/*************************************************************************
* *
* 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.sql.Types;
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 FeedingLCMSWell extends PlateWell<FeedingLCMSWell> {
public static final String TABLE_NAME = "wells_lcms_feeding";
protected static final FeedingLCMSWell INSTANCE = new FeedingLCMSWell();
public static FeedingLCMSWell 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"),
EXTRACT(7, 6, "extract"),
CHEMICAL(8, 7, "chemical"),
CONCENTRATION(9, 8, "concentration"),
NOTE(10, 9, "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<FeedingLCMSWell> fromResultSet(ResultSet resultSet) throws SQLException {
List<FeedingLCMSWell> 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 extract = resultSet.getString(DB_FIELD.EXTRACT.getOffset());
String chemical = resultSet.getString(DB_FIELD.CHEMICAL.getOffset());
Double concentration = resultSet.getDouble(DB_FIELD.CONCENTRATION.getOffset());
if (resultSet.wasNull()) {
concentration = null;
}
String note = resultSet.getString(DB_FIELD.NOTE.getOffset());
results.add(new FeedingLCMSWell(
id, plateId, plateRow, plateColumn, msid, composition, extract, chemical, concentration, note));
}
return results;
}
public static final String QUERY_GET_FEEDING_LCMS_WELL_BY_PLATE_ID = INSTANCE.makeGetQueryForSelectField("plate_id");
public List<FeedingLCMSWell> getFeedingLCMSWellByPlateId(DB db, Integer plateId) throws SQLException {
try (PreparedStatement stmt = db.getConn().prepareStatement(QUERY_GET_FEEDING_LCMS_WELL_BY_PLATE_ID)) {
stmt.setInt(1, plateId);
try (ResultSet resultSet = stmt.executeQuery()) {
return fromResultSet(resultSet);
}
}
}
// Insert/update
protected void bindInsertOrUpdateParameters(
PreparedStatement stmt, Integer plateId, Integer plateRow, Integer plateColumn, String msid,
String composition, String extract, String chemical, Double concentration, 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.EXTRACT.getInsertUpdateOffset(), extract);
stmt.setString(DB_FIELD.CHEMICAL.getInsertUpdateOffset(), chemical);
if (concentration != null) {
stmt.setDouble(DB_FIELD.CONCENTRATION.getInsertUpdateOffset(), concentration);
} else {
stmt.setNull(DB_FIELD.CONCENTRATION.getInsertUpdateOffset(), Types.DOUBLE);
}
stmt.setString(DB_FIELD.NOTE.getInsertUpdateOffset(), note);
}
@Override
protected void bindInsertOrUpdateParameters(PreparedStatement stmt, FeedingLCMSWell parameterSource)
throws SQLException {
bindInsertOrUpdateParameters(stmt, parameterSource.getPlateId(), parameterSource.getPlateRow(),
parameterSource.getPlateColumn(), parameterSource.getMsid(), parameterSource.getComposition(),
parameterSource.getExtract(), parameterSource.getChemical(), parameterSource.getConcentration(),
parameterSource.getNote());
}
public static String trimAndComplain(String val) {
String tval = val.trim();
if (!val.equals(tval)) {
System.err.format("WARNING: trimmed spurious whitespace from '%s'\n", val);
}
return tval;
}
// Parsing/loading
public List<FeedingLCMSWell> insertFromPlateComposition(DB db, PlateCompositionParser parser, Plate p)
throws SQLException, IOException {
Map<String, String> plateProperties = parser.getPlateProperties();
String msid = null, composition = null;
if (!plateProperties.containsKey("msid") && plateProperties.containsKey("composition")) {
throw new RuntimeException("ERROR: assumed plate properties 'msid' and 'composition' do not exist");
}
msid = trimAndComplain(plateProperties.get("msid"));
composition = trimAndComplain(plateProperties.get("composition"));
// If a few well dones't have a concentration, it's not work keeping.
Map<Pair<String, String>, String> concentrations = parser.getCompositionTables().get("concentration");
List<Pair<String, String>> sortedCoordinates = new ArrayList<>(concentrations.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<FeedingLCMSWell> results = new ArrayList<>();
for (Pair<String, String> coords : sortedCoordinates) {
String concentraitonStr = parser.getCompositionTables().get("concentration").get(coords);
if (concentraitonStr == null || concentraitonStr.isEmpty()) {
continue;
}
String extract = parser.getCompositionTables().get("extract").get(coords);
String chemical = parser.getCompositionTables().get("chemical").get(coords);
Double concentration = Double.parseDouble(concentraitonStr);
String note = null;
if (parser.getCompositionTables().get("note") != null) {
note = parser.getCompositionTables().get("note").get(coords);
}
Pair<Integer, Integer> index = parser.getCoordinatesToIndices().get(coords);
FeedingLCMSWell s = INSTANCE.insert(db, new FeedingLCMSWell(null, p.getId(), index.getLeft(), index.getRight(),
msid, composition, extract, chemical, concentration, note));
results.add(s);
}
return results;
}
private String msid;
private String composition;
private String extract;
private String chemical;
private Double concentration;
private String note;
private FeedingLCMSWell() { }
public FeedingLCMSWell(Integer id, Integer plateId, Integer plateRow, Integer plateColumn,
String msid, String composition, String extract, String chemical,
Double concentration, String note) {
this.id = id;
this.plateId = plateId;
this.plateRow = plateRow;
this.plateColumn = plateColumn;
this.msid = msid;
this.composition = composition;
this.extract = extract;
this.chemical = chemical;
this.concentration = concentration;
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 getExtract() {
return extract;
}
public void setExtract(String extract) {
this.extract = extract;
}
public String getChemical() {
return chemical;
}
public void setChemical(String chemical) {
this.chemical = chemical;
}
public Double getConcentration() {
return concentration;
}
public void setConcentration(Double concentration) {
this.concentration = concentration;
}
public String getNote() {
return note;
}
public void setNote(String note) {
this.note = note;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
FeedingLCMSWell that = (FeedingLCMSWell) o;
if (!msid.equals(that.msid)) return false;
if (!composition.equals(that.composition)) return false;
if (extract != null ? !extract.equals(that.extract) : that.extract != null) return false;
if (chemical != null ? !chemical.equals(that.chemical) : that.chemical != null) return false;
if (!concentration.equals(that.concentration)) return false;
return !(note != null ? !note.equals(that.note) : that.note != null);
}
@Override
public int hashCode() {
int result = msid.hashCode();
result = 31 * result + composition.hashCode();
result = 31 * result + (extract != null ? extract.hashCode() : 0);
result = 31 * result + (chemical != null ? chemical.hashCode() : 0);
result = 31 * result + concentration.hashCode();
result = 31 * result + (note != null ? note.hashCode() : 0);
return result;
}
}