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
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: 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.
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: issue https://github.com/Unidata/netcdf-c/issues/1251
Assume that you have the URL to a remote dataset
which is a normal netcdf-3 or netcdf-4 file.
This PR allows the netcdf-c to read that dataset's
contents as a netcdf file using HTTP byte ranges
if the remote server supports byte-range access.
Originally, this PR was set up to access Amazon S3 objects,
but it can also access other remote datasets such as those
provided by a Thredds server via the HTTPServer access protocol.
It may also work for other kinds of servers.
Note that this is not intended as a true production
capability because, as is known, this kind of access to
can be quite slow. In addition, the byte-range IO drivers
do not currently do any sort of optimization or caching.
An additional goal here is to gain some experience with
the Amazon S3 REST protocol.
This architecture and its use documented in
the file docs/byterange.dox.
There are currently two test cases:
1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle
for a remote netcdf-3 file and a remote netcdf-4 file.
2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote
datasets.
This PR also incorporates significantly changed model inference code
(see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259).
1. It centralizes the code that infers the dispatcher.
2. It adds support for byte-range URLs
Other changes:
1. NC_HDF5_finalize was not being properly called by nc_finalize().
2. Fix minor bug in ncgen3.l
3. fix memory leak in nc4info.c
4. add code to walk the .daprc triples and to replace protocol=
fragment tag with a more general mode= tag.
Final Note:
Th inference code is still way too complicated. We need to move
to the validfile() model used by netcdf Java, where each
dispatcher is asked if it can process the file. This decentralizes
the inference code. This will be done after all the major new
dispatchers (PIO, Zarr, etc) have been implemented.
In turn that caused some problems elsewhere because some files
did not include netcdf.h preceding netcdf_mem.h. Specifically,
building under visual studio fails.
So fix those cases that I can find. May need to
add more later.
The `typedef struct NC_Dispatch NC_Dispatch;` declaration is in both netcdf.h and in ncdispatch.h. Even though it is the same declaration, there are compilers which see this as an error and the compilation will fail:
```
In file included from /netcdf-c/include/nc4dispatch.h:15,
from /netcdf-c/libhdf5/hdf5attr.c:16:
/netcdf-c/include/ncdispatch.h:111: error: redefinition of typedef `NC_Dispatch`
/netcdf/netcdf-c/include/netcdf.h:515: note: previous declaration of `NC_Dispatch` was here
```
This is with a very old version of gcc-4.4.7 which isn't used much anymore, but this is the default gcc compiler on RHEL6 so it might be worth fixing.
and https://github.com/Unidata/netcdf-c/issues/708
Expand the NC_INMEMORY capabilities to support writing and accessing
the final modified memory.
Three new functions have been added:
nc_open_memio, nc_create_mem, and nc_close_memio.
The following new capabilities were added.
1. nc_open_memio() allows the NC_WRITE mode flag
so a chunk of memory can be passed in and be modified
2. nc_create_mem() allows the NC_INMEMORY flag to be set
to cause the created file to be kept in memory.
3. nc_close_mem() allows the final in-memory contents to be
retrieved at the time the file is closed.
4. A special flag, NC_MEMIO_LOCK, is provided to ensure that
the provided memory will not be freed or reallocated.
Note the following.
1. If nc_open_memio() is called with NC_WRITE, and NC_MEMIO_LOCK is not set,
then the netcdf-c library will take control of the incoming memory.
This means that the original memory block should not be freed
but the block returned by nc_close_mem() must be freed.
2. If nc_open_memio() is called with NC_WRITE, and NC_MEMIO_LOCK is set,
then modifications to the original memory may fail if the space available
is insufficient.
Documentation is provided in the file docs/inmemory.md.
A test case is provided: nc_test/tst_inmemory.c driven by
nc_test/run_inmemory.sh
WARNING: changes were made to the dispatch table for
the close entry. From int (*close)(int) to int (*close)(int,void*).
re pull request https://github.com/Unidata/netcdf-c/pull/405
re pull request https://github.com/Unidata/netcdf-c/pull/446
Notes:
1. This branch is a cleanup of the magic.dmh branch.
2. magic.dmh was originally merged, but caused problems with parallel IO.
It was re-issued as pull request https://github.com/Unidata/netcdf-c/pull/446.
3. This branch + pull request replace any previous pull requests and magic.dmh branch.
Given an otherwise valid netCDF file that has a corrupted header,
the netcdf library currently crashes. Instead, it should return
NC_ENOTNC.
Additionally, the NC_check_file_type code does not do the
forward search required by hdf5 files. It currently only looks
at file position 0 instead of 512, 1024, 2048,... Also, it turns
out that the HDF4 magic number is assumed to always be at the
beginning of the file (unlike HDF5).
The change is localized to libdispatch/dfile.c See
https://support.hdfgroup.org/release4/doc/DSpec_html/DS.pdf
Also, it turns out that the code in NC_check_file_type is duplicated
(mostly) in the function libsrc4/nc4file.c#nc_check_for_hdf.
This branch does the following.
1. Make NC_check_file_type return NC_ENOTNC instead of crashing.
2. Remove nc_check_for_hdf and centralize all file format checking
NC_check_file_type.
3. Add proper forward search for HDF5 files (but not HDF4 files)
to look for the magic number at offsets of 0, 512, 1024...
4. Add test tst_hdf5_offset.sh. This tests that hdf5 files with
an offset are properly recognized. It does so by prefixing
a legal file with some number of zero bytes: 512, 1024, etc.
5. Off-topic: Added -N flag to ncdump to force a specific output dataset name.
This relies on the HDF5 capability to
dynamically load compression filters.
Note that a compression filter is just
a subcase of filters.
The primary user-visible changes are as follows:
1. Add a standard header "netcdf_filter.h" that defines
the necessary API extensions
2. Modify ncgen to support two new special attributes
"_Filter_ID" and "_Filter_Parameters" so that compression
can be turned on when creating a file using ncgen.
4. Add a detailed description of filtering support
to the user's guide; see the file filters.md
5. Add a test case directory for this: nc_test4/filter_test.
It is fragile and a ./configure flags (-enable-filter-test)
is defined (default disabled) to shut this off this test
to avoid spurious 'make check' failures.
Note that the HDF5 documentation is not up-to-date, so
much of what is encoded here comes from examining the
actual code in the file H5PL.c in the HDF5 source code.
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
