This is a follow-on to pull request
````https://github.com/Unidata/netcdf-c/pull/1959````,
which fixed up type scoping.
The primary changes are to _nc\_inq\_dimid()_ and to ncdump.
The _nc\_inq\_dimid()_ function is supposed to allow the name to be
and FQN, but this apparently never got implemented. So if was modified
to support FQNs.
The ncdump program is supposed to output fully qualified dimension names
in its generated CDL file under certain conditions.
Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group
is G. For each dimension id D referenced by V, ncdump needs to determine
whether to print its name as a simple name or as a fully qualified name (FQN).
The algorithm is as follows:
1. Search up the tree of ancestor groups.
2. If one of those ancestor groups contains the dimid, then call it dimgrp.
3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true.
4. If dimgrp is defined and duplicate == false, then we do not need an fqn.
5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate.
6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid.
7. If found, then use the fqn of the first found such dimension location.
8. If not found, then fail.
Test case ncdump/test_scope.sh was modified to test the proper
operation of ncdump and _nc\_inq\_dimid()_.
Misc. Other Changes:
* Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL.
* Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
re: Github issue https://github.com/Unidata/netcdf-c/issues/1956
The function NC_compare_nc_types in libdispatch/dcopy.c uses an
incorrect algorithm to search for types. The core of this is the
function NC_rec_find_nc_type in libdispatch/dcopy.c. Currently
it searchs the current group and its subtree.
Additionally, the function NC4_inq_typeid in libsrc4/nc4internal.c
has been extended to handle fully qualified names. It was originally
designed to do this, but for some reason never completed.
The NC_rec_find_nc_type algorithm has been altered to match the
algorithm used by NC4_inq_typeid. It operates as follows.
Given a file F, group G and a type T. It searches file F2, group
G2, for another type T2 that is equivalent to T.
The search order is as follows.
1. Search G2 for a type T2 equivalent to T.
2. Search upwards in the ancestor groups of G2 for a type T2 equivalent to T.
3. Search the complete group tree of F2 in pre-order, breadth-first order to locate T2 equivalent to T.
Also add a test case to validate algorithm: ncdump/test_scope.sh.
Note, this change may cause compatibility problems, though it is
unlikely because two different equivalent type declarations in
one dataset is unlikely.
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.
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.
