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).
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.
Filter support has three goals:
1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled
Detailed usage directions are define in docs/filters.md.
For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.
This is a big change since filters affect many parts of the code.
In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.
### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.
### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.
### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
re: https://github.com/zarr-developers/zarr-specs/issues/41
After discussions with the Zarr community, it was decided to
convert to a new representation of the NCZarr meta-data extensions: version 2.
These extensions store information necessary to mapping the Zarr data model
to the netcdf-4 data model.
The basic change is to remove the NCZarr specific objects: .nczarr, .nczgroup, .nczarray, and .nczattr.
The contents of these objects is moved into the corresponding existing Zarr objects as special keys. The mapping is as follows:
* ''.nczarr'' => ''/.zgroup/_NCZARR_SUPERBLOCK_''
* ''.nczgroup => ''.zgroup/_NCZARR_GROUP_''
* ''.nczarray => ''.zarray/_NCZARR_ARRAY_''
* ''.nczattr => ''.zattr/_NCZARR_ATTR_''
Backward compatibility is maintained by looking for the object ''/.nczarr''
and if found, then assuming that the dataset is in the older version 1 format.
This compatibility only supports reading of such version 1 datasets.
Documentation and test cases are also added.
Misc. Other Changes:
1. The json parsing code was added to the general library instead of nczarr only (ncjson.c, ncjson.h).
2. Improved support for different platform paths by allowing conversion
to a single common path representation.
3. Add some new error codes.
4. Modify nccopy usage to mention the new chunking specification.
re: https://github.com/Unidata/netcdf-c/issues/2008
The fill_value key in a .zarray should have a single value,
but it currently has a value that is a 1 element array.
Fix is to pull out the single element.
This occurred because the fill_value is taken from the _FillValue attribute,
and all netcdf attributes are stored as arrays, of length 1 in this case.
In a related change, any attribute with length 1 is now stored in .zattrs
as a singleton rather than an array of length 1. This make the generated
Zarr more consistent with other Zarr implementations.
Misc. other changes:
1. Fix bug in testpathcvt caused by the way various shells handle backslash escapes.
2. Fix bug in testauth where test for MSVC is wrong.
re: github issue https://github.com/Unidata/netcdf-c/issues/1982
The problem was that the libnczarr/zsjon.c handling of strings with
embedded double quotes was wrong; a one line fix.
Also added a test case.
Misc. other changes:
1. I Discovered, en passant, that the handling of 64 bit constants
had an error that was fixed.
2. cleanup of the constant conversion code to recurse on arrays of values.
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
interoperability fixed. We were given a Zarr format dataset
stored as a directory+file tree. This dataset uses the XArray
conventions and was generated by some non-Unidata Zarr implementation.
In attempting to process it with NCZarr, several interoperability
problems were discovered and fixed. This gives us more confidence
that NCZarr -- using pure zarr -- can interoperate with other
Zarr implementations.
Specific changes:
* Add test nczarr_test/run_interop.sh
* Support attributes with single value not enclosed in JSON array tags.
* Add mode inferencing and use it in nczarr_test/run_purezarr.sh
* Reduce size of tst_err_enddef.nc because it is more than 3 GB.
The XArray implementation that uses Zarr for storage
provides a mechanism to simulate named dimensions.
It does this by adding a per-variable attribute called
_ARRAY_DIMENSIONS. This attribute contains a list of names
to be matched against the shape values of the variable.
In effect a named dimension is created with the name
_ARRAY_DIMENSIONS(i) and length shape(i) for all i
in range 0..rank(variable).
Both read and write support is provided.
This XArray support is only invoked if the mode value
of "xarray" is defined. So for example, as in this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,xarray,s3
````
Note that the "xarray" mode flag also implies mode flag "zarr", so the above
is equivalent to this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,zarr,xarray,s3
````
The primary change to implement this was to unify the handling
of dimension references in libnczarr/zsync.
A test for this and other pure-zarr features was added as
nczarr_test/run_purezarr.sh
Other changes:
* Make sure distcheck leaves no files around.
* Change the special attribute flag DIMSCALEFLAG to HIDDENATTRFLAG
to support the xarray attribute.
* Annotate the zmap implementations with feature flags such as
WRITEONCE (for zip files).
The primary change is to support the use of a zip file as a
storage format. Simultaneously the .nz4 support is made obsolete
Use of zip requires the libzip support library, so a number of
changes to the build files (Makefile.am, CMakeLists.txt) are
necessary to locate and incorporate libzip. The nczarr_tests
tests are also changed to add zip testing.
Other changes:
* Make sure distcheck leaves no files around.
* Add some functions to netcdf_aux to export some functions of libnetcdf.
* Add a new error NC_EFOUND as the complement of NC_EEMPTY.
* Add tracing support to nclog and use it in libnczarr.
* Modify the zmap interface to support the writeonce semantics of zip.
* Create a new s3util.c to support a variety of S3 auxilliary functions.
* EXTERNL'ize a number of functions so they can be used in s3util.
* Add support for the S3 ListObjects CommonPrefixes mechanism
to improve search.
* Add experimental support for running nczarr X s3 tests against
the actual Amazon S3 cloud.
Primary changes:
* Add an improved cache system to speed up performance.
* Fix NCZarr to properly handle scalar variables.
Misc. Related Changes:
* Added unit tests for extendible hash and for the generic cache.
* Add config parameter to set size of the NCZarr cache.
* Add initial performance tests but leave them unused.
* Add CRC64 support.
* Move location of ncdumpchunks utility from /ncgen to /ncdump.
* Refactor auth support.
Misc. Unrelated Changes:
* More cleanup of the S3 support
* Add support for S3 authentication in .rc files: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY.
* Remove the hashkey from the struct OBJHDR since it is never used.
re: https://github.com/Unidata/netcdf-c/issues/1836
Revert the internal filter code to simplify it. From the user's
point of view, the only visible changes should be:
1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h
2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter.
Internally,the dispatch table has been modified to get rid of the filter_actions
entry and associated complex structures. It has been replaced with
inq_var_filter_ids and inq_var_filter_info entries and the dispatch table
version has been bumped to 3. Corresponding NOOP and NOTNC4 functions
were added to libdispatch/dnotnc4.c. Also, the filter_action entries
in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2,
etc). This should only impact UDF users.
In the process, it became clear that the form of the filters
field in NC_VAR_INFO_T was format dependent, so I converted it to
be of type void* and pushed its management into the various dispatch
code bases. Specifically libhdf5 and libnczarr now manage the filters
field in their own way.
The auxilliary functions for parsing textual filter specifications
were moved to netcdf_aux.h and were renamed to the following:
* ncaux_h5filterspec_parse
* ncaux_h5filterspec_parselist
* ncaux_h5filterspec_free
* ncaux_h5filter_fix8
Misc. Other Changes:
1. Document NUG/filters.md updated to reflect the changes above.
2. All the old data types (structs and enums)
used by filter_actions actions were deleted.
The exception is the NC_H5_Filterspec because it is needed
by ncaux_h5filterspec_parselist.
3. Clientside filters were removed -- another enhancement
for which no-one ever asked.
4. The ability to remove filters was itself removed.
5. Some functionality needed by nczarr was moved from libhdf5
to libsrc4 e.g. nc4_find_default_chunksizes
6. All the filterx code was removed
7. ncfilter.h and nc4filter.c no longer used
Misc. Unrelated Changes:
1. The nczarr_test makefile clean was leaving some directories; so
add clean-local to take care of them.
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.
