were added to provide a path name converter from e.g. cygwin
paths to e.g. windows paths. This is necessary because
the shell scripts may produce cygwin paths, but the code
may have been compiled with Visual Studio. Similar issues
arise with Mingw.
At appropriate places, and if using Visual Studio or Mingw,
I added calls to the path conversion code.
Apparently I forgot to find all the places where this
conversion was needed. So this pr does the following:
1. Push the calls to the converter to the various libXXX
directories and out of libdispatch/dfile.c.
2. Add conversion calls to other parts of the code like oc2.
I also turns out that conversion code in dapcvt.c
had a bug when handling DAP Byte type under visual studio.
Notes:
1. there may still be places I missed that need to do path conversion.
2. need to make sure that calls to e.g. H5open also use converted path.
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.
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.
Github issue https://github.com/Unidata/netcdf-c/issues/152
requested that "orphaned" DAS attributes be included in the netcdf
metadata as global variables. The term orphaned here meant that
they were not connected to any variable in the DDS.
This was done in pull request https://github.com/Unidata/netcdf-c/pull/164
However, some servers (e.g. Thredds) include attributes for variables not
specified in a constraint expression, but which exist in the full DDS.
So I was adding these to the set of global attributes, but in retrospect
this should not have been done: they should have been elided.
Solution: modify oc2 code to be more distriminatory about
which orphaned attributes to include.
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
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.
Following command fails under visual studio.
ncdump -h http://thredds.ucar.edu/thredds/dodsC/nexrad/composite/gini/n0r/1km/20170216/Level3_Composite_n0r_1km_20170216_1635.gini
The problem is that sscanf for windows does not appear to support
scanning 8bit integers: it appears to only allow scanning of characters.
Solution:
Scan the input as an integer (for type Byte) or unsigned int (for type UByte)
and then recast the result as a char or unsigned char.
Primary code fix is in libdap2/dapcvt.c#dapcvtattrval
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.
the multiple definitions of
typedef struct DCEparsestate
near lines 10 and 42 causes compiler
problems with some versions of gcc.
remove the second typedef.
(Re: [netcdfgroup] nccopy fails with corrupted double link list)
shows that ncdump/nccopy was returning EPERM instead of
NC_EDAPCONSTRAINT as an error when we have a malformed constraint.
Also clean up a potential bug that might occur if the user invokes
nc_set_default_format before calling nc_open on a dap url.
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.
Re e-eupport VGQ-678069
It was noticed that an attribute value of "nan." was being treated as
legal (it should be "nan"). The reason is that sscanf was not be checked
to see that all the attribute value characters were being read.
Solution is to verify that all characters were being consumed.
It appears the problem is that synth9 was erroneously
included in testing. It involves a nested sequence which
is not translatable. Not sure why it was still there,
but fix is to suppress the test.
This supports better authorization
handling for DAP requests, especially redirection
based authorization. I also added a new test case
ncdap_tests/testauth.sh.
Specifically, suppose I have a netrc file /tmp/netrc
containing this.
machine uat.urs.earthdata.nasa.gov login xxxxxx password yyyyyy
Also suppose I have a .ocrc file containing these lines
HTTP.COOKIEJAR=/tmp/cookies
HTTP.NETRC=/tmp/netrc
Assume that .ocrc is in the local directory or HOME.
Then this command should work (assuming a valid login and password).
ncdump -h "https://54.86.135.31/opendap/data/nc/fnoc1.nc"
Jennifer Adams has requested a reversion in behavior so that
all dap requests include a constraint.
Problem is caused by change in prefetch where if all variables
are requested, then no constraint is generated.
Fix is to always generate a constraint in prefetch.
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.
using cygwin64 causes a couple of bugs during make check.
Fixes are as follows:
1. in ncdump.c and nccopy.c change all occurrences of
'return EXIT_FAILURE'
and
'return EXIT_SUCCESS'
with
exit(EXIT_FAILURE)
and
exit(EXIT_SUCCESS)
respectively.
I have no idea why this works.
2. in libdap2/ncdap3a.c#freeNCDAPCOMMON,
remove the call to nc_abort, it is
causing a loop; not sure why this
is not caught under other operating systems.
Some servers do not properly
implement the current DAP2 spec.
It turns out that this server is one of those:
http://nomads.ncep.noaa.gov:9090/
When a reference such as this is made:
http://nomads.ncep.noaa.gov:9090/dods/gens/gens20140123/gep_all_12z?prmslmsl[0][0][0][0:359]
tt is returning this:
Dataset {
float prmslmsl[ens=1][time=1][lat=1][lon=360];
} gens%2fgens20140123%2fgep_all_12z;
when it should be returning this:
Dataset {
Structure {
float prmslmsl[ens=1][time=1][lat=1][lon=360];
} prmslmsl;
} gens%2fgens20140123%2fgep_all_12z;
The reason is that when picking fields out of a grid,
one must maintain the fully qualified name, so the grid
is converted to an enclosing structure.
It turns out that the problem was that
when I create the new structure node, I was
improperly linking it into the existing graph.
This caused a null pointer failure.
Fix is to make sure the relevant field (node->root)
is set.
The code that tests if a path is a url is
faulting when the url does not end in a slash
(e.g. http://thredds-tests.ucar.edu).
The code that tests if a path is a url is
faulting when the url does not end in a slash
(e.g. http://thredds-tests.ucar.edu).
CF-273]/HZY-708311
Solution was to do a null pointer test.
Added a test (tst_misc).
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).
Add a new function called nc_inq_format_extended that
returns more detailed format information (vis-a-vis
nc_inq_format) about an open dataset.
Note that the netcdf API will present the file as if it had
the format specified by nc_inq_format. The true file
format, however, may not even be a netcdf file; it might be
DAP, HDF4, or PNETCDF, for example. This function returns
that true file type. It also returns the effective mode for
the file.
signature: nc_inq_format_extended(int ncid, int* formatp, int* modep)
where
* ncid is the NetCDF ID from a previous call to nc_open() or
nc_create().
* formatp is a pointer to a location for returned true format.
* modep is a pointer to a location for returned mode flags.
Refer to the actual list in the file netcdf.h to see the
currently defined set.
Also added test cases (tst_formatx*).
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.
Fix Http Basic Authorization.
The problem is really in oc2.0.
In order for it to work,
the CURLOPT_COOKIEJAR must have
a non-null value. The code
was already there, but not being
used for some reason.
1. fixed cookiejar code in oc2.0
2. synched oc2.0 with netcdf-c/oc2
3. added a test case
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.
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.
The DAP code compiles constraints into an internal
tree form. When it goes to fetch data, it converts
that tree form into a string suitable for use in a url.
The tree->string code was using '<' when it should be
using '<=' and vice versa.
The fix is to make sure the right operator is used.
revisions are simpler, and I hope, clearer than the all
previous versions. Part of the code taken from the
ucar.nc2.Range.compose function. Modified to handle edge
cases not handled in the Range.compose function.
Problem was that the NC_create
code was not checking for the NC_CLASSIC_MODEL
mode flag in deciding what dispatch table to use.
This meant that it was then defaulting to use
the default format, and if that was changed
to e.g. NC_FORMAT_NETCDF4, then it would try
to create a netcdf-4 format file, even is
NC_CLASSIC_MODEL mode flag was set.
for JIRA issue NCF-241.
This is only temporary
until I can make pnetcdf
operate as a separate dispatch table.
Also, fix nc_test4/tst_pnetcdf
to open with nc_open_par;
this is necessary because a pnetcdf
created file cannot be opened
as a netcdf classic file.
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.
to indicate that they only work for atomic types,
not user defined types.
2. modified NCDEFAULT_{get/put}_vars to no longer use
nc_get/put_varm. They now directly use nc_get/put_vara
directly. This means that nc_get/put_vars now work
properly for user defined types as well as atomic types.
3. Added test cases for get_vars/put_vars with a
user defined type. Tests placed into
nc_test/tst_compounds.c
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.
