mirror/netcdf-c
2
0
Fork 0
mirror of https://github.com/Unidata/netcdf-c.git synced 2024-12-21 08:39:46 +08:00
Code Issues Packages Projects Releases Wiki Activity
de403a0fe8
netcdf-c/libnczarr/zarr.h

82 lines
3.8 KiB
C
Raw Normal View History

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.
2020-06-29 08:02:47 +08:00
/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
/**
* Provide the zarr specific code to implement the netcdf-4 code.
*
* @author Dennis Heimbigner
*/
#ifndef ZARR_H
#define ZARR_H
Upgrade the nczarr code to match Zarr V2 Re: https://github.com/zarr-developers/zarr-python/pull/716 The Zarr version 2 spec has been extended to include the ability to choose the dimension separator in chunk name keys. The legal separators has been extended from {'.'} to {'.' '/'}. So now it is possible to use a key like "0/1/2/0" for chunk names. This PR implements this for NCZarr. The V2 spec now says that this separator can be set on a per-variable basis. For now, I have chosen to allow this be set only globally by adding a key named "ZARR.DIMENSION_SEPARATOR=<char>" in the .daprc/.dodsrc/ncrc file. Currently, the only legal separator characters are '.' (the default) and '/'. On writing, this key will only be written if its value is different than the default. This change caused problems because supporting a separator of '/' is difficult to parse when keys/paths use '/' as the path separator. A test case was added for this. Additionally, make nczarr be enabled default by default. This required some additional changes so that if zip and/or AWS S3 sdk are unavailable, then they are disabled for NCZarr. In addition the following unrelated changes were made. 1. Tested that pure-zarr mode could read an nczarr formatted store. 1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added. 1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl is not found then the other options that depend upon it properly are disabled. 1. I decided that xarray support should be enabled by default for pure zarr. In order to allow disabling, I added a new mode flag "noxarray". 1. Certain test in nczarr_test depend on use of .dodsrc. In order for these to work when testing in parallel, some inter-test dependencies needed to be added. 1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
struct ChunkKey;
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.
2020-06-29 08:02:47 +08:00
/* zarr.c */
extern int ncz_create_dataset(NC_FILE_INFO_T*, NC_GRP_INFO_T*, const char** controls);
extern int ncz_open_dataset(NC_FILE_INFO_T*, const char** controls);
extern int ncz_del_attr(NC_FILE_INFO_T* file, NC_OBJ* container, const char* name);
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.
2021-07-18 06:55:30 +08:00
/* HDF5 Mimics */
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.
2020-06-29 08:02:47 +08:00
extern int NCZ_isnetcdf4(struct NC_FILE_INFO*);
extern int NCZ_get_libversion(unsigned long* majorp, unsigned long* minorp,unsigned long* releasep);
extern int NCZ_get_superblock(NC_FILE_INFO_T* file, int* superblockp);
extern int ncz_unload_jatts(NCZ_FILE_INFO_T*, NC_OBJ* container, NCjson* jattrs, NCjson* jtypes);
/* zclose.c */
extern int ncz_close_file(NC_FILE_INFO_T* file, int abort);
/* zcvt.c */
Fix JSON quoted string processing in libnczarr re: github issue https://github.com/Unidata/netcdf-c/issues/1982 The problem was that the libnczarr/zsjon.c handling of strings with embedded double quotes was wrong; a one line fix. Also added a test case. Misc. other changes: 1. I Discovered, en passant, that the handling of 64 bit constants had an error that was fixed. 2. cleanup of the constant conversion code to recurse on arrays of values.
2021-05-07 06:39:44 +08:00
extern int NCZ_convert1(NCjson* jsrc, nc_type, unsigned char* memory0);
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'
2021-09-03 07:04:26 +08:00
extern int NCZ_stringconvert1(nc_type typid, size_t len, char* src, NCjson* jvalue);
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.
2020-06-29 08:02:47 +08:00
extern int NCZ_stringconvert(nc_type typid, size_t len, void* data0, NCjson** jdatap);
/* zsync.c */
Add zip file support The primary change is to support the use of a zip file as a storage format. Simultaneously the .nz4 support is made obsolete Use of zip requires the libzip support library, so a number of changes to the build files (Makefile.am, CMakeLists.txt) are necessary to locate and incorporate libzip. The nczarr_tests tests are also changed to add zip testing. Other changes: * Make sure distcheck leaves no files around. * Add some functions to netcdf_aux to export some functions of libnetcdf. * Add a new error NC_EFOUND as the complement of NC_EEMPTY. * Add tracing support to nclog and use it in libnczarr. * Modify the zmap interface to support the writeonce semantics of zip. * Create a new s3util.c to support a variety of S3 auxilliary functions. * EXTERNL'ize a number of functions so they can be used in s3util. * Add support for the S3 ListObjects CommonPrefixes mechanism to improve search. * Add experimental support for running nczarr X s3 tests against the actual Amazon S3 cloud.
2021-01-29 11:11:01 +08:00
extern int ncz_sync_file(NC_FILE_INFO_T* file, int isclose);
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'
2021-09-03 07:04:26 +08:00
extern int ncz_sync_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, int isclose);
extern int ncz_sync_atts(NC_FILE_INFO_T*, NC_OBJ* container, NCindex* attlist, int isclose);
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.
2020-06-29 08:02:47 +08:00
extern int ncz_read_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp);
extern int ncz_read_atts(NC_FILE_INFO_T* file, NC_OBJ* container);
extern int ncz_read_vars(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp);
extern int ncz_read_file(NC_FILE_INFO_T* file);
extern int ncz_write_var(NC_VAR_INFO_T* var);
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.
2021-07-18 06:55:30 +08:00
extern int ncz_read_superblock(NC_FILE_INFO_T* zinfo, char** nczarrvp, char** zarrfp);
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.
2020-06-29 08:02:47 +08:00
/* zutil.c */
extern int NCZ_grpkey(const NC_GRP_INFO_T* grp, char** pathp);
extern int NCZ_varkey(const NC_VAR_INFO_T* var, char** pathp);
extern int NCZ_dimkey(const NC_DIM_INFO_T* dim, char** pathp);
extern int ncz_splitkey(const char* path, NClist* segments);
extern int NCZ_readdict(NCZMAP* zmap, const char* key, NCjson** jsonp);
extern int NCZ_readarray(NCZMAP* zmap, const char* key, NCjson** jsonp);
extern int ncz_zarr_type_name(nc_type nctype, int little, const char** znamep);
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.
2021-07-18 06:55:30 +08:00
extern int ncz_nctype2typeinfo(const char* snctype, nc_type* nctypep);
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.
2020-06-29 08:02:47 +08:00
extern int ncz_dtype2typeinfo(const char* dtype, nc_type* nctypep, int* endianness);
extern int ncz_fill_value_sort(nc_type nctype, int*);
extern int NCZ_createobject(NCZMAP* zmap, const char* key, size64_t size);
extern int NCZ_uploadjson(NCZMAP* zmap, const char* key, NCjson* json);
extern int NCZ_downloadjson(NCZMAP* zmap, const char* key, NCjson** jsonp);
extern int NCZ_isLittleEndian(void);
Upgrade the nczarr code to match Zarr V2 Re: https://github.com/zarr-developers/zarr-python/pull/716 The Zarr version 2 spec has been extended to include the ability to choose the dimension separator in chunk name keys. The legal separators has been extended from {'.'} to {'.' '/'}. So now it is possible to use a key like "0/1/2/0" for chunk names. This PR implements this for NCZarr. The V2 spec now says that this separator can be set on a per-variable basis. For now, I have chosen to allow this be set only globally by adding a key named "ZARR.DIMENSION_SEPARATOR=<char>" in the .daprc/.dodsrc/ncrc file. Currently, the only legal separator characters are '.' (the default) and '/'. On writing, this key will only be written if its value is different than the default. This change caused problems because supporting a separator of '/' is difficult to parse when keys/paths use '/' as the path separator. A test case was added for this. Additionally, make nczarr be enabled default by default. This required some additional changes so that if zip and/or AWS S3 sdk are unavailable, then they are disabled for NCZarr. In addition the following unrelated changes were made. 1. Tested that pure-zarr mode could read an nczarr formatted store. 1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added. 1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl is not found then the other options that depend upon it properly are disabled. 1. I decided that xarray support should be enabled by default for pure zarr. In order to allow disabling, I added a new mode flag "noxarray". 1. Certain test in nczarr_test depend on use of .dodsrc. In order for these to work when testing in parallel, some inter-test dependencies needed to be added. 1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
extern int NCZ_subobjects(NCZMAP* map, const char* prefix, const char* tag, char dimsep, NClist* objlist);
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.
2020-06-29 08:02:47 +08:00
extern int NCZ_grpname_full(int gid, char** pathp);
extern int ncz_get_var_meta(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var);
extern int NCZ_comma_parse(const char* s, NClist* list);
extern int NCZ_swapatomicdata(size_t datalen, void* data, int typesize);
extern char** NCZ_clonestringvec(size_t len, const char** vec);
extern void NCZ_freestringvec(size_t len, char** vec);
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'
2021-09-03 07:04:26 +08:00
extern int NCZ_create_fill_chunk(size64_t chunksize, size_t typesize, const void* fill, void** fillchunkp);
Add zip file support The primary change is to support the use of a zip file as a storage format. Simultaneously the .nz4 support is made obsolete Use of zip requires the libzip support library, so a number of changes to the build files (Makefile.am, CMakeLists.txt) are necessary to locate and incorporate libzip. The nczarr_tests tests are also changed to add zip testing. Other changes: * Make sure distcheck leaves no files around. * Add some functions to netcdf_aux to export some functions of libnetcdf. * Add a new error NC_EFOUND as the complement of NC_EEMPTY. * Add tracing support to nclog and use it in libnczarr. * Modify the zmap interface to support the writeonce semantics of zip. * Create a new s3util.c to support a variety of S3 auxilliary functions. * EXTERNL'ize a number of functions so they can be used in s3util. * Add support for the S3 ListObjects CommonPrefixes mechanism to improve search. * Add experimental support for running nczarr X s3 tests against the actual Amazon S3 cloud.
2021-01-29 11:11:01 +08:00
extern int NCZ_s3clear(ZS3INFO* s3);
Upgrade the nczarr code to match Zarr V2 Re: https://github.com/zarr-developers/zarr-python/pull/716 The Zarr version 2 spec has been extended to include the ability to choose the dimension separator in chunk name keys. The legal separators has been extended from {'.'} to {'.' '/'}. So now it is possible to use a key like "0/1/2/0" for chunk names. This PR implements this for NCZarr. The V2 spec now says that this separator can be set on a per-variable basis. For now, I have chosen to allow this be set only globally by adding a key named "ZARR.DIMENSION_SEPARATOR=<char>" in the .daprc/.dodsrc/ncrc file. Currently, the only legal separator characters are '.' (the default) and '/'. On writing, this key will only be written if its value is different than the default. This change caused problems because supporting a separator of '/' is difficult to parse when keys/paths use '/' as the path separator. A test case was added for this. Additionally, make nczarr be enabled default by default. This required some additional changes so that if zip and/or AWS S3 sdk are unavailable, then they are disabled for NCZarr. In addition the following unrelated changes were made. 1. Tested that pure-zarr mode could read an nczarr formatted store. 1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added. 1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl is not found then the other options that depend upon it properly are disabled. 1. I decided that xarray support should be enabled by default for pure zarr. In order to allow disabling, I added a new mode flag "noxarray". 1. Certain test in nczarr_test depend on use of .dodsrc. In order for these to work when testing in parallel, some inter-test dependencies needed to be added. 1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
extern int NCZ_ischunkname(const char* name,char dimsep);
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'
2021-09-03 07:04:26 +08:00
extern char* NCZ_chunkpath(struct ChunkKey key);
Upgrade the nczarr code to match Zarr V2 Re: https://github.com/zarr-developers/zarr-python/pull/716 The Zarr version 2 spec has been extended to include the ability to choose the dimension separator in chunk name keys. The legal separators has been extended from {'.'} to {'.' '/'}. So now it is possible to use a key like "0/1/2/0" for chunk names. This PR implements this for NCZarr. The V2 spec now says that this separator can be set on a per-variable basis. For now, I have chosen to allow this be set only globally by adding a key named "ZARR.DIMENSION_SEPARATOR=<char>" in the .daprc/.dodsrc/ncrc file. Currently, the only legal separator characters are '.' (the default) and '/'. On writing, this key will only be written if its value is different than the default. This change caused problems because supporting a separator of '/' is difficult to parse when keys/paths use '/' as the path separator. A test case was added for this. Additionally, make nczarr be enabled default by default. This required some additional changes so that if zip and/or AWS S3 sdk are unavailable, then they are disabled for NCZarr. In addition the following unrelated changes were made. 1. Tested that pure-zarr mode could read an nczarr formatted store. 1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added. 1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl is not found then the other options that depend upon it properly are disabled. 1. I decided that xarray support should be enabled by default for pure zarr. In order to allow disabling, I added a new mode flag "noxarray". 1. Certain test in nczarr_test depend on use of .dodsrc. In order for these to work when testing in parallel, some inter-test dependencies needed to be added. 1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
Add zip file support The primary change is to support the use of a zip file as a storage format. Simultaneously the .nz4 support is made obsolete Use of zip requires the libzip support library, so a number of changes to the build files (Makefile.am, CMakeLists.txt) are necessary to locate and incorporate libzip. The nczarr_tests tests are also changed to add zip testing. Other changes: * Make sure distcheck leaves no files around. * Add some functions to netcdf_aux to export some functions of libnetcdf. * Add a new error NC_EFOUND as the complement of NC_EEMPTY. * Add tracing support to nclog and use it in libnczarr. * Modify the zmap interface to support the writeonce semantics of zip. * Create a new s3util.c to support a variety of S3 auxilliary functions. * EXTERNL'ize a number of functions so they can be used in s3util. * Add support for the S3 ListObjects CommonPrefixes mechanism to improve search. * Add experimental support for running nczarr X s3 tests against the actual Amazon S3 cloud.
2021-01-29 11:11:01 +08:00
/* Export */
EXTERNL int NCZ_s3urlprocess(NCURI* url, ZS3INFO* s3);
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.
2020-06-29 08:02:47 +08:00
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.
2020-11-20 08:01:04 +08:00
/* zwalk.c */
Fix a number of CMake problems
2020-11-20 13:24:13 +08:00
EXTERNL int NCZ_read_chunk(int ncid, int varid, size64_t* zindices, void* chunkdata);
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.
2020-11-20 08:01:04 +08:00
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.
2020-06-29 08:02:47 +08:00
#endif /*ZARR_H*/
Reference in New Issue Copy Permalink