netcdf-c/libdispatch/nc.c

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/*
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* Copyright 2018, University Corporation for Atmospheric Research
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*/
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/**
* @file
* @internal
*
* This file contains functions that work with the NC struct. There is
* an NC struct for every open netCDF file.
*
* @author Glenn Davis
*/
Primary change: add dap4 support Specific changes: 1. Add dap4 code: libdap4 and dap4_test. Note that until the d4ts server problem is solved, dap4 is turned off. 2. Modify various files to support dap4 flags: configure.ac, Makefile.am, CMakeLists.txt, etc. 3. Add nc_test/test_common.sh. This centralizes the handling of the locations of various things in the build tree: e.g. where is ncgen.exe located. See nc_test/test_common.sh for details. 4. Modify .sh files to use test_common.sh 5. Obsolete separate oc2 by moving it to be part of netcdf-c. This means replacing code with netcdf-c equivalents. 5. Add --with-testserver to configure.ac to allow override of the servers to be used for --enable-dap-remote-tests. 6. There were multiple versions of nctypealignment code. Try to centralize in libdispatch/doffset.c and include/ncoffsets.h 7. Add a unit test for the ncuri code because of its complexity. 8. Move the findserver code out of libdispatch and into a separate, self contained program in ncdap_test and dap4_test. 9. Move the dispatch header files (nc{3,4}dispatch.h) to .../include because they are now shared by modules. 10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts. 11. Make use of MREMAP if available 12. Misc. minor changes e.g. - #include <config.h> -> #include "config.h" - Add some no-install headers to /include - extern -> EXTERNL and vice versa as needed - misc header cleanup - clean up checking for misc. unix vs microsoft functions 13. Change copyright decls in some files to point to LICENSE file. 14. Add notes to RELEASENOTES.md
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#include "config.h"
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#if defined(LOCKNUMREC) /* && _CRAYMPP */
# include <mpp/shmem.h>
# include <intrinsics.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "ncdispatch.h"
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/** This is the default create format for nc_create and nc__create. */
static int default_create_format = NC_FORMAT_CLASSIC;
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/**
* Find the NC struct for an open file, using the ncid.
*
* @param ncid The ncid to find.
* @param ncpp Pointer that gets a pointer to the NC.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID ncid not found.
* @author Glenn Davis, Dennis Heimbigner
*/
int
NC_check_id(int ncid, NC** ncpp)
{
NC* nc = find_in_NCList(ncid);
if(nc == NULL) return NC_EBADID;
if(ncpp) *ncpp = nc;
return NC_NOERR;
}
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/**
* Free an NC struct and its related resources.
*
* @param ncp Pointer to the NC struct to be freed.
*
* @author Glenn Davis, Dennis Heimbigner
*/
void
free_NC(NC *ncp)
{
if(ncp == NULL)
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return;
if(ncp->path)
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free(ncp->path);
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
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if(ncp->model)
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free(ncp->model);
/* We assume caller has already cleaned up ncp->dispatchdata */
#if _CRAYMPP && defined(LOCKNUMREC)
shfree(ncp);
#else
free(ncp);
#endif /* _CRAYMPP && LOCKNUMREC */
}
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/**
* Create and initialize a new NC struct. The ncid is assigned later.
*
* @param dispatcher
* @param path The name of the file.
* @param mode The open or create mode.
* @param model
* @param ncpp A pointer that gets a pointer to the newlly allocacted
* and initialized NC struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Glenn Davis, Dennis Heimbigner
*/
int
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new_NC(const NC_Dispatch* dispatcher, const char* path, int mode,
NCmodel* model, NC** ncpp)
{
NC *ncp = (NC*)calloc(1,sizeof(NC));
if(ncp == NULL) return NC_ENOMEM;
ncp->dispatch = dispatcher;
ncp->path = nulldup(path);
ncp->mode = mode;
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
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if((ncp->model = malloc(sizeof(NCmodel)))==NULL)
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return NC_ENOMEM;
Provide byte-range reading of remote datasets re: issue https://github.com/Unidata/netcdf-c/issues/1251 Assume that you have the URL to a remote dataset which is a normal netcdf-3 or netcdf-4 file. This PR allows the netcdf-c to read that dataset's contents as a netcdf file using HTTP byte ranges if the remote server supports byte-range access. Originally, this PR was set up to access Amazon S3 objects, but it can also access other remote datasets such as those provided by a Thredds server via the HTTPServer access protocol. It may also work for other kinds of servers. Note that this is not intended as a true production capability because, as is known, this kind of access to can be quite slow. In addition, the byte-range IO drivers do not currently do any sort of optimization or caching. An additional goal here is to gain some experience with the Amazon S3 REST protocol. This architecture and its use documented in the file docs/byterange.dox. There are currently two test cases: 1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle for a remote netcdf-3 file and a remote netcdf-4 file. 2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote datasets. This PR also incorporates significantly changed model inference code (see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259). 1. It centralizes the code that infers the dispatcher. 2. It adds support for byte-range URLs Other changes: 1. NC_HDF5_finalize was not being properly called by nc_finalize(). 2. Fix minor bug in ncgen3.l 3. fix memory leak in nc4info.c 4. add code to walk the .daprc triples and to replace protocol= fragment tag with a more general mode= tag. Final Note: Th inference code is still way too complicated. We need to move to the validfile() model used by netcdf Java, where each dispatcher is asked if it can process the file. This decentralizes the inference code. This will be done after all the major new dispatchers (PIO, Zarr, etc) have been implemented.
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*ncp->model = *model; /* Make a copy */
if(ncp->path == NULL) { /* fail */
free_NC(ncp);
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return NC_ENOMEM;
}
if(ncpp) {
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*ncpp = ncp;
} else {
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free_NC(ncp);
}
return NC_NOERR;
}
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/**
* This function sets a default create flag that will be logically
* or'd to whatever flags are passed into nc_create for all future
* calls to nc_create.
*
* @param format The format that should become the default.
* @param old_formatp Pointer that gets the previous default. Ignored
* if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOTBUILD Requested format not built with this install.
* @return ::NC_EINVAL Invalid input.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
nc_set_default_format(int format, int *old_formatp)
{
/* Return existing format if desired. */
if (old_formatp)
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*old_formatp = default_create_format;
/* Make sure only valid format is set. */
#ifndef ENABLE_CDF5
if (format == NC_FORMAT_CDF5)
return NC_ENOTBUILT;
#endif
#ifdef USE_HDF5
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if (format != NC_FORMAT_CLASSIC && format != NC_FORMAT_64BIT_OFFSET &&
format != NC_FORMAT_NETCDF4 && format != NC_FORMAT_NETCDF4_CLASSIC &&
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format != NC_FORMAT_CDF5)
return NC_EINVAL;
#else
if (format == NC_FORMAT_NETCDF4 || format == NC_FORMAT_NETCDF4_CLASSIC)
return NC_ENOTBUILT;
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if (format != NC_FORMAT_CLASSIC && format != NC_FORMAT_64BIT_OFFSET &&
format != NC_FORMAT_CDF5)
return NC_EINVAL;
#endif
default_create_format = format;
return NC_NOERR;
}
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/**
* Get the current default format.
*
* @return the default format.
* @author Ed Hartnett
*/
int
nc_get_default_format(void)
{
return default_create_format;
}