Commit Graph

67 Commits

Author SHA1 Message Date
Dennis Heimbigner
53464e8963 Allow optional use of libxml2
re: https://github.com/Unidata/netcdf-c/issues/2119

H/T to [Egbert Eich](https://github.com/e4t) and [Bas Couwenberg](https://github.com/sebastic) for this PR.

It is undesirable to make netcdf be dependent on the availability
of libxml2, but it is desirable to allow its use if available.

In order to do this, a wrapper API (include/ncxml.h) was constructed
that supports either ezxml or libxml2 as the implementation.
Additionally, the xml support code was moved to a new directory
netcdf-c/libncxml.

Primary changes:
* Create a new sub-directory named netcdf-c/libncxml to hold all the xml implementation code.
* Move ezxml.c and ezxml.h to libncxml
* Create a wrapper API -- include/ncxml.h
* Create an implementation, ncxml_ezxml.c to support use of ezxml.
* Create an implementation, ncxml_xml2.c to support use of libxml2.
* Add a check for libxml2 in configure.ac and CMakeLists.txt
* Modify libdap to use the wrapper API instead of ezxml directly.

Misc. Other Changes:
* Change include/netcdf_json.h from built source to be part of the distribution.
2021-11-01 22:37:05 -06:00
Dennis Heimbigner
f6e25b695e Fix additional S3 support issues
re: https://github.com/Unidata/netcdf-c/issues/2117
re: https://github.com/Unidata/netcdf-c/issues/2119

* Modify libsrc to allow byte-range reading of netcdf-3 files in private S3 buckets; this required using the aws sdk. Also add a test case.
* The aws sdk can sometimes cause problems if the Awd::ShutdownAPI function is not called. So at optional atexit() support to ensure it is called. This is disabled for Windows.
* Add documentation to nczarr.md on how to build and use the aws sdk under windows. Currently it builds, but testing fails.
* Switch testing from stratus to the Unidata bucket on S3.
* Improve support for the s3: url protocol.
* Add a s3 specific utility code file: ds3util.c
* Modify NC_infermodel to attempt to read the magic number of byte-ranged files in S3.

## Misc.

* Move and rename the core S3 SDK wrapper code (libnczarr/zs3sdk.cpp) to libdispatch since it now used in libsrc as well as libnczarr.
* Add calls to nc_finalize in the utilities in case atexit is disabled.
* Add header only json parser to the distribution rather than as a built source.
2021-10-29 20:06:37 -06:00
Dennis Heimbigner
dc2ecc74ac (1) improve INI parser (2) Fix make discheck 2021-09-30 13:45:09 -06:00
Dennis Heimbigner
6b69b9c52c Significantly Improve Amazon S3 Cloud Storage Support
## 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.
2021-09-27 18:36:33 -06:00
Dennis Heimbigner
11fe00ea05 Add filter support to NCZarr
Filter support has three goals:

1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled

Detailed usage directions are define in docs/filters.md.

For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.

This is a big change since filters affect many parts of the code.

In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.

### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.

### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.

### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-02 17:04:26 -06:00
Dennis Heimbigner
d953899559 Move to Version 2 NCZarr Extended Meta-Data
re: https://github.com/zarr-developers/zarr-specs/issues/41

After discussions with the Zarr community, it was decided to
convert to a new representation of the NCZarr meta-data extensions: version 2.
These extensions store information necessary to mapping the Zarr data model
to the netcdf-4 data model.

The basic change is to remove the NCZarr specific objects: .nczarr, .nczgroup, .nczarray, and .nczattr.
The contents of these objects is moved into the corresponding existing Zarr objects as special keys. The mapping is as follows:

* ''.nczarr'' => ''/.zgroup/_NCZARR_SUPERBLOCK_''
* ''.nczgroup => ''.zgroup/_NCZARR_GROUP_''
* ''.nczarray => ''.zarray/_NCZARR_ARRAY_''
* ''.nczattr => ''.zattr/_NCZARR_ATTR_''

Backward compatibility is maintained by looking for the object ''/.nczarr''
and if found, then assuming that the dataset is in the older version 1 format.
This compatibility only supports reading of such version 1 datasets.

Documentation and test cases are also added.

Misc. Other Changes:
1. The json parsing code was added to the general library instead of nczarr only (ncjson.c, ncjson.h).
2. Improved support for different platform paths by allowing conversion
   to a single common path representation.
3. Add some new error codes.
4. Modify nccopy usage to mention the new chunking specification.
2021-07-17 16:55:30 -06:00
Ward Fisher
670fd2482f Corrected typo preventing success when running make dist or make distcheck 2021-03-30 14:08:00 -06:00
Ward Fisher
f75c1c4d7b
Merge branch 'master' into dispatchversion.dmh 2021-03-22 12:40:09 -06:00
Dennis Heimbigner
0b7a5382e7 Codify cross-platform file paths
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc.  These platforms differ
significantly in the kind of file paths that they accept.  So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.

A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.

The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.

The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.

As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.

In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.

Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
  tests to work under windows using shell scripts; the args do
  not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
  PR https://github.com/Unidata/netcdf-c/pull/1794,
  HDF5 changed its Windows file path handling.
2021-03-04 13:41:31 -07:00
Dennis Heimbigner
7a44ae9184 Unify definition of NC_DISPATCH_VERSION
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
2021-01-31 21:40:08 -07:00
Dennis Heimbigner
eb3d9eb0c9 Provide a Number of fixes/improvements to NCZarr
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.
2020-11-19 17:01:04 -07:00
Dennis Heimbigner
25d2e05444 Prepare for the path management code
Rename some files in prep for eventual implementation
of more comprehensive cross-platform file path management.
2020-10-13 19:12:15 -06:00
Dennis Heimbigner
aeb3ac2809 Mostly revert the filter code to reduce its complexity of use.
re: https://github.com/Unidata/netcdf-c/issues/1836

Revert the internal filter code to simplify it. From the user's
point of view, the only visible changes should be:

1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h
2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter.

Internally,the dispatch table has been modified to get rid of the filter_actions
entry and associated complex structures. It has been replaced with
inq_var_filter_ids and inq_var_filter_info entries and the dispatch table
version has been bumped to 3. Corresponding NOOP and NOTNC4 functions
were added to libdispatch/dnotnc4.c. Also, the filter_action entries
in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2,
etc). This should only impact UDF users.

In the process, it became clear that the form of the filters
field in NC_VAR_INFO_T was format dependent, so I converted it to
be of type void* and pushed its management into the various dispatch
code bases. Specifically libhdf5 and libnczarr now manage the filters
field in their own way.

The auxilliary functions for parsing textual filter specifications
were moved to netcdf_aux.h and were renamed to the following:
* ncaux_h5filterspec_parse
* ncaux_h5filterspec_parselist
* ncaux_h5filterspec_free
* ncaux_h5filter_fix8

Misc. Other Changes:

1. Document NUG/filters.md updated to reflect the changes above.
2. All the old data types (structs and enums)
   used by filter_actions actions were deleted.
   The exception is the NC_H5_Filterspec because it is needed
   by ncaux_h5filterspec_parselist.
3. Clientside filters were removed -- another enhancement
   for which no-one ever asked.
4. The ability to remove filters was itself removed.
5. Some functionality needed by nczarr was moved from libhdf5
   to libsrc4 e.g. nc4_find_default_chunksizes
6. All the filterx code was removed
7. ncfilter.h and nc4filter.c no longer used

Misc. Unrelated Changes:

1. The nczarr_test makefile clean was leaving some directories; so
   add clean-local to take care of them.
2020-09-27 12:43:46 -06:00
Ward Fisher
31dee0c4da
Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
Ward Fisher
16c27ca13f
Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries" 2020-08-17 15:51:01 -06:00
Dennis Heimbigner
d538cf38c2 Fix nczarr-experimental to better support CMake and find AWS libraries
The primary fix is to improve CMake build support.
Specific changes include:
* CMake: Provide a better soln to locating the AWS SDK
  libraries; the new way is the preferred method as described in
  the aws-cpp-sdk documentation.
* CMake (and Automake): allow -DENABLE_S3_SDK (default off) to suppress
  looking for AWS libraries.
* CMake: add the complete set of nczarr tests
* CMake: add EXTERNL as needed to various .h files.
* Improve support for windows drive letters in paths.
* Add nczarr and s3 flags to nc-config
* For VisualStudio X nczarr, cleanup the NAN+INFINITY handling
* Convert _MSC_VER -> _WIN32 and vice versa as needed
* NCZarr - support multiple platform paths including windows, cygwin.
  mingw, etc.
* NCZarr - sort the test outputs because different platforms
  produce directory contents in different orders.

One big change concerns netcdf-c/CMakeLists.txt and netcdf-c/configure.ac.
In the current versions, it was the case that --disable-hdf5
disabled netcdf-4 (libsrc4). With nczarr, this can no longer
be the case because nczarr requires libsrc4 even if libhdf5
is disabled. So, I modified the above files to move the
format options (HDF5, NCZarr, HDF4, etc) to a single place
near the front of the files. Now it is the case that:
* Enabling any of the formats that require libsrc4
  also does an implicit --enable-netcdf4.
* --disable-netcdf4 | --disable-netcdf-4 now becomes
  and alias for --disable-hdf5.

There are probably some bugs in this change in terms of
dependencies between format options.

Problems:
* CMake S3 support is still not working for Visual Studio
* A recent issue points out that there is work to do on handling
  UTF8 filenames, but that will be addressed in a separate fix.

Notes:
* Consider converting all of our includes/.h files to use EXTERNL
2020-07-12 12:21:56 -06:00
Dennis Heimbigner
59e04ae071 This PR adds EXPERIMENTAL support for accessing data in the
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.
2020-06-28 18:02:47 -06:00
Ed Hartnett
39ba4aae89 added netcdf_dispatch.h file 2019-07-05 04:50:36 -06:00
Dennis Heimbigner
0c59e13bf7 Master merge, conflict resolution, cleanup 2019-02-24 16:54:13 -07:00
Dennis Heimbigner
24510f2ffb Forgot to distribute ncmodel.h 2019-02-13 21:46:01 -07:00
Dennis Heimbigner
a1f080db19
Merge branch 'master' into byterange.dmh 2019-02-13 14:45:53 -07:00
Dennis Heimbigner
8714066b18 Fix errors when building on big-endian machine
re: issue https://github.com/Unidata/netcdf-c/issues/1278
re: issue https://github.com/Unidata/netcdf-c/issues/876
re: issue https://github.com/Unidata/netcdf-c/issues/806

* Major change to the handling of 8-byte parameters for nc_def_var_filter.
  The old code was not well thought out.
  * The new algorithm is documented in docs/filters.md.
  * Added new utility file plugins/H5Zutil.c to support
  * Modified plugins/H5Zmisc.c to use new algorithm
  the new algorithm.
  * Renamed include/ncfilter.h to include/netcdf_filter.h
    and made it an installed header so clients can access the
    new algorithm utility.
  * Fixed nc_test4/tst_filterparser.c and nc_test4/test_filter_misc.c
    to use the new algorithm
* libdap4/ fixes:
  * d4swap.c has an error in the endian pre-processing such
    that record counts were not being swapped correctly.
  * d4data.c had an error in that checksums were being computed
    after endian swapping rather than before.
* ocinitialize() was never being called, so xxdr bigendian handling
  was never set correctly.
  * Required adding debug statements to occompile
* Found and fixed memory leak in ncdump.c

Not tested:
* HDF4
* Pnetcdf
* parallel HDF5
2019-01-31 21:13:06 -07:00
Dennis Heimbigner
bf2746b8ea Provide byte-range reading of remote datasets
re: issue https://github.com/Unidata/netcdf-c/issues/1251

Assume that you have the URL to a remote dataset
which is a normal netcdf-3 or netcdf-4 file.

This PR allows the netcdf-c to read that dataset's
contents as a netcdf file using HTTP byte ranges
if the remote server supports byte-range access.

Originally, this PR was set up to access Amazon S3 objects,
but it can also access other remote datasets such as those
provided by a Thredds server via the HTTPServer access protocol.
It may also work for other kinds of servers.

Note that this is not intended as a true production
capability because, as is known, this kind of access to
can be quite slow. In addition, the byte-range IO drivers
do not currently do any sort of optimization or caching.

An additional goal here is to gain some experience with
the Amazon S3 REST protocol.

This architecture and its use documented in
the file docs/byterange.dox.

There are currently two test cases:

1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle
   for a remote netcdf-3 file and a remote netcdf-4 file.
2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote
   datasets.

This PR also incorporates significantly changed model inference code
(see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259).

1. It centralizes the code that infers the dispatcher.
2. It adds support for byte-range URLs

Other changes:

1. NC_HDF5_finalize was not being properly called by nc_finalize().
2. Fix minor bug in ncgen3.l
3. fix memory leak in nc4info.c
4. add code to walk the .daprc triples and to replace protocol=
   fragment tag with a more general mode= tag.

Final Note:
Th inference code is still way too complicated. We need to move
to the validfile() model used by netcdf Java, where each
dispatcher is asked if it can process the file. This decentralizes
the inference code. This will be done after all the major new
dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-01 18:27:36 -07:00
Ward Fisher
5be0126920 More standardizing of the copyright stanza. 2018-12-06 14:13:56 -07:00
Ward Fisher
0f72f42d3a Merge branch 'ejh_next_17' of https://github.com/NetCDF-World-Domination-Council/netcdf-c into pr-aggregation.wif 2018-11-28 13:28:26 -07:00
Ward Fisher
a8673c3dfe Moving provenance info out so that it doesn't depend on netCDF4 support to display. 2018-11-27 16:09:17 -07:00
Ed Hartnett
1f64c66cdf rename HDF5 dispatch functions to start with NC4_HDF5 2018-11-26 08:13:57 -07:00
Ed Hartnett
6dbcc42eb6 changes in support of separating HDF5 and libsrc4 2018-11-26 04:31:23 -07:00
Dennis Heimbigner
245961de00 re: github issues
https://github.com/Unidata/netcdf-c/issues/1168
    https://github.com/Unidata/netcdf-c/issues/1163
    https://github.com/Unidata/netcdf-c/issues/1162

This PR partially fixes memory leaks in the netcdf-c library,
in the ncdump utility, and in some test cases.

The netcdf-c library now runs memory clean with the assumption
that the --disable-utilities option is used. The primary remaining
problem is ncgen. Once that is fixed, I believe the netcdf-c library
will run memory clean with no limitations.

Notes
-----------
1. Memory checking was performed using gcc -fsanitize=address.
   Valgrind-based testing has yet to be performed.
2. The pnetcdf, hdf4, and examples code has not been tested.

Misc. Non-leak changes
1. Make tst_diskless2 only run when netcdf4 is enabled (issue 1162)
2. Fix CmakeLists.txt to turn off logging if ENABLE_NETCDF_4 is OFF
3. Isolated all my debug scripts into a single top-level directory
   called debug
4. Fix some USE_NETCDF4 dependencies in nc_test and nc_test4 Makefile.am
2018-10-30 20:48:12 -06:00
Ed Hartnett
786c5a8f2e moved hdf5 specific header stuff to hdf5internal.h 2018-07-12 07:05:21 -06:00
Dennis Heimbigner
3c7ffcc6d1 Fix https://github.com/Unidata/netcdf-c/issues/963
Fix https://github.com/Unidata/netcdf-c/issues/962

1. remove the --disable-diskless option since it is no
   longer needed. Similarly for CMakeLists.txt.
2. Fixed nc4files.c where BAIL and return were mixed
   leading to situation where cleanup code was not
   being invoked. This probably occurs elsewhere,
   but I did not find any specifically.
2018-05-11 15:30:19 -06:00
Dennis Heimbigner
fd089ab3d2 Oops, forgot to remove nc4xinternal from Makefile.am 2018-03-31 11:56:12 -06:00
Dennis Heimbigner
25f062528b This completes (for now) the refactoring of libsrc4.
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.
2018-03-16 11:46:18 -06:00
Ward Fisher
f9f27c5ab7
Merge branch 'master' into newhash0.dmh 2018-02-21 14:19:43 -07:00
Dennis Heimbigner
727b613459 This is the initial step in moving to the new higher performance
(I hope) metadata mechanism. This mostly just adds new pieces of
code (e.g. nclistmap) and does some minor fixes.

It should be transparent to everything else.
The next set of changes will be the big step.
2018-02-08 19:53:40 -07:00
Ed Hartnett
723cc840a3 added missing file 2018-02-08 08:02:28 -07:00
Ward Fisher
16d6f94f30 Merge branch 'master' into filters.dmh 2017-11-13 11:15:02 -07:00
Dennis Heimbigner
733da154c5 1. Keep up to date by merging master
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.
2017-10-08 15:56:45 -06:00
Dennis Heimbigner
8e2abdeed8 Initial version 2017-08-31 14:19:56 -06:00
Dennis Heimbigner
7c3164577e Finalize the compression support.
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.
2017-04-27 13:01:59 -06:00
Dennis Heimbigner
32fe709615 ckp 2017-04-14 11:05:30 -06:00
Dennis Heimbigner
6d8809100f Fix pull request https://github.com/Unidata/netcdf-c/pull/374 (dap4.dmh)
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.
2017-04-03 21:39:44 -06:00
Dennis Heimbigner
3db4f013bf Primary change: add dap4 support
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
2017-03-08 17:01:10 -07:00
Dennis Heimbigner
47daf33074 Resolves Github issue https://github.com/Unidata/netcdf-c/issues/349.
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.
2017-02-16 14:27:54 -07:00
Greg Sjaardema
d5cb4b9e3e Add hashmap for quick retrieval of dim and var 2016-03-24 06:38:45 -06:00
dmh
3dd807a155 The original mem branch somehow got
hosed, so I rebuilt it as a new mem2 branch.
2015-05-28 15:10:10 -06:00
Ward Fisher
028d564344 Have finished with autotools-based netcdf_meta.h template. Need to redo cmake-based template to match behavior.
Modified cmake to use the same netcdf_meta template as autotools.

Removed trace of old cmake template file.
2014-09-11 12:32:55 -06:00
Ward Fisher
37928ea229 Added generated file for cmake-based builds. 2014-09-10 13:35:27 -06:00
Ward Fisher
fe019785ba Update to include XGetopt.h when make dist is invoked. 2013-03-29 21:11:25 +00:00
Dennis Heimbigner
841f7c7148 Move onstack.h from libsrc
to include because it is used
both in libsrc and libdispatch
2013-03-08 18:08:11 +00:00