mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-27 08:49:16 +08:00
df3636b959
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.
387 lines
8.7 KiB
C
387 lines
8.7 KiB
C
/*
|
|
* Copyright 2018, University Corporation for Atmospheric Research
|
|
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
|
|
*/
|
|
|
|
#include "ut_includes.h"
|
|
|
|
#undef DEBUG
|
|
|
|
#if 0
|
|
#define FILE1 "testmapnc4.ncz"
|
|
#define URL1 "file://" FILE1 "#mode=zarr"
|
|
#endif
|
|
|
|
#define META1 "/meta1"
|
|
#define META2 "/meta2"
|
|
#define DATA1 "/data1"
|
|
#define DATA1LEN 25
|
|
|
|
static const char* metadata1 = "{\n\"foo\": 42,\n\"bar\": \"apples\",\n\"baz\": [1, 2, 3, 4]}";
|
|
|
|
static const char* metadata2 = "{\n\"foo\": 42,\n\"bar\": \"apples\",\n\"baz\": [1, 2, 3, 4],\n\"extra\": 137}";
|
|
|
|
static char* url = NULL;
|
|
static NCZM_IMPL impl = NCZM_UNDEF;
|
|
|
|
/* Forward */
|
|
static int simplecreate(void);
|
|
static int simpledelete(void);
|
|
static int writemeta(void);
|
|
static int writemeta2(void);
|
|
static int readmeta(void);
|
|
static int readmeta2(void);
|
|
static int writedata(void);
|
|
static int readdata(void);
|
|
static int search(void);
|
|
|
|
struct Test tests[] = {
|
|
{"create",simplecreate},
|
|
{"delete",simpledelete},
|
|
{"writemeta", writemeta},
|
|
{"writemeta2", writemeta2},
|
|
{"readmeta", readmeta},
|
|
{"readmeta2", readmeta2},
|
|
{"writedata", writedata},
|
|
{"readdata", readdata},
|
|
{"search", search},
|
|
{NULL,NULL}
|
|
};
|
|
|
|
int
|
|
main(int argc, char** argv)
|
|
{
|
|
int stat = NC_NOERR;
|
|
char* tmp = NULL;
|
|
|
|
if((stat = ut_init(argc, argv, &utoptions))) goto done;
|
|
if(utoptions.file == NULL && utoptions.output == NULL) { stat = NC_EINVAL; goto done; }
|
|
if(utoptions.file == NULL && utoptions.output != NULL) utoptions.file = strdup(utoptions.output);
|
|
if(utoptions.output == NULL && utoptions.file != NULL)utoptions.output = strdup(utoptions.file);
|
|
|
|
/* Canonicalize */
|
|
if((stat = NCpathcanonical(utoptions.file,&tmp))) goto done;
|
|
free(utoptions.file);
|
|
utoptions.file = tmp;
|
|
if((stat = NCpathcanonical(utoptions.output,&tmp))) goto done;
|
|
free(utoptions.output);
|
|
utoptions.output = tmp;
|
|
fprintf(stderr,"file=%s output=%s\n",utoptions.file,utoptions.output);
|
|
|
|
impl = kind2impl(utoptions.kind);
|
|
url = makeurl(utoptions.file,impl,&utoptions);
|
|
|
|
if((stat = runtests((const char**)utoptions.cmds,tests))) goto done;
|
|
|
|
done:
|
|
nullfree(tmp);
|
|
ut_final();
|
|
if(stat) usage(stat);
|
|
return 0;
|
|
}
|
|
|
|
/* Do a simple create */
|
|
static int
|
|
simplecreate(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
char* path = NULL;
|
|
|
|
if((stat = nczmap_create(impl,url,0,0,NULL,&map)))
|
|
goto done;
|
|
|
|
if((stat=nczm_concat(NULL,NCZMETAROOT,&path)))
|
|
goto done;
|
|
|
|
/* Write empty metadata content */
|
|
if((stat = nczmap_write(map, path, 0, (const void*)"")))
|
|
goto done;
|
|
|
|
done:
|
|
/* Do not delete so we can look at it with ncdump */
|
|
stat = nczmap_close(map,0);
|
|
nullfree(path);
|
|
return THROW(stat);
|
|
}
|
|
|
|
/* Do a simple delete of previously created file */
|
|
static int
|
|
simpledelete(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
|
|
if((stat = nczmap_open(impl,url,0,0,NULL,&map)))
|
|
goto done;
|
|
if((stat = nczmap_close(map,1)))
|
|
goto done;
|
|
|
|
done:
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
writemeta(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
char* path = NULL;
|
|
|
|
if((stat = nczmap_open(impl,url,NC_WRITE,0,NULL,&map)))
|
|
goto done;
|
|
|
|
if((stat=nczm_concat(META1,ZARRAY,&path)))
|
|
goto done;
|
|
if((stat = nczmap_write(map, path, strlen(metadata1), metadata1)))
|
|
goto done;
|
|
free(path); path = NULL;
|
|
|
|
done:
|
|
/* Do not delete so we can look at it with ncdump */
|
|
(void)nczmap_close(map,0);
|
|
nullfree(path);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
writemeta2(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
char* path = NULL;
|
|
|
|
if((stat = nczmap_open(impl,url,NC_WRITE,0,NULL,&map)))
|
|
goto done;
|
|
|
|
if((stat=nczm_concat(META2,NCZARRAY,&path)))
|
|
goto done;
|
|
if((stat = nczmap_write(map, path, strlen(metadata2), metadata2)))
|
|
goto done;
|
|
|
|
done:
|
|
/* Do not delete so we can look at it with ncdump */
|
|
(void)nczmap_close(map,0);
|
|
nullfree(path);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
readkey(NCZMAP* map, const char* prefix, const char* object)
|
|
{
|
|
int stat = NC_NOERR;
|
|
char* path = NULL;
|
|
size64_t olen;
|
|
char* content = NULL;
|
|
|
|
if((stat=nczm_concat(prefix,object,&path)))
|
|
goto done;
|
|
|
|
/* Get length */
|
|
if((stat = nczmap_len(map, path, &olen)))
|
|
goto done;
|
|
|
|
/* Allocate the space for reading the metadata (might be overkill) */
|
|
if((content = malloc(olen+1)) == NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
|
|
if((stat = nczmap_read(map, path, 0, olen, content)))
|
|
goto done;
|
|
|
|
/* nul terminate */
|
|
content[olen] = '\0';
|
|
|
|
printf("%s: |%s|\n",path,content);
|
|
|
|
done:
|
|
nullfree(content);
|
|
nullfree(path);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
readmeta(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
|
|
if((stat = nczmap_open(impl,url,0,0,NULL,&map)))
|
|
goto done;
|
|
|
|
if((stat = readkey(map,META1,ZARRAY))) goto done;
|
|
|
|
done:
|
|
(void)nczmap_close(map,0);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
readmeta2(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
|
|
if((stat = nczmap_open(impl,url,0,0,NULL,&map)))
|
|
goto done;
|
|
|
|
if((stat = readkey(map,META2,NCZARRAY)))
|
|
goto done;
|
|
|
|
done:
|
|
(void)nczmap_close(map,0);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
writedata(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
char* path = NULL;
|
|
int data1[DATA1LEN];
|
|
int i;
|
|
size64_t totallen;
|
|
char* data1p = (char*)&data1[0]; /* byte level version of data1 */
|
|
|
|
/* Create the data */
|
|
for(i=0;i<DATA1LEN;i++) data1[i] = i;
|
|
totallen = sizeof(int)*DATA1LEN;
|
|
|
|
if((stat = nczmap_open(impl,url,NC_WRITE,0,NULL,&map)))
|
|
goto done;
|
|
|
|
/* ensure object */
|
|
if((stat=nczm_concat(DATA1,"0",&path)))
|
|
goto done;
|
|
|
|
if((stat = nczmap_write(map, path, totallen, data1p)))
|
|
goto done;
|
|
|
|
done:
|
|
/* Do not delete so we can look at it with ncdump */
|
|
(void)nczmap_close(map,0);
|
|
nullfree(path);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
readdata(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
char* path = NULL;
|
|
int data1[DATA1LEN];
|
|
int i;
|
|
size64_t chunklen, totallen;
|
|
char* data1p = NULL; /* byte level pointer into data1 */
|
|
|
|
if((stat = nczmap_open(impl,url,0,0,NULL,&map)))
|
|
goto done;
|
|
|
|
/* ensure object */
|
|
if((stat=nczm_concat(DATA1,"0",&path)))
|
|
goto done;
|
|
|
|
if((stat = nczmap_exists(map,path)))
|
|
goto done;
|
|
|
|
/* Read chunks in size sizeof(int)*n, where is rndup(DATA1LEN/3) */
|
|
chunklen = sizeof(int) * ((DATA1LEN+2)/3);
|
|
data1p = (char*)&data1[0];
|
|
totallen = sizeof(int)*DATA1LEN;
|
|
|
|
/* Read in 3 chunks */
|
|
memset(data1,0,sizeof(data1));
|
|
for(i=0;i<3;i++) {
|
|
size64_t start, count, last;
|
|
start = i * chunklen;
|
|
last = start + chunklen;
|
|
if(last > totallen)
|
|
last = totallen;
|
|
count = last - start;
|
|
if((stat = nczmap_read(map, path, start, count, &data1p[start])))
|
|
goto done;
|
|
}
|
|
|
|
/* Validate */
|
|
for(i=0;i<DATA1LEN;i++) {
|
|
if(data1[i] != i) {
|
|
fprintf(stderr,"data mismatch: is: %d should be: %d\n",data1[i],i);
|
|
stat = NC_EINVAL;
|
|
goto done;
|
|
}
|
|
}
|
|
|
|
done:
|
|
/* Do not delete so we can look at it with ncdump */
|
|
(void)nczmap_close(map,0);
|
|
nullfree(path);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
searchR(NCZMAP* map, int depth, const char* prefix0, NClist* objects)
|
|
{
|
|
int i,stat = NC_NOERR;
|
|
NClist* matches = nclistnew();
|
|
char prefix[4096]; /* only ok because we know testdata */
|
|
size_t prefixlen;
|
|
|
|
nclistpush(objects,strdup(prefix0));
|
|
|
|
prefix[0] = '\0';
|
|
strlcat(prefix,prefix0,sizeof(prefix));
|
|
prefixlen = strlen(prefix);
|
|
|
|
/* get next level object keys **below** the prefix: should have form: <name> */
|
|
switch (stat = nczmap_search(map, prefix, matches)) {
|
|
case NC_NOERR: break;
|
|
case NC_ENOOBJECT: stat = NC_NOERR; break;/* prefix is not an object */
|
|
default: goto done;
|
|
}
|
|
/* recurse */
|
|
for(i=0;i<nclistlength(matches);i++) {
|
|
const char* key = nclistget(matches,i);
|
|
/* ensure trailing '/' */
|
|
if(prefix[prefixlen-1] != '/')
|
|
strlcat(prefix,"/",sizeof(prefix));
|
|
strlcat(prefix,key,sizeof(prefix));
|
|
if((stat = searchR(map,depth+1,prefix,objects))) goto done;
|
|
/* restore prefix */
|
|
prefix[prefixlen] = '\0';
|
|
if(stat != NC_NOERR)
|
|
goto done;
|
|
}
|
|
done:
|
|
nclistfreeall(matches);
|
|
return THROW(stat);
|
|
}
|
|
|
|
static int
|
|
search(void)
|
|
{
|
|
int i,stat = NC_NOERR;
|
|
NCZMAP* map = NULL;
|
|
NClist* objects = nclistnew();
|
|
|
|
if((stat = nczmap_open(impl,url,0,0,NULL,&map)))
|
|
goto done;
|
|
|
|
/* Do a recursive search on root to get all object keys */
|
|
if((stat=searchR(map,0,"/",objects)))
|
|
goto done;
|
|
/* Sort */
|
|
ut_sortlist(objects);
|
|
/* Print out the list */
|
|
for(i=0;i<nclistlength(objects);i++) {
|
|
const char* key = nclistget(objects,i);
|
|
printf("[%d] %s\n",i,key);
|
|
}
|
|
|
|
done:
|
|
/* Do not delete so later tests can use it */
|
|
(void)nczmap_close(map,0);
|
|
nclistfreeall(objects);
|
|
return THROW(stat);
|
|
}
|