re: Issue https://github.com/Unidata/netcdf-c/issues/2502
H/T Charlie Zender
* Fix NCZarr handling of endianness value NC_ENDIAN_NATIVE. This now matches how it is handled in libhdf5
* Fix NCZarr handling of char typed attribute with value "". This now matches how it is handled in libhdf5
* Add test for various char attribute values
* Change the mapping of NC_CHAR and NC_STRING to dtype; requires changing some test files also.
* Optimize the testing for NC_ENOTBUILT in NC_open.
* Turn off debugging left on accidentally
* Fix memory leak in tst_pnetcdf.c
* Fix blosc test
re: PR https://github.com/Unidata/netcdf-c/pull/2492
re: Issue https://github.com/Unidata/netcdf-c/issues/2494
This PR fixes some problems with the pull request https://github.com/Unidata/netcdf-c/pull/2492 in response to Issue https://github.com/Unidata/netcdf-c/issues/2494.
* Found and fixed more scalar handling problems and add a test case for scalars.
* Cleanup nczarr_test/run_string.sh test
* Document *_nczarr_default_maxstrlen* and *_nczarr_maxstrlen*.
* Support both "Nan" and *Nan* as being floating point constants
for attributes. It is unclear from the Zarr V2 spec if
unquoted *Nan* is legal or not, but support for reading.
Write the quoted versions when writing an attribute. Similar
for Infinity constants.
So NCZarr supports the following constants for use in Attributes
* *Nan*, "Nan", *-Nan*, "-Nan"
* *Nanf*, "Nanf", *-Nanf*, "-Nanf"
* *Infinity*, "Infinity", *-Infinity*, "-Infinity"
* *Infinityf*, "Infinityf", *-Infinityf*, "-Infinityf"
* 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.
Add options
"--enable-external-server-tests" (automake)
"-DENABLE_EXTERNAL_SERVER_TESTS" (cmake)
to enable/disable tests that access
external URLS, where an external URL refers to some server not
directly under the control of netcdf-c.
This option defaults to off.
The reason for this PR is that external servers can be up or down
or change content without any warning to us, thus causing some
of our tests to fail.
Additionally. and recently, the thredds-test server was shut
down and some of our tests used it. So these tests are disabled
until a suitable replacement server is available.
## Misc. Fixes
* Bump the depth of trace support in nclog.c to avoid overflow
re: https://github.com/Unidata/netcdf-c/issues/2159
There was error in libhdf5 that only allowed reading a single
value HDF5 fixed string. Fix to allow reading an array of such strings.
Also make sure it still works for scalars and for attributes.
Add a testcase: nc_test4/tst_fixedstring.sh.
re: Issue https://github.com/Unidata/netcdf-c/issues/2458
The above Github Issue revealed some bugs in the file netcdf-c/plugins/H5Zblosc.c. Fixed and added a testcase. Also discovered that the Blosc LZ sub-compressors do not work well with small datasets.
Misc. Other Change(s): I noticed that the file "dap4_test/baselinethredds/GOES16_CONUS_20170821_020218_0.47_1km_33.3N_91.4W.nc4.thredds" is still causing tar errors during "make distcheck", so I made some changes to do rename at test-time.
re: Issue https://github.com/Unidata/netcdf-c/issues/2419
There are effectively two json subsystems in netcdf-c.
1. ncjson.[ch] in libnetcdf
2. netcdf_json.h for use by plugins so they can be built without need
for libnetcdf.
The netcdf_json.h file is constructed from the concatenation of
ncjson.h plus ncjson.c. It turned out that in doing this, I was
leaving some symbols externally visible so that if, for some
reason, a plugin was built and needed libnetcdf, then symbol
conflicts arose.
The solution is to prefix the declarations in ncjson.[ch] with a
macro (OPTSTATIC) that can be resolved to either nothing or to
"static". Then in netcdf_json.h, it resolves to "static" and
prevents the symbol conflicts.
Note that netcdf_json.h is constructed once in
netcdf-c/include/Makefile.am with the rule named
"makepluginjson". This means that it is included in the
distribution. However, this also means that if ncjson.[ch] is
changed, then it is necessary to invoke makepluginjson
explicitly to rebuild netcdf_json.h
re: Issue https://github.com/Unidata/netcdf-c/issues/2429
The CMake tests for -DPLUGIN_INSTALL_DIR only accepted
"on" or "off" as boolean values. So extend to accept e.g.
-DPLUGIN_INSTALL_DIR=yes or -DPLUGIN_INSTALL_DIR=1, etc.
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.
