This change-set modifies PR https://github.com/Unidata/netcdf-c/pull/2555
to add the changes listed below. Most of these changes are required
by changes to the Java remotetest.unidata.ucar.edu server.
## DAP4 Related Changes
* Add tests *dap4_test/test_constraints.sh* and *dap4_test/test_hyrax.sh*.
* Provide explicit list of remotetest files to test.
* Cleanup local checksum computing and verification.
* Define a temporary Hyrax hack flag to deal with the way Hyrax handles checksums and add "#hyrax" fragment flag for it.
* Add a hack to get past an LGTM problem with using "http:".
* Improve debug support.
## Other Changes
* Cleanup the recipe in *docs/nczarr.md* for building *aws-sdk-cpp* library.
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.
NOTE: This PR should not be included in 4.9.1 since additional
DAP4 related PRs will be forthcoming.
This PR makes major changes to libdap4 and dap4_test driven by changes to TDS.
* Enable DAP4
* Clean up the test input files and the test baseline comparison files. This entails:
* Remove a multitude of unused test input and baseline data files; among them are dap4_test/: daptestfiles, dmrtestfiles, nctestfiles, and misctestfiles.
* Define a canonical set of test input files and record in dap4_test/cdltestfiles.
* Use the cdltestfiles to generate the .nc test inputs. This set of .nc files is then moved to the d4ts (DAP4 test server) war file in the tds repository. This set then becomes the canonical set of DAP4 test sources.
* Scrape d4ts to obtain copies of the raw streams of DAP4 encoded data. The .dmr and .dap streams are then stored in dap4_test/rawtestfiles.
* Disable some remote server tests until those servers are fixed.
* Add an option to ncdump (-XF) that forces the type of the _FillValue attribute; this is primarily to simplify testing of fill mismatch.
* Minor bug fixes to ncgen.
* Changes to libdap4:
* Replace old checksum hack with the dap4.checksum flag.
* Support the dap4.XXX controls.
* Cleanup _FillValue handling, especially var-attribute type mismatches.
* Fix enum handling based on changes to netcdf-java.
* Changes to dap4_test:
* Add getopt support to various test support programs.
* Remove unneeded shell scripts.
* Add new scripts: test_curlopt.sh
* 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.
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: 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
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.
The ncdump test set has a number of inter-test dependencies
that are not properly established in ncdump/CMakeLists.txt.
So this PR attempts to:
1. reorder the tests
2. change tests in CMakeLists.txt from build_bin_test_no_prefix to add_bin_test_no_prefix so they get executed
Plus a couple of minor bug fixes.
1. Change ENABLE_NC4 => ENABLE_HDF5 in github action.
2. fix a memory error in findtestserver.c.in
3. fix bug in ncdap_tests/tst_urls.sh
4. fix netcdf file name bug in tst_netcdf4_4.sh
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/Unidata/netcdf-c/pull/2075
The long file name fix fails when the build is manually repeated
because the source file has already been renamed. Solution is to
test if the dest file exists or not before doing the rename.
re: https://github.com/Unidata/netcdf-c/pull/2003#issuecomment-847637871
Turns out that mingw defines both _WIN32 and also defines getopt.
This means that this test:
````
#ifdef _WIN32
#include "XGetopt.h"
#endif
````
fails on this error:
````
../include/XGetopt.h:38:24: error: conflicting types for 'getopt'
````
Fix is to replace
````
#ifdef _WIN32
with
#if defined(_WIN32) && !defined(__MINGW32__)
````
re: e-support EOT-483791
* Add a new set of remote tests based on using the thredds-test server.
* Improve error reporting when server requests fail.
* Fix handing of _NCProperties attribute
re: Issue https://github.com/Unidata/netcdf-c/issues/1999
NCclosedir code is incorrect. Fix.
Note that this issue crops up when using a non-VisualStudio windows build
such as Mingw because Mingq defines dirent.h, but Visual Studio does not.
Addendum:
Fix some mingw bugs:
1. Modify XGetopt.h to be conditional on _WIN32 instead of _MSC_VER.
2. Make sure sys/stat.h is included in ncpathmgr.h
re: https://github.com/Unidata/netcdf-c/issues/1827
The issue is partly resolved by this PR. The proximate problem appears to be that the semantics of mkstemp in **nix is different than the semantics of _mktemp_s in Windows. I had thought they were the same but that is incorrect. The _mktemp_s function will only produce 26 different files and so the netcdf temp file code will fail after about that many iterations.
So, to solve this, I created my own version of mkstemp for windows that uses a random number generator. This appears to solve the reported issue. I also added the testcase ncdap_test/test_manyurls but made it conditional on --enable-dap-long-tests because it is very slow.
I did note that the provided test program now fails after some 800 iterations with a libcurl error claiming it cannot resolve the host name. My belief is that the library is just running out of resources at this point: too many open curl handles or some such. I doubt if this failure is fixable.
So bottom line is that it is really important to do nc_close when you are finished with a file.
Misc. Other Changes:
1. I took the opportunity to clean up some bad string hacks in the code. Specifically
* change all uses of strncat to strlcat
* remove old string hacks: occoncat and occopycat
2. Add heck to see if test.opendap.org is running and if not, then skip test
3. Make CYGWIN use TEMP environment variable
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.
re: esupport 31942
* Add a new set of remote tests based on using the opendap hyrax server
* Re-enable --enable-dap-remote-tests as default on
* Make it possible to query the DMR separate from the DAP
so that it is possible to delay reading data until it is actually
requested. This make things like ncdump -h much more efficient.
* Fix handling of <Map>s in DMRs.
* Fix some memory leaks
