Method main_

src/topp/SemanticValidator.cpp:72–130

  }

  ExitCodes main_(int, const char**) override
  {
    String in_file = getStringOption_("in");
    String mapping_file = getStringOption_("mapping_file");
    StringList cv_list = getStringList_("cv");

    CVMappings mappings;
    CVMappingFile().load(mapping_file, mappings, false);

    // Allow definition of the controlled vocabulary files on the commandlines.
    // If none are defined, the hardcoded obo files are used
    ControlledVocabulary cv;
    if (!cv_list.empty())
    {
      for (Size i = 0; i < cv_list.size(); i++)
      {
        // TODO do we need to provide the name of the namespace here?
        cv.loadFromOBO("", cv_list[i]);
      }
    }
    else
    {
      cv.loadFromOBO("PSI-MOD", File::find("/CHEMISTRY/PSI-MOD.obo"));
      cv.loadFromOBO("PATO", File::find("/CV/quality.obo"));
      cv.loadFromOBO("UO", File::find("/CV/unit.obo"));
      cv.loadFromOBO("brenda", File::find("/CV/brenda.obo"));
      cv.loadFromOBO("GO", File::find("/CV/goslim_goa.obo"));
      cv.loadFromOBO("UNIMOD", File::find("/CV/unimod.obo"));
      cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
    }

    // check cv params
    Internal::SemanticValidator semantic_validator(mappings, cv);
    semantic_validator.setCheckTermValueTypes(true);
    semantic_validator.setCheckUnits(true);

    StringList errors, warnings;

    bool valid = semantic_validator.validate(in_file, errors, warnings);
    for (Size i = 0; i < warnings.size(); ++i)
    {
      cout << "Warning: " << warnings[i] << endl;
    }
    for (Size i = 0; i < errors.size(); ++i)
    {
      cout << "Error: " << errors[i] << endl;
    }

    if (valid && warnings.empty() && errors.empty())
    {
      cout << "Congratulations, the file is valid!" << endl;
      return EXECUTION_OK;
    }
    else
    {
      return PARSE_ERROR;
    }