mirror of
https://github.com/Unidata/netcdf-c.git
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231ae96c4b
* re: https://github.com/Unidata/netcdf-c/pull/2278 * re: https://github.com/Unidata/netcdf-c/issues/2485 * re: https://github.com/Unidata/netcdf-c/issues/2474 This PR subsumes PR https://github.com/Unidata/netcdf-c/pull/2278. Actually is a bit an omnibus covering several issues. ## PR https://github.com/Unidata/netcdf-c/pull/2278 Add support for the Zarr string type. Zarr strings are restricted currently to be of fixed size. The primary issue to be addressed is to provide a way for user to specify the size of the fixed length strings. This is handled by providing the following new attributes special: 1. **_nczarr_default_maxstrlen** — This is an attribute of the root group. It specifies the default maximum string length for string types. If not specified, then it has the value of 64 characters. 2. **_nczarr_maxstrlen** — This is a per-variable attribute. It specifies the maximum string length for the string type associated with the variable. If not specified, then it is assigned the value of **_nczarr_default_maxstrlen**. This PR also requires some hacking to handle the existing netcdf-c NC_CHAR type, which does not exist in zarr. The goal was to choose numpy types for both the netcdf-c NC_STRING type and the netcdf-c NC_CHAR type such that if a pure zarr implementation read them, it would still work and an NC_CHAR type would be handled by zarr as a string of length 1. For writing variables and NCZarr attributes, the type mapping is as follows: * "|S1" for NC_CHAR. * ">S1" for NC_STRING && MAXSTRLEN==1 * ">Sn" for NC_STRING && MAXSTRLEN==n Note that it is a bit of a hack to use endianness, but it should be ok since for string/char, the endianness has no meaning. For reading attributes with pure zarr (i.e. with no nczarr atribute types defined), they will always be interpreted as of type NC_CHAR. ## Issue: https://github.com/Unidata/netcdf-c/issues/2474 This PR partly fixes this issue because it provided more comprehensive support for Zarr attributes that are JSON valued expressions. This PR still does not address the problem in that issue where the _ARRAY_DIMENSION attribute is incorrectly set. Than can only be fixed by the creator of the datasets. ## Issue: https://github.com/Unidata/netcdf-c/issues/2485 This PR also fixes the scalar failure shown in this issue. It generally cleans up scalar handling. It also adds a note to the documentation describing that NCZarr supports scalars while Zarr does not and also how scalar interoperability is achieved. ## Misc. Other Changes 1. Convert the nczarr special attributes and keys to be all lower case. So "_NCZARR_ATTR" now used "_nczarr_attr. Support back compatibility for the upper case names. 2. Cleanup my too-clever-by-half handling of scalars in libnczarr.
2238 lines
61 KiB
C
2238 lines
61 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 "netcdf_meta.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 <stdarg.h>
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#include "ncrc.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 (strcmp) 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|NAMEONLYFLAG|HIDDENATTRFLAG}, /*_ARRAY_DIMENSIONS*/
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{NC_ATT_CODECS, VARFLAG|READONLYFLAG|NAMEONLYFLAG}, /*_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|HIDDENATTRFLAG}, /*_NCProperties*/
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{NC_NCZARR_ATTR_UC, READONLYFLAG|HIDDENATTRFLAG}, /*_NCZARR_ATTR */
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{NC_ATT_COORDINATES, READONLYFLAG|HIDDENATTRFLAG}, /*_Netcdf4Coordinates*/
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{NC_ATT_DIMID_NAME, READONLYFLAG|HIDDENATTRFLAG}, /*_Netcdf4Dimid*/
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{SUPERBLOCKATT, READONLYFLAG|NAMEONLYFLAG}, /*_SuperblockVersion*/
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{NC_ATT_NC3_STRICT_NAME, READONLYFLAG}, /*_nc3_strict*/
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{NC_ATT_NC3_STRICT_NAME, READONLYFLAG}, /*_nc3_strict*/
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{NC_NCZARR_ATTR, READONLYFLAG|HIDDENATTRFLAG}, /*_nczarr_attr */
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};
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#define NRESERVED (sizeof(NC_reserved) / sizeof(NC_reservedatt)) /*|NC_reservedatt|*/
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static int NC4_move_in_NCList(NC* nc, int new_id);
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#if NC_HAS_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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#if NC_HAS_PARALLEL4
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/* File pointer for the parallel I/O log file. */
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FILE *LOG_FILE = NULL;
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#endif /* NC_HAS_PARALLEL4 */
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/* This function prints out a message, if the severity of
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* the message is lower than the global nc_log_level. To use it, do
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* something like this:
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*
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* nc_log(0, "this computer will explode in %d seconds", i);
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*
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* After the first arg (the severity), use the rest like a normal
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* printf statement. Output will appear on stderr for sequential
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* builds, and in a file nc4_log_R.log for each process for a parallel
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* build, where R is the rank of the process.
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*
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* Ed Hartnett
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*/
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void
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nc_log(int severity, const char *fmt, ...)
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{
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va_list argp;
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int t;
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FILE *f = stderr;
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/* If the severity is greater than the log level, we don't print
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* this message. */
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if (severity > nc_log_level)
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return;
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#if NC_HAS_PARALLEL4
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/* For parallel I/O build, if MPI has been initialized, instead of
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* printing logging output to stderr, it goes to a file for each
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* process. */
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{
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int mpi_initialized;
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int mpierr;
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/* Check to see if MPI has been initialized. */
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if ((mpierr = MPI_Initialized(&mpi_initialized)))
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return;
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/* If MPI has been initialized use a log file. */
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assert(LOG_FILE);
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if (mpi_initialized)
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f = LOG_FILE;
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}
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#endif /* NC_HAS_PARALLEL4 */
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/* If the severity is zero, this is an error. Otherwise insert that
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many tabs before the message. */
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if (!severity)
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fprintf(f, "ERROR: ");
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for (t = 0; t < severity; t++)
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fprintf(f, "\t");
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/* Print out the variable list of args with vprintf. */
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va_start(argp, fmt);
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vfprintf(f, fmt, argp);
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va_end(argp);
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/* Put on a final linefeed. */
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fprintf(f, "\n");
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fflush(f);
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}
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#endif /* NC_HAS_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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/**
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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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|
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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;
|
|
if (grp)
|
|
*grp = my_grp;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Given an ncid and varid, get pointers to the group and var
|
|
* metadata.
|
|
*
|
|
* @param ncid File ID.
|
|
* @param varid Variable ID.
|
|
* @param h5 Pointer that gets pointer to the NC_FILE_INFO_T struct
|
|
* for this file. Ignored if NULL.
|
|
* @param grp Pointer that gets pointer to group info. Ignored if
|
|
* NULL.
|
|
* @param var Pointer that gets pointer to var info. Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5, NC_GRP_INFO_T **grp,
|
|
NC_VAR_INFO_T **var)
|
|
{
|
|
NC_FILE_INFO_T *my_h5;
|
|
NC_GRP_INFO_T *my_grp;
|
|
NC_VAR_INFO_T *my_var;
|
|
int retval;
|
|
|
|
/* Look up file and group metadata. */
|
|
if ((retval = nc4_find_grp_h5(ncid, &my_grp, &my_h5)))
|
|
return retval;
|
|
assert(my_grp && my_h5);
|
|
|
|
/* Find the var. */
|
|
if (!(my_var = (NC_VAR_INFO_T *)ncindexith(my_grp->vars, varid)))
|
|
return NC_ENOTVAR;
|
|
assert(my_var && my_var->hdr.id == varid);
|
|
|
|
/* Return pointers that caller wants. */
|
|
if (h5)
|
|
*h5 = my_h5;
|
|
if (grp)
|
|
*grp = my_grp;
|
|
if (var)
|
|
*var = my_var;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Find a dim in the file.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
* @param dimid Dimension ID to find.
|
|
* @param dim Pointer that gets pointer to dim info if found.
|
|
* @param dim_grp Pointer that gets pointer to group info of group
|
|
* that contains dimension. Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADDIM Dimension not found.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim,
|
|
NC_GRP_INFO_T **dim_grp)
|
|
{
|
|
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;
|
|
NCglobalstate* gs = NC_getglobalstate();
|
|
|
|
/* 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->chunkcache.size = gs->chunkcache.size;
|
|
new_var->chunkcache.nelems = gs->chunkcache.nelems;
|
|
new_var->chunkcache.preemption = gs->chunkcache.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 stat = NC_NOERR;
|
|
|
|
assert(att);
|
|
LOG((3, "%s: name %s ", __func__, att->hdr.name));
|
|
|
|
/* Free the name. */
|
|
if (att->hdr.name)
|
|
free(att->hdr.name);
|
|
|
|
#ifdef SEPDATA
|
|
/* Free memory that was malloced to hold data for this
|
|
* attribute. */
|
|
if (att->data) {
|
|
free(att->data);
|
|
}
|
|
|
|
/* 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)
|
|
{
|
|
int i;
|
|
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)
|
|
{
|
|
int i;
|
|
for (i = 0; i < att->len; i++)
|
|
nc_free_vlen(&att->vldata[i]);
|
|
free(att->vldata);
|
|
}
|
|
#else
|
|
if (att->data) {
|
|
NC_OBJ* parent;
|
|
NC_FILE_INFO_T* h5 = NULL;
|
|
|
|
/* Locate relevant objects */
|
|
parent = att->container;
|
|
if(parent->sort == NCVAR) parent = (NC_OBJ*)(((NC_VAR_INFO_T*)parent)->container);
|
|
assert(parent->sort == NCGRP);
|
|
h5 = ((NC_GRP_INFO_T*)parent)->nc4_info;
|
|
/* Reclaim the attribute data */
|
|
if((stat = nc_reclaim_data(h5->controller->ext_ncid,att->nc_typeid,att->data,att->len))) goto done;
|
|
free(att->data); /* reclaim top level */
|
|
att->data = NULL;
|
|
}
|
|
#endif
|
|
|
|
done:
|
|
free(att);
|
|
return stat;
|
|
}
|
|
|
|
/**
|
|
* @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) {
|
|
int ncid = var->container->nc4_info->controller->ext_ncid;
|
|
int tid = var->type_info->hdr.id;
|
|
if((retval = nc_reclaim_data_all(ncid, tid, var->fill_value, 1))) return retval;
|
|
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 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_att_data(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_att_data((NC_GRP_INFO_T *)ncindexith(grp->children, i))))
|
|
return retval;
|
|
|
|
/* Free attribute data in this group */
|
|
for (i = 0; i < ncindexsize(grp->att); i++) {
|
|
NC_ATT_INFO_T * att = (NC_ATT_INFO_T*)ncindexith(grp->att, i);
|
|
if((retval = nc_reclaim_data_all(grp->nc4_info->controller->ext_ncid,att->nc_typeid,att->data,att->len)))
|
|
return retval;
|
|
att->data = NULL;
|
|
att->len = 0;
|
|
att->dirty = 0;
|
|
}
|
|
|
|
/* Delete att data from all contained vars in this group */
|
|
for (i = 0; i < ncindexsize(grp->vars); i++) {
|
|
int j;
|
|
NC_VAR_INFO_T* v = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
|
|
for(j=0;j<ncindexsize(v->att);j++) {
|
|
NC_ATT_INFO_T* att = (NC_ATT_INFO_T*)ncindexith(v->att, j);
|
|
if((retval = nc_reclaim_data_all(grp->nc4_info->controller->ext_ncid,att->nc_typeid,att->data,att->len)))
|
|
return retval;
|
|
att->data = NULL;
|
|
att->len = 0;
|
|
att->dirty = 0;
|
|
}
|
|
}
|
|
|
|
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);
|
|
|
|
/* Order is important here. We must delete the attribute contents
|
|
before deleteing any metadata because nc_reclaim_data depends
|
|
on the existence of the type info.
|
|
*/
|
|
|
|
/* Delete all the attribute data contents in each group and variable. */
|
|
if ((retval = nc4_rec_grp_del_att_data(h5->root_grp)))
|
|
return retval;
|
|
|
|
/* 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
|
|
|
|
/**
|
|
* Initialize parallel I/O logging. For parallel I/O builds, open log
|
|
* file, if not opened yet, or increment ref count if already open.
|
|
*
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_init_logging(void)
|
|
{
|
|
int ret = NC_NOERR;
|
|
|
|
#if NC_HAS_LOGGING
|
|
#if NC_HAS_PARALLEL4
|
|
if (!LOG_FILE && nc_log_level >= 0)
|
|
{
|
|
char log_filename[NC_MAX_NAME];
|
|
int my_rank = 0;
|
|
int mpierr;
|
|
int mpi_initialized;
|
|
|
|
/* If MPI has been initialized find the rank. */
|
|
if ((mpierr = MPI_Initialized(&mpi_initialized)))
|
|
return NC_EMPI;
|
|
if (mpi_initialized)
|
|
{
|
|
if ((mpierr = MPI_Comm_rank(MPI_COMM_WORLD, &my_rank)))
|
|
return NC_EMPI;
|
|
}
|
|
|
|
/* Create a filename with the rank in it. */
|
|
sprintf(log_filename, "nc4_log_%d.log", my_rank);
|
|
|
|
/* Open a file for this rank to log messages. */
|
|
if (!(LOG_FILE = fopen(log_filename, "w")))
|
|
return NC_EINTERNAL;
|
|
}
|
|
#endif /* NC_HAS_PARALLEL4 */
|
|
#endif /* NC_HAS_LOGGING */
|
|
|
|
return ret;
|
|
}
|
|
|
|
/**
|
|
* Finalize logging - close parallel I/O log files, if open. This does
|
|
* nothing if logging is not enabled.
|
|
*
|
|
* @author Ed Hartnett
|
|
*/
|
|
void
|
|
nc4_finalize_logging(void)
|
|
{
|
|
#if NC_HAS_LOGGING
|
|
#if NC_HAS_PARALLEL4
|
|
if (LOG_FILE)
|
|
{
|
|
fclose(LOG_FILE);
|
|
LOG_FILE = NULL;
|
|
}
|
|
#endif /* NC_HAS_PARALLEL4 */
|
|
#endif /* NC_HAS_LOGGING */
|
|
}
|
|
|
|
/**
|
|
* 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 when building
|
|
* netCDF, this function will do nothing.
|
|
*
|
|
* @param new_level The new logging level.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_set_log_level(int new_level)
|
|
{
|
|
#if NC_HAS_LOGGING
|
|
/* Remember the new level. */
|
|
nc_log_level = new_level;
|
|
|
|
#if NC_HAS_PARALLEL4
|
|
/* For parallel I/O builds, call the log init/finalize functions
|
|
* as needed, to open and close the log files. */
|
|
if (new_level >= 0)
|
|
{
|
|
if (!LOG_FILE)
|
|
nc4_init_logging();
|
|
}
|
|
else
|
|
nc4_finalize_logging();
|
|
#endif /* NC_HAS_PARALLEL4 */
|
|
|
|
LOG((1, "log_level changed to %d", nc_log_level));
|
|
#endif /*NC_HAS_LOGGING */
|
|
|
|
return NC_NOERR;
|
|
}
|
|
#endif /* ENABLE_SET_LOG_LEVEL */
|
|
|
|
#if NC_HAS_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 /*NC_HAS_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;
|
|
#if NC_HAS_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 /*NC_HAS_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;
|
|
}
|
|
|
|
/**************************************************/
|
|
/* NCglobal state management */
|
|
|
|
static NCglobalstate* nc_globalstate = NULL;
|
|
|
|
static int
|
|
NC_createglobalstate(void)
|
|
{
|
|
int stat = NC_NOERR;
|
|
const char* tmp = NULL;
|
|
|
|
if(nc_globalstate == NULL) {
|
|
nc_globalstate = calloc(1,sizeof(NCglobalstate));
|
|
}
|
|
/* Initialize struct pointers */
|
|
if((nc_globalstate->rcinfo = calloc(1,sizeof(struct NCRCinfo)))==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
if((nc_globalstate->rcinfo->entries = nclistnew())==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
if((nc_globalstate->rcinfo->s3profiles = nclistnew())==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
|
|
/* Get environment variables */
|
|
if(getenv(NCRCENVIGNORE) != NULL)
|
|
nc_globalstate->rcinfo->ignore = 1;
|
|
tmp = getenv(NCRCENVRC);
|
|
if(tmp != NULL && strlen(tmp) > 0)
|
|
nc_globalstate->rcinfo->rcfile = strdup(tmp);
|
|
/* Initialize chunk cache defaults */
|
|
nc_globalstate->chunkcache.size = CHUNK_CACHE_SIZE; /**< Default chunk cache size. */
|
|
nc_globalstate->chunkcache.nelems = CHUNK_CACHE_NELEMS; /**< Default chunk cache number of elements. */
|
|
nc_globalstate->chunkcache.preemption = CHUNK_CACHE_PREEMPTION; /**< Default chunk cache preemption. */
|
|
|
|
done:
|
|
return stat;
|
|
}
|
|
|
|
/* Get global state */
|
|
NCglobalstate*
|
|
NC_getglobalstate(void)
|
|
{
|
|
if(nc_globalstate == NULL)
|
|
NC_createglobalstate();
|
|
return nc_globalstate;
|
|
}
|
|
|
|
void
|
|
NC_freeglobalstate(void)
|
|
{
|
|
if(nc_globalstate != NULL) {
|
|
nullfree(nc_globalstate->tempdir);
|
|
nullfree(nc_globalstate->home);
|
|
nullfree(nc_globalstate->cwd);
|
|
NC_rcclear(nc_globalstate->rcinfo);
|
|
free(nc_globalstate->rcinfo);
|
|
free(nc_globalstate);
|
|
nc_globalstate = NULL;
|
|
}
|
|
}
|
|
/**************************************************/
|
|
/* Specific property functions */
|
|
|
|
/**
|
|
Provide a function to store global data alignment
|
|
information.
|
|
Repeated calls to nc_set_alignment will overwrite any existing values.
|
|
|
|
If defined, then for every file created or opened after the call to
|
|
nc_set_alignment, and for every new variable added to the file, the
|
|
most recently set threshold and alignment values will be applied
|
|
to that variable.
|
|
|
|
The nc_set_alignment function causes new data written to a
|
|
netCDF-4 file to be aligned on disk to a specified block
|
|
size. To be effective, alignment should be the system disk block
|
|
size, or a multiple of it. This setting is effective with MPI
|
|
I/O and other parallel systems.
|
|
|
|
This is a trade-off of write speed versus file size. Alignment
|
|
leaves holes between file objects. The default of no alignment
|
|
writes file objects contiguously, without holes. Alignment has
|
|
no impact on file readability.
|
|
|
|
Alignment settings apply only indirectly, through the file open
|
|
functions. Call nc_set_alignment first, then nc_create or
|
|
nc_open for one or more files. Current alignment settings are
|
|
locked in when each file is opened, then forgotten when the same
|
|
file is closed. For illustration, it is possible to write
|
|
different files at the same time with different alignments, by
|
|
interleaving nc_set_alignment and nc_open calls.
|
|
|
|
Alignment applies to all newly written low-level file objects at
|
|
or above the threshold size, including chunks of variables,
|
|
attributes, and internal infrastructure. Alignment is not locked
|
|
in to a data variable. It can change between data chunks of the
|
|
same variable, based on a file's history.
|
|
|
|
Refer to H5Pset_alignment in HDF5 documentation for more
|
|
specific details, interactions, and additional rules.
|
|
|
|
@param threshold The minimum size to which alignment is applied.
|
|
@param alignment The alignment value.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EINVAL Invalid input.
|
|
@author Dennis Heimbigner
|
|
@ingroup datasets
|
|
*/
|
|
int
|
|
nc_set_alignment(int threshold, int alignment)
|
|
{
|
|
NCglobalstate* gs = NC_getglobalstate();
|
|
gs->alignment.threshold = threshold;
|
|
gs->alignment.alignment = alignment;
|
|
gs->alignment.defined = 1;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
Provide get function to retrieve global data alignment
|
|
information.
|
|
|
|
The nc_get_alignment function return the last values set by
|
|
nc_set_alignment. If nc_set_alignment has not been called, then
|
|
it returns the value 0 for both threshold and alignment.
|
|
|
|
@param thresholdp Return the current minimum size to which alignment is applied or zero.
|
|
@param alignmentp Return the current alignment value or zero.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EINVAL Invalid input.
|
|
@author Dennis Heimbigner
|
|
@ingroup datasets
|
|
*/
|
|
|
|
int
|
|
nc_get_alignment(int* thresholdp, int* alignmentp)
|
|
{
|
|
NCglobalstate* gs = NC_getglobalstate();
|
|
if(thresholdp) *thresholdp = gs->alignment.threshold;
|
|
if(alignmentp) *alignmentp = gs->alignment.alignment;
|
|
return NC_NOERR;
|
|
}
|