netcdf-c/ncgen/main.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

596 lines
15 KiB
C

/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
/* $Id: main.c,v 1.33 2010/05/26 21:43:36 dmh Exp $ */
/* $Header: /upc/share/CVS/netcdf-3/ncgen/main.c,v 1.33 2010/05/26 21:43:36 dmh Exp $ */
#include "includes.h"
#include "ncoffsets.h"
#include "ncwinpath.h"
#ifdef HAVE_GETOPT_H
#include <getopt.h>
#endif
#ifdef _MSC_VER
#include "XGetopt.h"
#endif
/* Default is netcdf-3 mode 1 */
#define DFALTCMODE 0
/*Mnemonic*/
#define DEPRECATED 1
/* For error messages */
char* progname; /* Global: not reclaimed */
char* cdlname; /* Global: not reclaimed */
/* option flags */
int nofill_flag;
char* mainname; /* name to use for main function; defaults to "main"*/
Language l_flag;
int syntax_only;
int header_only;
/* flags for tracking what output format to use */
int k_flag; /* > 0 => -k was specified on command line*/
int format_attribute; /* 1=>format came from format attribute */
int enhanced_flag; /* 1 => netcdf-4 */
int cdf5_flag; /* 1 => cdf5 | maybe netcdf-4 */
int specials_flag; /* 1=> special attributes are present */
int usingclassic;
int cmode_modifier;
int diskless;
int ncloglevel;
int wholevarsize;
GlobalSpecialData globalspecials;
size_t zerosvector[NC_MAX_VAR_DIMS];
size_t onesvector[NC_MAX_VAR_DIMS];
char* binary_ext = ".nc";
struct Vlendata* vlendata;
char *netcdf_name = NULL; /* command line -o file name */
char *datasetname = NULL; /* name from the netcdf <name> {} || from -N */
extern FILE *ncgin;
/* Forward */
static char* ubasename(char*);
void usage( void );
int main( int argc, char** argv );
/* Define tables vs modes for legal -k values*/
struct Kvalues legalkinds[] = {
/* NetCDF-3 classic format (32-bit offsets) */
{"classic", NC_FORMAT_CLASSIC, !DEPRECATED}, /* canonical format name */
{"nc3", NC_FORMAT_CLASSIC, !DEPRECATED}, /* short format name */
{"1", NC_FORMAT_CLASSIC, !DEPRECATED}, /* deprecated, use "-3" or "-k nc3" instead */
/* NetCDF-3 64-bit offset format */
{"64-bit offset", NC_FORMAT_64BIT_OFFSET, !DEPRECATED}, /* canonical format name */
{"nc6", NC_FORMAT_64BIT_OFFSET, !DEPRECATED}, /* short format name */
{"2", NC_FORMAT_64BIT_OFFSET, !DEPRECATED}, /* deprecated, use "-6" or "-k nc6" instead */
{"64-bit-offset", NC_FORMAT_64BIT_OFFSET, !DEPRECATED}, /* aliases */
/* NetCDF-4 HDF5-based format */
{"netCDF-4", NC_FORMAT_NETCDF4, !DEPRECATED}, /* canonical format name */
{"nc4", NC_FORMAT_NETCDF4, !DEPRECATED}, /* short format name */
{"3", NC_FORMAT_NETCDF4, !DEPRECATED}, /* deprecated, use "-4" or "-k nc4" instead */
{"netCDF4", NC_FORMAT_NETCDF4, !DEPRECATED}, /* aliases */
{"hdf5", NC_FORMAT_NETCDF4, !DEPRECATED},
{"enhanced", NC_FORMAT_NETCDF4, !DEPRECATED},
{"netcdf-4", NC_FORMAT_NETCDF4, !DEPRECATED},
{"netcdf4", NC_FORMAT_NETCDF4, !DEPRECATED},
/* NetCDF-4 HDF5-based format, restricted to classic data model */
{"netCDF-4 classic model", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED}, /* canonical format name */
{"nc7", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED}, /* short format name */
{"4", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED}, /* deprecated, use "-7" or -k nc7" instead */
{"netCDF-4-classic", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED}, /* aliases */
{"netCDF-4_classic", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED},
{"netCDF4_classic", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED},
{"hdf5-nc3", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED},
{"enhanced-nc3", NC_FORMAT_NETCDF4_CLASSIC, !DEPRECATED},
/* CDF-5 format */
{"5", NC_FORMAT_64BIT_DATA, !DEPRECATED},
{"64-bit-data", NC_FORMAT_64BIT_DATA, !DEPRECATED},
{"64-bit data", NC_FORMAT_64BIT_DATA, !DEPRECATED},
{"nc5", NC_FORMAT_64BIT_DATA, !DEPRECATED},
{"cdf5", NC_FORMAT_64BIT_DATA, !DEPRECATED},
{"cdf-5", NC_FORMAT_64BIT_DATA, !DEPRECATED},
/* null terminate*/
{NULL,0,0}
};
#ifndef _MSC_VER
struct Languages {
char* name;
Language flag;
} legallanguages[] = {
{"b", L_BINARY},
{"c", L_C},
{"C", L_C},
{"f77", L_F77},
{"fortran77", L_F77},
{"Fortran77", L_F77},
{"j", L_JAVA},
{"java", L_JAVA},
{NULL,L_UNDEFINED}
};
#else
typedef struct Languages {
char* name;
Language flag;
} Languages;
struct Languages legallanguages[] = {
{"b", L_BINARY},
{"c", L_C},
{"C", L_C},
{"f77", L_F77},
{"fortran77", L_F77},
{"Fortran77", L_F77},
{"j", L_JAVA},
{"java", L_JAVA},
{NULL,L_UNDEFINED}
};
#endif
/* strip off leading path */
/* result is malloc'd */
static char *
ubasename(char *logident)
{
char* sep;
sep = strrchr(logident,'/');
#ifdef MSDOS
if(sep == NULL) sep = strrchr(logident,'\\');
#endif
if(sep == NULL) return logident;
sep++; /* skip past the separator */
return sep;
}
void
usage(void)
{
derror("Usage: %s"
" [-1]"
" [-3]"
" [-4]"
" [-5]"
" [-6]"
" [-7]"
" [-b]"
" [-d]"
" [-D debuglevel]"
" [-h]"
" [-k kind ]"
" [-l language=b|c|f77|java]"
" [-M <name>]"
" [-n]"
" [-o outfile]"
" [-P]"
" [-x]"
" [-N datasetname]"
" [-L loglevel]"
" [-H]"
" [-W generate whole var upload]"
" [file ... ]",
progname);
derror("netcdf library version %s", nc_inq_libvers());
}
int
main(
int argc,
char *argv[])
{
int code = 0;
int c;
FILE *fp;
struct Languages* langs;
#ifdef __hpux
setlocale(LC_CTYPE,"");
#endif
init_netcdf();
opterr = 1; /* print error message if bad option */
progname = nulldup(ubasename(argv[0]));
cdlname = NULL;
netcdf_name = NULL;
datasetname = NULL;
l_flag = 0;
nofill_flag = 0;
syntax_only = 0;
header_only = 0;
mainname = "main";
k_flag = 0;
format_attribute = 0;
enhanced_flag = 0;
cdf5_flag = 0;
specials_flag = 0;
diskless = 0;
wholevarsize = 1024;
#ifdef LOGGING
ncloglevel = NC_TURN_OFF_LOGGING;
#else
ncloglevel = -1;
#endif
memset(&globalspecials,0,sizeof(GlobalSpecialData));
while ((c = getopt(argc, argv, "134567bcdD:fhHk:l:M:no:Pv:xL:N:B:W:")) != EOF)
switch(c) {
case 'b': /* for binary netcdf output, ".nc" extension */
if(l_flag != 0) {
fprintf(stderr,"Please specify only one language\n");
return 1;
}
l_flag = L_BINARY;
break;
case 'B':
/* Ignore, but keep for back compatibility */
break;
case 'c': /* for c output, old version of "-lc" */
if(l_flag != 0) {
fprintf(stderr,"Please specify only one language\n");
return 1;
}
l_flag = L_C;
fprintf(stderr,"-c is deprecated: please use -lc\n");
break;
case 'd':
debug = 1;
break;
case 'D':
debug = atoi(optarg);
break;
case 'f': /* for f77 output, old version of "-lf" */
if(l_flag != 0) {
fprintf(stderr,"Please specify only one language\n");
return 1;
}
l_flag = L_F77;
fprintf(stderr,"-f is deprecated: please use -lf77\n");
break;
case 'h':
usage();
goto done;
case 'H':
header_only = 1;
break;
case 'v': /* a deprecated alias for "kind" option */
/*FALLTHRU*/
case 'k': { /* for specifying variant of netCDF format to be generated
Possible values are:
Format names:
"classic" or "nc3"
"64-bit offset" or "nc6"
"64-bit data" or "nc5" or "cdf-5"
"netCDF-4" or "nc4"
"netCDF-4 classic model" or "nc7"
"netCDF-5" or "nc5" or "cdf5"
Format version numbers (deprecated):
1 (=> classic)
2 (=> 64-bit offset)
3 (=> netCDF-4)
4 (=> netCDF-4 classic model)
5 (=> classic 64 bit data aka CDF-5)
*/
struct Kvalues* kvalue;
if(optarg == NULL) {
derror("-k flag has no value");
return 2;
}
for(kvalue=legalkinds;kvalue->name;kvalue++) {
if(strcmp(optarg,kvalue->name) == 0) {
k_flag = kvalue->k_flag;
if(kvalue->deprecated)
fprintf(stderr,"-k%s is deprecated; use corresponding -k<name> or -3|-4|-5|-6|-7\n",optarg);
break;
}
}
if(kvalue->name == NULL) {
derror("Invalid format: %s",optarg);
return 2;
}
} break;
case 'l': /* specify language, instead of using -c or -f or -b */
{
char* lang_name = NULL;
if(l_flag != 0) {
fprintf(stderr,"Please specify only one language\n");
return 1;
}
if(!optarg) {
derror("%s: output language is null", progname);
return(1);
}
lang_name = (char*) emalloc(strlen(optarg)+1);
(void)strcpy(lang_name, optarg);
for(langs=legallanguages;langs->name != NULL;langs++) {
if(strcmp(lang_name,langs->name)==0) {
l_flag = langs->flag;
break;
}
}
if(langs->name == NULL) {
derror("%s: output language %s not implemented",progname, lang_name);
nullfree(lang_name);
return(1);
}
nullfree(lang_name);
}; break;
case 'L':
ncloglevel = atoi(optarg);
break;
case 'M': /* Determine the name for the main function */
mainname = nulldup(optarg);
break;
case 'n': /* old version of -b, uses ".cdf" extension */
if(l_flag != 0) {
fprintf(stderr,"Please specify only one language\n");
return 1;
}
l_flag = L_BINARY;
binary_ext = ".cdf";
break;
case 'N': /* to explicitly specify dataset name */
if(datasetname) efree(datasetname);
datasetname = nulldup(optarg);
break;
case 'o': /* to explicitly specify output name */
if(netcdf_name) efree(netcdf_name);
netcdf_name = NCdeescape(optarg);
break;
case 'P': /* diskless with persistence */
diskless = 1;
case 'W':
wholevarsize = atoi(optarg);
break;
case 'x': /* set nofill mode to speed up creation of large files */
nofill_flag = 1;
break;
case '3': /* output format is classic (netCDF-3) */
k_flag = NC_FORMAT_CLASSIC;
break;
case '6': /* output format is 64-bit-offset (netCDF-3 version 2) */
k_flag = NC_FORMAT_64BIT_OFFSET;
break;
case '4': /* output format is netCDF-4 (variant of HDF5) */
k_flag = NC_FORMAT_NETCDF4;
break;
case '5': /* output format is CDF5 */
k_flag = NC_FORMAT_CDF5;
break;
case '7': /* output format is netCDF-4 (restricted to classic model)*/
k_flag = NC_FORMAT_NETCDF4_CLASSIC;
break;
case '?':
usage();
return(8);
}
if(l_flag == 0) {
l_flag = L_BINARY; /* default */
/* Treat -k or -o as an implicit -lb assuming no other -l flags */
if(k_flag == 0 && netcdf_name == NULL)
syntax_only = 1;
}
#ifndef ENABLE_C
if(l_flag == L_C) {
fprintf(stderr,"C not currently supported\n");
code=1; goto done;
}
#endif
#ifndef ENABLE_BINARY
if(l_flag == L_BINARY) {
fprintf(stderr,"Binary netcdf not currently supported\n");
code=1; goto done;
}
#endif
#ifndef ENABLE_JAVA
if(l_flag == L_JAVA) {
fprintf(stderr,"Java not currently supported\n");
code=1; goto done;
}
#else
if(l_flag == L_JAVA && mainname != NULL && strcmp(mainname,"main")==0)
mainname = "Main";
#endif
#ifndef ENABLE_F77
if(l_flag == L_F77) {
fprintf(stderr,"F77 not currently supported\n");
code=1; goto done;
}
#endif
if(l_flag != L_BINARY)
diskless = 0;
argc -= optind;
argv += optind;
if (argc > 1) {
derror ("%s: only one input file argument permitted",progname);
return(6);
}
fp = stdin;
if (argc > 0 && strcmp(argv[0], "-") != 0) {
char bom[4];
size_t count;
if ((fp = NCfopen(argv[0], "r")) == NULL) {
derror ("can't open file %s for reading: ", argv[0]);
perror("");
return(7);
}
/* Check the leading bytes for an occurrence of a BOM */
/* re: http://www.unicode.org/faq/utf_bom.html#BOM */
/* Attempt to read the first four bytes */
memset(bom,0,sizeof(bom));
count = fread(bom,1,2,fp);
if(count == 2) {
switch (bom[0]) {
case '\x00':
case '\xFF':
case '\xFE':
/* Only UTF-* is allowed; complain and exit */
fprintf(stderr,"Input file contains a BOM indicating a non-UTF8 encoding\n");
return 1;
case '\xEF':
/* skip the BOM */
(void)fread(bom,1,1,fp);
break;
default: /* legal printable char, presumably; rewind */
rewind(fp);
break;
}
}
}
cdlname = nulldup(argv[0]);
if(cdlname != NULL) {
if(strlen(cdlname) > NC_MAX_NAME)
cdlname[NC_MAX_NAME] = '\0';
}
parse_init();
ncgin = fp;
if(debug >= 2) {ncgdebug=1;}
if(ncgparse() != 0)
return 1;
/* Compute the k_flag (1st pass) using rules in the man page (ncgen.1).*/
#ifndef ENABLE_CDF5
if(k_flag == NC_FORMAT_CDF5) {
derror("Output format CDF5 requested, but netcdf was built without cdf5 support.");
return 0;
}
#endif
#ifndef USE_NETCDF4
if(enhanced_flag) {
derror("CDL input is enhanced mode, but --disable-netcdf4 was specified during build");
return 0;
}
#endif
if(l_flag == L_JAVA || l_flag == L_F77) {
k_flag = NC_FORMAT_CLASSIC;
if(enhanced_flag) {
derror("Java or Fortran requires classic model CDL input");
return 0;
}
}
if(k_flag == 0)
k_flag = globalspecials._Format;
if(cdf5_flag && !enhanced_flag && k_flag == 0)
k_flag = NC_FORMAT_64BIT_DATA;
if(enhanced_flag && k_flag == 0)
k_flag = NC_FORMAT_NETCDF4;
if(enhanced_flag && k_flag != NC_FORMAT_NETCDF4) {
if(enhanced_flag && k_flag != NC_FORMAT_NETCDF4 && k_flag != NC_FORMAT_64BIT_DATA) {
derror("-k or _Format conflicts with enhanced CDL input");
return 0;
}
}
if(specials_flag > 0 && k_flag == 0)
#ifdef USE_NETCDF4
k_flag = NC_FORMAT_NETCDF4;
#else
k_flag = NC_FORMAT_CLASSIC;
#endif
if(k_flag == 0)
k_flag = NC_FORMAT_CLASSIC;
/* Figure out usingclassic */
switch (k_flag) {
case NC_FORMAT_64BIT_DATA:
case NC_FORMAT_CLASSIC:
case NC_FORMAT_64BIT_OFFSET:
case NC_FORMAT_NETCDF4_CLASSIC:
usingclassic = 1;
break;
case NC_FORMAT_NETCDF4:
default:
usingclassic = 0;
break;
}
/* compute cmode_modifier */
switch (k_flag) {
case NC_FORMAT_CLASSIC:
cmode_modifier = 0; break;
case NC_FORMAT_64BIT_OFFSET:
cmode_modifier = NC_64BIT_OFFSET; break;
case NC_FORMAT_NETCDF4:
cmode_modifier = NC_NETCDF4; break;
case NC_FORMAT_NETCDF4_CLASSIC:
cmode_modifier = NC_NETCDF4 | NC_CLASSIC_MODEL; break;
case NC_FORMAT_64BIT_DATA:
cmode_modifier = NC_CDF5; break;
default: ASSERT(0); /* cannot happen */
}
if(diskless)
cmode_modifier |= (NC_DISKLESS|NC_NOCLOBBER);
processsemantics();
if(!syntax_only && error_count == 0)
define_netcdf();
done:
nullfree(netcdf_name);
nullfree(datasetname);
finalize_netcdf(code);
return code;
}
void
init_netcdf(void) /* initialize global counts, flags */
{
int i;
memset((void*)&nullconstant,0,sizeof(NCConstant));
fillconstant = nullconstant;
fillconstant.nctype = NC_FILLVALUE;
filldatalist = builddatalist(1);
dlappend(filldatalist,&fillconstant);
filldatalist->readonly = 1;
codebuffer = bbNew();
stmt = bbNew();
error_count = 0; /* Track # of errors */
for(i=0;i<NC_MAX_VAR_DIMS;i++) onesvector[i] = 1;
memset(zerosvector,0,sizeof(zerosvector));
}
void
finalize_netcdf(int retcode)
{
nc_finalize();
exit(retcode);
}