/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * 
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * CommandLineParser.cpp
 *
 *  Created on: May 8, 2010
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include <boost/filesystem.hpp>
#include <boost/program_options.hpp>
#include <fstream>
#include <iostream>
#include <set>
#include <map>

#include "Actions/Action.hpp"
#include "Actions/ActionQueue.hpp"
#include "Actions/ActionTrait.hpp"
#include "Actions/OptionRegistry.hpp"
#include "Actions/OptionTrait.hpp"
#include "Actions/Values.hpp"
#include "CodePatterns/Log.hpp"
#include "CodePatterns/Verbose.hpp"
#include "CommandLineParser.hpp"
#include "CommandLineParser_validate.hpp"
#include "World.hpp"

#include "CodePatterns/Singleton_impl.hpp"

using namespace MoleCuilder;

class element;

/** Constructor of class CommandLineParser.
 *
 */
CommandLineParser::CommandLineParser() :
  analysis("Analysis options"),
  atom("Atom options"),
  bond("Bond options"),
  command("Command options"),
  fill("fill options"),
  shape("shape options"),
  fragmentation("Fragmentation options"),
  graph("Graph options"),
  molecule("Molecule options"),
  options("Secondary options"),
  parser("Parser options"),
  potential("Potential options"),
  selection("Selection options"),
  tesselation("Tesselation options"),
  world("World options")
{
  // put all options lists into a lookup
  CmdParserLookup["analysis"] = &analysis;
  CmdParserLookup["atom"] = &atom;
  CmdParserLookup["bond"] = &bond;
  CmdParserLookup["command"] = &command;
  CmdParserLookup["edit"] = &edit;
  CmdParserLookup["fill"] = &fill;
  CmdParserLookup["shape"] = &shape;
  CmdParserLookup["fragmentation"] = &fragmentation;
  CmdParserLookup["graph"] = &graph;
  CmdParserLookup["options"] = &options;
  CmdParserLookup["molecule"] = &molecule;
  CmdParserLookup["parser"] = &parser;
  CmdParserLookup["potential"] = &potential;
  CmdParserLookup["selection"] = &selection;
  CmdParserLookup["tesselation"] = &tesselation;
  CmdParserLookup["world"] = &world;
}

/** Destructor of class CommandLineParser.
 *
 */
CommandLineParser::~CommandLineParser()
{}

/** Initializes command arguments to accept.
 * Goes through ActionRegistry and puts all actions therein into the map.
 */
void CommandLineParser::InitializeCommandArguments()
{
  // we need a list of already added options, otherwise we get ambigious exceptions
  std::set<std::string> AlreadyAddedOptionNames;

  bool ActionAlreadyAdded_flag = false;
  ActionQueue &AQ = ActionQueue::getInstance();
  ActionQueue::ActionTokens_t tokens = AQ.getListOfActions();
  for (ActionQueue::ActionTokens_t::const_iterator iter = tokens.begin();
      iter != tokens.end(); ++iter) {
    const ActionTrait &CurrentTrait = AQ.getActionsTrait(*iter);
    ActionAlreadyAdded_flag = false;
    //std::cout << "Current Action to initialize is: " << actioniter->first << std::endl;

    for (ActionTrait::options_const_iterator optioniter = CurrentTrait.getBeginIter();
        optioniter != CurrentTrait.getEndIter();
        ++optioniter) {
      if (optioniter->first == *iter)
        ActionAlreadyAdded_flag = true;
      ASSERT( OptionRegistry::getInstance().isOptionPresentByName(optioniter->first),
          "CommandLineParser::Init() - Option "+optioniter->first+" not present in OptionRegistry." );
      const OptionTrait* const currentOption = OptionRegistry::getInstance().getOptionByName(optioniter->first);

      if (AlreadyAddedOptionNames.find(optioniter->first) == AlreadyAddedOptionNames.end()) {
        // add the option
//        std::cout << "Registering Option "
//            << currentOption->getName()
//            << " with type '" << currentOption->getTypeName() << "' "
//            << " with description '" << currentOption->getDescription() << "' ";
//        if (currentOption->hasShortForm())
//          std::cout << ", with short form " << currentOption->getShortForm();
//        else
//          std::cout << ", with no short form ";
//        if (currentOption->hasDefaultValue())
//          std::cout << ", with default value " << currentOption->getDefaultValue();
//        else
//          std::cout << ", with no default value ";
//        std::cout << std::endl;

        AddOptionToParser(currentOption, (CmdParserLookup["options"]),
            (optioniter->first == *iter) ?
                true : false);

        AlreadyAddedOptionNames.insert(optioniter->first);
      } else {
//        std::cout << "Option " << currentOption->getName() << " already registered." << std::endl;
      }
    }

    if (!ActionAlreadyAdded_flag) {
      // add the action
//      std::cout << "Registering Action "
//          << currentAction->Traits.getName()
//          << " in menu " << currentAction->Traits.getMenuName()
//          << " with type '" << currentAction->Traits.getTypeName() << "' "
//          << " with description '" << currentAction->Traits.getDescription() << "' ";
//      if (currentAction->Traits.hasShortForm())
//        std::cout << ", with short form " << currentAction->Traits.getShortForm();
//      else
//        std::cout << ", with no short form ";
//      if (currentAction->Traits.hasDefaultValue())
//        std::cout << ", with default value " << currentAction->Traits.getDefaultValue();
//      else
//        std::cout << ", with no default value ";
//      std::cout  << std::endl;

      ASSERT(CmdParserLookup.find(CurrentTrait.getMenuName()) != CmdParserLookup.end(),
          "CommandLineParser: boost::program_options::options_description for this Action not present.");
      AddOptionToParser(
          dynamic_cast<const OptionTrait * const>(&CurrentTrait),
          (CmdParserLookup[CurrentTrait.getMenuName()]),
          false);
    }
  }
  // note: positioning is not important on the command line
}

/** Adds an Action or Option to the CommandLineParser.
 * Note that Action is derived from Option(Trait)
 *
 * This ugly switch function is necessary because of the compile-time problem:
 * po::value<T> has to be instantiated at compile-time however we do know the type not until run-time.
 * Not even a templated function like po::value<T> getProgramOptionValuefromType() does help, specialized
 * to each available type, as the signatures of all the functions differ. Hence, they cannot not put into
 * one type_info -> po::value<T> map ...
 *
 * \param *currentOption pointer to Action/Option to add
 * \param *OptionList program_options list to add to
 * \param _DefaultAsImplicit whether to add a default value as default_value or
 *        as implicit_value (default = option token present or not, implicit =
          option token present but not necessarily followed by argument)
 */
void CommandLineParser::AddOptionToParser(
    const OptionTrait * const currentOption, 
    po::options_description* OptionList,
    const bool _DefaultAsImplicit)
{
  // check whether dynamic_cast in Init() suceeded
  ASSERT(currentOption != NULL, "CommandLineParser::AddOptionToParser() - currentOption is NULL!");
  // add other options
//  std::cout << "Adding Action " << currentOption->getName() << " with type "
//      << currentOption->getType()->name() << ", " << (currentOption->hasDefaultValue() ? "with" : "without")
//      << " default value, and KeyandShortform " << currentOption->getKeyAndShortForm()
//      << " to CommandLineParser." << std::endl;
  switch(TypeToEnums.getEnumforType(currentOption->getType())) {
    default:
    case TypeEnumContainer::NoneType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(), currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::BooleanType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
            currentOption->hasDefaultValue() ?
                  (_DefaultAsImplicit ? 
                      po::value < bool >()->implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) :
                      po::value < bool >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
                  po::value < bool >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::FileType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < boost::filesystem::path >()->default_value(boost::lexical_cast<boost::filesystem::path>(currentOption->getDefaultValue().c_str())) :
                  po::value < boost::filesystem::path >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfFilesType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<boost::filesystem::path> >()->default_value(boost::lexical_cast< std::vector<boost::filesystem::path> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<boost::filesystem::path> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::IntegerType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
            currentOption->hasDefaultValue() ?
                  (_DefaultAsImplicit ? 
                      po::value < int >()->implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) :
                      po::value < int >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
                  po::value < int >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfIntegersType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<int> >()->default_value(boost::lexical_cast< std::vector<int> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<int> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::UnsignedIntegerType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
            currentOption->hasDefaultValue() ?
                  (_DefaultAsImplicit ? 
                      po::value < unsigned int >()->implicit_value(boost::lexical_cast<unsigned int>(currentOption->getDefaultValue().c_str())) :
                      po::value < unsigned int >()->default_value(boost::lexical_cast<unsigned int>(currentOption->getDefaultValue().c_str()))) :
                  po::value < unsigned int >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfUnsignedIntegersType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<unsigned int> >()->default_value(boost::lexical_cast< std::vector<unsigned int> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<unsigned int> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::DoubleType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
            currentOption->hasDefaultValue() ?
                  (_DefaultAsImplicit ? 
                      po::value < double >()->implicit_value(boost::lexical_cast<double>(currentOption->getDefaultValue().c_str())) :
                      po::value < double >()->default_value(boost::lexical_cast<double>(currentOption->getDefaultValue().c_str()))) :
                  po::value < double >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfDoublesType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<double> >()->default_value(boost::lexical_cast< std::vector<double> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<double> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::StringType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
            currentOption->hasDefaultValue() ?
                  (_DefaultAsImplicit ? 
                      po::value < std::string >()->implicit_value(currentOption->getDefaultValue()) :
                      po::value < std::string >()->default_value(currentOption->getDefaultValue())) :
                  po::value < std::string >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfStringsType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<std::string> >()->default_value(boost::lexical_cast< std::vector<std::string> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<std::string> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::VectorType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < VectorValue >()->default_value(boost::lexical_cast<VectorValue>(currentOption->getDefaultValue().c_str())) :
                  po::value < VectorValue >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfVectorsType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<VectorValue> >()->default_value(boost::lexical_cast< std::vector<VectorValue> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<VectorValue> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::MoleculeType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < const molecule * >()->default_value(boost::lexical_cast<const molecule *>(currentOption->getDefaultValue().c_str())) :
                  po::value < int >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfMoleculesType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<const molecule *> >()->default_value(boost::lexical_cast< std::vector<const molecule *> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<int> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::AtomType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
            currentOption->hasDefaultValue() ?
                  (_DefaultAsImplicit ? 
                      po::value < int >()->implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) :
                      po::value < int >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
                  po::value < int >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfAtomsType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<const atom *> >()->default_value(boost::lexical_cast< std::vector<const atom *> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<int> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ElementType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < const element * >()->default_value(boost::lexical_cast<const element *>(currentOption->getDefaultValue().c_str())) :
                  po::value < int >(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::ListOfElementsType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < std::vector<const element *> >()->default_value(boost::lexical_cast< std::vector<const element *> >(currentOption->getDefaultValue().c_str())) :
                  po::value < std::vector<int> >()->multitoken(),
                  currentOption->getDescription().c_str())
        ;
      break;
    case TypeEnumContainer::RealSpaceMatrixType:
      OptionList->add_options()
        (currentOption->getKeyAndShortForm().c_str(),
//            currentOption->hasDefaultValue() ?
//                  po::value < RealSpaceMatrixValue >()->default_value(boost::lexical_cast<BoxValue>(currentOption->getDefaultValue().c_str())) :
                  po::value < RealSpaceMatrixValue >(),
                  currentOption->getDescription().c_str())
        ;
      break;
  }
}

/** States whether there are command line arguments.
 * \return true - there are none, false - there is at least one command line argument
 */
bool CommandLineParser::isEmpty()
{
  return vm.empty();
}

/** Sets the options.
 * \param _argc arg count from main()
 * \param **_argv argument array from main()
 */
void CommandLineParser::setOptions(int _argc, char **_argv)
{
  argc = _argc;
  argv = _argv;
  config_file_options.add(options);
  // append all option_descriptions to both cmdline_options and visible
  for (CmdParserLookupMap::iterator iter = CmdParserLookup.begin();
      iter != CmdParserLookup.end();
      ++iter) {
    cmdline_options.add(*(iter->second));
    visible.add(*(iter->second));
  }
}

/** Parses the command line arguments.
 * Calls program_options::store() and program_options::notify()
 *
 * @return true - all is ok, false - command-line options could not be parsed 
 *         correctly
 */
bool CommandLineParser::Parse()
{
  bool status = true;
  try {
    po::store(po::command_line_parser(argc,argv).options(cmdline_options).run(), vm);
  } catch (std::exception &e) {
    std::cerr << "Something went wrong with parsing the command-line arguments: " 
        << e.what() << std::endl;
    World::getInstance().setExitFlag(134);
#ifdef HAVE_ACTION_THREAD
    // force action queue to stop thread
    ActionQueue::getInstance().stop();
    ActionQueue::getInstance().clearTempQueue();
#endif
    ActionQueue::getInstance().clearQueue();
    status = false;
  }
  if (status) {
    std::ifstream input;
    input.open("example.cfg");
    if (!input.fail())
      po::store(po::parse_config_file(input, config_file_options), vm);
    input.close();
    po::notify(vm);
  }
  return status;
}

/** Scan the argument list for -a or --arguments and store their order for later use.
 */
void CommandLineParser::scanforSequenceOfArguments()
{
  std::map <std::string, std::string> ShortFormToActionMap = getShortFormToActionMap();
  LOG(0, "Scanning command line arguments and recognizing Actions.");
  // go through all arguments
  for (int i=1;i<argc;i++) {
    LOG(2, "Checking on " << argv[i]);
    // check whether they
    if (argv[i][0] == '-') { // .. begin with -
      LOG(2, "Possible argument: " << argv[i]);
      if (argv[i][1] == '-') { // .. or --
        LOG(1, "Putting " << argv[i] << " into the sequence.");
        SequenceOfActions.push_back(&(argv[i][2]));
        //  .. and check that next letter is not numeric, if so insert
      } else if (((argv[i][1] < '0') || (argv[i][1] > '9')) && ((argv[i][1] != '.'))) {
        std::map <std::string, std::string>::iterator iter = ShortFormToActionMap.find(&(argv[i][1]));
        if (iter != ShortFormToActionMap.end()) {
          LOG(1, "Putting " << iter->second << " for " << iter->first << " into the sequence.");
          SequenceOfActions.push_back(iter->second);
        }
      }
    }
  }
}

/** Makes the Parser parse the command line options with current known options.
 * \param _argc arg count from main()
 * \param **_argv argument array from main()
 */
void CommandLineParser::Run(int _argc, char **_argv)
{
  setOptions(_argc,_argv);
  const bool status = Parse();
  if (status)
    scanforSequenceOfArguments();
}

/** Go through all Actions and create a map from short form to their token.
 * \return map from Action's ShortForm to token.
 */
std::map <std::string, std::string> CommandLineParser::getShortFormToActionMap() const
{
  std::map <std::string, std::string> result;

  ActionQueue &AQ = ActionQueue::getInstance();
  ActionQueue::ActionTokens_t tokens = AQ.getListOfActions();
  for (ActionQueue::ActionTokens_t::const_iterator iter = tokens.begin();
      iter != tokens.end(); ++iter) {
    const ActionTrait &CurrentTrait = AQ.getActionsTrait(*iter);
    if (CurrentTrait.hasShortForm()) {
      ASSERT(result.find(CurrentTrait.getShortForm()) == result.end(),
          "Short form "+toString(CurrentTrait.getShortForm())+
          " for action "+toString(*iter)+" already present from "+
          std::string(result[CurrentTrait.getShortForm()])+"!");
      result[CurrentTrait.getShortForm()] = *iter;
    }
  }

  return result;
}

CONSTRUCT_SINGLETON(CommandLineParser)