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update against main

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This commit is contained in:
Dennis Heimbigner 2023-01-28 13:45:35 -07:00
parent d1d2808919
commit ebf86ac637
18 changed files with 212 additions and 261 deletions
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20
.github/workflows/run_tests_osx.yml vendored
View File

@ -21,14 +21,14 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
###
# libhdf5
###
- name: Cache libhdf5-${{ runner.os }}-${{ matrix.hdf5 }}
id: cache-hdf5-osx
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -61,7 +61,7 @@ jobs:
use_nczarr: [ nczarr_off, nczarr_on ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
###
# Set Environmental Variables
@ -93,7 +93,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf-osx
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -167,7 +167,7 @@ jobs:
use_nczarr: [ nczarr_off, nczarr_on ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
###
# Set Environmental Variables
@ -199,7 +199,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf5-osx
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -260,7 +260,7 @@ jobs:
hdf5: [ 1.12.2 ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
###
# Set Environmental Variables
@ -277,7 +277,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf-osx
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -342,7 +342,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
###
# Set Environmental Variables
@ -357,7 +357,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf5-osx
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}

50
.github/workflows/run_tests_ubuntu.yml vendored
View File

@ -18,7 +18,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -29,7 +29,7 @@ jobs:
###
- name: Cache libhdf5-${{ matrix.hdf5 }}
id: cache-hdf5
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -67,7 +67,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -78,7 +78,7 @@ jobs:
###
- name: Cache libhdf5-parallel-${{ matrix.hdf5 }}
id: cache-hdf5
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-parallel-${{ runner.os }}-${{ matrix.hdf5 }}
@ -128,7 +128,7 @@ jobs:
hdf5: [ 1.12.2 ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -149,7 +149,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -208,7 +208,7 @@ jobs:
hdf5: [ 1.12.2 ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -224,7 +224,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-parallel-${{ runner.os }}-${{ matrix.hdf5 }}
@ -289,7 +289,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -308,7 +308,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -369,7 +369,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -388,7 +388,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-parallel-${{ runner.os }}-${{ matrix.hdf5 }}
@ -448,7 +448,7 @@ jobs:
use_nczarr: [ nczarr_off, nczarr_on ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -482,7 +482,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@ -501,31 +501,37 @@ jobs:
- name: Configure
shell: bash -l {0}
run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure ${ENABLE_HDF5} ${ENABLE_DAP} ${ENABLE_NCZARR}
run: |
current_directory="$(pwd)"
mkdir ../build
cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} "${current_directory}/configure" ${ENABLE_HDF5} ${ENABLE_DAP} ${ENABLE_NCZARR}
if: ${{ success() }}
- name: Look at config.log if error
shell: bash -l {0}
run: cat config.log
run: cd ../build && cat config.log
if: ${{ failure() }}
- name: Print Summary
shell: bash -l {0}
run: cat libnetcdf.settings
run: cd ../build && cat libnetcdf.settings
- name: Build Library and Utilities
shell: bash -l {0}
run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j
run: |
cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j
if: ${{ success() }}
- name: Build Tests
shell: bash -l {0}
run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j
run: |
cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j
if: ${{ success() }}
- name: Run Tests
shell: bash -l {0}
run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
run: |
cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
if: ${{ success() }}
nc-cmake:
@ -541,7 +547,7 @@ jobs:
use_nczarr: [ nczarr_off, nczarr_on ]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Install System dependencies
shell: bash -l {0}
@ -575,7 +581,7 @@ jobs:
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}

2
.github/workflows/run_tests_win_cygwin.yml vendored
View File

@ -20,7 +20,7 @@ jobs:
- name: Fix line endings
run: git config --global core.autocrlf input
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: cygwin/cygwin-install-action@v2
with:

2
.github/workflows/run_tests_win_mingw.yml vendored
View File

@ -22,7 +22,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: msys2/setup-msys2@v2
with:
msystem: MINGW64

2
docs/CMakeLists.txt
View File

@ -95,6 +95,6 @@ obsolete/fan_utils.html bestpractices.md filters.md indexing.md
inmemory.md DAP2.dox FAQ.md
known_problems.md
COPYRIGHT.dox user_defined_formats.md DAP4.md DAP4.dox
testserver.dox byterange.dox filters.md nczarr.md auth.md quantize.md)
testserver.dox byterange.md filters.md nczarr.md auth.md quantize.md)
ADD_EXTRA_DIST("${CUR_EXTRA_DIST}")

8
docs/Doxyfile.in
View File

@ -809,13 +809,10 @@ INPUT = @abs_top_srcdir@/docs/mainpage.dox \
@abs_top_srcdir@/RELEASE_NOTES.md \
@abs_top_srcdir@/docs/install-fortran.md \
@abs_top_srcdir@/docs/windows-binaries.md \
@abs_top_srcdir@/docs/attribute_conventions.md \
@abs_top_srcdir@/docs/file_format_specifications.md \
@abs_top_srcdir@/docs/all-error-codes.md \
@abs_top_srcdir@/docs/inmemory.md \
@abs_top_srcdir@/docs/filter_quickstart.md \
@abs_top_srcdir@/docs/filters.md \
@abs_top_srcdir@/docs/byterange.dox \
@abs_top_srcdir@/docs/byterange.md \
@abs_top_srcdir@/docs/nczarr.md \
@abs_top_srcdir@/docs/notes.md \
@abs_top_srcdir@/docs/building-with-cmake.md \
@ -829,6 +826,9 @@ INPUT = @abs_top_srcdir@/docs/mainpage.dox \
@abs_top_srcdir@/docs/indexing.dox \
@abs_top_srcdir@/docs/testserver.dox \
@abs_top_srcdir@/docs/quantize.md \
@abs_top_srcdir@/docs/attribute_conventions.md \
@abs_top_srcdir@/docs/file_format_specifications.md \
@abs_top_srcdir@/docs/all-error-codes.md \
@abs_top_srcdir@/include/netcdf.h \
@abs_top_srcdir@/include/netcdf_mem.h \
@abs_top_srcdir@/include/netcdf_par.h \

2
docs/Doxyfile.user
View File

@ -748,7 +748,7 @@ INPUT = \
./docs/windows-binaries.md \
./docs/attribute_conventions.md \
./docs/file_format_specifications.md \
./docs/byterange.dox \
./docs/byterange.md \
./docs/inmemory.md \
./docs/auth.md \
./docs/filters.md \

14
docs/Makefile.am
View File

@ -7,15 +7,13 @@
# See netcdf-c/COPYRIGHT file for more info.
# These files will be included with the dist.
EXTRA_DIST = CMakeLists.txt COPYRIGHT.md FAQ.md \
netcdf.m4 DoxygenLayout.xml Doxyfile.in footer.html \
mainpage.dox tutorial.dox architecture.dox \
groups.dox indexing.dox inmeminternal.dox testserver.dox \
byterange.dox \
windows-binaries.md dispatch.md building-with-cmake.md \
EXTRA_DIST = netcdf.m4 DoxygenLayout.xml Doxyfile.in footer.html \
mainpage.dox tutorial.dox architecture.dox internal.dox \
windows-binaries.md dispatch.md building-with-cmake.md CMakeLists.txt groups.dox \
notes.md install-fortran.md credits.md auth.md filters.md \
obsolete/fan_utils.html inmemory.md known_problems.md \
nczarr.md quantize.md all-error-codes.md
obsolete/fan_utils.html indexing.dox inmemory.md FAQ.md \
known_problems.md COPYRIGHT.md inmeminternal.dox testserver.dox \
byterange.md nczarr.md quantize.md all-error-codes.md
# Turn off parallel builds in this directory.
.NOTPARALLEL:

156
docs/byterange.dox
View File

@ -1,156 +0,0 @@
/**
@if INTERNAL
@page byterange Remote Dataset Access Using HTTP Byte Ranges
\tableofcontents
<!-- Note that this file has the .dox extension, but is mostly markdown -->
<!-- Begin MarkDown -->
# Introduction {#byterange_intro}
Suppose that you have the URL to a remote dataset
which is a normal netcdf-3 or netcdf-4 file.
The netCDF-c library now supports read-only access to such
datasets using the HTTP byte range capability [], assuming that
the remote server supports byte-range access.
Two examples:
1. An Amazon S3 object containing a netcdf classic file.
- location: "https://remotetest.unidata.ucar.edu/thredds/fileServer/testdata/2004050300_eta_211.nc#mode=bytes"
2. A Thredds Server dataset supporting the Thredds HTTPServer protocol.
and containing a netcdf enhanced file.
- location: "http://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadC/2017/059/03/OR_ABI-L1b-RadC-M3C13_G16_s20170590337505_e20170590340289_c20170590340316.nc#mode=bytes"
Other remote servers may also provide byte-range access in a similar form.
It is important to note that this is not intended as a true
production capability because it is believed that this kind of access
can be quite slow. In addition, the byte-range IO drivers do not
currently do any sort of optimization or caching.
# Configuration {#byterange_config}
This capability is enabled using the option *--enable-byterange* option
to the *./configure* command for Automake. For Cmake, the option flag is
*-DENABLE_BYTERANGE=true*.
This capability requires access to *libcurl*, and an error will occur
if byterange is enabled, but no *libcurl* could not be located.
In this, it is similar to the DAP2 and DAP4 capabilities.
Note also that here, the term "http" is often used as a synonym for *byterange*.
# Run-time Usage {#byterange_url}
In order to use this capability at run-time, with *ncdump* for
example, it is necessary to provide a URL pointing to the basic
dataset to be accessed. The URL must be annotated to tell the
netcdf-c library that byte-range access should be used. This is
indicated by appending the phrase ````#mode=bytes````
to the end of the URL.
The two examples above show how this will look.
In order to determine the kind of file being accessed, the
netcdf-c library will read what is called the "magic number"
from the beginning of the remote dataset. This magic number
is a specific set of bytes that indicates the kind of file:
classic, enhanced, cdf5, etc.
# Architecture {#byterange_arch}
Internally, this capability is implemented with three files:
1. libdispatch/dhttp.c -- wrap libcurl operations.
2. libsrc/httpio.c -- provide byte-range reading to the netcdf-3 dispatcher.
3. libhdf5/H5FDhttp.c -- provide byte-range reading to the netcdf-4 dispatcher.
Both *httpio.c* and *H5FDhttp.c* are adapters that use *dhttp.c*
to do the work. Testing for the magic number is also carried out
by using the *dhttp.c* code.
## NetCDF Classic Access
The netcdf-3 code in the directory *libsrc* is built using
a secondary dispatch mechanism called *ncio*. This allows the
netcdf-3 code be independent of the lowest level IO access mechanisms.
This is how in-memory and mmap based access is implemented.
The file *httpio.c* is the dispatcher used to provide byte-range
IO for the netcdf-3 code.
Note that *httpio.c* is mostly just an
adapter between the *ncio* API and the *dhttp.c* code.
## NetCDF Enhanced Access
Similar to the netcdf-3 code, the HDF5 library
provides a secondary dispatch mechanism *H5FD*. This allows the
HDF5 code to be independent of the lowest level IO access mechanisms.
The netcdf-4 code in libhdf5 is built on the HDF5 library, so
it indirectly inherits the H5FD mechanism.
The file *H5FDhttp.c* implements the H5FD dispatcher API
and provides byte-range IO for the netcdf-4 code
(and for the HDF5 library as a side effect).
Note that *H5FDhttp.c* is mostly just an
adapter between the *H5FD* API and the *dhttp.c* code.
# The dhttp.c Code {#byterange_dhttp}
The core of all this is *dhttp.c* (and its header
*include/nchttp.c*). It is a wrapper over *libcurl*
and so exposes the libcurl handles -- albeit as _void*_.
The API for *dhttp.c* consists of the following procedures:
- int nc_http_open(const char* objecturl, void** curlp, fileoffset_t* filelenp);
- int nc_http_read(void* curl, const char* url, fileoffset_t start, fileoffset_t count, NCbytes* buf);
- int nc_http_close(void* curl);
- typedef long long fileoffset_t;
The type *fileoffset_t* is used to avoid use of *off_t* or *off64_t*
which are too volatile. It is intended to be represent file lengths
and offsets.
## nc_http_open
The *nc_http_open* procedure creates a *Curl* handle and returns it
in the *curlp* argument. It also obtains and searches the headers
looking for two headers:
1. "Accept-Ranges: bytes" -- to verify that byte-range access is supported.
2. "Content-Length: ..." -- to obtain the size of the remote dataset.
The dataset length is returned in the *filelenp* argument.
## nc_http_read
The *nc_http_read* procedure reads a specified set of contiguous bytes
as specified by the *start* and *count* arguments. It takes the *Curl*
handle produced by *nc_http_open* to indicate the server from which to read.
The *buf* argument is a pointer to an instance of type *NCbytes*, which
is a dynamically expandable byte vector (see the file *include/ncbytes.h*).
This procedure reads *count* bytes from the remote dataset starting at
the offset *start* position. The bytes are stored in *buf*.
## nc_http_close
The *nc_http_close* function closes the *Curl* handle and does any
necessary cleanup.
# Point of Contact {#byterange_poc}
__Author__: Dennis Heimbigner<br>
__Email__: dmh at ucar dot edu<br>
__Initial Version__: 12/30/2018<br>
__Last Revised__: 12/30/2018
<!-- End MarkDown -->
@endif
*/

38
libdispatch/dfile.c
View File

@ -125,8 +125,6 @@ int
nc_def_user_format(int mode_flag, NC_Dispatch *dispatch_table, char *magic_number)
{
/* Check inputs. */
if (mode_flag != NC_UDF0 && mode_flag != NC_UDF1)
return NC_EINVAL;
if (!dispatch_table)
return NC_EINVAL;
if (magic_number && strlen(magic_number) > NC_MAX_MAGIC_NUMBER_LEN)
@ -135,21 +133,29 @@ nc_def_user_format(int mode_flag, NC_Dispatch *dispatch_table, char *magic_numbe
/* Check the version of the dispatch table provided. */
if (dispatch_table->dispatch_version != NC_DISPATCH_VERSION)
return NC_EINVAL;
/* user defined magic numbers not allowed with netcdf3 modes */
if (magic_number && (fIsSet(mode_flag, NC_64BIT_OFFSET) ||
fIsSet(mode_flag, NC_64BIT_DATA) ||
(fIsSet(mode_flag, NC_CLASSIC_MODEL) &&
!fIsSet(mode_flag, NC_NETCDF4))))
return NC_EINVAL;
/* Retain a pointer to the dispatch_table and a copy of the magic
* number, if one was provided. */
switch(mode_flag)
if (fIsSet(mode_flag,NC_UDF0))
{
case NC_UDF0:
UDF0_dispatch_table = dispatch_table;
if (magic_number)
strncpy(UDF0_magic_number, magic_number, NC_MAX_MAGIC_NUMBER_LEN);
break;
case NC_UDF1:
}
else if(fIsSet(mode_flag, NC_UDF1))
{
UDF1_dispatch_table = dispatch_table;
if (magic_number)
strncpy(UDF1_magic_number, magic_number, NC_MAX_MAGIC_NUMBER_LEN);
break;
}
else
{
return NC_EINVAL;
}
return NC_NOERR;
@ -175,23 +181,23 @@ int
nc_inq_user_format(int mode_flag, NC_Dispatch **dispatch_table, char *magic_number)
{
/* Check inputs. */
if (mode_flag != NC_UDF0 && mode_flag != NC_UDF1)
return NC_EINVAL;
switch(mode_flag)
if (fIsSet(mode_flag,NC_UDF0))
{
case NC_UDF0:
if (dispatch_table)
*dispatch_table = UDF0_dispatch_table;
if (magic_number)
strncpy(magic_number, UDF0_magic_number, NC_MAX_MAGIC_NUMBER_LEN);
break;
case NC_UDF1:
}
else if(fIsSet(mode_flag,NC_UDF1))
{
if (dispatch_table)
*dispatch_table = UDF1_dispatch_table;
if (magic_number)
strncpy(magic_number, UDF1_magic_number, NC_MAX_MAGIC_NUMBER_LEN);
break;
}
else
{
return NC_EINVAL;
}
return NC_NOERR;

83
libdispatch/dinfermodel.c
View File

@ -118,8 +118,8 @@ static struct FORMATMODES {
{"classic",NC_FORMATX_NC3,0}, /* ditto */
{"netcdf-4",NC_FORMATX_NC4,NC_FORMAT_NETCDF4},
{"enhanced",NC_FORMATX_NC4,NC_FORMAT_NETCDF4},
{"udf0",NC_FORMATX_UDF0,NC_FORMAT_NETCDF4},
{"udf1",NC_FORMATX_UDF1,NC_FORMAT_NETCDF4},
{"udf0",NC_FORMATX_UDF0,0},
{"udf1",NC_FORMATX_UDF1,0},
{"nczarr",NC_FORMATX_NCZARR,NC_FORMAT_NETCDF4},
{"zarr",NC_FORMATX_NCZARR,NC_FORMAT_NETCDF4},
{"bytes",NC_FORMATX_NC4,NC_FORMAT_NETCDF4}, /* temporary until 3 vs 4 is determined */
@ -182,8 +182,8 @@ static struct Readable {
{NC_FORMATX_PNETCDF,1},
{NC_FORMATX_DAP2,0},
{NC_FORMATX_DAP4,0},
{NC_FORMATX_UDF0,0},
{NC_FORMATX_UDF1,0},
{NC_FORMATX_UDF0,1},
{NC_FORMATX_UDF1,1},
{NC_FORMATX_NCZARR,0}, /* eventually make readable */
{0,0},
};
@ -762,13 +762,31 @@ NC_omodeinfer(int useparallel, int cmode, NCmodel* model)
* use some of the other flags, like NC_NETCDF4, so we must first
* check NC_UDF0 and NC_UDF1 before checking for any other
* flag. */
if(fIsSet(cmode,(NC_UDF0|NC_UDF1))) {
model->format = NC_FORMAT_NETCDF4;
if(fIsSet(cmode,NC_UDF0)) {
if(fIsSet(cmode, NC_UDF0) || fIsSet(cmode, NC_UDF1))
{
if(fIsSet(cmode, NC_UDF0))
{
model->impl = NC_FORMATX_UDF0;
} else {
model->impl = NC_FORMATX_UDF1;
}
if(fIsSet(cmode,NC_64BIT_OFFSET))
{
model->format = NC_FORMAT_64BIT_OFFSET;
}
else if(fIsSet(cmode,NC_64BIT_DATA))
{
model->format = NC_FORMAT_64BIT_DATA;
}
else if(fIsSet(cmode,NC_NETCDF4))
{
if(fIsSet(cmode,NC_CLASSIC_MODEL))
model->format = NC_FORMAT_NETCDF4_CLASSIC;
else
model->format = NC_FORMAT_NETCDF4;
}
if(! model->format)
model->format = NC_FORMAT_CLASSIC;
goto done;
}
@ -981,8 +999,6 @@ NC_infermodel(const char* path, int* omodep, int iscreate, int useparallel, void
case NC_FORMATX_NC4:
case NC_FORMATX_NC_HDF4:
case NC_FORMATX_DAP4:
case NC_FORMATX_UDF0:
case NC_FORMATX_UDF1:
case NC_FORMATX_NCZARR:
omode |= NC_NETCDF4;
if(model->format == NC_FORMAT_NETCDF4_CLASSIC)
@ -1001,6 +1017,17 @@ NC_infermodel(const char* path, int* omodep, int iscreate, int useparallel, void
case NC_FORMATX_DAP2:
omode &= ~(NC_NETCDF4|NC_64BIT_OFFSET|NC_64BIT_DATA|NC_CLASSIC_MODEL);
break;
case NC_FORMATX_UDF0:
case NC_FORMATX_UDF1:
if(model->format == NC_FORMAT_64BIT_OFFSET)
omode |= NC_64BIT_OFFSET;
else if(model->format == NC_FORMAT_64BIT_DATA)
omode |= NC_64BIT_DATA;
else if(model->format == NC_FORMAT_NETCDF4)
omode |= NC_NETCDF4;
else if(model->format == NC_FORMAT_NETCDF4_CLASSIC)
omode |= NC_NETCDF4|NC_CLASSIC_MODEL;
break;
default:
{stat = NC_ENOTNC; goto done;}
}
@ -1513,23 +1540,10 @@ static int
NC_interpret_magic_number(char* magic, NCmodel* model)
{
int status = NC_NOERR;
int tmpimpl = 0;
/* Look at the magic number */
#ifdef USE_NETCDF4
if (strlen(UDF0_magic_number) && !strncmp(UDF0_magic_number, magic,
strlen(UDF0_magic_number)))
{
model->impl = NC_FORMATX_UDF0;
model->format = NC_FORMAT_NETCDF4;
goto done;
}
if (strlen(UDF1_magic_number) && !strncmp(UDF1_magic_number, magic,
strlen(UDF1_magic_number)))
{
model->impl = NC_FORMATX_UDF1;
model->format = NC_FORMAT_NETCDF4;
goto done;
}
#endif /* USE_NETCDF4 */
if(model->impl == NC_FORMATX_UDF0 || model->impl == NC_FORMATX_UDF1)
tmpimpl = model->impl;
/* Use the complete magic number string for HDF5 */
if(memcmp(magic,HDF5_SIGNATURE,sizeof(HDF5_SIGNATURE))==0) {
@ -1561,10 +1575,29 @@ NC_interpret_magic_number(char* magic, NCmodel* model)
}
}
/* No match */
if (!tmpimpl)
status = NC_ENOTNC;
goto done;
done:
/* if model->impl was UDF0 or UDF1 on entry, make it so on exit */
if(tmpimpl)
model->impl = tmpimpl;
/* if this is a UDF magic_number update the model->impl */
if (strlen(UDF0_magic_number) && !strncmp(UDF0_magic_number, magic,
strlen(UDF0_magic_number)))
{
model->impl = NC_FORMATX_UDF0;
status = NC_NOERR;
}
if (strlen(UDF1_magic_number) && !strncmp(UDF1_magic_number, magic,
strlen(UDF1_magic_number)))
{
model->impl = NC_FORMATX_UDF1;
status = NC_NOERR;
}
return check(status);
}

3
libdispatch/dvar.c
View File

@ -1303,6 +1303,9 @@ NC_check_nulls(int ncid, int varid, const size_t *start, size_t **count,
pointer back to this function, when you're done with the data, and
it will free the string memory.
WARNING: This does not free the data vector itself, only
the strings to which it points.
@param len The number of character arrays in the array.
@param data The pointer to the data array.

7
nc_test4/tst_udf.c
View File

@ -307,7 +307,7 @@ main(int argc, char **argv)
* priority. If NC_NETCDF4 flag were given priority, then
* nc_abort() will not return TEST_VAL_42, but instead will
* return 0. */
if (nc_open(FILE_NAME, mode[i]|NC_NETCDF4, &ncid)) ERR;
if (nc_open(FILE_NAME, mode[i], &ncid)) ERR;
if (nc_inq_format(ncid, NULL) != TEST_VAL_42) ERR;
if (nc_inq_format_extended(ncid, NULL, NULL) != TEST_VAL_42) ERR;
if (nc_abort(ncid) != TEST_VAL_42) ERR;
@ -336,6 +336,7 @@ main(int argc, char **argv)
for (i = 0; i < NUM_UDFS; i++)
{
/* Add our test user defined format. */
mode[i] = mode[i]|NC_NETCDF4;
if (nc_def_user_format(mode[i], &tst_dispatcher, magic_number)) ERR;
/* Check that our user-defined format has been added. */
@ -360,6 +361,7 @@ main(int argc, char **argv)
printf("*** testing bad version causes dispatch table to be rejected...");
{
int i;
char magic_number[5] = "1111";
/* Test all available user-defined format slots. */
for (i = 0; i < NUM_UDFS; i++)
@ -367,6 +369,9 @@ main(int argc, char **argv)
/* Make sure our bad version format is rejected. */
if (nc_def_user_format(mode[i], &tst_dispatcher_bad_version,
NULL) != NC_EINVAL) ERR;
/* Make sure defining a magic number with netcdf3 is rejected. */
if (nc_def_user_format(NC_CLASSIC_MODEL, &tst_dispatcher,
magic_number) != NC_EINVAL) ERR;
}
}
SUMMARIZE_ERR;

1
ncdump/CMakeLists.txt
View File

@ -263,6 +263,7 @@ endif()
add_sh_test(ncdump tst_ncgen4)
add_sh_test(ncdump tst_netcdf4_4)
add_sh_test(ncdump tst_nccopy4)
add_sh_test(ncdump tst_calendars_nc4)
SET_TESTS_PROPERTIES(ncdump_tst_nccopy4 PROPERTIES DEPENDS "ncdump_run_ncgen_tests;ncdump_tst_output;ncdump_tst_ncgen4;ncdump_sh_tst_fillbug;ncdump_tst_netcdf4_4;ncdump_tst_h_scalar;tst_comp;tst_comp2;tst_nans;tst_opaque_data;tst_create_files;tst_special_atts")
SET_TESTS_PROPERTIES(ncdump_tst_nccopy5 PROPERTIES DEPENDS "ncdump_tst_nccopy4")

8
ncdump/Makefile.am
View File

@ -151,7 +151,7 @@ TESTS += tst_output.sh
TESTS += tst_nccopy3.sh
if USE_HDF5
TESTS += run_back_comp_tests.sh tst_netcdf4_4.sh
TESTS += tst_nccopy4.sh tst_nccopy5.sh
TESTS += tst_nccopy4.sh tst_nccopy5.sh tst_calendars_nc4.sh
endif
endif
endif
@ -177,7 +177,7 @@ ref_tst_noncoord.cdl ref_tst_compounds2.nc ref_tst_compounds2.cdl \
ref_tst_compounds3.nc ref_tst_compounds3.cdl ref_tst_compounds4.nc \
ref_tst_compounds4.cdl ref_tst_group_data_v23.cdl tst_mslp.cdl \
tst_bug321.cdl ref_tst_format_att.cdl ref_tst_format_att_64.cdl \
tst_nccopy3.sh tst_nccopy4.sh tst_nccopy5.sh \
tst_nccopy3.sh tst_nccopy4.sh tst_nccopy5.sh tst_calendars_nc4.sh \
ref_nc_test_netcdf4_4_0.nc run_back_comp_tests.sh \
ref_nc_test_netcdf4.cdl ref_tst_special_atts3.cdl tst_brecs.cdl \
ref_tst_grp_spec0.cdl ref_tst_grp_spec.cdl tst_grp_spec.sh \
@ -205,7 +205,7 @@ test_keywords.sh ref_keyword1.cdl ref_keyword2.cdl ref_keyword3.cdl ref_keyword4
ref_tst_nofilters.cdl test_scope.sh \
test_rcmerge.sh ref_rcmerge1.txt ref_rcmerge2.txt ref_rcmerge3.txt \
scope_ancestor_only.cdl scope_ancestor_subgroup.cdl scope_group_only.cdl scope_preorder.cdl \
ref_rcapi.txt ref_tst_enum_undef.cdl
ref_rcapi.txt ref_tst_enum_undef.cdl tst_calendars_nc4.cdl ref_times_nc4.cdl
# The L512.bin file is file containing exactly 512 bytes each of value 0.
# It is used for creating hdf5 files with varying offsets for testing.
@ -247,7 +247,7 @@ tst_roman_szip_unlim.cdl tst_perdimpspecs.nc tmppds.* \
keyword1.nc keyword2.nc keyword3.nc keyword4.nc \
tmp_keyword1.cdl tmp_keyword2.cdl tmp_keyword3.cdl tmp_keyword4.cdl \
type_*.nc copy_type_*.cdl \
scope_*.nc copy_scope_*.cdl keyword5.nc tst_enum_undef.cdl
scope_*.nc copy_scope_*.cdl keyword5.nc tst_enum_undef.cdl tst_times_nc4.cdl
# Remove directories
clean-local:

24
ncdump/nctime0.c
View File

@ -79,13 +79,18 @@ calendar_type(int ncid, int varid) {
int ncals = (sizeof calmap)/(sizeof calmap[0]);
ctype = cdMixed; /* default mixed Gregorian/Julian ala udunits */
stat = nc_inq_att(ncid, varid, CF_CAL_ATT_NAME, &catt.type, &catt.len);
if(stat == NC_NOERR && catt.type == NC_CHAR && catt.len > 0) {
char *calstr = (char *)emalloc(catt.len + 1);
if(stat == NC_NOERR && (catt.type == NC_CHAR || catt.type == NC_STRING) && catt.len > 0) {
char *calstr;
size_t cf_cal_att_name_len = strlen(CF_CAL_ATT_NAME);
strncpy(catt.name, CF_CAL_ATT_NAME, cf_cal_att_name_len);
catt.name[cf_cal_att_name_len] = '\0';
catt.tinfo = get_typeinfo(catt.type);
nc_get_att_single_string(ncid, varid, &catt, &calstr);
int itype;
NC_CHECK(nc_get_att(ncid, varid, CF_CAL_ATT_NAME, calstr));
calstr[catt.len] = '\0';
int calstr_len = strlen(calstr);
for(itype = 0; itype < ncals; itype++) {
if(strncasecmp(calstr, calmap[itype].attname, catt.len) == 0) {
if(strncasecmp(calstr, calmap[itype].attname, calstr_len) == 0) {
ctype = calmap[itype].type;
break;
}
@ -204,10 +209,11 @@ get_timeinfo(int ncid1, int varid1, ncvar_t *vp) {
/* time variables must have appropriate units attribute or be a bounds variable */
nc_status = nc_inq_att(ncid, varid, "units", &uatt.type, &uatt.len);
if(nc_status == NC_NOERR && uatt.type == NC_CHAR) { /* TODO: NC_STRING? */
units = emalloc(uatt.len + 1);
NC_CHECK(nc_get_att(ncid, varid, "units", units));
units[uatt.len] = '\0';
if(nc_status == NC_NOERR && (uatt.type == NC_CHAR || uatt.type == NC_STRING)) {
strncpy(uatt.name, "units", 5);
uatt.name[5] = '\0';
uatt.tinfo = get_typeinfo(uatt.type);
nc_get_att_single_string(ncid, varid, &uatt, &units);
if(!is_valid_time_unit(units)) {
free(units);
return;

37
ncdump/utils.c
View File

@ -13,6 +13,7 @@
#include <assert.h>
#include <ctype.h>
#include "utils.h"
#include "nccomps.h"
#ifndef isascii
EXTERNL int isascii(int c);
#endif
@ -959,3 +960,39 @@ done:
}
#endif
/*********************************************************************************/
void nc_get_att_single_string(const int ncid, const int varid,
const struct ncatt_t *att, char **str_out) {
if (att->type == NC_CHAR) {
// NC_CHAR type attribute
// Use a call to nc_get_att_text which expects to output the attribute value
// into a char * pointing to allocated memory. The number of bytes to allocate
// is the attribute length (which is the number of elements in a vector, 1 for
// scalar) times the size of each element in bytes. The attribute length is
// held in att->len, and the attribute element size is in att->tinfo->size.
*str_out = emalloc((att->len + 1) * att->tinfo->size);
(*str_out)[att->len] = '\0';
NC_CHECK(nc_get_att_text(ncid, varid, att->name, *str_out));
} else if (att->type == NC_STRING) {
// NC_STRING type attribute
// Use a call to nc_get_att_string which expects to output the attribute value
// into a vector of char pointers, where each entry points to allocated memory.
// The vector of char pointers needs to be allocated to the length (number of strings)
// times the size of each entry (size of a char *).
char **att_strings = emalloc((att->len + 1) * att->tinfo->size);
NC_CHECK(nc_get_att_string(ncid, varid, att->name, att_strings));
// str_out needs to be allocated to a size large enough to hold the string that
// the first pointer in att_strings is pointing to.
size_t att_str_len = strlen(att_strings[0]);
*str_out = emalloc((att_str_len + 1) * att->tinfo->size);
(*str_out)[att_str_len] = '\0';
strncpy(*str_out, att_strings[0], att_str_len);
nc_free_string(att->len, att_strings); /* Warning: does not free att_strings */
free(att_strings);
} else {
fprintf(stderr,"nc_get_att_single_string: unknown attribute type: %d\n", att->type);
fprintf(stderr," must use one of: NC_CHAR, NC_STRING\n");
fflush(stderr); fflush(stdout);
exit(2);
}
}

12
ncdump/utils.h
View File

@ -10,6 +10,8 @@
#include "config.h"
struct ncatt_t;
#ifndef NCSTREQ
#define NCSTREQ(a, b) (*(a) == *(b) && strcmp((a), (b)) == 0)
#endif
@ -181,6 +183,16 @@ extern int nc_next_giter(ncgiter_t *iterp, int *grpid);
extern void nc_free_giter(ncgiter_t *iterp);
extern int getrootid(int grpid);
/*
* Get attribute value for a single string value from either of NC_CHAR or NC_STRING types.
* This routine assumes that the attribute holds a single string value. If there are more
* than one string, subequent strings after the first one will be ignored.
*
* The caller is responsible for allocating and freeing memory for the str_out parameter.
*/
extern void nc_get_att_single_string(const int ncid, const int varid,
const struct ncatt_t *att, char **str_out);
#ifdef __cplusplus
}
#endif