL) var->filters = (void*)nclistnew();
if((stat = NCZ_filter_initialize())) goto done;
if((stat = NCJdictget(jvar,"compressor",&jfilter))) goto done;
if(jfilter != NULL && NCJsort(jfilter) != NCJ_NULL) {
if(NCJsort(jfilter) != NCJ_DICT) {stat = NC_EFILTER; goto done;}
if((stat = NCZ_filter_build(file,var,jfilter,chainindex++))) goto done;
}
}
/* Suppress variable if there are filters and var is not fixed-size */
if(varsized && nclistlength((NClist*)var->filters) > 0)
suppress = 1;
#endif
if(zarr_rank > 0) {
if((stat = computedimrefs(file, var, purezarr, xarray, rank, dimnames, shapes, var->dim)))
goto done;
if(!zvar->scalar) {
/* Extract the dimids */
for(j=0;j<rank;j++)
var->dimids[j] = var->dim[j]->hdr.id;
}
}
#ifdef ENABLE_NCZARR_FILTERS
if(!suppress) {
/* At this point, we can finalize the filters */
if((stat = NCZ_filter_setup(var))) goto done;
}
#endif
suppressvar:
if(suppress) {
/* Reclaim NCZarr variable specific info */
(void)NCZ_zclose_var1(var);
/* Remove from list of variables and reclaim the top level var object */
(void)nc4_var_list_del(grp, var);
var = NULL;
}
/* Clean up from last cycle */
nclistfreeall(dimnames); dimnames = NULL;
nullfree(varpath); varpath = NULL;
nullfree(shapes); shapes = NULL;
nullfree(key); key = NULL;
if(formatv1) {NCJreclaim(jncvar); jncvar = NULL;}
NCJreclaim(jvar); jvar = NULL;
var = NULL;
}
done:
return ZUNTRACE(THROW(stat));
}
/**
* @internal Materialize subgroups into memory
*
* @param file Pointer to file info struct.
* @param grp Pointer to grp info struct.
* @param subgrpnames List of names of subgroups in this group
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
define_subgrps(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, NClist* subgrpnames)
{
int i,stat = NC_NOERR;
ZTRACE(3,"file=%s grp=%s |subgrpnames|=%u",file->controller->path,grp->hdr.name,nclistlength(subgrpnames));
/* Load each subgroup name in turn */
for(i = 0; i < nclistlength(subgrpnames); i++) {
NC_GRP_INFO_T* g = NULL;
const char* gname = nclistget(subgrpnames,i);
char norm_name[NC_MAX_NAME];
/* Check and normalize the name. */
if((stat = nc4_check_name(gname, norm_name)))
goto done;
if((stat = nc4_grp_list_add(file, grp, norm_name, &g)))
goto done;
if(!(g->format_grp_info = calloc(1, sizeof(NCZ_GRP_INFO_T))))
{stat = NC_ENOMEM; goto done;}
((NCZ_GRP_INFO_T*)g->format_grp_info)->common.file = file;
}
/* Recurse to fill in subgroups */
for(i=0;i<ncindexsize(grp->children);i++) {
NC_GRP_INFO_T* g = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if((stat = define_grp(file,g)))
goto done;
}
done:
return ZUNTRACE(THROW(stat));
}
int
ncz_read_superblock(NC_FILE_INFO_T* file, char** nczarrvp, char** zarrfp)
{
int stat = NC_NOERR;
NCjson* jnczgroup = NULL;
NCjson* jzgroup = NULL;
NCjson* jsuper = NULL;
NCjson* jtmp = NULL;
char* nczarr_version = NULL;
char* zarr_format = NULL;
NCZ_FILE_INFO_T* zinfo = (NCZ_FILE_INFO_T*)file->format_file_info;
ZTRACE(3,"file=%s",file->controller->path);
/* See if the V1 META-Root is being used */
switch(stat = NCZ_downloadjson(zinfo->map, NCZMETAROOT, &jnczgroup)) {
case NC_EEMPTY: /* not there */
stat = NC_NOERR;
break;
case NC_NOERR:
if((stat = NCJdictget(jnczgroup,"nczarr_version",&jtmp))) goto done;
nczarr_version = strdup(NCJstring(jtmp));
break;
default: goto done;
}
/* Get Zarr Root Group, if any */
switch(stat = NCZ_downloadjson(zinfo->map, ZMETAROOT, &jzgroup)) {
case NC_NOERR:
break;
case NC_EEMPTY: /* not there */
stat = NC_NOERR;
assert(jzgroup == NULL);
break;
default: goto done;
}
if(jzgroup != NULL) {
/* See if this NCZarr V2 */
if((stat = NCJdictget(jzgroup,NCZ_V2_SUPERBLOCK,&jsuper))) goto done;
if(!stat && jsuper == NULL) { /* try uppercase name */
if((stat = NCJdictget(jzgroup,NCZ_V2_SUPERBLOCK_UC,&jsuper))) goto done;
}
if(jsuper != NULL) {
/* Extract the equivalent attribute */
if(jsuper->sort != NCJ_DICT)
{stat = NC_ENCZARR; goto done;}
if((stat = NCJdictget(jsuper,"version",&jtmp))) goto done;
nczarr_version = nulldup(NCJstring(jtmp));
}
/* In any case, extract the zarr format */
if((stat = NCJdictget(jzgroup,"zarr_format",&jtmp))) goto done;
assert(zarr_format == NULL);
zarr_format = nulldup(NCJstring(jtmp));
}
/* Set the format flags */
if(jnczgroup == NULL && jsuper == NULL) {
/* See if this is looks like a NCZarr/Zarr dataset at all
by looking for anything here of the form ".z*" */
if((stat = ncz_validate(file))) goto done;
/* ok, assume pure zarr with no groups */
zinfo->controls.flags |= FLAG_PUREZARR;
zinfo->controls.flags &= ~(FLAG_NCZARR_V1);
if(zarr_format == NULL) zarr_format = strdup("2");
} else if(jnczgroup != NULL) {
zinfo->controls.flags |= FLAG_NCZARR_V1;
/* Also means file is read only */
file->no_write = 1;
} else if(jsuper != NULL) {
/* ! FLAG_NCZARR_V1 && ! FLAG_PUREZARR */
}
if(nczarrvp) {*nczarrvp = nczarr_version; nczarr_version = NULL;}
if(zarrfp) {*zarrfp = zarr_format; zarr_format = NULL;}
done:
nullfree(zarr_format);
nullfree(nczarr_version);
NCJreclaim(jzgroup);
NCJreclaim(jnczgroup);
return ZUNTRACE(THROW(stat));
}
/**************************************************/
/* Utilities */
static int
parse_group_content(NCjson* jcontent, NClist* dimdefs, NClist* varnames, NClist* subgrps)
{
int i,stat = NC_NOERR;
NCjson* jvalue = NULL;
ZTRACE(3,"jcontent=|%s| |dimdefs|=%u |varnames|=%u |subgrps|=%u",NCJtotext(jcontent),(unsigned)nclistlength(dimdefs),(unsigned)nclistlength(varnames),(unsigned)nclistlength(subgrps));
if((stat=NCJdictget(jcontent,"dims",&jvalue))) goto done;
if(jvalue != NULL) {
if(NCJsort(jvalue) != NCJ_DICT) {stat = (THROW(NC_ENCZARR)); goto done;}
/* Extract the dimensions defined in this group */
for(i=0;i<NCJlength(jvalue);i+=2) {
NCjson* jname = NCJith(jvalue,i);
NCjson* jleninfo = NCJith(jvalue,i+1);
NCjson* jtmp = NULL;
const char* slen = "0";
const char* sunlim = "0";
char norm_name[NC_MAX_NAME + 1];
/* Verify name legality */
if((stat = nc4_check_name(NCJstring(jname), norm_name)))
{stat = NC_EBADNAME; goto done;}
/* check the length */
if(NCJsort(jleninfo) == NCJ_DICT) {
if((stat = NCJdictget(jleninfo,"size",&jtmp))) goto done;
if(jtmp== NULL)
{stat = NC_EBADNAME; goto done;}
slen = NCJstring(jtmp);
/* See if unlimited */
if((stat = NCJdictget(jleninfo,"unlimited",&jtmp))) goto done;
if(jtmp == NULL) sunlim = "0"; else sunlim = NCJstring(jtmp);
} else if(jleninfo != NULL && NCJsort(jleninfo) == NCJ_INT) {
slen = NCJstring(jleninfo);
} else
{stat = NC_ENCZARR; goto done;}
nclistpush(dimdefs,strdup(norm_name));
nclistpush(dimdefs,strdup(slen));
nclistpush(dimdefs,strdup(sunlim));
}
}
if((stat=NCJdictget(jcontent,"vars",&jvalue))) goto done;
if(jvalue != NULL) {
/* Extract the variable names in this group */
for(i=0;i<NCJlength(jvalue);i++) {
NCjson* jname = NCJith(jvalue,i);
char norm_name[NC_MAX_NAME + 1];
/* Verify name legality */
if((stat = nc4_check_name(NCJstring(jname), norm_name)))
{stat = NC_EBADNAME; goto done;}
nclistpush(varnames,strdup(norm_name));
}
}
if((stat=NCJdictget(jcontent,"groups",&jvalue))) goto done;
if(jvalue != NULL) {
/* Extract the subgroup names in this group */
for(i=0;i<NCJlength(jvalue);i++) {
NCjson* jname = NCJith(jvalue,i);
char norm_name[NC_MAX_NAME + 1];
/* Verify name legality */
if((stat = nc4_check_name(NCJstring(jname), norm_name)))
{stat = NC_EBADNAME; goto done;}
nclistpush(subgrps,strdup(norm_name));
}
}
done:
return ZUNTRACE(THROW(stat));
}
static int
parse_group_content_pure(NCZ_FILE_INFO_T* zinfo, NC_GRP_INFO_T* grp, NClist* varnames, NClist* subgrps)
{
int stat = NC_NOERR;
ZTRACE(3,"zinfo=%s grp=%s |varnames|=%u |subgrps|=%u",zinfo->common.file->controller->path,grp->hdr.name,(unsigned)nclistlength(varnames),(unsigned)nclistlength(subgrps));
nclistclear(varnames);
if((stat = searchvars(zinfo,grp,varnames))) goto done;
nclistclear(subgrps);
if((stat = searchsubgrps(zinfo,grp,subgrps))) goto done;
done:
return ZUNTRACE(THROW(stat));
}
#if 0
static int
parse_var_dims_pure(NCZ_FILE_INFO_T* zinfo, NC_GRP_INFO_T* grp, NC_VAR_INFO_T* var, size64_t* shapes)
{
int stat = NC_NOERR;
char* varkey = NULL;
char* zakey = NULL;
NCjson* jvar = NULL;
NCjson* jvalue = NULL;
/* Construct var path */
if((stat = NCZ_varkey(var,&varkey))) goto done;
/* Construct .zarray path */
if((stat = nczm_concat(varkey,ZARRAY,&zakey))) goto done;
/* Download the zarray object */
if((stat=NCZ_readdict(zinfo->map,zakey,&jvar)))
goto done;
assert((NCJsort(jvar) == NCJ_DICT));
nullfree(varkey); varkey = NULL;
nullfree(zakey); zakey = NULL;
/* Extract the shape */
if((stat=NCJdictget(jvar,"shape",&jvalue))) goto done;
if((stat = decodeints(jvalue, shapes))) goto done;
done:
NCJreclaim(jvar);
NCJreclaim(jvalue);
nullfree(varkey); varkey = NULL;
nullfree(zakey); zakey = NULL;
return ZUNTRACE(THROW(stat));
}
#endif
static int
searchvars(NCZ_FILE_INFO_T* zfile, NC_GRP_INFO_T* grp, NClist* varnames)
{
int i,stat = NC_NOERR;
char* grpkey = NULL;
char* varkey = NULL;
char* zarray = NULL;
NClist* matches = nclistnew();
/* Compute the key for the grp */
if((stat = NCZ_grpkey(grp,&grpkey))) goto done;
/* Get the map and search group */
if((stat = nczmap_search(zfile->map,grpkey,matches))) goto done;
for(i=0;i<nclistlength(matches);i++) {
const char* name = nclistget(matches,i);
if(name[0] == NCZM_DOT) continue; /* zarr/nczarr specific */
/* See if name/.zarray exists */
if((stat = nczm_concat(grpkey,name,&varkey))) goto done;
if((stat = nczm_concat(varkey,ZARRAY,&zarray))) goto done;
if((stat = nczmap_exists(zfile->map,zarray)) == NC_NOERR)
nclistpush(varnames,strdup(name));
stat = NC_NOERR;
nullfree(varkey); varkey = NULL;
nullfree(zarray); zarray = NULL;
}
done:
nullfree(grpkey);
nullfree(varkey);
nullfree(zarray);
nclistfreeall(matches);
return stat;
}
static int
searchsubgrps(NCZ_FILE_INFO_T* zfile, NC_GRP_INFO_T* grp, NClist* subgrpnames)
{
int i,stat = NC_NOERR;
char* grpkey = NULL;
char* subkey = NULL;
char* zgroup = NULL;
NClist* matches = nclistnew();
/* Compute the key for the grp */
if((stat = NCZ_grpkey(grp,&grpkey))) goto done;
/* Get the map and search group */
if((stat = nczmap_search(zfile->map,grpkey,matches))) goto done;
for(i=0;i<nclistlength(matches);i++) {
const char* name = nclistget(matches,i);
if(name[0] == NCZM_DOT) continue; /* zarr/nczarr specific */
/* See if name/.zgroup exists */
if((stat = nczm_concat(grpkey,name,&subkey))) goto done;
if((stat = nczm_concat(subkey,ZGROUP,&zgroup))) goto done;
if((stat = nczmap_exists(zfile->map,zgroup)) == NC_NOERR)
nclistpush(subgrpnames,strdup(name));
stat = NC_NOERR;
nullfree(subkey); subkey = NULL;
nullfree(zgroup); zgroup = NULL;
}
done:
nullfree(grpkey);
nullfree(subkey);
nullfree(zgroup);
nclistfreeall(matches);
return stat;
}
/* Convert a list of integer strings to 64 bit dimension sizes (shapes) */
static int
decodeints(NCjson* jshape, size64_t* shapes)
{
int i, stat = NC_NOERR;
for(i=0;i<NCJlength(jshape);i++) {
struct ZCVT zcvt;
nc_type typeid = NC_NAT;
NCjson* jv = NCJith(jshape,i);
if((stat = NCZ_json2cvt(jv,&zcvt,&typeid))) goto done;
switch (typeid) {
case NC_INT64:
if(zcvt.int64v < 0) {stat = (THROW(NC_ENCZARR)); goto done;}
shapes[i] = (size64_t)zcvt.int64v;
break;
case NC_UINT64:
shapes[i] = (size64_t)zcvt.uint64v;
break;
default: {stat = (THROW(NC_ENCZARR)); goto done;}
}
}
done:
return THROW(stat);
}
/* This code is a subset of NCZ_def_dim */
static int
createdim(NC_FILE_INFO_T* file, const char* name, size64_t dimlen, NC_DIM_INFO_T** dimp)
{
int stat = NC_NOERR;
NC_GRP_INFO_T* root = file->root_grp;
NC_DIM_INFO_T* thed = NULL;
if((stat = nc4_dim_list_add(root, name, (size_t)dimlen, -1, &thed)))
goto done;
assert(thed != NULL);
/* Create struct for NCZ-specific dim info. */
if (!(thed->format_dim_info = calloc(1, sizeof(NCZ_DIM_INFO_T))))
{stat = NC_ENOMEM; goto done;}
((NCZ_DIM_INFO_T*)thed->format_dim_info)->common.file = file;
*dimp = thed; thed = NULL;
done:
return stat;
}
/*
Given a list of segments, find corresponding group.
*/
static int
locategroup(NC_FILE_INFO_T* file, size_t nsegs, NClist* segments, NC_GRP_INFO_T** grpp)
{
int i, j, found, stat = NC_NOERR;
NC_GRP_INFO_T* grp = NULL;
grp = file->root_grp;
for(i=0;i<nsegs;i++) {
const char* segment = nclistget(segments,i);
char norm_name[NC_MAX_NAME];
found = 0;
if((stat = nc4_check_name(segment,norm_name))) goto done;
for(j=0;j<ncindexsize(grp->children);j++) {
NC_GRP_INFO_T* subgrp = (NC_GRP_INFO_T*)ncindexith(grp->children,j);
if(strcmp(subgrp->hdr.name,norm_name)==0) {
grp = subgrp;
found = 1;
break;
}
}
if(!found) {stat = NC_ENOGRP; goto done;}
}
/* grp should be group of interest */
if(grpp) *grpp = grp;
done:
return THROW(stat);
}
static int
parsedimrefs(NC_FILE_INFO_T* file, NClist* dimnames, size64_t* shape, NC_DIM_INFO_T** dims, int create)
{
int i, stat = NC_NOERR;
NClist* segments = NULL;
for(i=0;i<nclistlength(dimnames);i++) {
NC_GRP_INFO_T* g = NULL;
NC_DIM_INFO_T* d = NULL;
int j;
const char* dimpath = nclistget(dimnames,i);
const char* dimname = NULL;
/* Locate the corresponding NC_DIM_INFO_T* object */
nclistfreeall(segments);
segments = nclistnew();
if((stat = ncz_splitkey(dimpath,segments)))
goto done;
if((stat=locategroup(file,nclistlength(segments)-1,segments,&g)))
goto done;
/* Lookup the dimension */
dimname = nclistget(segments,nclistlength(segments)-1);
d = NULL;
dims[i] = NULL;
for(j=0;j<ncindexsize(g->dim);j++) {
d = (NC_DIM_INFO_T*)ncindexith(g->dim,j);
if(strcmp(d->hdr.name,dimname)==0) {
dims[i] = d;
break;
}
}
if(dims[i] == NULL && create) {
/* If not found and create then create it */
if((stat = createdim(file, dimname, shape[i], &dims[i])))
goto done;
} else {
/* Verify consistency */
if(dims[i]->len != shape[i])
{stat = NC_EDIMSIZE; goto done;}
}
assert(dims[i] != NULL);
}
done:
nclistfreeall(segments);
return THROW(stat);
}
/**
* @internal Get the metadata for a variable.
*
* @param var Pointer to var info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EVARMETA Error with var metadata.
* @author Ed Hartnett
*/
int
ncz_get_var_meta(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var)
{
int retval = NC_NOERR;
assert(file && var && var->format_var_info);
LOG((3, "%s: var %s", __func__, var->hdr.name));
ZTRACE(3,"file=%s var=%s",file->controller->path,var->hdr.name);
/* Have we already read the var metadata? */
if (var->meta_read)
goto done;
#ifdef LOOK
/* Get the current chunk cache settings. */
if ((access_pid = H5Dget_access_plist(hdf5_var->hdf_datasetid)) < 0)
BAIL(NC_EVARMETA);
/* Learn about current chunk cache settings. */
if ((H5Pget_chunk_cache(access_pid, &(var->chunk_cache_nelems),
&(var->chunk_cache_size), &rdcc_w0)) < 0)
BAIL(NC_EHDFERR);
var->chunk_cache_preemption = rdcc_w0;
/* Get the dataset creation properties. */
if ((propid = H5Dget_create_plist(hdf5_var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
/* Get var chunking info. */
if ((retval = get_chunking_info(propid, var)))
BAIL(retval);
/* Get filter info for a var. */
if ((retval = get_filter_info(propid, var)))
BAIL(retval);
/* Get fill value, if defined. */
if ((retval = get_fill_info(propid, var)))
BAIL(retval);
/* Is this a deflated variable with a chunksize greater than the
* current cache size? */
if ((retval = nc4_adjust_var_cache(var)))
BAIL(retval);
/* Is there an attribute which means quantization was used? */
if ((retval = get_quantize_info(var)))
BAIL(retval);
if (var->coords_read && !var->dimscale)
if ((retval = get_attached_info(var, hdf5_var, var->ndims, hdf5_var->hdf_datasetid)))
goto done;;
#endif
/* Remember that we have read the metadata for this var. */
var->meta_read = NC_TRUE;
done:
return ZUNTRACE(retval);
}
#if 0
int
ncz_create_superblock(NCZ_FILE_INFO_T* zinfo)
{
int stat = NC_NOERR;
NCjson* json = NULL;
NCZMAP* map = NULL;
char version[1024];
ZTRACE(4,"zinfo=%s",zinfo->common.file->controller->path);
/* If V2, then do not create a superblock per-se */
if(!(zinfo->controls.flags & FLAG_NCZARR_V1)) goto done;
map = zinfo->map;
/* create superblock json */
if((stat = NCJnew(NCJ_DICT,&json)))
goto done;
/* fill */
snprintf(version,sizeof(version),"%d",zinfo->zarr.zarr_version);
if((stat = NCJaddstring(json,NCJ_STRING,"zarr_format"))) goto done;
if((stat = NCJaddstring(json,NCJ_INT,version))) goto done;
if((stat = NCJaddstring(json,NCJ_STRING,NCZ_V2_VERSION))) goto done;
{
char ver[1024];
snprintf(ver,sizeof(ver),"%lu.%lu.%lu",
zinfo->zarr.nczarr_version.major,
zinfo->zarr.nczarr_version.minor,
zinfo->zarr.nczarr_version.release);
if((stat = NCJaddstring(json,NCJ_STRING,ver))) goto done;
}
/* Write back to map */
if((stat=NCZ_uploadjson(map,NCZMETAROOT,json)))
goto done;
done:
NCJreclaim(json);
return ZUNTRACE(stat);
}
#endif
/* Compute the set of dim refs for this variable, taking purezarr and xarray into account */
static int
computedimrefs(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int purezarr, int xarray, int ndims, NClist* dimnames, size64_t* shapes, NC_DIM_INFO_T** dims)
{
int stat = NC_NOERR;
int i;
int createdims = 0; /* 1 => we need to create the dims in root if they do not already exist */
NCZ_FILE_INFO_T* zfile = (NCZ_FILE_INFO_T*)file->format_file_info;
NCZ_VAR_INFO_T* zvar = (NCZ_VAR_INFO_T*)(var->format_var_info);
NCjson* jatts = NULL;
ZTRACE(3,"file=%s var=%s purezarr=%d xarray=%d ndims=%d shape=%s",
file->controller->path,var->hdr.name,purezarr,xarray,(int)ndims,nczprint_vector(ndims,shapes));
assert(zfile && zvar);
if(purezarr && xarray) {/* Read in the attributes to get xarray dimdef attribute; Note that it might not exist */
/* Note that if xarray && !purezarr, then xarray will be superceded by the nczarr dimensions key */
char zdimname[4096];
if(zvar->xarray == NULL) {
assert(nclistlength(dimnames) == 0);
if((stat = ncz_read_atts(file,(NC_OBJ*)var))) goto done;
}
if(zvar->xarray != NULL) {
/* convert xarray to the dimnames */
for(i=0;i<nclistlength(zvar->xarray);i++) {
snprintf(zdimname,sizeof(zdimname),"/%s",(const char*)nclistget(zvar->xarray,i));
nclistpush(dimnames,strdup(zdimname));
}
}
createdims = 1; /* may need to create them */
}
/* If pure zarr and we have no dimref names, then fake it */
if(purezarr && nclistlength(dimnames) == 0) {
createdims = 1;
for(i=0;i<ndims;i++) {
/* Compute the set of absolute paths to dimrefs */
char zdimname[4096];
snprintf(zdimname,sizeof(zdimname),"/%s_%llu",ZDIMANON,shapes[i]);
nclistpush(dimnames,strdup(zdimname));
}
}
/* Now, use dimnames to get the dims; create if necessary */
if((stat = parsedimrefs(file,dimnames,shapes,dims,createdims)))
goto done;
done:
NCJreclaim(jatts);
return ZUNTRACE(THROW(stat));
}
/**
Implement the JSON convention:
Stringify it as the value and make the attribute be of type "char".
*/
static int
json_convention_read(NCjson* json, NCjson** jtextp)
{
int stat = NC_NOERR;
NCjson* jtext = NULL;
char* text = NULL;
if(json == NULL) {stat = NC_EINVAL; goto done;}
if(NCJunparse(json,0,&text)) {stat = NC_EINVAL; goto done;}
if(NCJnewstring(NCJ_STRING,text,&jtext)) {stat = NC_EINVAL; goto done;}
*jtextp = jtext; jtext = NULL;
done:
NCJreclaim(jtext);
nullfree(text);
return stat;
}
#if 0
/**
Implement the JSON convention:
Parse it as JSON and use that as its value in .zattrs.
*/
static int
json_convention_write(size_t len, const void* data, NCjson** jsonp, int* isjsonp)
{
int stat = NC_NOERR;
NCjson* jexpr = NULL;
int isjson = 0;
assert(jsonp != NULL);
if(NCJparsen(len,(char*)data,0,&jexpr)) {
/* Ok, just treat as sequence of chars */
if((stat = NCJnewstringn(NCJ_STRING, len, data, &jexpr))) goto done;
}
isjson = 1;
*jsonp = jexpr; jexpr = NULL;
if(isjsonp) *isjsonp = isjson;
done:
NCJreclaim(jexpr);
return stat;
}
#endif
/* Convert an attribute "types list to an envv style list */
static int
jtypes2atypes(NCjson* jtypes, NClist* atypes)
{
int i, stat = NC_NOERR;
for(i=0;i<NCJlength(jtypes);i+=2) {
const NCjson* key = NCJith(jtypes,i);
const NCjson* value = NCJith(jtypes,i+1);
if(NCJsort(key) != NCJ_STRING) {stat = (THROW(NC_ENCZARR)); goto done;}
if(NCJsort(value) != NCJ_STRING) {stat = (THROW(NC_ENCZARR)); goto done;}
nclistpush(atypes,strdup(NCJstring(key)));
nclistpush(atypes,strdup(NCJstring(value)));
}
done:
return stat;
}
/* See if there is reason to believe the specified path is a legitimate (NC)Zarr file
* Do a breadth first walk of the tree starting at file path.
* @param file to validate
* @return NC_NOERR if it looks ok
* @return NC_ENOTNC if it does not look ok
*/
static int
ncz_validate(NC_FILE_INFO_T* file)
{
int stat = NC_NOERR;
NCZ_FILE_INFO_T* zinfo = (NCZ_FILE_INFO_T*)file->format_file_info;
int validate = 0;
NCbytes* prefix = ncbytesnew();
NClist* queue = nclistnew();
NClist* nextlevel = nclistnew();
NCZMAP* map = zinfo->map;
char* path = NULL;
char* segment = NULL;
size_t seglen;
ZTRACE(3,"file=%s",file->controller->path);
path = strdup("/");
nclistpush(queue,path);
path = NULL;
do {
nullfree(path); path = NULL;
/* This should be full path key */
path = nclistremove(queue,0); /* remove from front of queue */
/* get list of next level segments (partial keys) */
assert(nclistlength(nextlevel)==0);
if((stat=nczmap_search(map,path,nextlevel))) {validate = 0; goto done;}
/* For each s in next level, test, convert to full path, and push onto queue */
while(nclistlength(nextlevel) > 0) {
segment = nclistremove(nextlevel,0);
seglen = nulllen(segment);
if((seglen >= 2 && memcmp(segment,".z",2)==0) || (seglen >= 4 && memcmp(segment,".ncz",4)==0)) {
validate = 1;
goto done;
}
/* Convert to full path */
ncbytesclear(prefix);
ncbytescat(prefix,path);
if(strlen(path) > 1) ncbytescat(prefix,"/");
ncbytescat(prefix,segment);
/* push onto queue */
nclistpush(queue,ncbytesextract(prefix));
nullfree(segment); segment = NULL;
}
} while(nclistlength(queue) > 0);
done:
if(!validate) stat = NC_ENOTNC;
nullfree(path);
nullfree(segment);
nclistfreeall(queue);
nclistfreeall(nextlevel);
ncbytesfree(prefix);
return ZUNTRACE(THROW(stat));
}
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