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#ifndef TAKANE_SINGLE_CELL_EXPERIMENT_HPP
#define TAKANE_SINGLE_CELL_EXPERIMENT_HPP
#include "millijson/millijson.hpp"
#include "byteme/byteme.hpp"
#include "summarized_experiment.hpp"
#include "ranged_summarized_experiment.hpp"
#include <filesystem>
#include <stdexcept>
#include <unordered_set>
#include <string>
/**
* @file single_cell_experiment.hpp
* @brief Validation for single cell experiments.
*/
namespace takane {
/**
* @cond
*/
void validate(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&);
/**
* @endcond
*/
/**
* @namespace takane::single_cell_experiment
* @brief Definitions for single cell experiments.
*/
namespace single_cell_experiment {
/**
* @param path Path to the directory containing the single cell 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::ranged_summarized_experiment::validate(path, metadata, options);
auto sedims = ::takane::summarized_experiment::dimensions(path, metadata, options);
size_t num_cols = sedims[1];
const auto& scemap = internal_json::extract_typed_object_from_metadata(metadata.other, "single_cell_experiment");
const std::string& vstring = internal_json::extract_string_from_typed_object(scemap, "version", "single_cell_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 + "'");
}
// Check the reduced dimensions.
auto rddir = path / "reduced_dimensions";
if (std::filesystem::exists(rddir)) {
auto num_rd = internal_summarized_experiment::check_names_json(rddir);
for (size_t i = 0; i < num_rd; ++i) {
auto rdname = std::to_string(i);
auto rdpath = rddir / rdname;
auto rdmeta = read_object_metadata(rdpath);
::takane::validate(rdpath, rdmeta, options);
auto dims = ::takane::dimensions(rdpath, rdmeta, options);
if (dims.size() < 1) {
throw std::runtime_error("object in 'reduced_dimensions/" + rdname + "' should have at least one dimension");
}
if (dims[0] != num_cols) {
throw std::runtime_error("object in 'reduced_dimensions/" + rdname + "' should have the same number of rows as the columns of its parent '" + metadata.type + "'");
}
}
size_t num_dir_obj = internal_other::count_directory_entries(rddir);
if (num_dir_obj - 1 != num_rd) { // -1 to account for the names.json file itself.
throw std::runtime_error("more objects than expected inside the 'reduced_dimensions' subdirectory");
}
}
// Check the alternative experiments.
auto aedir = path / "alternative_experiments";
std::unordered_set<std::string> alt_names;
if (std::filesystem::exists(aedir)) {
internal_summarized_experiment::check_names_json(aedir, alt_names);
size_t num_ae = alt_names.size();
for (size_t i = 0; i < num_ae; ++i) {
auto aename = std::to_string(i);
auto aepath = aedir / aename;
auto aemeta = read_object_metadata(aepath);
if (!satisfies_interface(aemeta.type, "SUMMARIZED_EXPERIMENT", options)) {
throw std::runtime_error("object in 'alternative_experiments/" + aename + "' should satisfy the 'SUMMARIZED_EXPERIMENT' interface");
}
::takane::validate(aepath, aemeta, options);
auto dims = ::takane::dimensions(aepath, aemeta, options);
if (dims[1] != num_cols) {
throw std::runtime_error("object in 'alternative_experiments/" + aename + "' should have the same number of columns as its parent '" + metadata.type + "'");
}
}
size_t num_dir_obj = internal_other::count_directory_entries(aedir);
if (num_dir_obj - 1 != num_ae) { // -1 to account for the names.json file itself.
throw std::runtime_error("more objects than expected inside the 'alternative_experiments' subdirectory");
}
}
// Validating the main experiment name.
auto mIt = scemap.find("main_experiment_name");
if (mIt != scemap.end()) {
const auto& ver = mIt->second;
if (ver->type() != millijson::STRING) {
throw std::runtime_error("expected 'main_experiment_name' to be a string");
}
const auto& mname = reinterpret_cast<const millijson::String*>(ver.get())->value;
if (mname.empty()) {
throw std::runtime_error("expected 'main_experiment_name' to be a non-empty string");
}
if (alt_names.find(mname) != alt_names.end()) {
throw std::runtime_error("expected 'main_experiment_name' to not overlap with 'alternative_experiment' names (found '" + mname + "')");
}
}
}
}
}
#endif
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