summarized_experiment.hpp

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#ifndef TAKANE_SUMMARIZED_EXPERIMENT_HPP
#define TAKANE_SUMMARIZED_EXPERIMENT_HPP
 
#include "millijson/millijson.hpp"
 
#include "utils_public.hpp"
#include "utils_other.hpp"
#include "utils_summarized_experiment.hpp"
 
#include <filesystem>
#include <stdexcept>
#include <string>
 
namespace takane {
 
void validate(const std::filesystem::path&, const ObjectMetadata&, Options& options);
size_t height(const std::filesystem::path&, const ObjectMetadata&, Options& options);
std::vector<size_t> dimensions(const std::filesystem::path&, const ObjectMetadata&, Options& options);
bool satisfies_interface(const std::string&, const std::string&, const Options&);
namespace summarized_experiment {
 
inline void validate(const std::filesystem::path& path, const ObjectMetadata& metadata, Options& options) {
    const std::string type_name = "summarized_experiment"; // use a separate variable to avoid dangling reference warnings from GCC.
    const auto& semap = internal_json::extract_typed_object_from_metadata(metadata.other, type_name);
 
    const std::string version_name = "version"; // again, avoid dangling reference warnings.
    const std::string& vstring = internal_json::extract_string_from_typed_object(semap, version_name, type_name);
    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 dimensions.
    auto dims = internal_summarized_experiment::extract_dimensions_json(semap, type_name);
    size_t num_rows = dims.first;
    size_t num_cols = dims.second;
 
    // Checking the assays. The directory is also allowed to not exist, 
    // in which case we have no assays.
    auto adir = path / "assays";
    if (std::filesystem::exists(adir)) {
        size_t num_assays = internal_summarized_experiment::check_names_json(adir);
        for (size_t i = 0; i < num_assays; ++i) {
            auto aname = std::to_string(i);
            auto apath = adir / aname;
            auto ameta = read_object_metadata(apath);
            ::takane::validate(apath, ameta, options);
 
            auto dims = ::takane::dimensions(apath, ameta, options);
            if (dims.size() < 2) {
                throw std::runtime_error("object in 'assays/" + aname + "' should have two or more dimensions");
            }
            if (dims[0] != num_rows) {
                throw std::runtime_error("object in 'assays/" + aname + "' should have the same number of rows as its parent '" + metadata.type + "'");
            }
            if (dims[1] != num_cols) {
                throw std::runtime_error("object in 'assays/" + aname + "' should have the same number of columns as its parent '" + metadata.type + "'");
            }
        }
 
        size_t num_dir_obj = internal_other::count_directory_entries(adir);
        if (num_dir_obj - 1 != num_assays) { // -1 to account for the names.json file itself.
            throw std::runtime_error("more objects than expected inside the 'assays' subdirectory");
        }
    }
 
    auto rd_path = path / "row_data";
    if (std::filesystem::exists(rd_path)) {
        auto rdmeta = read_object_metadata(rd_path);
        if (!satisfies_interface(rdmeta.type, "DATA_FRAME", options)) {
            throw std::runtime_error("object in 'row_data' should satisfy the 'DATA_FRAME' interface");
        }
        ::takane::validate(rd_path, rdmeta, options);
        if (::takane::height(rd_path, rdmeta, options) != num_rows) {
            throw std::runtime_error("data frame at 'row_data' should have number of rows equal to that of the '" + metadata.type + "'");
        }
    }
 
    auto cd_path = path / "column_data";
    if (std::filesystem::exists(cd_path)) {
        auto cdmeta = read_object_metadata(cd_path);
        if (!satisfies_interface(cdmeta.type, "DATA_FRAME", options)) {
            throw std::runtime_error("object in 'column_data' should satisfy the 'DATA_FRAME' interface");
        }
        ::takane::validate(cd_path, cdmeta, options);
        if (::takane::height(cd_path, cdmeta, options) != num_cols) {
            throw std::runtime_error("data frame at 'column_data' should have number of rows equal to the number of columns of its parent '" + metadata.type + "'");
        }
    }
 
    internal_other::validate_metadata(path, "other_data", options);
}
 
inline size_t height([[maybe_unused]] const std::filesystem::path& path, const ObjectMetadata& metadata, [[maybe_unused]] Options& options) {
    const std::string type_name = "summarized_experiment"; // use a separate variable to avoid dangling reference warnings from GCC.
    // Assume it's all valid, so we go straight for the kill.
    const auto& semap = internal_json::extract_object(metadata.other, type_name);
    auto dims = internal_summarized_experiment::extract_dimensions_json(semap, type_name);
    return dims.first;
}
 
inline std::vector<size_t> dimensions([[maybe_unused]] const std::filesystem::path& path, const ObjectMetadata& metadata, [[maybe_unused]] Options& options) {
    const std::string type_name = "summarized_experiment"; // use a separate variable to avoid dangling reference warnings from GCC.
    // Assume it's all valid, so we go straight for the kill.
    const auto& semap = internal_json::extract_object(metadata.other, type_name);
    auto dims = internal_summarized_experiment::extract_dimensions_json(semap, type_name);
    return std::vector<size_t>{ dims.first, dims.second };
}
 
}
 
}
 
#endif