XMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Macros.h>
 
#include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
#include <OpenMS/DATASTRUCTURES/DateTime.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
 
#include <xercesc/util/XMLString.hpp>
#include <xercesc/sax2/DefaultHandler.hpp>
#include <xercesc/sax/Locator.hpp>
#include <xercesc/sax2/Attributes.hpp>
 
#include <algorithm>
#include <iosfwd>
#include <string>
 
namespace OpenMS
{
  class ProteinIdentification;
 
 
  namespace Internal
  {
 
    /*
     * @brief Helper class for XML parsing that handles the conversions of Xerces strings
     *
     * It provides the convert() function which internally calls
     * XMLString::transcode and ensures that the memory is released properly
     * through XMLString::release internally. It returns a std::string or
     * std::basic_string<XMLCh> to the caller who takes ownership of the data.
     *
    */
    class OPENMS_DLLAPI StringManager
    {
 
      typedef std::basic_string<XMLCh> XercesString;
 
      // Converts from a narrow-character string to a wide-character string.
      inline XercesString fromNative_(const char* str) const
      {
        XMLCh* ptr(xercesc::XMLString::transcode(str));
        XercesString result(ptr);
        xercesc::XMLString::release(&ptr);
        return result;
      }
 
      // Converts from a narrow-character string to a wide-character string.
      inline XercesString fromNative_(const String& str) const
      {
        return fromNative_(str.c_str());
      }
 
      // Converts from a wide-character string to a narrow-character string.
      inline String toNative_(const XMLCh* str) const
      {
        char* ptr(xercesc::XMLString::transcode(str));
        String result(ptr);
        xercesc::XMLString::release(&ptr);
        return result;
      }
 
      // Converts from a wide-character string to a narrow-character string.
      inline String toNative_(const XercesString& str) const
      {
        return toNative_(str.c_str());
      }
 
 
public:
      StringManager();
 
      ~StringManager();
 
      inline XercesString convert(const char * str) const
      {
        return fromNative_(str);
      }
 
      inline XercesString convert(const std::string & str) const
      {
        return fromNative_(str.c_str());
      }
 
      inline XercesString convert(const String & str) const
      {
        return fromNative_(str.c_str());
      }
 
      inline String convert(const XMLCh * str) const
      {
        return toNative_(str);
      }
 
      static void appendASCII(const XMLCh * str, const XMLSize_t length, String & result);
 
    };
 
    class OPENMS_DLLAPI XMLHandler :
      public xercesc::DefaultHandler
    {
public:
 
      class OPENMS_DLLAPI EndParsingSoftly :
        public Exception::BaseException
      {
      public:
        EndParsingSoftly(const char * file, int line, const char * function) :
          Exception::BaseException(file, line, function)
        {
        }
 
      };
 
      enum ActionMode
      {
        LOAD,               
        STORE               
      };
 
      enum LOADDETAIL 
      {  
        LD_ALLDATA,       // default; load all data
        LD_RAWCOUNTS,     // only count the total number of spectra and chromatograms (usually very fast)
        LD_COUNTS_WITHOPTIONS // count the number of spectra, while respecting PeakFileOptions (msLevel and RTRange) and chromatograms (fast)
      };
 
 
      XMLHandler(const String & filename, const String & version);
      ~XMLHandler() override;
 
      void reset();
 
 
      void fatalError(const xercesc::SAXParseException & exception) override;
      void error(const xercesc::SAXParseException & exception) override;
      void warning(const xercesc::SAXParseException & exception) override;
 
      void fatalError(ActionMode mode, const String & msg, UInt line = 0, UInt column = 0) const;
      void error(ActionMode mode, const String & msg, UInt line = 0, UInt column = 0) const;
      void warning(ActionMode mode, const String & msg, UInt line = 0, UInt column = 0) const;
 
      void characters(const XMLCh * const chars, const XMLSize_t length) override;
      void startElement(const XMLCh * const uri, const XMLCh * const localname, const XMLCh * const qname, const xercesc::Attributes & attrs) override;
      void endElement(const XMLCh * const uri, const XMLCh * const localname, const XMLCh * const qname) override;
 
      virtual void writeTo(std::ostream & /*os*/);
 
      String errorString();
 
      virtual LOADDETAIL getLoadDetail() const;
 
      virtual void setLoadDetail(const LOADDETAIL d);
 
      static String writeXMLEscape(const String& to_escape)
      {
        String _copy = to_escape;
        // has() is cheap, so check before calling substitute(), since substitute() will usually happen rarely
        if (_copy.has('&')) _copy.substitute("&","&amp;");
        if (_copy.has('>')) _copy.substitute(">","&gt;");
        if (_copy.has('"')) _copy.substitute("\"","&quot;");
        if (_copy.has('<')) _copy.substitute("<","&lt;");
        if (_copy.has('\'')) _copy.substitute("'","&apos;");
 
        return _copy;
      }
 
      void checkUniqueIdentifiers_(const std::vector<ProteinIdentification>& prot_ids);
 
protected:
      mutable String error_message_;
 
      String file_;
 
      String version_;
 
      StringManager sm_;
 
      std::vector<String> open_tags_;
 
      LOADDETAIL load_detail_; 
 
 
      inline bool equal_(const XMLCh * a, const XMLCh * b) const
      {
        return xercesc::XMLString::compareString(a, b) == 0;
      }
 
 
 
      void writeUserParam_(const String & tag_name, std::ostream & os, const MetaInfoInterface & meta, UInt indent) const;
 
 
 
 
      std::vector<std::vector<String> > cv_terms_;
 
      inline SignedSize cvStringToEnum_(const Size section, const String & term, const char * message, const SignedSize result_on_error = 0)
      {
        OPENMS_PRECONDITION(section < cv_terms_.size(), "cvStringToEnum_: Index overflow (section number too large)");
 
        std::vector<String>::const_iterator it = std::find(cv_terms_[section].begin(), cv_terms_[section].end(), term);
        if (it != cv_terms_[section].end())
        {
          return it - cv_terms_[section].begin();
        }
        else
        {
          warning(LOAD, String("Unexpected CV entry '") + message + "'='" + term + "'");
          return result_on_error;
        }
      }
 
 
 
 
      inline Int asInt_(const String & in)
      {
        Int res = 0;
        try
        {
          res = in.toInt();
        }
        catch (Exception::ConversionError&)
        {
          error(LOAD, String("Int conversion error of \"") + in + "\"");
        }
        return res;
      }
 
      inline Int asInt_(const XMLCh * in)
      {
        return xercesc::XMLString::parseInt(in);
      }
 
      inline UInt asUInt_(const String & in)
      {
        UInt res = 0;
        try
        {
          Int tmp = in.toInt();
          if (tmp < 0)
          {
            throw Exception::ConversionError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "");
          }
          res = UInt(tmp);
        }
        catch (Exception::ConversionError& )
        {
          error(LOAD, String("UInt conversion error of \"") + in + "\"");
        }
        return res;
      }
 
      inline double asDouble_(const String & in)
      {
        double res = 0.0;
        try
        {
          res = in.toDouble();
        }
        catch (Exception::ConversionError& )
        {
          error(LOAD, String("Double conversion error of \"") + in + "\"");
        }
        return res;
      }
 
      inline float asFloat_(const String & in)
      {
        float res = 0.0;
        try
        {
          res = in.toFloat();
        }
        catch (Exception::ConversionError& )
        {
          error(LOAD, String("Float conversion error of \"") + in + "\"");
        }
        return res;
      }
 
      inline bool asBool_(const String & in)
      {
        if (in == "true" || in == "TRUE" || in == "True" || in == "1")
        {
          return true;
        }
        else if (in == "false" || in == "FALSE" || in == "False" || in == "0")
        {
          return false;
        }
        else
        {
          error(LOAD, String("Boolean conversion error of \"") + in + "\"");
        }
        return false;
      }
 
      inline DateTime asDateTime_(String date_string)
      {
        DateTime date_time;
        if (date_string != "")
        {
          try
          {
            //strip away milliseconds
            date_string.trim();
            date_string = date_string.substr(0, 19);
            date_time.set(date_string);
          }
          catch (Exception::ParseError& /*err*/ )
          {
            error(LOAD, String("DateTime conversion error of \"") + date_string + "\"");
          }
        }
        return date_time;
      }
 
 
 
 
      inline String attributeAsString_(const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val == nullptr) fatalError(LOAD, String("Required attribute '") + name + "' not present!");
        return sm_.convert(val);
      }
 
      inline Int attributeAsInt_(const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val == nullptr) fatalError(LOAD, String("Required attribute '") + name + "' not present!");
        return xercesc::XMLString::parseInt(val);
      }
 
      inline double attributeAsDouble_(const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val == nullptr) fatalError(LOAD, String("Required attribute '") + name + "' not present!");
        return String(sm_.convert(val)).toDouble();
      }
 
      inline DoubleList attributeAsDoubleList_(const xercesc::Attributes & a, const char * name) const
      {
        String tmp(expectList_(attributeAsString_(a, name)));
        return ListUtils::create<double>(tmp.substr(1, tmp.size() - 2));
      }
 
      inline IntList attributeAsIntList_(const xercesc::Attributes & a, const char * name) const
      {
        String tmp(expectList_(attributeAsString_(a, name)));
        return ListUtils::create<Int>(tmp.substr(1, tmp.size() - 2));
      }
 
      inline StringList attributeAsStringList_(const xercesc::Attributes & a, const char * name) const
      {
        String tmp(expectList_(attributeAsString_(a, name)));
        return ListUtils::create<String>(tmp.substr(1, tmp.size() - 2));
      }
 
      inline bool optionalAttributeAsString_(String & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = sm_.convert(val);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsInt_(Int & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = xercesc::XMLString::parseInt(val);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsUInt_(UInt & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = xercesc::XMLString::parseInt(val);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsDouble_(double & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = String(sm_.convert(val)).toDouble();
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsDoubleList_(DoubleList & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = attributeAsDoubleList_(a, name);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsStringList_(StringList & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = attributeAsStringList_(a, name);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsIntList_(IntList & value, const xercesc::Attributes & a, const char * name) const
      {
        const XMLCh * val = a.getValue(sm_.convert(name).c_str());
        if (val != nullptr)
        {
          value = attributeAsIntList_(a, name);
          return true;
        }
        return false;
      }
 
      inline String attributeAsString_(const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val == nullptr) fatalError(LOAD, String("Required attribute '") + sm_.convert(name) + "' not present!");
        return sm_.convert(val);
      }
 
      inline Int attributeAsInt_(const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val == nullptr) fatalError(LOAD, String("Required attribute '") + sm_.convert(name) + "' not present!");
        return xercesc::XMLString::parseInt(val);
      }
 
      inline double attributeAsDouble_(const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val == nullptr) fatalError(LOAD, String("Required attribute '") + sm_.convert(name) + "' not present!");
        return sm_.convert(val).toDouble();
      }
 
      inline DoubleList attributeAsDoubleList_(const xercesc::Attributes & a, const XMLCh * name) const
      {
        String tmp(expectList_(attributeAsString_(a, name)));
        return ListUtils::create<double>(tmp.substr(1, tmp.size() - 2));
      }
 
      inline IntList attributeAsIntList_(const xercesc::Attributes & a, const XMLCh * name) const
      {
        String tmp(expectList_(attributeAsString_(a, name)));
        return ListUtils::create<Int>(tmp.substr(1, tmp.size() - 2));
      }
 
      inline StringList attributeAsStringList_(const xercesc::Attributes & a, const XMLCh * name) const
      {
        String tmp(expectList_(attributeAsString_(a, name)));
        return ListUtils::create<String>(tmp.substr(1, tmp.size() - 2));
      }
 
      inline bool optionalAttributeAsString_(String& value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = sm_.convert(val);
          return !value.empty();
        }
        return false;
      }
 
      inline bool optionalAttributeAsInt_(Int & value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = xercesc::XMLString::parseInt(val);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsUInt_(UInt & value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = xercesc::XMLString::parseInt(val);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsDouble_(double & value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = sm_.convert(val).toDouble();
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsDoubleList_(DoubleList & value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = attributeAsDoubleList_(a, name);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsIntList_(IntList & value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = attributeAsIntList_(a, name);
          return true;
        }
        return false;
      }
 
      inline bool optionalAttributeAsStringList_(StringList & value, const xercesc::Attributes & a, const XMLCh * name) const
      {
        const XMLCh * val = a.getValue(name);
        if (val != nullptr)
        {
          value = attributeAsStringList_(a, name);
          return true;
        }
        return false;
      }
 
 
private:
      XMLHandler();
 
      inline const String& expectList_(const String& str) const
      {
        if (!(str.hasPrefix('[') && str.hasSuffix(']')))
        {
          fatalError(LOAD, String("List argument is not a string representation of a list!"));
        }
        return str;
      }
 
    };
 
  }   // namespace Internal
} // namespace OpenMS