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
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173
Sorry that it is so big, but leak suppression can be complex.
This PR fixes all remaining memory leaks -- as determined by
-fsanitize=address, and with the exceptions noted below.
Unfortunately. there remains a significant leak that I cannot
solve. It involves vlens, and it is unclear if the leak is
occurring in the netcdf-c library or the HDF5 library.
I have added a check_PROGRAM to the ncdump directory to show the
problem. The program is called tst_vlen_demo.c To exercise it,
build the netcdf library with -fsanitize=address enabled. Then
go into ncdump and do a "make clean check". This should build
tst_vlen_demo without actually executing it. Then do the
command "./tst_vlen_demo" to see the output of the memory
checker. Note the the lost malloc is deep in the HDF5 library
(in H5Tvlen.c).
I am temporarily working around this error in the following way.
1. I modified several test scripts to not execute known vlen tests
that fail as described above.
2. Added an environment variable called NC_VLEN_NOTEST.
If set, then those specific tests are suppressed.
This should mean that the --disable-utilities option to
./configure should not need to be set to get a memory leak clean
build. This should allow for detection of any new leaks.
Note: I used an environment variable rather than a ./configure
option to control the vlen tests. This is because it is
temporary (I hope) and because it is a bit tricky for shell
scripts to access ./configure options.
Finally, as before, this only been tested with netcdf-4 and hdf5 support.
dap code will create a real temporary file in which to store the
converted metadata for the DAP .dds or .dmr.
It was assumed that the nc_close code would reclaim the
temporary file. For DAP2, reclamation occurs in the ncio
code. For DAP4, it was assumed that the libsrc4 code would do
the reclamation, but for whatever reason, this is not happening.
Thus, in this situation, a temporary file is left in the file
system. Aside from being irritating to users, this screws up
'make distcheck'.
So the DAP4 code is fixed to ensure that the temporary file is
properly reclaimed independent of the libsrc4 code.
The problem was that for opendap, it is possible to use keywords
as identifiers
when there is no ambiguity. However, the DAP2
parser lost the case of the identifier used the lower case version.
Fix is to use the actual text of the symbol when it is used as an identifier.
Also added a test case for this (kwcase.*).
Additionally cleaned up some misc. dap2 testing problems.
1. ncdap_test/tst_ncdap3.sh was using an empty test set.
restored the testing of datasets.
2. as a consequence of #1, some tests needed to be updated with minor
tweeks.
3. fix dapmerge to handle multiple DODS_EXTRAS attributes.
4. modify buildattribute to suppress nul characters and terminate
the name at the first nul.
5. clean up various test scripts to remove residual, unused
references to obsolete netcdf-4 translation.
6. export e.g. NCDUMP from test_common.in so that non-top-level
shell scripts can access it.
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
effectively o(n cubed); modified to be
o(n squared).
2. If the list of prefetched variables is too long,
(something on the order of 400 variables), then
the server may reject it. Modified code so that
in the case that the set of prefetch'd vars is
the in fact all variables, it does not create a long
request. This does not actually solve the problem
if the prefetch list is long, but not all inclusive.
effectively o(n cubed); modified to be
o(n squared).
2. If the list of prefetched variables is too long,
(something on the order of 400 variables), then
the server may reject it. Modified code so that
in the case that the set of prefetch'd vars is
the in fact all variables, it does not create a long
request. This does not actually solve the problem
if the prefetch list is long, but not all inclusive.
to do prefetch on either a lazy
or eager basis. Lazy means that
the prefetch does not occur
until and unless the client actually
makes a get_var request.
Also repaired a problem where
doing prefetch wrt a url that
has a constraint will prefetch
a whole variable if its constrained
size is small enough, even if the
underlying variable is too large
to warrant prefetch.
contain as little file-type specific info as possible. It
modifies especially libsrc so that all of the netcdf-3 data
that used to be in struct NC is now kept in a separate chunk
of data pointed to by the struct NC. This makes all of
current protocols consistent: netcdf-3, netcdf-4, and dap.
The in-memory files can be made persistent if nc_create is called with
NC_DISKLESS|NC_WRITE flags set. Initial test case also included.
- Modified ncio mechanism to support
multiple ncio packages; this is so we
can have posixio and memio operating
at the same time.
- cleanup up a bunch of lint issues (unused variables, etc).
- Fix NCF-157 to modify DAP code to support
partial variable retrieval.
- Fix of NCF-154 to solve problem of ncgen
improperly processing data lists for variables
of size greater than 2**18 bytes.
- Fix ncgen processing of char variables that have
multiple unlimited dimensions.
- Partly fix Jira issue: NCF-145 (vlen issues).
- Benchmark program nc_test4/tst_ar4_*) requires arguments
and should only be invoked inside a shell
script; fixed so that they terminate cleanly
if invoked with no arguments.
- Fix the Doxygen processing so it will work
with make distcheck.
- Begin switchover to using an alternative to ncio.
- Begin support for in-memory (diskless) files.
NCF-42: _Format attribute sometimes being ignored
NCF-43: Fixed unsigned long long parsing.
NCF-47: Make opendap code properly handle illegal names like "x.y" by
supressing them
NCF-49: check for uint type
NCF-50: properly handle username:pwd embedded in urls.
