netcdf-c/ncgen/data.c
Dennis Heimbigner 68a98f6e81 Fix ncgen handling of big data sections
The current ncgen does not properly handle very large
data sections. Apparently this is very uncommon because
it was only discovered in testing the new zarr code.

The fix required a new approach to processing data sections.
Unfortunately, the resulting ncgen is slower than before
but at least it is, I think, now correct.

The added test cases are in libnczarr, and so will
not show up until that is incorporated into master.

Note also that fortran code generation changed, but
has not been tested here.

Misc. Changes
1. Cleanup error handling in ncgen -lc and -lb output
2. Cleanup Makefiles for ncgen to remove unused code
3. Added a program, ncgen/ncdumpchunks, to print
   the data for a .nc file on a per-chunk format.
4. Made the XGetOpt change in PR https://github.com/Unidata/netcdf-c/pull/1694
   for ncdump/ncvalidator
2020-05-14 11:20:46 -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;
}