mirror of
https://github.com/Unidata/netcdf-c.git
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d953899559
re: https://github.com/zarr-developers/zarr-specs/issues/41 After discussions with the Zarr community, it was decided to convert to a new representation of the NCZarr meta-data extensions: version 2. These extensions store information necessary to mapping the Zarr data model to the netcdf-4 data model. The basic change is to remove the NCZarr specific objects: .nczarr, .nczgroup, .nczarray, and .nczattr. The contents of these objects is moved into the corresponding existing Zarr objects as special keys. The mapping is as follows: * ''.nczarr'' => ''/.zgroup/_NCZARR_SUPERBLOCK_'' * ''.nczgroup => ''.zgroup/_NCZARR_GROUP_'' * ''.nczarray => ''.zarray/_NCZARR_ARRAY_'' * ''.nczattr => ''.zattr/_NCZARR_ATTR_'' Backward compatibility is maintained by looking for the object ''/.nczarr'' and if found, then assuming that the dataset is in the older version 1 format. This compatibility only supports reading of such version 1 datasets. Documentation and test cases are also added. Misc. Other Changes: 1. The json parsing code was added to the general library instead of nczarr only (ncjson.c, ncjson.h). 2. Improved support for different platform paths by allowing conversion to a single common path representation. 3. Add some new error codes. 4. Modify nccopy usage to mention the new chunking specification.
1861 lines
50 KiB
C
1861 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_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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/* 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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if (!(my_grp = nclistget(my_h5->allgroups, (ncid & GRP_ID_MASK))))
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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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* @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);
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LOG((4, "%s: dimid %d", __func__, dimid));
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/* Find the dim info. */
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if (!((*dim) = nclistget(grp->nc4_info->alldims, dimid)))
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return NC_EBADDIM;
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/* Give the caller the group the dimension is in. */
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if (dim_grp)
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*dim_grp = (*dim)->container;
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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 var (by name) in a grp.
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*
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* @param grp Pointer to group info.
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* @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);
|
|
|
|
/* 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
|
|
strcat(storage_str, "chunked");
|
|
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;
|
|
}
|