netcdf-c/libnczarr/zmap.c
Dennis Heimbigner df3636b959 Mitigate S3 test interference + Unlimited Dimensions in NCZarr
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.

The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.

## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
   - "size" with an integer value representing the (current) size of the dimension.
   - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.

For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.

Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.

## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
   AWS Transfer Utility mechanism. This is controlled by the
   ```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
2023-09-26 16:56:48 -06:00

547 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 */
/**************************************************/
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
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;
if((mode & NC_NOCLOBBER) == 0) {
/* Truncate the file */
if((stat = nczmap_truncate(impl,path))) goto done;
}
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
case NCZM_S3:
stat = zmap_s3sdk.create(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#endif
default:
{stat = REPORT(NC_ENOTBUILT,"nczmap_create"); 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
case NCZM_S3:
stat = zmap_s3sdk.open(path, mode, flags, parameters, &map);
if(stat) goto done;
break;
#endif
default:
{stat = REPORT(NC_ENOTBUILT,"nczmap_open"); goto done;}
}
done:
ncurifree(uri);
if(!stat) {
if(mapp) *mapp = map;
}
return THROW(stat);
}
int
nczmap_truncate(NCZM_IMPL impl, const char *path)
{
int stat = NC_NOERR;
switch (impl) {
case NCZM_FILE:
if((stat = zmap_file.truncate(path))) goto done;
break;
#ifdef ENABLE_NCZARR_ZIP
case NCZM_ZIP:
if((stat = zmap_zip.truncate(path))) goto done;
break;
#endif
#ifdef ENABLE_S3
case NCZM_S3:
if((stat = zmap_s3sdk.truncate(path))) goto done;
break;
#endif
default:
{stat = REPORT(NC_ENOTBUILT,"nczmap_truncate"); goto done;}
}
done:
return 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 count, const void* content)
{
return map->api->write(map, key, 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)
{
return NC_split_delim(path,delim,segments);
}
/* 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;
static const char* windrive = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
#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(strlen(path) >= 4
&& path[0] == '/' && strchr(windrive,path[1]) != NULL
&& path[2] == ':' && path[3] == '/')
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* tmp1 = NULL;
if(path == NULL)
{cpath = NULL; goto done;}
/* Process path to make it be absolute*/
if((tmp1 = NCpathabsolute(path))==NULL) {ret = NC_ENOMEM; goto done;}
/* Fix slashes to be forward for now */
if((ret = nczm_localize(tmp1,&cpath,!LOCALIZE))) goto done;
if(cpathp) {*cpathp = cpath; cpath = NULL;}
done:
nullfree(tmp1);
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));
}
static int
nczm_compare(const void* arg1, const void* arg2)
{
char* n1 = *((char**)arg1);
char* n2 = *((char**)arg2);
return strcmp(n1,n2);
}
/* quick sort a list of strings */
void
nczm_sortenvv(int n, char** envv)
{
if(n <= 1) return;
qsort(envv, n, sizeof(char*), nczm_compare);
#if 0
{int i;
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);
}