re: Issue https://github.com/Unidata/netcdf-c/issues/2748
This PR fixes a number of issues and bugs.
## s3cleanup fixes
* Delete extraneous s3cleanup.sh related files.
* Remove duplicate s3cleanup.uids entries.
## Support the Google S3 API
* Add code to recognize "storage.gooleapis.com"
* Add extra code to track the kind of server being accessed: unknown, Amazon, Google.
* Add a new mode flag "gs3" (analog to "s3") to support this api.
* Modify the S3 URL code to support this case.
* Modify the listobjects result parsing because Google returns some non-standard XML elements.
* Change signature and calls for NC_s3urlrebuild.
## Handle corrupt Zarr files where shape is empty for a variable.
Modify behavior when a variable's "shape" dictionary entry.
Previously it returned an error, but now it suppresses such a variable.
This change makes it possible to read non-corrupt data from the file.
Also added a test case.
## Misc. Other Changes
* Fix the nclog level handling to suppress output by default.
* Fix de-duplicates code in ncuri.c
* Restore testing of iridl.ldeo.columbia.edu.
* Fix bug in define_vars() which did not always do a proper reclaim between variables.
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.
The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.
## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
- "size" with an integer value representing the (current) size of the dimension.
- "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.
For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.
Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.
## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
AWS Transfer Utility mechanism. This is controlled by the
```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
re: https://github.com/Unidata/netcdf-c/issues/2733
When addressing the above issue, I noticed that there was a disconnect
in NCZarr between nc_set_chunk_cache and nc_set_var_chunk cache.
Specifically, setting nc_set_chunk_cache had no impact on the per-variable cache parameters when nc_set_var_chunk_cache was not used.
So, modified the NCZarr code so that the per-variable cache parameters are set in this order (#1 is first choice):
1. The values set by nc_set_var_chunk_cache
2. The values set by nc_set_chunk_cache
3. The defaults set by configure.ac
re: PR https://github.com/Unidata/netcdf-c/pull/2716).
re: Issue https://github.com/Unidata/netcdf-c/issues/2189
The basic change is to make use of the fact that HDF5 automatically suppresses optional filters when an attempt is made to apply them to variable-length typed arrays.
This means that e.g. ncdump or nccopy will properly see meaningful data.
Note that if a filter is defined as HDF5 mandatory, then the corresponding variable will be suppressed and will be invisible to ncdump and nccopy.
This functionality is also propagated to NCZarr.
This PR makes some minor changes to PR https://github.com/Unidata/netcdf-c/pull/2716 as follows:
* Move the test for filter X variable-length from dfilter.c down into the dispatch table functions.
* Make all filters for HDF5 optional rather than mandatory so that the built-in HDF5 test for filter X variable-length will be invoked.
The test case for this was expanded to verify that the filters are defined, but suppressed.
re: PR https://github.com/Unidata/netcdf-c/pull/2655
This PR modifies the transient types PR so that all created
transient types are given a created unique name (within a
group). The form of the name is "_Anonymous<Class>NN". The class
is the user-defined type class: Enum, Compound, Opaque, or
Vlen. NN is an integer identifier to ensure uniqueness.
Additionally, this was applied to DAP/4 anonymous dimensions.
This also required some test baseline data changes.
The transient test case is modified to verify that the name exists.
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2554
re: PR https://github.com/Unidata/netcdf-c/pull/2231
re: Issue https://github.com/Unidata/netcdf-c/issues/2189
After some discussion, the issue of applying filters on variables
whose type is not fixed size, was resolved as follows:
1. A call to nc_def_var_filter will ignore such filters, but will issue a log warning.
2. Loading (from an existing file) a variable whose type is not fixed-size and which has filters, will cause the variable to be suppressed.
This PR enforces those rules.
### Misc. Other changes
* Add a test case to test the vlen change.
* Make some minor clean-ups in various cmake and automake files.
* Remove unused test
re: Issue https://github.com/Unidata/netcdf-c/issues/2685
re: PR https://github.com/Unidata/netcdf-c/pull/2179
As noted in PR https://github.com/Unidata/netcdf-c/pull/2179,
the old code did not allow for reclaiming instances of types,
nor for properly copying them. That PR provided new functions
capable of reclaiming/copying instances of arbitrary types.
However, as noted by Issue https://github.com/Unidata/netcdf-c/issues/2685, using these
most general functions resulted in a significant performance
degradation, even for common cases.
This PR attempts to mitigate the cost of using the general
reclaim/copy functions in two ways.
First, the previous functions operating at the top level by
using ncid and typeid arguments. These functions were augmented
with equivalent versions that used the netcdf-c library internal
data structures to allow direct access to needed information.
These new functions are used internally to the library.
The second mitigation involves optimizing the internal functions
by providing early tests for common cases. This avoids
unnecessary recursive function calls.
The overall result is a significant improvement in speed by a
factor of roughly twenty -- your mileage may vary. These
optimized functions are still not as fast as the original (more
limited) functions, but they are getting close. Additional optimizations are
possible. But the cost is a significant "uglification" of the
code that I deemed a step too far, at least for now.
## Misc. Changes
1. Added a test case to check the proper reclamation/copy of complex types.
2. Found and fixed some places where nc_reclaim/copy should have been used.
3. Replaced, in the netcdf-c library, (almost all) occurrences of nc_reclaim_copy with calls to NC_reclaim/copy. This plus the optimizations is the primary speed-up mechanism.
4. In DAP4, the metadata is held in a substrate in-memory file; this required some changes so that the reclaim/copy code accessed that substrate dispatcher rather than the DAP4 dispatcher.
5. Re-factored and isolated the code that computes if a type is (transitively) variable-sized or not.
6. Clean up the reclamation code in ncgen; adding the use of nc_reclaim exposed some memory problems.
## Improvements to S3 Documentation
* Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths.
* Modify *nczarr.md* to remove most of the S3 related text.
* Move the S3 text from *nczarr.md* to a new document *cloud.md*.
* Add some S3-related text to the *byterange.md* document.
Hopefully, this will make it easier for users to find the information they want.
## Rebuild NCZarr Testing
In order to avoid problems with running make check in parallel, two changes were made:
1. The *nczarr_test* test system was rebuilt. Now, for each test.
any generated files are kept in a test-specific directory, isolated
from all other test executions.
2. Similarly, since the S3 test bucket is shared, any generated S3 objects
are isolated using a test-specific key path.
## Other S3 Related Changes
* Add code to ensure that files created on S3 are reclaimed at end of testing.
* Used the bash "trap" command to ensure S3 cleanup even if the test fails.
* Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former.
* Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket.
* Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in.
* Merge partial S3 support into dhttp.c.
* Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it.
* Move some definitions from ncrc.h to ncs3sdk.h
## Other Changes
* Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
* main: (56 commits)
Fix a mismatched if,endif block label.
Update issue with make distcheck
Update dap4_test for systems without getopt
Missed unit_test
Update release notes
Fix bug in szip handling.
Update release notes
"Simplify" XGetopt usage
added fortran
documenting logging
documenting logging
documenting logging
Fix issue #2674
Update to latest main
ubuntufix1
ub1"
bad file reference
oops
Maintainer mode should only be turned on prior to minting a release.
Fix run_jsonconvention.sh to be resilient against irrelevant changes to _NCProperties.
...
These are compound or enum datatypes stored directly in the dataset
itself, and so aren't read as standalone objects during the initial
metadata gathering when the file is opened
re: Issue
The byterange handling of the following URLS fails.
### Problem 1: "https://crudata.uea.ac.uk/cru/data/temperature/HadCRUT.4.6.0.0.median.nc#mode=bytes"
It turns out that byterange in hdf5 has two possible targets: S3 and not-S3 (e.g. a thredds server or the crudata URL above). Each uses a different HDF5 Virtual File Driver (VFD).
I incorrectly set up the byterange code in libhdf5 so that it would choose one or the other of the two VFD's for any netcdf-c library build. The fix is to allow it to choose either one at run-time.
### Problem 2: "https://noaa-goes16.s3.amazonaws.com/ABI-L1b-RadF/2022/001/18/OR_ABI-L1b-RadF-M6C01_G16_s20220011800205_e20220011809513_c20220011809562.nc#mode=bytes,s3"
When given what appears to be an S3-related URL, the netcdf-c library code converts it into a canonical, so-called "path" format. In casing out the possible input URL formats, I missed the case where the host contains the bucket ("noaa-goes16"), but not the region. So the fix was to check for this case.
## Misc. Related Changes
1. Since S3 is used in more than just NCZarr, I changed the automake/cmake options to replace "--enable-nczarr-s3" with "--enable-s3", but keeping the former option as a synonym for the latter. This also entailed cleaning up libnetcdf.settings WRT S3 support
2. Added the above URLS as additional test cases
## Misc. Un-Related Changes
1. CURLOPT_PUT is deprecated in favor to CURLOPT_UPLOAD
2. Fix some minor warnings
## Open Problems
* Under Ubuntu, either libcrypto or aws-sdk-cpp has a memory leak.
re: https://github.com/Unidata/netcdf-c/issues/2614
Most of the changes are minor comment changes.
But the dispatch table for H5FD has changed, requiring changes
to H5FDhttp.c, which is derived from the HDF5 source file H5FDstdio.c.
The patch is to conditionally modify the dispatch table
to conform to the HDF5-1.14.0 version.
I was able to build and successfully test 1.14 for a reasonable
set of (non-parallel) ./configure options.
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.
re: https://github.com/Unidata/netcdf-c/issues/2159
There was error in libhdf5 that only allowed reading a single
value HDF5 fixed string. Fix to allow reading an array of such strings.
Also make sure it still works for scalars and for attributes.
Add a testcase: nc_test4/tst_fixedstring.sh.
re: Github Issue https://github.com/Unidata/netcdf-c/issues/2401
The nc_def_var_fletcher32 code in hdf5 is always setting fletcher32
when invoked.
Fix is to properly test value of the fletcher32 argument.
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.
