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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"
/**
* @file data_frame_factor.hpp
* @brief Validation for data frame factors.
*/
namespace takane {
/**
* @cond
*/
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&);
/**
* @endcond
*/
/**
* @namespace takane::data_frame_factor
* @brief Definitions for data frame factors.
*/
namespace data_frame_factor {
/**
* If `Options::data_frame_factor_any_duplicated` provided, it enables stricter checking of the uniqueness of the data frame levels.
* Currently, we don't provide a default method for `data_frame` objects, as it's kind of tedious and we haven't gotten around to it yet.
*
* @param path Path to the directory containing the data frame factor.
* @param metadata Metadata for the object, typically read from its `OBJECT` file.
* @param options Validation options.
*/
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);
}
/**
* @param path Path to the directory containing the data frame factor.
* @param metadata Metadata for the object, typically read from its `OBJECT` file.
* @param options Validation options.
* @return Length of the factor.
*/
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
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