Commit Graph

105 Commits

Author SHA1 Message Date
Dennis Heimbigner
1a45ee025f Fix some addtional errors in NCZarr
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
2022-09-09 14:25:24 -06:00
Dennis Heimbigner
7e48f2ad7b Fix missing files 2022-09-03 14:57:48 -06:00
Dennis Heimbigner
be88b66390 Update Release Notes 2022-09-03 14:54:18 -06:00
Dennis Heimbigner
6abaab967b Fix some problems with PR https://github.com/Unidata/netcdf-c/pull/2492
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"
2022-09-03 14:21:48 -06:00
Dennis Heimbigner
57b1d9f7f8 update file permission 2022-09-03 14:21:36 -06:00
Dennis Heimbigner
231ae96c4b Add support for Zarr string type to NCZarr
* 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.
2022-08-27 20:21:13 -06:00
Ward Fisher
ba37c0af9f
Merge branch 'main' into enumdfalt.dmh 2022-07-26 15:23:40 -06:00
Magnus Ulimoen
aa394b5ebc Prevent cmake writing to source dir 2022-07-19 15:55:42 +02:00
Dennis Heimbigner
eeb215bf4e debug1 2022-07-17 14:43:59 -06:00
Dennis Heimbigner
d7e57d261a Update to default --with-plugin-dir to yes 2022-05-24 20:05:19 -06:00
Dennis Heimbigner
cad946cde4 merged 2022-05-24 19:59:36 -06:00
Dennis Heimbigner
d16a894458 conflicts 2022-05-24 14:40:54 -06:00
Ward Fisher
d8959f170b
Merge branch 'main' into install.dmh 2022-05-24 14:35:33 -06:00
Ward Fisher
c59f626219 Add missing file to EXTRA_DIST 2022-05-24 10:56:25 -06:00
Dennis Heimbigner
6ae3289701 I made a major update to this PR with the following changes:
## Overwriting
I think I solved the file overwrite problem by doing light name
mangling of the shared library names. With this change the probabilty
is very small that installing our filter wrappers in a directory will
overwrite code produced by others.

## Default Install Location
I have setup the --with-plugin-dir option default to install in
the following locations in order of preference

1. If HDF5_PLUGIN_PATH is defined (at build time remember), then the last directory in that path will be where the filter wrapper shared libraries will be installed.
2. Otherwise the default is "/usr/local/hdf5/lib/plugin" (on *nix*) or "%ALLUSERSPROFILE%\\hdf5\\lib\\plugin" for Windows or Mingw.

Currently, --with-plugin-dir is disabled by default.
I should note that even if I enable it by default, installing
netcdf-c will still not run "out of the box" because the hypothetical
naive user will not know which compressor libraries need to be
pre-installed before netcdf is installed. Nor will that user have any
way to find out what needs to be installed.
2022-05-19 22:00:40 -06:00
Dennis Heimbigner
e05f5c36a8 Merge master 2022-05-17 15:11:31 -06:00
Ward Fisher
c9727c2a65
Merge branch 'main' into distcheck.dmh 2022-05-17 13:26:58 -06:00
Ward Fisher
771b959cad
Merge branch 'main' into jsonconvention.dmh 2022-05-17 13:24:53 -06:00
Ward Fisher
375e5adfe4
Merge branch 'main' into alwaysxarray.dmh 2022-05-17 13:23:19 -06:00
Dennis Heimbigner
7b09290a3a Improve filter installation process to avoid use of an extra shell script
re: https://github.com/Unidata/netcdf-c/issues/2338
re: https://github.com/Unidata/netcdf-c/issues/2294

In issue https://github.com/Unidata/netcdf-c/issues/2338,
Ed Hartnett suggested a better way to install filters to a user
defined location -- for Automake, anyway.

This PR implements that suggestion. It turns out to be more
complicated than it appears, so there are fair number of changes;
mostly to shell scripts. Most of the change is in plugins/Makefile.am.

NOTE: this PR still does NOT address the use of HDF5_PLUGIN_PATH
as the default; this turns out to be complex when dealing with NCZarr.
So this will be addressed in a subsequent post 4.9.0 PR.

## Misc. Changes
1. Record the occurrences of incomplete codecs in libnczarr so that
   they can be included in _Codecs attribute correctly. This allows
   users to see what missing filters are referenced in the Zarr file.
   Primarily affects libnczarr/zfilter.[ch]. Also required creating a
   new no-effect filter: H5Zunknown.c.
2. Move the unknown filter test to a separate test file.
3. Incorporates PR https://github.com/Unidata/netcdf-c/pull/2343
2022-05-14 16:05:48 -06:00
Dennis Heimbigner
5b400442ff Merge branch 'master' into jsonconvention.dmh 2022-05-09 12:43:52 -06:00
Dennis Heimbigner
53890fd3a0 Fix distcheck problems
re: https://github.com/Unidata/netcdf-c/issues/2342
This PR replaces PR https://github.com/Unidata/netcdf-c/pull/2342

This PR extends the distcheck corrections in PR
https://github.com/Unidata/netcdf-c/pull/2342.  That original PR
exposed some errors in the file naming in the plugins and
nczarr_test directories.  This PR corrects those problems and
should be used instead of https://github.com/Unidata/netcdf-c/pull/2342

Ed Hartnett's suggestion about how to install the plugins in the
user specified directory will be addressed in a subsequent PR.
2022-05-09 12:10:53 -06:00
Dennis Heimbigner
444024a7be Merge branch 'master' into jsonconvention.dmh 2022-05-01 13:16:58 -06:00
Dennis Heimbigner
909884ffb3 cleanup 2022-04-30 21:54:00 -06:00
Dennis Heimbigner
f897b458ea Fix szip handling 2022-04-30 19:06:01 -06:00
Dennis Heimbigner
126b3f9423 Support installation of filters into user-specified location
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.
2022-04-29 14:31:55 -06:00
Edward Hartnett
336b7d7222 turning off tests that depend on ncpathcvt when --disable-utilities is used 2022-04-09 13:28:01 -06:00
Dennis Heimbigner
9f78be8bb8 Allow the read/write of JSON-valued Zarr attributes.
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.
2022-04-06 18:22:59 -06:00
Ward Fisher
127c139618
Merge pull request #2263 from wkliao/vpath
vpath build: use top_srcdir
2022-04-05 16:57:27 -06:00
Ward Fisher
3446aa0c13 Merge branch 'winutf8.dmh' of https://github.com/DennisHeimbigner/netcdf-c into gh2222.wif 2022-04-05 10:46:22 -06:00
wkliao
15c75bf5d3 vpath build: use top_srcdir 2022-03-27 17:37:43 -05:00
Dennis Heimbigner
a5cae51efc Turn on the xarray convention for NCZarr format
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.
2022-03-23 19:28:06 -06:00
Dennis Heimbigner
3ffe7be446 Enhance/Fix filter support
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.
2022-03-14 12:39:37 -06:00
Ward Fisher
7c113cfae4 Merge branch 'h5align.dmh' of https://github.com/DennisHeimbigner/netcdf-c into gh2206.wif 2022-03-01 09:49:13 -08:00
Dennis Heimbigner
9b7202bf06 Explicitly disallow variable length type compression
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
2022-02-19 16:47:31 -07:00
Dennis Heimbigner
36102e3c32 Improve UTF8 Support On Windows
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.
2022-02-08 20:53:30 -07:00
Ward Fisher
375beee9f1 Cleaning up make dist, it's generating tarballs that don't work with cmake. 2022-02-01 11:40:01 -07:00
Dennis Heimbigner
f3e711e2b8 Add support for setting HDF5 alignment property when creating a file
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.
2022-01-29 15:27:52 -07:00
Dennis Heimbigner
610d8ebf51 Fix conflicts with main 2022-01-28 13:12:03 -07:00
Ward Fisher
4d13f8ef7e Merge branch 'stratus.dmh' of https://github.com/DennisHeimbigner/netcdf-c into gh2152.wif 2022-01-25 11:20:20 -07:00
Ward Fisher
e2d917575d Remove stray character. 2022-01-24 15:30:01 -07:00
Dennis Heimbigner
446348ed18 Add complete bitgroom support to NCZarr
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).
2022-01-24 15:22:24 -07:00
Ward Fisher
27db0f2354 More tweaks. 2022-01-24 15:21:29 -07:00
Mark Harfouche
458fa0b8c7 Fix a few memory leaks and erroneous logic in nczarr_test/testfilter_misc 2022-01-09 14:41:35 -05:00
Dennis Heimbigner
9380790ea8 Support MSYS2/Mingw platform
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.
2021-12-23 22:18:56 -07:00
Dennis Heimbigner
c01cf995c0 Fix use of S3 with a non-aws appliances
re: https://github.com/Unidata/netcdf-c/issues/2151

The of a non-aws appliance broke during the switch to testing
against Amazon S3.
So make necessary changes to get non-aws appliances work correctly.
2021-11-25 18:26:03 -07:00
Dennis Heimbigner
53464e8963 Allow optional use of libxml2
re: https://github.com/Unidata/netcdf-c/issues/2119

H/T to [Egbert Eich](https://github.com/e4t) and [Bas Couwenberg](https://github.com/sebastic) for this PR.

It is undesirable to make netcdf be dependent on the availability
of libxml2, but it is desirable to allow its use if available.

In order to do this, a wrapper API (include/ncxml.h) was constructed
that supports either ezxml or libxml2 as the implementation.
Additionally, the xml support code was moved to a new directory
netcdf-c/libncxml.

Primary changes:
* Create a new sub-directory named netcdf-c/libncxml to hold all the xml implementation code.
* Move ezxml.c and ezxml.h to libncxml
* Create a wrapper API -- include/ncxml.h
* Create an implementation, ncxml_ezxml.c to support use of ezxml.
* Create an implementation, ncxml_xml2.c to support use of libxml2.
* Add a check for libxml2 in configure.ac and CMakeLists.txt
* Modify libdap to use the wrapper API instead of ezxml directly.

Misc. Other Changes:
* Change include/netcdf_json.h from built source to be part of the distribution.
2021-11-01 22:37:05 -06:00
Dennis Heimbigner
f6e25b695e Fix additional S3 support issues
re: https://github.com/Unidata/netcdf-c/issues/2117
re: https://github.com/Unidata/netcdf-c/issues/2119

* Modify libsrc to allow byte-range reading of netcdf-3 files in private S3 buckets; this required using the aws sdk. Also add a test case.
* The aws sdk can sometimes cause problems if the Awd::ShutdownAPI function is not called. So at optional atexit() support to ensure it is called. This is disabled for Windows.
* Add documentation to nczarr.md on how to build and use the aws sdk under windows. Currently it builds, but testing fails.
* Switch testing from stratus to the Unidata bucket on S3.
* Improve support for the s3: url protocol.
* Add a s3 specific utility code file: ds3util.c
* Modify NC_infermodel to attempt to read the magic number of byte-ranged files in S3.

## Misc.

* Move and rename the core S3 SDK wrapper code (libnczarr/zs3sdk.cpp) to libdispatch since it now used in libsrc as well as libnczarr.
* Add calls to nc_finalize in the utilities in case atexit is disabled.
* Add header only json parser to the distribution rather than as a built source.
2021-10-29 20:06:37 -06:00
Dennis Heimbigner
dc2ecc74ac (1) improve INI parser (2) Fix make discheck 2021-09-30 13:45:09 -06:00
Dennis Heimbigner
6b69b9c52c Significantly Improve Amazon S3 Cloud Storage Support
## S3 Related Fixes

* Add comprehensive support for specifying AWS profiles to provide access credentials.
* Parse the files "~/.aws/config" and "~/.aws/credentials to provide credentials for the HDF5 ROS3 driver and to locate default region.
* Add a function to obtain the currently active S3 credentials. The search rules are defined in docs/nczarr.md.
* Provide documentation for the new features.
* Modify the struct NCauth (in include/ncauth.h) to replace specific S3 credentials with a profile name.
* Add a unit test to test the operation of profile and credentials management.
* Add support for URLS of the form "s3://<bucket>/<key>"; this requires obtaining a default region.
* Allows the specification of profile and/or region in a URL of the form "#mode=nczarr,...&aws.region=...&aws.profile=..."

## Misc. Fixes

* Move the ezxml code to libdispatch so that it can be used both by DAP4 and nczarr.
* Modify nclist to provide a deep clone operation.
* Modify ncuri to provide a deep clone operation.
* Modify the .rc file format to allow the specification of a path to be tested when looking for an entry in the .rc file.
* Ensure that the NC_rcload function is called.
* Modify nchttp to support setting request headers.
2021-09-27 18:36:33 -06:00