Primary Fixes:
* Add a whole variable optimization -- used in the rare case that nc_get/put_vara covers the whole of a variable and the variable has a single chunk.
* Fix chunking error when stride causes whole chunks to be skipped.
* Fix some memory leaks
* Add test cases
* Add one performance test to nczarr_test/. This uses the timer utils from unit_test: timer_utils.[ch].
* Move ncdumpchunks utility from ncdump to nczarr_test
Misc. Other Changes:
* Make check for aws libraries conditional on --enable-nczarr-s3
* Remove all but one bm tests from nczarr_test until they are working.
* Remove another dependency on HDF5 from supposedly non-HDF5 specific code; specifically hdf5_log_hdf5.
* Make the BAIL2 macro be hdf5 specific and replace elsewhere with an HDF5 independent equivalent.
* Move hdf5cache.c to libsrc4/nc4cache.c because it is used by nczarr.
* Modify unit_tests so that some of them are run even if using Windows.
* Misc. small bug fixes and refactors and memory leaks.
* Rename some conflicting tests for cmake.
* Attempted to make nc_perf work with cmake and failed.
re: https://github.com/Unidata/netcdf-c/issues/1876
and: https://github.com/Unidata/netcdf-c/pull/1835
and: https://github.com/Unidata/netcdf4-python/issues/1041
The change in PR 1835 was correct with respect to using %20 instead of '+'
for encoding blanks. However, it was a mistake to assume everything was
unencoded and then to do encoding ourselves. The problem is that
different servers do different things, with Columbia being an outlier.
So, I have added a set of client controls that can at least give
the caller some control over this. The caller can append
the following fragment to his URL to control what gets encoded before
sending it to the server. The syntax is as follows:
````
https://<host>/<path>/<query>#encode=path|query|all|none
````
The possible values:
* path -- URL encode (i.e. %xx encode) as needed in the path part of the URL.
* query -- URL encode as needed in the query part of the URL.
* all -- equivalent to ````#encode=path,query````.
* none -- do not url encode any part of the URL sent to the server; not strictly necessary, so mostly for completeness.
Note that if "encode=" is used, then before it is processed, all encoding
is turned of so that ````#encode=path```` will only encode the path
and not the query.
The default is ````#encode=query````, so the path is left untouched,
but the query is always encoded.
Internally, this required changes to pass the encode flags down into
the OC2 library.
Misc. Unrelated Changes:
* Shut up those irritating warning from putget.m4
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.
re: https://github.com/Unidata/netcdf-c/issues/1373 (partial)
* Mark some global constants be const to indicate to make them easier to track.
* Hide direct access to the ncrc_globalstate behind a function call.
* Convert dispatch tables to constants (except the user defined ones)
This has some consequences in terms of function arguments needing to be marked
as const also.
* Remove some no longer needed global fields
* Aggregate all the globals in nclog.c
* Uniformly replace nc_sizevector{0,1} with NC_coord_{zero,one}
* Uniformly replace nc_ptrdffvector1 with NC_stride_one
* Remove some obsolete code
re: https://github.com/Unidata/thredds/issues/1224
[note that this is an issue in thredds, but the fix is in netcdf-c]
A thredds server can encode a netcdf-4 file into DAP2
by flattening names to include the containing group path,
where the group names are separated by '/'.
But the '/' is prohibited in netcdf names even if escaped
(a decision before my time).
So, if the netcdf-c/libdap2 code encounters a DAP2 name with '/'
characters, the '/' characters are converted to the string
%2f. Unfortunately, there is a glitch, namely that converting
the leading '/' produces a name that is still illegal. This PR
modifies the code to just drop the leading '/' character.
re: issue https://github.com/Unidata/netcdf-c/issues/1151
Modify DAP2 and DAP4 code to handle case when _FillValue type is not
same as the parent variable type.
Specifically:
1. Define a parameter [fillmismatch] to allow this mismatch;
default is to disallow.
2. If allowed, forcibly change the type of the _FillValue to match
the parent variable.
3. If allowed Convert the values to match new type
4. Generate a log message
5. if not allowed, then fail
Implementing this required some changes to ncdap_test/dapcvt.c
Also added test cases.
Minor Unrelated Changes:
1. There were a number of warnings about e.g.
assigning a const char* to a char*. Fix these
2. In nccopy.1, replace .NP with .IP "n"
(re PR https://github.com/Unidata/netcdf-c/pull/1144)
3. fix minor error in ncdump/ocprint
strlcat provides better protection against buffer overflows.
Code is taken from the FreeBSD project source code. Specifically:
https://github.com/freebsd/freebsd/blob/master/lib/libc/string/strlcat.c
License appears to be acceptable, but needs to be checked by e.g. Debian.
Step 1:
1. Add to netcdf-c/include/ncconfigure.h to use our version
if not already available as determined by HAVE_STRLCAT in config.h.
2. Add the strlcat code to libdispatch/dstring.c
3. Turns out that strlcat was already defined in several places.
So remove it from:
ncgen3/genlib.c
ncdump/dumplib.c
3. Define strlcat extern definition in ncconfigure.h.
4. Modify following directories to use strlcat:
libdap2 libdap4 ncdap_test dap4_test
Will do others in subsequent steps.
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
The code that tests if a path is a url is
faulting when the url does not end in a slash
(e.g. http://thredds-tests.ucar.edu).
The code that tests if a path is a url is
faulting when the url does not end in a slash
(e.g. http://thredds-tests.ucar.edu).
CF-273]/HZY-708311
Solution was to do a null pointer test.
Added a test (tst_misc).
to do prefetch on either a lazy
or eager basis. Lazy means that
the prefetch does not occur
until and unless the client actually
makes a get_var request.
Also repaired a problem where
doing prefetch wrt a url that
has a constraint will prefetch
a whole variable if its constrained
size is small enough, even if the
underlying variable is too large
to warrant prefetch.
NCF-42: _Format attribute sometimes being ignored
NCF-43: Fixed unsigned long long parsing.
NCF-47: Make opendap code properly handle illegal names like "x.y" by
supressing them
NCF-49: check for uint type
NCF-50: properly handle username:pwd embedded in urls.
