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#ifndef TAKANE_ATOMIC_VECTOR_HPP
#define TAKANE_ATOMIC_VECTOR_HPP
#include <string>
#include <stdexcept>
#include <filesystem>
#include "ritsuko/hdf5/hdf5.hpp"
#include "utils_public.hpp"
#include "utils_string.hpp"
#include "utils_json.hpp"
/**
* @file atomic_vector.hpp
* @brief Validation for atomic vectors.
*/
namespace takane {
/**
* @namespace takane::atomic_vector
* @brief Definitions for atomic vectors.
*/
namespace atomic_vector {
/**
* @param path Path to the directory containing the atomic vector.
* @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, "atomic_vector");
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 + "'");
}
auto handle = ritsuko::hdf5::open_file(path / "contents.h5");
auto ghandle = ritsuko::hdf5::open_group(handle, "atomic_vector");
auto dhandle = ritsuko::hdf5::open_dataset(ghandle, "values");
auto vlen = ritsuko::hdf5::get_1d_length(dhandle.getSpace(), false);
auto type = ritsuko::hdf5::open_and_load_scalar_string_attribute(ghandle, "type");
const char* missing_attr_name = "missing-value-placeholder";
if (type == "string") {
if (!ritsuko::hdf5::is_utf8_string(dhandle)) {
throw std::runtime_error("expected a datatype for 'values' that can be represented by a UTF-8 encoded string");
}
auto missingness = ritsuko::hdf5::open_and_load_optional_string_missing_placeholder(dhandle, missing_attr_name);
std::string format = internal_string::fetch_format_attribute(ghandle);
internal_string::validate_string_format(dhandle, vlen, format, missingness.first, missingness.second, options.hdf5_buffer_size);
} else {
if (type == "integer") {
if (ritsuko::hdf5::exceeds_integer_limit(dhandle, 32, true)) {
throw std::runtime_error("expected a datatype for 'values' that fits in a 32-bit signed integer");
}
} else if (type == "boolean") {
if (ritsuko::hdf5::exceeds_integer_limit(dhandle, 32, true)) {
throw std::runtime_error("expected a datatype for 'values' that fits in a 32-bit signed integer");
}
} else if (type == "number") {
if (ritsuko::hdf5::exceeds_float_limit(dhandle, 64)) {
throw std::runtime_error("expected a datatype for 'values' that fits in a 64-bit float");
}
} else {
throw std::runtime_error("unsupported type '" + type + "'");
}
if (dhandle.attrExists(missing_attr_name)) {
auto missing_attr = dhandle.openAttribute(missing_attr_name);
ritsuko::hdf5::check_missing_placeholder_attribute(dhandle, missing_attr);
}
}
internal_string::validate_names(ghandle, "names", vlen, options.hdf5_buffer_size);
}
/**
* @param path Path to the directory containing the atomic vector.
* @param metadata Metadata for the object, typically read from its `OBJECT` file.
* @param options Validation options.
* @return Length of the vector.
*/
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("atomic_vector");
auto dhandle = ghandle.openDataSet("values");
return ritsuko::hdf5::get_1d_length(dhandle.getSpace(), false);
}
}
}
#endif
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