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Fix some problems with PR 2492 #2497

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merged 7 commits into from
Sep 6, 2022
Merged

Fix some problems with PR 2492 #2497

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57b1d9f
update file permission
DennisHeimbigner Sep 3, 2022
6abaab9
Fix some problems with PR https://github.com/Unidata/netcdf-c/pull/2492
DennisHeimbigner Sep 3, 2022
85577f4
Update release notes
DennisHeimbigner Sep 3, 2022
be88b66
Update Release Notes
DennisHeimbigner Sep 3, 2022
0349acb
Merge branch 'zarrfixes3.dmh' of https://github.com/DennisHeimbigner/…
DennisHeimbigner Sep 3, 2022
7e48f2a
Fix missing files
DennisHeimbigner Sep 3, 2022
00a80ec
Catch Xarray dimension inconsistencies
DennisHeimbigner Sep 4, 2022
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2 changes: 1 addition & 1 deletion .github/workflows/run_tests_osx.yml
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Expand Up @@ -7,7 +7,7 @@
name: Run macOS-based netCDF Tests


on: [push,pull_request, workflow_dispatch]
on: [pull_request, workflow_dispatch]

jobs:

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_tests_ubuntu.yml
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Expand Up @@ -4,7 +4,7 @@

name: Run Ubuntu/Linux netCDF Tests

on: [push,pull_request, workflow_dispatch]
on: [pull_request, workflow_dispatch]

jobs:

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_tests_win_mingw.yml
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Expand Up @@ -7,7 +7,7 @@
name: Run MSYS2, MinGW64-based Tests


on: [push,pull_request, workflow_dispatch]
on: [pull_request, workflow_dispatch]

jobs:

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1 change: 1 addition & 0 deletions RELEASE_NOTES.md
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Expand Up @@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release

## 4.9.1 - T.B.D.

* [Bug Fix] Fix some errors detected in [PR #2492](https://github.com/Unidata/netcdf-c/pull/2492) . See [Github #2497](https://github.com/Unidata/netcdf-c/pull/2497).
* [Enhancement] Add support for Zarr (fixed length) string type in nczarr. See [Github #2492](https://github.com/Unidata/netcdf-c/pull/2492).
* [Bug Fix] Split the remote tests into two parts: one for the remotetest server and one for all other external servers. Also add a configure option to enable the latter set. See [Github #2491](https://github.com/Unidata/netcdf-c/pull/2491).
* [Bug Fix] Fix support for reading arrays of HDF5 fixed size strings. See [Github #2462](https://github.com/Unidata/netcdf-c/pull/2466).
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2 changes: 1 addition & 1 deletion docs/nczarr.md
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Expand Up @@ -891,7 +891,7 @@ handled by providing the following new attributes:
1. **_nczarr_default_maxstrlen** —
This is an attribute of the root group. It specifies the default
maximum string length for string types. If not specified, then
it has the value of 64 characters.
it has the value of 128 characters.
2. **_nczarr_maxstrlen** —
This is a per-variable attribute. It specifies the maximum
string length for the string type associated with the variable.
Expand Down
12 changes: 6 additions & 6 deletions libdispatch/ncjson.c
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Expand Up @@ -467,13 +467,13 @@ testdouble(const char* word)
double d;
int count = 0;
/* Check for Nan and Infinity */
if(strcasecmp("nan",word)==0) return NCJTHROW(NCJ_OK);
if(strcasecmp("infinity",word)==0) return NCJTHROW(NCJ_OK);
if(strcasecmp("-infinity",word)==0) return NCJTHROW(NCJ_OK);
if(0==(int)strcasecmp("nan",word)) return NCJTHROW(NCJ_OK);
if(0==(int)strcasecmp("infinity",word)) return NCJTHROW(NCJ_OK);
if(0==(int)strcasecmp("-infinity",word)) return NCJTHROW(NCJ_OK);
/* Allow the XXXf versions as well */
if(strcasecmp("nanf",word)==0) return NCJTHROW(NCJ_OK);
if(strcasecmp("infinityf",word)==0) return NCJTHROW(NCJ_OK);
if(strcasecmp("-infinityf",word)==0) return NCJTHROW(NCJ_OK);
if(0==(int)strcasecmp("nanf",word)) return NCJTHROW(NCJ_OK);
if(0==(int)strcasecmp("infinityf",word)) return NCJTHROW(NCJ_OK);
if(0==(int)strcasecmp("-infinityf",word)) return NCJTHROW(NCJ_OK);
/* Try to convert to number */
ncvt = sscanf(word,"%lg%n",&d,&count);
return NCJTHROW((ncvt == 1 && strlen(word)==count ? NCJ_OK : NCJ_ERR));
Expand Down
143 changes: 117 additions & 26 deletions libnczarr/zcvt.c
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Expand Up @@ -33,6 +33,7 @@ sizeof(char *), /*NC_STRING*/

/* Forward */
static int typeid2jtype(nc_type typeid);
static int naninftest(const char* s, double* dcase, float* fcase);

#if 0
/* Convert a JSON value to a struct ZCVT value and also return the type */
Expand Down Expand Up @@ -104,6 +105,8 @@ NCZ_json2cvt(NCjson* jsrc, struct ZCVT* zcvt, nc_type* typeidp)
{
int stat = NC_NOERR;
nc_type srctype = NC_NAT;
double naninf;
float naninff;

/* Convert the incoming jsrc to a restricted set of values */
switch (NCJsort(jsrc)) {
Expand All @@ -119,18 +122,14 @@ NCZ_json2cvt(NCjson* jsrc, struct ZCVT* zcvt, nc_type* typeidp)
}
break;
case NCJ_DOUBLE:
/* Capture nan and infinity values */
if(strcasecmp(NCJstring(jsrc),"nan")==0)
zcvt->float64v = NAN;
else if(strcasecmp(NCJstring(jsrc),"-nan")==0)
zcvt->float64v = - NAN;
else if(strcasecmp(NCJstring(jsrc),"infinity")==0)
zcvt->float64v = INFINITY;
else if(strcasecmp(NCJstring(jsrc),"-infinity")==0)
zcvt->float64v = (- INFINITY);
else {
switch (naninftest(NCJstring(jsrc),&naninf,&naninff)) {
case NC_NAT:
if(sscanf(NCJstring(jsrc),"%lg",&zcvt->float64v) != 1)
{stat = NC_EINVAL; goto done;}
break;
default:
zcvt->float64v = naninf;
break;
}
srctype = NC_DOUBLE;
break;
Expand Down Expand Up @@ -162,6 +161,8 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
struct ZCVT zcvt = zcvt_empty;
int outofrange = 0;
size_t len = 0;
double naninf;
float naninff;

assert(dsttype != NC_NAT && dsttype <= NC_MAX_ATOMIC_TYPE && buf);

Expand Down Expand Up @@ -192,6 +193,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
c = (signed char)zcvt.uint64v;
ncbytesappend(buf,(char)c);
break;
default: abort();
}
} break;
case NC_UBYTE: {
Expand All @@ -210,6 +212,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
c = (unsigned char)zcvt.uint64v;
ncbytesappend(buf,(char)c);
break;
default: abort();
}
} break;
case NC_SHORT: {
Expand All @@ -228,6 +231,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
s = (signed short)zcvt.uint64v;
ncbytesappendn(buf,(char*)&s,sizeof(s));
break;
default: abort();
}
} break;
case NC_USHORT: {
Expand All @@ -246,6 +250,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
s = (unsigned short)zcvt.uint64v;
ncbytesappendn(buf,(char*)&s,sizeof(s));
break;
default: abort();
}
} break;
case NC_INT: {
Expand All @@ -264,6 +269,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
ii = (signed int)zcvt.uint64v;
ncbytesappendn(buf,(char*)&ii,sizeof(ii));
break;
default: abort();
}
} break;
case NC_UINT: {
Expand All @@ -282,6 +288,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
ii = (unsigned int)zcvt.uint64v;
ncbytesappendn(buf,(char*)&ii,sizeof(ii));
break;
default: abort();
}
} break;
case NC_INT64: {
Expand All @@ -299,6 +306,7 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
ll = (signed long long)zcvt.uint64v;
ncbytesappendn(buf,(char*)&ll,sizeof(ll));
break;
default: abort();
}
} break;
case NC_UINT64: {
Expand All @@ -316,40 +324,58 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
ll = (unsigned long long)zcvt.uint64v;
ncbytesappendn(buf,(char*)&ll,sizeof(ll));
break;
default: abort();
}
} break;
case NC_FLOAT: {
float f = 0;
switch (srctype) {
case NC_DOUBLE:
f = (float)zcvt.float64v;
ncbytesappendn(buf,(char*)&f,sizeof(f));
break;
case NC_INT64:
f = (float)zcvt.int64v;
ncbytesappendn(buf,(char*)&f,sizeof(f));
break;
case NC_UINT64:
f = (float)zcvt.uint64v;
ncbytesappendn(buf,(char*)&f,sizeof(f));
break;
case NC_STRING: /* Detect special constants encoded as strings e.g. "Nan" */
switch (naninftest(zcvt.strv,&naninf,&naninff)) {
case NC_NAT: abort();
case NC_FLOAT:
case NC_DOUBLE:
f = naninff; break;
break;
}
break;
default: abort();
}
ncbytesappendn(buf,(char*)&f,sizeof(f));
} break;
case NC_DOUBLE: {
double d = 0;
switch (srctype) {
case NC_DOUBLE:
d = (double)zcvt.float64v;
ncbytesappendn(buf,(char*)&d,sizeof(d));
break;
case NC_INT64:
d = (double)zcvt.int64v;
ncbytesappendn(buf,(char*)&d,sizeof(d));
break;
case NC_UINT64:
d = (double)zcvt.uint64v;
ncbytesappendn(buf,(char*)&d,sizeof(d));
break;
case NC_STRING: /* NaN might be quoted */
switch (naninftest(zcvt.strv,&naninf,&naninff)) {
case NC_NAT: abort();
case NC_FLOAT:
case NC_DOUBLE:
d = naninf; break;
break;
}
break;
default: abort();
}
ncbytesappendn(buf,(char*)&d,sizeof(d));
} break;
case NC_STRING: {
char* scopy = NULL;
Expand All @@ -360,10 +386,25 @@ NCZ_convert1(NCjson* jsrc, nc_type dsttype, NCbytes* buf)
scopy = NULL;
} break;
case NC_CHAR: {
if(srctype != NC_STRING) {stat = NC_EINVAL; goto done;}
len = strlen(zcvt.strv);
ncbytesappendn(buf,zcvt.strv,len);
} break;
char digits[64];
switch (srctype) {
case NC_DOUBLE:
snprintf(digits,sizeof(digits),"%lf",(double)zcvt.float64v);
ncbytesappendn(buf,digits,strlen(digits));
break;
case NC_INT64:
snprintf(digits,sizeof(digits),"%lli",(long long)zcvt.int64v);
ncbytesappendn(buf,digits,strlen(digits));
case NC_UINT64:
snprintf(digits,sizeof(digits),"%lli",(unsigned long long)zcvt.uint64v);
ncbytesappendn(buf,digits,strlen(digits));
break;
case NC_STRING:
len = strlen(zcvt.strv);
ncbytesappendn(buf,zcvt.strv,len);
default: abort();
}
} break;
default: stat = NC_EINTERNAL; goto done;
}

Expand All @@ -380,7 +421,9 @@ NCZ_stringconvert1(nc_type srctype, char* src, NCjson* jvalue)
struct ZCVT zcvt;
nc_type dsttype = NC_NAT;
char s[1024];
char sq[1024+2+1];
char* p = NULL;
int isnanorinf = 0;

assert(srctype >= NC_NAT && srctype != NC_CHAR && srctype <= NC_STRING);
/* Convert to a restricted set of values */
Expand Down Expand Up @@ -444,26 +487,35 @@ NCZ_stringconvert1(nc_type srctype, char* src, NCjson* jvalue)
#ifdef _MSC_VER
switch (_fpclass(zcvt.float64v)) {
case _FPCLASS_SNAN: case _FPCLASS_QNAN:
strcpy(s,"NaN"); break;
strcpy(s,"NaN"); isnanorinf = 1; break;
case _FPCLASS_NINF:
strcpy(s,"-Infinity"); break;
strcpy(s,"-Infinity"); isnanorinf = 1; break;
case _FPCLASS_PINF:
strcpy(s,"Infinity"); break;
strcpy(s,"Infinity"); isnanorinf = 1; break;
default:
snprintf(s,sizeof(s),"%lg",zcvt.float64v); /* handles NAN? */
break;
}
#else
if(isnan(zcvt.float64v))
strcpy(s,"NaN");
{strcpy(s,"NaN"); isnanorinf = 1;}
else if(isinf(zcvt.float64v) && zcvt.float64v < 0)
strcpy(s,"-Infinity");
{strcpy(s,"-Infinity"); isnanorinf = 1;}
else if(isinf(zcvt.float64v) && zcvt.float64v > 0)
strcpy(s,"Infinity");
{strcpy(s,"Infinity"); isnanorinf = 1;}
else {
snprintf(s,sizeof(s),"%lg",zcvt.float64v); /* handles NAN? */
}
#endif
/* Quote the nan/inf constant */
if(isnanorinf) {
size_t l = strlen(s);
memcpy(sq,s,l+1);
s[0] = '"';
memcpy(s+1,sq,l);
s[l+1] = '"';
s[l+2] = '\0';
}
} break;
case NC_STRING: {
p = nulldup(zcvt.strv);
Expand Down Expand Up @@ -543,3 +595,42 @@ typeid2jtype(nc_type typeid)
}
return NCJ_UNDEF;
}

/* Test for Nan(f) and Inf(f)
return 0 if not nan or inf
return NC_FLOAT if nanf or inff
return NC_DOUBLE if nan or inf
Always fill in both double and float cases so caller can choose
*/
static int
naninftest(const char* s, double* dcase, float* fcase)
{
nc_type nctype= NC_NAT;
assert(dcase && fcase);
if(strcasecmp(s,"nan")==0) {
*dcase = NAN; *fcase = NANF;
nctype = NC_DOUBLE;
} else if(strcasecmp(s,"-nan")==0) {
*dcase = (- NAN); *fcase = (- NANF);
nctype = NC_DOUBLE;
} else if(strcasecmp(s,"nanf")==0) {
*dcase = NAN; *fcase = NANF;
nctype = NC_FLOAT;
} else if(strcasecmp(s,"-nan")==0) {
*dcase = (- NAN); *fcase = (- NANF);
nctype = NC_FLOAT;
} else if(strcasecmp(s,"infinity")==0) {
*dcase = INFINITY; *fcase = INFINITYF;
nctype = NC_DOUBLE;
} else if(strcasecmp(s,"-infinity")==0) {
*dcase = (- INFINITY); *fcase = (- INFINITYF);
nctype = NC_DOUBLE;
} else if(strcasecmp(s,"infinityf")==0) {
*dcase = INFINITY; *fcase = INFINITYF;
nctype = NC_FLOAT;
} else if(strcasecmp(s,"-infinityf")==0) {
*dcase = (- INFINITY); *fcase = (- INFINITYF);
nctype = NC_FLOAT;
}
return nctype;
}
2 changes: 1 addition & 1 deletion libnczarr/zinternal.h
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Expand Up @@ -100,7 +100,7 @@ Inserted into any .zattrs ? or should it go into the container?
#define DFALT_DIM_SEPARATOR '.'

/* Default max string length for fixed length strings */
#define NCZ_MAXSTR_DEFAULT 64
#define NCZ_MAXSTR_DEFAULT 128

#define islegaldimsep(c) ((c) != '\0' && strchr(LEGAL_DIM_SEPARATORS,(c)) != NULL)

Expand Down
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