SemanticValidator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/DATASTRUCTURES/CVMappings.h>
 
 
namespace OpenMS
{
  class ControlledVocabulary;
  namespace Internal
  {
 
    class OPENMS_DLLAPI SemanticValidator :
      protected Internal::XMLHandler,
      public Internal::XMLFile
    {
public:
      SemanticValidator(const CVMappings & mapping, const ControlledVocabulary & cv);
 
      ~SemanticValidator() override;
 
      struct CVTerm
      {
        String accession;
        String name;
        String value;
        bool has_value;
        String unit_accession;
        bool has_unit_accession;
        String unit_name;
        bool has_unit_name;
      };
 
      bool validate(const String & filename, StringList & errors, StringList & warnings);
 
      bool locateTerm(const String & path, const CVTerm & parsed_term) const;
 
      void setTag(const String & tag);
 
      void setAccessionAttribute(const String & accession);
 
      void setNameAttribute(const String & name);
 
      void setValueAttribute(const String & value);
 
      void setCheckTermValueTypes(bool check);
 
      void setCheckUnits(bool check);
 
      void setUnitAccessionAttribute(const String & accession);
 
      void setUnitNameAttribute(const String & name);
 
protected:
 
      // Docu in base class
      void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
 
      // Docu in base class
      void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
 
      // Docu in base class
      void characters(const XMLCh * const chars, const XMLSize_t /*length*/) override;
 
      virtual String getPath_(UInt remove_from_end = 0) const;
 
      virtual void getCVTerm_(const xercesc::Attributes & attributes, CVTerm & parsed_term);
 
      //~ forward dekl. of a inner struct/class not possible in C++ - or our Library is overtemplated
      //~ /// make a SemanticValidator::CVTerm from a ControlledVocabulary::CVTerm (without any value or unit), needed for writing only cvs at the right places in the xml (i.e. with cvmapping)
      //~ virtual void makeCVTerm_(const ControlledVocabulary::CVTerm & lc, CVTerm & parsed_term);
 
      virtual void handleTerm_(const String & path, const CVTerm & parsed_term);
 
      const CVMappings & mapping_;
 
      const ControlledVocabulary & cv_;
 
      StringList errors_;
 
      StringList warnings_;
 
      StringList open_tags_;
 
      Map<String, std::vector<CVMappingRule> > rules_;
 
      Map<String, Map<String, Map<String, UInt> > > fulfilled_;
 
 
 
      String cv_tag_;
      String accession_att_;
      String name_att_;
      String value_att_;
      String unit_accession_att_;
      String unit_name_att_;
      bool check_term_value_types_;
      bool check_units_;
 
private:
 
      SemanticValidator();
 
      SemanticValidator(const SemanticValidator & rhs);
 
      SemanticValidator & operator=(const SemanticValidator & rhs);
 
    };
 
  }   // namespace Internal
 
} // namespace OpenMS