mirror of
https://github.com/Unidata/netcdf-c.git
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59e04ae071
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.
670 lines
14 KiB
C
670 lines
14 KiB
C
/*********************************************************************
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* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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* $Header: /upc/share/CVS/netcdf-3/ncgen/util.c,v 1.4 2010/04/14 22:04:59 dmh Exp $
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*********************************************************************/
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#include "includes.h"
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/* Track primitive symbol instances (initialized in ncgen.y) */
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Symbol* primsymbols[PRIMNO];
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char*
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append(const char* s1, const char* s2)
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{
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int len = (s1?strlen(s1):0)+(s2?strlen(s2):0);
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char* result = (char*)ecalloc(len+1);
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result[0] = '\0';
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if(s1) strcat(result,s1);
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if(s2) strcat(result,s2);
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return result;
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}
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unsigned int
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chartohex(char c)
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{
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switch (c) {
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case '0': case '1': case '2': case '3': case '4':
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case '5': case '6': case '7': case '8': case '9':
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return (c - '0');
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case 'A': case 'B': case 'C':
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case 'D': case 'E': case 'F':
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return (c - 'A') + 0x0a;
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case 'a': case 'b': case 'c':
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case 'd': case 'e': case 'f':
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return (c - 'a') + 0x0a;
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}
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return 0;
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}
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/*
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* For generated Fortran, change 'e' to 'd' in exponent of double precision
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* constants.
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*/
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void
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expe2d(
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char *cp) /* string containing double constant */
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{
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char *expchar = strrchr(cp,'e');
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if (expchar) {
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*expchar = 'd';
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}
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}
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/* Returns non-zero if n is a power of 2, 0 otherwise */
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int
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pow2(
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int n)
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{
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int m = n;
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int p = 1;
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while (m > 0) {
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m /= 2;
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p *= 2;
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}
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return p == 2*n;
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}
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/*
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* Remove trailing zeros (after decimal point) but not trailing decimal
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* point from ss, a string representation of a floating-point number that
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* might include an exponent part.
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*/
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void
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tztrim(
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char *ss /* returned string representing dd */
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)
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{
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char *cp, *ep;
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cp = ss;
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if (*cp == '-')
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cp++;
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while(isdigit((int)*cp) || *cp == '.')
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cp++;
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if (*--cp == '.')
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return;
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ep = cp+1;
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while (*cp == '0')
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cp--;
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cp++;
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if (cp == ep)
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return;
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while (*ep)
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*cp++ = *ep++;
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*cp = '\0';
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return;
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}
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static void
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clearSpecialdata(Specialdata* data)
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{
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if(data == NULL) return;
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reclaimdatalist(data->_Fillvalue);
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if(data->_ChunkSizes)
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efree(data->_ChunkSizes);
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if(data->_Filters) {
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int i;
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for(i=0;i<data->nfilters;i++) {
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NC_Filterspec* f = (NC_Filterspec*)data->_Filters[i];
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ncaux_filterspec_free(f);
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}
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efree(data->_Filters);
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}
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}
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void
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freeSymbol(Symbol* sym)
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{
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if(sym == NULL) return;
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switch (sym->objectclass) {
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case NC_VAR:
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clearSpecialdata(&sym->var.special);
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listfree(sym->var.attributes);
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break;
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case NC_TYPE:
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if(sym->typ.econst)
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reclaimconstant(sym->typ.econst);
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if(sym->typ._Fillvalue)
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reclaimdatalist(sym->typ._Fillvalue);
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break;
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case NC_GRP:
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if(sym->file.filename)
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efree(sym->file.filename);
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break;
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default: break;
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}
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/* Universal */
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if(sym->name) efree(sym->name);
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if(sym->fqn) efree(sym->fqn);
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listfree(sym->prefix);
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if(sym->data)
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reclaimdatalist(sym->data);
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listfree(sym->subnodes);
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efree(sym);
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}
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char* nctypenames[17] = {
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"NC_NAT",
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"NC_BYTE", "NC_CHAR", "NC_SHORT", "NC_INT",
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"NC_FLOAT", "NC_DOUBLE",
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"NC_UBYTE", "NC_USHORT", "NC_UINT",
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"NC_INT64", "NC_UINT64",
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"NC_STRING",
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"NC_VLEN", "NC_OPAQUE", "NC_ENUM", "NC_COMPOUND"
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};
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char* nctypenamesextend[9] = {
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"NC_GRP", "NC_DIM", "NC_VAR", "NC_ATT", "NC_TYPE",
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"NC_ECONST","NC_FIELD", "NC_ARRAY","NC_PRIM"
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};
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char*
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nctypename(nc_type nctype)
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{
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char* s;
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if(nctype >= NC_NAT && nctype <= NC_COMPOUND)
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return nctypenames[nctype];
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if(nctype >= NC_GRP && nctype <= NC_PRIM)
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return nctypenamesextend[(nctype - NC_GRP)];
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if(nctype == NC_FILLVALUE) return "NC_FILL";
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if(nctype == NC_NIL) return "NC_NIL";
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s = poolalloc(128);
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sprintf(s,"NC_<%d>",nctype);
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return s;
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}
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/* These are the augmented NC_ values (0 based from NC_GRP)*/
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char* ncclassnames[9] = {
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"NC_GRP", "NC_DIM", "NC_VAR", "NC_ATT",
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"NC_TYP", "NC_ECONST", "NC_FIELD", "NC_ARRAY",
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"NC_PRIM"
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};
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char*
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ncclassname(nc_class ncc)
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{
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char* s;
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if(ncc >= NC_NAT && ncc <= NC_COMPOUND)
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return nctypename((nc_type)ncc);
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if(ncc == NC_FILLVALUE) return "NC_FILL";
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if(ncc >= NC_GRP && ncc <= NC_PRIM)
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return ncclassnames[ncc - NC_GRP];
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s = poolalloc(128);
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sprintf(s,"NC_<%d>",ncc);
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return s;
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}
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int ncsizes[17] = {
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0,
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1,1,2,4,
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4,8,
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1,2,4,
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8,8,
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sizeof(char*),
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sizeof(nc_vlen_t),
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0,0,0
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};
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int
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ncsize(nc_type nctype)
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{
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if(nctype >= NC_NAT && nctype <= NC_COMPOUND)
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return ncsizes[nctype];
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return 0;
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}
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int
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hasunlimited(Dimset* dimset)
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{
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int i;
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for(i=0;i<dimset->ndims;i++) {
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Symbol* dim = dimset->dimsyms[i];
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if(dim->dim.declsize == NC_UNLIMITED) return 1;
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}
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return 0;
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}
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/* return 1 if first dimension is unlimited*/
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int
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isunlimited0(Dimset* dimset)
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{
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return (dimset->ndims > 0 && dimset->dimsyms[0]->dim.declsize == NC_UNLIMITED);
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}
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/* True only if dim[0] is unlimited all rest are bounded*/
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/* or all are bounded*/
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int
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classicunlimited(Dimset* dimset)
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{
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int i;
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int last = -1;
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for(i=0;i<dimset->ndims;i++) {
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Symbol* dim = dimset->dimsyms[i];
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if(dim->dim.declsize == NC_UNLIMITED) last = i;
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}
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return (last < 1);
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}
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/* True only iff no dimension is unlimited*/
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int
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isbounded(Dimset* dimset)
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{
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int i;
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for(i=0;i<dimset->ndims;i++) {
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Symbol* dim = dimset->dimsyms[i];
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if(dim->dim.declsize == NC_UNLIMITED) return 0;
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}
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return 1;
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}
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int
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signedtype(nc_type nctype)
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{
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switch (nctype) {
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case NC_BYTE:
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case NC_SHORT:
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case NC_INT:
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case NC_INT64:
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return nctype;
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case NC_UBYTE: return NC_BYTE;
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case NC_USHORT: return NC_SHORT;
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case NC_UINT: return NC_INT;
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case NC_UINT64: return NC_INT64;
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default: break;
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}
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return nctype;
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}
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int
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unsignedtype(nc_type nctype)
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{
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switch (nctype) {
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case NC_UBYTE:
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case NC_USHORT:
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case NC_UINT:
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case NC_UINT64:
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return nctype;
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case NC_BYTE: return NC_UBYTE;
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case NC_SHORT: return NC_USHORT;
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case NC_INT: return NC_UINT;
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case NC_INT64: return NC_UINT64;
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default: break;
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}
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return nctype;
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}
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int
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isinttype(nc_type nctype)
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{
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return (nctype != NC_CHAR)
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&& ((nctype >= NC_BYTE && nctype <= NC_INT)
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|| (nctype >= NC_UBYTE && nctype <= NC_UINT64));
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}
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int
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isuinttype(nc_type t)
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{
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return isinttype(t)
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&& t >= NC_UBYTE
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&& t <= NC_UINT64
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&& t != NC_INT64;
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}
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int
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isfloattype(nc_type nctype)
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{
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return (nctype == NC_FLOAT || nctype <= NC_DOUBLE);
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}
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int
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isclassicprim(nc_type nctype)
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{
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return (nctype >= NC_BYTE && nctype <= NC_DOUBLE)
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;
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}
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int
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isclassicprimplus(nc_type nctype)
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{
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return (nctype >= NC_BYTE && nctype <= NC_DOUBLE)
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|| (nctype == NC_STRING)
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;
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}
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int
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isprim(nc_type nctype)
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{
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return (nctype >= NC_BYTE && nctype <= NC_STRING)
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;
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}
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int
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isprimplus(nc_type nctype)
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{
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return (nctype >= NC_BYTE && nctype <= NC_STRING)
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|| (nctype == NC_ECONST)
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|| (nctype == NC_OPAQUE)
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;
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}
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void
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collectpath(Symbol* grp, List* grpstack)
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{
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while(grp != NULL) {
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listpush(grpstack,(void*)grp);
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grp = grp->container;
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}
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}
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#ifdef USE_NETCDF4
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/* Result is pool'd*/
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char*
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prefixtostring(List* prefix, char* separator)
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{
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int slen=0;
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int plen;
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int i;
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char* result;
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if(prefix == NULL) return pooldup("");
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plen = prefixlen(prefix);
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if(plen == 0) { /* root prefix*/
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slen=0;
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/* slen += strlen(separator);*/
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slen++; /* for null terminator*/
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result = poolalloc(slen);
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result[0] = '\0';
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/*strcat(result,separator);*/
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} else {
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for(i=0;i<plen;i++) {
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Symbol* sym = (Symbol*)listget(prefix,i);
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slen += (strlen(separator)+strlen(sym->name));
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}
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slen++; /* for null terminator*/
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result = poolalloc(slen);
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result[0] = '\0';
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for(i=0;i<plen;i++) {
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Symbol* sym = (Symbol*)listget(prefix,i);
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strcat(result,separator);
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strcat(result,sym->name); /* append "/<prefix[i]>"*/
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}
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}
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return result;
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}
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#endif
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/* Result is pool'd*/
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char*
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fullname(Symbol* sym)
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{
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#ifdef USE_NETCDF4
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char* s1;
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char* result;
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char* prefix;
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prefix = prefixtostring(sym->prefix,PATHSEPARATOR);
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s1 = poolcat(prefix,PATHSEPARATOR);
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result = poolcat(s1,sym->name);
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return result;
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#else
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return nulldup(sym->name);
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#endif
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}
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int
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prefixeq(List* x1, List* x2)
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{
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Symbol** l1;
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Symbol** l2;
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int len,i;
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if((len=listlength(x1)) != listlength(x2)) return 0;
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l1=(Symbol**)listcontents(x1);
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l2=(Symbol**)listcontents(x2);
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for(i=0;i<len;i++) {
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if(strcmp(l1[i]->name,l2[i]->name) != 0) return 0;
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}
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return 1;
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}
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List*
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prefixdup(List* prefix)
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{
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List* dupseq;
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int i;
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if(prefix == NULL) return listnew();
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dupseq = listnew();
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listsetalloc(dupseq,listlength(prefix));
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for(i=0;i<listlength(prefix);i++) listpush(dupseq,listget(prefix,i));
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return dupseq;
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}
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/*
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Many of the generate routines need to construct
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heap strings for short periods. Remembering to
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free such space is error prone, so provide a
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pseudo-GC to handle these short term requests.
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The idea is to have a fixed size pool
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tracking malloc requests and automatically
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releasing when the pool gets full.
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*/
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/* Max number of allocated pool items*/
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#define POOLMAX 100
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static char* pool[POOLMAX];
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static int poolindex = -1;
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#define POOL_DEFAULT 256
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char*
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poolalloc(size_t length)
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{
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if(poolindex == -1) { /* initialize*/
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memset((void*)pool,0,sizeof(pool));
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poolindex = 0;
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}
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if(poolindex == POOLMAX) poolindex=0;
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if(length == 0) length = POOL_DEFAULT;
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if(pool[poolindex] != NULL) efree(pool[poolindex]);
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pool[poolindex] = (char*)ecalloc(length);
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return pool[poolindex++];
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}
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char*
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pooldup(const char* s)
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{
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char* sdup = poolalloc(strlen(s)+1);
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strncpy(sdup,s,(strlen(s)+1));
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return sdup;
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}
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|
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char*
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poolcat(const char* s1, const char* s2)
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|
{
|
|
int len1, len2;
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|
char* cat;
|
|
if(s1 == NULL && s2 == NULL) return NULL;
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len1 = (s1?strlen(s1):0);
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len2 = (s2?strlen(s2):0);
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cat = poolalloc(len1+len2+1);
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cat[0] = '\0';
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if(s1 != NULL) strcat(cat,s1);
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if(s2 != NULL) strcat(cat,s2);
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return cat;
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}
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|
|
/* Result is malloc'd*/
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|
unsigned char*
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|
makebytestring(char* s, size_t* lenp)
|
|
{
|
|
unsigned char* bytes;
|
|
unsigned char* b;
|
|
size_t slen = strlen(s); /* # nibbles */
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|
size_t blen = slen/2; /* # bytes */
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|
int i;
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|
|
ASSERT((slen%2) == 0);
|
|
ASSERT(blen > 0);
|
|
bytes = (unsigned char*)ecalloc(blen);
|
|
b = bytes;
|
|
for(i=0;i<slen;i+=2) {
|
|
unsigned int digit1 = chartohex(*s++);
|
|
unsigned int digit2 = chartohex(*s++);
|
|
unsigned int byte = (digit1 << 4) | digit2;
|
|
*b++ = byte;
|
|
}
|
|
if(lenp) *lenp = blen;
|
|
return bytes;
|
|
}
|
|
|
|
int
|
|
getpadding(int offset, int alignment)
|
|
{
|
|
int rem = (alignment==0?0:(offset % alignment));
|
|
int pad = (rem==0?0:(alignment - rem));
|
|
return pad;
|
|
}
|
|
|
|
static void
|
|
reclaimSymbols(void)
|
|
{
|
|
int i;
|
|
for(i=0;i<listlength(symlist);i++) {
|
|
Symbol* sym = listget(symlist,i);
|
|
freeSymbol(sym);
|
|
}
|
|
}
|
|
|
|
void
|
|
cleanup()
|
|
{
|
|
reclaimSymbols();
|
|
listfree(symlist);
|
|
listfree(grpdefs);
|
|
listfree(dimdefs);
|
|
listfree(attdefs);
|
|
listfree(gattdefs);
|
|
listfree(xattdefs);
|
|
listfree(typdefs);
|
|
listfree(vardefs);
|
|
filldatalist->readonly = 0;
|
|
freedatalist(filldatalist);
|
|
}
|
|
|
|
/* compute the total n-dimensional size as 1 long array;
|
|
if stop == 0, then stop = dimset->ndims.
|
|
*/
|
|
size_t
|
|
crossproduct(Dimset* dimset, int start, int stop)
|
|
{
|
|
size_t totalsize = 1;
|
|
int i;
|
|
for(i=start;i<stop;i++) {
|
|
totalsize = totalsize * dimset->dimsyms[i]->dim.declsize;
|
|
}
|
|
return totalsize;
|
|
}
|
|
|
|
/* Do the "complement" of crossproduct;
|
|
compute the total n-dimensional size of an array
|
|
starting at 0 thru the 'last' array index.
|
|
stop if we encounter an unlimited dimension
|
|
*/
|
|
size_t
|
|
prefixarraylength(Dimset* dimset, int last)
|
|
{
|
|
return crossproduct(dimset,0,last+1);
|
|
}
|
|
|
|
|
|
|
|
#ifdef USE_HDF5
|
|
extern int H5Eprint1(FILE * stream);
|
|
#endif
|
|
|
|
void
|
|
check_err(const int stat, const int line, const char* file, const char* func)
|
|
{
|
|
check_err2(stat,-1,line,file,func);
|
|
}
|
|
|
|
void check_err2(const int stat, const int cdlline, const int line, const char* file, const char* func)
|
|
{
|
|
if (stat != NC_NOERR) {
|
|
if(cdlline >= 0)
|
|
fprintf(stderr, "ncgen: cdl line %d; %s\n", cdlline, nc_strerror(stat));
|
|
else
|
|
fprintf(stderr, "ncgen: %s\n", nc_strerror(stat));
|
|
fprintf(stderr, "\t(%s:%s:%d)\n", file,func,line);
|
|
#ifdef USE_HDF5
|
|
H5Eprint1(stderr);
|
|
#endif
|
|
fflush(stderr);
|
|
finalize_netcdf(1);
|
|
}
|
|
}
|
|
|
|
/**
|
|
Find the index of the first unlimited
|
|
dimension at or after 'start'.
|
|
If no unlimited exists, return |dimset|
|
|
*/
|
|
int
|
|
findunlimited(Dimset* dimset, int start)
|
|
{
|
|
for(;start<dimset->ndims;start++) {
|
|
if(dimset->dimsyms[start]->dim.isunlimited)
|
|
return start;
|
|
}
|
|
return dimset->ndims;
|
|
}
|
|
|
|
/**
|
|
Find the index of the last unlimited
|
|
dimension.
|
|
If no unlimited exists, return |dimset|
|
|
*/
|
|
int
|
|
findlastunlimited(Dimset* dimset)
|
|
{
|
|
int i;
|
|
for(i=dimset->ndims-1;i>=0;i--) {
|
|
if(dimset->dimsyms[i]->dim.isunlimited)
|
|
return i;
|
|
}
|
|
return dimset->ndims;
|
|
}
|
|
|
|
/**
|
|
Count the number of unlimited dimensions.
|
|
*/
|
|
int
|
|
countunlimited(Dimset* dimset)
|
|
{
|
|
int i, count;
|
|
for(count=0,i=dimset->ndims-1;i>=0;i--) {
|
|
if(dimset->dimsyms[i]->dim.isunlimited)
|
|
count++;
|
|
}
|
|
return count;
|
|
}
|
|
|
|
/* Return standard format string */
|
|
const char *
|
|
kind_string(int kind)
|
|
{
|
|
switch (kind) {
|
|
case 1: return "classic";
|
|
case 2: return "64-bit offset";
|
|
case 3: return "netCDF-4";
|
|
case 4: return "netCDF-4 classic model";
|
|
default:
|
|
derror("Unknown format index: %d\n",kind);
|
|
}
|
|
return NULL;
|
|
}
|
|
|