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.lcms.db.model;
  
  import com.act.lcms.db.io.DB;
  import com.act.lcms.db.io.parser.PlateCompositionParser;
  import org.apache.commons.lang3.StringUtils;
  import org.apache.commons.lang3.tuple.Pair;
  
  import java.io.IOException;
  import java.sql.PreparedStatement;
  import java.sql.ResultSet;
  import java.sql.SQLException;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.Comparator;
  import java.util.List;
  import java.util.Map;
  
  public class LCMSWell extends PlateWell<LCMSWell> {
    public static final String TABLE_NAME = "wells_lcms";
    protected static final LCMSWell INSTANCE = new LCMSWell();
  
    public static LCMSWell getInstance() {
      return INSTANCE;
    }
  
    private enum DB_FIELD implements DBFieldEnumeration {
      ID(1, -1, "id"),
      PLATE_ID(2, 1, "plate_id"),
      PLATE_ROW(3, 2, "plate_row"),
      PLATE_COLUMN(4, 3, "plate_column"),
      MSID(5, 4, "msid"),
      COMPOSITION(6, 5, "composition"),
      CHEMICAL(7, 6, "chemical"),
      NOTE(8, 7, "note"),
      ;
  
      private final int offset;
      private final int insertUpdateOffset;
      private final String fieldName;
  
      DB_FIELD(int offset, int insertUpdateOffset, String fieldName) {
        this.offset = offset;
        this.insertUpdateOffset = insertUpdateOffset;
        this.fieldName = fieldName;
      }
  
      @Override
      public int getOffset() {
        return offset;
      }
  
      @Override
      public int getInsertUpdateOffset() {
        return insertUpdateOffset;
      }
  
      @Override
      public String getFieldName() {
        return fieldName;
      }
  
      @Override
      public String toString() {
        return this.fieldName;
      }
  
      public static String[] names() {
        DB_FIELD[] values = DB_FIELD.values();
        String[] names = new String[values.length];
        for (int i = 0; i < values.length; i++) {
          names[i] = values[i].getFieldName();
        }
        return names;
      }
    }
  
    protected static final List<String> ALL_FIELDS = Collections.unmodifiableList(Arrays.asList(DB_FIELD.names()));
  
    // id is auto-generated on insertion.
    protected static final List<String> INSERT_UPDATE_FIELDS = INSTANCE.makeInsertUpdateFields();
  
    @Override
    public String getTableName() {
      return TABLE_NAME;
    }
  
    @Override
    public List<String> getAllFields() {
      return ALL_FIELDS;
    }
  
    @Override
    public List<String> getInsertUpdateFields() {
      return INSERT_UPDATE_FIELDS;
    }
  
    protected static final String GET_BY_ID_QUERY = INSTANCE.makeGetByIDQuery();
    @Override
    protected String getGetByIDQuery() {
      return GET_BY_ID_QUERY;
    }
  
    protected static final String GET_BY_PLATE_ID_QUERY = INSTANCE.makeGetByPlateIDQuery();
    @Override
    protected String getGetByPlateIDQuery() {
      return GET_BY_PLATE_ID_QUERY;
    }
  
    protected static final String INSERT_QUERY = INSTANCE.makeInsertQuery();
    @Override
    public String getInsertQuery() {
      return INSERT_QUERY;
    }
  
    protected static final String UPDATE_QUERY = INSTANCE.makeUpdateQuery();
    @Override
    public String getUpdateQuery() {
      return UPDATE_QUERY;
    }
  
    @Override
    protected List<LCMSWell> fromResultSet(ResultSet resultSet) throws SQLException {
      List<LCMSWell> results = new ArrayList<>();
      while (resultSet.next()) {
        Integer id = resultSet.getInt(DB_FIELD.ID.getOffset());
        Integer plateId = resultSet.getInt(DB_FIELD.PLATE_ID.getOffset());
        Integer plateRow = resultSet.getInt(DB_FIELD.PLATE_ROW.getOffset());
        Integer plateColumn = resultSet.getInt(DB_FIELD.PLATE_COLUMN.getOffset());
        String msid = resultSet.getString(DB_FIELD.MSID.getOffset());
        String composition = resultSet.getString(DB_FIELD.COMPOSITION.getOffset());
        String chemical = resultSet.getString(DB_FIELD.CHEMICAL.getOffset());
        String note = resultSet.getString(DB_FIELD.NOTE.getOffset());
  
        results.add(new LCMSWell(id, plateId, plateRow, plateColumn, msid, composition, chemical, note));
      }
      return results;
    }
  
    protected void bindInsertOrUpdateParameters(
        PreparedStatement stmt, Integer plateId, Integer plateRow, Integer plateColumn,
        String msid, String composition, String chemical, String note) throws SQLException {
      stmt.setInt(DB_FIELD.PLATE_ID.getInsertUpdateOffset(), plateId);
      stmt.setInt(DB_FIELD.PLATE_ROW.getInsertUpdateOffset(), plateRow);
      stmt.setInt(DB_FIELD.PLATE_COLUMN.getInsertUpdateOffset(), plateColumn);
      stmt.setString(DB_FIELD.MSID.getInsertUpdateOffset(), msid);
      stmt.setString(DB_FIELD.COMPOSITION.getInsertUpdateOffset(), composition);
      stmt.setString(DB_FIELD.CHEMICAL.getInsertUpdateOffset(), chemical);
      stmt.setString(DB_FIELD.NOTE.getInsertUpdateOffset(), note);
    }
  
    // Extra access patterns.
    public static final String GET_BY_CONSTRUCT_ID_QUERY = INSTANCE.makeGetQueryForSelectField("composition");
    public List<LCMSWell> getByConstructID(DB db, String construct) throws SQLException {
      try (PreparedStatement stmt = db.getConn().prepareStatement(GET_BY_CONSTRUCT_ID_QUERY)) {
        stmt.setString(1, construct);
        try (ResultSet resultSet = stmt.executeQuery()) {
          return fromResultSet(resultSet);
        }
      }
    }
  
    public static final String GET_BY_STRAIN_QUERY = INSTANCE.makeGetQueryForSelectField("msid");
    public List<LCMSWell> getByStrain(DB db, String strainId) throws SQLException {
      try (PreparedStatement stmt = db.getConn().prepareStatement(GET_BY_STRAIN_QUERY)) {
        stmt.setString(1, strainId);
        try (ResultSet resultSet = stmt.executeQuery()) {
          return fromResultSet(resultSet);
        }
      }
    }
  
    public static final String GET_BY_PLATE_ID_AND_COORDINATES =
        StringUtils.join(new String[]{
            "SELECT", StringUtils.join(INSTANCE.getAllFields(), ','),
            "from", INSTANCE.getTableName(),
            "where plate_id = ?",
            "  and plate_row = ?",
            "  and plate_column = ?",
        }, " ");
    public LCMSWell getByPlateIdAndCoordinates(DB db, Integer plateId, Integer plateRow, Integer plateColumn)
      throws SQLException, IOException, ClassNotFoundException {
      try (PreparedStatement stmt = db.getConn().prepareStatement(GET_BY_PLATE_ID_AND_COORDINATES)) {
        stmt.setInt(1, plateId);
        stmt.setInt(2, plateRow);
        stmt.setInt(3, plateColumn);
        try (ResultSet resultSet = stmt.executeQuery()) {
          return expectOneResult(resultSet,
              String.format("plate_id = %d, plate_row = %d, plate_column = %d", plateId, plateRow, plateColumn));
        }
      }
    }
  
    @Override
    protected void bindInsertOrUpdateParameters(PreparedStatement stmt, LCMSWell sw) throws SQLException {
      bindInsertOrUpdateParameters(stmt, sw.getPlateId(), sw.getPlateRow(), sw.getPlateColumn(),
          sw.getMsid(), sw.getComposition(), sw.getChemical(), sw.getNote());
    }
  
    public LCMSWell insert(
        DB db, Integer plateId, Integer plateRow, Integer plateColumn,
        String msid, String composition, String chemical, String note) throws SQLException, IOException {
      return INSTANCE.insert(db, new LCMSWell(null, plateId, plateRow, plateColumn, msid, composition, chemical, note));
    }
  
    // Parsing/loading
    public List<LCMSWell> insertFromPlateComposition(DB db, PlateCompositionParser parser, Plate p)
        throws SQLException, IOException {
      Map<Pair<String, String>, String> msids = parser.getCompositionTables().get("msid");
      List<Pair<String, String>> sortedCoordinates = new ArrayList<>(msids.keySet());
      Collections.sort(sortedCoordinates, new Comparator<Pair<String, String>>() {
        // TODO: parse the values of these pairs as we read them so we don't need this silly comparator.
        @Override
        public int compare(Pair<String, String> o1, Pair<String, String> o2) {
          if (o1.getKey().equals(o2.getKey())) {
            return Integer.valueOf(Integer.parseInt(o1.getValue())).compareTo(Integer.parseInt(o2.getValue()));
          }
          return o1.getKey().compareTo(o2.getKey());
        }
      });
  
      List<LCMSWell> results = new ArrayList<>();
      for (Pair<String, String> coords : sortedCoordinates) {
        String msid = msids.get(coords);
        if (msid == null || msid.isEmpty()) {
          continue;
        }
        String composition = parser.getCompositionTables().get("composition").get(coords);
        String chemical = parser.getCompositionTables().get("chemical").get(coords);
        String note = null;
        if (parser.getCompositionTables().get("note") != null) {
          note = parser.getCompositionTables().get("note").get(coords);
        }
        Pair<Integer, Integer> index = parser.getCoordinatesToIndices().get(coords);
        LCMSWell s = INSTANCE.insert(db, p.getId(), index.getLeft(), index.getRight(),
            msid, composition, chemical, note);
  
        results.add(s);
      }
  
      return results;
    }
  
  
    private String msid;
    private String composition;
    private String chemical;
    private String note;
  
    private LCMSWell() { }
  
    protected LCMSWell(Integer id, Integer plateId, Integer plateRow, Integer plateColumn, String msid,
                       String composition, String chemical, String note) {
      this.id = id;
      this.plateId = plateId;
      this.plateRow = plateRow;
      this.plateColumn = plateColumn;
      this.msid = msid;
      this.composition = composition;
      this.chemical = chemical;
      this.note = note;
    }
  
    public String getMsid() {
      return msid;
    }
  
    public void setMsid(String msid) {
      this.msid = msid;
    }
  
    public String getComposition() {
      return composition;
    }
  
    public void setComposition(String composition) {
      this.composition = composition;
    }
  
    public String getChemical() {
      return chemical;
    }
  
    public void setChemical(String chemical) {
      this.chemical = chemical;
    }
  
    public String getNote() {
      return note;
    }
  
    public void setNote(String note) {
      this.note = note;
    }
  }
  