netcdf-c/libnczarr/zinternal.c

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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 2003-2018, University Corporation for Atmospheric
* Research. See the COPYRIGHT file for copying and redistribution
* conditions.
*/
/**
* @file @internal Internal netcdf-4 functions.
*
* This file contains functions internal to the netcdf4 library. None of
* the functions in this file are exposed in the exetnal API. These
* functions all relate to the manipulation of netcdf-4's in-memory
* buffer of metadata information, i.e. the linked list of NC
* structs.
*
* @author Dennis Heimbigner, Ed Hartnett
*/
#include "zincludes.h"
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
#include "zfilter.h"
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
/* Forward */
#ifdef LOGGING
/* This is the severity level of messages which will be logged. Use
severity 0 for errors, 1 for important log messages, 2 for less
important, etc. */
extern int nc_log_level;
#endif /* LOGGING */
#ifdef LOOK
/**
* @internal Provide a wrapper for H5Eset_auto
* @param func Pointer to func.
* @param client_data Client data.
*
* @return 0 for success
*/
static herr_t
set_auto(void* func, void *client_data)
{
#ifdef DEBUGH5
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)h5catch,client_data);
#else
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)func,client_data);
#endif
}
#endif
/**
* @internal Provide a function to do any necessary initialization of
* the ZARR library.
*/
int
NCZ_initialize_internal(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
int stat = NC_NOERR;
char* dimsep = NULL;
Add support for setting HDF5 alignment property when creating a file re: https://github.com/Unidata/netcdf-c/issues/2177 re: https://github.com/Unidata/netcdf-c/pull/2178 Provide get/set functions to store global data alignment information and apply it when a file is created. The api is as follows: ```` int nc_set_alignment(int threshold, int alignment); int nc_get_alignment(int* thresholdp, int* alignmentp); ```` If defined, then for every file created opened after the call to nc_set_alignment, for every new variable added to the file, the most recently set threshold and alignment values will be applied to that variable. The nc_get_alignment function return the last values set by nc_set_alignment. If nc_set_alignment has not been called, then it returns the value 0 for both threshold and alignment. The alignment parameters are stored in the NCglobalstate object (see below) for use as needed. Repeated calls to nc_set_alignment will overwrite any existing values in NCglobalstate. The alignment parameters are applied in libhdf5/hdf5create.c and libhdf5/hdf5open.c The set/get alignment functions are defined in libsrc4/nc4internal.c. A test program was added as nc_test4/tst_alignment.c. ## Misc. Changes Unrelated to Alignment * The NCRCglobalstate type was renamed to NCglobalstate to indicate that it represented more general global state than just .rc data. It was also moved to nc4internal.h. This led to a large number of small changes: mostly renaming. The global state management functions were moved to nc4internal.c. * The global chunk cache variables have been moved into NCglobalstate. As warranted, other global state will be moved as well. * Some misc. problems with the nczarr performance tests were corrected.
2022-01-30 06:27:52 +08:00
NCglobalstate* ngs = NULL;
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
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
ncz_initialized = 1;
Add support for setting HDF5 alignment property when creating a file re: https://github.com/Unidata/netcdf-c/issues/2177 re: https://github.com/Unidata/netcdf-c/pull/2178 Provide get/set functions to store global data alignment information and apply it when a file is created. The api is as follows: ```` int nc_set_alignment(int threshold, int alignment); int nc_get_alignment(int* thresholdp, int* alignmentp); ```` If defined, then for every file created opened after the call to nc_set_alignment, for every new variable added to the file, the most recently set threshold and alignment values will be applied to that variable. The nc_get_alignment function return the last values set by nc_set_alignment. If nc_set_alignment has not been called, then it returns the value 0 for both threshold and alignment. The alignment parameters are stored in the NCglobalstate object (see below) for use as needed. Repeated calls to nc_set_alignment will overwrite any existing values in NCglobalstate. The alignment parameters are applied in libhdf5/hdf5create.c and libhdf5/hdf5open.c The set/get alignment functions are defined in libsrc4/nc4internal.c. A test program was added as nc_test4/tst_alignment.c. ## Misc. Changes Unrelated to Alignment * The NCRCglobalstate type was renamed to NCglobalstate to indicate that it represented more general global state than just .rc data. It was also moved to nc4internal.h. This led to a large number of small changes: mostly renaming. The global state management functions were moved to nc4internal.c. * The global chunk cache variables have been moved into NCglobalstate. As warranted, other global state will be moved as well. * Some misc. problems with the nczarr performance tests were corrected.
2022-01-30 06:27:52 +08:00
ngs = NC_getglobalstate();
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
if(ngs != NULL) {
/* Defaults */
ngs->zarr.dimension_separator = DFALT_DIM_SEPARATOR;
dimsep = NC_rclookup("ZARR.DIMENSION_SEPARATOR",NULL,NULL);
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
if(dimsep != NULL) {
/* Verify its value */
if(dimsep != NULL && strlen(dimsep) == 1 && islegaldimsep(dimsep[0]))
ngs->zarr.dimension_separator = dimsep[0];
}
}
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
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
return stat;
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
}
/**
* @internal Provide a function to do any necessary finalization of
* the ZARR library.
*/
int
NCZ_finalize_internal(void)
{
/* Reclaim global resources */
ncz_initialized = 0;
Support MSYS2/Mingw platform re: The current netcdf-c release has some problems with the mingw platform on windows. Mostly they are path issues. Changes to support mingw+msys2: ------------------------------- * Enable option of looking into the windows registry to find the mingw root path. In aid of proper path handling. * Add mingw+msys as a specific platform in configure.ac and move testing of the platform to the front so it is available early. * Handle mingw X libncpoco (dynamic loader) properly even though mingw does not yet support it. * Handle mingw X plugins properly even though mingw does not yet support it. * Alias pwd='pwd -W' to better handle paths in shell scripts. * Plus a number of other minor compile irritations. * Disallow the use of multiple nc_open's on the same file for windows (and mingw) because windows does not seem to handle these properly. Not sure why we did not catch this earlier. * Add mountpoint info to dpathmgr.c to help support mingw. * Cleanup dpathmgr conversions. Known problems: --------------- * I have not been able to get shared libraries to work, so plugins/filters must be disabled. * There is some kind of problem with libcurl that I have not solved, so all uses of libcurl (currently DAP+Byterange) must be disabled. Misc. other fixes: ------------------ * Cleanup the relationship between ENABLE_PLUGINS and various other flags in CMakeLists.txt and configure.ac. * Re-arrange the TESTDIRS order in Makefile.am. * Add pseudo-breakpoint to nclog.[ch] for debugging. * Improve the documentation of the path manager code in ncpathmgr.h * Add better support for relative paths in dpathmgr.c * Default the mode args to NCfopen to include "b" (binary) for windows. * Add optional debugging output in various places. * Make sure that everything builds with plugins disabled. * Fix numerous (s)printf inconsistencies betweenb the format spec and the arguments.
2021-12-24 13:18:56 +08:00
#ifdef ENABLE_NCZARR_FILTERS
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
NCZ_filter_finalize();
Support MSYS2/Mingw platform re: The current netcdf-c release has some problems with the mingw platform on windows. Mostly they are path issues. Changes to support mingw+msys2: ------------------------------- * Enable option of looking into the windows registry to find the mingw root path. In aid of proper path handling. * Add mingw+msys as a specific platform in configure.ac and move testing of the platform to the front so it is available early. * Handle mingw X libncpoco (dynamic loader) properly even though mingw does not yet support it. * Handle mingw X plugins properly even though mingw does not yet support it. * Alias pwd='pwd -W' to better handle paths in shell scripts. * Plus a number of other minor compile irritations. * Disallow the use of multiple nc_open's on the same file for windows (and mingw) because windows does not seem to handle these properly. Not sure why we did not catch this earlier. * Add mountpoint info to dpathmgr.c to help support mingw. * Cleanup dpathmgr conversions. Known problems: --------------- * I have not been able to get shared libraries to work, so plugins/filters must be disabled. * There is some kind of problem with libcurl that I have not solved, so all uses of libcurl (currently DAP+Byterange) must be disabled. Misc. other fixes: ------------------ * Cleanup the relationship between ENABLE_PLUGINS and various other flags in CMakeLists.txt and configure.ac. * Re-arrange the TESTDIRS order in Makefile.am. * Add pseudo-breakpoint to nclog.[ch] for debugging. * Improve the documentation of the path manager code in ncpathmgr.h * Add better support for relative paths in dpathmgr.c * Default the mode args to NCfopen to include "b" (binary) for windows. * Add optional debugging output in various places. * Make sure that everything builds with plugins disabled. * Fix numerous (s)printf inconsistencies betweenb the format spec and the arguments.
2021-12-24 13:18:56 +08:00
#endif
#ifdef ENABLE_S3_SDK
NCZ_s3finalize();
#endif
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
return NC_NOERR;
}
/**
* @internal Given a varid, return the maximum length of a dimension
* using dimid.
*
* @param grp Pointer to group info struct.
* @param varid Variable ID.
* @param dimid Dimension ID.
* @param maxlen Pointer that gets the max length.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid,
size_t *maxlen)
{
NC_VAR_INFO_T *var;
int retval = NC_NOERR;
*maxlen = 0;
/* Find this var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if (!var) return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* If the var hasn't been created yet, its size is 0. */
if (!var->created)
{
*maxlen = 0;
}
else
{
/* Get the number of records in the dataset. */
#ifdef LOOK
#if 0
not needed if ((retval = ncz_open_var_grp2(grp, var->hdr.id, &datasetid)))
BAIL(retval);
#endif
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
/* If it's a scalar dataset, it has length one. */
if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
{
*maxlen = (var->dimids && var->dimids[0] == dimid) ? 1 : 0;
}
else
{
/* Check to make sure ndims is right, then get the len of each
dim in the space. */
if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
if (dataset_ndims != var->ndims)
BAIL(NC_EHDFERR);
if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
h5dimlen, h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
LOG((5, "find_var_dim_max_length: varid %d len %d max: %d",
varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
for (d=0; d<dataset_ndims; d++) {
if (var->dimids[d] == dimid) {
*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
}
}
}
#endif /*LOOK*/
}
#ifdef LOOK
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (h5dimlen) free(h5dimlen);
if (h5dimlenmax) free(h5dimlenmax);
#endif
return retval;
}
#ifdef LOOK
/**
* @internal Search for type with a given HDF type id.
*
* @param h5 File
* @param target_hdf_typeid ZARR type ID to find.
*
* @return Pointer to type info struct, or NULL if not found.
* @author Dennis Heimbigner, Ed Hartnett
*/
NC_TYPE_INFO_T *
ncz_rec_find_hdf_type(NC_FILE_INFO_T *h5, hid_t target_hdf_typeid)
{
NC_TYPE_INFO_T *type;
int i;
assert(h5);
for (i = 0; i < nclistlength(h5->alltypes); i++)
{
type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes, i);
if(type == NULL) continue;
#ifdef LOOK
/* Select the ZARR typeid to use. */
hdf_typeid = ncz_type->native_hdf_typeid ?
ncz_type->native_hdf_typeid : ncz_type->hdf_typeid;
/* Is this the type we are searching for? */
if ((equal = H5Tequal(hdf_typeid, target_hdf_typeid)) < 0)
return NULL;
if (equal)
return type;
#endif
}
/* Can't find it. Fate, why do you mock me? */
return NULL;
}
#endif
/**
* @internal Find the actual length of a dim by checking the length of
* that dim in all variables that use it, in grp or children. **len
* must be initialized to zero before this function is called.
*
* @param grp Pointer to group info struct.
* @param dimid Dimension ID.
* @param len Pointer to pointer that gets length.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
ncz_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len)
{
NC_VAR_INFO_T *var;
int retval;
int i;
assert(grp && len);
LOG((3, "%s: grp->name %s dimid %d", __func__, grp->hdr.name, dimid));
/* If there are any groups, call this function recursively on
* them. */
for (i = 0; i < ncindexsize(grp->children); i++) {
if ((retval = ncz_find_dim_len((NC_GRP_INFO_T*)ncindexith(grp->children, i),
dimid, len)))
return retval;
}
/* For all variables in this group, find the ones that use this
* dimension, and remember the max length. */
for (i = 0; i < ncindexsize(grp->vars); i++)
{
size_t mylen;
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
assert(var);
/* Find max length of dim in this variable... */
if ((retval = find_var_dim_max_length(grp, var->hdr.id, dimid, &mylen)))
return retval;
**len = **len > mylen ? **len : mylen;
}
return NC_NOERR;
}
#if 0
/**
* @internal Close ZARR resources for global atts in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR ZARR error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
close_gatts(NC_GRP_INFO_T *grp)
{
NC_ATT_INFO_T *att;
int a;
for (a = 0; a < ncindexsize(grp->att); a++)
{
att = (NC_ATT_INFO_T *)ncindexith(grp->att, a);
assert(att && att->format_att_info);
#ifdef LOOK
/* Close the ZARR typeid. */
if (ncz_att->native_hdf_typeid &&
H5Tclose(ncz_att->native_hdf_typeid) < 0)
return NC_EHDFERR;
#endif
}
return NC_NOERR;
}
#endif /*0*/
#if 0
/**
* @internal Close ZARR resources for vars in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR ZARR error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
close_vars(NC_GRP_INFO_T *grp)
{
NC_VAR_INFO_T *var;
NC_ATT_INFO_T *att;
int a, i;
for (i = 0; i < ncindexsize(grp->vars); i++)
{
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
assert(var && var->format_var_info);
/* Close the ZARR dataset associated with this var. */
#ifdef LOOK
if (ncz_var->hdf_datasetid)
#endif
{
#ifdef LOOK
LOG((3, "closing ZARR dataset %lld", ncz_var->hdf_datasetid));
if (H5Dclose(ncz_var->hdf_datasetid) < 0)
return NC_EHDFERR;
#endif
if (var->fill_value)
{
if (var->type_info)
{
Fix various problem around VLEN's re: https://github.com/Unidata/netcdf-c/issues/541 re: https://github.com/Unidata/netcdf-c/issues/1208 re: https://github.com/Unidata/netcdf-c/issues/2078 re: https://github.com/Unidata/netcdf-c/issues/2041 re: https://github.com/Unidata/netcdf-c/issues/2143 For a long time, there have been known problems with the management of complex types containing VLENs. This also involves the string type because it is stored as a VLEN of chars. This PR (mostly) fixes this problem. But note that it adds new functions to netcdf.h (see below) and this may require bumping the .so number. These new functions can be removed, if desired, in favor of functions in netcdf_aux.h, but netcdf.h seems the better place for them because they are intended as alternatives to the nc_free_vlen and nc_free_string functions already in netcdf.h. The term complex type refers to any type that directly or transitively references a VLEN type. So an array of VLENS, a compound with a VLEN field, and so on. In order to properly handle instances of these complex types, it is necessary to have function that can recursively walk instances of such types to perform various actions on them. The term "deep" is also used to mean recursive. At the moment, the two operations needed by the netcdf library are: * free'ing an instance of the complex type * copying an instance of the complex type. The current library does only shallow free and shallow copy of complex types. This means that only the top level is properly free'd or copied, but deep internal blocks in the instance are not touched. Note that the term "vector" will be used to mean a contiguous (in memory) sequence of instances of some type. Given an array with, say, dimensions 2 X 3 X 4, this will be stored in memory as a vector of length 2*3*4=24 instances. The use cases are primarily these. ## nc_get_vars Suppose one is reading a vector of instances using nc_get_vars (or nc_get_vara or nc_get_var, etc.). These functions will return the vector in the top-level memory provided. All interior blocks (form nested VLEN or strings) will have been dynamically allocated. After using this vector of instances, it is necessary to free (aka reclaim) the dynamically allocated memory, otherwise a memory leak occurs. So, the recursive reclaim function is used to walk the returned instance vector and do a deep reclaim of the data. Currently functions are defined in netcdf.h that are supposed to handle this: nc_free_vlen(), nc_free_vlens(), and nc_free_string(). Unfortunately, these functions only do a shallow free, so deeply nested instances are not properly handled by them. Note that internally, the provided data is immediately written so there is no need to copy it. But the caller may need to reclaim the data it passed into the function. ## nc_put_att Suppose one is writing a vector of instances as the data of an attribute using, say, nc_put_att. Internally, the incoming attribute data must be copied and stored so that changes/reclamation of the input data will not affect the attribute. Again, the code inside the netcdf library does only shallow copying rather than deep copy. As a result, one sees effects such as described in Github Issue https://github.com/Unidata/netcdf-c/issues/2143. Also, after defining the attribute, it may be necessary for the user to free the data that was provided as input to nc_put_att(). ## nc_get_att Suppose one is reading a vector of instances as the data of an attribute using, say, nc_get_att. Internally, the existing attribute data must be copied and returned to the caller, and the caller is responsible for reclaiming the returned data. Again, the code inside the netcdf library does only shallow copying rather than deep copy. So this can lead to memory leaks and errors because the deep data is shared between the library and the user. # Solution The solution is to build properly recursive reclaim and copy functions and use those as needed. These recursive functions are defined in libdispatch/dinstance.c and their signatures are defined in include/netcdf.h. For back compatibility, corresponding "ncaux_XXX" functions are defined in include/netcdf_aux.h. ```` int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy); int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp); ```` There are two variants. The first two, nc_reclaim_data() and nc_copy_data(), assume the top-level vector is managed by the caller. For reclaim, this is so the user can use, for example, a statically allocated vector. For copy, it assumes the user provides the space into which the copy is stored. The second two, nc_reclaim_data_all() and nc_copy_data_all(), allows the functions to manage the top-level. So for nc_reclaim_data_all, the top level is assumed to be dynamically allocated and will be free'd by nc_reclaim_data_all(). The nc_copy_data_all() function will allocate the top level and return a pointer to it to the user. The user can later pass that pointer to nc_reclaim_data_all() to reclaim the instance(s). # Internal Changes The netcdf-c library internals are changed to use the proper reclaim and copy functions. It turns out that the places where these functions are needed is quite pervasive in the netcdf-c library code. Using these functions also allows some simplification of the code since the stdata and vldata fields of NC_ATT_INFO are no longer needed. Currently this is commented out using the SEPDATA \#define macro. When any bugs are largely fixed, all this code will be removed. # Known Bugs 1. There is still one known failure that has not been solved. All the failures revolve around some variant of this .cdl file. The proximate cause of failure is the use of a VLEN FillValue. ```` netcdf x { types: float(*) row_of_floats ; dimensions: m = 5 ; variables: row_of_floats ragged_array(m) ; row_of_floats ragged_array:_FillValue = {-999} ; data: ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32}, {40, 41}, _ ; } ```` When a solution is found, I will either add it to this PR or post a new PR. # Related Changes * Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data. * Remove the --enable-unfixed-memory-leaks option. * Remove the NC_VLENS_NOTEST code that suppresses some vlen tests. * Document this change in docs/internal.md * Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh. * Mark types as fixed size or not (transitively) to optimize the reclaim and copy functions. # Misc. Changes * Make Doxygen process libdispatch/daux.c * Make sure the NC_ATT_INFO_T.container field is set.
2022-01-09 09:30:00 +08:00
int stat = NC_NOERR;
if((stat = nc_reclaim_data(grp->nc4_info->controller->ext_ncid,var->type_info->hdr.id,var->fill_value,1)))
return stat;
nullfree(var->fill_value);
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
}
}
}
#ifdef LOOK
/* Delete any ZARR dimscale objid information. */
if (ncz_var->dimscale_ncz_objids)
free(ncz_var->dimscale_ncz_objids);
#endif
for (a = 0; a < ncindexsize(var->att); a++)
{
att = (NC_ATT_INFO_T *)ncindexith(var->att, a);
assert(att && att->format_att_info);
#ifdef LOOK
/* Close the ZARR typeid if one is open. */
if (ncz_att->native_hdf_typeid &&
H5Tclose(ncz_att->native_hdf_typeid) < 0)
return NC_EHDFERR;
#endif
}
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.
2020-09-28 02:43:46 +08:00
/* Reclaim filters */
if(var->filters != NULL) {
(void)NCZ_filter_freelists(var);
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.
2020-09-28 02:43:46 +08:00
}
var->filters = NULL;
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
}
return NC_NOERR;
}
#endif /*0*/
#if 0
/**
* @internal Close ZARR resources for dims in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR ZARR error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
close_dims(NC_GRP_INFO_T *grp)
{
NC_DIM_INFO_T *dim;
int i;
for (i = 0; i < ncindexsize(grp->dim); i++)
{
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, i);
assert(dim && dim->format_dim_info);
#ifdef LOOK
/* If this is a dim without a coordinate variable, then close
* the ZARR DIM_WITHOUT_VARIABLE dataset associated with this
* dim. */
if (ncz_dim->hdf_dimscaleid && H5Dclose(ncz_dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
#endif
}
return NC_NOERR;
}
#endif /*0*/
#if 0
/**
* @internal Close ZARR resources for types in a group. Set values to
* 0 after closing types. Because of type reference counters, these
* closes can be called multiple times.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR ZARR error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
close_types(NC_GRP_INFO_T *grp)
{
int i;
for (i = 0; i < ncindexsize(grp->type); i++)
{
NC_TYPE_INFO_T *type;
type = (NC_TYPE_INFO_T *)ncindexith(grp->type, i);
assert(type && type->format_type_info);
#ifdef LOOK
/* Close any open user-defined ZARR typeids. */
if (ncz_type->hdf_typeid && H5Tclose(ncz_type->hdf_typeid) < 0)
return NC_EHDFERR;
ncz_type->hdf_typeid = 0;
if (ncz_type->native_hdf_typeid &&
H5Tclose(ncz_type->native_hdf_typeid) < 0)
return NC_EHDFERR;
ncz_type->native_hdf_typeid = 0;
#endif
}
return NC_NOERR;
}
#endif /*0*/
#if 0
/**
* @internal Recursively free ZARR objects for a group (and everything
* it contains).
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR ZARR error.
* @author Dennis Heimbigner, Ed Hartnett
*/
static int
ncz_rec_grp_NCZ_del(NC_GRP_INFO_T *grp)
{
int i;
int retval;
assert(grp && grp->format_grp_info);
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
/* Recursively call this function for each child, if any, stopping
* if there is an error. */
for (i = 0; i < ncindexsize(grp->children); i++)
if ((retval = ncz_rec_grp_NCZ_del((NC_GRP_INFO_T *)ncindexith(grp->children,
i))))
return retval;
/* Close ZARR resources associated with global attributes. */
if ((retval = close_gatts(grp)))
return retval;
/* Close ZARR resources associated with vars. */
if ((retval = close_vars(grp)))
return retval;
/* Close ZARR resources associated with dims. */
if ((retval = close_dims(grp)))
return retval;
/* Close ZARR resources associated with types. */
if ((retval = close_types(grp)))
return retval;
/* Close the ZARR group. */
LOG((4, "%s: closing group %s", __func__, grp->hdr.name));
#ifdef LOOK
if (ncz_grp->hdf_grpid && H5Gclose(ncz_grp->hdf_grpid) < 0)
return NC_EHDFERR;
#endif
return NC_NOERR;
}
#endif /*0*/
/**
* @internal Given an ncid and varid, get pointers to the group and var
* metadata. Lazy var metadata reads are done as needed.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param h5 Pointer that gets pointer to the NC_FILE_INFO_T struct
* for this file. Ignored if NULL.
* @param grp Pointer that gets pointer to group info. Ignored if
* NULL.
* @param var Pointer that gets pointer to var info. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOTVAR Variable not found.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
ncz_find_grp_file_var(int ncid, int varid, NC_FILE_INFO_T **h5,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var)
{
NC_FILE_INFO_T *my_h5;
NC_VAR_INFO_T *my_var;
int retval;
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.
2020-09-28 02:43:46 +08:00
/* Delegate to libsrc4 */
if((retval = nc4_find_grp_h5_var(ncid,varid,&my_h5,grp,&my_var))) return retval;
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
/* Do we need to read var metadata? */
if (!my_var->meta_read && my_var->created)
if ((retval = ncz_get_var_meta(my_h5, my_var)))
return retval;
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.
2020-09-28 02:43:46 +08:00
if (var) *var = my_var;
if (h5) *h5 = my_h5;
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
return NC_NOERR;
}
/**
* @internal Given an ncid, varid, and attribute name, return
* normalized name and (optionally) pointers to the file, group,
* var, and att info structs.
* Lazy reads of attributes and variable metadata are done as needed.
*
* @param ncid File/group ID.
* @param varid Variable ID.
* @param name Name to of attribute.
* @param attnum Number of attribute.
* @param use_name If true, use the name to get the
* attribute. Otherwise use the attnum.
* @param norm_name Pointer to storage of size NC_MAX_NAME + 1,
* which will get the normalized name, if use_name is true. Ignored if
* NULL.
* @param h5 Pointer to pointer that gets file info struct. Ignored if
* NULL.
* @param grp Pointer to pointer that gets group info struct. Ignored
* if NULL.
* @param h5 Pointer to pointer that gets variable info
* struct. Ignored if NULL.
* @param att Pointer to pointer that gets attribute info
* struct. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTVAR Variable not found.
* @return ::NC_ENOTATT Attribute not found.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
ncz_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
int use_name, char *norm_name, NC_FILE_INFO_T **h5,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var,
NC_ATT_INFO_T **att)
{
NC_FILE_INFO_T *my_h5;
NC_GRP_INFO_T *my_grp;
NC_VAR_INFO_T *my_var = NULL;
NC_ATT_INFO_T *my_att;
char my_norm_name[NC_MAX_NAME + 1] = "";
NCindex *attlist = NULL;
int retval;
LOG((4, "%s: ncid %d varid %d attnum %d use_name %d", __func__, ncid, varid,
attnum, use_name));
/* Don't need to provide name unless getting att pointer and using
* use_name. */
assert(!att || ((use_name && name) || !use_name));
/* Find info for this file, group, and h5 info. */
if ((retval = nc4_find_nc_grp_h5(ncid, NULL, &my_grp, &my_h5)))
return retval;
assert(my_grp && my_h5);
/* Read the attributes for this var, if any */
switch (retval = ncz_getattlist(my_grp, varid, &my_var, &attlist)) {
case NC_NOERR: assert(attlist); break;
case NC_EEMPTY: retval = NC_NOERR; attlist = NULL; break; /* variable has no attributes */
default: return retval; /* significant error */
}
/* Need a name if use_name is true. */
if (use_name && !name)
return NC_EBADNAME;
/* Normalize the name. */
if (use_name)
if ((retval = nc4_normalize_name(name, my_norm_name)))
return retval;
/* Now find the attribute by name or number. */
if (att)
{
my_att = use_name ? (NC_ATT_INFO_T *)ncindexlookup(attlist, my_norm_name) :
(NC_ATT_INFO_T *)ncindexith(attlist, attnum);
if (!my_att)
return NC_ENOTATT;
}
/* Give the people what they want. */
if (norm_name)
strncpy(norm_name, my_norm_name, NC_MAX_NAME);
if (h5)
*h5 = my_h5;
if (grp)
*grp = my_grp;
if (var)
*var = my_var;
if (att)
*att = my_att;
return retval;
}
/**
* @internal Ensure that either var->no_fill || var->fill_value != NULL.
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
* Side effects: set as default if necessary and build _FillValue attribute.
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
*
* @param h5 Pointer to file info struct.
* @param var Pointer to variable info struct.
*
* @returns NC_NOERR No error.
* @returns NC_ENOMEM Out of memory.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NCZ_ensure_fill_value(NC_VAR_INFO_T *var)
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
{
size_t size;
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
int retval = NC_NOERR;
NC_FILE_INFO_T *h5 = var->container->nc4_info;
if(var->no_fill)
return NC_NOERR;
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
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
#if 0 /*LOOK*/
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
/* Find out how much space we need for this type's fill value. */
if (var->type_info->nc_type_class == NC_VLEN)
size = sizeof(nc_vlen_t);
else if (var->type_info->nc_type_class == NC_STRING)
size = sizeof(char *);
else
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
#endif
if ((retval = nc4_get_typelen_mem(h5, var->type_info->hdr.id, &size))) goto done;
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
assert(size);
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
/* If the user has set a fill_value for this var, use, otherwise find the default fill value. */
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
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
if (var->fill_value == NULL) {
/* initialize the fill_value to the default */
/* Allocate the fill_value space. */
if((var->fill_value = calloc(1, size))==NULL)
{retval = NC_ENOMEM; goto done;}
if((retval = nc4_get_default_fill_value(var->type_info, var->fill_value))) {
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
/* Note: release memory, but don't return error on failure */
(void)NCZ_reclaim_fill_value(var);
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
retval = NC_NOERR;
goto done;
}
}
assert(var->fill_value != NULL);
LOG((4, "Found a fill value for var %s", var->hdr.name));
#if 0 /*LOOK*/
/* Need to copy both vlen and a single basetype */
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
if (var->type_info->nc_type_class == NC_VLEN)
{
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
nc_vlen_t *in_vlen = (nc_vlen_t *)(var->fill_value);
nc_vlen-t *fv_vlen = (nc_vlen_t *)fill;
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
size_t basetypesize = 0;
if((retval=nc4_get_typelen_mem(h5, var->type_info->u.v.base_nc_typeid, &basetypesize)))
return retval;
fv_vlen->len = in_vlen->len;
if (!(fv_vlen->p = malloc(basetypesize * in_vlen->len)))
{
free(*fillp);
*fillp = NULL;
return NC_ENOMEM;
}
memcpy(fv_vlen->p, in_vlen->p, in_vlen->len * basetypesize);
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if (*(char **)var->fill_value)
if (!(**(char ***)fillp = strdup(*(char **)var->fill_value)))
{
free(*fillp);
*fillp = NULL;
return NC_ENOMEM;
}
}
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
#endif /*0*/
done:
return retval;
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
}
#ifdef LOGGING
/* We will need to check against nc log level from nc4internal.c. */
extern int nc_log_level;
/**
* @internal This is like nc_set_log_level(), but will also turn on
* ZARR internal logging, in addition to netCDF logging. This should
* never be called by the user. It is called in open/create when the
* nc logging level has changed.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
NCZ_set_log_level()
{
/* If the user wants to completely turn off logging, turn off NCZ
logging too. Now I truely can't think of what to do if this
fails, so just ignore the return code. */
if (nc_log_level == NC_TURN_OFF_LOGGING)
{
#ifdef LOOK
set_auto(NULL, NULL);
#endif
LOG((1, "NCZ error messages turned off!"));
}
else
{
#ifdef LOOK
if (set_auto((H5E_auto_t)&H5Eprint1, stderr) < 0)
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
LOG((0, "H5Eset_auto failed!"));
#endif
LOG((1, "NCZ error messages turned on."));
}
return NC_NOERR;
}
#endif /* LOGGING */
/**
* @internal Get the format (i.e. NC_FORMAT_NETCDF4 pr
* NC_FORMAT_NETCDF4_CLASSIC) of an open netCDF-4 file.
*
* @param ncid File ID (ignored).
* @param formatp Pointer that gets the constant indicating format.
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Ed Hartnett
*/
int
NCZ_inq_format(int ncid, int *formatp)
{
int stat = NC_NOERR;
ZTRACE(0,"ncid=%d formatp=%p",ncid,formatp);
stat = NC4_inq_format(ncid,formatp);
return ZUNTRACEX(stat,"formatp=%d",(formatp?-1:*formatp));
}
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
/**
* @internal Return the extended format (i.e. the dispatch model),
* plus the mode associated with an open file.
*
* @param ncid File ID (ignored).
* @param formatp a pointer that gets the extended format. Note that
* this is not the same as the format provided by nc_inq_format(). The
* extended foramt indicates the dispatch layer model. NetCDF-4 files
* will always get NC_FORMATX_NC4.
* @param modep a pointer that gets the open/create mode associated with
* this file. Ignored if NULL.
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Dennis Heimbigner
*/
int
NCZ_inq_format_extended(int ncid, int *formatp, int *modep)
{
NC *nc;
int retval;
LOG((2, "%s: ncid 0x%x", __func__, ncid));
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, NULL, NULL)))
return NC_EBADID;
if(modep)
*modep = nc->mode|NC_NETCDF4;
if (formatp)
*formatp = NC_FORMATX_NCZARR;
return NC_NOERR;
}