The file docs/indexing.dox tries to provide design
information for the refactoring.
The primary change is to replace all walking of linked
lists with the use of the NCindex data structure.
Ncindex is a combination of a hash table (for name-based
lookup) and a vector (for walking the elements in the index).
Additionally, global vectors are added to NC_HDF5_FILE_INFO_T
to support direct mapping of an e.g. dimid to the NC_DIM_INFO_T
object. These global vectors exist for dimensions, types, and groups
because they have globally unique id numbers.
WARNING:
1. since libsrc4 and libsrchdf4 share code, there are also
changes in libsrchdf4.
2. Any outstanding pull requests that change libsrc4 or libhdf4
are likely to cause conflicts with this code.
3. The original reason for doing this was for performance improvements,
but as noted elsewhere, this may not be significant because
the meta-data read performance apparently is being dominated
by the hdf5 library because we do bulk meta-data reading rather
than lazy reading.
2. Fixed plugin building (nc_test4/hdf5plugins)
to be done properly by cmake and automake.
4. Duplicated part of the nc_test4 filter test code
in examples/C
An incomplete and untested set of hooks exist
for OS-X in nc_test4/findplugins.in. They need testing.
tst_h_rdc0 depends on ncdump_tst_netcdf4, which isn't build if HAVE_BASH
isn't true. But CMake errors out with:
-- Bash shell not found; disabling shell script tests.
CMake Error at CMakeLists.txt:1521 (SET_PROPERTY):
SET_PROPERTY given TEST names that do not exist:
tst_h_rdc0
There are also some tests which cdl_do_maps depends on, but it is
also not defined if HAVE_BASH isn't true. CMake errors out with:
CMake Error at examples/CDL/CMakeLists.txt:10 (SET_TESTS_PROPERTIES):
SET_TESTS_PROPERTIES Can not find test to add properties to:
cdl_do_comps
This patch makes these tests conditional, making CMake happy.
strlcat provides better protection against buffer overflows.
Code is taken from the FreeBSD project source code. Specifically:
https://github.com/freebsd/freebsd/blob/master/lib/libc/string/strlcat.c
License appears to be acceptable, but needs to be checked by e.g. Debian.
Step 1:
1. Add to netcdf-c/include/ncconfigure.h to use our version
if not already available as determined by HAVE_STRLCAT in config.h.
2. Add the strlcat code to libdispatch/dstring.c
3. Turns out that strlcat was already defined in several places.
So remove it from:
ncgen3/genlib.c
ncdump/dumplib.c
3. Define strlcat extern definition in ncconfigure.h.
4. Modify following directories to use strlcat:
libdap2 libdap4 ncdap_test dap4_test
Will do others in subsequent steps.
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.
2. Factored out the parameter string parsing for ncgen and nccopy
int libdispatch/dfilter.c + include/ncfilter.h
3. Allow a parameter string to use constant types other than
unsigned int. See docs/filters.md for details.
4. Moved the old content of include/netcdf_filter.h into include/netcdf.h
and removed include/netcdf_filter.h as no longer needed.
5. Force the test filter (bzip2) in nc_test4/filter_test to
be built using BUILT_SOURCES.
Primary change is to cleanup code and remove duplicated code.
1. Unify the rc file reading into libdispatch/drc.c. Eventually extend
if we need rc file for netcdf itself as opposed to the dap code.
2. Unify the extraction from the rc file of DAP authorization info.
3. Misc. other small unifications: make temp file, read file.
4. Avoid use of libcurl when reading file:// because
there is some kind of problem with the Visual Studio version.
Might be related to the winpath problem.
In any case, do direct read instead.
5. Add new error code NC_ERCFILE for errors in reading RC file.
6. Complete documentation cleanup as indicated in this comment
https://github.com/Unidata/netcdf-c/pull/472#issuecomment-325926426
7. Convert some occurrences of #ifdef _WIN32 to #ifdef _MSC_VER
from e-support OYW-455599.
Problem was that in nctime.c#CDMonthDay, it was setting up
the month -> #days table correctly, but it did not use it
because it forgot to check for Cd366, it only checked for Cd365.
from e-support OYW-455599.
Problem was that in nctime.c#CDMonthDay, it was setting up
the month -> #days table correctly, but it did not use it
because it forgot to check for Cd366, it only checked for Cd365.
1. Allow nccopy to apply filters, especially on the output file.
This provides a third way to do this other than using ncgen or
programatically
2. Make sure that even if the filter code is not available, it is
possible to see the filter id and parameters for variables using
e.g ncdump -hs.
3. Fix bug in nccopy so that the input file does
not necessarily have to be netcdf-4.
4. At last minute decided to change to using a
single "_Filter" attribute for ncgen
5. Added a test to tst_filter.sh to generate C code using ncgen.
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.
1. When running under windows (as opposed to cygwin)
we need to make sure to not user /cygdrive/ file paths.
This was ocurring in libdap4/d4read.c, but may occur
elsewhere.
2. Shell scripts in the git repo are not being checked-out
with the executable mode set. Had core.filemode set to false.
Was a major hassle to fix.
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
A set of typecasts in the function
print_enum_type in ncdump/ncdump.c cause some
compilers to complain about type punning:
warning: dereferencing type-punned pointer will
break strict-aliasing rules
Fix is to cast to void* before casting to final
value. There may be other occurrences in some
of the older netcdf-c code.
to get TOPSRCDIR that avoids use of
TEST_ENVIRONMENT and makes automake and cmake
more consistent.
Basic assumption is that abs_top_srcdir (and
cmake equivalent) is known at 'make check' time,
so we can use -D flag to compile a program that
has the value of abs_top_srcdir embedded into it
as a constant.
We define two new files in ncdap_test:
1. t_srcdir.h -- provide a gettopsrcdir() function
to return the topsrcdir value to the test program.
2. topsrcdir.c -- a program that calls gettopsrcdir()
and prints its output (minus any newline) on stdout.
This is used in .sh files to get topsrcdir.
Modified provenance code to allocate the minimal space
needed for _NCProperties attribute in file. Basically
required using malloc in the provenance code and in ncdump.
Otherwise should cause no externally visible effects.
Also removed the ENABLE_FILEINFO from configure.ac since
the provenance code is no longer optional.
not being computed. Fix in nc4file.c.
Not sure how this ever worked for any variable.
What is also weird is that the dim hash is
apparently being computed.
re: github netcdf-c issue #271
This occurs for several reasons, including:
1. using H5Aopen_name instead of H5Aexists to test if attribute exists.
2. using H5Eset_auto instead of H5Eset_auto2.
There are probably others that will have to be extinguished as encountered.
p.s Hope I did not overdo this and kill too much.
Charlie Zender noted that we forgot to define what happens for
various netcdf API attribute operations, notably nc_inq_att()
and nc_get_att().
So, I added a list of legal and illegal api calls for the provenance
attributes in docs/attribute_conventions.md.
I also added more test cases to ncdump/tst_fileinfo.c to verify
and fixed resultant errors.
This consists of a persistent attribute named
_NCProperties plus two computed attributes
_IsNetcdf4 and _SuperblockVersion.
See the 'Provenance Attributes' section
of docs/attribute_conventions.md for details.
If a char valued attribute contains embedded nul characters,
then illegal xml will be generated when using the -x (ncml) flag.
There is not good solution since we have a char value '\0' that
is legal in a netcdf-c char valued attribute, but is completely
illegal in ncml (i.e. xml).
So, implemented hack is to go ahead and generate '�' entities
and then complain that we are generating illegal ncml.
NetCDF-c Github issue #185
The code in libsrc/dim.c has not been upgraded to support
CDF-5 format.
Rule we are implementing sets the max dimension sizes as follows:
Classic: CDF-1 NC_MAX_INT - 3 = 2147483647 - 3
64 bit Offset: CDF-2 NC_MAX_UINT - 3 = 4294967295 - 3
64 bit Data: CDF-5 NC_MAX_UINT64 - 3 = 18446744073709551615 - 3
The -3 is to handle rounding.
NetCDF-c Github issue #178 / esupport BNL-694121
The ncgen man pages says:
> Note also that the words variable',dimension', data',group', and
> `types' are legal CDL names, but be careful that there is a space be-
> tween them and any following colon character when used as a variable
> name. This is mostly an issue with attribute declarations.
Ncdump does not obey this rule.
The fix is to modify ncdump/ncdump.c to check if a variable name is
a keyword.
Also added test case.
that were not taking the CDF-5 format into account.
2. Had to update ncgen.1 man page to define the new
k-flag rules to deal with cdf-5.
3. Had to fix some tests that use 'cmp' for comparison;
this really should be deprecated.
3. There was a bug in configure.ac with respect
to using the enable-netcdf-4 flag vs
using disable-netcdf-4.
AC_CHECK_SIZEOF is not working because anti-virus
will not allow very rapid creation/deletion of a
file with same name.
2. modified some test baselines to attempt to fix
Ward's issue
AC_CHECK_SIZEOF is not working because anti-virus
will not allow very rapid creation/deletion of a
file with same name.
2. modified some test baselines to attempt to fix
Ward's issue
AC_CHECK_SIZEOF is not working because anti-virus
will not allow very rapid creation/deletion of a
file with same name.
2. modified some test baselines to attempt to fix
Ward's issue
If the netCDF-C library is built with the
HDF5 library but without the HDF4 library and one attempts
to open an HDF4 file, an abort occurs rather than returning
a proper error code (NC_ENOTNC).
Fix is to modify dfile.c#NC_check_file_type to properly
#ifdef relevant tests.
The code for handling character constants
in datalists in ncgen has some problems.
1. It failed on large constants
2. It did not handle e.g. var = 'a', 'b', ...
in the same way that ncgen3 did.
3. The code for generate.c and genchar.c needed
some refactoring to make it a little simpler
(but not simple).
re: e support ZCL-340681 and CPW-270700
HDF4 supports compression (and chunking)
but the chunking was not being recorded
for HDF4 files. So, I modified the necessary
files to support HDF4 chunking.
Fixed indentation.
Updated .gitignore.
Added a macro to make it easy to check to see if the linker supports a particular flag. Debug builds now pass the -w1,--no-undefined if it is detected the linker supports it.
Add -c '/' option to specify changing layout for all variables from chunked to contiguous.
Fix logic for chunking and compression depending on input and output formats.
should be under ENABLE_DAP_REMOTE_TESTS.
Fixed to make sure that this is so.
Also attempted to fix ncdap_test/CMakeLists.txt,
but probably got it wrong.
HT to Nico Schlomer.
2. Attempted to reduce the number of conversion errors
when -Wconversion is set. Fixed oc2, but
rest of netcdf remains to be done.
HT to Nico Schlomer.
3. When doing #2, I discovered an error in ncgen.y
that has remained hidden. This required some other
test case fixes.
times, but returning the same ncid.
2. Separate out the dap auth tests
and make them disabled by default.
3. turn of ncdap_test/test_varm3 until
we can find a copy of coads_climatology.nc
