2010-06-03 21:24:43 +08:00
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#!/bin/sh
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2017-11-17 04:03:35 +08:00
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# This shell script runs extra tests ncdump for netcdf-4
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# Dennis Heimbigner, Ward Fisher
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2017-03-09 08:01:10 +08:00
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2018-09-07 05:53:25 +08:00
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if test "x$srcdir" = x ; then srcdir=`pwd`; fi
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2017-03-09 08:01:10 +08:00
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. ../test_common.sh
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2010-06-03 21:24:43 +08:00
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set -e
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2012-07-18 04:13:17 +08:00
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2018-08-26 11:44:41 +08:00
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# Remove the version information from _NCProperties
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cleanncprops() {
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src="$1"
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dst="$2"
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rm -f $dst
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cat $src \
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This PR adds EXPERIMENTAL support for accessing data in the
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-29 08:02:47 +08:00
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| sed -e '/:_Endianness/d' \
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2021-01-12 05:13:21 +08:00
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| sed -e 's/_SuperblockVersion = [12]/_SuperblockVersion = 0/' \
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2018-08-26 11:44:41 +08:00
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| sed -e 's/\(netcdflibversion\|netcdf\)=.*|/\1=NNNN|/' \
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| sed -e 's/\(hdf5libversion\|hdf5\)=.*"/\1=HHHH"/' \
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2018-09-07 05:53:25 +08:00
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| grep -v '_NCProperties' \
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2018-08-26 11:44:41 +08:00
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| cat >$dst
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}
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2010-06-03 21:24:43 +08:00
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echo ""
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echo "*** Running extra netcdf-4 tests."
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2012-06-19 00:56:45 +08:00
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#
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# In windows, these tests fail because srcdir is prepended.
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# e.g., Instead of 'ncdump ref_tst_compounds2' the file would
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# contain:
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# 'ncdump ./ref_tst_compounds2'. This causes the test to fail.
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# But, 'srcdir' is necessary for make distcheck.
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#
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2018-09-07 05:53:25 +08:00
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# Short term solution, use sed when on windows/MSYS to
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2012-06-19 00:56:45 +08:00
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# remove the './','../../ncdump'.
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2017-11-17 04:03:35 +08:00
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#
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2018-03-21 11:31:31 +08:00
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# I am undoing this because libdispatch/dwinpath.c
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# should be taking care of this. If not, then that is
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# what we need to fix. Alternatively, we can use top_srcdir,
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# which is an absolute path
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2017-11-17 04:03:35 +08:00
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echo "*** running tst_string_data to create test files..."
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${execdir}/tst_string_data
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2012-06-19 00:56:45 +08:00
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2018-03-21 11:31:31 +08:00
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echo "*** dumping tst_string_data.nc to tst_string_data.cdl..."
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${NCDUMP} tst_string_data.nc > tst_string_data.cdl
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2018-08-26 11:44:41 +08:00
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cleanncprops tst_string_data.cdl tst_string_data.tmp
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cleanncprops ${srcdir}/ref_tst_string_data.cdl ref_tst_string_data.tmp
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2018-03-21 11:31:31 +08:00
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echo "*** comparing tst_string_data.cdl with ref_tst_string_data.cdl..."
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2018-08-26 11:44:41 +08:00
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diff -b tst_string_data.tmp ref_tst_string_data.tmp
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2010-06-03 21:24:43 +08:00
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#echo '*** testing non-coordinate variable of same name as dimension...'
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2018-03-21 11:31:31 +08:00
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#${NCGEN} -v4 -b -o tst_noncoord.nc ${top_srcdir}/ncdump/ref_tst_noncoord.cdl
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2010-06-03 21:24:43 +08:00
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2018-03-21 11:31:31 +08:00
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echo '*** testing reference file ref_tst_compounds2.nc...'
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2021-12-21 06:13:08 +08:00
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${NCDUMP} -n ref_tst_compounds2 ${top_srcdir}/ncdump/ref_tst_compounds2.nc > tst_compounds2.cdl
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2018-03-21 11:31:31 +08:00
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diff -b tst_compounds2.cdl ${top_srcdir}/ncdump/ref_tst_compounds2.cdl
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2010-06-03 21:24:43 +08:00
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2018-03-21 11:31:31 +08:00
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echo '*** testing reference file ref_tst_compounds3.nc...'
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2021-12-21 06:13:08 +08:00
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${NCDUMP} -n ref_tst_compounds3 ${top_srcdir}/ncdump/ref_tst_compounds3.nc > tst_compounds3.cdl
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2018-03-21 11:31:31 +08:00
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diff -b tst_compounds3.cdl ${top_srcdir}/ncdump/ref_tst_compounds3.cdl
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2010-06-03 21:24:43 +08:00
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2018-03-21 11:31:31 +08:00
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echo '*** testing reference file ref_tst_compounds4.nc...'
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2021-12-21 06:13:08 +08:00
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${NCDUMP} -n ref_tst_compounds4 ${top_srcdir}/ncdump/ref_tst_compounds4.nc > tst_compounds4.cdl
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2018-03-21 11:31:31 +08:00
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diff -b tst_compounds4.cdl ${top_srcdir}/ncdump/ref_tst_compounds4.cdl
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2012-06-19 00:56:45 +08:00
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2018-03-21 11:31:31 +08:00
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# Exercise Jira NCF-213 bug fix
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2014-03-09 11:41:30 +08:00
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# rm -f tst_ncf213.cdl tst_ncf213.nc
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2018-08-26 11:44:41 +08:00
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# Remove specific _NCProperties values
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${NCGEN} -b -o tst_ncf213.nc $srcdir/ref_tst_ncf213.cdl
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Enhance/Fix filter support
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214
The primary change is to support so-called "standard filters".
A standard filter is one that is defined by the following
netcdf-c API:
````
int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params);
int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params);
````
So for example, zstandard would be a standard filter by defining
the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*.
In order to define these functions, we need a new dispatch function:
````
int nc_inq_filter_avail(int ncid, unsigned filterid);
````
This function, combined with the existing filter API can be used
to implement arbitrary standard filters using a simple code pattern.
Note that I would have preferred that this function return a list
of all available filters, but HDF5 does not support that functionality.
So this PR implements the dispatch function and implements
the following standard functions:
+ bzip2
+ zstandard
+ blosc
Specific test cases are also provided for HDF5 and NCZarr.
Over time, other specific standard filters will be defined.
## Primary Changes
* Add nc_inq_filter_avail() to netcdf-c API.
* Add standard filter implementations to test use of *nc_inq_filter_avail*.
* Bump the dispatch table version number and add to all the relevant
dispatch tables (libsrc, libsrcp, etc).
* Create a program to invoke nc_inq_filter_avail so that it is accessible
to shell scripts.
* Cleanup szip support to properly support szip
when HDF5 is disabled. This involves detecting
libsz separately from testing if HDF5 supports szip.
* Integrate shuffle and fletcher32 into the existing
filter API. This means that, for example, nc_def_var_fletcher32
is now a wrapper around nc_def_var_filter.
* Extend the Codec defaulting to allow multiple default shared libraries.
## Misc. Changes
* Modify configure.ac/CMakeLists.txt to look for the relevant
libraries implementing standard filters.
* Modify libnetcdf.settings to list available standard filters
(including deflate and szip).
* Add CMake test modules to locate libbz2 and libzstd.
* Cleanup the HDF5 memory manager function use in the plugins.
* remove unused file include//ncfilter.h
* remove tests for the HDF5 memory operations e.g. H5allocate_memory.
* Add flag to ncdump to force use of _Filter instead of _Deflate
or _Shuffle or _Fletcher32. Used for testing.
2022-03-15 02:39:37 +08:00
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${NCDUMP} -shF tst_ncf213.nc > tst_ncf213.cdl
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2018-08-26 11:44:41 +08:00
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cleanncprops tst_ncf213.cdl tst_ncf213.tmp
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cleanncprops ${srcdir}/ref_tst_ncf213.cdl ref_tst_ncf213.tmp
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2018-03-21 11:31:31 +08:00
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# Now compare
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Codify cross-platform file paths
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc. These platforms differ
significantly in the kind of file paths that they accept. So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.
A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.
The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.
The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.
As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.
In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.
Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
tests to work under windows using shell scripts; the args do
not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
PR https://github.com/Unidata/netcdf-c/pull/1794,
HDF5 changed its Windows file path handling.
2021-03-05 04:41:31 +08:00
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diff -b tst_ncf213.tmp ref_tst_ncf213.tmp
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2010-06-03 21:24:43 +08:00
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echo "*** All ncgen and ncdump extra test output for netCDF-4 format passed!"
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exit 0
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Codify cross-platform file paths
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc. These platforms differ
significantly in the kind of file paths that they accept. So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.
A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.
The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.
The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.
As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.
In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.
Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
tests to work under windows using shell scripts; the args do
not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
PR https://github.com/Unidata/netcdf-c/pull/1794,
HDF5 changed its Windows file path handling.
2021-03-05 04:41:31 +08:00
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