/*************************************************************************
* *
* 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;
}
}