data_frame_factor.hpp

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#ifndef TAKANE_DATA_FRAME_FACTOR_HPP
#define TAKANE_DATA_FRAME_FACTOR_HPP
 
#include <string>
#include <stdexcept>
#include <filesystem>
 
#include "ritsuko/hdf5/hdf5.hpp"
 
#include "utils_public.hpp"
#include "utils_string.hpp"
#include "utils_factor.hpp"
#include "utils_json.hpp"
#include "utils_other.hpp"
 
namespace takane {
 
void validate(const std::filesystem::path&, const ObjectMetadata&, Options&);
size_t height(const std::filesystem::path&, const ObjectMetadata&, Options&);
bool satisfies_interface(const std::string&, const std::string&, const Options&);
namespace data_frame_factor {
 
inline void validate(const std::filesystem::path& path, const ObjectMetadata& metadata, Options& options) {
    const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame_factor");
    auto version = ritsuko::parse_version_string(vstring.c_str(), vstring.size(), /* skip_patch = */ true);
    if (version.major != 1) {
        throw std::runtime_error("unsupported version string '" + vstring + "'");
    }
 
    // Validating the levels.
    auto lpath = path / "levels";
    auto lmeta = read_object_metadata(lpath);
    if (!satisfies_interface(lmeta.type, "DATA_FRAME", options)) {
        throw std::runtime_error("expected 'levels' to be an object that satifies the 'DATA_FRAME' interface");
    }
 
    try {
        ::takane::validate(lpath, lmeta, options);
    } catch (std::exception& e) {
        throw std::runtime_error("failed to validate 'levels'; " + std::string(e.what()));
    }
    size_t num_levels = ::takane::height(lpath, lmeta, options);
 
    if (options.data_frame_factor_any_duplicated) {
        if (options.data_frame_factor_any_duplicated(lpath, lmeta, options)) {
            throw std::runtime_error("'levels' should not contain duplicated rows");
        }
    }
 
    auto handle = ritsuko::hdf5::open_file(path / "contents.h5");
    auto ghandle = ritsuko::hdf5::open_group(handle, "data_frame_factor");
    size_t num_codes = internal_factor::validate_factor_codes(ghandle, "codes", num_levels, options.hdf5_buffer_size, /* allow_missing = */ false);
 
    internal_other::validate_mcols(path, "element_annotations", num_codes, options);
    internal_other::validate_metadata(path, "other_annotations", options);
 
    internal_string::validate_names(ghandle, "names", num_codes, options.hdf5_buffer_size);
}
 
inline size_t height(const std::filesystem::path& path, [[maybe_unused]] const ObjectMetadata& metadata, [[maybe_unused]] Options& options) {
    auto handle = ritsuko::hdf5::open_file(path / "contents.h5");
    auto ghandle = handle.openGroup("data_frame_factor");
    auto dhandle = ghandle.openDataSet("codes");
    return ritsuko::hdf5::get_1d_length(dhandle.getSpace(), false);
}
 
}
 
}
 
#endif