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fix appel problems with data lists

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This commit is contained in:
Dennis Heimbigner 2012-01-09 18:39:37 +00:00
parent 2d46d44e96
commit 599f35d2e6
15 changed files with 141 additions and 79 deletions
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6
cf
View File

@ -1,7 +1,7 @@
#!/bin/bash
#X="-x"
#HDF5=1
HDF5=1
#DAP=1
#CDMR=1
#RPC=1
@ -98,8 +98,8 @@ FLAGS="$FLAGS --disable-pnetcdf"
#FLAGS="$FLAGS --enable-dap-long-tests"
#FLAGS="$FLAGS --with-udunits"
#FLAGS="$FLAGS --with-libcf"
FLAGS="$FLAGS --enable-benchmarks"
FLAGS="$FLAGS --enable-extra-tests"
#FLAGS="$FLAGS --enable-benchmarks"
#FLAGS="$FLAGS --enable-extra-tests"
FLAGS="$FLAGS --disable-shared"
#FLAGS="$FLAGS --enable-shared"

2
configure.ac
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@ -15,7 +15,7 @@ AC_REVISION([$Id: configure.ac,v 1.450 2010/05/28 19:42:47 dmh Exp $])
AC_PREREQ([2.59])
# Initialize with name, version, and support email address.
AC_INIT([netCDF], [4.2-rc1], [support-netcdf@unidata.ucar.edu])
AC_INIT([netCDF], [4.2-rc2], [support-netcdf@unidata.ucar.edu])
# Create the VERSION file, which contains the package version from
# AC_INIT.

10
h5_test/tst_h_mem.c
View File

@ -8,13 +8,21 @@
either.
*/
#include <nc_tests.h>
#include "nc_tests.h"
#include <hdf5.h>
#include <H5DSpublic.h>
#define FILE_NAME "tst_h_mem.h5"
#define STR_LEN 255
const char*
nc_strerror(int ncerr)
{
static char msg[1024];
snprintf(msg,sizeof(msg),"error: %d\n",ncerr);
return msg;
}
int
main()
{

48
ncgen/bindata.c
View File

@ -129,22 +129,42 @@ bindata_basetype(Symbol* tsym, Datasrc* datasrc, Bytebuffer* memory, Datalist* f
case NC_VLEN: {
Constant* con;
nc_vlen_t ptr;
if(!isfillvalue(datasrc) && !issublist(datasrc)) {/* fail on no compound*/
semerror(srcline(datasrc),"Vlen data must be enclosed in {..}");
}
con = srcnext(datasrc);
if(con == NULL || con->nctype == NC_FILLVALUE) {
Datalist* filler = getfiller(tsym,fillsrc);
ASSERT(filler->length == 1);
con = &filler->data[0];
if(con->nctype != NC_COMPOUND) {
semerror(con->lineno,"Vlen data fill value is not enclosed in {..}");
Bytebuffer* vlenmem;
int count;
int pushed = 0;
Datasrc* olddatasrc = NULL;
if(isfillvalue(datasrc)) {
con = srcnext(datasrc);
if(con == NULL || con->nctype == NC_FILLVALUE) {
Datalist* filler = getfiller(tsym,fillsrc);
ASSERT(filler->length == 1);
con = &filler->data[0];
if(con->nctype != NC_COMPOUND) {
semerror(con->lineno,"Vlen data fill value is not enclosed in {..}");
} else {
olddatasrc = datasrc;
datasrc = const2src(con);
}
}
}
/* generate the nc_vlen_t instance*/
ptr.p = vlendata[con->value.compoundv->vlen.uid].data;
ptr.len = vlendata[con->value.compoundv->vlen.uid].count;
if(!issublist(datasrc)) {
semerror(srcline(datasrc),"Vlen data must be enclosed in {..}");
} else {
SRCPUSH(pushed,datasrc);
}
/* collect the nc_vlen_t instance*/
vlenmem = bbNew();
for(count=0;srcmore(datasrc);count++) {
bindata_basetype(tsym->typ.basetype,datasrc,vlenmem,NULL);
}
ptr.len = count;
ptr.p = bbDup(vlenmem);
bbFree(vlenmem);
bbAppendn(memory,(char*)&ptr,sizeof(ptr));
if(pushed) srcpop(datasrc);
if(olddatasrc) datasrc = olddatasrc;
} break;
case NC_FIELD:
@ -305,6 +325,7 @@ done:
}
#ifdef IGNORE
/*
This walk of the data lists collects
vlen sublists and constructs separate C constants
@ -353,5 +374,6 @@ bindata_vlenconstants(List* vlenconstants)
}
bbFree(memory);
}
#endif /*IGNORE*/
#endif /*ENABLE_BINARY*/

3
ncgen/bytebuffer.h
View File

@ -26,6 +26,9 @@ EXTERNC int bbFill(Bytebuffer*, const char fill);
/* Produce a duplicate of the contents*/
EXTERNC char* bbDup(const Bytebuffer*);
/* pull a duplicate of the contents*/
EXTERNC char* bbDup(const Bytebuffer*);
/* Return the ith char; -1 if no such char */
EXTERNC int bbGet(Bytebuffer*,unsigned int);

53
ncgen/cdata.c
View File

@ -21,6 +21,9 @@
static void cdata_primdata(Symbol*, Datasrc*, Bytebuffer*, Datalist*);
static void cdata_fieldarray(Symbol*, Datasrc*, Odometer*, int, Bytebuffer*, Datalist* fillsrc);
/* vlen uid generator */
static int uid = 0;
/* Specialty wrappers for cdata_data */
void
cdata_attrdata(Symbol* asym, Bytebuffer* codebuf)
@ -128,23 +131,47 @@ cdata_basetype(Symbol* tsym, Datasrc* datasrc, Bytebuffer* codebuf, Datalist* fi
case NC_VLEN: {
Constant* con;
if(!isfillvalue(datasrc) && !issublist(datasrc)) {/* fail on no compound*/
semerror(srcline(datasrc),"Vlen data must be enclosed in {..}");
}
con = srcnext(datasrc);
if(con == NULL || con->nctype == NC_FILLVALUE) {
Datalist* filler = getfiller(tsym,fillsrc);
ASSERT(filler->length == 1);
con = &filler->data[0];
if(con->nctype != NC_COMPOUND) {
semerror(con->lineno,"Vlen data fill value is not enclosed in {..}");
nc_vlen_t ptr;
Bytebuffer* vlenmem;
int count;
int pushed = 0;
Datasrc* olddatasrc = NULL;
if(isfillvalue(datasrc)) {
con = srcnext(datasrc);
if(con == NULL || con->nctype == NC_FILLVALUE) {
Datalist* filler = getfiller(tsym,fillsrc);
ASSERT(filler->length == 1);
con = &filler->data[0];
if(con->nctype != NC_COMPOUND) {
semerror(con->lineno,"Vlen data fill value is not enclosed in {..}");
} else {
olddatasrc = datasrc;
datasrc = const2src(con);
}
}
}
if(!issublist(datasrc)) {
semerror(srcline(datasrc),"Vlen data must be enclosed in {..}");
} else {
SRCPUSH(pushed,datasrc);
}
/* generate the nc_vlen_t instance*/
bbprintf0(stmt,"{%u (void*)vlen_%u}",
con->value.compoundv->vlen.count,
con->value.compoundv->vlen.uid);
vlenmem = bbNew();
for(count=0;srcmore(datasrc);count++) {
cdata_basetype(tsym->typ.basetype,datasrc,vlenmem,NULL);
}
/* generate the nc_vlen_t instance*/
bbprintf0(stmt,"{%u (void*)vlen_%u}",count,++uid);
bbCatbuf(codebuf,stmt);
ptr.len = count;
ptr.p = bbDup(vlenmem);
bbFree(vlenmem);
if(pushed) srcpop(datasrc);
if(olddatasrc) datasrc = olddatasrc;
} break;
case NC_FIELD:

3
ncgen/data.h
View File

@ -97,7 +97,6 @@ int isstringable(nc_type nctype);
void bindata_array(struct Symbol*,Bytebuffer*,Datasrc*,Odometer*,int,Datalist*);
void bindata_attrdata(struct Symbol* asym, Bytebuffer*);
void bindata_vardata(struct Symbol* vsym, Bytebuffer*);
void bindata_vlenconstants(List*);
void bindata_basetype(struct Symbol*,struct Datasrc*,Bytebuffer*,struct Datalist*);
#endif
@ -208,7 +207,7 @@ extern Constant fillconstant;
/* From genchar.c */
void gen_charattr(struct Symbol* asym, Bytebuffer* databuf);
void gen_chararray(struct Symbol* vsym, Bytebuffer* databuf, Datalist* fillsrc);
void gen_chararray(struct Symbol* vsym, Datasrc*, Bytebuffer* databuf, Datalist* fillsrc);
void gen_charfield(Datasrc* src, Odometer*, Bytebuffer* databuf);
void gen_charvlen(Datasrc*, Bytebuffer*);
int collectstring(struct Constant*, size_t, Bytebuffer*, int);

18
ncgen/genbin.c
View File

@ -13,7 +13,9 @@
#undef TRACE
#ifdef IGNORE
extern List* vlenconstants;
#endif
/* Forward*/
static void genbin_defineattr(Symbol* asym,Bytebuffer*);
@ -124,7 +126,9 @@ gen_netcdf(const char *filename)
#ifdef USE_NETCDF4
/* Collect vlen data*/
#ifdef IGNORE
bindata_vlenconstants(vlenconstants);
#endif
/* define special variable properties */
if(nvars > 0) {
@ -443,8 +447,6 @@ genbin_defineattr(Symbol* asym,Bytebuffer* databuf)
static void
genbin_definevardata(Symbol* vsym)
{
int varid, grpid;
int rank;
Bytebuffer* memory;
nciter_t iter;
Odometer* odom = NULL;
@ -452,10 +454,13 @@ genbin_definevardata(Symbol* vsym)
int chartype = (vsym->typ.basetype->typ.typecode == NC_CHAR);
Datalist* fillsrc = vsym->var.special._Fillvalue;
int isscalar = (vsym->typ.dimset.ndims == 0);
Datasrc* src;
#ifdef IGNORE
grpid = vsym->container->ncid,
varid = vsym->ncid;
rank = vsym->typ.dimset.ndims;
#endif
memory = bbNew();
/* give the buffer a running start to be large enough*/
@ -463,14 +468,15 @@ genbin_definevardata(Symbol* vsym)
if(vsym->data == NULL) return;
src = datalist2src(vsym->data);
/* Generate character constants separately */
if(!isscalar && chartype) {
gen_chararray(vsym,memory,fillsrc);
gen_chararray(vsym,src,memory,fillsrc);
/* generate a corresponding odometer */
odom = newodometer(&vsym->typ.dimset,NULL,NULL);
genbin_write(vsym,memory,odom,0);
} else { /* not character constant */
Datasrc* src = datalist2src(vsym->data);
if(isscalar) { /*scalar */
bindata_basetype(vsym->typ.basetype,src,memory,fillsrc); /*scalar*/
if(bbLength(memory) > 0)
@ -504,6 +510,10 @@ fprintf(stderr,"]\n");
}
odometerfree(odom);
bbFree(memory);
/* See if we have too much data */
if(srcmore(src)) {
semerror(srcline(src),"Extra data found at end of datalist");
}
}
static void

4
ncgen/genc.c
View File

@ -1081,19 +1081,19 @@ genc_definevardata(Symbol* vsym)
int chartype = (vsym->typ.basetype->typ.typecode == NC_CHAR);
if(vsym->data == NULL) return;
src = datalist2src(vsym->data);
code = bbNew();
/* give the buffer a running start to be large enough*/
bbSetalloc(code, nciterbuffersize);
if(!isscalar && chartype) {
gen_chararray(vsym,code,fillsrc);
gen_chararray(vsym,src,code,fillsrc);
/* generate a corresponding odometer */
odom = newodometer(&vsym->typ.dimset,NULL,NULL);
/* patch the odometer to use the right counts */
genc_write(vsym,code,odom,0);
} else { /* not character constant */
src = datalist2src(vsym->data);
fillsrc = vsym->var.special._Fillvalue;
/* Handle special cases first*/
if(isscalar) {

27
ncgen/genchar.c
View File

@ -21,7 +21,7 @@ So, this rather ugly code is kept in this file
and a variety of heuristics are used to mimic ncgen.
*/
static void gen_chararrayr(Dimset*, Bytebuffer*, int index, Datalist*, int fillchar, size_t);
static void gen_chararrayr(Dimset*, Bytebuffer*, int index, Datasrc*, int fillchar, size_t);
extern List* vlenconstants;
@ -120,20 +120,17 @@ datalistpad(Datalist* data, size_t targetlen)
1. pad
*/
void
gen_chararray(Symbol* vsym, Bytebuffer* databuf, Datalist* fillsrc)
gen_chararray(Symbol* vsym, Datasrc* data, Bytebuffer* databuf, Datalist* fillsrc)
{
int i,fillchar = getfillchar(fillsrc);
Datalist* data = vsym->data;
int lastunlimitedindex = lastunlimited(&vsym->typ.dimset);
/* If there is no unlimited, then treat similarly to a field array */
if(lastunlimitedindex < 0) {
/* Semantics.c:walkchararray will have done all the hard work */
for(i=0;i<data->length;i++) {
Constant* con = data->data+i;
while(srcmore(data)) {
Constant* con = srcnext(data);
ASSERT(con->nctype == NC_STRING);
bbAppendn(databuf,con->value.stringv.stringv,con->value.stringv.len);
}
@ -152,7 +149,7 @@ gen_chararray(Symbol* vsym, Bytebuffer* databuf, Datalist* fillsrc)
}
static void
gen_chararrayr(Dimset* dimset, Bytebuffer* databuf, int index, Datalist* data,
gen_chararrayr(Dimset* dimset, Bytebuffer* databuf, int index, Datasrc* data,
int fillchar, size_t subsize)
{
int i;
@ -164,8 +161,8 @@ gen_chararrayr(Dimset* dimset, Bytebuffer* databuf, int index, Datalist* data,
if(index == lastunlimitedindex) {
Constant* con;
/* pad to the unlimited size of the dimension * subsize */
ASSERT(data->length == 1);
con = data->data;
ASSERT(srcmore(data));
con = srcnext(data);
ASSERT(con->nctype == NC_STRING);
padstring(con,dim->dim.unlimitedsize*subsize,fillchar);
bbAppendn(databuf,con->value.stringv.stringv,con->value.stringv.len);
@ -173,16 +170,16 @@ gen_chararrayr(Dimset* dimset, Bytebuffer* databuf, int index, Datalist* data,
/* data should be a set of compounds */
size_t expected = (isunlimited ? dim->dim.unlimitedsize : dim->dim.declsize );
for(i=0;i<expected;i++) {
if(i >= data->length) {/* pad buffer */
if(!srcmore(data)) { /* pad buffer */
int j;
for(j=0;j<subsize;j++) bbAppend(databuf,fillchar);
} else {
Constant* con = data->data+i;
Datasrc* subdata;
Constant* con = srcnext(data);
if(con->nctype != NC_COMPOUND) continue;
/* recurse */
gen_chararrayr(dimset,databuf,index+1,con->value.compoundv,
fillchar,subsize);
subdata = datalist2src(con->value.compoundv);
gen_chararrayr(dimset,databuf,index+1,subdata,fillchar,subsize);
}
}
}

11
ncgen/genf77.c
View File

@ -50,15 +50,13 @@ void
gen_ncf77(const char *filename)
{
int idim, ivar, iatt;
int ndims, nvars, natts, ngatts, ngrps, ntyps;
int ndims, nvars, natts, ngatts;
char* cmode_string;
ndims = listlength(dimdefs);
nvars = listlength(vardefs);
natts = listlength(attdefs);
ngatts = listlength(gattdefs);
ngrps = listlength(grpdefs);
ntyps = listlength(typdefs);
/* Construct the main program */
@ -544,12 +542,10 @@ f77fold(Bytebuffer* lines)
char* s;
char* line0;
char* linen;
int linesize;
static char trimchars[] = " \t\r\n";
s = bbDup(lines);
bbClear(lines);
linesize = 0;
line0 = s;
/* Start by trimming leading blanks and empty lines */
while(*line0 && strchr(trimchars,*line0) != NULL) line0++;
@ -771,18 +767,17 @@ genf77_definevardata(Symbol* vsym)
int chartype = (vsym->typ.basetype->typ.typecode == NC_CHAR);
if(vsym->data == NULL) return;
src = datalist2src(vsym->data);
code = bbNew();
/* give the buffer a running start to be large enough*/
bbSetalloc(code, nciterbuffersize);
if(!isscalar && chartype) {
gen_chararray(vsym,code,fillsrc);
gen_chararray(vsym,src,code,fillsrc);
genf77_write(vsym,code,NULL,0,0);
} else { /* not character constant */
src = datalist2src(vsym->data);
fillsrc = vsym->var.special._Fillvalue;
/* Handle special cases first*/
if(isscalar) {
f77data_basetype(vsym->typ.basetype,src,code,fillsrc);

12
ncgen/genj.c
View File

@ -41,15 +41,12 @@ void
gen_ncjava(const char *filename)
{
int idim, ivar, iatt, maxdims;
int ndims, nvars, natts, ngatts, ngrps, ntyps;
char* cmode_string;
int ndims, nvars, natts, ngatts;
ndims = listlength(dimdefs);
nvars = listlength(vardefs);
natts = listlength(attdefs);
ngatts = listlength(gattdefs);
ngrps = listlength(grpdefs);
ntyps = listlength(typdefs);
/* Construct the main class */
codeline("import java.util.*;");
@ -105,6 +102,7 @@ gen_ncjava(const char *filename)
codeline("");
codelined(1,"/* enter define mode */");
#ifdef IGNORE
if(!cmode_modifier) {
cmode_string = "NC_CLOBBER";
} else if(cmode_modifier & NC_64BIT_OFFSET) {
@ -113,6 +111,7 @@ gen_ncjava(const char *filename)
derror("unknown cmode modifier");
cmode_string = "NC_CLOBBER";
}
#endif
bbprintf0(stmt,
"%sNetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(\"%s\", %s);\n",
@ -554,18 +553,17 @@ genj_definevardata(Symbol* vsym)
int chartype = (vsym->typ.basetype->typ.typecode == NC_CHAR);
if(vsym->data == NULL) return;
src = datalist2src(vsym->data);
code = bbNew();
/* give the buffer a running start to be large enough*/
bbSetalloc(code, nciterbuffersize);
if(!isscalar && chartype) {
gen_chararray(vsym,code,fillsrc);
gen_chararray(vsym,src,code,fillsrc);
genj_write(vsym,code,NULL,0,0);
} else { /* not character constant */
src = datalist2src(vsym->data);
fillsrc = vsym->var.special._Fillvalue;
/* Handle special cases first*/
if(isscalar) {
jdata_basetype(vsym->typ.basetype,src,code,fillsrc);

17
ncgen/ncgen.1
View File

@ -638,17 +638,20 @@ the variable
Specifying datalists for variables in the `data:` section can be somewhat
complicated. There are some rules that must be followed
to ensure that datalists are parsed correctly by ncgen.
.LP
First, the top level is automatically assumed to be a list of items, so it should not be inside {...}.
That means that if the variable is a scalar, there will be a single top-level element
and if the variable is an array, there will be N top-level elements.
For each element of the top level list, the following rules should be applied.
.IP 1. 3
The top level is automatically assumed to be a list of items, so it should not be inside {...}.
.IP 2. 3
Instances of UNLIMITED dimensions (other than the first dimension) must be surrounded by {...} in order to specify the size.
.IP 3. 3
Instances of vlens must be surrounded by {...} in order to specify the size.
.IP 4. 3
.IP 2. 3
Compound instances must be embedded in {...}
.IP 5. 3
.IP 3. 3
Non-scalar fields of compound instances must be embedded in {...}.
.IP 6. 3
.IP 4. 3
Instances of vlens must be surrounded by {...} in order to specify the size.
.LP
Datalists associated with attributes are implicitly a vector (i.e., a list) of values of the type of the attribute and the above rules must apply with that in mind.
.IP 7. 3
No other use of braces is allowed.

1
ncgen/ncgen.h
View File

@ -33,6 +33,7 @@
#define NC_ARRAY 107
#define NC_PRIM 108 /*Including NC_STRING */
#define NC_STRUCT NC_COMPOUND /* alias */
#define NC_LIST NC_COMPOUND /* alias */
/* Extend nc types with generic fill value*/
#define NC_FILLVALUE 31

5
ncgen/semantics.c
View File

@ -1088,10 +1088,8 @@ walkfieldarray(Symbol* basetype, Datasrc* src, Dimset* dimset, int index)
int lastdim = (index == (rank-1));
Symbol* dim = dimset->dimsyms[index];
size_t datasize = dim->dim.declsize;
size_t count = 0;
ASSERT(datasize != 0);
count = datasize;
for(i=0;i<datasize;i++) {
if(lastdim)
walktype(basetype,src,NULL);
@ -1214,7 +1212,6 @@ walkchararray(Symbol* vsym, Datalist* fillsrc)
{
Dimset* dimset = &vsym->typ.dimset;
int lastunlimindex;
int simpleunlim;
int rank = dimset->ndims;
Symbol* lastdim = dimset->dimsyms[rank-1];
size_t lastdimsize = lastdim->dim.declsize;
@ -1222,7 +1219,9 @@ walkchararray(Symbol* vsym, Datalist* fillsrc)
int fillchar = getfillchar(fillsrc);
lastunlimindex = lastunlimited(dimset);
#ifdef IGNORE
simpleunlim = (lastunlimindex == 0);
#endif
/* If the unlimited is also the last dimension, then do no padding */
if(lastdimsize == 0) lastdimsize = 1;