re: https://github.com/Unidata/netcdf-c/issues/2177
re: https://github.com/Unidata/netcdf-c/pull/2178
Provide get/set functions to store global data alignment
information and apply it when a file is created.
The api is as follows:
````
int nc_set_alignment(int threshold, int alignment);
int nc_get_alignment(int* thresholdp, int* alignmentp);
````
If defined, then for every file created opened after the call to
nc_set_alignment, for every new variable added to the file, the
most recently set threshold and alignment values will be applied
to that variable.
The nc_get_alignment function return the last values set by
nc_set_alignment. If nc_set_alignment has not been called, then
it returns the value 0 for both threshold and alignment.
The alignment parameters are stored in the NCglobalstate object
(see below) for use as needed. Repeated calls to nc_set_alignment
will overwrite any existing values in NCglobalstate.
The alignment parameters are applied in libhdf5/hdf5create.c
and libhdf5/hdf5open.c
The set/get alignment functions are defined in libsrc4/nc4internal.c.
A test program was added as nc_test4/tst_alignment.c.
## Misc. Changes Unrelated to Alignment
* The NCRCglobalstate type was renamed to NCglobalstate to
indicate that it represented more general global state than
just .rc data. It was also moved to nc4internal.h. This led
to a large number of small changes: mostly renaming. The
global state management functions were moved to nc4internal.c.
* The global chunk cache variables have been moved into
NCglobalstate. As warranted, other global state will be moved
as well.
* Some misc. problems with the nczarr performance tests were corrected.
## S3 Related Fixes
* Add comprehensive support for specifying AWS profiles to provide access credentials.
* Parse the files "~/.aws/config" and "~/.aws/credentials to provide credentials for the HDF5 ROS3 driver and to locate default region.
* Add a function to obtain the currently active S3 credentials. The search rules are defined in docs/nczarr.md.
* Provide documentation for the new features.
* Modify the struct NCauth (in include/ncauth.h) to replace specific S3 credentials with a profile name.
* Add a unit test to test the operation of profile and credentials management.
* Add support for URLS of the form "s3://<bucket>/<key>"; this requires obtaining a default region.
* Allows the specification of profile and/or region in a URL of the form "#mode=nczarr,...&aws.region=...&aws.profile=..."
## Misc. Fixes
* Move the ezxml code to libdispatch so that it can be used both by DAP4 and nczarr.
* Modify nclist to provide a deep clone operation.
* Modify ncuri to provide a deep clone operation.
* Modify the .rc file format to allow the specification of a path to be tested when looking for an entry in the .rc file.
* Ensure that the NC_rcload function is called.
* Modify nchttp to support setting request headers.
re: https://github.com/Unidata/netcdf-c/issues/1827
The issue is partly resolved by this PR. The proximate problem appears to be that the semantics of mkstemp in **nix is different than the semantics of _mktemp_s in Windows. I had thought they were the same but that is incorrect. The _mktemp_s function will only produce 26 different files and so the netcdf temp file code will fail after about that many iterations.
So, to solve this, I created my own version of mkstemp for windows that uses a random number generator. This appears to solve the reported issue. I also added the testcase ncdap_test/test_manyurls but made it conditional on --enable-dap-long-tests because it is very slow.
I did note that the provided test program now fails after some 800 iterations with a libcurl error claiming it cannot resolve the host name. My belief is that the library is just running out of resources at this point: too many open curl handles or some such. I doubt if this failure is fixable.
So bottom line is that it is really important to do nc_close when you are finished with a file.
Misc. Other Changes:
1. I took the opportunity to clean up some bad string hacks in the code. Specifically
* change all uses of strncat to strlcat
* remove old string hacks: occoncat and occopycat
2. Add heck to see if test.opendap.org is running and if not, then skip test
3. Make CYGWIN use TEMP environment variable
Primary changes:
* Add an improved cache system to speed up performance.
* Fix NCZarr to properly handle scalar variables.
Misc. Related Changes:
* Added unit tests for extendible hash and for the generic cache.
* Add config parameter to set size of the NCZarr cache.
* Add initial performance tests but leave them unused.
* Add CRC64 support.
* Move location of ncdumpchunks utility from /ncgen to /ncdump.
* Refactor auth support.
Misc. Unrelated Changes:
* More cleanup of the S3 support
* Add support for S3 authentication in .rc files: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY.
* Remove the hashkey from the struct OBJHDR since it is never used.
re: https://github.com/Unidata/netcdf-c/issues/1876
and: https://github.com/Unidata/netcdf-c/pull/1835
and: https://github.com/Unidata/netcdf4-python/issues/1041
The change in PR 1835 was correct with respect to using %20 instead of '+'
for encoding blanks. However, it was a mistake to assume everything was
unencoded and then to do encoding ourselves. The problem is that
different servers do different things, with Columbia being an outlier.
So, I have added a set of client controls that can at least give
the caller some control over this. The caller can append
the following fragment to his URL to control what gets encoded before
sending it to the server. The syntax is as follows:
````
https://<host>/<path>/<query>#encode=path|query|all|none
````
The possible values:
* path -- URL encode (i.e. %xx encode) as needed in the path part of the URL.
* query -- URL encode as needed in the query part of the URL.
* all -- equivalent to ````#encode=path,query````.
* none -- do not url encode any part of the URL sent to the server; not strictly necessary, so mostly for completeness.
Note that if "encode=" is used, then before it is processed, all encoding
is turned of so that ````#encode=path```` will only encode the path
and not the query.
The default is ````#encode=query````, so the path is left untouched,
but the query is always encoded.
Internally, this required changes to pass the encode flags down into
the OC2 library.
Misc. Unrelated Changes:
* Shut up those irritating warning from putget.m4
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: Partly addresses issue https://github.com/Unidata/netcdf-c/issues/1712.
1. Turn on Hyrax Hack to accept Hyrax style attribute containers.
2. Support Url type as alias for String.
3. Accept the special attribute, "__DAP4_Checksum_CRC32",
to control per-variable checksums.
4. Make _DAP4_xxx attributes be reserved and only accessible
by name (ala _SuperBlock attribute).
5. Fix handling of checksums. There is a hack in the code
that uses an extra flag in the chunk header to indicate
that all variables have checksums. This violates the spec
and will be removed once it is possible to regenerate the
test cases.
Note that checksumming with the Hyrax test server has not
been tested. This, along with some other probable inconsistencies,
needs fixing when OPeNDAP and Unidata can agree on the proper
specification. Testing will be included.
Fix Issue https://github.com/Unidata/netcdf-c/issues/1725.
Replace PR https://github.com/Unidata/netcdf-c/pull/1726
Also replace PR https://github.com/Unidata/netcdf-c/pull/1694
The general problem is that under Visual Studio, we are seeing
a number of undefined reference and other scoping errors.
The reason is that the code is not properly using Visual Studio
_declspec() declarations.
The basic solution is to ensure that when compiling the code itself
one needs to ensure that _declspec(dllexport) is used. There
are several sets of macros to handle this, but they all rely
on the flag DLL_EXPORT being define when the code is compiled,
but not being defined when the code is used via a .h file.
As a test, I modified XGetOpt.c to build properly. I also
fixed the oc2 library to properly _declspec things like ocdebug.
I also made some misc. changes to get all the tests to run
if cygwin is installed (to get bash, sed, etc).
Misc. Changes:
* Put XGetOpt.c into libsrc and copy at build time
to the other directories where it is needed.
* For URL paths, the new approach essentially centralizes all information
in the URL into the "#mode=" fragment key and uses that value
to determine the dispatcher for (most) URLs.
* The new approach has the following steps:
1. canonicalize the path if it is a URL.
2. use the mode= fragment key to determine the dispatcher
3. if dispatcher still not determined, then use the mode flags
argument to nc_open/nc_create to determine the dispatcher.
4. if the path points to something readable, attempt to read the
magic number at the front, and use that to determine the dispatcher.
this case may override all previous cases.
* Misc changes.
1. Update documentation
2. Moved some unit tests from libdispatch to unit_test directory.
3. Fixed use of wrong #ifdef macro in test_filter_reg.c
[I think this may fix an previously reported esupport query].
re: github issue #1425
The 'ncdump -v' command causes a constraint to be sent
to the opendap code (in libdap2). This is a separate path
from specifying the constraint via a URL.
This separate path encoded its constraint using code independent
of and duplicative of that provided by ncuri.c and this duplicate
code did not properly encode the constraint, which might include
square brackets.
Solution chosen here was to get rid of the duplicate code and
ensure that all URL escaping is performed in the ncuribuild function
in the ncuri.c file.
Also removed the use of the NEWESCAPE conditional in ncuri.c
because it is no longer needed.
re: https://github.com/Unidata/netcdf-c/issues/1388
1. Centralize calls to curl_global_init and curl_global_cleanup
to libdispatch/ddispatch.c
2. Make the above calls if options require curl: currently
any of DAP2, DAP4, or byterange.
3. Side issue: Fix obscure bug in mmapio.c involving non-persistent mmap.
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
Add the ability to set some additional curlopt values via .daprc (aka .dodsrc).
This effects both DAP2 and DAP4 protocols.
Related issues:
[1] re: esupport: KOZ-821332
[2] re: github issue https://github.com/Unidata/netcdf4-python/issues/836
[3] re: github issue https://github.com/Unidata/netcdf-c/issues/1074
1. CURLOPT_BUFFERSIZE: Relevant to [1]. Allow user to set the read/write
buffersizes used by curl.
This is done by adding the following to .daprc (aka .dodsrc):
HTTP.READ.BUFFERSIZE=n
where n is the buffersize in bytes. There is a built-in (to curl)
limit of 512k for this value.
2. CURLOPT_TCP_KEEPALIVE (and CURLOPT_TCP_KEEPIDLE and CURLOPT_TCP_KEEPINTVL):
Relevant (maybe) to [2] and [3]. Allow the user to turn on KEEPALIVE
This is done by adding the following to .daprc (aka .dodsrc):
HTTP.KEEPALIVE=on|n/m
If the value is "on", then simply enable default KEEPALIVE. If the value
is n/m, then enable KEEPALIVE and set KEEPIDLE to n and KEEPINTVL to m.
url parameter handling, the parameter
lookup code was ignoring parameters
because I was giving it a url stripped
of parameters instead of the one with
parameters.
This code change fixes the parameter processing
so it again used the correct url.
reference:
docs/OPeNDAP.dox#section Defined Client Parameters
v4.5-release-candidate branch and master branch ASAP.
The bug occurs in d4rc.c where strcmp is being applied to NULL.
Also, the code in which it occurs is debugging code, so it needs
to be #ifdef'd. This fix may cause minor conflicts with other
outstanding pull requests that fix the same bug. But the
conflicts should be minor and easy to resolve.
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
generates garbage. This in turn interferes with using .netrc
because the garbage user+pwd can will override the
.netrc. Note that this may work ok sometimes
if the garbage happens to start with a nul character.
2. It turns out that the user:pwd combination needs to support
character escaping. One reason is the user may contain an '@' character.
The other is that modern password rules make it not unlikely that
the password will contain characters that interfere with url parsing.
So, the rule I have implemented is that all occurrences of the user:pwd
format must escape any dodgy characters. The escape format is URL escaping
of the form %XX. This applies both to user:pwd
embedded in a URL as well as the use of HTTP.CREDENTIALS.USERPASSWORD
in a .dodsrc/.daprc file. The user and password in .netrc must not
be escaped. This is now documented in docs/auth.md
The fix for #2 actually obviated #1. Now, internally, the user and pwd
are stored separately and not in the user:pwd format. They are combined
(and escaped) only when needed.
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.
Some temporary files are being left in a tempdir (e.g. /tmp
under *nix*).
The situation is described tersely in
netcdf-c/docs/auth.html#REDIR Basically, when a url is used that
requires redirection, a physical cookiejar file is required
to exist in the file system in order for this to work.
Since it was difficult to figure out when redirection was
being used (it was internal to libcurl) I needed to be prepared for that
eventuality. The result was that I always created a cookiejar file if one
was not specified in the rc file. This actually occurs in two places:
one inside oc2 and one inside libdap4.
The solution was two-fold:
1. do not use a cookiejar directory -- create cookiejar file directly
2. ensure that all cookiejar related files are reclaimed by nc_close().
Note that if nc_close (or nc_abort) is not called for whatever reason,
then reclamation will not occur.
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
DAPRCFILE. Note that the value of this environment
variable should be the absolute path of the rc file, not
the path to its containing directory.
2. fixup testauth.sh and add some new tests
3. synch oc
