content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program 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 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program 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 this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package com.act.biointerpretation.sars;
  
  import act.server.MongoDB;
  import act.shared.Chemical;
  import act.shared.Reaction;
  import chemaxon.formats.MolFormatException;
  import chemaxon.struc.Molecule;
  import chemaxon.struc.RxnMolecule;
  
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.stream.Collectors;
  
  public class DbAPI {
  
    private final MongoDB db;
    private Map<Long, Chemical> chemicalCache;
    private Map<Long, Reaction> reactionCache;
  
    public DbAPI(MongoDB db) {
      this.db = db;
      chemicalCache = new HashMap<>();
      reactionCache = new HashMap<>();
    }
  
    public static boolean areAllOneSubstrate(List<RxnMolecule> reactions) {
      for (RxnMolecule reaction : reactions) {
        if (reaction.getReactantCount() != 1) {
          return false;
        }
      }
      return true;
    }
  
    public static boolean areAllOneProduct(List<RxnMolecule> reactions) {
      for (RxnMolecule reaction : reactions) {
        if (reaction.getProductCount() != 1) {
          return false;
        }
      }
      return true;
    }
  
    public void clearCaches() {
      chemicalCache = new HashMap<>();
      reactionCache = new HashMap<>();
    }
  
    public Chemical getChemical(Long id) {
      Chemical result = chemicalCache.get(id);
      if (result == null) {
        result = db.getChemicalFromChemicalUUID(id);
        chemicalCache.put(id, result);
      }
      return result;
    }
  
    public Reaction getReaction(Long id) {
      Reaction result = reactionCache.get(id);
      if (result == null) {
        result = db.getReactionFromUUID(id);
        reactionCache.put(id, result);
      }
      return result;
    }
  
    public List<Reaction> getReactions(ReactionGroup group) {
      return new ArrayList<>(group.getReactionIds()).stream()
          .map(id -> getReaction(id)).collect(Collectors.toList());
    }
  
    public List<RxnMolecule> getRxnMolecules(List<Reaction> reactions) {
      return reactions.stream().map(reaction -> getRxnMolecule(reaction)).collect(Collectors.toList());
    }
  
    public RxnMolecule getRxnMolecule(Reaction reaction) {
      RxnMolecule result = new RxnMolecule();
      getSubstratesAsMolecules(reaction).forEach(mol -> result.addComponent(mol, RxnMolecule.REACTANTS));
      getProductsAsMolecules(reaction).forEach(mol -> result.addComponent(mol, RxnMolecule.PRODUCTS));
      return result;
    }
  
    public List<Molecule> getSubstratesAsMolecules(Reaction reaction) {
      return Arrays.asList(reaction.getSubstrates()).stream()
          .map(id -> importMolecule(getChemical(id))).collect(Collectors.toList());
    }
  
    public List<Molecule> getProductsAsMolecules(Reaction reaction) {
      return Arrays.asList(reaction.getSubstrates()).stream()
          .map(id -> importMolecule(getChemical(id))).collect(Collectors.toList());
    }
  
    public Molecule importMolecule(Chemical chemical) {
      try {
        return chemical.importAsMolecule();
      } catch (MolFormatException e) {
        throw new IllegalArgumentException("DbAPI couldn't import chemical:" + e.getMessage());
      }
    }
  
  }
  