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#ifndef TAKANE_UTILS_FILES_HPP
#define TAKANE_UTILS_FILES_HPP
#include <string>
#include <stdexcept>
#include <filesystem>
#include <array>
#include "utils_other.hpp"
#include "utils_json.hpp"
#include "byteme/byteme.hpp"
namespace takane {
namespace internal_files {
template<class Reader_ = byteme::RawFileReader>
void check_signature(const std::filesystem::path& path, const char* expected, size_t len, const char* msg) {
auto reader = internal_other::open_reader<Reader_>(path, /* buffer_size = */ len);
byteme::PerByte<> pb(&reader);
bool okay = pb.valid();
for (size_t i = 0; i < len; ++i) {
if (!okay) {
throw std::runtime_error("incomplete " + std::string(msg) + " file signature for '" + path.string() + "'");
}
if (pb.get() != expected[i]) {
throw std::runtime_error("incorrect " + std::string(msg) + " file signature for '" + path.string() + "'");
}
okay = pb.advance();
}
}
template<class Reader_ = byteme::RawFileReader>
void check_signature(const std::filesystem::path& path, const unsigned char* expected, size_t len, const char* msg) {
auto reader = internal_other::open_reader<Reader_>(path, /* buffer_size = */ len);
byteme::PerByte<unsigned char> pb(&reader);
bool okay = pb.valid();
for (size_t i = 0; i < len; ++i) {
if (!okay) {
throw std::runtime_error("incomplete " + std::string(msg) + " file signature for '" + path.string() + "'");
}
if (pb.get() != expected[i]) {
throw std::runtime_error("incorrect " + std::string(msg) + " file signature for '" + path.string() + "'");
}
okay = pb.advance();
}
}
inline void check_gzip_signature(const std::filesystem::path& path) {
std::array<unsigned char, 2> gzmagic { 0x1f, 0x8b };
check_signature(path, gzmagic.data(), gzmagic.size(), "GZIP");
}
inline void extract_signature(const std::filesystem::path& path, unsigned char* store, size_t len) {
auto reader = internal_other::open_reader<byteme::RawFileReader>(path, /* buffer_size = */ len);
byteme::PerByte<unsigned char> pb(&reader);
bool okay = pb.valid();
for (size_t i = 0; i < len; ++i) {
if (!okay) {
throw std::runtime_error("file at '" + path.string() + "' is too small to extract a signature of length " + std::to_string(len));
}
store[i] = pb.get();
okay = pb.advance();
}
}
inline bool is_indexed(const internal_json::JsonObjectMap& objmap) {
auto iIt = objmap.find("indexed");
if (iIt == objmap.end()) {
return false;
}
const auto& val = iIt->second;
if (val->type() != millijson::BOOLEAN) {
throw std::runtime_error("property should be a JSON boolean");
}
return reinterpret_cast<const millijson::Boolean*>(val.get())->value;
}
inline void check_sequence_type(const internal_json::JsonObjectMap& objmap, const char* msg) {
auto sIt = objmap.find("sequence_type");
if (sIt == objmap.end()) {
throw std::runtime_error("expected a '" + std::string(msg) + ".sequence_type' property");
}
const auto& val = sIt->second;
if (val->type() != millijson::STRING) {
throw std::runtime_error("'" + std::string(msg) + ".sequence_type' property should be a JSON string");
}
const auto& stype = reinterpret_cast<const millijson::String*>(val.get())->value;
if (stype != "RNA" && stype != "DNA" && stype != "AA" && stype != "custom") {
throw std::runtime_error("unsupported value '" + stype + "' for the '" + std::string(msg) + ".sequence_type' property");
}
}
}
}
#endif
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