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: 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: 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
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
* Replace wholevar with more useful wholechunk optimization
* Add optimization to read multiple values at one time
* Replace NCDEFAULT_get/put_vars with native nczarr versions.
* Clarify chunk projection computations
* zdebdispatch.h
* Add more chunking test cases and re-enable run_chunkcases
* If !szip, then suppress deflate interference test
* Make H5Znoop(1) filter produce more information
* cleanup bzlib.c API
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: GH Issue https://github.com/Unidata/netcdf-c/issues/1900
Apparently the clock_gettime() function is not always available.
It is used in unit_test/tst_exhash.c and unit_test/tst_xcache.c.
To solve this, a number of things were changed:
* Move the timing code to a new file unit_tests/timer_utils.[ch]
* Modify the timing code to choose one of several timing methods
depending on availability. The prioritized order is as follows:
1. If Windows, use the QueryPerformanceCounter mechanism else
2. Use clock_gettime if available else
3. Use gettimeofday if available else
4. Use getrusage if available
Note that the resolution of 3 and 4 is less than 1 or 2.
Misc. Other Changes:
* Move the test in CMakeLists.txt that disables unit tests for WIN32 to unit_test/CMakeLists.txt since some unit tests actually work under Visual Studio.
* Fix some of the unit tests to work under visual studio
* Fix problem with using remove() in zmap_nzf.c
* Remove some warning about use of EXTERNL
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: Partly addresses issue https://github.com/Unidata/netcdf-c/issues/1712.
1. Turn on Hyrax Hack to accept Hyrax style attribute containers.
2. Support Url type as alias for String.
3. Accept the special attribute, "__DAP4_Checksum_CRC32",
to control per-variable checksums.
4. Make _DAP4_xxx attributes be reserved and only accessible
by name (ala _SuperBlock attribute).
5. Fix handling of checksums. There is a hack in the code
that uses an extra flag in the chunk header to indicate
that all variables have checksums. This violates the spec
and will be removed once it is possible to regenerate the
test cases.
Note that checksumming with the Hyrax test server has not
been tested. This, along with some other probable inconsistencies,
needs fixing when OPeNDAP and Unidata can agree on the proper
specification. Testing will be included.
re: https://github.com/Unidata/netcdf-c/issues/1451
The situation with the various DAP (and other) remote test
servers is currently in a state of flux. For example, Unidata
admin is planning to forcibly shift the remote test server to
remotetest.unidata.ucar.edu soon. In addition, the server
test.opendap.org has shown some recent instability.
The result is that various DAP (and byterange) tests can fail
unexpectedly. This is an irritant to users and reveals nothing
about test sucess or failure.
Solve by modifying tests to report server inaccessibility and
otherwise pretend to succeed.
This puts an onus on Unidata to detect such server failures, but
will not cause users to see spurious failures. [Note. Do similar
fix for netcdf-java]. The check is:
1. export SETX=1 to cause all the shell scripts to trace
2. search the log files for the phrase "WARNING" (in upper case)
and see if it is complaining about not finding a server.
Misc. Changes
-------------
1. Added a pingurl program to see if a server was up.
2. modified some test case url targets
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
re: github issue https://github.com/Unidata/netcdf-c/issues/1111
One of the less common use cases for the in-memory feature is
apparently failing with HDF5-1.10.x. The fix is complicated and
requires significant changes to libhdf5/nc4memcb.c. The current
setup is detailed in the file docs/inmeminternal.dox.
Additionally, it was discovered that the program
nc_test/tst_inmemory.c, which is invoked by
nc_test/run_inmemory.sh, actually was failing because of the
above problem. But the failure is not detected since the script
does not return non-zero value.
Other Changes:
1. Fix nc_test_tst_inmemory to return errors correctly.
2. Make ncdap_tests/findtestserver.c and dap4_tests/findtestserver4.c
be generated from ncdap_test/findtestserver.c.in.
3. Make LOG() print output to stderr instead of stdout to
avoid contaminating e.g. ncdump output.
4. Modify the handling of NC_INMEMORY and NC_DISKLESS flags
to properly handle that NC_DISKLESS => NC_INMEMORY. This
affects a number of code pieces, especially memio.c.
Add the ability to set some additional curlopt values via .daprc (aka .dodsrc).
This effects both DAP2 and DAP4 protocols.
Related issues:
[1] re: esupport: KOZ-821332
[2] re: github issue https://github.com/Unidata/netcdf4-python/issues/836
[3] re: github issue https://github.com/Unidata/netcdf-c/issues/1074
1. CURLOPT_BUFFERSIZE: Relevant to [1]. Allow user to set the read/write
buffersizes used by curl.
This is done by adding the following to .daprc (aka .dodsrc):
HTTP.READ.BUFFERSIZE=n
where n is the buffersize in bytes. There is a built-in (to curl)
limit of 512k for this value.
2. CURLOPT_TCP_KEEPALIVE (and CURLOPT_TCP_KEEPIDLE and CURLOPT_TCP_KEEPINTVL):
Relevant (maybe) to [2] and [3]. Allow the user to turn on KEEPALIVE
This is done by adding the following to .daprc (aka .dodsrc):
HTTP.KEEPALIVE=on|n/m
If the value is "on", then simply enable default KEEPALIVE. If the value
is n/m, then enable KEEPALIVE and set KEEPIDLE to n and KEEPINTVL to m.
So it now becomes the first default test server to try.
This also means that the dap4 remote testing is enabled.
The only issue to watch is to see if the jetstream-based
server can stay up for significant periods of time.
A uptimerobot (https://uptimerobot.com) has been set ups
to monitor this hourly, so we shall see.
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
