netcdf-c/libnczarr/zmap.c
Dennis Heimbigner 74b40fd788 Upgrade the nczarr code to match Zarr V2
Re: https://github.com/zarr-developers/zarr-python/pull/716

The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}.  So now it
is possible to use a key like "0/1/2/0" for chunk names.

This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.

Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.

In addition the following unrelated changes were made.

1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
   is not found then the other options that depend upon it properly
   are disabled.
1. I decided that xarray support should be enabled by default for pure
   zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
   to work when testing in parallel, some inter-test dependencies needed to
   be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-24 19:48:15 -06:00

553 lines
12 KiB
C

/*
* Copyright 2018, University Corporation for Atmospheric Research
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*/
#include "zincludes.h"
#include <stdarg.h>
#include "ncpathmgr.h"
/**************************************************/
/* Import the current implementations */
extern NCZMAP_DS_API zmap_file;
#ifdef USE_HDF5
extern NCZMAP_DS_API zmap_nz4;
#endif
#ifdef ENABLE_NCZARR_ZIP
extern NCZMAP_DS_API zmap_zip;
#endif
#ifdef ENABLE_S3_SDK
extern NCZMAP_DS_API zmap_s3sdk;
#endif
/**************************************************/
NCZM_FEATURES
nczmap_features(NCZM_IMPL impl)
{
switch (impl) {
case NCZM_FILE: return zmap_file.features;
#ifdef ENABLE_NCZARR_ZIP
case NCZM_ZIP: return zmap_zip.features;
#endif
#ifdef ENABLE_S3_SDK
case NCZM_S3: return zmap_s3sdk.features;
#endif
default: break;
}
return NCZM_UNIMPLEMENTED;
}
int
nczmap_create(NCZM_IMPL impl, const char *path, int mode, size64_t flags, void* parameters, NCZMAP** mapp)
{
int stat = NC_NOERR;
NCZMAP* map = NULL;
NCURI* uri = NULL;
if(path == NULL || strlen(path) == 0)
{stat = NC_EINVAL; goto done;}
if(mapp) *mapp = NULL;
switch (impl) {
case NCZM_FILE:
stat = zmap_file.create(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#ifdef ENABLE_NCZARR_ZIP
case NCZM_ZIP:
stat = zmap_zip.create(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#endif
#ifdef ENABLE_S3_SDK
case NCZM_S3:
stat = zmap_s3sdk.create(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#endif
default:
{stat = NC_ENOTBUILT; goto done;}
}
if(mapp) *mapp = map;
done:
ncurifree(uri);
return THROW(stat);
}
int
nczmap_open(NCZM_IMPL impl, const char *path, int mode, size64_t flags, void* parameters, NCZMAP** mapp)
{
int stat = NC_NOERR;
NCZMAP* map = NULL;
NCURI* uri = NULL;
if(path == NULL || strlen(path) == 0)
{stat = NC_EINVAL; goto done;}
if(mapp) *mapp = NULL;
switch (impl) {
case NCZM_FILE:
stat = zmap_file.open(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#ifdef ENABLE_NCZARR_ZIP
case NCZM_ZIP:
stat = zmap_zip.open(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#endif
#ifdef ENABLE_S3_SDK
case NCZM_S3:
stat = zmap_s3sdk.open(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#endif
default:
{stat = NC_ENOTBUILT; goto done;}
}
done:
ncurifree(uri);
if(!stat) {
if(mapp) *mapp = map;
}
return THROW(stat);
}
/**************************************************/
/* API Wrapper */
int
nczmap_close(NCZMAP* map, int delete)
{
int stat = NC_NOERR;
if(map && map->api)
stat = map->api->close(map,delete);
return THROW(stat);
}
int
nczmap_exists(NCZMAP* map, const char* key)
{
return map->api->exists(map, key);
}
int
nczmap_len(NCZMAP* map, const char* key, size64_t* lenp)
{
return map->api->len(map, key, lenp);
}
int
nczmap_read(NCZMAP* map, const char* key, size64_t start, size64_t count, void* content)
{
return map->api->read(map, key, start, count, content);
}
int
nczmap_write(NCZMAP* map, const char* key, size64_t start, size64_t count, const void* content)
{
return map->api->write(map, key, start, count, content);
}
/* Define a static qsort comparator for strings for use with qsort */
static int
cmp_strings(const void* a1, const void* a2)
{
const char** s1 = (const char**)a1;
const char** s2 = (const char**)a2;
return strcmp(*s1,*s2);
}
int
nczmap_search(NCZMAP* map, const char* prefix, NClist* matches)
{
int stat = NC_NOERR;
if((stat = map->api->search(map, prefix, matches)) == NC_NOERR) {
/* sort the list */
if(nclistlength(matches) > 1) {
void* base = nclistcontents(matches);
qsort(base, nclistlength(matches), sizeof(char*), cmp_strings);
}
}
return stat;
}
/**************************************************/
/* Utilities */
int
nczm_split(const char* path, NClist* segments)
{
return nczm_split_delim(path,NCZM_SEP[0],segments);
}
int
nczm_split_delim(const char* path, char delim, NClist* segments)
{
int stat = NC_NOERR;
const char* p = NULL;
const char* q = NULL;
ptrdiff_t len = 0;
char* seg = NULL;
if(path == NULL || strlen(path)==0 || segments == NULL)
{stat = NC_EINVAL; goto done;}
p = path;
if(p[0] == delim) p++;
for(;*p;) {
q = strchr(p,delim);
if(q==NULL)
q = p + strlen(p); /* point to trailing nul */
len = (q - p);
if(len == 0)
{stat = NC_EURL; goto done;}
if((seg = malloc(len+1)) == NULL)
{stat = NC_ENOMEM; goto done;}
memcpy(seg,p,len);
seg[len] = '\0';
nclistpush(segments,seg);
seg = NULL; /* avoid mem errors */
if(*q) p = q+1; else p = q;
}
done:
nullfree(seg);
return THROW(stat);
}
/* concat the the segments with each segment preceded by '/' */
int
nczm_join(NClist* segments, char** pathp)
{
int stat = NC_NOERR;
int i;
NCbytes* buf = NULL;
if(segments == NULL)
{stat = NC_EINVAL; goto done;}
if((buf = ncbytesnew())==NULL)
{stat = NC_ENOMEM; goto done;}
if(nclistlength(segments) == 0)
ncbytescat(buf,"/");
else for(i=0;i<nclistlength(segments);i++) {
const char* seg = nclistget(segments,i);
if(seg[0] != '/')
ncbytescat(buf,"/");
ncbytescat(buf,seg);
}
done:
if(!stat) {
if(pathp) *pathp = ncbytesextract(buf);
}
ncbytesfree(buf);
return THROW(stat);
}
int
nczm_concat(const char* prefix, const char* suffix, char** pathp)
{
NCbytes* buf = ncbytesnew();
if(prefix == NULL || strlen(prefix)==0) prefix = NCZM_SEP;
if(suffix == NULL) suffix = "";
ncbytescat(buf,prefix);
if(ncbytesget(buf,ncbyteslength(buf)-1) == NCZM_SEP[0])
ncbytessetlength(buf,ncbyteslength(buf)-1);
if(strlen(suffix) > 0 && suffix[0] != NCZM_SEP[0])
ncbytescat(buf,NCZM_SEP);
ncbytescat(buf,suffix);
if(pathp) *pathp = ncbytesextract(buf);
ncbytesfree(buf);
return NC_NOERR;
}
/* Concat multiple strings, but with no intervening separators */
int
nczm_appendn(char** resultp, int n, ...)
{
va_list args;
NCbytes* buf = ncbytesnew();
int i;
va_start(args, n);
for(i=0;i<n;i++) {
char* s = va_arg(args,char*);
if(s != NULL) ncbytescat(buf,s);
}
ncbytesnull(buf);
va_end(args);
if(resultp) {*resultp = ncbytesextract(buf);}
ncbytesfree(buf);
return NC_NOERR;
}
/* A segment is defined as a '/' plus characters following up
to the end or upto the next '/'
*/
int
nczm_divide_at(const char* key, int nsegs, char** prefixp, char** suffixp)
{
int stat = NC_NOERR;
char* prefix = NULL;
char* suffix = NULL;
size_t len, i;
ptrdiff_t delta;
const char* p;
int abssegs = (nsegs >= 0 ?nsegs: -nsegs);
int presegs = 0;
/* Special case */
if(key == NULL || strlen(key) == 0) goto done;
p = (key[0] == '/' ? key+1 : key);
/* Count number of segments */
for(len=0;;) {
const char* q = strchr(p,'/');
len++;
if(q == NULL) break;
p = q+1; /* start past leading '/' of next segment */
}
if(abssegs > len)
{stat = NC_EINVAL; goto done;}
/* find split point */
if(nsegs >= 0)
{presegs = abssegs;}
else
{presegs = (len - abssegs);}
/* skip past the first presegs segments */
for(p=key,i=0;i<presegs;i++) {
const char* q = strchr(p+1,'/');
if(q == NULL) {p = (p + strlen(p)); break;}
else p = q;
}
/* p should point at the presegs+1 start point */
delta = (p-key);
if(prefixp) {
prefix = malloc(delta+1);
memcpy(prefix,key,delta);
prefix[delta] = '\0';
*prefixp = prefix;
}
if(suffixp) {
suffix = strdup(p);
*suffixp = suffix;
}
done:
return stat;
}
int
nczm_clear(NCZMAP* map)
{
if(map)
nullfree(map->url);
return NC_NOERR;
}
int
nczm_isabsolutepath(const char* path)
{
if(path == NULL) return 0;
switch (path[0]) {
case '\\': return 1;
case '/': return 1;
case '\0': break;
default:
/* Check for windows drive letter */
if(NChasdriveletter(path)) return 1;
break;
}
return 0;
}
/* Convert forward slash to backslash ( !localize) or vice-versa (localize)*/
int
nczm_localize(const char* path, char** localpathp, int localize)
{
int stat = NC_NOERR;
char* localpath = NULL;
char* p;
int forward = 1;
int offset = 0;
#ifdef _MSC_VER
forward = (localize?0:1);
#endif
/* If path comes from a url, then it may start with: /x:/...
where x is a drive letter. If so, then remove leading / */
if(path[0] == '/' && NChasdriveletter(path+1))
offset = 1;
if((localpath = strdup(path+offset))==NULL) return NC_ENOMEM;
for(p=localpath;*p;p++) {
if(forward && *p == '\\') *p = '/';
else if(!forward && *p == '/') *p = '\\';
}
if(localpathp) {*localpathp = localpath; localpath = NULL;}
nullfree(localpath);
return stat;
}
/* Convert path0 to be:
1. absolute -- including drive letters
2. forward slashed -- we will convert back to back slash in nczm_fixpath
*/
int
nczm_canonicalpath(const char* path, char** cpathp)
{
int ret = NC_NOERR;
char* cpath = NULL;
char* tmp = NULL;
if(path == NULL)
{cpath = NULL; goto done;}
/* Process path to make it be windows compatible */
if((tmp = NCpathcvt(path))==NULL) {ret = NC_ENOMEM; goto done;}
/* Fix slashes to be forward for now */
if((ret = nczm_localize(tmp,&cpath,!LOCALIZE))) goto done;
if(cpathp) {*cpathp = cpath; cpath = NULL;}
done:
nullfree(tmp);
nullfree(cpath);
return THROW(ret);
}
/* extract the first segment of a path */
int
nczm_segment1(const char* path, char** seg1p)
{
int ret = NC_NOERR;
char* seg1 = NULL;
const char* p = NULL;
const char* q = NULL;
ptrdiff_t delta;
if(path == NULL)
{seg1 = NULL; goto done;}
p = path;
if(*p == '/') p++; /* skip any leading '/' */
q = strchr(p,'/');
if(q == NULL) q = p+strlen(p); /* point to stop character */
delta = (q-p);
if((seg1 = (char*)malloc(delta+1))==NULL)
{ret = NC_ENOMEM; goto done;}
memcpy(seg1,p,delta);
seg1[delta] = '\0';
if(seg1p) {*seg1p = seg1; seg1 = NULL;}
done:
nullfree(seg1);
return THROW(ret);
}
/*
Extract the last segment from path.
*/
int
nczm_lastsegment(const char* path, char** lastp)
{
int ret = NC_NOERR;
const char* last = NULL;
if(path == NULL)
{if(lastp) *lastp = NULL; goto done;}
last = strrchr(path,'/');
if(last == NULL) last = path; else last++;
if(lastp) *lastp = strdup(last);
done:
return THROW(ret);
}
/*
Extract the basename from a path.
Basename is last segment minus one extension.
*/
int
nczm_basename(const char* path, char** basep)
{
int stat = NC_NOERR;
char* base = NULL;
char* last = NULL;
const char* p = NULL;
ptrdiff_t delta;
if((stat=nczm_lastsegment(path,&last))) goto done;
if(last == NULL) goto done;
p = strrchr(last,'.');
if(p == NULL) p = last+strlen(last);
delta = (p - last);
if((base = (char*)malloc(delta+1))==NULL)
{stat = NC_ENOMEM; goto done;}
memcpy(base,last,delta);
base[delta] = '\0';
if(basep) {*basep = base; base = NULL;}
done:
nullfree(last);
nullfree(base);
return THROW(stat);
}
/* bubble sort a list of strings */
void
nczm_sortlist(NClist* l)
{
nczm_sortenvv(nclistlength(l),(char**)nclistcontents(l));
}
/* bubble sort a list of strings */
void
nczm_sortenvv(int n, char** envv)
{
size_t i, switched;
if(n <= 1) return;
do {
switched = 0;
for(i=0;i<n-1;i++) {
char* ith = envv[i];
char* ith1 = envv[i+1];
if(strcmp(ith,ith1) > 0) {
envv[i] = ith1;
envv[i+1] = ith;
switched = 1;
}
}
} while(switched);
#if 0
for(i=0;i<n;i++)
fprintf(stderr,"sorted: [%d] %s\n",i,(const char*)envv[i]);
#endif
}
void
NCZ_freeenvv(int n, char** envv)
{
int i;
char** p;
if(envv == NULL) return;
if(n < 0)
{for(n=0, p = envv; *p; n++); /* count number of strings */}
for(i=0;i<n;i++)
if(envv[i]) free(envv[i]);
free(envv);
}