netcdf-c/ncgen/data.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

802 lines
17 KiB
C

/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
/* $Id: data.c,v 1.7 2010/05/24 19:59:56 dmh Exp $ */
/* $Header: /upc/share/CVS/netcdf-3/ncgen/data.c,v 1.7 2010/05/24 19:59:56 dmh Exp $ */
#include "includes.h"
#include "ncoffsets.h"
#include "netcdf_aux.h"
#include "dump.h"
#undef VERIFY
#define XVSNPRINTF vsnprintf
/*
#define XVSNPRINTF lvsnprintf
extern int lvsnprintf(char*, size_t, const char*, va_list);
*/
#define DATALISTINIT 32
/* Track all known datalist*/
List* alldatalists = NULL;
NCConstant nullconstant;
NCConstant fillconstant;
Datalist* filldatalist;
Bytebuffer* codebuffer;
Bytebuffer* codetmp;
Bytebuffer* stmt;
/* Forward */
static void setconstlist(NCConstant* con, Datalist* dl);
#ifdef VERIFY
/* index of match */
static int
verify(List* all, Datalist* dl)
{
int i;
for(i=0;i<listlength(all);i++) {
void* pi = listget(all,i);
if(pi == dl)
return i;
}
return -1;
}
#endif
/**************************************************/
/**************************************************/
NCConstant*
nullconst(void)
{
NCConstant* n = ecalloc(sizeof(NCConstant));
return n;
}
int
isstringable(nc_type nctype)
{
switch (nctype) {
case NC_CHAR: case NC_STRING:
case NC_BYTE: case NC_UBYTE:
case NC_FILLVALUE:
return 1;
default: break;
}
return 0;
}
NCConstant*
list2const(Datalist* list)
{
NCConstant* con = nullconst();
ASSERT(list != NULL);
con->nctype = NC_COMPOUND;
if(!list->readonly) con->lineno = list->data[0]->lineno;
setconstlist(con,list);
con->filled = 0;
return con;
}
Datalist*
const2list(NCConstant* con)
{
Datalist* list;
ASSERT(con != NULL);
list = builddatalist(1);
if(list != NULL) {
dlappend(list,con);
}
return list;
}
/**************************************************/
#ifdef GENDEBUG
void
report(char* lead, Datalist* list)
{
extern void bufdump(Datalist*,Bytebuffer*);
Bytebuffer* buf = bbNew();
bufdump(list,buf);
fprintf(stderr,"\n%s::%s\n",lead,bbContents(buf));
fflush(stderr);
bbFree(buf);
}
#endif
/**************************************************/
static void
setconstlist(NCConstant* con, Datalist* dl)
{
#ifdef VERIFY
int pos = verify(alldatalists,dl);
if(pos >= 0) {
dumpdatalist(listget(alldatalists,pos),"XXX");
}
#endif
con->value.compoundv = dl;
}
/* Deep constant cloning; return struct not pointer to struct*/
NCConstant*
cloneconstant(NCConstant* con)
{
NCConstant* newcon = NULL;
Datalist* newdl = NULL;
char* s = NULL;
newcon = nullconst();
if(newcon == NULL) return newcon;
*newcon = *con;
switch (newcon->nctype) {
case NC_STRING:
if(newcon->value.stringv.len == 0)
s = NULL;
else {
s = (char*)ecalloc(newcon->value.stringv.len+1);
if(newcon->value.stringv.len > 0)
memcpy(s,newcon->value.stringv.stringv,newcon->value.stringv.len);
s[newcon->value.stringv.len] = '\0';
}
newcon->value.stringv.stringv = s;
break;
case NC_OPAQUE:
s = (char*)ecalloc(newcon->value.opaquev.len+1);
if(newcon->value.opaquev.len > 0)
memcpy(s,newcon->value.opaquev.stringv,newcon->value.opaquev.len);
s[newcon->value.opaquev.len] = '\0';
newcon->value.opaquev.stringv = s;
break;
case NC_COMPOUND:
newdl = clonedatalist(con->value.compoundv);
setconstlist(newcon,newdl);
break;
default: break;
}
return newcon;
}
/* Deep constant clear*/
void
clearconstant(NCConstant* con)
{
if(con == NULL) return;
switch (con->nctype) {
case NC_STRING:
if(con->value.stringv.stringv != NULL)
efree(con->value.stringv.stringv);
break;
case NC_OPAQUE:
if(con->value.opaquev.stringv != NULL)
efree(con->value.opaquev.stringv);
break;
case NC_COMPOUND:
con->value.compoundv = NULL;
break;
default: break;
}
memset((void*)con,0,sizeof(NCConstant));
}
void
freeconstant(NCConstant* con, int shallow)
{
if(!shallow) clearconstant(con);
nullfree(con);
}
/**************************************************/
int
datalistline(Datalist* ds)
{
if(ds == NULL || ds->length == 0) return 0;
return ds->data[0]->lineno;
}
/* Go thru a databuf of possibly nested constants
and insert commas as needed; ideally, this
operation should be idempotent so that
the caller need not worry about it having already
been applied. Also, handle situation where there may be missing
matching right braces.
*/
static char* commifyr(char* p, Bytebuffer* buf);
static char* wordstring(char* p, Bytebuffer* buf, int quote);
void
commify(Bytebuffer* buf)
{
char* list,*p;
if(bbLength(buf) == 0) return;
list = bbDup(buf);
p = list;
bbClear(buf);
commifyr(p,buf);
bbNull(buf);
efree(list);
}
/* Requires that the string be balanced
WRT to braces
*/
static char*
commifyr(char* p, Bytebuffer* buf)
{
int comma = 0;
int c;
while((c=*p++)) {
if(c == ' ') continue;
if(c == ',') continue;
else if(c == '}') {
break;
}
if(comma) bbCat(buf,", "); else comma=1;
if(c == '{') {
bbAppend(buf,'{');
p = commifyr(p,buf);
bbAppend(buf,'}');
} else if(c == '\'' || c == '\"') {
p = wordstring(p,buf,c);
} else {
bbAppend(buf,c);
p=word(p,buf);
}
}
return p;
}
char*
word(char* p, Bytebuffer* buf)
{
int c;
while((c=*p++)) {
if(c == '}' || c == ' ' || c == ',') break;
if(c == '\\') {
bbAppend(buf,c);
c=*p++;
if(!c) break;
}
bbAppend(buf,(char)c);
}
p--; /* leave terminator for parent */
return p;
}
static char*
wordstring(char* p, Bytebuffer* buf, int quote)
{
int c;
bbAppend(buf,quote);
while((c=*p++)) {
if(c == '\\') {
bbAppend(buf,c);
c = *p++;
if(c == '\0') return --p;
} else if(c == quote) {
bbAppend(buf,c);
return p;
}
bbAppend(buf,c);
}
return p;
}
static const char zeros[] =
"\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
void
alignbuffer(NCConstant* prim, Bytebuffer* buf)
{
int alignment,pad,offset;
ASSERT(prim->nctype != NC_COMPOUND);
if(prim->nctype == NC_ECONST)
alignment = ncaux_class_alignment(prim->value.enumv->typ.typecode);
else if(usingclassic && prim->nctype == NC_STRING)
alignment = ncaux_class_alignment(NC_CHAR);
else if(prim->nctype == NC_CHAR)
alignment = ncaux_class_alignment(NC_CHAR);
else
alignment = ncaux_class_alignment(prim->nctype);
offset = bbLength(buf);
pad = getpadding(offset,alignment);
if(pad > 0) {
bbAppendn(buf,(void*)zeros,pad);
}
}
/*
Following routines are in support of language-oriented output
*/
void
codedump(Bytebuffer* buf)
{
bbCatbuf(codebuffer,buf);
bbClear(buf);
}
void
codepartial(const char* txt)
{
bbCat(codebuffer,txt);
}
void
codeline(const char* line)
{
codepartial(line);
codepartial("\n");
}
void
codelined(int n, const char* txt)
{
bbindent(codebuffer,n);
bbCat(codebuffer,txt);
codepartial("\n");
}
void
codeflush(void)
{
if(bbLength(codebuffer) > 0) {
bbNull(codebuffer);
fputs(bbContents(codebuffer),stdout);
fflush(stdout);
bbClear(codebuffer);
}
}
void
bbindent(Bytebuffer* buf, const int n)
{
bbCat(buf,indented(n));
}
/* Provide an restrict snprintf that writes to an expandable buffer */
/* Simulates a simple snprintf because apparently
the IRIX one is broken wrt return value.
Supports only %u %d %f %s and %% specifiers
with optional leading hh or ll.
*/
static void
vbbprintf(Bytebuffer* buf, const char* fmt, va_list argv)
{
char tmp[128];
const char* p;
int c;
int hcount;
int lcount;
char* text;
for(p=fmt;(c=*p++);) {
hcount = 0; lcount = 0;
switch (c) {
case '%':
retry: switch ((c=*p++)) {
case '\0': bbAppend(buf,'%'); p--; break;
case '%': bbAppend(buf,c); break;
case 'h':
hcount++;
while((c=*p) && (c == 'h')) {hcount++; p++;}
if(hcount > 2) hcount = 2;
goto retry;
case 'l':
lcount++;
while((c=*p) && (c == 'l')) {
lcount++;
p++;
}
if(lcount > 2) lcount = 2;
goto retry;
case 'u':
if(hcount == 2) {
snprintf(tmp,sizeof(tmp),"%hhu",
(unsigned char)va_arg(argv,unsigned int));
} else if(hcount == 1) {
snprintf(tmp,sizeof(tmp),"%hu",
(unsigned short)va_arg(argv,unsigned int));
} else if(lcount == 2) {
snprintf(tmp,sizeof(tmp),"%llu",
(unsigned long long)va_arg(argv,unsigned long long));
} else if(lcount == 1) {
snprintf(tmp,sizeof(tmp),"%lu",
(unsigned long)va_arg(argv,unsigned long));
} else {
snprintf(tmp,sizeof(tmp),"%u",
(unsigned int)va_arg(argv,unsigned int));
}
bbCat(buf,tmp);
break;
case 'd':
if(hcount == 2) {
snprintf(tmp,sizeof(tmp),"%hhd",
(signed char)va_arg(argv,signed int));
} else if(hcount == 1) {
snprintf(tmp,sizeof(tmp),"%hd",
(signed short)va_arg(argv,signed int));
} else if(lcount == 2) {
snprintf(tmp,sizeof(tmp),"%lld",
(signed long long)va_arg(argv,signed long long));
} else if(lcount == 1) {
snprintf(tmp,sizeof(tmp),"%ld",
(signed long)va_arg(argv,signed long));
} else {
snprintf(tmp,sizeof(tmp),"%d",
(signed int)va_arg(argv,signed int));
}
bbCat(buf,tmp);
break;
case 'f':
if(lcount > 0) {
snprintf(tmp,sizeof(tmp),"((double)%.16g)",
(double)va_arg(argv,double));
} else {
snprintf(tmp,sizeof(tmp),"((float)%.8g)",
(double)va_arg(argv,double));
}
bbCat(buf,tmp);
break;
case 's':
text = va_arg(argv,char*);
bbCat(buf,text);
break;
case 'c':
c = va_arg(argv,int);
bbAppend(buf,(char)c);
break;
default:
PANIC1("vbbprintf: unknown specifier: %c",(char)c);
}
break;
default:
bbAppend(buf,c);
}
}
}
void
bbprintf(Bytebuffer* buf, const char *fmt, ...)
{
va_list argv;
va_start(argv,fmt);
vbbprintf(buf,fmt,argv);
va_end(argv);
}
void
bbprintf0(Bytebuffer* buf, const char *fmt, ...)
{
va_list argv;
va_start(argv,fmt);
bbClear(buf);
vbbprintf(buf,fmt,argv);
va_end(argv);
}
void
codeprintf(const char *fmt, ...)
{
va_list argv;
va_start(argv,fmt);
vbbprintf(codebuffer,fmt,argv);
va_end(argv);
}
NCConstant*
emptycompoundconst(int lineno)
{
NCConstant* c = nullconst();
c->lineno = lineno;
c->nctype = NC_COMPOUND;
setconstlist(c,builddatalist(0));
c->filled = 0;
return c;
}
/* Make an empty string constant*/
NCConstant*
emptystringconst(int lineno)
{
NCConstant* c = nullconst();
ASSERT(c != NULL);
c->lineno = lineno;
c->nctype = NC_STRING;
c->value.stringv.len = 0;
c->value.stringv.stringv = NULL;
c->filled = 0;
return c;
}
#define INDENTMAX 256
static char* dent = NULL;
char*
indented(int n)
{
char* indentation;
if(dent == NULL) {
dent = (char*)ecalloc(INDENTMAX+1);
memset((void*)dent,' ',INDENTMAX);
dent[INDENTMAX] = '\0';
}
if(n*4 >= INDENTMAX) n = INDENTMAX/4;
indentation = dent+(INDENTMAX - 4*n);
return indentation;
}
void
dlsetalloc(Datalist* dl, size_t need)
{
NCConstant** newdata = NULL;
if(dl->readonly) abort();
if(dl->alloc < need) {
newdata = (NCConstant**)ecalloc(need*sizeof(NCConstant*));
if(dl->length > 0)
memcpy(newdata,dl->data,sizeof(NCConstant*)*dl->length);
dl->alloc = need;
nullfree(dl->data);
dl->data = newdata;
}
}
void
dlextend(Datalist* dl)
{
size_t newalloc;
if(dl->readonly) abort();
newalloc = (dl->alloc > 0?2*dl->alloc:2);
dlsetalloc(dl,newalloc);
}
void
capture(Datalist* dl)
{
if(alldatalists == NULL) alldatalists = listnew();
listpush(alldatalists,dl);
}
Datalist*
builddatalist(int initial)
{
Datalist* ci;
if(initial <= 0) initial = DATALISTINIT;
initial++; /* for header*/
ci = (Datalist*)ecalloc(sizeof(Datalist));
if(ci == NULL) semerror(0,"out of memory\n");
ci->data = (NCConstant**)ecalloc(sizeof(NCConstant*)*initial);
ci->alloc = initial;
ci->length = 0;
return ci;
}
void
dlappend(Datalist* dl, NCConstant* constant)
{
if(dl->readonly) abort();
if(dl->length >= dl->alloc)
dlextend(dl);
dl->data[dl->length++] = (constant);
}
void
dlset(Datalist* dl, size_t pos, NCConstant* constant)
{
ASSERT(pos < dl->length);
dl->data[pos] = (constant);
}
NCConstant*
dlremove(Datalist* dl, size_t pos)
{
int i;
NCConstant* con = NULL;
ASSERT(dl->length > 0 && pos < dl->length);
con = dl->data[pos];
for(i=pos+1;i<dl->length;i++)
dl->data[i-1] = dl->data[i];
dl->length--;
return con;
}
void
dlinsert(Datalist* dl, size_t pos, Datalist* insertion)
{
int i;
int len1 = datalistlen(dl);
int len2 = datalistlen(insertion);
int delta = len1 - pos;
dlsetalloc(dl,len2+len1+1);
/* move contents of dl up to make room for insertion */
if(delta > 0)
memmove(&dl->data[pos+len2],&dl->data[pos],delta*sizeof(NCConstant*));
dl->length += len2;
for(i=0;i<len2;i++) {
NCConstant* con = insertion->data[i];
con = cloneconstant(con);
dl->data[pos+i] = con;
}
}
/* Convert a datalist to a compound constant */
NCConstant*
builddatasublist(Datalist* dl)
{
NCConstant* d = nullconst();
d->nctype = NC_COMPOUND;
d->lineno = (dl->length > 0?dl->data[0]->lineno:0);
setconstlist(d,dl);
d->filled = 0;
return d;
}
/* Convert a subsequence of a datalist to its own datalist */
Datalist*
builddatasubset(Datalist* dl, size_t start, size_t count)
{
Datalist* subset;
if(dl == NULL || start >= datalistlen(dl)) return NULL;
if((start + count) > datalistlen(dl))
count = (datalistlen(dl) - start);
subset = (Datalist*)ecalloc(sizeof(Datalist));
subset->readonly = 1;
subset->length = count;
subset->alloc = count;
subset->data = &dl->data[start];
return subset;
}
/* Deep copy */
Datalist*
clonedatalist(Datalist* dl)
{
int i;
size_t len;
Datalist* newdl;
if(dl == NULL) return NULL;
len = datalistlen(dl);
newdl = builddatalist(len);
/* initialize */
for(i=0;i<len;i++) {
NCConstant* con = datalistith(dl,i);
con = cloneconstant(con);
dlappend(newdl,con);
}
return newdl;
}
/* recursive helpers */
void
reclaimconstant(NCConstant* con)
{
if(con == NULL) return;
switch (con->nctype) {
case NC_STRING:
if(con->value.stringv.stringv != NULL)
efree(con->value.stringv.stringv);
break;
case NC_OPAQUE:
if(con->value.opaquev.stringv != NULL)
efree(con->value.opaquev.stringv);
break;
case NC_COMPOUND:
#ifdef VERIFY
{int pos;
if((pos=verify(alldatalists,con->value.compoundv)) >= 0) {
dumpdatalist(listget(alldatalists,pos),"XXX");
abort();
}
}
#endif
reclaimdatalist(con->value.compoundv);
con->value.compoundv = NULL;
break;
default: break;
}
efree(con);
}
void
reclaimdatalist(Datalist* list)
{
int i;
if(list == NULL) return;
if(!list->readonly) {
if(list->data != NULL) {
for(i=0;i<list->length;i++) {
NCConstant* con = list->data[i];
if(con != NULL) reclaimconstant(con);
}
}
}
freedatalist(list);
}
/* Like reclaimdatalist, but do not try to reclaim contained constants */
void
freedatalist(Datalist* list)
{
if(list == NULL) return;
if(!list->readonly) {
efree(list->data);
list->data = NULL;
}
efree(list);
}
void
reclaimalldatalists(void)
{
int i;
for(i=0;i<listlength(alldatalists);i++) {
Datalist* di = listget(alldatalists,i);
if(di != NULL)
reclaimdatalist(di);
}
efree(alldatalists);
alldatalists = NULL;
}
static void
flattenR(Datalist* result, Datalist* data, int rank, int depth)
{
int i;
NCConstant* con;
if(rank == depth) return;
if(datalistlen(data) == 0) return;
for(i=0;i<datalistlen(data);i++) {
con = datalistith(data,i);
if(depth < rank - 1) {
/* Is this is a char list, then we might have short depth */
if(islistconst(con))
flattenR(result,compoundfor(con),rank,depth+1);
else
dlappend(result,con);
} else { /* depth == rank -1, last dimension */
dlappend(result,con);
}
}
}
/* Produce a new list that is the concat of all the leaf constants */
Datalist*
flatten(Datalist* list,int rank)
{
Datalist* result = builddatalist(0);
flattenR(result,list,rank,0);
return result;
}