Method readFromJSON_

src/openms/source/CHEMISTRY/RibonucleotideDB.cpp:212–266

Read from a JSON file into a RibonucleotideDB

   // Read from a JSON file into a RibonucleotideDB
  void RibonucleotideDB::readFromJSON_(const std::string& path)
  {
    using json = nlohmann::json;

    String full_path = File::find(path);

    // the input file is Unicode encoded, so we need Qt to read it:
    QFile file(full_path.toQString());
    if (!file.open(QIODevice::ReadOnly | QIODevice::Text))
    {
      throw Exception::FileNotReadable(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, full_path);
    }

    QTextStream source(&file);
    source.setCodec("UTF-8");
    Size line_count = 0;
    json mod_obj;
    try
    {
      mod_obj = json::parse(String(source.readAll()));
    }
    catch (Exception::ParseError& e)
    {
      OPENMS_LOG_ERROR << "Error: Failed to parse Modomics JSON. Reason:\n" << e.getName() << " - " << e.what() << endl;
      throw;
    }
    for (auto& element : mod_obj)
    {
      line_count++;
      try
      {
        // Throw an exception if we are straight up missing necessary elements of the JSON
        entryIsWellFormed_(element);

        ParsedEntry_ entry = parseEntry_(element);

        unique_ptr<Ribonucleotide> ribo = std::move(entry.ribo);
        if (entry.isAmbiguous()) // Handle the ambiguity map
        {
          ambiguity_map_[ribo->getCode()] = make_pair(getRibonucleotide(entry.alternative_1), getRibonucleotide(entry.alternative_2));
        }
        // there are some weird exotic mods in modomics that don't have codes. We ignore them
        if (ribo->getCode() != "")
        {
          code_map_[ribo->getCode()] = ribonucleotides_.size();
          max_code_length_ = max(max_code_length_, ribo->getCode().size());
          ribonucleotides_.push_back(std::move(ribo));
        }
      }
      catch (Exception::BaseException& e)
      {
        OPENMS_LOG_ERROR << "Error: Failed to parse input element " << line_count << ". Reason:\n" << e.getName() << " - " << e.what() << "\nSkipping this line." << endl;
      }
    }
  }
  
  // Read entries from a TSV file
  void RibonucleotideDB::readFromFile_(const std::string& path)