re: Issue
The byterange handling of the following URLS fails.
### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes"
It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD).
I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time.
### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3"
When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case.
## Misc. Related Changes
1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support
2. Added the above URLS as additional test cases
## Misc. Un-Related Changes
1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD
2. Fix some minor warnings
## Open Problems
* Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
Warning: This PR is a follow on to PR https://github.com/Unidata/netcdf-c/pull/2555 and should not be merged until that prior PR has been merged. The changeset for this PR is a delta on the PR https://github.com/Unidata/netcdf-c/pull/2555.
This PR re-enables the use of the server *remotetest.unidata.ucar.edu/d4ts*
to test several features:
1. Show that access over the Internet to servers using the DAP4 protocol works.
2. Test that DAP4 support in the [Thredds Data Server](https://github.com/Unidata/tds) is operating correctly.
4. Test that the DAP4 support in the [netcdf-java library](https://github.com/Unidata/netcdf-java) library and the DAP4 support in the netcdf-c library are consistent and are interoperable.
The test inputs (primarily *\*.nc* files) provided in the netcdf-c library
are also used by the DAP4 Test Server (aka d4ts) to present web access to a
collection of data files accessible via the DAP4 protocol and which can be
used for testing Internet access to a working server.
To be precise, this version of d4ts is currently in unmerged branches
of the *netcdf-java* and *tds* Github repositories and so are not actually
in the main repositories *yet*. However, the *d4ts.war* file was created
from that branch and used to populate the *remotetest.unidata.ucar.edu*
server
The two other remote servers that were used in the past are *Hyrax* (OPenDAP.org)
and *thredds-test*. These will continue to remain disabled until
those servers can be fixed.
## Primary Changes
* Rebuild the *baselineremote* directory. This directory contains the validation data needed to test the remote servers.
* Re-enable using remotetest.unidata.ucar.edu as part of the DAP4 testing process.
* Fix the *dap4_test/test_remote.sh* test script to match the current available test data.
* Make some changes to libdap4 to improve the ability to catch malformed data streams [affects a lot of files in libdap4].
## Misc. Unrelated Changes
* Remove a raft of warnings, especially in nc_test4/tst_quantize.c.
* Add some additional explanatory information to the NCZarr documentation.
* Cleanup some Doxygen errors in the docs file and reorder some files.
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: 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).
re:
The current netcdf-c release has some problems with the mingw platform
on windows. Mostly they are path issues.
Changes to support mingw+msys2:
-------------------------------
* Enable option of looking into the windows registry to find
the mingw root path. In aid of proper path handling.
* Add mingw+msys as a specific platform in configure.ac and move testing
of the platform to the front so it is available early.
* Handle mingw X libncpoco (dynamic loader) properly even though
mingw does not yet support it.
* Handle mingw X plugins properly even though mingw does not yet support it.
* Alias pwd='pwd -W' to better handle paths in shell scripts.
* Plus a number of other minor compile irritations.
* Disallow the use of multiple nc_open's on the same file for windows
(and mingw) because windows does not seem to handle these properly.
Not sure why we did not catch this earlier.
* Add mountpoint info to dpathmgr.c to help support mingw.
* Cleanup dpathmgr conversions.
Known problems:
---------------
* I have not been able to get shared libraries to work, so
plugins/filters must be disabled.
* There is some kind of problem with libcurl that I have not solved,
so all uses of libcurl (currently DAP+Byterange) must be disabled.
Misc. other fixes:
------------------
* Cleanup the relationship between ENABLE_PLUGINS and various other flags
in CMakeLists.txt and configure.ac.
* Re-arrange the TESTDIRS order in Makefile.am.
* Add pseudo-breakpoint to nclog.[ch] for debugging.
* Improve the documentation of the path manager code in ncpathmgr.h
* Add better support for relative paths in dpathmgr.c
* Default the mode args to NCfopen to include "b" (binary) for windows.
* Add optional debugging output in various places.
* Make sure that everything builds with plugins disabled.
* Fix numerous (s)printf inconsistencies betweenb the format spec
and the arguments.
