First experimental release of nczarr #1769
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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.
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This pull request introduces 2 alerts when merging 59e04ae into ba24e3c - view on LGTM.com new alerts:
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This pull request fixes 2 alerts when merging 9e1ff15 into ba24e3c - view on LGTM.com fixed alerts:
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This will be very welcome by the user community! Great work @DennisHeimbigner ! |
They rely on access to the unidata S3 bucket on stratus, so only Unidata NetCDF personnel can execute them, To enable them, one needs to do this at command level: export NETCDF_S3_TESTS=1
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This pull request fixes 2 alerts when merging d21c017 into ba24e3c - view on LGTM.com fixed alerts:
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This pull request fixes 2 alerts when merging b47bee4 into ba24e3c - view on LGTM.com fixed alerts:
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…imbigner/netcdf-c into nczarr-experimental.dmh
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This pull request fixes 2 alerts when merging 5c6fb13 into ba24e3c - view on LGTM.com fixed alerts:
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Thanks @DennisHeimbigner ! The travis validation passed, but appeared to be stuck on the GitHub side. I've restarted the travis build, we'll see if that clears it. I'll get this merged ASAP. |
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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.
WARNING: this code has had limited testing, so do not use this version for production work. Also, performance improvements are ongoing. Note especially the following platform matrix of successful tests:
Additionally, and as a consequence of the addition of NCZarr, major changes have been made to the Filter API. Note that 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, previous 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:
Changes directly related to Zarr:
Changes not directly related to Zarr:
Changes Left TO-DO: