R lists to HDF5 or JSON

Overview

The uzuki2 repository describes a language-agnostic file format for serializing basic R lists. List elements may be atomic vectors, NULL, or nested lists of such objects. It also supports missing values in the vectors and per-element names on the vectors or lists. A mechanism is also provided to handle external references to more complex objects (e.g., S4 classes) that cannot be directly saved into the format.

Specifications

We support serialization in either HDF5 or (possibly Gzip-compressed) JSON. Both of these are widely used formats and have complementary strengths for list representation. HDF5 supports random access into list components, which can provide optimization opportunities when the list is large and/or contains large atomic vectors. In contrast, JSON is easier to parse and has less storage overhead per list element.

Both the HDF5 and JSON specifications have multiple versions. Links to the version-specific HDF5 specifications are listed below, along with the minimum version of the C++ library required to parse them:

• 1.3, supported by uzuki2 version ≥ 1.3.
• 1.2, supported by uzuki2 version ≥ 1.2.
• 1.1, supported by uzuki2 version ≥ 1.1.
• 1.0, supported by uzuki2 version ≥ 1.0.

Similarly, different versions of the JSON specification are listed below:

• 1.2, supported by uzuki2 version ≥ 1.2.
• 1.1, supported by uzuki2 version ≥ 1.1.
• 1.0, supported by uzuki2 version ≥ 1.0.

Validation

Quick start

A reference implementation of the validator is provided as a header-only C++ library in include/uzuki2. This is useful for portable deployment in different frameworks like R, Python, etc. We can check that a JSON/HDF5 file complies with the uzuki specification:

#include "uzuki2/uzuki2.hpp"
uzuki2::hdf5::validate(h5_file_path, h5_group_name);
uzuki2::json::validate(json_file_path);

This will raise an error if any violations of the specification are observed. If a non-zero expected number of external objects is present:

uzuki2::hdf5::validate(h5_file_path, h5_group_name, num_externals);

Advanced users can also use the uzuki2 parser to load the list into memory. This is achieved by calling parse() with custom provisioner and external reference classes. For example, tests/src/test_subclass.h defines the DefaultProvisioner and DefaultExternals classes, which can be used to load the HDF5 contents into std::vectors for easier downstream operations.

DefaultExternals ext(nexpected);
auto ptr = uzuki2::hdf5::parse<DefaultProvisioner>(file_path, group_name, ext);

See the reference documentation for more details.

Building projects

CMake with FetchContent

If you're using CMake, you just need to add something like this to your CMakeLists.txt:

include(FetchContent)
 
FetchContent_Declare(
  uzuki2 
  GIT_REPOSITORY https://github.com/ArtifactDB/uzuki2
  GIT_TAG master # or any version of interest
)
 
FetchContent_MakeAvailable(uzuki2)

Then you can link to uzuki2 to make the headers available during compilation:

# For executables:
target_link_libraries(myexe uzuki2)
 
# For libaries
target_link_libraries(mylib INTERFACE uzuki2)

CMake with find_package()

You can install the library by cloning a suitable version of this repository and running the following commands:

mkdir build && cd build
cmake .. -DUZUKI2_TESTS=OFF
cmake --build . --target install

Then you can use find_package() as usual:

find_package(artifactdb_uzuki2 CONFIG REQUIRED)
target_link_libraries(mylib INTERFACE artifactdb::uzuki2)

Manual

If you're not using CMake, the simple approach is to just copy the files in the include/ subdirectory - either directly or with Git submodules - and include their path during compilation with, e.g., GCC's -I. You will also need to link to the dependencies listed in the extern/CMakeLists.txt directory, along with the HDF5 and Zlib libraries.

Further comments

See here for a list of changes from the original uzuki library.

Just like the original uzuki, we're just re-using the reference to Uzuki Shimamura for the name: