re: https://github.com/Unidata/netcdf-c/issues/2337
re: https://github.com/Unidata/netcdf-c/issues/2407
Add two functions to netcdf.h to allow programs to get/set
selected entries into the internal .rc tables. This should fix
the above issues by allowing HTTP.CAINFO to be set to the
certificates directory. Note that the changes should be
performed as early as possible in the program because some of
the .rc table entries may get cached internally and changing the
entry after that caching occurs may have no effect.
The new signatures are as follows:
1. Get the value of a simple .rc entry of the form "key=value".
Note that caller must free the returned value, which might be NULL.
````
char* nc_rc_get(char* const * key);
@param key table entry key
@return value if .rc table has entry of the form key=value
@return NULL if no such entry is found.
````
2. Insert/Overwrite the specified key=value pair in the .rc table.
````
int nc_rc_set(const char* key, const char* value);
@param key table entry key -- may not be NULL
@param value table entry value -- may not be NULL
@return NC_NOERR if no error
@return NC_EINVAL if error
````
Addendum:
re: https://github.com/Unidata/netcdf-c/issues/2407
Modify dhttp.c to use the .rc entry HTTP.CAINFO if defined.
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
A number of other packages that read/write Zarr insert
attributes whose value is a dictionary containing specialized
information. An example is the GDAL Driver convention (see
https://gdal.org/drivers/raster/zarr.html).
In order to handle such attributes, this PR enforces a special
convention. It applies to both pure Zarr an NCZarr format as
written by the netdf-c library.
The convention is as follows:
## Reading
Suppose an attribute is read from *.zattrs* and it has a JSON
value that is a a dictionary. In this case, the JSON dictionary
is converted to a string value. It then appears in the netcdf-c
API as if it is a character valued attribute of the same name,
and whose value is the "stringified" dictionary.
# Writing
Suppose an attribute is of type character and its *value* *looks like*
a JSON dictionary. In this case, it is parsed to JSON
and written as the value of the attribute in the NCZarr file.
Here the *value* is the concatenation of all the characters
in the attributes netcdf-c value.
The term "looks like" means that the *value*'s first character is
"{", its last value is "}", and it can be successfully parsed
by a JSON parser.
A test case, *nczarr_test/run_jsonconventions.sh* was also added.
## Misc. Unrelated Changes
1. Fix an error in nc_test4/tst_broken_files.c
2. Modify the internal JSON parser API.
3. Modify the nczarr_test/zisjson program is modified to support
this convention.
re: https://github.com/pydata/xarray/issues/6374
As a result of a discussion about Xarray (see above issue),
I decided to turn on the xarray convention for NCZarr datasets
where possible so that xarray can read a larger set of nczarr
generated datasets.
This causes the following changes:
* If the user wants to generate a pure zarr file, then the mode "zarr" must be explicitly used; it is no longer the case that "mode=xarray" or mode="noxarray"
implies "mode=zarr".
* It is still the case that "mode=noxarray" will turn off the XArray convention.
The following conditions will cause ''_ARRAY_DIMENSIONS'' to not be written.
* The variable is not in the root group,
* Any dimension referenced by the variable is not in the root group.
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.
re: https://github.com/Unidata/netcdf-c/issues/2189
Compression of a variable whose type is variable length
fails for all current filters. This is because at some point,
the compression buffer will contain pointers to data instead
of the actual data. Compression of pointers of course is meaningless.
The PR changes the behavior of nc_def_var_filter so that it will
fail with error NC_EFILTER if an attempt is made to add a filter
to a variable whose type is variable-length.
A variable is variable-length if it is of type string or VLEN
or transitively (via a compound type) contains a string or VLEN.
Also added a test case for this.
## Misc Changes
1. Turn off a number of debugging statements
re: Issue https://github.com/Unidata/netcdf-c/issues/2190
The primary purpose of this PR is to improve the utf8 support
for windows. This is persuant to a change in Windows that
supports utf8 natively (almost). The almost means that it is
still utf16 internally and the set of characters representable
by utf8 is larger than those representable by utf16.
This leaves open the question in the Issue about handling
the Windows 1252 character set.
This required the following changes:
1. Test the Windows build and major version in order to see if
native utf8 is supported.
2. If native utf8 is supported, Modify dpathmgr.c to call the 8-bit
version of the windows fopen() and open() functions.
3. In support of this, programs that use XGetOpt (Windows versions)
need to get the command line as utf8 and then parse to
arc+argv as utf8. This requires using a homegrown command line parser
named XCommandLineToArgvA.
4. Add a utility program called "acpget" that prints out the
current Windows code page and locale.
Additionally, some technical debt was cleaned up as follows:
1. Unify all the places which attempt to read all or a part
of a file into the dutil.c#NC_readfile code.
2. Similary unify all the code that creates temp files into
dutil.c#NC_mktmp code.
3. Convert almost all remaining calls to fopen() and open()
to NCfopen() and NCopen3(). This is to ensure that path management
is used consistently. This touches a number of files.
4. extern->EXTERNL as needed to get it to work under Windows.
re: https://github.com/Unidata/netcdf-c/issues/2177
re: https://github.com/Unidata/netcdf-c/pull/2178
Provide get/set functions to store global data alignment
information and apply it when a file is created.
The api is as follows:
````
int nc_set_alignment(int threshold, int alignment);
int nc_get_alignment(int* thresholdp, int* alignmentp);
````
If defined, then for every file created opened after the call to
nc_set_alignment, for every new variable added to the file, the
most recently set threshold and alignment values will be applied
to that variable.
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.
The alignment parameters are stored in the NCglobalstate object
(see below) for use as needed. Repeated calls to nc_set_alignment
will overwrite any existing values in NCglobalstate.
The alignment parameters are applied in libhdf5/hdf5create.c
and libhdf5/hdf5open.c
The set/get alignment functions are defined in libsrc4/nc4internal.c.
A test program was added as nc_test4/tst_alignment.c.
## Misc. Changes Unrelated to Alignment
* The NCRCglobalstate type was renamed to NCglobalstate to
indicate that it represented more general global state than
just .rc data. It was also moved to nc4internal.h. This led
to a large number of small changes: mostly renaming. The
global state management functions were moved to nc4internal.c.
* The global chunk cache variables have been moved into
NCglobalstate. As warranted, other global state will be moved
as well.
* Some misc. problems with the nczarr performance tests were corrected.
re: PR https://github.com/Unidata/netcdf-c/pull/2088
re: PR https://github.com/Unidata/netcdf-c/pull/2130
replaces: https://github.com/Unidata/netcdf-c/pull/2140
Changes:
* Add NCZarr-specific quantize functions to the dispatch table.
* Copy (modified) quantize code from libhdf5 to NCZarr
* Add quantize invocation to zvar.c
* Add support for _QuantizeBitgroomNumberOfSignificantDigits
and _QuantizeGranularBitgroomNumberOfSignificantDigits to ncgen.
* Modify nc_test4/tst_quantize.c to allow it to be used both for hdf5
and for nczarr.
* Make dap4 properly handle quantize functions in dispatch table.
* Add quantize attribute support to ncgen.
Other changes:
* Caught and fixed some S3 problems
* Fixed some nczarr fillvalue problems.
* Fixed some nczarr cache problems.
* Cleanup some flaws in libdispatch/dinfermodel.c
* Allow byterange requests to S3 be readable by dinfermodel.c/check_file_type
* Remove the libnczarr ztracedispatch code (big change).
