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https://github.com/Unidata/netcdf-c.git
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946a7ab8b5
netCDF classic or 64-bit offset files that have a UINT32_MAX flag for large last record size of a variable that has values larger than 1 byte. This problem had previously been fixed for *writing* such data, but was only tested with an ncbyte variable. Fixed test to demonstrate problem and the fix. More updates to chunking documentation, cosmetic fixes for some "--option=" documentation that doxygen turns into mdash.
1401 lines
28 KiB
C
1401 lines
28 KiB
C
/*
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* Copyright 1996, University Corporation for Atmospheric Research
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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*/
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/* $Id: v1hpg.c,v 1.70 2010/05/26 21:43:34 dmh Exp $ */
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#include "config.h"
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#include "nc3internal.h"
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#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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#include <assert.h>
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#include "rnd.h"
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#include "ncx.h"
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/*
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* This module defines the external representation
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* of the "header" of a netcdf version one file and
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* the version two variant that uses 64-bit file
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* offsets instead of the 32-bit file offsets in version
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* one files.
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* For each of the components of the NC structure,
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* There are (static) ncx_len_XXX(), v1h_put_XXX()
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* and v1h_get_XXX() functions. These define the
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* external representation of the components.
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* The exported entry points for the whole NC structure
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* are built up from these.
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*/
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/*
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* "magic number" at beginning of file: 0x43444601 (big endian)
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* assert(sizeof(ncmagic) % X_ALIGN == 0);
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*/
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static const schar ncmagic[] = {'C', 'D', 'F', 0x02};
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static const schar ncmagic1[] = {'C', 'D', 'F', 0x01};
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/*
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* v1hs == "Version 1 Header Stream"
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*
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* The netcdf file version 1 header is
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* of unknown and potentially unlimited size.
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* So, we don't know how much to get() on
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* the initial read. We build a stream, 'v1hs'
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* on top of ncio to do the header get.
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*/
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typedef struct v1hs {
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ncio *nciop;
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off_t offset; /* argument to nciop->get() */
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size_t extent; /* argument to nciop->get() */
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int flags; /* set to RGN_WRITE for write */
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int version; /* format variant: NC_FORMAT_CLASSIC or NC_FORMAT_64BIT */
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void *base; /* beginning of current buffer */
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void *pos; /* current position in buffer */
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void *end; /* end of current buffer = base + extent */
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} v1hs;
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/*
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* Release the stream, invalidate buffer
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*/
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static int
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rel_v1hs(v1hs *gsp)
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{
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int status;
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if(gsp->offset == OFF_NONE || gsp->base == NULL)
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return ENOERR;
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status = ncio_rel(gsp->nciop, gsp->offset,
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gsp->flags == RGN_WRITE ? RGN_MODIFIED : 0);
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gsp->end = NULL;
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gsp->pos = NULL;
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gsp->base = NULL;
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return status;
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}
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/*
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* Release the current chunk and get the next one.
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* Also used for initialization when gsp->base == NULL.
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*/
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static int
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fault_v1hs(v1hs *gsp, size_t extent)
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{
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int status;
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if(gsp->base != NULL)
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{
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const ptrdiff_t incr = (char *)gsp->pos - (char *)gsp->base;
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status = rel_v1hs(gsp);
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if(status)
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return status;
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gsp->offset += incr;
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}
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if(extent > gsp->extent)
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gsp->extent = extent;
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status = ncio_get(gsp->nciop,
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gsp->offset, gsp->extent,
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gsp->flags, &gsp->base);
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if(status)
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return status;
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gsp->pos = gsp->base;
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gsp->end = (char *)gsp->base + gsp->extent;
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return ENOERR;
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}
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/*
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* Ensure that 'nextread' bytes are available.
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*/
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static int
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check_v1hs(v1hs *gsp, size_t nextread)
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{
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#if 0 /* DEBUG */
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fprintf(stderr, "nextread %lu, remaining %lu\n",
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(unsigned long)nextread,
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(unsigned long)((char *)gsp->end - (char *)gsp->pos));
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#endif
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if((char *)gsp->pos + nextread <= (char *)gsp->end)
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return ENOERR;
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return fault_v1hs(gsp, nextread);
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}
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/* End v1hs */
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/* Write a size_t to the header */
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static int
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v1h_put_size_t(v1hs *psp, const size_t *sp)
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{
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int status = check_v1hs(psp, X_SIZEOF_SIZE_T);
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if(status != ENOERR)
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return status;
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return ncx_put_size_t(&psp->pos, sp);
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}
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/* Read a size_t from the header */
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static int
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v1h_get_size_t(v1hs *gsp, size_t *sp)
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{
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int status = check_v1hs(gsp, X_SIZEOF_SIZE_T);
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if(status != ENOERR)
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return status;
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return ncx_get_size_t((const void **)(&gsp->pos), sp);
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}
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/* Begin nc_type */
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#define X_SIZEOF_NC_TYPE X_SIZEOF_INT
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/* Write a nc_type to the header */
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static int
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v1h_put_nc_type(v1hs *psp, const nc_type *typep)
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{
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const int itype = (int) *typep;
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int status = check_v1hs(psp, X_SIZEOF_INT);
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if(status != ENOERR)
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return status;
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status = ncx_put_int_int(psp->pos, &itype);
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psp->pos = (void *)((char *)psp->pos + X_SIZEOF_INT);
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return status;
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}
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/* Read a nc_type from the header */
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static int
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v1h_get_nc_type(v1hs *gsp, nc_type *typep)
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{
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int type = 0;
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int status = check_v1hs(gsp, X_SIZEOF_INT);
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if(status != ENOERR)
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return status;
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status = ncx_get_int_int(gsp->pos, &type);
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gsp->pos = (void *)((char *)gsp->pos + X_SIZEOF_INT);
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if(status != ENOERR)
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return status;
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assert(type == NC_BYTE
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|| type == NC_CHAR
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|| type == NC_SHORT
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|| type == NC_INT
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|| type == NC_FLOAT
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|| type == NC_DOUBLE);
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/* else */
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*typep = (nc_type) type;
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return ENOERR;
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}
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/* End nc_type */
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/* Begin NCtype (internal tags) */
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#define X_SIZEOF_NCTYPE X_SIZEOF_INT
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/* Write a NCtype to the header */
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static int
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v1h_put_NCtype(v1hs *psp, NCtype type)
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{
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const int itype = (int) type;
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int status = check_v1hs(psp, X_SIZEOF_INT);
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if(status != ENOERR)
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return status;
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status = ncx_put_int_int(psp->pos, &itype);
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psp->pos = (void *)((char *)psp->pos + X_SIZEOF_INT);
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return status;
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}
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/* Read a NCtype from the header */
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static int
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v1h_get_NCtype(v1hs *gsp, NCtype *typep)
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{
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int type = 0;
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int status = check_v1hs(gsp, X_SIZEOF_INT);
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if(status != ENOERR)
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return status;
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status = ncx_get_int_int(gsp->pos, &type);
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gsp->pos = (void *)((char *)gsp->pos + X_SIZEOF_INT);
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if(status != ENOERR)
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return status;
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/* else */
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*typep = (NCtype) type;
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return ENOERR;
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}
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/* End NCtype */
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/* Begin NC_string */
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/*
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* How much space will the xdr'd string take.
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* Formerly
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NC_xlen_string(cdfstr)
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*/
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static size_t
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ncx_len_NC_string(const NC_string *ncstrp)
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{
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size_t sz = X_SIZEOF_SIZE_T; /* nchars */
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assert(ncstrp != NULL);
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if(ncstrp->nchars != 0)
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{
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#if 0
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assert(ncstrp->nchars % X_ALIGN == 0);
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sz += ncstrp->nchars;
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#else
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sz += _RNDUP(ncstrp->nchars, X_ALIGN);
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#endif
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}
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return sz;
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}
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/* Write a NC_string to the header */
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static int
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v1h_put_NC_string(v1hs *psp, const NC_string *ncstrp)
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{
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int status;
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#if 0
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assert(ncstrp->nchars % X_ALIGN == 0);
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#endif
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status = v1h_put_size_t(psp, &ncstrp->nchars);
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if(status != ENOERR)
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return status;
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status = check_v1hs(psp, _RNDUP(ncstrp->nchars, X_ALIGN));
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if(status != ENOERR)
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return status;
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status = ncx_pad_putn_text(&psp->pos, ncstrp->nchars, ncstrp->cp);
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if(status != ENOERR)
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return status;
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return ENOERR;
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}
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/* Read a NC_string from the header */
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static int
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v1h_get_NC_string(v1hs *gsp, NC_string **ncstrpp)
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{
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int status;
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size_t nchars = 0;
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NC_string *ncstrp;
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status = v1h_get_size_t(gsp, &nchars);
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if(status != ENOERR)
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return status;
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ncstrp = new_NC_string(nchars, NULL);
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if(ncstrp == NULL)
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{
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return NC_ENOMEM;
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}
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#if 0
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/* assert(ncstrp->nchars == nchars || ncstrp->nchars - nchars < X_ALIGN); */
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assert(ncstrp->nchars % X_ALIGN == 0);
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status = check_v1hs(gsp, ncstrp->nchars);
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#else
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status = check_v1hs(gsp, _RNDUP(ncstrp->nchars, X_ALIGN));
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#endif
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if(status != ENOERR)
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goto unwind_alloc;
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status = ncx_pad_getn_text((const void **)(&gsp->pos),
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nchars, ncstrp->cp);
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if(status != ENOERR)
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goto unwind_alloc;
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*ncstrpp = ncstrp;
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return ENOERR;
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unwind_alloc:
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free_NC_string(ncstrp);
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return status;
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}
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/* End NC_string */
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/* Begin NC_dim */
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/*
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* How much space will the xdr'd dim take.
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* Formerly
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NC_xlen_dim(dpp)
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*/
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static size_t
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ncx_len_NC_dim(const NC_dim *dimp)
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{
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size_t sz;
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assert(dimp != NULL);
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sz = ncx_len_NC_string(dimp->name);
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sz += X_SIZEOF_SIZE_T;
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return(sz);
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}
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/* Write a NC_dim to the header */
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static int
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v1h_put_NC_dim(v1hs *psp, const NC_dim *dimp)
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{
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int status;
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status = v1h_put_NC_string(psp, dimp->name);
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if(status != ENOERR)
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return status;
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status = v1h_put_size_t(psp, &dimp->size);
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if(status != ENOERR)
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return status;
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return ENOERR;
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}
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/* Read a NC_dim from the header */
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static int
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v1h_get_NC_dim(v1hs *gsp, NC_dim **dimpp)
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{
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int status;
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NC_string *ncstrp;
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NC_dim *dimp;
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status = v1h_get_NC_string(gsp, &ncstrp);
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if(status != ENOERR)
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return status;
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dimp = new_x_NC_dim(ncstrp);
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if(dimp == NULL)
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{
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status = NC_ENOMEM;
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goto unwind_name;
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}
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status = v1h_get_size_t(gsp, &dimp->size);
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if(status != ENOERR)
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{
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free_NC_dim(dimp); /* frees name */
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return status;
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}
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*dimpp = dimp;
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return ENOERR;
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unwind_name:
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free_NC_string(ncstrp);
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return status;
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}
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/* How much space in the header is required for this NC_dimarray? */
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static size_t
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ncx_len_NC_dimarray(const NC_dimarray *ncap)
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{
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size_t xlen = X_SIZEOF_NCTYPE; /* type */
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xlen += X_SIZEOF_SIZE_T; /* count */
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if(ncap == NULL)
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return xlen;
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/* else */
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{
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const NC_dim **dpp = (const NC_dim **)ncap->value;
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const NC_dim *const *const end = &dpp[ncap->nelems];
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for( /*NADA*/; dpp < end; dpp++)
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{
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xlen += ncx_len_NC_dim(*dpp);
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}
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}
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return xlen;
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}
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/* Write a NC_dimarray to the header */
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static int
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v1h_put_NC_dimarray(v1hs *psp, const NC_dimarray *ncap)
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{
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int status;
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assert(psp != NULL);
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if(ncap == NULL
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#if 1
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/* Backward:
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* This clause is for 'byte for byte'
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* backward compatibility.
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* Strickly speaking, it is 'bug for bug'.
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*/
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|| ncap->nelems == 0
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#endif
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)
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{
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/*
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* Handle empty netcdf
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*/
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const size_t nosz = 0;
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status = v1h_put_NCtype(psp, NC_UNSPECIFIED);
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if(status != ENOERR)
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return status;
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status = v1h_put_size_t(psp, &nosz);
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if(status != ENOERR)
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return status;
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return ENOERR;
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}
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/* else */
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status = v1h_put_NCtype(psp, NC_DIMENSION);
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if(status != ENOERR)
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return status;
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status = v1h_put_size_t(psp, &ncap->nelems);
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if(status != ENOERR)
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return status;
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{
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const NC_dim **dpp = (const NC_dim **)ncap->value;
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const NC_dim *const *const end = &dpp[ncap->nelems];
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for( /*NADA*/; dpp < end; dpp++)
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{
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status = v1h_put_NC_dim(psp, *dpp);
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if(status)
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return status;
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}
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}
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return ENOERR;
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}
|
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|
|
|
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/* Read a NC_dimarray from the header */
|
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static int
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v1h_get_NC_dimarray(v1hs *gsp, NC_dimarray *ncap)
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{
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int status;
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NCtype type = NC_UNSPECIFIED;
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|
|
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assert(gsp != NULL && gsp->pos != NULL);
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assert(ncap != NULL);
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assert(ncap->value == NULL);
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|
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status = v1h_get_NCtype(gsp, &type);
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if(status != ENOERR)
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return status;
|
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|
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status = v1h_get_size_t(gsp, &ncap->nelems);
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if(status != ENOERR)
|
|
return status;
|
|
|
|
if(ncap->nelems == 0)
|
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return ENOERR;
|
|
/* else */
|
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if(type != NC_DIMENSION)
|
|
return EINVAL;
|
|
|
|
ncap->value = (NC_dim **) malloc(ncap->nelems * sizeof(NC_dim *));
|
|
if(ncap->value == NULL)
|
|
return NC_ENOMEM;
|
|
ncap->nalloc = ncap->nelems;
|
|
|
|
{
|
|
NC_dim **dpp = ncap->value;
|
|
NC_dim *const *const end = &dpp[ncap->nelems];
|
|
for( /*NADA*/; dpp < end; dpp++)
|
|
{
|
|
status = v1h_get_NC_dim(gsp, dpp);
|
|
if(status)
|
|
{
|
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ncap->nelems = (size_t)(dpp - ncap->value);
|
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free_NC_dimarrayV(ncap);
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|
return status;
|
|
}
|
|
}
|
|
}
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/* End NC_dim */
|
|
/* Begin NC_attr */
|
|
|
|
|
|
/*
|
|
* How much space will 'attrp' take in external representation?
|
|
* Formerly
|
|
NC_xlen_attr(app)
|
|
*/
|
|
static size_t
|
|
ncx_len_NC_attr(const NC_attr *attrp)
|
|
{
|
|
size_t sz;
|
|
|
|
assert(attrp != NULL);
|
|
|
|
sz = ncx_len_NC_string(attrp->name);
|
|
sz += X_SIZEOF_NC_TYPE; /* type */
|
|
sz += X_SIZEOF_SIZE_T; /* nelems */
|
|
sz += attrp->xsz;
|
|
|
|
return(sz);
|
|
}
|
|
|
|
|
|
#undef MIN
|
|
#define MIN(mm,nn) (((mm) < (nn)) ? (mm) : (nn))
|
|
|
|
/*
|
|
* Put the values of an attribute
|
|
* The loop is necessary since attrp->nelems
|
|
* could potentially be quite large.
|
|
*/
|
|
static int
|
|
v1h_put_NC_attrV(v1hs *psp, const NC_attr *attrp)
|
|
{
|
|
int status;
|
|
const size_t perchunk = psp->extent;
|
|
size_t remaining = attrp->xsz;
|
|
void *value = attrp->xvalue;
|
|
size_t nbytes;
|
|
|
|
assert(psp->extent % X_ALIGN == 0);
|
|
|
|
do {
|
|
nbytes = MIN(perchunk, remaining);
|
|
|
|
status = check_v1hs(psp, nbytes);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
(void) memcpy(psp->pos, value, nbytes);
|
|
|
|
psp->pos = (void *)((char *)psp->pos + nbytes);
|
|
value = (void *)((char *)value + nbytes);
|
|
remaining -= nbytes;
|
|
|
|
} while(remaining != 0);
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
/* Write a NC_attr to the header */
|
|
static int
|
|
v1h_put_NC_attr(v1hs *psp, const NC_attr *attrp)
|
|
{
|
|
int status;
|
|
|
|
status = v1h_put_NC_string(psp, attrp->name);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_nc_type(psp, &attrp->type);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_size_t(psp, &attrp->nelems);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_NC_attrV(psp, attrp);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/*
|
|
* Get the values of an attribute
|
|
* The loop is necessary since attrp->nelems
|
|
* could potentially be quite large.
|
|
*/
|
|
static int
|
|
v1h_get_NC_attrV(v1hs *gsp, NC_attr *attrp)
|
|
{
|
|
int status;
|
|
const size_t perchunk = gsp->extent;
|
|
size_t remaining = attrp->xsz;
|
|
void *value = attrp->xvalue;
|
|
size_t nget;
|
|
|
|
do {
|
|
nget = MIN(perchunk, remaining);
|
|
|
|
status = check_v1hs(gsp, nget);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
(void) memcpy(value, gsp->pos, nget);
|
|
|
|
gsp->pos = (void *)((char *)gsp->pos + nget);
|
|
value = (void *)((char *)value + nget);
|
|
remaining -= nget;
|
|
|
|
} while(remaining != 0);
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/* Read a NC_attr from the header */
|
|
static int
|
|
v1h_get_NC_attr(v1hs *gsp, NC_attr **attrpp)
|
|
{
|
|
NC_string *strp;
|
|
int status;
|
|
nc_type type;
|
|
size_t nelems;
|
|
NC_attr *attrp;
|
|
|
|
status = v1h_get_NC_string(gsp, &strp);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_get_nc_type(gsp, &type);
|
|
if(status != ENOERR)
|
|
goto unwind_name;
|
|
|
|
status = v1h_get_size_t(gsp, &nelems);
|
|
if(status != ENOERR)
|
|
goto unwind_name;
|
|
|
|
attrp = new_x_NC_attr(strp, type, nelems);
|
|
if(attrp == NULL)
|
|
{
|
|
status = NC_ENOMEM;
|
|
goto unwind_name;
|
|
}
|
|
|
|
status = v1h_get_NC_attrV(gsp, attrp);
|
|
if(status != ENOERR)
|
|
{
|
|
free_NC_attr(attrp); /* frees strp */
|
|
return status;
|
|
}
|
|
|
|
*attrpp = attrp;
|
|
|
|
return ENOERR;
|
|
|
|
unwind_name:
|
|
free_NC_string(strp);
|
|
return status;
|
|
}
|
|
|
|
|
|
/* How much space in the header is required for this NC_attrarray? */
|
|
static size_t
|
|
ncx_len_NC_attrarray(const NC_attrarray *ncap)
|
|
{
|
|
size_t xlen = X_SIZEOF_NCTYPE; /* type */
|
|
xlen += X_SIZEOF_SIZE_T; /* count */
|
|
if(ncap == NULL)
|
|
return xlen;
|
|
/* else */
|
|
{
|
|
const NC_attr **app = (const NC_attr **)ncap->value;
|
|
const NC_attr *const *const end = &app[ncap->nelems];
|
|
for( /*NADA*/; app < end; app++)
|
|
{
|
|
xlen += ncx_len_NC_attr(*app);
|
|
}
|
|
}
|
|
return xlen;
|
|
}
|
|
|
|
|
|
/* Write a NC_attrarray to the header */
|
|
static int
|
|
v1h_put_NC_attrarray(v1hs *psp, const NC_attrarray *ncap)
|
|
{
|
|
int status;
|
|
|
|
assert(psp != NULL);
|
|
|
|
if(ncap == NULL
|
|
#if 1
|
|
/* Backward:
|
|
* This clause is for 'byte for byte'
|
|
* backward compatibility.
|
|
* Strickly speaking, it is 'bug for bug'.
|
|
*/
|
|
|| ncap->nelems == 0
|
|
#endif
|
|
)
|
|
{
|
|
/*
|
|
* Handle empty netcdf
|
|
*/
|
|
const size_t nosz = 0;
|
|
|
|
status = v1h_put_NCtype(psp, NC_UNSPECIFIED);
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = v1h_put_size_t(psp, &nosz);
|
|
if(status != ENOERR)
|
|
return status;
|
|
return ENOERR;
|
|
}
|
|
/* else */
|
|
|
|
status = v1h_put_NCtype(psp, NC_ATTRIBUTE);
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = v1h_put_size_t(psp, &ncap->nelems);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
{
|
|
const NC_attr **app = (const NC_attr **)ncap->value;
|
|
const NC_attr *const *const end = &app[ncap->nelems];
|
|
for( /*NADA*/; app < end; app++)
|
|
{
|
|
status = v1h_put_NC_attr(psp, *app);
|
|
if(status)
|
|
return status;
|
|
}
|
|
}
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/* Read a NC_attrarray from the header */
|
|
static int
|
|
v1h_get_NC_attrarray(v1hs *gsp, NC_attrarray *ncap)
|
|
{
|
|
int status;
|
|
NCtype type = NC_UNSPECIFIED;
|
|
|
|
assert(gsp != NULL && gsp->pos != NULL);
|
|
assert(ncap != NULL);
|
|
assert(ncap->value == NULL);
|
|
|
|
status = v1h_get_NCtype(gsp, &type);
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = v1h_get_size_t(gsp, &ncap->nelems);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
if(ncap->nelems == 0)
|
|
return ENOERR;
|
|
/* else */
|
|
if(type != NC_ATTRIBUTE)
|
|
return EINVAL;
|
|
|
|
ncap->value = (NC_attr **) malloc(ncap->nelems * sizeof(NC_attr *));
|
|
if(ncap->value == NULL)
|
|
return NC_ENOMEM;
|
|
ncap->nalloc = ncap->nelems;
|
|
|
|
{
|
|
NC_attr **app = ncap->value;
|
|
NC_attr *const *const end = &app[ncap->nelems];
|
|
for( /*NADA*/; app < end; app++)
|
|
{
|
|
status = v1h_get_NC_attr(gsp, app);
|
|
if(status)
|
|
{
|
|
ncap->nelems = (size_t)(app - ncap->value);
|
|
free_NC_attrarrayV(ncap);
|
|
return status;
|
|
}
|
|
}
|
|
}
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
/* End NC_attr */
|
|
/* Begin NC_var */
|
|
|
|
/*
|
|
* How much space will the xdr'd var take.
|
|
* Formerly
|
|
NC_xlen_var(vpp)
|
|
*/
|
|
static size_t
|
|
ncx_len_NC_var(const NC_var *varp, size_t sizeof_off_t)
|
|
{
|
|
size_t sz;
|
|
|
|
assert(varp != NULL);
|
|
assert(sizeof_off_t != 0);
|
|
|
|
sz = ncx_len_NC_string(varp->name);
|
|
sz += X_SIZEOF_SIZE_T; /* ndims */
|
|
sz += ncx_len_int(varp->ndims); /* dimids */
|
|
sz += ncx_len_NC_attrarray(&varp->attrs);
|
|
sz += X_SIZEOF_NC_TYPE; /* type */
|
|
sz += X_SIZEOF_SIZE_T; /* len */
|
|
sz += sizeof_off_t; /* begin */
|
|
|
|
return(sz);
|
|
}
|
|
|
|
|
|
/* Write a NC_var to the header */
|
|
static int
|
|
v1h_put_NC_var(v1hs *psp, const NC_var *varp)
|
|
{
|
|
int status;
|
|
|
|
status = v1h_put_NC_string(psp, varp->name);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_size_t(psp, &varp->ndims);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = check_v1hs(psp, ncx_len_int(varp->ndims));
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = ncx_putn_int_int(&psp->pos,
|
|
varp->ndims, varp->dimids);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_NC_attrarray(psp, &varp->attrs);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_nc_type(psp, &varp->type);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_put_size_t(psp, &varp->len);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = check_v1hs(psp, psp->version == 1 ? 4 : 8);
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = ncx_put_off_t(&psp->pos, &varp->begin, psp->version == 1 ? 4 : 8);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/* Read a NC_var from the header */
|
|
static int
|
|
v1h_get_NC_var(v1hs *gsp, NC_var **varpp)
|
|
{
|
|
NC_string *strp;
|
|
int status;
|
|
size_t ndims;
|
|
NC_var *varp;
|
|
|
|
status = v1h_get_NC_string(gsp, &strp);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_get_size_t(gsp, &ndims);
|
|
if(status != ENOERR)
|
|
goto unwind_name;
|
|
|
|
varp = new_x_NC_var(strp, ndims);
|
|
if(varp == NULL)
|
|
{
|
|
status = NC_ENOMEM;
|
|
goto unwind_name;
|
|
}
|
|
|
|
status = check_v1hs(gsp, ncx_len_int(ndims));
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
status = ncx_getn_int_int((const void **)(&gsp->pos),
|
|
ndims, varp->dimids);
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
|
|
status = v1h_get_NC_attrarray(gsp, &varp->attrs);
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
|
|
status = v1h_get_nc_type(gsp, &varp->type);
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
|
|
status = v1h_get_size_t(gsp, &varp->len);
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
|
|
status = check_v1hs(gsp, gsp->version == 1 ? 4 : 8);
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
status = ncx_get_off_t((const void **)&gsp->pos,
|
|
&varp->begin, gsp->version == 1 ? 4 : 8);
|
|
if(status != ENOERR)
|
|
goto unwind_alloc;
|
|
|
|
*varpp = varp;
|
|
return ENOERR;
|
|
|
|
unwind_alloc:
|
|
free_NC_var(varp); /* frees name */
|
|
return status;
|
|
|
|
unwind_name:
|
|
free_NC_string(strp);
|
|
return status;
|
|
}
|
|
|
|
|
|
/* How much space in the header is required for this NC_vararray? */
|
|
static size_t
|
|
ncx_len_NC_vararray(const NC_vararray *ncap, size_t sizeof_off_t)
|
|
{
|
|
size_t xlen = X_SIZEOF_NCTYPE; /* type */
|
|
xlen += X_SIZEOF_SIZE_T; /* count */
|
|
if(ncap == NULL)
|
|
return xlen;
|
|
/* else */
|
|
{
|
|
const NC_var **vpp = (const NC_var **)ncap->value;
|
|
const NC_var *const *const end = &vpp[ncap->nelems];
|
|
for( /*NADA*/; vpp < end; vpp++)
|
|
{
|
|
xlen += ncx_len_NC_var(*vpp, sizeof_off_t);
|
|
}
|
|
}
|
|
return xlen;
|
|
}
|
|
|
|
|
|
/* Write a NC_vararray to the header */
|
|
static int
|
|
v1h_put_NC_vararray(v1hs *psp, const NC_vararray *ncap)
|
|
{
|
|
int status;
|
|
|
|
assert(psp != NULL);
|
|
|
|
if(ncap == NULL
|
|
#if 1
|
|
/* Backward:
|
|
* This clause is for 'byte for byte'
|
|
* backward compatibility.
|
|
* Strickly speaking, it is 'bug for bug'.
|
|
*/
|
|
|| ncap->nelems == 0
|
|
#endif
|
|
)
|
|
{
|
|
/*
|
|
* Handle empty netcdf
|
|
*/
|
|
const size_t nosz = 0;
|
|
|
|
status = v1h_put_NCtype(psp, NC_UNSPECIFIED);
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = v1h_put_size_t(psp, &nosz);
|
|
if(status != ENOERR)
|
|
return status;
|
|
return ENOERR;
|
|
}
|
|
/* else */
|
|
|
|
status = v1h_put_NCtype(psp, NC_VARIABLE);
|
|
if(status != ENOERR)
|
|
return status;
|
|
status = v1h_put_size_t(psp, &ncap->nelems);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
{
|
|
const NC_var **vpp = (const NC_var **)ncap->value;
|
|
const NC_var *const *const end = &vpp[ncap->nelems];
|
|
for( /*NADA*/; vpp < end; vpp++)
|
|
{
|
|
status = v1h_put_NC_var(psp, *vpp);
|
|
if(status)
|
|
return status;
|
|
}
|
|
}
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/* Read a NC_vararray from the header */
|
|
static int
|
|
v1h_get_NC_vararray(v1hs *gsp, NC_vararray *ncap)
|
|
{
|
|
int status;
|
|
NCtype type = NC_UNSPECIFIED;
|
|
|
|
assert(gsp != NULL && gsp->pos != NULL);
|
|
assert(ncap != NULL);
|
|
assert(ncap->value == NULL);
|
|
|
|
status = v1h_get_NCtype(gsp, &type);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
status = v1h_get_size_t(gsp, &ncap->nelems);
|
|
if(status != ENOERR)
|
|
return status;
|
|
|
|
if(ncap->nelems == 0)
|
|
return ENOERR;
|
|
/* else */
|
|
if(type != NC_VARIABLE)
|
|
return EINVAL;
|
|
|
|
ncap->value = (NC_var **) malloc(ncap->nelems * sizeof(NC_var *));
|
|
if(ncap->value == NULL)
|
|
return NC_ENOMEM;
|
|
ncap->nalloc = ncap->nelems;
|
|
|
|
{
|
|
NC_var **vpp = ncap->value;
|
|
NC_var *const *const end = &vpp[ncap->nelems];
|
|
for( /*NADA*/; vpp < end; vpp++)
|
|
{
|
|
status = v1h_get_NC_var(gsp, vpp);
|
|
if(status)
|
|
{
|
|
ncap->nelems = (size_t)(vpp - ncap->value);
|
|
free_NC_vararrayV(ncap);
|
|
return status;
|
|
}
|
|
}
|
|
}
|
|
|
|
return ENOERR;
|
|
}
|
|
|
|
|
|
/* End NC_var */
|
|
/* Begin NC */
|
|
|
|
/*
|
|
* Recompute the shapes of all variables
|
|
* Sets ncp->begin_var to start of first variable.
|
|
* Sets ncp->begin_rec to start of first record variable.
|
|
* Returns -1 on error. The only possible error is a reference
|
|
* to a non existent dimension, which could occur for a corrupted
|
|
* netcdf file.
|
|
*/
|
|
static int
|
|
NC_computeshapes(NC3_INFO* ncp)
|
|
{
|
|
NC_var **vpp = (NC_var **)ncp->vars.value;
|
|
NC_var *const *const end = &vpp[ncp->vars.nelems];
|
|
NC_var *first_var = NULL; /* first "non-record" var */
|
|
NC_var *first_rec = NULL; /* first "record" var */
|
|
int status;
|
|
|
|
ncp->begin_var = (off_t) ncp->xsz;
|
|
ncp->begin_rec = (off_t) ncp->xsz;
|
|
ncp->recsize = 0;
|
|
|
|
if(ncp->vars.nelems == 0)
|
|
return(0);
|
|
|
|
for( /*NADA*/; vpp < end; vpp++)
|
|
{
|
|
status = NC_var_shape(*vpp, &ncp->dims);
|
|
if(status != ENOERR)
|
|
return(status);
|
|
|
|
if(IS_RECVAR(*vpp))
|
|
{
|
|
if(first_rec == NULL)
|
|
first_rec = *vpp;
|
|
if((*vpp)->len == UINT32_MAX) /* Flag for large last record */
|
|
ncp->recsize += (*vpp)->dsizes[0] * (*vpp)->xsz;
|
|
else
|
|
ncp->recsize += (*vpp)->len;
|
|
}
|
|
else
|
|
{
|
|
if(first_var == NULL)
|
|
first_var = *vpp;
|
|
/*
|
|
* Overwritten each time thru.
|
|
* Usually overwritten in first_rec != NULL clause below.
|
|
*/
|
|
ncp->begin_rec = (*vpp)->begin + (off_t)(*vpp)->len;
|
|
}
|
|
}
|
|
|
|
if(first_rec != NULL)
|
|
{
|
|
assert(ncp->begin_rec <= first_rec->begin);
|
|
ncp->begin_rec = first_rec->begin;
|
|
/*
|
|
* for special case of exactly one record variable, pack value
|
|
*/
|
|
if(ncp->recsize == first_rec->len)
|
|
ncp->recsize = *first_rec->dsizes * first_rec->xsz;
|
|
}
|
|
|
|
if(first_var != NULL)
|
|
{
|
|
ncp->begin_var = first_var->begin;
|
|
}
|
|
else
|
|
{
|
|
ncp->begin_var = ncp->begin_rec;
|
|
}
|
|
|
|
assert(ncp->begin_var > 0);
|
|
assert(ncp->xsz <= (size_t)ncp->begin_var);
|
|
assert(ncp->begin_rec > 0);
|
|
assert(ncp->begin_var <= ncp->begin_rec);
|
|
|
|
return(ENOERR);
|
|
}
|
|
|
|
/* How much space in the header is required for the NC data structure? */
|
|
size_t
|
|
ncx_len_NC(const NC3_INFO* ncp, size_t sizeof_off_t)
|
|
{
|
|
size_t xlen = sizeof(ncmagic);
|
|
|
|
assert(ncp != NULL);
|
|
|
|
xlen += X_SIZEOF_SIZE_T; /* numrecs */
|
|
xlen += ncx_len_NC_dimarray(&ncp->dims);
|
|
xlen += ncx_len_NC_attrarray(&ncp->attrs);
|
|
xlen += ncx_len_NC_vararray(&ncp->vars, sizeof_off_t);
|
|
|
|
return xlen;
|
|
}
|
|
|
|
|
|
/* Write the file header */
|
|
int
|
|
ncx_put_NC(const NC3_INFO* ncp, void **xpp, off_t offset, size_t extent)
|
|
{
|
|
int status = ENOERR;
|
|
v1hs ps; /* the get stream */
|
|
|
|
assert(ncp != NULL);
|
|
|
|
/* Initialize stream ps */
|
|
|
|
ps.nciop = ncp->nciop;
|
|
ps.flags = RGN_WRITE;
|
|
|
|
if (ncp->flags & NC_64BIT_OFFSET)
|
|
ps.version = 2;
|
|
else
|
|
ps.version = 1;
|
|
|
|
if(xpp == NULL)
|
|
{
|
|
/*
|
|
* Come up with a reasonable stream read size.
|
|
*/
|
|
extent = ncp->xsz;
|
|
if(extent <= MIN_NC_XSZ)
|
|
{
|
|
/* first time read */
|
|
extent = ncp->chunk;
|
|
/* Protection for when ncp->chunk is huge;
|
|
* no need to read hugely. */
|
|
if(extent > 4096)
|
|
extent = 4096;
|
|
}
|
|
else if(extent > ncp->chunk)
|
|
extent = ncp->chunk;
|
|
|
|
ps.offset = 0;
|
|
ps.extent = extent;
|
|
ps.base = NULL;
|
|
ps.pos = ps.base;
|
|
|
|
status = fault_v1hs(&ps, extent);
|
|
if(status)
|
|
return status;
|
|
}
|
|
else
|
|
{
|
|
ps.offset = offset;
|
|
ps.extent = extent;
|
|
ps.base = *xpp;
|
|
ps.pos = ps.base;
|
|
ps.end = (char *)ps.base + ps.extent;
|
|
}
|
|
|
|
if (ps.version == 2)
|
|
status = ncx_putn_schar_schar(&ps.pos, sizeof(ncmagic), ncmagic);
|
|
else
|
|
status = ncx_putn_schar_schar(&ps.pos, sizeof(ncmagic1), ncmagic1);
|
|
if(status != ENOERR)
|
|
goto release;
|
|
|
|
{
|
|
const size_t nrecs = NC_get_numrecs(ncp);
|
|
status = ncx_put_size_t(&ps.pos, &nrecs);
|
|
if(status != ENOERR)
|
|
goto release;
|
|
}
|
|
|
|
assert((char *)ps.pos < (char *)ps.end);
|
|
|
|
status = v1h_put_NC_dimarray(&ps, &ncp->dims);
|
|
if(status != ENOERR)
|
|
goto release;
|
|
|
|
status = v1h_put_NC_attrarray(&ps, &ncp->attrs);
|
|
if(status != ENOERR)
|
|
goto release;
|
|
|
|
status = v1h_put_NC_vararray(&ps, &ncp->vars);
|
|
if(status != ENOERR)
|
|
goto release;
|
|
|
|
release:
|
|
(void) rel_v1hs(&ps);
|
|
|
|
return status;
|
|
}
|
|
|
|
|
|
/* Make the in-memory NC structure from reading the file header */
|
|
int
|
|
nc_get_NC(NC3_INFO* ncp)
|
|
{
|
|
int status;
|
|
v1hs gs; /* the get stream */
|
|
|
|
assert(ncp != NULL);
|
|
|
|
/* Initialize stream gs */
|
|
|
|
gs.nciop = ncp->nciop;
|
|
gs.offset = 0; /* beginning of file */
|
|
gs.extent = 0;
|
|
gs.flags = 0;
|
|
gs.version = 0;
|
|
gs.base = NULL;
|
|
gs.pos = gs.base;
|
|
|
|
{
|
|
/*
|
|
* Come up with a reasonable stream read size.
|
|
*/
|
|
off_t filesize;
|
|
size_t extent = MIN_NC_XSZ;
|
|
|
|
extent = ncp->xsz;
|
|
if(extent <= MIN_NC_XSZ)
|
|
{
|
|
status = ncio_filesize(ncp->nciop, &filesize);
|
|
if(status)
|
|
return status;
|
|
if(filesize < sizeof(ncmagic)) { /* too small, not netcdf */
|
|
|
|
status = NC_ENOTNC;
|
|
return status;
|
|
}
|
|
/* first time read */
|
|
extent = ncp->chunk;
|
|
/* Protection for when ncp->chunk is huge;
|
|
* no need to read hugely. */
|
|
if(extent > 4096)
|
|
extent = 4096;
|
|
if(extent > filesize)
|
|
extent = filesize;
|
|
}
|
|
else if(extent > ncp->chunk)
|
|
extent = ncp->chunk;
|
|
|
|
/*
|
|
* Invalidate the I/O buffers to force a read of the header
|
|
* region.
|
|
*/
|
|
status = ncio_sync(gs.nciop);
|
|
if(status)
|
|
return status;
|
|
|
|
status = fault_v1hs(&gs, extent);
|
|
if(status)
|
|
return status;
|
|
}
|
|
|
|
/* get the header from the stream gs */
|
|
|
|
{
|
|
/* Get & check magic number */
|
|
schar magic[sizeof(ncmagic)];
|
|
(void) memset(magic, 0, sizeof(magic));
|
|
|
|
status = ncx_getn_schar_schar(
|
|
(const void **)(&gs.pos), sizeof(magic), magic);
|
|
if(status != ENOERR)
|
|
goto unwind_get;
|
|
|
|
if(memcmp(magic, ncmagic, sizeof(ncmagic)-1) != 0)
|
|
{
|
|
status = NC_ENOTNC;
|
|
goto unwind_get;
|
|
}
|
|
/* Check version number in last byte of magic */
|
|
if (magic[sizeof(ncmagic)-1] == 0x1) {
|
|
gs.version = 1;
|
|
} else if (magic[sizeof(ncmagic)-1] == 0x2) {
|
|
gs.version = 2;
|
|
fSet(ncp->flags, NC_64BIT_OFFSET);
|
|
/* Now we support version 2 file access on non-LFS systems -- rkr */
|
|
#if 0
|
|
if (sizeof(off_t) != 8) {
|
|
fprintf(stderr, "NETCDF WARNING: Version 2 file on 32-bit system.\n");
|
|
}
|
|
#endif
|
|
} else {
|
|
status = NC_ENOTNC;
|
|
goto unwind_get;
|
|
}
|
|
}
|
|
|
|
{
|
|
size_t nrecs = 0;
|
|
status = ncx_get_size_t((const void **)(&gs.pos), &nrecs);
|
|
if(status != ENOERR)
|
|
goto unwind_get;
|
|
NC_set_numrecs(ncp, nrecs);
|
|
}
|
|
|
|
assert((char *)gs.pos < (char *)gs.end);
|
|
|
|
status = v1h_get_NC_dimarray(&gs, &ncp->dims);
|
|
if(status != ENOERR)
|
|
goto unwind_get;
|
|
|
|
status = v1h_get_NC_attrarray(&gs, &ncp->attrs);
|
|
if(status != ENOERR)
|
|
goto unwind_get;
|
|
|
|
status = v1h_get_NC_vararray(&gs, &ncp->vars);
|
|
if(status != ENOERR)
|
|
goto unwind_get;
|
|
|
|
ncp->xsz = ncx_len_NC(ncp, (gs.version == 1) ? 4 : 8);
|
|
|
|
status = NC_computeshapes(ncp);
|
|
if(status != ENOERR)
|
|
goto unwind_get;
|
|
|
|
unwind_get:
|
|
(void) rel_v1hs(&gs);
|
|
return status;
|
|
}
|