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netcdf-c/nczarr_test/itmeta.c
Dennis Heimbigner 59e04ae071 This PR adds EXPERIMENTAL support for accessing data in the 
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.
2020-06-28 18:02:47 -06:00

725 lines
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/*
* Copyright 2018, University Corporation for Atmospheric Research
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*/
#include "ut_includes.h"
#define SETUP
#define DEBUG
#define FILE "testmeta.ncz"
#define VAR1 "var1"
#define VAR2 "var2"
static char* url = NULL;
/* Arguments from command line */
struct Options {
int debug;
char* cmd;
} options;
typedef union AtomicsR {
char bytev[1];
short shortv[1];
int intv[1];
float floatv[1];
double doublev[1];
unsigned char ubytev[1];
unsigned short ushortv[1];
unsigned int uintv[1];
long long int64v[1];
unsigned long long uint64v[1];
char charv[1];
} AtomicsR;
typedef struct AtomicsW {
char bytev[1];
short shortv[1];
int intv[1];
float floatv[1];
double doublev[1];
unsigned char ubytev[1];
unsigned short ushortv[1];
unsigned int uintv[1];
long long int64v[1];
unsigned long long uint64v[1];
char charv[1];
} AtomicsW;
/* Forward */
static int testcreate(void);
static int testdim1(void);
static int testvar1(void);
static int testvar2(void);
static int testattr1(void);
static int testattr2(void);
static int testread1(void);
static int testread2(void);
static int testread3(void);
struct Test {
const char* cmd;
int (*test)(void);
} tests[] = {
{"create", testcreate},
{"dim1", testdim1},
{"var1", testvar1},
{"var2", testvar2},
{"attr1", testattr1},
{"attr2", testattr2},
{"read1", testread1},
{"read2", testread2},
{"read3", testread3},
{NULL, NULL}
};
#ifdef SETUP
#define NCCHECK(expr) nccheck((expr),__LINE__)
void nccheck(int stat, int line)
{
if(stat) {
fprintf(stderr,"%d: %s\n",line,nc_strerror(stat));
fflush(stderr);
exit(1);
}
}
#endif
static void
makeurl(const char* file)
{
char wd[4096];
NCbytes* buf = ncbytesnew();
ncbytescat(buf,"file://");
(void)getcwd(wd, sizeof(wd));
ncbytescat(buf,wd);
ncbytescat(buf,"/");
ncbytescat(buf,file);
ncbytescat(buf,"#mode=zarr"); /* => use default file: format */
url = ncbytesextract(buf);
ncbytesfree(buf);
}
int
main(int argc, char** argv)
{
int stat = NC_NOERR;
int c;
struct Test* t = NULL;
struct Test* test = NULL;
char* file = NULL;
memset((void*)&options,0,sizeof(options));
while ((c = getopt(argc, argv, "dc:o:")) != EOF) {
switch(c) {
case 'd':
options.debug = 1;
break;
case 'c':
if(options.cmd != NULL) {
fprintf(stderr,"error: multiple tests specified\n");
stat = NC_EINVAL;
goto done;
}
options.cmd = strdup(optarg);
break;
case 'o':
if(file != NULL) {
fprintf(stderr,"error: multiple output files specified\n");
stat = NC_EINVAL;
goto done;
}
file = strdup(optarg);
break;
case '?':
fprintf(stderr,"unknown option\n");
stat = NC_EINVAL;
goto done;
}
}
if(options.cmd == NULL) {
fprintf(stderr,"no command specified\n");
stat = NC_EINVAL;
goto done;
}
if(file == NULL)
file = strdup(FILE);
makeurl(file);
#ifdef DEBUG
fprintf(stderr,"test: %s url=|%s|\n",options.cmd,url);
fflush(stderr);
#endif
/* Find the corresponding test for command */
for(t=tests;t->cmd;t++) {
if(strcmp(options.cmd,t->cmd)==0) {test = t; break;}
}
if(test == NULL) {
fprintf(stderr,"unknown command: %s\n",optarg);
stat = NC_EINVAL;
goto done;
}
/* Execute */
test->test();
done:
if(stat)
nc_strerror(stat);
return (stat ? 1 : 0);
}
/* Create test netcdf4 file via netcdf.h API*/
static int
testcreate(void)
{
int stat = NC_NOERR;
int ncid;
unlink(FILE);
if((stat = nc_create(url, 0, &ncid)))
goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
/* Create file and add a dimension */
static int
testdim1(void)
{
int stat = NC_NOERR;
int ncid, dimid;
unlink(FILE);
if((stat = nc_create(url, 0, &ncid)))
goto done;
if((stat = nc_def_dim(ncid, "dim1", (size_t)1, &dimid)))
goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
/* Create file and add a variable */
static int
testvar1(void)
{
int stat = NC_NOERR;
int ncid, varid;
unlink(FILE);
if((stat = nc_create(url, 0, &ncid)))
goto done;
if((stat = nc_def_var(ncid, VAR1, NC_INT, 0, NULL, &varid)))
goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
/* Create file and add a rank 2 variable */
static int
testvar2(void)
{
int stat = NC_NOERR;
int ncid, varid1, varid2;
int dimids[2];
int ndims;
int fillval;
unlink(FILE);
if((stat = nc_create(url, 0, &ncid)))
goto done;
ndims = 0;
if((stat = nc_def_dim(ncid, "dim2", 2, &dimids[0])))
goto done;
ndims++;
if((stat = nc_def_dim(ncid, "dim3", 3, &dimids[1])))
goto done;
ndims++;
if((stat = nc_def_var(ncid, VAR1, NC_INT, ndims, dimids, &varid1)))
goto done;
/* make VAR1 no-fill */
if((stat = nc_def_var_fill(ncid,varid1,NC_NOFILL,NULL)))
goto done;
/* make VAR1 contiguous */
if((stat = nc_def_var_chunking(ncid,varid1,NC_CONTIGUOUS,NULL)))
goto done;
/* Define var2 as chunked, but use default chunking */
if((stat = nc_def_var(ncid, VAR2, NC_INT, ndims, dimids, &varid2)))
goto done;
if((stat = nc_def_var_chunking(ncid,varid2,NC_CHUNKED,NULL)))
goto done;
/* make VAR1 use non-default fill */
fillval = 137;
if((stat = nc_def_var_fill(ncid,varid2,NC_FILL,&fillval)))
goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
/* Create file and add global attributes of all supported types */
static int
testattr1(void)
{
int stat = NC_NOERR;
int ncid;
AtomicsW atoms = {
{-17},
{-17},
{-17},
{17.0f},
{17.0},
{17u},
{17u},
{17u},
{17ll},
{17ull},
{'7'}};
unlink(FILE);
if((stat = nc_create(url, 0, &ncid)))
goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"byte_a",NC_BYTE,1,atoms.bytev))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"short_a",NC_SHORT,1,atoms.shortv))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"int_a",NC_INT,1,atoms.intv))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"float_a",NC_FLOAT,1,atoms.floatv))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"double_a",NC_DOUBLE,1,atoms.doublev))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"ubyte_a",NC_UBYTE,1,atoms.ubytev))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"ushort_a",NC_USHORT,1,atoms.ushortv))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"uint_a",NC_UINT,1,atoms.uintv))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"int64_a",NC_INT64,1,atoms.int64v))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"uint64_a",NC_UINT64,1,atoms.uint64v))) goto done;
if((stat = nc_put_att(ncid,NC_GLOBAL,"char_a",NC_CHAR,1,atoms.charv))) goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
/* Create file and a var and add some attributes to the var */
static int
testattr2(void)
{
int stat = NC_NOERR;
int ncid, varid1;
int intv[1] = {-17};
float floatv[1] = {17.0f};
long long int64v[1] = {17ll};
char charv[1] = {'7'};
unlink(FILE);
if((stat = nc_create(url, 0, &ncid)))
goto done;
if((stat = nc_def_var(ncid, VAR1, NC_INT, 0, NULL, &varid1)))
goto done;
if((stat = nc_put_att(ncid,varid1,"int_a",NC_INT,1,intv))) goto done;
if((stat = nc_put_att(ncid,varid1,"float_a",NC_FLOAT,1,floatv))) goto done;
if((stat = nc_put_att(ncid,varid1,"int64_a",NC_INT64,1,int64v))) goto done;
if((stat = nc_put_att(ncid,varid1,"char_a",NC_CHAR,1,charv))) goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
static int
fv2string(nc_type xtype, size_t xtypesize, void* fill_value, char** fillstringp)
{
char sval[1024];
switch (xtype) {
case NC_BYTE:
snprintf(sval,sizeof(sval),"%d",*((char*)fill_value));
break;
case NC_CHAR:
snprintf(sval,sizeof(sval),"'%c'",*((char*)fill_value));
break;
case NC_SHORT:
snprintf(sval,sizeof(sval),"%d",*((short*)fill_value));
break;
case NC_INT:
snprintf(sval,sizeof(sval),"%d",*((int*)fill_value));
break;
case NC_FLOAT:
snprintf(sval,sizeof(sval),"%g",*((float*)fill_value));
break;
case NC_DOUBLE:
snprintf(sval,sizeof(sval),"%lg",*((double*)fill_value));
break;
case NC_UBYTE:
snprintf(sval,sizeof(sval),"%u",*((unsigned char*)fill_value));
break;
case NC_USHORT:
snprintf(sval,sizeof(sval),"%u",*((unsigned short*)fill_value));
break;
case NC_UINT:
snprintf(sval,sizeof(sval),"%u",*((unsigned int*)fill_value));
break;
case NC_INT64:
snprintf(sval,sizeof(sval),"%lld",*((long long*)fill_value));
break;
case NC_UINT64:
snprintf(sval,sizeof(sval),"%llu",*((unsigned long long*)fill_value));
break;
default:
strlcat(sval,"<unknown>",sizeof(sval));
break;
}
if(fillstringp) *fillstringp = strdup(sval);
return NC_NOERR;
}
static int
reportvar(int ncid, int varid)
{
int i,stat = NC_NOERR;
char varname[NC_MAX_NAME];
nc_type xtype;
int ndims, natts;
char typename[NC_MAX_NAME];
size_t typesize;
int dimids[NC_MAX_VAR_DIMS];
char* dimname[NC_MAX_VAR_DIMS];
size_t dimsize[NC_MAX_VAR_DIMS];
int no_fill;
void* fill_value = NULL;
int shuffle, deflate, deflate_level;
int fletcher32;
int endian;
unsigned int* filterids
size_t nfilters;
int storage;
size_t chunksizes[NC_MAX_VAR_DIMS];
const char* tmp = NULL;
char* fillstring = NULL;
if((stat = nc_inq_var(ncid,varid,varname,&xtype,&ndims,dimids,&natts)))
goto done;
/* get basetype name and size*/
if((stat = nc_inq_type(ncid, xtype, typename, &typesize))) goto done;
/* Get dimension sizes */
for(i=0;i<ndims;i++) {
char name[NC_MAX_NAME];
if((stat = nc_inq_dim(ncid, dimids[i], name, &dimsize[i])))
goto done;
dimname[i] = strdup(name);
}
if((stat = nc_inq_var_endian(ncid, varid, &endian)))
goto done;
if((stat = nc_inq_var_deflate(ncid, varid, &shuffle, &deflate, &deflate_level)))
goto done;
if((stat = nc_inq_var_fletcher32(ncid, varid, &fletcher32)))
goto done;
if((stat = nc_inq_var_filters(ncid, varid, &nfilters, NULL)))
goto done;
filterids = NULL;
if(nfilters > 0)
filterids = malloc(sizeof(unsigned int)*nfilters);
if((stat = nc_inq_var_filters(ncid, varid, &nfilters, filterids)))
goto done;
/* Allocate space for fill_value */
if((fill_value = calloc(1,typesize)) == NULL)
{stat = NC_ENOMEM; goto done;}
if((stat = nc_inq_var_fill(ncid, varid, &no_fill, fill_value)))
goto done;
if((stat = nc_inq_var_chunking(ncid, varid, &storage, chunksizes)))
goto done;
/* Now dump everything */
printf("%s %s",typename, varname);
printf("(");
for(i=0;i<ndims;i++) {
if(i > 0) printf(",");
printf("%s=%lu",dimname[i],(unsigned long)dimsize[i]);
}
printf(");\n");
switch (endian) {
case NC_ENDIAN_NATIVE: tmp = "native"; break;
case NC_ENDIAN_LITTLE: tmp = "little"; break;
case NC_ENDIAN_BIG: tmp = "big"; break;
default: tmp = "unknown"; break;
}
printf("\t_Endianness=%s\n",tmp);
printf("\t_Fletcher32=%s\n",(fletcher32?"true":"false"));
printf("\t_Shuffle=%s\n",(shuffle?"true":"false"));
if(deflate) printf("\t_DeflateLevel=%d\n",deflate_level);
if(filterids != NULL) {
printf("\t_Filters=(");
for(i=0;i<nfilters;i++) {
if(i>0) printf(",");
printf("%u",filterids[i]);
}
printf(")\n");
}
if((stat=fv2string(xtype,typesize,fill_value,&fillstring))) goto done;
printf("\t_FillValue=%s\n",fillstring);
if(storage == NC_CONTIGUOUS) {
printf("\t_Storage=contiguous\n");
} else { /* chunked */
printf("\t_Storage=chunked\n");
printf("\t_ChunkSizes=");
for(i=0;i<ndims;i++) {
if(i>0) printf(",");
printf("%lu",(unsigned long)chunksizes[i]);
}
printf("\n");
}
done:
return stat;
}
/* Report variables from testvar2 */
static int
testread1(void)
{
int stat = NC_NOERR;
int ncid, varid1, varid2;
int ndims,nvars,natts,unlimdimid;
unlink(FILE);
#ifdef SETUP
NCCHECK(testvar2());
#endif
if((stat = nc_open(url, 0, &ncid)))
goto done;
/* Report file level info */
if((stat = nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)))
goto done;
printf("file info: ndims=%d nvars=%d natts=%d unlimdimid=%d\n",
ndims,nvars,natts,unlimdimid);
if((stat = nc_inq_varid(ncid, VAR1, &varid1))) goto done;
/* Report info about the var */
if((stat = reportvar(ncid,varid1))) goto done;
if((stat = nc_inq_varid(ncid, VAR2, &varid2))) goto done;
/* Report info about the var */
if((stat = reportvar(ncid,varid2))) goto done;
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
static int
reportatt(int ncid, int varid, int natts, int index)
{
int i,stat = NC_NOERR;
void* data = NULL;
char aname[NC_MAX_NAME];
nc_type atype;
size_t alen;
char typename[NC_MAX_NAME];
size_t typesize;
char* p = NULL; /* char* so we can do arithmetic */
/* Get some meta info about the attribute */
if((stat = nc_inq_attname(ncid,varid,index,aname)))
goto done;
if((stat = nc_inq_att(ncid, varid, aname, &atype, &alen))) goto done;
/* Get type info about atype */
if((stat = nc_inq_type(ncid, atype, typename, &typesize))) goto done;
/* Allocate space to read the attribute */
if((data = malloc(typesize * alen)) == NULL)
{stat = NC_ENOMEM; goto done;}
/* Read the attribute */
if((stat = nc_get_att(ncid,varid,aname,data))) goto done;
/* Now report */
printf("\t[%d] %s:%s(%lu) = ",index,typename,aname,(unsigned long)alen);
for(p=(char*)data,i=0;i<alen;i++,p+=typesize) {
AtomicsR* atom = (AtomicsR*)p;
printf("%s",(i==0?"{":" "));
switch (atype) {
case NC_BYTE: printf("%db",atom->bytev[0]); break;
case NC_SHORT: printf("%ds",atom->shortv[0]); break;
case NC_INT: printf("%d",atom->intv[0]); break;
case NC_FLOAT: printf("%gf",atom->floatv[0]); break;
case NC_DOUBLE: printf("%lg",atom->doublev[0]); break;
case NC_UBYTE: printf("%uub",atom->ubytev[0]); break;
case NC_USHORT: printf("%uus",atom->ushortv[0]); break;
case NC_UINT: printf("%uu",atom->intv[0]); break;
case NC_INT64: printf("%lldll",atom->int64v[0]); break;
case NC_UINT64: printf("%lluull",atom->uint64v[0]); break;
case NC_CHAR: printf("'%c'",atom->charv[0]); break;
}
}
printf("}\n");
done:
return stat;
}
/* Print out selected reserved attributes by name */
static int
reportreserved(int ncid)
{
int stat = NC_NOERR;
char* ncpropdata = NULL;
size_t len;
int superblockversion;
int isnetcdf4;
nc_type xtype;
/* Get and print _NCProperties */
if((stat = nc_inq_attlen(ncid, NC_GLOBAL, "_NCProperties", &len)))
goto done;
if((ncpropdata = calloc(1,len+1)) == NULL) {stat = NC_ENOMEM; goto done;}
if((stat = nc_get_att(ncid,NC_GLOBAL, "_NCProperties", ncpropdata)))
goto done;
ncpropdata[len] = '\0'; /* nul term */
printf("\t%s:%s(%lu) = |%s|\n", "char","_NCProperties", (unsigned long)len, ncpropdata);
/* Get and print _SuperblockVersion */
if((stat = nc_inq_att(ncid, NC_GLOBAL, "_SuperblockVersion", &xtype,&len)))
goto done;
if(len != 1 || xtype != NC_INT) {stat = NC_ENCZARR; goto done;}
if((stat = nc_get_att_int(ncid,NC_GLOBAL, "_SuperblockVersion", &superblockversion)))
goto done;
printf("\t%s:%s(%lu) = %d\n", "int","_SuperblockVersion", (unsigned long)len, superblockversion);
/* Get and print _Isnetcdf4 */
if((stat = nc_inq_att(ncid, NC_GLOBAL, "_IsNetcdf4", &xtype,&len)))
goto done;
if(len != 1 || xtype != NC_INT) {stat = NC_ENCZARR; goto done;}
if((stat = nc_get_att_int(ncid,NC_GLOBAL, "_IsNetcdf4", &isnetcdf4)))
goto done;
printf("\t%s:%s(%lu) = %d\n", "int","_IsNetcdf4", (unsigned long)len, isnetcdf4);
done:
nullfree(ncpropdata);
return stat;
}
/* Read the global attributes in testattr1 */
static int
testread2(void)
{
int i,stat = NC_NOERR;
int ncid;
int natts;
unlink(FILE);
#ifdef SETUP
NCCHECK(testattr1());
#endif
if((stat = nc_open(url, 0, &ncid)))
goto done;
printf("Reserved Attributes:\n");
if((stat = reportreserved(ncid))) goto done;
fflush(stdout);
printf("\nGlobal Attributes:\n");
/* Get and print the global attributes */
if((stat = nc_inq(ncid, NULL, NULL, &natts, NULL))) goto done;
for(i=0;i<natts;i++) {
if((stat = reportatt(ncid,NC_GLOBAL,natts,i))) goto done;
}
fflush(stdout);
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
/* Read the variable attributes in testattr2 */
static int
testread3(void)
{
int i,stat = NC_NOERR;
int ncid, varid1;
int natts;
unlink(FILE);
#ifdef SETUP
NCCHECK(testattr2());
#endif
if((stat = nc_open(url, 0, &ncid)))
goto done;
/* Get and print the variable attributes */
printf("\nVariable Attributes:\n");
if((stat = nc_inq_varid(ncid, VAR1, &varid1))) goto done;
if((stat = nc_inq_var(ncid,varid1,NULL,NULL,NULL,NULL,&natts)))
goto done;
for(i=0;i<natts;i++) {
if((stat = reportatt(ncid,varid1,natts,i))) goto done;
}
fflush(stdout);
if((stat = nc_close(ncid)))
goto done;
done:
return THROW(stat);
}
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