1. Cleanup test_common.sh to expunge (mostly) the use of the VS
path value. This has the effect of being unable to use the
Visual Studio C compiler for shell tests.
2. There is a missing case in CMakeLists.txt so add
defaulting for HDF5_C_LIBRARY_hdf5 using HDF5_C_LIBRARY.
Ward should probably examine this to get it fixed correctly.
3. Put back ref to esg.md in docs/Doxyfile.in
4. Fix minor warning in dut8proc.h
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.
a global attribute whose type is an enum.
Turns out this case fails because of an
oversight in ncgen.
This pr fixes that problem (in semantics.c).
Also added test case .cdl file: tst_gattenum.cdl
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
is somehow in interference with something
in the HDF4 code. So, I changed
the OPAQUE -> OPAQUE_ and that appears
to fix the problem with bison when HDF4
is enabled.
ps. when Visual Studio complained about token
'constant' it turn out that it mean token type,
not the actual token named 'constant'. Instead
the actual token that was causing the problem
was 'OPAQUE'.
re: https://github.com/Unidata/netcdf-c/issues/365
1. Added to RELEASENOTES.md
2. Add a range check to more closely
mimic unix sscanf
3. locate and fix same sscanf problems in ncgen/cvt.c
Still need a stable url for a test case.
Update utf8proc.[ch] to use the version now
maintained by the Julia Language project
(https://github.com/JuliaLang/utf8proc/blob/master/LICENSE.md).
The license for the previous version was
unacceptable for the Debian and Ubuntu release
systems. The new version both updates the code
and addresses the license issue.
It turns out that the utf8proc software we are using
was turned over to the Julia Language developers
and the license terms changed to allow modification.
(https://github.com/JuliaLang/utf8proc/blob/master/LICENSE.md).
So the fix here is as follows:
1. Wrap the library with a fixed interface: libdispatch/dutf8.c
and include/ncutf8.h.
2. Replace the existing utf8proc code with the new version
from https://github.com/JuliaLang/utf8proc.
3. Add a couple more test cases: nc_test/tst_utf8_validate.c
and nc_test_utf8_phrases.c. If/when I can find a usable
normalization test, I will incorporate that later.
Problem was in oc2/dap.y.
In definition of errormsg:, change WORD_WORD to WORD_STRING
since the msg field of an opendap error response is a quoted
string.
Also took the opportunity to modify ncgen to
transfer the logging level (-L flag) into the c-code
generated using -lc.
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.
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.
User request to have all orphaned DAP2 attributes kept as netcdf
global attributes. This is primarily a change in the oc code
nplus testcase dataset changes.
Result may be inconsistent with netcdf-Java output.
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.
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).
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).
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.
error occurs after an "exit:" label.
Corrected a dozen Coverity errors (mainly allocation issues, along with a few
other things):
711711, 711802, 711803, 711905, 970825, 996123, 996124, 1025787,
1047274, 1130013, 1130014, 1139538
Refactored internal fill-value code to correctly handle string types, and
especially to allow NULL pointers and null strings (ie. "") to be
distinguished. The code now avoids partially aliasing the two together
(which only happened on the 'write' side of things and wasn't reflected on
the 'read' side, adding to the previous confusion).
Probably still weak on handling fill-values of variable-length and compound
datatypes.
Refactored the recursive metadata reads a bit more, to process HDF5 named
datatypes and datasets immediately, avoiding chewing up memory for those
types of objects, etc.
Finished uncommenting and updating the nc_test4/tst_fills2.c code (as I'm
proceeding alphabetically through the nc_test4 code files).
to clean up resources properly on failure.
Refactored doubly-linked list code for objects in the libsrc4 directory,
cleaning up the add/del routines, breaking out the common next/prev
pointers into a struct and extracting the add/del operations on them,
changed the list of dims to add new dims in the same order as the other
types, made all add routines able to optionally return a pointer to the
newly created object.
Removed some dead code (pg_var(), nc4_pg_var1(), nc4_pg_varm(), misc. small
routines, etc)
Fixed fill value handling for string types in nc4_get_vara().
Changed many malloc()+strcpy() pairs into calls to strdup().
Cleaned up misc. other minor Coverity issues.
many cleanups to fix compiler warnings, streamline iteration over objects
in HDF5 file when opening the file, and generally straightening out the code
to be cleaner and simpler.
Tested on Mac OS/X with gcc 4.8 and OpenMPI (which uses clang).
Fix bug where leading backslash digit
in name was not being properly handled.
The reason was that I accidentally attemped to allow \x... and \0...
escapes in identifiers. This make identifiers
with leading escaped digits not work any more.
Also added test case.
Columbia server does not serve up proper
opendap DDS replies. The Dataset {...} name
changes depending on if the request has certain
kinds of constraints.
Code for a hack was not being used, so restore it.
The fix is to effectively ignore differences in
Dataset node names if the code is coming from
columbia.edu.
2. [NCF-278]
The ncgen code is improperly typing int64 integer constants
as uint64.
3. [NCF-279]
Empty string constants were not being properly
filled when their target array is length 1 or more.
Fix bug introduced by [NCF-267].
The bug was that octal constants that had
the highest bit set (e.g. '\200')
were not recognized as proper octal
constants. Fix was to keep as integer
until it was needed as an 8-bit byte.
Add support for embedded NUL characters
in character arrays and added some test cases.
Note that embedded NULs in netcdf-4
string constants are still illegal. This is
because strings are not counted in the netcdf
API, so they are implicitly NUL terminated.
1. Updated the ncgen manual (ncgen.1)
to discuss handling of ambiguous
enumeration constant references.
2. Fixed the test case. It is currently
XFAIL'd until such time as ncdump
is modified to output properly
disambiguated enumeration constant
references.
Added code to verify that enum constants
(and other constants) are consistent
with the type of the variable or
attribute to which they are assigned.
This addresses the ncdump failure.
Ncgen is unable to resolve
ambiguous references to an enum
constant when two different enums
have same econstant name.
Solved by allowing more specific
forms for econstant references.
1. /.../enumname.enumconstname
2. enumname.enumconstname
3. enumconstname
Case 1 is resolved by using the econstant
in the specific enum definition. If none is
found, an error is reported.
Case 2 is resolved by
1. finding an enclosing group with an
enum definition with the specified name
and containing the specified econstant.
If there are more than one, then an error is reported
2. finding all enum definitions in the dataset that have
the specified enum name and contain the specified
econstant. If more than one is found, then an error is reported.
If the above two methods fail, then report an error.
Case 3 is similar to case 2, but all enums, irrespective
of name are used if they contains the specified enum constant.
The ref_tst_econst.cdl test in ncdump is causing ncdump
to fail. So there may be yet some problem.
group renaming. The primary API
is 'nc_rename_grp(int grpid, const char* name)'.
No test cases provided yet.
This also required adding a rename_grp entry
to the dispatch tables.
CMake related changes in CMakeLists.txt files,
cmake_config.h.in. Other changes relate to
Windows-specific issues, and changes made
when regenerating generated source files.
o Changed variable names 'typeid' to 'typeid1' to avoid a namespace conflict
in visual studio.
o Cleaned up a handful of warnings in Visual Studio.
o Addressed a few Coverity-discovered issuesl
o Made changes to CMake-based builds.
Primarily focused on memory errors falling into a couple different types:
1) Static overrun errors.
2) Dereference uninitialized memory errors.
make distcheck works after applying these fixes, and coverity no longer sees an issue, so hopefully they are properly resolved.
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.
