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https://github.com/Unidata/netcdf-c.git
synced 2024-11-21 03:13:42 +08:00
751300ec59
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
543 lines
18 KiB
C
543 lines
18 KiB
C
/*********************************************************************
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* Copyright 2009, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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*********************************************************************/
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#include "includes.h"
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#include "nc_iter.h"
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#include "odom.h"
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#include "ncoffsets.h"
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#include "netcdf_aux.h"
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/**************************************************/
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/* Code for generating data lists*/
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/**************************************************/
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/* For datalist constant rules: see the rules on the man page */
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/* Forward*/
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static void generate_array(Symbol*,Bytebuffer*,Datalist*,Generator*,Writer);
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static void generate_arrayr(Symbol*,Bytebuffer*,Datalist*,Odometer*,int,Datalist*,Generator*);
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static void generate_primdata(Symbol*, NCConstant*, Bytebuffer*, Datalist* fillsrc, Generator*);
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static void generate_fieldarray(Symbol*, NCConstant*, Dimset*, Bytebuffer*, Datalist* fillsrc, Generator*);
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/* Mnemonics */
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#define VLENLIST1
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#define FIELDARRAY 1
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/**************************************************/
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int
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generator_getstate(Generator* generator ,void** statep)
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{
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if(statep) *statep = (void*)generator->globalstate;
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return 1;
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}
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int generator_reset(Generator* generator, void* state)
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{
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generator->globalstate = state;
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return 1;
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}
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#ifdef IGNORe
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static void
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checkodom(Odometer* odom)
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{
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int i;
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for(i=0;i<odom->rank;i++) {
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ASSERT(odom->index[i] == odom->start[i]+odom->count[i]);
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}
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}
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#endif
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/**************************************************/
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void
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generate_attrdata(Symbol* asym, Generator* generator, Writer writer, Bytebuffer* codebuf)
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{
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Symbol* basetype = asym->typ.basetype;
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nc_type typecode = basetype->typ.typecode;
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if(typecode == NC_CHAR) {
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gen_charattr(asym->data,codebuf);
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} else {
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int uid;
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size_t count;
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generator->listbegin(generator,asym,NULL,LISTATTR,asym->data->length,codebuf,&uid);
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for(count=0;count<asym->data->length;count++) {
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NCConstant* con = datalistith(asym->data,count);
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generator->list(generator,asym,NULL,LISTATTR,uid,count,codebuf);
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generate_basetype(asym->typ.basetype,con,codebuf,NULL,generator);
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}
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generator->listend(generator,asym,NULL,LISTATTR,uid,count,codebuf);
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}
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writer(generator,asym,codebuf,0,NULL,NULL);
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}
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void
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generate_vardata(Symbol* vsym, Generator* generator, Writer writer, Bytebuffer* code)
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{
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Dimset* dimset = &vsym->typ.dimset;
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int rank = dimset->ndims;
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Symbol* basetype = vsym->typ.basetype;
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Datalist* filler = getfiller(vsym);
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if(vsym->data == NULL) return;
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/* give the buffer a running start to be large enough*/
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if(!bbSetalloc(code, nciterbuffersize))
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return;
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if(rank == 0) {/*scalar case*/
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NCConstant* c0 = datalistith(vsym->data,0);
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generate_basetype(basetype,c0,code,filler,generator);
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writer(generator,vsym,code,0,NULL,NULL);
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} else {/*rank > 0*/
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#if 0
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/* First, create an odometer using all of the dimensions */
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odom = newodometer(dimset,NULL,NULL);
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start = odometerstartvector(odom);
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count = odometercountvector(odom);
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#endif
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generate_array(vsym,code,filler,generator,writer);
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}
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}
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/**
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The basic idea is to split the set of dimensions into
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groups and iterate over each group by recursion.
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A group is defined as the range of indices starting at an
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unlimited dimension upto (but not including) the next
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unlimited.
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The first group starts at index 0, even if dimension 0 is not
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unlimited. The last group is everything from the last
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unlimited dimension thru the last dimension (index rank-1).
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*/
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static void
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generate_array(Symbol* vsym,
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Bytebuffer* code,
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Datalist* filler,
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Generator* generator,
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Writer writer
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)
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{
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Dimset* dimset = &vsym->typ.dimset;
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int rank = dimset->ndims;
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Symbol* basetype = vsym->typ.basetype;
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nc_type typecode = basetype->typ.typecode;
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nciter_t iter;
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int firstunlim = findunlimited(dimset,1);
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int nunlim = countunlimited(dimset);
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int isnc3unlim = (nunlim <= 1 && (firstunlim == 0 || firstunlim == rank)); /* netcdf-3 case of at most 1 unlim in 0th dimension */
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ASSERT(rank > 0);
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if(isnc3unlim) {
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/* Handle NC_CHAR case separately */
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if(typecode == NC_CHAR) {
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Odometer* odom = newodometer(dimset,NULL,NULL);
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Bytebuffer* charbuf = bbNew();
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gen_chararray(dimset,0,vsym->data,charbuf,filler);
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generator->charconstant(generator,vsym,code,charbuf);
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/* Create an odometer to get the dimension info */
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writer(generator,vsym,code,odom->rank,odom->start,odom->count);
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#if 0
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writer(generator,vsym,code,odom->rank,0,bbLength(charbuf));
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#endif
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bbFree(charbuf);
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odometerfree(odom);
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} else { /* typecode != NC_CHAR */
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Odometer* odom = newodometer(dimset,NULL,NULL);
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/* Case: dim 1..rank-1 are not unlimited, dim 0 might be */
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size_t offset = 0; /* where are we in the data list */
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size_t nelems = 0; /* # of data list items to generate */
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/* Create an iterator and odometer and just walk the datalist */
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nc_get_iter(vsym,nciterbuffersize,&iter);
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for(;;offset+=nelems) {
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int i,uid;
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nelems=nc_next_iter(&iter,odometerstartvector(odom),odometercountvector(odom));
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if(nelems == 0)
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break;
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bbClear(code);
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generator->listbegin(generator,vsym,NULL,LISTDATA,vsym->data->length,code,&uid);
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for(i=0;i<nelems;i++) {
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NCConstant* con = datalistith(vsym->data,i+offset);
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generator->list(generator,vsym,NULL,LISTDATA,uid,i,code);
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generate_basetype(basetype,con,code,filler,generator);
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}
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generator->listend(generator,vsym,NULL,LISTDATA,uid,i,code);
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writer(generator,vsym,code,rank,odom->start,odom->count);
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}
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odometerfree(odom);
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}
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} else { /* Hard case: multiple unlimited dimensions or unlim in dim > 0*/
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Odometer* odom = newodometer(dimset,NULL,NULL);
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/* Setup iterator and odometer */
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nc_get_iter(vsym,NC_MAX_UINT,&iter); /* effectively infinite */
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for(;;) {/* iterate in nelem chunks */
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/* get nelems count and modify odometer */
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size_t nelems=nc_next_iter(&iter,odom->start,odom->count);
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if(nelems == 0) break;
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generate_arrayr(vsym,code,vsym->data,
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odom,
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/*dim index=*/0,
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filler,generator
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);
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writer(generator,vsym,code,odom->rank,odom->start,odom->count);
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}
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odometerfree(odom);
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}
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}
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/**
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The basic idea is to split the set of dimensions into groups
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and iterate over each group. A group is defined as the
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range of indices starting at an unlimited dimension upto
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(but not including) the next unlimited. The first group
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starts at index 0, even if dimension 0 is not unlimited.
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The last group is everything from the last unlimited
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dimension thru the last dimension (index rank-1).
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*/
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static void
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generate_arrayr(Symbol* vsym,
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Bytebuffer* code,
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Datalist* list,
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Odometer* odom,
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int dimindex,
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Datalist* filler,
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Generator* generator
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)
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{
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int uid,i;
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Symbol* basetype = vsym->typ.basetype;
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Dimset* dimset = &vsym->typ.dimset;
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int rank = dimset->ndims;
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int lastunlimited = findlastunlimited(dimset);
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int nextunlimited = findunlimited(dimset,dimindex+1);
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int typecode = basetype->typ.typecode;
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int islastgroup = (lastunlimited == rank || dimindex >= lastunlimited || dimindex == rank-1);
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Odometer* subodom = NULL;
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ASSERT(rank > 0);
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ASSERT((dimindex >= 0 && dimindex < rank));
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if(islastgroup) {
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/* Handle NC_CHAR case separately */
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if(typecode == NC_CHAR) {
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Bytebuffer* charbuf = bbNew();
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gen_chararray(dimset,dimindex,list,charbuf,filler);
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generator->charconstant(generator,vsym,code,charbuf);
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bbFree(charbuf);
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} else {
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/* build a special odometer to walk the last few dimensions */
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subodom = newsubodometer(odom,dimset,dimindex,rank);
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generator->listbegin(generator,vsym,NULL,LISTDATA,list->length,code,&uid);
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for(i=0;odometermore(subodom);i++) {
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size_t offset = odometeroffset(subodom);
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NCConstant* con = datalistith(list,offset);
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generator->list(generator,vsym,NULL,LISTDATA,uid,i,code);
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generate_basetype(basetype,con,code,filler,generator);
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odometerincr(subodom);
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}
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generator->listend(generator,vsym,NULL,LISTDATA,uid,i,code);
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odometerfree(subodom); subodom = NULL;
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}
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} else {/* !islastgroup */
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/* Our datalist must be a list of compounds representing
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the next unlimited; so walk the subarray from this index
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upto next unlimited.
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*/
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ASSERT((dimindex < nextunlimited));
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ASSERT((isunlimited(dimset,nextunlimited)));
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/* build a sub odometer */
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subodom = newsubodometer(odom,dimset,dimindex,nextunlimited);
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for(i=0;odometermore(subodom);i++) {
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size_t offset = odometeroffset(subodom);
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NCConstant* con = datalistith(list,offset);
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if(con == NULL || con->nctype == NC_FILL) {
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if(filler == NULL)
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filler = getfiller(vsym);
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generate_arrayr(vsym,code,filler,odom,nextunlimited,NULL,generator);
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} else if(islistconst(con)) {
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Datalist* sublist = compoundfor(con);
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generate_arrayr(vsym,code,sublist,odom,nextunlimited,filler,generator);
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} else {
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semerror(constline(con),"Expected {...} representing unlimited list");
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return;
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}
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odometerincr(subodom);
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}
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odometerfree(subodom); subodom = NULL;
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}
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if(subodom != NULL)
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odometerfree(subodom);
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return;
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}
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/* Generate an instance of the basetype using the value of con*/
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void
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generate_basetype(Symbol* tsym, NCConstant* con, Bytebuffer* codebuf, Datalist* filler, Generator* generator)
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{
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Datalist* data;
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int offsetbase = 0;
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switch (tsym->subclass) {
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case NC_ENUM:
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case NC_OPAQUE:
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case NC_PRIM:
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if(islistconst(con)) {
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semerror(constline(con),"Expected primitive found {..}");
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}
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generate_primdata(tsym,con,codebuf,filler,generator);
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break;
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case NC_COMPOUND: {
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int i,uid, nfields, dllen;
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if(con == NULL || isfillconst(con)) {
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Datalist* fill = (filler==NULL?getfiller(tsym):filler);
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ASSERT(fill->length == 1);
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con = fill->data[0];
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if(!islistconst(con)) {
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if(con)
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semerror(con->lineno,"Compound data fill value is not enclosed in {..}");
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else
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semerror(0,"Compound data fill value not enclosed in {..}, con is NULL.");
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}
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}
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if(!con) { /* fail on null compound. */
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semerror(constline(con),"NULL compound data.");
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break;
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}
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if(!islistconst(con)) {/* fail on no compound*/
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semerror(constline(con),"Compound data must be enclosed in {..}");
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}
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data = con->value.compoundv;
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nfields = listlength(tsym->subnodes);
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dllen = datalistlen(data);
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if(dllen > nfields) {
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semerror(con->lineno,"Datalist longer than the number of compound fields");
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break;
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}
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generator->listbegin(generator,tsym,&offsetbase,LISTCOMPOUND,listlength(tsym->subnodes),codebuf,&uid);
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for(i=0;i<nfields;i++) {
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Symbol* field = (Symbol*)listget(tsym->subnodes,i);
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con = datalistith(data,i);
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generator->list(generator,field,&offsetbase,LISTCOMPOUND,uid,i,codebuf);
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generate_basetype(field,con,codebuf,NULL,generator);
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}
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generator->listend(generator,tsym,&offsetbase,LISTCOMPOUND,uid,i,codebuf);
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} break;
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case NC_VLEN: {
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Bytebuffer* vlenbuf;
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int uid;
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size_t count;
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if(con == NULL || isfillconst(con)) {
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Datalist* fill = (filler==NULL?getfiller(tsym):filler);
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ASSERT(fill->length == 1);
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con = fill->data[0];
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if(con->nctype != NC_COMPOUND) {
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semerror(con->lineno,"Vlen data fill value is not enclosed in {..}");
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}
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}
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if(!islistconst(con)) {
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semerror(constline(con),"Vlen data must be enclosed in {..}");
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}
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data = con->value.compoundv;
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/* generate the nc_vlen_t instance*/
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vlenbuf = bbNew();
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if(tsym->typ.basetype->typ.typecode == NC_CHAR) {
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gen_charseq(data,vlenbuf);
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generator->vlenstring(generator,tsym,vlenbuf,&uid,&count);
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} else {
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generator->listbegin(generator,tsym,NULL,LISTVLEN,data->length,codebuf,&uid);
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for(count=0;count<data->length;count++) {
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NCConstant* con;
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generator->list(generator,tsym,NULL,LISTVLEN,uid,count,vlenbuf);
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con = datalistith(data,count);
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generate_basetype(tsym->typ.basetype,con,vlenbuf,NULL,generator);
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}
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generator->listend(generator,tsym,NULL,LISTVLEN,uid,count,codebuf,(void*)vlenbuf);
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}
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generator->vlendecl(generator,tsym,codebuf,uid,count,vlenbuf); /* Will extract contents of vlenbuf */
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bbFree(vlenbuf);
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} break;
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case NC_FIELD:
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if(tsym->typ.dimset.ndims > 0) {
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/* Verify that we have a sublist (or fill situation) */
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if(con != NULL && !isfillconst(con) && !islistconst(con))
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semerror(constline(con),"Dimensioned fields must be enclose in {...}");
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generate_fieldarray(tsym->typ.basetype,con,&tsym->typ.dimset,codebuf,filler,generator);
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} else {
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generate_basetype(tsym->typ.basetype,con,codebuf,NULL,generator);
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}
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break;
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default: PANIC1("generate_basetype: unexpected subclass %d",tsym->subclass);
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}
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}
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/* Used only for structure field arrays*/
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static void
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generate_fieldarray(Symbol* basetype, NCConstant* con, Dimset* dimset,
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Bytebuffer* codebuf, Datalist* filler, Generator* generator)
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{
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int i;
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int chartype = (basetype->typ.typecode == NC_CHAR);
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Datalist* data;
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int rank = rankfor(dimset);
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ASSERT(dimset->ndims > 0);
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if(con != NULL && !isfillconst(con))
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data = con->value.compoundv;
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else
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data = NULL;
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if(chartype) {
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Bytebuffer* charbuf = bbNew();
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gen_chararray(dimset,0,data,charbuf,filler);
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generator->charconstant(generator,basetype,codebuf,charbuf);
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bbFree(charbuf);
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} else {
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int uid;
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size_t xproduct = crossproduct(dimset,0,rank); /* compute total number of elements */
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generator->listbegin(generator,basetype,NULL,LISTFIELDARRAY,xproduct,codebuf,&uid);
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for(i=0;i<xproduct;i++) {
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con = (data == NULL ? NULL : datalistith(data,i));
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generator->list(generator,basetype,NULL,LISTFIELDARRAY,uid,i,codebuf);
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generate_basetype(basetype,con,codebuf,NULL,generator);
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}
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generator->listend(generator,basetype,NULL,LISTFIELDARRAY,uid,i,codebuf);
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}
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}
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/* An opaque string value might not conform
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to the size of the opaque to which it is being
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assigned. Normalize it to match the required
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opaque length (in bytes).
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Note that the string is a sequence of nibbles (4 bits).
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*/
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static void
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normalizeopaquelength(NCConstant* prim, unsigned long nbytes)
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{
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int nnibs = 2*nbytes;
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ASSERT(prim->nctype==NC_OPAQUE);
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if(prim->value.opaquev.len == nnibs) {
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/* do nothing*/
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} else if(prim->value.opaquev.len > nnibs) { /* truncate*/
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prim->value.opaquev.stringv[nnibs] = '\0';
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prim->value.opaquev.len = nnibs;
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} else {/* prim->value.opaquev.len < nnibs => expand*/
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char* s;
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s = (char*)ecalloc(nnibs+1);
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memset(s,'0',nnibs); /* Fill with '0' characters */
|
|
memcpy(s,prim->value.opaquev.stringv,prim->value.opaquev.len);
|
|
s[nnibs] = '\0';
|
|
efree(prim->value.opaquev.stringv);
|
|
prim->value.opaquev.stringv=s;
|
|
prim->value.opaquev.len = nnibs;
|
|
}
|
|
}
|
|
|
|
static void
|
|
generate_primdata(Symbol* basetype, NCConstant* prim, Bytebuffer* codebuf,
|
|
Datalist* filler, Generator* generator)
|
|
{
|
|
NCConstant* target;
|
|
int match;
|
|
|
|
if(prim == NULL || isfillconst(prim)) {
|
|
Datalist* fill = (filler==NULL?getfiller(basetype):filler);
|
|
ASSERT(fill->length == 1);
|
|
prim = datalistith(fill,0);
|
|
}
|
|
|
|
ASSERT((prim->nctype != NC_COMPOUND));
|
|
|
|
/* Verify that the constant is consistent with the type */
|
|
match = 1;
|
|
switch (prim->nctype) {
|
|
case NC_CHAR:
|
|
case NC_BYTE:
|
|
case NC_SHORT:
|
|
case NC_INT:
|
|
case NC_FLOAT:
|
|
case NC_DOUBLE:
|
|
case NC_UBYTE:
|
|
case NC_USHORT:
|
|
case NC_UINT:
|
|
case NC_INT64:
|
|
case NC_UINT64:
|
|
case NC_STRING:
|
|
match = (basetype->subclass == NC_PRIM ? 1 : 0);
|
|
break;
|
|
|
|
#ifdef USE_NETCDF4
|
|
case NC_NIL:
|
|
match = (basetype->subclass == NC_PRIM && basetype->typ.typecode == NC_STRING ? 1 : 0);
|
|
break;
|
|
|
|
case NC_OPAQUE:
|
|
/* OPAQUE is also consistent with numbers */
|
|
match = (basetype->subclass == NC_OPAQUE
|
|
|| basetype->subclass == NC_PRIM ? 1 : 0);
|
|
break;
|
|
case NC_ECONST:
|
|
match = (basetype->subclass == NC_ENUM ? 1 : 0);
|
|
if(match) {
|
|
/* Make sure this econst belongs to this enum */
|
|
Symbol* ec = prim->value.enumv;
|
|
Symbol* en = ec->container;
|
|
match = (en == basetype);
|
|
}
|
|
break;
|
|
#endif
|
|
default:
|
|
match = 0;
|
|
}
|
|
if(!match) {
|
|
semerror(constline(prim),"Data value is not consistent with the expected type: %s",
|
|
basetype->name);
|
|
}
|
|
|
|
target = nullconst();
|
|
target->nctype = basetype->typ.typecode;
|
|
|
|
if(target->nctype != NC_ECONST) {
|
|
convert1(prim,target);
|
|
}
|
|
|
|
switch (target->nctype) {
|
|
case NC_ECONST:
|
|
if(basetype->subclass != NC_ENUM) {
|
|
semerror(constline(prim),"Conversion to enum not supported (yet)");
|
|
} break;
|
|
case NC_OPAQUE:
|
|
normalizeopaquelength(target,basetype->typ.size);
|
|
break;
|
|
default:
|
|
break;
|
|
}
|
|
generator->constant(generator,basetype,target,codebuf);
|
|
reclaimconstant(target);
|
|
target = NULL;
|
|
return;
|
|
}
|