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.
## 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.
The thredds-test server now has some password protected datasets
that can be used to test DAP2 authorization support.
The general location is
````
https://thredds.ucar.edu/thredds/tdscapabilities/authTest.html
````
and specifically:
````
https://thredds.ucar.edu/thredds/dodsC/test3/testData.nc.html
````
This PR replaces old testcases with ncdap_test/testauth.sh.
This testcase allows us to test use of the .dodsrc file and .netrc file
and embedded user+pwd.
As part of this, I had to create a program (ncdap_test/pathcvt.c)
that is essentially the equivalent to cygpath. Given a path in
windows, unix, msys or cygwin format, it converts it to the
equivalent format in one of those four cases. So it can be used
to convert a cygwin path to a windows path, for example. This is
needed in testpathcvt and testauth to make sure that the paths
in .daprc (e.g. the reference to .netrc) are of the proper
format.
Misc. Other Changes:
1. Fix some memory leaks in libdap2
2. Setting the env variable CURLOPT_VERBOSE allows tracking of curl
operations.
3. Make tst_charvlenbug be conditional on NC_VLEN_NOTEST.
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: 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
re: Issue
The netcdf dispatch table version was defined in several places.
Modify to only require defining it in CMakeLists.txt and configure.ac.
Fix entailed the following changes:
* Up the NC_DISPATCH_VERSION from 2 to 3 in configure.ac and CMakeLists.txt
* Create include/netcdf_dispatch.h.in and use it to configure include/netcdf_dispatch.h
* For CMAKE, make it search CMAKE_CURRENT_BINARY_DIR so code can locate the configured netcdf_dispatch.h
* Add entry to config.h.cmake.in for NC_DISPATCH_VERSION
* Move NCerror from include/ncdispatch.h to libdap2/nccomon.h
* Fix an API problem re nchttp.h
* Fix a conversion warning in libdispatch/dinfermodel.c
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 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/1854
Apparently some older Arm processors will fail if asked to
read a 64 bit value from memory if not on an 8 byte boundary.
The primary problem is in reading counter values in the dap4 stream.
So if the Arm processor is detected, then memcpy the value
to an aligned 64 bit value before using it.
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.
As it was, nccopy -c dim/x was sometimes being ignored. So
modify nccopy to properly take into account. This also required
a change to the nczarr code because it was not applying default
chunking in the same way as libhdf5.
Modify ncdump/tst_nccopy4.sh to test this feature properly.
Also add a similar test to nczarr_test.
Additionally, fix some other things that were causing Visual
Studio builds with testing to not work.
* fix curl testing under CMake to properly handle case
where DAP is disabled, but byterange support is enabled.
* properly test and/or define uintptr_t
* Convert _O_XXX to O_XXX flags used by open();
disengagement of enable-netcdf4 from enable-hdf5.
That is, with the advent of nczarr, it is possible
to turn off hdf5 but still need netcdf-4 enabled
because nczarr uses libsrc4, but not libhdf5.
This change involves a bunch of things:
1. Modify configure.ac and CMakelist to make enable_hdf5
control if hdf5 support is provided. For back compatibility,
disable-netcdf4 is treated as disable-hdf5. But internally,
netcdf4 support is controlled only by the enabling of formats
that require it.
2. In support of #1, modify .travis.yml to use enable/disable-hdf5
instead of enable/disable-netcdf4.
3. test_common.in is modified to track selected features,
including enable-hdf5 and enable-s3-tests. This is used in
selected tests that mix netcdf-3 and netcdf4 tests.
4. The conflation of USE_HDF5 and USE_NETCDF4 is common in
code, tests, and build files, so all of those had to be weeded out.
5. It turns out that some of the NC4_dim functions really are HDF5 specific,
but are not treated as such. So they are moved from nc4dim.c to
hdf5dim.c or hdf5dispatch.c
6. Some generic functions in libhdf5 can be (and were) moved to libsrc4.
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.
The current ncgen does not properly handle very large
data sections. Apparently this is very uncommon because
it was only discovered in testing the new zarr code.
The fix required a new approach to processing data sections.
Unfortunately, the resulting ncgen is slower than before
but at least it is, I think, now correct.
The added test cases are in libnczarr, and so will
not show up until that is incorporated into master.
Note also that fortran code generation changed, but
has not been tested here.
Misc. Changes
1. Cleanup error handling in ncgen -lc and -lb output
2. Cleanup Makefiles for ncgen to remove unused code
3. Added a program, ncgen/ncdumpchunks, to print
the data for a .nc file on a per-chunk format.
4. Made the XGetOpt change in PR https://github.com/Unidata/netcdf-c/pull/1694
for ncdump/ncvalidator
re: Github issue https://github.com/Unidata/netcdf-c/issues/1713
If nc_def_var_filter or nc_def_var_deflate or nc_def_var_szip is
called multiple times with the same filter id, but possibly with
different sets of parameters, then the first invocation is
sticky and later invocations are ignored. The desired behavior
is to have the last invocation be used.
This PR implements that desired behavior, with some special
cases. If you call nc_def_var_deflate multiple times, then the
last invocation rule applies with respect to deflate. However,
the shuffle filter, if enabled, is always applied just before
applying deflate.
Misc unrelated changes:
1. Make client-side filters be disabled by default
2. Fix the definition of uintptr_t and use in oc2 and libdap4
3. Add some test cases
4. modify filter order tests to use plugin filters rather
than client-side filters
re: https://github.com/Unidata/netcdf-c/issues/1693
1. Add functions to libdispatch/dnotnc4.c to support
dispatch table operations that should work for any
dispatch table, even if they do not do anything.
Functions such as nc_inq_var_filter.
2. Modify selected dispatch tables to utilize
the noop functions.
3. Extend nc_test/tst_formats.c to test.
This is an extension of Ed's work to do this for
chunking and deflate and szip. See PRs
https://github.com/Unidata/netcdf-c/pull/1697
and
https://github.com/Unidata/netcdf-c/pull/1692
As a side effect, elide libdispatch/dnotnc3.c since
it is no longer used.
re: https://github.com/Unidata/netcdf-c/issues/1684
re: e-support VZL-904142
Two issues:
1. As of libcurl 7.66, the semantics of CURLOPT_SSL_VERIFYHOST
changed so that the non-zero values affects certificate processing.
2. The current library was forcing the values of VERIFYPEER
and VERIFYHOST to zero instead of leaving them to the default values.
Solution was first to leave the defaults in place for VERIFYPEER and VERIFYHOST
as long as they are not set in .ocrc/.dodsrc file.
Second, the value of HTTP.SSL.VERIFYPEER or HTTP.SSL.VERIFYHOST
as set in .ocrc/.dodrc is used to set the corresponding CURLOPT flags.
So for example, adding
> HTTP.SSL.VERIFYHOST=2
will set the value of CURLOPT_SSL_VERIFYHOST to 2, the default.
Using
> HTTP.SSL.VERIFYHOST=0
will set the value of CURLOPT_SSL_VERIFYHOST to 0, which disables it.
Similarly for VERIFYPEER.
Finally the semantics of HTTP.SSL.VALIDATE is now equivalent to
> HTTP.SSL.VERIFYPEER=1
> HTTP.SSL.VERIFYHOST=2
re: https://github.com/Unidata/netcdf-c/issues/1584
Support has been added for multiple filters per variable. This
affects a number of components in netcdf. The new APIs are
documented in NUG/filters.md.
The primary changes are:
* A set of new functions are provided (see __include/netcdf_filter.h__).
- Obtain a list of the filters associated with a variable
- Obtain the parameters for a specific filter.
* The existing __nc_inq_var_filter__ function now returns info
about the first defined filter.
* The utilities (ncgen, ncdump, and nccopy) now support
an extended format for specifying a sequence of filters.
The general form is __<filter>|<filter>..._.
* The ncdump **_Filter** attribute now dumps a list of all the
filters associated with a variable using the above new format.
* Filter specifications can now use a filter name instead of number
for filters known to the netcdf library, which in turn is taken
from the HDF5 filter registration page.
* New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter
is returned if an attempt is made to access an unknown filter.
* Internally, the dispatch table has been extended to add a function
to handle all of the filter functions.
* New, filter-related, tests were added to nc_test4.
* A new plugin was added to the plugins directory to help with testing.
Notes:
1. The shuffle and fletcher32 filters are not part of the multifilter system.
Misc. changes:
1. A debug module was added to libhdf5 to help catch error locations.
I see that there is no way to set CURLOPT_CONNECTTIMEOUT,
but there is support for CURLOPT_TIMEOUT.
So, accept the line 'HTTP.CONNECTTIMEOUT'
in .rc file to allow user to set CURLOPT_CONNECTTIMEOUT.
Some versions of some servers are returning malformed responses.
Make the library either handle them or gracefully fail.
The three server errors "fixed" here are as follows.
1. The attribute _NCProperties sometimes has a trailing nul character
in its value. Soln is to elide the nul(s).
2. Sometimes a DAP response has no data part, only a DMR.
Soln is to detect and return an error code instead of crashing.
3. Sometimes a server returns a redirection, but our current
openmagic() function was not following the redirect. Soln
is to follow redirects.
Also because of #2, I am temporarily making --disable-dap-remote-tests
be the default.
* For URL paths, the new approach essentially centralizes all information
in the URL into the "#mode=" fragment key and uses that value
to determine the dispatcher for (most) URLs.
* The new approach has the following steps:
1. canonicalize the path if it is a URL.
2. use the mode= fragment key to determine the dispatcher
3. if dispatcher still not determined, then use the mode flags
argument to nc_open/nc_create to determine the dispatcher.
4. if the path points to something readable, attempt to read the
magic number at the front, and use that to determine the dispatcher.
this case may override all previous cases.
* Misc changes.
1. Update documentation
2. Moved some unit tests from libdispatch to unit_test directory.
3. Fixed use of wrong #ifdef macro in test_filter_reg.c
[I think this may fix an previously reported esupport query].
Partially address: https://github.com/Unidata/netcdf-c/issues/1056
Currently, some of the entries in the dispatch table
are conditional'd on USE_NETCDF4.
As a step in upgrading the dispatch table for use
with user-defined tables, we remove that conditional.
This means that all dispatch tables must implement the
netcdf-4 specific functions even if only to make them
return NC_ENOTNC4. To simplify this, a set of default
functions are defined in libdispatch/dnotnc4.c to provide this
behavior. The file libdispatch/dnotnc3.c is also relevant to
this.
The primary fix is to modify the various dispatch tables to
remove the conditional and use the functions in
libdispatch/dnotnc4.c as appropriate. In practice, all of the
existing tables are prepared to handle this, so the only
real change is to remove the conditionals.
Misc. Unrelated fixes
1. Fix some annoying warnings in ncvalidator.
Notes:
1. This has not been tested with either pnetcdf or hdf4 enabled.
When those are enabled, it is possible that there are still
some conditionals that need to be fixed.
re: https://github.com/Unidata/netcdf-c/issues/1388
1. Centralize calls to curl_global_init and curl_global_cleanup
to libdispatch/ddispatch.c
2. Make the above calls if options require curl: currently
any of DAP2, DAP4, or byterange.
3. Side issue: Fix obscure bug in mmapio.c involving non-persistent mmap.
re: https://github.com/Unidata/netcdf-c/issues/1373 (partial)
* Mark some global constants be const to indicate to make them easier to track.
* Hide direct access to the ncrc_globalstate behind a function call.
* Convert dispatch tables to constants (except the user defined ones)
This has some consequences in terms of function arguments needing to be marked
as const also.
* Remove some no longer needed global fields
* Aggregate all the globals in nclog.c
* Uniformly replace nc_sizevector{0,1} with NC_coord_{zero,one}
* Uniformly replace nc_ptrdffvector1 with NC_stride_one
* Remove some obsolete code
re: https://github.com/Unidata/thredds/issues/1224
[note that this is an issue in thredds, but the fix is in netcdf-c]
A thredds server can encode a netcdf-4 file into DAP2
by flattening names to include the containing group path,
where the group names are separated by '/'.
But the '/' is prohibited in netcdf names even if escaped
(a decision before my time).
So, if the netcdf-c/libdap2 code encounters a DAP2 name with '/'
characters, the '/' characters are converted to the string
%2f. Unfortunately, there is a glitch, namely that converting
the leading '/' produces a name that is still illegal. This PR
modifies the code to just drop the leading '/' character.
