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.
## 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*.
## 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.
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/zarr-developers/zarr-specs/issues/41
After discussions with the Zarr community, it was decided to
convert to a new representation of the NCZarr meta-data extensions: version 2.
These extensions store information necessary to mapping the Zarr data model
to the netcdf-4 data model.
The basic change is to remove the NCZarr specific objects: .nczarr, .nczgroup, .nczarray, and .nczattr.
The contents of these objects is moved into the corresponding existing Zarr objects as special keys. The mapping is as follows:
* ''.nczarr'' => ''/.zgroup/_NCZARR_SUPERBLOCK_''
* ''.nczgroup => ''.zgroup/_NCZARR_GROUP_''
* ''.nczarray => ''.zarray/_NCZARR_ARRAY_''
* ''.nczattr => ''.zattr/_NCZARR_ATTR_''
Backward compatibility is maintained by looking for the object ''/.nczarr''
and if found, then assuming that the dataset is in the older version 1 format.
This compatibility only supports reading of such version 1 datasets.
Documentation and test cases are also added.
Misc. Other Changes:
1. The json parsing code was added to the general library instead of nczarr only (ncjson.c, ncjson.h).
2. Improved support for different platform paths by allowing conversion
to a single common path representation.
3. Add some new error codes.
4. Modify nccopy usage to mention the new chunking specification.
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc. These platforms differ
significantly in the kind of file paths that they accept. So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.
A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.
The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.
The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.
As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.
In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.
Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
tests to work under windows using shell scripts; the args do
not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
PR https://github.com/Unidata/netcdf-c/pull/1794,
HDF5 changed its Windows file path handling.
The XArray implementation that uses Zarr for storage
provides a mechanism to simulate named dimensions.
It does this by adding a per-variable attribute called
_ARRAY_DIMENSIONS. This attribute contains a list of names
to be matched against the shape values of the variable.
In effect a named dimension is created with the name
_ARRAY_DIMENSIONS(i) and length shape(i) for all i
in range 0..rank(variable).
Both read and write support is provided.
This XArray support is only invoked if the mode value
of "xarray" is defined. So for example, as in this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,xarray,s3
````
Note that the "xarray" mode flag also implies mode flag "zarr", so the above
is equivalent to this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,zarr,xarray,s3
````
The primary change to implement this was to unify the handling
of dimension references in libnczarr/zsync.
A test for this and other pure-zarr features was added as
nczarr_test/run_purezarr.sh
Other changes:
* Make sure distcheck leaves no files around.
* Change the special attribute flag DIMSCALEFLAG to HIDDENATTRFLAG
to support the xarray attribute.
* Annotate the zmap implementations with feature flags such as
WRITEONCE (for zip files).
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.
The primary fix is to improve CMake build support.
Specific changes include:
* CMake: Provide a better soln to locating the AWS SDK
libraries; the new way is the preferred method as described in
the aws-cpp-sdk documentation.
* CMake (and Automake): allow -DENABLE_S3_SDK (default off) to suppress
looking for AWS libraries.
* CMake: add the complete set of nczarr tests
* CMake: add EXTERNL as needed to various .h files.
* Improve support for windows drive letters in paths.
* Add nczarr and s3 flags to nc-config
* For VisualStudio X nczarr, cleanup the NAN+INFINITY handling
* Convert _MSC_VER -> _WIN32 and vice versa as needed
* NCZarr - support multiple platform paths including windows, cygwin.
mingw, etc.
* NCZarr - sort the test outputs because different platforms
produce directory contents in different orders.
One big change concerns netcdf-c/CMakeLists.txt and netcdf-c/configure.ac.
In the current versions, it was the case that --disable-hdf5
disabled netcdf-4 (libsrc4). With nczarr, this can no longer
be the case because nczarr requires libsrc4 even if libhdf5
is disabled. So, I modified the above files to move the
format options (HDF5, NCZarr, HDF4, etc) to a single place
near the front of the files. Now it is the case that:
* Enabling any of the formats that require libsrc4
also does an implicit --enable-netcdf4.
* --disable-netcdf4 | --disable-netcdf-4 now becomes
and alias for --disable-hdf5.
There are probably some bugs in this change in terms of
dependencies between format options.
Problems:
* CMake S3 support is still not working for Visual Studio
* A recent issue points out that there is work to do on handling
UTF8 filenames, but that will be addressed in a separate fix.
Notes:
* Consider converting all of our includes/.h files to use 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.
