mcell/utils/data_model_to_pymcell/generator_structs.h

/******************************************************************************
 *
 * Copyright (C) 2020 by
 * The Salk Institute for Biological Studies
 *
 * Use of this source code is governed by an MIT-style
 * license that can be found in the LICENSE file or at
 * https://opensource.org/licenses/MIT.
 *
******************************************************************************/

#ifndef UTILS_DATA_MODEL_TO_PYMCELL_GENERATOR_STRUCTS_H_
#define UTILS_DATA_MODEL_TO_PYMCELL_GENERATOR_STRUCTS_H_

#include <string>
#include <algorithm>
#include <set>
#include "json/json.h"
#include "datamodel_defines.h"
#include "generator_utils.h"

namespace MCell {

// auxiliary struct used when generating species or molecule types
struct SpeciesOrMolType {
  SpeciesOrMolType(const std::string& name_, const bool is_species_ = true)
    : name(name_), is_species(is_species_) {
  }

  SpeciesOrMolType(const SpeciesOrMolType& other)
    : name(other.name), is_species(other.is_species) {
  }

  // ignores type
  bool operator == (const SpeciesOrMolType& other) const {
    return name == other.name;
  }

  std::string name;
  bool is_species; // mol type when false
};


struct IdLoc {
  IdLoc(const std::string& name_, const bool in_python_ = true)
    : name(name_), in_python(in_python_) {
  }

  // ignores type
  bool operator == (const IdLoc& other) const {
    return name == other.name;
  }

  std::string name;
  bool in_python; // BNGL when false
};



// data and configuration shared among generators
struct SharedGenData {
  void reset() {
    input_file = "";
    output_files_prefix = "";
    debug_mode = false;
    testing_mode = false;
    bng_mode = false;
    not_overridable_python_params = false;

    unnamed_rxn_counter = 0;
    all_species_and_mol_type_names.clear();
    all_reaction_rules_names.clear();
    bngl_reaction_rules_used_in_observables.clear();
    all_count_term_names.clear();
    defined_python_objects.clear();
    surface_to_volume_compartments_map.clear();
    has_default_compartment_object = false;
  }

  uint unnamed_rxn_counter;

  std::string input_file;
  std::string output_files_prefix;

  bool bng_mode;
  bool debug_mode;
  bool testing_mode;
  std::vector<int> checkpoint_iterations;
  bool not_overridable_python_params;

  std::vector<SpeciesOrMolType> all_species_and_mol_type_names;
  std::vector<IdLoc> all_reaction_rules_names;
  std::vector<std::string> bngl_reaction_rules_used_in_observables;
  std::vector<std::string> all_count_term_names;

  // set in PythonGenerator::generate_geometry
  bool has_default_compartment_object;

  // set in MCell4Generator::analyze_and_generate_bngl_compartments
  std::set<std::string> used_compartments;

  // key is object name, value is class name
  std::map<std::string, std::string> defined_python_objects;

  // key is surface compartment name, value is volume compartment name
  std::map<std::string, std::string> surface_to_volume_compartments_map;

  // output file name to be used when loading observables from BNGL,
  // empty for DAT format
  std::string bng_observables_output_gdat_file;

  const SpeciesOrMolType* find_species_or_mol_type_info(const std::string& name) const {
    auto it = std::find(
        all_species_and_mol_type_names.begin(), all_species_and_mol_type_names.end(),
        SpeciesOrMolType(name));
    if (it != all_species_and_mol_type_names.end()) {
      return &*it;
    }
    else {
      return nullptr;
    }
  }

  const IdLoc* find_reaction_rule_info(const std::string& rxn_name) const {
    auto it = std::find(all_reaction_rules_names.begin(), all_reaction_rules_names.end(), IdLoc(rxn_name));
    if (it != all_reaction_rules_names.end()) {
      return &*it;
    }
    else {
      return nullptr;
    }
  }

  bool is_used_compartment(Json::Value& model_object) {
    const std::string& vol_comp = model_object[KEY_NAME].asString();
    assert(vol_comp != "");
    const std::string& surf_comp = model_object[KEY_MEMBRANE_NAME].asString();

    return used_compartments.count(vol_comp) != 0 || (surf_comp != "" && used_compartments.count(surf_comp) != 0);
  }


  bool is_already_defined(const std::string& obj_name, const char* class_name) {
    //return false;
    if (defined_python_objects.count(obj_name) != 0) {
      return defined_python_objects[obj_name] == std::string(class_name);
    }
    else {
      return false;
    }
  }

  // also adds
  void check_if_already_defined_and_add(const std::string& obj_name, const char* class_name) {
    //return;
    if (defined_python_objects.count(obj_name) != 0) {
      ERROR("Duplicate object name '" + obj_name + "', used for '" + class_name + "' and '" +
          defined_python_objects[obj_name] + "'. Object names must be unique.");
    }
    else {
      defined_python_objects[obj_name] = class_name;
    }
  }

  // mcell node of the loaded JSON file
  Json::Value mcell;
};


} // namespace MCell

#endif /* UTILS_DATA_MODEL_TO_PYMCELL_GENERATOR_STRUCTS_H_ */