Java tutorial
/************************************************************************* * * * 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; } }