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11fe00ea05
Filter support has three goals: 1. Use the existing HDF5 filter implementations, 2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr, 3. Allow filters to be used even when HDF5 is disabled Detailed usage directions are define in docs/filters.md. For now, the existing filter API is left in place. So filters are defined using ''nc_def_var_filter'' using the HDF5 style where the id and parameters are unsigned integers. This is a big change since filters affect many parts of the code. In the following, the terms "compressor" and "filter" and "codec" are generally used synonomously. ### Filter-Related Changes: * In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms. * Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h. * Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out. * Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h. * Add a number of new test to test the new nczarr filters. * Let ncgen parse _Codecs attribute, although it is ignored. ### Plugin directory changes: * Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file * Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip * Add a Codec defaulter (see docs/filters.md) for the big four filters. * Make plugins work with windows by properly adding __declspec declaration. ### Misc. Non-Filter Changes * Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5. * Improve support for caching * More fixes for path conversion code * Fix misc. memory leaks * Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath. * Add a number of new test to test the non-filter fixes. * Update the parsers * Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
1869 lines
50 KiB
C
1869 lines
50 KiB
C
/* Copyright 2003-2018, University Corporation for Atmospheric
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* Research. See the COPYRIGHT file for copying and redistribution
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* conditions.
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*/
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/**
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* @file
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* @internal
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* Internal netcdf-4 functions.
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*
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* This file contains functions internal to the netcdf4 library. None of
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* the functions in this file are exposed in the exetnal API. These
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* functions all relate to the manipulation of netcdf-4's in-memory
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* buffer of metadata information, i.e. the linked list of NC
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* structs.
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*
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* @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
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*/
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#include "config.h"
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#include "netcdf.h"
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#include "netcdf_filter.h"
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#include "nc4internal.h"
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#include "nc.h" /* from libsrc */
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#include "ncdispatch.h" /* from libdispatch */
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#include "ncutf8.h"
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#include "netcdf_aux.h"
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/** @internal Number of reserved attributes. These attributes are
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* hidden from the netcdf user, but exist in the implementation
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* datasets to help netcdf read the dataset.
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* Moved here from hdf5file.c.
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* These tables need to capture all reserved attributes
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* across all possible dispatchers
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*/
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/** @internal List of reserved attributes.
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WARNING: This list must be in sorted order for binary search. */
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static const NC_reservedatt NC_reserved[] = {
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{NC_ATT_CLASS, READONLYFLAG|HIDDENATTRFLAG}, /*CLASS*/
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{NC_ATT_DIMENSION_LIST, READONLYFLAG|HIDDENATTRFLAG}, /*DIMENSION_LIST*/
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{NC_ATT_NAME, READONLYFLAG|HIDDENATTRFLAG}, /*NAME*/
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{NC_ATT_REFERENCE_LIST, READONLYFLAG|HIDDENATTRFLAG}, /*REFERENCE_LIST*/
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{NC_XARRAY_DIMS, READONLYFLAG|HIDDENATTRFLAG}, /*_ARRAY_DIMENSIONS*/
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{NC_ATT_CODECS, VARFLAG|READONLYFLAG|NAMEONLYFLAG|HIDDENATTRFLAG}, /*_Codecs*/
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{NC_ATT_FORMAT, READONLYFLAG}, /*_Format*/
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{ISNETCDF4ATT, READONLYFLAG|NAMEONLYFLAG}, /*_IsNetcdf4*/
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{NCPROPS, READONLYFLAG|NAMEONLYFLAG|MATERIALIZEDFLAG}, /*_NCProperties*/
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{NC_NCZARR_ATTR, READONLYFLAG|HIDDENATTRFLAG}, /*_NCZARR_ATTR*/
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{NC_ATT_COORDINATES, READONLYFLAG|HIDDENATTRFLAG|MATERIALIZEDFLAG}, /*_Netcdf4Coordinates*/
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{NC_ATT_DIMID_NAME, READONLYFLAG|HIDDENATTRFLAG|MATERIALIZEDFLAG}, /*_Netcdf4Dimid*/
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{SUPERBLOCKATT, READONLYFLAG|NAMEONLYFLAG}, /*_SuperblockVersion*/
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{NC_ATT_NC3_STRICT_NAME, READONLYFLAG|MATERIALIZEDFLAG}, /*_nc3_strict*/
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};
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#define NRESERVED (sizeof(NC_reserved) / sizeof(NC_reservedatt)) /*|NC_reservedatt|*/
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/* These hold the file caching settings for the library. */
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size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE; /**< Default chunk cache size. */
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size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /**< Default chunk cache number of elements. */
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float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION; /**< Default chunk cache preemption. */
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static int NC4_move_in_NCList(NC* nc, int new_id);
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#ifdef LOGGING
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/* This is the severity level of messages which will be logged. Use
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severity 0 for errors, 1 for important log messages, 2 for less
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important, etc. */
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int nc_log_level = NC_TURN_OFF_LOGGING;
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#endif /* LOGGING */
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/**
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* @internal Check and normalize and name.
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*
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* @param name Name to normalize.
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* @param norm_name The normalized name.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EMAXNAME Name too long.
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* @return ::NC_EINVAL NULL given for name.
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* @return ::NC_ENOMEM Out of memory.
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* @author Dennis Heimbigner
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*/
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int
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nc4_check_name(const char *name, char *norm_name)
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{
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char *temp;
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int retval;
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assert(norm_name);
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/* Check for NULL. */
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if (!name)
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return NC_EINVAL;
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/* Make sure this is a valid netcdf name. This should be done
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* before the name is normalized, because it gives better error
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* codes for bad utf8 strings. */
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if ((retval = NC_check_name(name)))
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return retval;
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/* Normalize the name. */
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if ((retval = nc_utf8_normalize((const unsigned char *)name,
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(unsigned char **)&temp)))
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return retval;
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/* Check length of normalized name. */
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if (strlen(temp) > NC_MAX_NAME)
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{
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free(temp);
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return NC_EMAXNAME;
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}
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/* Copy the normalized name. */
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strcpy(norm_name, temp);
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free(temp);
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return NC_NOERR;
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}
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/**
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* @internal Add a file to the list of libsrc4 open files. This is
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* used by dispatch layers that wish to use the libsrc4 metadata
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* model, but don't know about struct NC. This is the same as
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* nc4_nc4f_list_add(), except it takes an ncid instead of an NC *,
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* and also passes back the dispatchdata pointer.
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*
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* @param ncid The (already-assigned) ncid of the file (aka ext_ncid).
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* @param path The file name of the new file.
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* @param mode The mode flag.
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* @param dispatchdata Void * that gets pointer to dispatch data,
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* which is the NC_FILE_INFO_T struct allocated for this file and its
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* metadata. Ignored if NULL. (This is passed as a void to allow
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* external user-defined formats to use this function.)
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID No NC struct with this ext_ncid.
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* @return ::NC_ENOMEM Out of memory.
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* @author Ed Hartnett
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*/
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int
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nc4_file_list_add(int ncid, const char *path, int mode, void **dispatchdata)
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{
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NC *nc;
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int ret;
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/* Find NC pointer for this file. */
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if ((ret = NC_check_id(ncid, &nc)))
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return ret;
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/* Add necessary structs to hold netcdf-4 file data. This is where
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* the NC_FILE_INFO_T struct is allocated for the file. */
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if ((ret = nc4_nc4f_list_add(nc, path, mode)))
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return ret;
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/* If the user wants a pointer to the NC_FILE_INFO_T, then provide
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* it. */
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if (dispatchdata)
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*dispatchdata = nc->dispatchdata;
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return NC_NOERR;
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}
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/**
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* @internal Change the ncid of an open file. This is needed for PIO
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* integration.
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*
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* @param ncid The ncid of the file (aka ext_ncid).
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* @param new_ncid The new ncid index to use (i.e. the first two bytes
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* of the ncid).
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID No NC struct with this ext_ncid.
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* @return ::NC_ENOMEM Out of memory.
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* @author Ed Hartnett
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*/
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int
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nc4_file_change_ncid(int ncid, unsigned short new_ncid_index)
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{
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NC *nc;
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int ret;
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LOG((2, "%s: ncid %d new_ncid_index %d", __func__, ncid, new_ncid_index));
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/* Find NC pointer for this file. */
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if ((ret = NC_check_id(ncid, &nc)))
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return ret;
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/* Move it in the list. It will faile if list spot is already
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* occupied. */
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LOG((3, "moving nc->ext_ncid %d nc->ext_ncid >> ID_SHIFT %d",
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nc->ext_ncid, nc->ext_ncid >> ID_SHIFT));
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if (NC4_move_in_NCList(nc, new_ncid_index))
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return NC_EIO;
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LOG((3, "moved to new_ncid_index %d new nc->ext_ncid %d", new_ncid_index,
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nc->ext_ncid));
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return NC_NOERR;
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}
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/**
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* @internal Get info about a file on the list of libsrc4 open
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* files. This is used by dispatch layers that wish to use the libsrc4
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* metadata model, but don't know about struct NC.
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*
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* @param ncid The ncid of the file (aka ext_ncid).
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* @param path A pointer that gets file name (< NC_MAX_NAME). Ignored
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* if NULL.
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* @param mode A pointer that gets the mode flag. Ignored if NULL.
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* @param dispatchdata Void * that gets pointer to dispatch data,
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* which is the NC_FILE_INFO_T struct allocated for this file and its
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* metadata. Ignored if NULL. (This is passed as a void to allow
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* external user-defined formats to use this function.)
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID No NC struct with this ext_ncid.
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* @return ::NC_ENOMEM Out of memory.
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* @author Ed Hartnett
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*/
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int
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nc4_file_list_get(int ncid, char **path, int *mode, void **dispatchdata)
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{
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NC *nc;
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int ret;
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/* Find NC pointer for this file. */
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if ((ret = NC_check_id(ncid, &nc)))
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return ret;
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/* If the user wants path, give it. */
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if (path)
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strncpy(*path, nc->path, NC_MAX_NAME);
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/* If the user wants mode, give it. */
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if (mode)
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*mode = nc->mode;
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/* If the user wants dispatchdata, give it. */
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if (dispatchdata)
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*dispatchdata = nc->dispatchdata;
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return NC_NOERR;
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}
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/**
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* @internal Given an NC pointer, add the necessary stuff for a
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* netcdf-4 file. This allocates the NC_FILE_INFO_T struct for the
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* file, which is used by libhdf5 and libhdf4 (and perhaps other
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* future dispatch layers) to hold the metadata for the file.
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*
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* @param nc Pointer to file's NC struct.
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* @param path The file name of the new file.
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* @param mode The mode flag.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_ENOMEM Out of memory.
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* @author Ed Hartnett, Dennis Heimbigner
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*/
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int
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nc4_nc4f_list_add(NC *nc, const char *path, int mode)
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{
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NC_FILE_INFO_T *h5;
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int retval;
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assert(nc && !NC4_DATA(nc) && path);
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/* We need to malloc and initialize the substructure
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NC_FILE_INFO_T. */
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if (!(h5 = calloc(1, sizeof(NC_FILE_INFO_T))))
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return NC_ENOMEM;
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nc->dispatchdata = h5;
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h5->controller = nc;
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h5->hdr.sort = NCFIL;
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h5->hdr.name = strdup(path);
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h5->hdr.id = nc->ext_ncid;
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/* Hang on to cmode, and note that we're in define mode. */
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h5->cmode = mode | NC_INDEF;
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/* The next_typeid needs to be set beyond the end of our atomic
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* types. */
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h5->next_typeid = NC_FIRSTUSERTYPEID;
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/* Initialize lists for dimensions, types, and groups. */
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h5->alldims = nclistnew();
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h5->alltypes = nclistnew();
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h5->allgroups = nclistnew();
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/* There's always at least one open group - the root
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* group. Allocate space for one group's worth of information. Set
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* its grp id, name, and allocate associated empty lists. */
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if ((retval = nc4_grp_list_add(h5, NULL, NC_GROUP_NAME, &h5->root_grp)))
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return retval;
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return NC_NOERR;
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}
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/**
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* @internal Given an ncid, find the relevant group and return a
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* pointer to it.
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*
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* @param ncid File and group ID.
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* @param grp Pointer that gets pointer to group info struct. Ignored
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* if NULL.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_ENOTNC4 Not a netCDF-4 file.
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* @author Ed Hartnett
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*/
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int
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nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp)
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{
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return nc4_find_nc_grp_h5(ncid, NULL, grp, NULL);
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}
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/**
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* @internal Given an ncid, find the relevant group and return a
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* pointer to it, also set a pointer to the nc4_info struct of the
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* related file.
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*
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* @param ncid File and group ID.
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* @param grp Pointer that gets pointer to group info struct. Ignored
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* if NULL.
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* @param h5 Pointer that gets pointer to file info struct. Ignored if
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* NULL.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID Bad ncid.
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* @author Ed Hartnett
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*/
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int
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nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_FILE_INFO_T **h5)
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{
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return nc4_find_nc_grp_h5(ncid, NULL, grp, h5);
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}
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/**
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* @internal Find info for this file and group, and set pointers.
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*
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* @param ncid File and group ID.
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* @param nc Pointer that gets a pointer to the file's NC
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* struct. Ignored if NULL.
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* @param grp Pointer that gets a pointer to the group
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* struct. Ignored if NULL.
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* @param h5 Pointer that gets HDF5 file struct. Ignored if NULL.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADID Bad ncid.
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* @author Ed Hartnett, Dennis Heimbigner
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*/
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int
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nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grp, NC_FILE_INFO_T **h5)
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{
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NC_GRP_INFO_T *my_grp = NULL;
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NC_FILE_INFO_T *my_h5 = NULL;
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NC *my_nc;
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int retval;
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size_t index;
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/* Look up file metadata. */
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if ((retval = NC_check_id(ncid, &my_nc)))
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return retval;
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my_h5 = my_nc->dispatchdata;
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assert(my_h5 && my_h5->root_grp);
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/* If we can't find it, the grp id part of ncid is bad. */
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index = (ncid & GRP_ID_MASK);
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if (!(my_grp = nclistget(my_h5->allgroups,index)))
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return NC_EBADID;
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/* Return pointers to caller, if desired. */
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if (nc)
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*nc = my_nc;
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if (h5)
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*h5 = my_h5;
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if (grp)
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*grp = my_grp;
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return NC_NOERR;
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}
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/**
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* @internal Given an ncid and varid, get pointers to the group and var
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* metadata.
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param h5 Pointer that gets pointer to the NC_FILE_INFO_T struct
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* for this file. Ignored if NULL.
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* @param grp Pointer that gets pointer to group info. Ignored if
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* NULL.
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* @param var Pointer that gets pointer to var info. Ignored if NULL.
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*
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* @return ::NC_NOERR No error.
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* @author Ed Hartnett
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*/
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int
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nc4_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5, NC_GRP_INFO_T **grp,
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NC_VAR_INFO_T **var)
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{
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NC_FILE_INFO_T *my_h5;
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NC_GRP_INFO_T *my_grp;
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NC_VAR_INFO_T *my_var;
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int retval;
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/* Look up file and group metadata. */
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if ((retval = nc4_find_grp_h5(ncid, &my_grp, &my_h5)))
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return retval;
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assert(my_grp && my_h5);
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/* Find the var. */
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if (!(my_var = (NC_VAR_INFO_T *)ncindexith(my_grp->vars, varid)))
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return NC_ENOTVAR;
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assert(my_var && my_var->hdr.id == varid);
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/* Return pointers that caller wants. */
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if (h5)
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*h5 = my_h5;
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if (grp)
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*grp = my_grp;
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if (var)
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*var = my_var;
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return NC_NOERR;
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}
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|
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/**
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* @internal Find a dim in the file.
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*
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* @param grp Pointer to group info struct.
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* @param dimid Dimension ID to find.
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* @param dim Pointer that gets pointer to dim info if found.
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* @param dim_grp Pointer that gets pointer to group info of group
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* that contains dimension. Ignored if NULL.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EBADDIM Dimension not found.
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* @author Ed Hartnett, Dennis Heimbigner
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*/
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int
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nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim,
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NC_GRP_INFO_T **dim_grp)
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|
{
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assert(grp && grp->nc4_info && dim);
|
|
LOG((4, "%s: dimid %d", __func__, dimid));
|
|
|
|
/* Find the dim info. */
|
|
if (!((*dim) = nclistget(grp->nc4_info->alldims, dimid)))
|
|
return NC_EBADDIM;
|
|
|
|
/* Give the caller the group the dimension is in. */
|
|
if (dim_grp)
|
|
*dim_grp = (*dim)->container;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Find a var (by name) in a grp.
|
|
*
|
|
* @param grp Pointer to group info.
|
|
* @param name Name of var to find.
|
|
* @param var Pointer that gets pointer to var info struct, if found.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_find_var(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var)
|
|
{
|
|
assert(grp && var && name);
|
|
|
|
/* Find the var info. */
|
|
*var = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Locate netCDF type by name.
|
|
*
|
|
* @param start_grp Pointer to starting group info.
|
|
* @param name Name of type to find.
|
|
*
|
|
* @return Pointer to type info, or NULL if not found.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
NC_TYPE_INFO_T *
|
|
nc4_rec_find_named_type(NC_GRP_INFO_T *start_grp, char *name)
|
|
{
|
|
NC_GRP_INFO_T *g;
|
|
NC_TYPE_INFO_T *type, *res;
|
|
int i;
|
|
|
|
assert(start_grp);
|
|
|
|
/* Does this group have the type we are searching for? */
|
|
type = (NC_TYPE_INFO_T*)ncindexlookup(start_grp->type,name);
|
|
if(type != NULL)
|
|
return type;
|
|
|
|
/* Search subgroups. */
|
|
for(i=0;i<ncindexsize(start_grp->children);i++) {
|
|
g = (NC_GRP_INFO_T*)ncindexith(start_grp->children,i);
|
|
if(g == NULL) continue;
|
|
if ((res = nc4_rec_find_named_type(g, name)))
|
|
return res;
|
|
}
|
|
/* Can't find it. Oh, woe is me! */
|
|
return NULL;
|
|
}
|
|
|
|
/**
|
|
* @internal Use a netCDF typeid to find a type in a type_list.
|
|
*
|
|
* @param h5 Pointer to HDF5 file info struct.
|
|
* @param typeid The netCDF type ID.
|
|
* @param type Pointer to pointer to the list of type info structs.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EINVAL Invalid input.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_find_type(const NC_FILE_INFO_T *h5, nc_type typeid, NC_TYPE_INFO_T **type)
|
|
{
|
|
/* Check inputs. */
|
|
assert(h5);
|
|
if (typeid < 0 || !type)
|
|
return NC_EINVAL;
|
|
*type = NULL;
|
|
|
|
/* Atomic types don't have associated NC_TYPE_INFO_T struct, just
|
|
* return NOERR. */
|
|
if (typeid <= NC_STRING)
|
|
return NC_NOERR;
|
|
|
|
/* Find the type. */
|
|
if (!(*type = nclistget(h5->alltypes,typeid)))
|
|
return NC_EBADTYPID;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Given a group, find an att. If name is provided, use that,
|
|
* otherwise use the attnum.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
* @param varid Variable ID.
|
|
* @param name Name to of attribute.
|
|
* @param attnum Number of attribute.
|
|
* @param att Pointer to pointer that gets attribute info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOTVAR Variable not found.
|
|
* @return ::NC_ENOTATT Attribute not found.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_find_grp_att(NC_GRP_INFO_T *grp, int varid, const char *name, int attnum,
|
|
NC_ATT_INFO_T **att)
|
|
{
|
|
NC_VAR_INFO_T *var;
|
|
NC_ATT_INFO_T *my_att;
|
|
NCindex *attlist = NULL;
|
|
|
|
assert(grp && grp->hdr.name && att);
|
|
|
|
LOG((4, "%s: grp->name %s varid %d attnum %d", __func__, grp->hdr.name,
|
|
varid, attnum));
|
|
|
|
/* Get either the global or a variable attribute list. */
|
|
if (varid == NC_GLOBAL)
|
|
{
|
|
attlist = grp->att;
|
|
}
|
|
else
|
|
{
|
|
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
|
|
if (!var) return NC_ENOTVAR;
|
|
|
|
attlist = var->att;
|
|
}
|
|
assert(attlist);
|
|
|
|
/* Now find the attribute by name or number. If a name is provided,
|
|
* ignore the attnum. */
|
|
if (name)
|
|
my_att = (NC_ATT_INFO_T *)ncindexlookup(attlist, name);
|
|
else
|
|
my_att = (NC_ATT_INFO_T *)ncindexith(attlist, attnum);
|
|
|
|
if (!my_att)
|
|
return NC_ENOTATT;
|
|
|
|
*att = my_att;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Given an ncid, varid, and name or attnum, find and return
|
|
* pointer to NC_ATT_INFO_T metadata.
|
|
*
|
|
* @param ncid File and group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name to of attribute.
|
|
* @param attnum Number of attribute.
|
|
* @param att Pointer to pointer that gets attribute info struct.
|
|
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOTVAR Variable not found.
|
|
* @return ::NC_ENOTATT Attribute not found.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_find_nc_att(int ncid, int varid, const char *name, int attnum,
|
|
NC_ATT_INFO_T **att)
|
|
{
|
|
NC_GRP_INFO_T *grp;
|
|
int retval;
|
|
|
|
LOG((4, "nc4_find_nc_att: ncid 0x%x varid %d name %s attnum %d",
|
|
ncid, varid, name, attnum));
|
|
|
|
/* Find info for this file and group, and set pointer to each. */
|
|
if ((retval = nc4_find_grp_h5(ncid, &grp, NULL)))
|
|
return retval;
|
|
assert(grp);
|
|
|
|
return nc4_find_grp_att(grp, varid, name, attnum, att);
|
|
}
|
|
|
|
/**
|
|
* @internal Add NC_OBJ to allXXX lists in a file
|
|
*
|
|
* @param file Pointer to the containing file
|
|
* @param obj Pointer to object to add.
|
|
*
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
static void
|
|
obj_track(NC_FILE_INFO_T* file, NC_OBJ* obj)
|
|
{
|
|
NClist* list = NULL;
|
|
/* record the object in the file */
|
|
switch (obj->sort) {
|
|
case NCDIM: list = file->alldims; break;
|
|
case NCTYP: list = file->alltypes; break;
|
|
case NCGRP: list = file->allgroups; break;
|
|
default:
|
|
assert(NC_FALSE);
|
|
}
|
|
/* Insert at the appropriate point in the list */
|
|
nclistset(list,obj->id,obj);
|
|
}
|
|
|
|
/**
|
|
* @internal Create a new variable and insert into relevant
|
|
* lists. Dimensionality info need not be known.
|
|
*
|
|
* @param grp the containing group
|
|
* @param name the name for the new variable
|
|
* @param var Pointer in which to return a pointer to the new var.
|
|
*
|
|
* @param var Pointer to pointer that gets variable info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_var_list_add2(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var)
|
|
{
|
|
NC_VAR_INFO_T *new_var = NULL;
|
|
|
|
/* Allocate storage for new variable. */
|
|
if (!(new_var = calloc(1, sizeof(NC_VAR_INFO_T))))
|
|
return NC_ENOMEM;
|
|
new_var->hdr.sort = NCVAR;
|
|
new_var->container = grp;
|
|
|
|
/* These are the HDF5-1.8.4 defaults. */
|
|
new_var->chunk_cache_size = nc4_chunk_cache_size;
|
|
new_var->chunk_cache_nelems = nc4_chunk_cache_nelems;
|
|
new_var->chunk_cache_preemption = nc4_chunk_cache_preemption;
|
|
|
|
/* Now fill in the values in the var info structure. */
|
|
new_var->hdr.id = ncindexsize(grp->vars);
|
|
if (!(new_var->hdr.name = strdup(name))) {
|
|
if(new_var)
|
|
free(new_var);
|
|
return NC_ENOMEM;
|
|
}
|
|
|
|
/* Create an indexed list for the attributes. */
|
|
new_var->att = ncindexnew(0);
|
|
|
|
/* Officially track it */
|
|
ncindexadd(grp->vars, (NC_OBJ *)new_var);
|
|
|
|
/* Set the var pointer, if one was given */
|
|
if (var)
|
|
*var = new_var;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Set the number of dims in an NC_VAR_INFO_T struct.
|
|
*
|
|
* @param var Pointer to the var.
|
|
* @param ndims Number of dimensions for this var.
|
|
*
|
|
* @param var Pointer to pointer that gets variable info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_var_set_ndims(NC_VAR_INFO_T *var, int ndims)
|
|
{
|
|
assert(var);
|
|
|
|
/* Remember the number of dimensions. */
|
|
var->ndims = ndims;
|
|
|
|
/* Allocate space for dimension information. */
|
|
if (ndims)
|
|
{
|
|
if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *))))
|
|
return NC_ENOMEM;
|
|
if (!(var->dimids = calloc(ndims, sizeof(int))))
|
|
return NC_ENOMEM;
|
|
|
|
/* Initialize dimids to illegal values (-1). See the comment
|
|
in nc4_rec_match_dimscales(). */
|
|
memset(var->dimids, -1, ndims * sizeof(int));
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Create a new variable and insert int relevant list.
|
|
*
|
|
* @param grp the containing group
|
|
* @param name the name for the new variable
|
|
* @param ndims the rank of the new variable
|
|
* @param var Pointer in which to return a pointer to the new var.
|
|
*
|
|
* @param var Pointer to pointer that gets variable info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims,
|
|
NC_VAR_INFO_T **var)
|
|
{
|
|
int retval;
|
|
|
|
if ((retval = nc4_var_list_add2(grp, name, var)))
|
|
return retval;
|
|
if ((retval = nc4_var_set_ndims(*var, ndims)))
|
|
return retval;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Add a dimension to the dimension list for a group.
|
|
*
|
|
* @param grp container for the dim
|
|
* @param name for the dim
|
|
* @param len for the dim
|
|
* @param assignedid override dimid if >= 0
|
|
* @param dim Pointer to pointer that gets the new dim info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_dim_list_add(NC_GRP_INFO_T *grp, const char *name, size_t len,
|
|
int assignedid, NC_DIM_INFO_T **dim)
|
|
{
|
|
NC_DIM_INFO_T *new_dim = NULL;
|
|
|
|
assert(grp && name);
|
|
|
|
/* Allocate memory for dim metadata. */
|
|
if (!(new_dim = calloc(1, sizeof(NC_DIM_INFO_T))))
|
|
return NC_ENOMEM;
|
|
|
|
new_dim->hdr.sort = NCDIM;
|
|
|
|
/* Assign the dimension ID. */
|
|
if (assignedid >= 0)
|
|
new_dim->hdr.id = assignedid;
|
|
else
|
|
new_dim->hdr.id = grp->nc4_info->next_dimid++;
|
|
|
|
/* Remember the name and create a hash. */
|
|
if (!(new_dim->hdr.name = strdup(name))) {
|
|
if(new_dim)
|
|
free(new_dim);
|
|
|
|
return NC_ENOMEM;
|
|
}
|
|
|
|
/* Is dimension unlimited? */
|
|
new_dim->len = len;
|
|
if (len == NC_UNLIMITED)
|
|
new_dim->unlimited = NC_TRUE;
|
|
|
|
/* Remember the containing group. */
|
|
new_dim->container = grp;
|
|
|
|
/* Add object to dimension list for this group. */
|
|
ncindexadd(grp->dim, (NC_OBJ *)new_dim);
|
|
obj_track(grp->nc4_info, (NC_OBJ *)new_dim);
|
|
|
|
/* Set the dim pointer, if one was given */
|
|
if (dim)
|
|
*dim = new_dim;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Add to an attribute list.
|
|
*
|
|
* @param list NCindex of att info structs.
|
|
* @param name name of the new attribute
|
|
* @param att Pointer to pointer that gets the new att info
|
|
* struct. Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_att_list_add(NCindex *list, const char *name, NC_ATT_INFO_T **att)
|
|
{
|
|
NC_ATT_INFO_T *new_att = NULL;
|
|
|
|
LOG((3, "%s: name %s ", __func__, name));
|
|
|
|
if (!(new_att = calloc(1, sizeof(NC_ATT_INFO_T))))
|
|
return NC_ENOMEM;
|
|
new_att->hdr.sort = NCATT;
|
|
|
|
/* Fill in the information we know. */
|
|
new_att->hdr.id = ncindexsize(list);
|
|
if (!(new_att->hdr.name = strdup(name))) {
|
|
if(new_att)
|
|
free(new_att);
|
|
return NC_ENOMEM;
|
|
}
|
|
|
|
/* Add object to list as specified by its number */
|
|
ncindexadd(list, (NC_OBJ *)new_att);
|
|
|
|
/* Set the attribute pointer, if one was given */
|
|
if (att)
|
|
*att = new_att;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Add a group to a group list.
|
|
*
|
|
* @param h5 Pointer to the file info.
|
|
* @param parent Pointer to the parent group. Will be NULL when adding
|
|
* the root group.
|
|
* @param name Name of the group.
|
|
* @param grp Pointer to pointer that gets new group info
|
|
* struct. Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_grp_list_add(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *parent, char *name,
|
|
NC_GRP_INFO_T **grp)
|
|
{
|
|
NC_GRP_INFO_T *new_grp;
|
|
|
|
/* Check inputs. */
|
|
assert(h5 && name);
|
|
LOG((3, "%s: name %s ", __func__, name));
|
|
|
|
/* Get the memory to store this groups info. */
|
|
if (!(new_grp = calloc(1, sizeof(NC_GRP_INFO_T))))
|
|
return NC_ENOMEM;
|
|
|
|
/* Fill in this group's information. */
|
|
new_grp->hdr.sort = NCGRP;
|
|
new_grp->nc4_info = h5;
|
|
new_grp->parent = parent;
|
|
|
|
/* Assign the group ID. The root group will get id 0. */
|
|
new_grp->hdr.id = h5->next_nc_grpid++;
|
|
assert(parent || !new_grp->hdr.id);
|
|
|
|
/* Handle the group name. */
|
|
if (!(new_grp->hdr.name = strdup(name)))
|
|
{
|
|
free(new_grp);
|
|
return NC_ENOMEM;
|
|
}
|
|
|
|
/* Set up new indexed lists for stuff this group can contain. */
|
|
new_grp->children = ncindexnew(0);
|
|
new_grp->dim = ncindexnew(0);
|
|
new_grp->att = ncindexnew(0);
|
|
new_grp->type = ncindexnew(0);
|
|
new_grp->vars = ncindexnew(0);
|
|
|
|
/* Add object to lists */
|
|
if (parent)
|
|
ncindexadd(parent->children, (NC_OBJ *)new_grp);
|
|
obj_track(h5, (NC_OBJ *)new_grp);
|
|
|
|
/* Set the group pointer, if one was given */
|
|
if (grp)
|
|
*grp = new_grp;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Names for groups, variables, and types must not be the
|
|
* same. This function checks that a proposed name is not already in
|
|
* use. Normalzation of UTF8 strings should happen before this
|
|
* function is called.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
* @param name Name to check.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENAMEINUSE Name is in use.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_check_dup_name(NC_GRP_INFO_T *grp, char *name)
|
|
{
|
|
NC_TYPE_INFO_T *type;
|
|
NC_GRP_INFO_T *g;
|
|
NC_VAR_INFO_T *var;
|
|
|
|
/* Any types of this name? */
|
|
type = (NC_TYPE_INFO_T*)ncindexlookup(grp->type,name);
|
|
if(type != NULL)
|
|
return NC_ENAMEINUSE;
|
|
|
|
/* Any child groups of this name? */
|
|
g = (NC_GRP_INFO_T*)ncindexlookup(grp->children,name);
|
|
if(g != NULL)
|
|
return NC_ENAMEINUSE;
|
|
|
|
/* Any variables of this name? */
|
|
var = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name);
|
|
if(var != NULL)
|
|
return NC_ENAMEINUSE;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Create a type, but do not add to various lists nor
|
|
* increment its ref count
|
|
*
|
|
* @param size Size of type in bytes.
|
|
* @param name Name of type.
|
|
* @param assignedid if >= 0 then override the default type id.
|
|
* @param type Pointer that gets pointer to new type info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett, Ward Fisher
|
|
*/
|
|
int
|
|
nc4_type_new(size_t size, const char *name, int assignedid,
|
|
NC_TYPE_INFO_T **type)
|
|
{
|
|
NC_TYPE_INFO_T *new_type;
|
|
|
|
LOG((4, "%s: size %d name %s assignedid %d", __func__, size, name, assignedid));
|
|
|
|
/* Check inputs. */
|
|
assert(type);
|
|
|
|
/* Allocate memory for the type */
|
|
if (!(new_type = calloc(1, sizeof(NC_TYPE_INFO_T))))
|
|
return NC_ENOMEM;
|
|
new_type->hdr.sort = NCTYP;
|
|
new_type->hdr.id = assignedid;
|
|
|
|
/* Remember info about this type. */
|
|
new_type->size = size;
|
|
if (!(new_type->hdr.name = strdup(name))) {
|
|
free(new_type);
|
|
return NC_ENOMEM;
|
|
}
|
|
|
|
/* Return a pointer to the new type. */
|
|
*type = new_type;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Add to the type list.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
* @param size Size of type in bytes.
|
|
* @param name Name of type.
|
|
* @param type Pointer that gets pointer to new type info
|
|
* struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_type_list_add(NC_GRP_INFO_T *grp, size_t size, const char *name,
|
|
NC_TYPE_INFO_T **type)
|
|
{
|
|
NC_TYPE_INFO_T *new_type;
|
|
int retval;
|
|
|
|
/* Check inputs. */
|
|
assert(grp && name && type);
|
|
LOG((4, "%s: size %d name %s", __func__, size, name));
|
|
|
|
/* Create the new TYPE_INFO struct. */
|
|
if ((retval = nc4_type_new(size, name, grp->nc4_info->next_typeid,
|
|
&new_type)))
|
|
return retval;
|
|
grp->nc4_info->next_typeid++;
|
|
|
|
/* Increment the ref. count on the type */
|
|
new_type->rc++;
|
|
|
|
/* Add object to lists */
|
|
ncindexadd(grp->type, (NC_OBJ *)new_type);
|
|
obj_track(grp->nc4_info,(NC_OBJ*)new_type);
|
|
|
|
/* Return a pointer to the new type. */
|
|
*type = new_type;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Add to the compound field list.
|
|
*
|
|
* @param parent parent type
|
|
* @param name Name of the field.
|
|
* @param offset Offset in bytes.
|
|
* @param xtype The netCDF type of the field.
|
|
* @param ndims The number of dimensions of the field.
|
|
* @param dim_sizesp An array of dim sizes for the field.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_field_list_add(NC_TYPE_INFO_T *parent, const char *name,
|
|
size_t offset, nc_type xtype, int ndims,
|
|
const int *dim_sizesp)
|
|
{
|
|
NC_FIELD_INFO_T *field;
|
|
|
|
/* Name has already been checked and UTF8 normalized. */
|
|
if (!name)
|
|
return NC_EINVAL;
|
|
|
|
/* Allocate storage for this field information. */
|
|
if (!(field = calloc(1, sizeof(NC_FIELD_INFO_T))))
|
|
return NC_ENOMEM;
|
|
field->hdr.sort = NCFLD;
|
|
|
|
/* Store the information about this field. */
|
|
if (!(field->hdr.name = strdup(name)))
|
|
{
|
|
free(field);
|
|
return NC_ENOMEM;
|
|
}
|
|
field->nc_typeid = xtype;
|
|
field->offset = offset;
|
|
field->ndims = ndims;
|
|
if (ndims)
|
|
{
|
|
int i;
|
|
if (!(field->dim_size = malloc(ndims * sizeof(int))))
|
|
{
|
|
free(field->hdr.name);
|
|
free(field);
|
|
return NC_ENOMEM;
|
|
}
|
|
for (i = 0; i < ndims; i++)
|
|
field->dim_size[i] = dim_sizesp[i];
|
|
}
|
|
|
|
/* Add object to lists */
|
|
field->hdr.id = nclistlength(parent->u.c.field);
|
|
nclistpush(parent->u.c.field,field);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Add a member to an enum type.
|
|
*
|
|
* @param parent Containing NC_TYPE_INFO_T object
|
|
* @param size Size in bytes of new member.
|
|
* @param name Name of the member.
|
|
* @param value Value to associate with member.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM Out of memory.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_enum_member_add(NC_TYPE_INFO_T *parent, size_t size,
|
|
const char *name, const void *value)
|
|
{
|
|
NC_ENUM_MEMBER_INFO_T *member;
|
|
|
|
/* Name has already been checked. */
|
|
assert(name && size > 0 && value);
|
|
LOG((4, "%s: size %d name %s", __func__, size, name));
|
|
|
|
/* Allocate storage for this field information. */
|
|
if (!(member = calloc(1, sizeof(NC_ENUM_MEMBER_INFO_T))))
|
|
return NC_ENOMEM;
|
|
if (!(member->value = malloc(size))) {
|
|
free(member);
|
|
return NC_ENOMEM;
|
|
}
|
|
if (!(member->name = strdup(name))) {
|
|
free(member->value);
|
|
free(member);
|
|
return NC_ENOMEM;
|
|
}
|
|
|
|
/* Store the value for this member. */
|
|
memcpy(member->value, value, size);
|
|
|
|
/* Add object to list */
|
|
nclistpush(parent->u.e.enum_member,member);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Free up a field
|
|
*
|
|
* @param field Pointer to field info of field to delete.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
static void
|
|
field_free(NC_FIELD_INFO_T *field)
|
|
{
|
|
/* Free some stuff. */
|
|
if (field->hdr.name)
|
|
free(field->hdr.name);
|
|
if (field->dim_size)
|
|
free(field->dim_size);
|
|
|
|
/* Nc_Free the memory. */
|
|
free(field);
|
|
}
|
|
|
|
/**
|
|
* @internal Free allocated space for type information.
|
|
*
|
|
* @param type Pointer to type info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_type_free(NC_TYPE_INFO_T *type)
|
|
{
|
|
int i;
|
|
|
|
assert(type && type->rc && type->hdr.name);
|
|
|
|
/* Decrement the ref. count on the type */
|
|
type->rc--;
|
|
|
|
/* Release the type, if the ref. count drops to zero */
|
|
if (type->rc == 0)
|
|
{
|
|
LOG((4, "%s: deleting type %s", __func__, type->hdr.name));
|
|
|
|
/* Free the name. */
|
|
free(type->hdr.name);
|
|
|
|
/* Enums and compound types have lists of fields to clean up. */
|
|
switch (type->nc_type_class)
|
|
{
|
|
case NC_COMPOUND:
|
|
{
|
|
NC_FIELD_INFO_T *field;
|
|
|
|
/* Delete all the fields in this type (there will be some if its a
|
|
* compound). */
|
|
for(i=0;i<nclistlength(type->u.c.field);i++) {
|
|
field = nclistget(type->u.c.field,i);
|
|
field_free(field);
|
|
}
|
|
nclistfree(type->u.c.field);
|
|
}
|
|
break;
|
|
|
|
case NC_ENUM:
|
|
{
|
|
NC_ENUM_MEMBER_INFO_T *enum_member;
|
|
|
|
/* Delete all the enum_members, if any. */
|
|
for(i=0;i<nclistlength(type->u.e.enum_member);i++) {
|
|
enum_member = nclistget(type->u.e.enum_member,i);
|
|
free(enum_member->value);
|
|
free(enum_member->name);
|
|
free(enum_member);
|
|
}
|
|
nclistfree(type->u.e.enum_member);
|
|
}
|
|
break;
|
|
|
|
default:
|
|
break;
|
|
}
|
|
|
|
/* Release the memory. */
|
|
free(type);
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Free memory of an attribute object
|
|
*
|
|
* @param att Pointer to attribute info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_att_free(NC_ATT_INFO_T *att)
|
|
{
|
|
int i;
|
|
|
|
assert(att);
|
|
LOG((3, "%s: name %s ", __func__, att->hdr.name));
|
|
|
|
/* Free memory that was malloced to hold data for this
|
|
* attribute. */
|
|
if (att->data)
|
|
free(att->data);
|
|
|
|
/* Free the name. */
|
|
if (att->hdr.name)
|
|
free(att->hdr.name);
|
|
|
|
/* If this is a string array attribute, delete all members of the
|
|
* string array, then delete the array of pointers to strings. (The
|
|
* array was filled with pointers by HDF5 when the att was read,
|
|
* and memory for each string was allocated by HDF5. That's why I
|
|
* use free and not nc_free, because the netCDF library didn't
|
|
* allocate the memory that is being freed.) */
|
|
if (att->stdata)
|
|
{
|
|
for (i = 0; i < att->len; i++)
|
|
if(att->stdata[i])
|
|
free(att->stdata[i]);
|
|
free(att->stdata);
|
|
}
|
|
|
|
/* If this att has vlen data, release it. */
|
|
if (att->vldata)
|
|
{
|
|
for (i = 0; i < att->len; i++)
|
|
nc_free_vlen(&att->vldata[i]);
|
|
free(att->vldata);
|
|
}
|
|
|
|
free(att);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Delete a var, and free the memory. All HDF5 objects for
|
|
* the var must be closed before this is called.
|
|
*
|
|
* @param var Pointer to the var info struct of var to delete.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
static int
|
|
var_free(NC_VAR_INFO_T *var)
|
|
{
|
|
int i;
|
|
int retval;
|
|
|
|
assert(var);
|
|
LOG((4, "%s: deleting var %s", __func__, var->hdr.name));
|
|
|
|
/* First delete all the attributes attached to this var. */
|
|
for (i = 0; i < ncindexsize(var->att); i++)
|
|
if ((retval = nc4_att_free((NC_ATT_INFO_T *)ncindexith(var->att, i))))
|
|
return retval;
|
|
ncindexfree(var->att);
|
|
|
|
/* Free some things that may be allocated. */
|
|
if (var->chunksizes)
|
|
free(var->chunksizes);
|
|
|
|
if (var->alt_name)
|
|
free(var->alt_name);
|
|
|
|
if (var->dimids)
|
|
free(var->dimids);
|
|
|
|
if (var->dim)
|
|
free(var->dim);
|
|
|
|
/* Delete any fill value allocation. */
|
|
if (var->fill_value)
|
|
{free(var->fill_value); var->fill_value = NULL;}
|
|
|
|
/* Release type information */
|
|
if (var->type_info)
|
|
if ((retval = nc4_type_free(var->type_info)))
|
|
return retval;
|
|
|
|
/* Do this last because debugging may need it */
|
|
if (var->hdr.name)
|
|
free(var->hdr.name);
|
|
|
|
/* Delete the var. */
|
|
free(var);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Delete a var, and free the memory.
|
|
*
|
|
* @param grp Pointer to the strct for the containing group.
|
|
* @param var Pointer to the var info struct of var to delete.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_var_list_del(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
|
|
{
|
|
int i;
|
|
|
|
assert(var && grp);
|
|
|
|
/* Remove from lists */
|
|
i = ncindexfind(grp->vars, (NC_OBJ *)var);
|
|
if (i >= 0)
|
|
ncindexidel(grp->vars, i);
|
|
|
|
return var_free(var);
|
|
}
|
|
|
|
/**
|
|
* @internal Free a dim
|
|
*
|
|
* @param dim Pointer to dim info struct of type to delete.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett, Ward Fisher
|
|
*/
|
|
static int
|
|
dim_free(NC_DIM_INFO_T *dim)
|
|
{
|
|
assert(dim);
|
|
LOG((4, "%s: deleting dim %s", __func__, dim->hdr.name));
|
|
|
|
/* Free memory allocated for names. */
|
|
if (dim->hdr.name)
|
|
free(dim->hdr.name);
|
|
|
|
free(dim);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Free a dim and unlist it
|
|
*
|
|
* @param grp Pointer to dim's containing group
|
|
* @param dim Pointer to dim info struct of type to delete.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_dim_list_del(NC_GRP_INFO_T *grp, NC_DIM_INFO_T *dim)
|
|
{
|
|
if (grp && dim)
|
|
{
|
|
int pos = ncindexfind(grp->dim, (NC_OBJ *)dim);
|
|
if(pos >= 0)
|
|
ncindexidel(grp->dim, pos);
|
|
}
|
|
|
|
return dim_free(dim);
|
|
}
|
|
|
|
/**
|
|
* @internal Recursively delete the data for a group (and everything
|
|
* it contains) in our internal metadata store.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_rec_grp_del(NC_GRP_INFO_T *grp)
|
|
{
|
|
int i;
|
|
int retval;
|
|
|
|
assert(grp);
|
|
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
|
|
|
|
/* Recursively call this function for each child, if any, stopping
|
|
* if there is an error. */
|
|
for (i = 0; i < ncindexsize(grp->children); i++)
|
|
if ((retval = nc4_rec_grp_del((NC_GRP_INFO_T *)ncindexith(grp->children,
|
|
i))))
|
|
return retval;
|
|
ncindexfree(grp->children);
|
|
|
|
/* Free attributes */
|
|
for (i = 0; i < ncindexsize(grp->att); i++)
|
|
if ((retval = nc4_att_free((NC_ATT_INFO_T *)ncindexith(grp->att, i))))
|
|
return retval;
|
|
ncindexfree(grp->att);
|
|
|
|
/* Delete all vars. */
|
|
for (i = 0; i < ncindexsize(grp->vars); i++) {
|
|
NC_VAR_INFO_T* v = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
|
|
if ((retval = var_free(v)))
|
|
return retval;
|
|
}
|
|
ncindexfree(grp->vars);
|
|
|
|
/* Delete all dims, and free the list of dims. */
|
|
for (i = 0; i < ncindexsize(grp->dim); i++)
|
|
if ((retval = dim_free((NC_DIM_INFO_T *)ncindexith(grp->dim, i))))
|
|
return retval;
|
|
ncindexfree(grp->dim);
|
|
|
|
/* Delete all types. */
|
|
for (i = 0; i < ncindexsize(grp->type); i++)
|
|
if ((retval = nc4_type_free((NC_TYPE_INFO_T *)ncindexith(grp->type, i))))
|
|
return retval;
|
|
ncindexfree(grp->type);
|
|
|
|
/* Free the name. */
|
|
free(grp->hdr.name);
|
|
|
|
/* Free up this group */
|
|
free(grp);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Remove a NC_ATT_INFO_T from an index.
|
|
* This will nc_free the memory too.
|
|
*
|
|
* @param list Pointer to pointer of list.
|
|
* @param att Pointer to attribute info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_att_list_del(NCindex *list, NC_ATT_INFO_T *att)
|
|
{
|
|
assert(att && list);
|
|
ncindexidel(list, ((NC_OBJ *)att)->id);
|
|
return nc4_att_free(att);
|
|
}
|
|
|
|
/**
|
|
* @internal Free all resources and memory associated with a
|
|
* NC_FILE_INFO_T. This is the same as nc4_nc4f_list_del(), except it
|
|
* takes ncid. This function allows external dispatch layers, like
|
|
* PIO, to manipulate the file list without needing to know about
|
|
* internal netcdf structures.
|
|
*
|
|
* @param ncid The ncid of the file to release.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_file_list_del(int ncid)
|
|
{
|
|
NC_FILE_INFO_T *h5;
|
|
int retval;
|
|
|
|
/* Find our metadata for this file. */
|
|
if ((retval = nc4_find_grp_h5(ncid, NULL, &h5)))
|
|
return retval;
|
|
assert(h5);
|
|
|
|
/* Delete the file resources. */
|
|
if ((retval = nc4_nc4f_list_del(h5)))
|
|
return retval;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Free all resources and memory associated with a
|
|
* NC_FILE_INFO_T.
|
|
*
|
|
* @param h5 Pointer to NC_FILE_INFO_T to be freed.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_nc4f_list_del(NC_FILE_INFO_T *h5)
|
|
{
|
|
int retval;
|
|
|
|
assert(h5);
|
|
|
|
/* Delete all the list contents for vars, dims, and atts, in each
|
|
* group. */
|
|
if ((retval = nc4_rec_grp_del(h5->root_grp)))
|
|
return retval;
|
|
|
|
/* Cleanup these (extra) lists of all dims, groups, and types. */
|
|
nclistfree(h5->alldims);
|
|
nclistfree(h5->allgroups);
|
|
nclistfree(h5->alltypes);
|
|
|
|
/* Free the NC_FILE_INFO_T struct. */
|
|
nullfree(h5->hdr.name);
|
|
free(h5);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Normalize a UTF8 name. Put the result in norm_name, which
|
|
* can be NC_MAX_NAME + 1 in size. This function makes sure the free()
|
|
* gets called on the return from utf8proc_NFC, and also ensures that
|
|
* the name is not too long.
|
|
*
|
|
* @param name Name to normalize.
|
|
* @param norm_name The normalized name.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EMAXNAME Name too long.
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_normalize_name(const char *name, char *norm_name)
|
|
{
|
|
char *temp_name;
|
|
int stat = nc_utf8_normalize((const unsigned char *)name,(unsigned char **)&temp_name);
|
|
if(stat != NC_NOERR)
|
|
return stat;
|
|
if (strlen(temp_name) > NC_MAX_NAME)
|
|
{
|
|
free(temp_name);
|
|
return NC_EMAXNAME;
|
|
}
|
|
strcpy(norm_name, temp_name);
|
|
free(temp_name);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
#ifdef ENABLE_SET_LOG_LEVEL
|
|
|
|
/**
|
|
* @internal Use this to set the global log level. Set it to
|
|
* NC_TURN_OFF_LOGGING (-1) to turn off all logging. Set it to 0 to
|
|
* show only errors, and to higher numbers to show more and more
|
|
* logging details. If logging is not enabled with --enable-logging at
|
|
* configure when building netCDF, this function will do nothing.
|
|
* Note that it is possible to set the log level using the environment
|
|
* variable named _NETCDF_LOG_LEVEL_ (e.g. _export NETCDF_LOG_LEVEL=4_).
|
|
*
|
|
* @param new_level The new logging level.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_set_log_level(int new_level)
|
|
{
|
|
#ifdef LOGGING
|
|
/* Remember the new level. */
|
|
nc_log_level = new_level;
|
|
LOG((4, "log_level changed to %d", nc_log_level));
|
|
#endif /*LOGGING */
|
|
return 0;
|
|
}
|
|
#endif /* ENABLE_SET_LOG_LEVEL */
|
|
|
|
#ifdef LOGGING
|
|
#define MAX_NESTS 10
|
|
/**
|
|
* @internal Recursively print the metadata of a group.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
* @param tab_count Number of tabs.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
static int
|
|
rec_print_metadata(NC_GRP_INFO_T *grp, int tab_count)
|
|
{
|
|
NC_ATT_INFO_T *att;
|
|
NC_VAR_INFO_T *var;
|
|
NC_DIM_INFO_T *dim;
|
|
NC_TYPE_INFO_T *type;
|
|
NC_FIELD_INFO_T *field;
|
|
char tabs[MAX_NESTS+1] = "";
|
|
char temp_string[10];
|
|
int t, retval, d, i;
|
|
|
|
/* Come up with a number of tabs relative to the group. */
|
|
for (t = 0; t < tab_count && t < MAX_NESTS; t++)
|
|
tabs[t] = '\t';
|
|
tabs[t] = '\0';
|
|
|
|
LOG((2, "%s GROUP - %s nc_grpid: %d nvars: %d natts: %d",
|
|
tabs, grp->hdr.name, grp->hdr.id, ncindexsize(grp->vars), ncindexsize(grp->att)));
|
|
|
|
for (i = 0; i < ncindexsize(grp->att); i++)
|
|
{
|
|
att = (NC_ATT_INFO_T *)ncindexith(grp->att, i);
|
|
assert(att);
|
|
LOG((2, "%s GROUP ATTRIBUTE - attnum: %d name: %s type: %d len: %d",
|
|
tabs, att->hdr.id, att->hdr.name, att->nc_typeid, att->len));
|
|
}
|
|
|
|
for (i = 0; i < ncindexsize(grp->dim); i++)
|
|
{
|
|
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, i);
|
|
assert(dim);
|
|
LOG((2, "%s DIMENSION - dimid: %d name: %s len: %d unlimited: %d",
|
|
tabs, dim->hdr.id, dim->hdr.name, dim->len, dim->unlimited));
|
|
}
|
|
|
|
for (i = 0; i < ncindexsize(grp->vars); i++)
|
|
{
|
|
int j;
|
|
char storage_str[NC_MAX_NAME] = "";
|
|
char *dims_string = NULL;
|
|
|
|
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
|
|
assert(var);
|
|
if (var->ndims > 0)
|
|
{
|
|
if (!(dims_string = malloc(sizeof(char) * var->ndims * 4)))
|
|
return NC_ENOMEM;
|
|
strcpy(dims_string, "");
|
|
for (d = 0; d < var->ndims; d++)
|
|
{
|
|
sprintf(temp_string, " %d", var->dimids[d]);
|
|
strcat(dims_string, temp_string);
|
|
}
|
|
}
|
|
if (!var->meta_read)
|
|
strcat(storage_str, "unknown");
|
|
else if (var->storage == NC_CONTIGUOUS)
|
|
strcat(storage_str, "contiguous");
|
|
else if (var->storage == NC_COMPACT)
|
|
strcat(storage_str, "compact");
|
|
else if (var->storage == NC_CHUNKED)
|
|
strcat(storage_str, "chunked");
|
|
else if (var->storage == NC_VIRTUAL)
|
|
strcat(storage_str, "virtual");
|
|
else
|
|
strcat(storage_str, "unknown");
|
|
LOG((2, "%s VARIABLE - varid: %d name: %s ndims: %d "
|
|
"dimids:%s storage: %s", tabs, var->hdr.id, var->hdr.name,
|
|
var->ndims,
|
|
(dims_string ? dims_string : " -"), storage_str));
|
|
for (j = 0; j < ncindexsize(var->att); j++)
|
|
{
|
|
att = (NC_ATT_INFO_T *)ncindexith(var->att, j);
|
|
assert(att);
|
|
LOG((2, "%s VAR ATTRIBUTE - attnum: %d name: %s type: %d len: %d",
|
|
tabs, att->hdr.id, att->hdr.name, att->nc_typeid, att->len));
|
|
}
|
|
if (dims_string)
|
|
free(dims_string);
|
|
}
|
|
|
|
for (i = 0; i < ncindexsize(grp->type); i++)
|
|
{
|
|
type = (NC_TYPE_INFO_T*)ncindexith(grp->type, i);
|
|
assert(type);
|
|
LOG((2, "%s TYPE - nc_typeid: %d size: %d committed: %d name: %s",
|
|
tabs, type->hdr.id, type->size, (int)type->committed, type->hdr.name));
|
|
/* Is this a compound type? */
|
|
if (type->nc_type_class == NC_COMPOUND)
|
|
{
|
|
int j;
|
|
LOG((3, "compound type"));
|
|
for (j = 0; j < nclistlength(type->u.c.field); j++)
|
|
{
|
|
field = (NC_FIELD_INFO_T *)nclistget(type->u.c.field, j);
|
|
LOG((4, "field %s offset %d nctype %d ndims %d", field->hdr.name,
|
|
field->offset, field->nc_typeid, field->ndims));
|
|
}
|
|
}
|
|
else if (type->nc_type_class == NC_VLEN)
|
|
{
|
|
LOG((3, "VLEN type"));
|
|
LOG((4, "base_nc_type: %d", type->u.v.base_nc_typeid));
|
|
}
|
|
else if (type->nc_type_class == NC_OPAQUE)
|
|
LOG((3, "Opaque type"));
|
|
else if (type->nc_type_class == NC_ENUM)
|
|
{
|
|
LOG((3, "Enum type"));
|
|
LOG((4, "base_nc_type: %d", type->u.e.base_nc_typeid));
|
|
}
|
|
else
|
|
{
|
|
LOG((0, "Unknown class: %d", type->nc_type_class));
|
|
return NC_EBADTYPE;
|
|
}
|
|
}
|
|
|
|
/* Call self for each child of this group. */
|
|
for (i = 0; i < ncindexsize(grp->children); i++)
|
|
if ((retval = rec_print_metadata((NC_GRP_INFO_T *)ncindexith(grp->children, i),
|
|
tab_count + 1)))
|
|
return retval;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Print out the internal metadata for a file. This is
|
|
* useful to check that netCDF is working! Nonetheless, this function
|
|
* will print nothing if logging is not set to at least two.
|
|
*
|
|
* @param Pointer to the file info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
log_metadata_nc(NC_FILE_INFO_T *h5)
|
|
{
|
|
LOG((2, "*** NetCDF-4 Internal Metadata: int_ncid 0x%x ext_ncid 0x%x",
|
|
h5->root_grp->nc4_info->controller->int_ncid,
|
|
h5->root_grp->nc4_info->controller->ext_ncid));
|
|
if (!h5)
|
|
{
|
|
LOG((2, "This is a netCDF-3 file."));
|
|
return NC_NOERR;
|
|
}
|
|
LOG((2, "FILE - path: %s cmode: 0x%x parallel: %d redef: %d "
|
|
"fill_mode: %d no_write: %d next_nc_grpid: %d", h5->root_grp->nc4_info->controller->path,
|
|
h5->cmode, (int)h5->parallel, (int)h5->redef, h5->fill_mode, (int)h5->no_write,
|
|
h5->next_nc_grpid));
|
|
if(nc_log_level >= 2)
|
|
return rec_print_metadata(h5->root_grp, 0);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
#endif /*LOGGING */
|
|
|
|
/**
|
|
* @internal Show the in-memory metadata for a netcdf file. This
|
|
* function does nothing unless netCDF was built with
|
|
* the configure option --enable-logging.
|
|
*
|
|
* @param ncid File and group ID.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
NC4_show_metadata(int ncid)
|
|
{
|
|
int retval = NC_NOERR;
|
|
#ifdef LOGGING
|
|
NC_FILE_INFO_T *h5;
|
|
int old_log_level = nc_log_level;
|
|
|
|
/* Find file metadata. */
|
|
if ((retval = nc4_find_grp_h5(ncid, NULL, &h5)))
|
|
return retval;
|
|
|
|
/* Log level must be 2 to see metadata. */
|
|
nc_log_level = 2;
|
|
retval = log_metadata_nc(h5);
|
|
nc_log_level = old_log_level;
|
|
#endif /*LOGGING*/
|
|
return retval;
|
|
}
|
|
|
|
/**
|
|
* @internal Define a binary searcher for reserved attributes
|
|
* @param name for which to search
|
|
* @return pointer to the matching NC_reservedatt structure.
|
|
* @return NULL if not found.
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
const NC_reservedatt*
|
|
NC_findreserved(const char* name)
|
|
{
|
|
int n = NRESERVED;
|
|
int L = 0;
|
|
int R = (n - 1);
|
|
|
|
for(;;) {
|
|
if(L > R) break;
|
|
int m = (L + R) / 2;
|
|
const NC_reservedatt* p = &NC_reserved[m];
|
|
int cmp = strcmp(p->name,name);
|
|
if(cmp == 0) return p;
|
|
if(cmp < 0)
|
|
L = (m + 1);
|
|
else /*cmp > 0*/
|
|
R = (m - 1);
|
|
}
|
|
return NULL;
|
|
}
|
|
|
|
static int
|
|
NC4_move_in_NCList(NC* nc, int new_id)
|
|
{
|
|
int stat = move_in_NCList(nc,new_id);
|
|
if(stat == NC_NOERR) {
|
|
/* Synchronize header */
|
|
if(nc->dispatchdata)
|
|
((NC_OBJ*)nc->dispatchdata)->id = nc->ext_ncid;
|
|
}
|
|
return stat;
|
|
}
|