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#ifndef TAKANE_RANGED_SUMMARIZED_EXPERIMENT_HPP
#define TAKANE_RANGED_SUMMARIZED_EXPERIMENT_HPP
#include "millijson/millijson.hpp"
#include "byteme/byteme.hpp"
#include "summarized_experiment.hpp"
#include <filesystem>
#include <stdexcept>
#include <string>
/**
* @file ranged_summarized_experiment.hpp
* @brief Validation for ranged summarized experiments.
*/
namespace takane {
/**
* @cond
*/
void validate(const std::filesystem::path&, const ObjectMetadata&, Options& options);
size_t height(const std::filesystem::path&, const ObjectMetadata&, Options& options);
bool derived_from(const std::string&, const std::string&, const Options&);
/**
* @endcond
*/
/**
* @namespace takane::ranged_summarized_experiment
* @brief Definitions for ranged summarized experiments.
*/
namespace ranged_summarized_experiment {
/**
* @param path Path to the directory containing the ranged summarized experiment.
* @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) {
::takane::summarized_experiment::validate(path, metadata, options);
const auto& rsemap = internal_json::extract_typed_object_from_metadata(metadata.other, "ranged_summarized_experiment");
const std::string& vstring = internal_json::extract_string_from_typed_object(rsemap, "version", "ranged_summarized_experiment");
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 rangedir = path / "row_ranges";
if (std::filesystem::exists(rangedir)) {
auto rangemeta = read_object_metadata(rangedir);
if (!derived_from(rangemeta.type, "genomic_ranges", options) && !derived_from(rangemeta.type, "genomic_ranges_list", options)) {
throw std::runtime_error("object in 'row_ranges' must be a 'genomic_ranges' or 'genomic_ranges_list'");
}
::takane::validate(rangedir, rangemeta, options);
auto num_row = ::takane::summarized_experiment::height(path, metadata, options);
if (::takane::height(rangedir, rangemeta, options) != num_row) {
throw std::runtime_error("object in 'row_ranges' must have length equal to the number of rows of its parent '" + metadata.type + "'");
}
}
}
}
}
#endif
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