Method createFragment_

src/topp/GenericWrapper.cpp:194–304

  void createFragment_(String & fragment, const Param & param, const std::map<int, std::string>& optional_mappings = (std::map<int, std::string>()))
  {

    //std::cerr << "FRAGMENT: " << fragment << "\n\n";

    // e.g.:  -input %BASENAME[%%in].mzML

    // we have to make this little detour param -> vector<String>
    // to sort the param names by length, otherwise we have a
    // problem with parameter substitution
    // i.e., if A is a prefix of B and gets replaced first, the
    // suffix of B remains and will cause trouble, e.g.: "%%out" vs. "%%out_fm"
    vector<String> param_names;
    param_names.reserve(param.size());
    for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
    {
      param_names.push_back(it->name);
    }
    // sort by length
    std::sort(param_names.begin(), param_names.end(), [](auto &left, auto &right) {StringSizeLess cmp; return cmp(right, left);});

    // iterate through all input params and replace with values:
    SignedSize allowed_percent(0); // filenames might contain '%', which are allowed to remain there (and even must remain)
    for (vector<String>::iterator it = param_names.begin(); it != param_names.end(); ++it)
    {
      if (!fragment.hasSubstring("%%" + *it)) continue;

      String s_new = paramToString_(param.getEntry(*it));
      allowed_percent += s_new.length() - String(s_new).substitute("%", "").length();
      //std::cerr << "IN: " << s_new << "(" << allowed_percent << "\n";
      fragment.substitute("%%" + *it, s_new);
    }
    if (fragment.hasSubstring("%%"))
    {
      throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Invalid '%%' found in '" + fragment + "' after replacing all parameters!", fragment);
    }
    // mapping replace> e.g.: %2
    // do it reverse, since %10 should precede %1
    for (std::map<int, std::string>::const_reverse_iterator it = optional_mappings.rbegin(); it != optional_mappings.rend(); ++it)
    {
      String m = String("%") + it->first;
      if (fragment.hasSubstring(m)) {
        writeDebug_(String("Replacing '") + m + "' in '" + fragment + "' by '" + it->second + "'\n", 10);
        fragment.substitute(m, it->second);
      }
    }

    // %TMP replace:
    fragment.substitute("%TMP", File::getTempDirectory());

    // %RND replace:
    fragment.substitute("%RND", String(UniqueIdGenerator::getUniqueId()));

    // %WORKINGDIR replace:
    fragment.substitute("%WORKINGDIR", tde_.working_directory);

    // %DIR% replace
    {