Method main_

src/topp/SageAdapter.cpp:429–646

  ExitCodes main_(int, const char**) override
  {
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------

    // do this early, to see if Sage is installed
    String sage_executable = getStringOption_("sage_executable");
    String proc_stdout, proc_stderr;
    TOPPBase::ExitCodes exit_code = runExternalProcess_(sage_executable.toQString(), QStringList() << "--help", proc_stdout, proc_stderr, "");
    auto major_minor_patch = getVersionNumber_(proc_stdout);
    String sage_version = std::get<0>(major_minor_patch) + "." + std::get<1>(major_minor_patch) + "." + std::get<2>(major_minor_patch);
    
    //-------------------------------------------------------------
    // run sage
    //-------------------------------------------------------------
    StringList input_files = getStringList_("in");
    String output_file = getStringOption_("out");
    String output_folder = File::path(output_file);
    String fasta_file = getStringOption_("database");
    int batch = getIntOption_("batch_size");
    String decoy_prefix = getStringOption_("decoy_prefix");

    // create config
    String config = imputeConfigIntoTemplate();

    // store config in config_file
    OPENMS_LOG_INFO << "Creating temp file name..." << std::endl;
    String config_file = File::getTempDirectory() + "/" + File::getUniqueName() + ".json";
    OPENMS_LOG_INFO << "Creating Sage config file..." << config_file << std::endl;
    ofstream config_stream(config_file.c_str());
    config_stream << config;
    config_stream.close();

    // keep config file if debug mode is set
    if (getIntOption_("debug") > 1)
    {
      String debug_config_file = output_folder + "/" + File::getUniqueName() + ".json";
      ofstream debug_config_stream(debug_config_file.c_str());
      debug_config_stream << config;
      debug_config_stream.close();     
    }

    QStringList arguments;
    arguments << config_file.toQString() 
              << "-f" << fasta_file.toQString() 
              << "-o" << output_folder.toQString() 
              << "--write-pin";
    if (batch >= 1) arguments << "--batch-size" << QString(batch);
    for (auto s : input_files) arguments << s.toQString();

    OPENMS_LOG_INFO << "Sage command line: " << sage_executable << " " << arguments.join(' ').toStdString() << std::endl;

    // Sage execution with the executable and the arguments StringList
    exit_code = runExternalProcess_(sage_executable.toQString(), arguments);
    if (exit_code != EXECUTION_OK)
    {
      return exit_code;