mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-27 08:49:16 +08:00
59e04ae071
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.
473 lines
11 KiB
C
473 lines
11 KiB
C
/*
|
|
* Copyright 2018, University Corporation for Atmospheric Research
|
|
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
|
|
*/
|
|
|
|
#include "ut_includes.h"
|
|
|
|
#define OPEN "[{("
|
|
#define CLOSE "]})"
|
|
|
|
#define LPAREN '('
|
|
#define RPAREN ')'
|
|
#define BLANK ' '
|
|
|
|
NCbytes* buf = NULL;
|
|
|
|
static Dimdef* finddim(const char* name, NClist* defs);
|
|
|
|
#if 0
|
|
static void
|
|
ranktest(int rank, char c, int count)
|
|
{
|
|
if(rank != count) {
|
|
fprintf(stderr,"Option '%c': rank mismatch: rank=%d count=%d\n",
|
|
c,rank,count);
|
|
exit(1);
|
|
}
|
|
}
|
|
#endif
|
|
|
|
int
|
|
parseslices(const char* s0, int* nslicesp, NCZSlice* slices)
|
|
{
|
|
int count,nchars,nslices,i;
|
|
const char* s = NULL;
|
|
unsigned long start,stop,stride;
|
|
|
|
/* First, compute number of slices */
|
|
for(s=s0,nslices=0;*s;s++) {
|
|
if(*s == '[') nslices++;
|
|
}
|
|
|
|
if(nslices > NC_MAX_VAR_DIMS) return NC_EINVAL; /* too many */
|
|
if(nslicesp) *nslicesp = nslices;
|
|
|
|
/* Extract the slices */
|
|
for(i=0,s=s0;*s;s+=nchars,i++) {
|
|
NCZSlice* sl = &slices[i];
|
|
/* Try 3-element slice first */
|
|
stride = 1; /* default */
|
|
nchars = -1;
|
|
count = sscanf(s,"[%lu:%lu]%n",&start,&stop,&nchars);
|
|
if(nchars == -1) {
|
|
nchars = -1;
|
|
count = sscanf(s,"[%lu:%lu:%lu]%n",&start,&stop,&stride,&nchars);
|
|
if(count != 3) return NC_EINVAL;
|
|
}
|
|
sl->start = start;
|
|
sl->stop = stop;
|
|
sl->stride = stride;
|
|
}
|
|
return NC_NOERR;
|
|
}
|
|
|
|
int
|
|
parsedimdef(const char* s0, Dimdef** defp)
|
|
{
|
|
int nchars;
|
|
const char* s = NULL;
|
|
Dimdef* def = NULL;
|
|
unsigned l;
|
|
const char* p;
|
|
ptrdiff_t count;
|
|
|
|
if((def = calloc(1,sizeof(struct Dimdef)))==NULL)
|
|
return NC_ENOMEM;
|
|
|
|
/* Extract */
|
|
s = s0;
|
|
if((p = strchr(s,'=')) == NULL) abort();
|
|
if((count = (p - s)) == 0) return NC_EINVAL;
|
|
def->name = malloc(count+1);
|
|
memcpy(def->name,s,count);
|
|
def->name[count] = '\0';
|
|
s = p+1;
|
|
sscanf(s,"%u%n",&l,&nchars);
|
|
if(nchars == -1) return NC_EINVAL;
|
|
def->size = (size_t)l;
|
|
s += nchars;
|
|
if(*s != '\0') return NC_EINVAL;
|
|
if(defp) *defp = def;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
int
|
|
parsevardef(const char* s0, NClist* dimdefs, Vardef** varp)
|
|
{
|
|
int count;
|
|
const char* s = NULL;
|
|
Vardef* vd = NULL;
|
|
const char* p;
|
|
ptrdiff_t len;
|
|
char name[NC_MAX_NAME];
|
|
|
|
if((vd = calloc(1,sizeof(Vardef)))==NULL)
|
|
return NC_ENOMEM;
|
|
|
|
s=s0;
|
|
|
|
/* Scan for the end of type name */
|
|
p = strchr(s,BLANK);
|
|
if(p == NULL) return NC_EINVAL;
|
|
len = (p - s);
|
|
if(len == 0) return NC_EINVAL;
|
|
memcpy(name,s,len);
|
|
name[len] = '\0';
|
|
vd->typeid = ut_typeforname(name);
|
|
vd->typesize = ut_typesize(vd->typeid);
|
|
while(*p == BLANK) p++;
|
|
s = p;
|
|
|
|
/* Scan for the end of var name */
|
|
p = strchr(s,LPAREN);
|
|
if(p == NULL) return NC_EINVAL;
|
|
len = (p - s);
|
|
if(len == 0) return NC_EINVAL;
|
|
memcpy(name,s,len);
|
|
name[len] = '\0';
|
|
vd->name = strdup(name);
|
|
/* parse a vector of dimnames and chunksizes and convert */
|
|
s = p;
|
|
if(*s == LPAREN) {
|
|
char** names = NULL;
|
|
char* p;
|
|
s++;
|
|
count = parsestringvector(s,RPAREN,&names);
|
|
if(count >= NC_MAX_VAR_DIMS) return NC_EINVAL;
|
|
vd->rank = count;
|
|
if(vd->rank > 0) {
|
|
int j;
|
|
for(j=0;j<vd->rank;j++) {
|
|
Dimdef* dimref = NULL;
|
|
/* Split on / to get chunksize */
|
|
p = strchr(names[j],'/');
|
|
if(p) *p++ = '\0';
|
|
if((dimref = finddim(names[j],dimdefs)) == NULL)
|
|
return NC_EINVAL;
|
|
vd->dimrefs[j] = dimref;
|
|
vd->dimsizes[j] = dimref->size;
|
|
if(p == NULL)
|
|
vd->chunksizes[j] = dimref->size;
|
|
else {
|
|
unsigned long l;
|
|
sscanf(p,"%lu",&l);
|
|
vd->chunksizes[j] = (size_t)l;
|
|
}
|
|
}
|
|
/* Skip past the trailing rparen */
|
|
if((p = strchr(s,RPAREN)) == NULL) abort();
|
|
p++;
|
|
}
|
|
freestringvec(names);
|
|
}
|
|
if(varp) *varp = vd;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
int
|
|
parsestringvector(const char* s0, int stopchar, char*** namesp)
|
|
{
|
|
int nelems,i;
|
|
const char* s;
|
|
char** names = NULL;
|
|
|
|
/* First, compute number of elements */
|
|
for(s=s0,nelems=1;*s;s++) {if(*s == ',') nelems++; if(*s == stopchar) break;}
|
|
if(nelems == 0) return NC_EINVAL;
|
|
names = calloc(nelems+1,sizeof(char*));
|
|
for(s=s0,i=0;i<nelems;i++) {
|
|
ptrdiff_t len;
|
|
const char* p = strchr(s,',');
|
|
if(p == NULL) p = strchr(s,stopchar);
|
|
if(p == NULL) p = s + strlen(s);
|
|
if(names[i] == NULL) {
|
|
char* q;
|
|
len = (p - s);
|
|
q = malloc(1+len);
|
|
memcpy(q,s,len);
|
|
q[len] = '\0';
|
|
names[i] = q;
|
|
}
|
|
if(*p == '\0' || *p == stopchar) s = p; else s = p+1;
|
|
}
|
|
names[nelems] = NULL;
|
|
if(namesp) *namesp = names;
|
|
return nelems;
|
|
}
|
|
|
|
int
|
|
parseintvector(const char* s0, int typelen, void** vectorp)
|
|
{
|
|
int count,nchars,nelems,index;
|
|
const char* s = NULL;
|
|
void* vector = NULL;
|
|
|
|
/* First, compute number of elements */
|
|
for(s=s0,nelems=1;*s;s++) {
|
|
if(*s == ',') nelems++;
|
|
}
|
|
|
|
vector = calloc(nelems,typelen);
|
|
|
|
/* Extract the elements of the vector */
|
|
/* Skip any leading bracketchar */
|
|
s=s0;
|
|
if(strchr(OPEN,*s0) != NULL) s++;
|
|
for(index=0;*s;index++) {
|
|
long long elem;
|
|
nchars = -1;
|
|
count = sscanf(s,"%lld%n",&elem,&nchars);
|
|
if(nchars == -1 || count != 1) return NC_EINVAL;
|
|
s += nchars;
|
|
if(*s == ',') s++;
|
|
switch (typelen) {
|
|
case 1: ((char*)vector)[index] = (char)elem; break;
|
|
case 2: ((short*)vector)[index] = (short)elem; break;
|
|
case 4: ((int*)vector)[index] = (int)elem; break;
|
|
case 8: ((long long*)vector)[index] = (long long)elem; break;
|
|
default: abort();
|
|
}
|
|
}
|
|
assert(nelems == index);
|
|
if(vectorp) *vectorp = vector;
|
|
return nelems;
|
|
}
|
|
|
|
void
|
|
freedimdefs(NClist* defs)
|
|
{
|
|
int i;
|
|
for(i=0;i<nclistlength(defs);i++) {
|
|
Dimdef* dd = nclistget(defs,i);
|
|
nullfree(dd->name);
|
|
nullfree(dd);
|
|
}
|
|
}
|
|
|
|
void
|
|
freevardefs(NClist* defs)
|
|
{
|
|
int i;
|
|
for(i=0;i<nclistlength(defs);i++) {
|
|
Vardef* vd = nclistget(defs,i);
|
|
nullfree(vd->name);
|
|
nullfree(vd);
|
|
}
|
|
}
|
|
|
|
void
|
|
freeranges(NCZChunkRange* ranges)
|
|
{
|
|
}
|
|
|
|
void
|
|
freeslices(NCZSlice* slices)
|
|
{
|
|
}
|
|
|
|
void
|
|
freestringvec(char** vec)
|
|
{
|
|
if(vec != NULL) {
|
|
char** p;
|
|
for(p=vec;*p;p++) free(*p);
|
|
}
|
|
nullfree(vec);
|
|
}
|
|
|
|
void
|
|
freeprojvector(int rank, NCZProjection** vec)
|
|
{
|
|
if(vec != NULL) {
|
|
int r;
|
|
for(r=0;r<rank;r++) free(vec[r]);
|
|
}
|
|
nullfree(vec);
|
|
}
|
|
|
|
/**************************************************/
|
|
|
|
#if 0
|
|
char*
|
|
printvec(int len, size64_t* vec)
|
|
{
|
|
char* result = NULL;
|
|
int i;
|
|
char value[128];
|
|
NCbytes* buf = ncbytesnew();
|
|
|
|
ncbytescat(buf,"(");
|
|
for(i=0;i<len;i++) {
|
|
if(i > 0) ncbytescat(buf,",");
|
|
snprintf(value,sizeof(value),"%lu",(unsigned long)vec[i]);
|
|
ncbytescat(buf,value);
|
|
}
|
|
ncbytescat(buf,")");
|
|
result = ncbytesextract(buf);
|
|
ncbytesfree(buf);
|
|
return result;
|
|
}
|
|
#endif /*0*/
|
|
|
|
/**************************************************/
|
|
int
|
|
ut_typesize(nc_type t)
|
|
{
|
|
switch (t) {
|
|
case NC_BYTE: case NC_UBYTE: return 1;
|
|
case NC_SHORT: case NC_USHORT: return 2;
|
|
case NC_INT: case NC_UINT: return 4;
|
|
case NC_INT64: case NC_UINT64: return 8;
|
|
case NC_FLOAT: return 4;
|
|
case NC_DOUBLE: return 8;
|
|
default: usage(NC_EINVAL);
|
|
}
|
|
return 0;
|
|
}
|
|
|
|
nc_type
|
|
ut_typeforname(const char* tname)
|
|
{
|
|
if(strcasecmp("byte",tname)==0) return NC_BYTE;
|
|
if(strcasecmp("ubyte",tname)==0) return NC_UBYTE;
|
|
if(strcasecmp("short",tname)==0) return NC_SHORT;
|
|
if(strcasecmp("ushort",tname)==0) return NC_USHORT;
|
|
if(strcasecmp("int",tname)==0) return NC_INT;
|
|
if(strcasecmp("uint",tname)==0) return NC_UINT;
|
|
if(strcasecmp("int64",tname)==0) return NC_INT64;
|
|
if(strcasecmp("uint64",tname)==0) return NC_UINT64;
|
|
if(strcasecmp("float",tname)==0) return NC_FLOAT;
|
|
if(strcasecmp("double",tname)==0) return NC_DOUBLE;
|
|
usage(NC_EINVAL);
|
|
return NC_NAT;
|
|
}
|
|
|
|
static Dimdef*
|
|
finddim(const char* name, NClist* defs)
|
|
{
|
|
int i;
|
|
for(i=0;i<nclistlength(defs);i++) {
|
|
Dimdef* dd = nclistget(defs,i);
|
|
if(strcmp(dd->name,name) == 0)
|
|
return dd;
|
|
}
|
|
return NULL;
|
|
}
|
|
|
|
NCZM_IMPL
|
|
kind2impl(const char* kind)
|
|
{
|
|
if(strcasecmp("s3",kind)==0) return NCZM_S3;
|
|
else if(strcasecmp("nz4",kind)==0) return NCZM_NC4;
|
|
else if(strcasecmp("nzf",kind)==0) return NCZM_FILE;
|
|
else return NCZM_UNDEF;
|
|
}
|
|
|
|
const char*
|
|
impl2kind(NCZM_IMPL impl)
|
|
{
|
|
switch (impl) {
|
|
case NCZM_S3: return "s3";
|
|
case NCZM_NC4: return "nz4";
|
|
case NCZM_FILE: return "nzf";
|
|
case NCZM_UNDEF: break;
|
|
}
|
|
return NULL;
|
|
}
|
|
|
|
/* Goal: Given a set of per-dimension indices,
|
|
compute the corresponding linear position.
|
|
*/
|
|
size64_t
|
|
computelinearoffset(int R, const size64_t* indices, const size64_t* max, size64_t* productp)
|
|
{
|
|
size64_t offset, product;
|
|
int i;
|
|
|
|
offset = 0; product = 1;
|
|
for(i=0;i<R;i++) {
|
|
offset *= max[i];
|
|
offset += indices[i];
|
|
product *= max[i];
|
|
}
|
|
if(productp) *productp = product;
|
|
return offset;
|
|
}
|
|
|
|
void
|
|
slices2vector(int rank, NCZSlice* slices, size64_t** startp, size64_t** stopp, size64_t** stridep, size64_t** maxp)
|
|
{
|
|
static size64_t start[NC_MAX_VAR_DIMS];
|
|
static size64_t stop[NC_MAX_VAR_DIMS];
|
|
static size64_t stride[NC_MAX_VAR_DIMS];
|
|
static size64_t max[NC_MAX_VAR_DIMS];
|
|
int i;
|
|
for(i=0;i<rank;i++) {
|
|
start[i] = slices[i].start;
|
|
stop[i] = slices[i].stop;
|
|
stride[i] = slices[i].stride;
|
|
max[i] = slices[i].len;
|
|
}
|
|
if(startp) *startp = start;
|
|
if(stopp) *stopp = stop;
|
|
if(stridep) *stridep = stride;
|
|
if(maxp) *maxp = max;
|
|
}
|
|
|
|
void
|
|
printoptions(struct Options* opts)
|
|
{
|
|
char** p;
|
|
int i;
|
|
printf("Options:");
|
|
#if 0
|
|
printf(" debug=%d",opts->debug);
|
|
printf(" file=|%s|",opts->file);
|
|
printf(" output=|%s|",opts->output);
|
|
#endif
|
|
if(opts->kind)
|
|
printf(" kind=%s",opts->kind);
|
|
if(opts->cmds) {
|
|
printf(" cmds=");
|
|
for(i=0,p=opts->cmds;*p;p++,i++)
|
|
printf("%s%s",(i==0?"(":","),*p);
|
|
printf(")");
|
|
}
|
|
|
|
for(i=0;i<nclistlength(opts->dimdefs);i++) {
|
|
struct Dimdef* dd = (struct Dimdef*)nclistget(opts->dimdefs,i);
|
|
printf(" -d%s=%llu",dd->name,dd->size);
|
|
}
|
|
|
|
for(i=0;i<nclistlength(opts->vardefs);i++) {
|
|
int j;
|
|
struct Vardef* vd = (struct Vardef*)nclistget(opts->vardefs,i);
|
|
printf(" -v '%d %s[",vd->typeid,vd->name);
|
|
for(j=0;j<vd->rank;j++) {
|
|
Dimdef* vdd = vd->dimrefs[j];
|
|
if(j > 0) printf(",");
|
|
printf("%s/%llu",vdd->name,vd->chunksizes[j]);
|
|
}
|
|
printf("]'");
|
|
}
|
|
|
|
printf(" -s ");
|
|
for(i=0;i<opts->nslices;i++) {
|
|
NCZSlice* sl = &opts->slices[i];
|
|
printf("%s",nczprint_slicex(*sl,1));
|
|
}
|
|
printf("\n");
|
|
}
|
|
|
|
int
|
|
hasdriveletter(const char* f)
|
|
{
|
|
if(f == NULL || *f == '\0' || strlen(f) < 3) return 0;
|
|
if(f[1] != ':') return 0;
|
|
if(f[2] != '/' && f[2] != '\\') return 0;
|
|
if((f[0] < 'z' && f[0] >= 'a') || (f[0] < 'Z' && f[0] >= 'A'))
|
|
return 1;
|
|
return 0;
|
|
}
|