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netcdf-c/libdap4/ncd4.h
Dennis Heimbigner 8b9253fef2 Fix various problem around VLEN's 
re: https://github.com/Unidata/netcdf-c/issues/541
re: https://github.com/Unidata/netcdf-c/issues/1208
re: https://github.com/Unidata/netcdf-c/issues/2078
re: https://github.com/Unidata/netcdf-c/issues/2041
re: https://github.com/Unidata/netcdf-c/issues/2143

For a long time, there have been known problems with the
management of complex types containing VLENs.  This also
involves the string type because it is stored as a VLEN of
chars.

This PR (mostly) fixes this problem. But note that it adds new
functions to netcdf.h (see below) and this may require bumping
the .so number.  These new functions can be removed, if desired,
in favor of functions in netcdf_aux.h, but netcdf.h seems the
better place for them because they are intended as alternatives
to the nc_free_vlen and nc_free_string functions already in
netcdf.h.

The term complex type refers to any type that directly or
transitively references a VLEN type. So an array of VLENS, a
compound with a VLEN field, and so on.

In order to properly handle instances of these complex types, it
is necessary to have function that can recursively walk
instances of such types to perform various actions on them.  The
term "deep" is also used to mean recursive.

At the moment, the two operations needed by the netcdf library are:
* free'ing an instance of the complex type
* copying an instance of the complex type.

The current library does only shallow free and shallow copy of
complex types. This means that only the top level is properly
free'd or copied, but deep internal blocks in the instance are
not touched.

Note that the term "vector" will be used to mean a contiguous (in
memory) sequence of instances of some type. Given an array with,
say, dimensions 2 X 3 X 4, this will be stored in memory as a
vector of length 2*3*4=24 instances.

The use cases are primarily these.

## nc_get_vars
Suppose one is reading a vector of instances using nc_get_vars
(or nc_get_vara or nc_get_var, etc.).  These functions will
return the vector in the top-level memory provided.  All
interior blocks (form nested VLEN or strings) will have been
dynamically allocated.

After using this vector of instances, it is necessary to free
(aka reclaim) the dynamically allocated memory, otherwise a
memory leak occurs.  So, the recursive reclaim function is used
to walk the returned instance vector and do a deep reclaim of
the data.

Currently functions are defined in netcdf.h that are supposed to
handle this: nc_free_vlen(), nc_free_vlens(), and
nc_free_string().  Unfortunately, these functions only do a
shallow free, so deeply nested instances are not properly
handled by them.

Note that internally, the provided data is immediately written so
there is no need to copy it. But the caller may need to reclaim the
data it passed into the function.

## nc_put_att
Suppose one is writing a vector of instances as the data of an attribute
using, say, nc_put_att.

Internally, the incoming attribute data must be copied and stored
so that changes/reclamation of the input data will not affect
the attribute.

Again, the code inside the netcdf library does only shallow copying
rather than deep copy. As a result, one sees effects such as described
in Github Issue https://github.com/Unidata/netcdf-c/issues/2143.

Also, after defining the attribute, it may be necessary for the user
to free the data that was provided as input to nc_put_att().

## nc_get_att
Suppose one is reading a vector of instances as the data of an attribute
using, say, nc_get_att.

Internally, the existing attribute data must be copied and returned
to the caller, and the caller is responsible for reclaiming
the returned data.

Again, the code inside the netcdf library does only shallow copying
rather than deep copy. So this can lead to memory leaks and errors
because the deep data is shared between the library and the user.

# Solution

The solution is to build properly recursive reclaim and copy
functions and use those as needed.
These recursive functions are defined in libdispatch/dinstance.c
and their signatures are defined in include/netcdf.h.
For back compatibility, corresponding "ncaux_XXX" functions
are defined in include/netcdf_aux.h.
````
int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count);
int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count);
int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy);
int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp);
````
There are two variants. The first two, nc_reclaim_data() and
nc_copy_data(), assume the top-level vector is managed by the
caller. For reclaim, this is so the user can use, for example, a
statically allocated vector. For copy, it assumes the user
provides the space into which the copy is stored.

The second two, nc_reclaim_data_all() and
nc_copy_data_all(), allows the functions to manage the
top-level.  So for nc_reclaim_data_all, the top level is
assumed to be dynamically allocated and will be free'd by
nc_reclaim_data_all().  The nc_copy_data_all() function
will allocate the top level and return a pointer to it to the
user. The user can later pass that pointer to
nc_reclaim_data_all() to reclaim the instance(s).

# Internal Changes
The netcdf-c library internals are changed to use the proper
reclaim and copy functions.  It turns out that the places where
these functions are needed is quite pervasive in the netcdf-c
library code.  Using these functions also allows some
simplification of the code since the stdata and vldata fields of
NC_ATT_INFO are no longer needed.  Currently this is commented
out using the SEPDATA \#define macro.  When any bugs are largely
fixed, all this code will be removed.

# Known Bugs

1. There is still one known failure that has not been solved.
   All the failures revolve around some variant of this .cdl file.
   The proximate cause of failure is the use of a VLEN FillValue.
````
        netcdf x {
        types:
          float(*) row_of_floats ;
        dimensions:
          m = 5 ;
        variables:
          row_of_floats ragged_array(m) ;
              row_of_floats ragged_array:_FillValue = {-999} ;
        data:
          ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32},
                         {40, 41}, _ ;
        }
````
When a solution is found, I will either add it to this PR or post a new PR.

# Related Changes

* Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data.
* Remove the --enable-unfixed-memory-leaks option.
* Remove the NC_VLENS_NOTEST code that suppresses some vlen tests.
* Document this change in docs/internal.md
* Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh.
* Mark types as fixed size or not (transitively) to optimize the reclaim
  and copy functions.

# Misc. Changes

* Make Doxygen process libdispatch/daux.c
* Make sure the NC_ATT_INFO_T.container field is set.
2022-01-08 18:30:00 -07:00

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/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
/*
External functions and state variables are
defined here, including function-like #defines.
*/
#ifndef NCD4_H
#define NCD4_H 1
#include "d4includes.h"
#include "d4util.h"
#include "d4debug.h"
#include "nc4internal.h"
/**************************************************/
/* Constants */
#define RCFILEENV "DAPRCFILE"
/* Figure out a usable max path name max */
#ifdef PATH_MAX /* *nix* */
#define NC_MAX_PATH PATH_MAX
#else
# ifdef MAX_PATH /*windows*/
# define NC_MAX_PATH MAX_PATH
# else
# define NC_MAX_PATH 4096
# endif
#endif
#define COUNTERTYPE unsigned long long
#define COUNTERSIZE sizeof(COUNTERTYPE)
/* Clear allocated memory (see e.g. d4data.c); Potentially costly*/
#undef CLEARMEM
/* Clear empty structure alignment space; Potentially costly, but probably less than CLEARMEM */
#define CLEARSTRUCT
/* Always use fixed size opaques */
#define FIXEDOPAQUE
#define DFALTOPAQUESIZE 16
/* Size of a chunk header */
#define CHUNKHDRSIZE 4
/* Special attributes */
#define D4CHECKSUMATTR "_DAP4_Checksum_CRC32"
#define D4LEATTR "_DAP4_Little_Endian"
/**************************************************/
#undef nullfree
#ifndef nullfree
#define nullfree(m) ((m)==NULL?NULL:(free(m),NULL))
#endif
#define nulldup(s) ((s)==NULL?NULL:strdup(s))
/**************************************************/
/* DSP API wrappers */
#ifdef FIX
extern int dsp_getDMR(ND4dsp* dsp, DCR** dcrp);
extern int dsp_getDAP(ND4dsp* dsp, DCR** dcrp);
extern int dsp_close(ND4dsp* dsp);
/* DSP API */
extern int dsp_open(const char* path, ND4dsp** dspp);
#endif
/**************************************************/
/* From d4http.c */
extern long NCD4_fetchhttpcode(CURL* curl);
extern int NCD4_fetchurl_file(CURL* curl, const char* url, FILE* stream, d4size_t* sizep, long* filetime);
extern int NCD4_fetchurl(CURL* curl, const char* url, NCbytes* buf, long* filetime, int* httpcode);
extern int NCD4_curlopen(CURL** curlp);
extern void NCD4_curlclose(CURL* curl);
extern int NCD4_fetchlastmodified(CURL* curl, char* url, long* filetime);
extern int NCD4_ping(const char* url);
/* From d4read.c */
extern int NCD4_readDMR(NCD4INFO* state, int flags);
extern int NCD4_readDAP(NCD4INFO* state, int flags);
extern int NCD4_seterrormessage(NCD4meta* metadata, size_t len, char* msg);
/* From d4parser.c */
extern int NCD4_parse(NCD4meta*);
extern NCD4node* NCD4_findAttr(NCD4node* container, const char* attrname);
extern NCD4node* NCD4_groupFor(NCD4node* node);
extern int NCD4_defineattr(NCD4meta* meta, NCD4node* parent, const char* aname, const char* typename, NCD4node** attrp);
/* From d4printer.c */
extern int NCD4_print(NCD4meta*, NCbytes* output);
/* From d4meta.c */
extern NCD4meta* NCD4_newmeta(NCD4INFO*);
extern void NCD4_attachraw(NCD4meta*, size_t size, void* rawdata);
extern void NCD4_reclaimMeta(NCD4meta*);
extern void NCD4_resetMeta(NCD4meta*);
extern void reclaimNode(NCD4node* node);
extern void NCD4_setdebuglevel(NCD4meta*,int);
extern int NCD4_metabuild(NCD4meta*, int ncid);
extern size_t NCD4_computeTypeSize(NCD4meta*, NCD4node* type);
extern int NCD4_findvar(NC* ncp, int ncid, int varid, NCD4node** varp, NCD4node** grpp);
/* From d4chunk.c */
extern int NCD4_dechunk(NCD4meta*);
extern int NCD4_infermode(NCD4meta* meta);
struct NCD4serial;
extern void NCD4_resetSerial(struct NCD4serial* serial, size_t rawsize, void* rawdata);
/* From d4swap.c */
extern int NCD4_swapdata(NCD4meta*, NClist* topvars);
/* From d4fix.c */
extern int NCD4_delimit(NCD4meta*, NCD4node* var, void** offsetp);
extern int NCD4_moveto(NCD4meta*, NCD4node* var, d4size_t count, void** offsetp);
extern int NCD4_toposort(NCD4meta*);
/* From d4data.c */
extern int NCD4_processdata(NCD4meta*);
extern int NCD4_fillinstance(NCD4meta*, NCD4node* type, void** offsetp, void** dstp, NClist* blobs);
extern int NCD4_getToplevelVars(NCD4meta* meta, NCD4node* group, NClist* toplevel);
/* From d4util.c */
extern d4size_t NCD4_dimproduct(NCD4node* node);
extern size_t NCD4_typesize(nc_type tid);
extern int NCD4_isLittleEndian(void);/* Return 1 if this machine is little endian */
extern int NCD4_errorNC(int code, const int line, const char* file);
extern int NCD4_error(int code, const int line, const char* file, const char* fmt, ...);
extern char* NCD4_makeFQN(NCD4node* node);
extern char* NCD4_makeName(NCD4node*,const char* sep);
extern int NCD4_parseFQN(const char* fqn0, NClist* pieces);
extern char* NCD4_deescape(const char* esc);
extern char* NCD4_entityescape(const char* s);
extern size_t NCD4_elidenuls(char* s, size_t slen);
extern void* NCD4_getheader(void* p, NCD4HDR* hdr, int hostlittleendian);
extern void NCD4_reporterror(NCD4INFO* state);
/* From d4dump.c */
extern void NCD4_dumpbytes(size_t size, const void* data0, int swap);
extern void NCD4_tagdump(size_t size, const void* data0, int swap, const char* tag);
extern void NCD4_dumpvars(NCD4node* group);
extern union ATOMICS* NCD4_dumpatomic(NCD4node* var, void* data);
/* From d4rc.c */
extern int NCD4_rcload(void);
extern int NCD4_rcprocess(NCD4INFO* info);
extern void NCD4_rcfree(NClist* rc);
extern char* NCD4_rclookup(char* key, char* hostport);
extern int NCD4_parseproxy(NCD4INFO* info, const char* surl);
extern int NCD4_rcdefault(NCD4INFO*);
/* From d4cvt.c */
extern int NCD4_convert(nc_type srctype, nc_type dsttype, char* memory0, char* value0, size_t count);
/* d4file.c */
extern void NCD4_applyclientparamcontrols(NCD4INFO*);
extern int NCD4_readDMRorDAP(NCD4INFO* d4info, NCD4mode mode);
/* ncd4dispatch.c */
struct NC_reservedatt; /*forward*/
extern const struct NC_reservedatt* NCD4_lookupreserved(const char* name);
/* Add an extra function whose sole purpose is to allow
configure(.ac) to test for the presence of this code.
*/
extern int nc__dap4(void);
/**************************************************/
/* Macro defined functions */
#undef NCCHECK
#undef FAIL
#define NCCHECK(expr) if((ret=(expr))) {ret = NCD4_errorNC(ret,__LINE__,__FILE__); goto done;}else{}
#define FAIL(code,fmt,...) do{ret=NCD4_error(code,__LINE__,__FILE__,fmt , ##__VA_ARGS__); goto done;}while(0)
#undef INCR
#undef DECR
#undef DELTA
#define INCR(offset,size) ((void*)(((char*)(offset))+(size)))
#define DECR(offset,size) ((void*)(((char*)(offset))-(size)))
#define DELTA(p1,p2) ((ptrdiff_t)(((char*)(p1))-((char*)(p2))))
#undef GETCOUNTER
#undef SKIPCOUNTER
/* Unclear which macros are defined for which compilers.
see: https://sourceforge.net/p/predef/wiki/Architectures/
*/
#if defined(__arm__) && __ARM_ARCH < 8
EXTERNL d4size_t NCD4_getcounter(void* p);
#define GETCOUNTER(p) NCD4_getcounter(p)
#else
#define GETCOUNTER(p) ((d4size_t)*((COUNTERTYPE*)(p)))
#endif /*defined(__arm__) && __ARM_ARCH < 8*/
#define SKIPCOUNTER(p) {p=INCR(p,COUNTERSIZE);}
#undef PUSH
#define PUSH(list,value) do{if((list)==NULL) {(list)=nclistnew();} else{}; nclistpush((list),(value));}while(0)
#define getnc3id(d4) (getdap(d4)->nc4id)
#define ISTOPLEVEL(var) ((var)->container == NULL || (var)->container->sort == NCD4_GROUP)
#define FILEIDPART(NCID) (((unsigned int) (NCID)) >> ID_SHIFT)
#define GROUPIDPART(NCID) (((unsigned int) (NCID)) & GRP_ID_MASK)
#define MAKENCID(grp,file) ((((unsigned int)(file)) << ID_SHIFT) | (grp))
#define getdap(ncp) ((NCD4INFO*)((NC*)ncp)->dispatchdata)
#define getnc4id(ncp) (getdap(ncp)->substrate.nc4id)
/* Convert a dap4 grpid to a substrate id */
#define makenc4id(ncp,dap4id) (((dap4id) & GRP_ID_MASK) | getdap(ncp)->substrate.nc4id)
/* and the inverse */
#define makedap4id(ncp,nc4id) (((nc4id) & GRP_ID_MASK) | (ncp)->ext_ncid)
#ifdef CLEARMEM
#define d4alloc(n) (calloc(1,(size_t)(n)))
#else
#define d4alloc(n) (malloc((size_t)(n)))
#endif
/* A number of hacks have been inserted
to deal with issues in accessing hyrax
using DAP4.
*/
#define HYRAXHACK
EXTERNL int NCD4_get_substrate(int ncid);
#endif /*NCD4_H*/
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