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.analysis.Utils; import com.act.lcms.db.io.DB; import com.act.lcms.db.io.parser.PlateCompositionParser; 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.HashMap; import java.util.List; import java.util.Map; import java.util.regex.Matcher; import java.util.regex.Pattern; public class DeliveredStrainWell extends PlateWell<DeliveredStrainWell> { public static final String TABLE_NAME = "wells_delivered_strain"; protected static final DeliveredStrainWell INSTANCE = new DeliveredStrainWell(); public static DeliveredStrainWell 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"), WELL(5, 4, "well"), MSID(6, 5, "msid"), COMPOSITION(7, 6, "composition"),; 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<DeliveredStrainWell> fromResultSet(ResultSet resultSet) throws SQLException { List<DeliveredStrainWell> 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 well = resultSet.getString(DB_FIELD.WELL.getOffset()); String msid = resultSet.getString(DB_FIELD.MSID.getOffset()); String composition = resultSet.getString(DB_FIELD.COMPOSITION.getOffset()); results.add(new DeliveredStrainWell(id, plateId, plateRow, plateColumn, well, msid, composition)); } return results; } // Insert/Update protected void bindInsertOrUpdateParameters(PreparedStatement stmt, Integer plateId, Integer plateRow, Integer plateColumn, String well, String msid, String composition) 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.WELL.getInsertUpdateOffset(), well); stmt.setString(DB_FIELD.MSID.getInsertUpdateOffset(), msid); stmt.setString(DB_FIELD.COMPOSITION.getInsertUpdateOffset(), composition); } @Override protected void bindInsertOrUpdateParameters(PreparedStatement stmt, DeliveredStrainWell dsw) throws SQLException { bindInsertOrUpdateParameters(stmt, dsw.getPlateId(), dsw.getPlateRow(), dsw.getPlateColumn(), dsw.getWell(), dsw.getMsid(), dsw.getComposition()); } public DeliveredStrainWell insert(DB db, Integer plateId, Integer plateRow, Integer plateColumn, String well, String msid, String composition) throws SQLException, IOException { return INSTANCE.insert(db, new DeliveredStrainWell(null, plateId, plateRow, plateColumn, well, msid, composition)); } // Parsing/loading public List<DeliveredStrainWell> insertFromPlateComposition(DB db, PlateCompositionParser parser, Plate p) throws SQLException, IOException { List<DeliveredStrainWell> results = new ArrayList<>(); Map<Pair<String, String>, String> featuresTable = parser.getCompositionTables().get("well"); /* The composition tables are usually constructed with well coordinates as the X and Y axes. Amyris strain plates, * however, have the combined well coordinates in the first column and the msid/composition in related columns. * We'll collect the features in each row by traversing the per-cell entries in the parser's table and merging on * the first coordinate component. */ Map<Pair<Integer, Integer>, Map<String, String>> wellToFeaturesMap = new HashMap<>(); for (Map.Entry<Pair<String, String>, String> entry : featuresTable.entrySet()) { String wellCoordinates = entry.getKey().getLeft(); String featureName = entry.getKey().getRight(); String featureValue = entry.getValue(); Pair<Integer, Integer> coordinates = Utils.parsePlateCoordinates(wellCoordinates); Map<String, String> featuresForWell = wellToFeaturesMap.get(coordinates); if (featuresForWell == null) { featuresForWell = new HashMap<>(); wellToFeaturesMap.put(coordinates, featuresForWell); } if (featuresForWell.containsKey(featureName)) { throw new RuntimeException( String.format("Found duplicate feature %s for well %s", wellCoordinates, featureName)); } featuresForWell.put(featureName, featureValue); // Also save the original well coordinates string. featuresForWell.put("well", wellCoordinates); } List<Map.Entry<Pair<Integer, Integer>, Map<String, String>>> sortedEntries = new ArrayList<>( wellToFeaturesMap.entrySet()); Collections.sort(sortedEntries, new Comparator<Map.Entry<Pair<Integer, Integer>, Map<String, String>>>() { @Override public int compare(Map.Entry<Pair<Integer, Integer>, Map<String, String>> o1, Map.Entry<Pair<Integer, Integer>, Map<String, String>> o2) { return o1.getKey().compareTo(o2.getKey()); } }); for (Map.Entry<Pair<Integer, Integer>, Map<String, String>> entry : sortedEntries) { Pair<Integer, Integer> coords = entry.getKey(); Map<String, String> attrs = entry.getValue(); DeliveredStrainWell s = INSTANCE.insert(db, p.getId(), coords.getLeft(), coords.getRight(), attrs.get("well"), attrs.get("msid"), attrs.get("composition")); results.add(s); } return results; } private String well; private String msid; private String composition; private DeliveredStrainWell() { } protected DeliveredStrainWell(Integer id, Integer plateId, Integer plateRow, Integer plateColumn, String well, String msid, String composition) { this.id = id; this.plateId = plateId; this.plateRow = plateRow; this.plateColumn = plateColumn; this.well = well; this.msid = msid; this.composition = composition; } public String getWell() { return well; } public void setWell(String well) { this.well = well; } 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; } }