genepi.db.DatabaseUpdater.java Source code

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Here is the source code for genepi.db.DatabaseUpdater.java

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/*******************************************************************************
 * Copyright (C) 2009-2016 Lukas Forer and Sebastian Schnherr
 *  
 * 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 genepi.db;

import genepi.io.FileUtil;

import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URISyntaxException;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.SQLException;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

public class DatabaseUpdater {

    protected static final Log log = LogFactory.getLog(DatabaseUpdater.class);

    private DatabaseConnector connector;

    private String oldVersion;

    private String currentVersion;

    private String filename;

    private InputStream updateFileStram;

    private boolean needUpdate = false;

    public DatabaseUpdater(DatabaseConnector connector, String filename, InputStream updateFileStram,
            String currentVersion) {

        this.connector = connector;
        this.filename = filename;
        this.updateFileStram = updateFileStram;
        this.currentVersion = currentVersion;

        oldVersion = readVersion(filename);

        needUpdate = (compareVersion(currentVersion, oldVersion) > 0);

    }

    public boolean update() {

        if (needUpdate) {

            try {

                log.info("Updating database from " + oldVersion + " to " + currentVersion + "....");

                executeSQLClasspath(updateFileStram, oldVersion, currentVersion);

                log.info("Updating database successful.");

                FileUtil.writeStringBufferToFile(filename, new StringBuffer(currentVersion));

            } catch (SQLException e) {

                log.error("Updating database failed.", e);
                return false;

            } catch (IOException e) {

                log.error("Updating database failed.", e);
                return false;

            } catch (URISyntaxException e) {

                log.error("Updating database failed.", e);
                return false;

            }

        }

        return true;

    }

    public boolean needUpdate() {
        return needUpdate;
    }

    public String readVersion(String versionFile) {

        File file = new File(versionFile);

        if (file.exists()) {

            try {

                return readFileAsString(versionFile);

            } catch (Exception e) {

                return "1.0.0";

            }

        } else {

            return "1.0.0";

        }

    }

    public static String readFileAsString(String filename) throws java.io.IOException, URISyntaxException {

        InputStream is = new FileInputStream(filename);

        DataInputStream in = new DataInputStream(is);
        BufferedReader br = new BufferedReader(new InputStreamReader(in));
        String strLine;
        StringBuilder builder = new StringBuilder();
        while ((strLine = br.readLine()) != null) {
            // builder.append("\n");
            builder.append(strLine);
        }

        in.close();

        return builder.toString();
    }

    public void executeSQLFile(String filename, String minVersion, String maxVersion)
            throws SQLException, IOException, URISyntaxException {

        String sqlContent = readFileAsStringFile(filename, minVersion, maxVersion);

        Connection connection = connector.getDataSource().getConnection();

        PreparedStatement ps = connection.prepareStatement(sqlContent);
        ps.executeUpdate();
        connection.close();
    }

    public static String readFileAsStringFile(String filename, String minVersion, String maxVersion)
            throws java.io.IOException, URISyntaxException {

        InputStream is = new FileInputStream(filename);

        DataInputStream in = new DataInputStream(is);
        BufferedReader br = new BufferedReader(new InputStreamReader(in));
        String strLine;
        StringBuilder builder = new StringBuilder();
        boolean reading = false;
        while ((strLine = br.readLine()) != null) {

            if (strLine.startsWith("--")) {

                String version = strLine.replace("--", "").trim();
                reading = (compareVersion(version, minVersion) > 0 && compareVersion(version, maxVersion) <= 0);
                if (reading) {
                    log.info("Loading update for version " + version);
                }

            }

            if (reading) {
                builder.append("\n");
                builder.append(strLine);
            }
        }

        in.close();

        return builder.toString();
    }

    public void executeSQLClasspath(InputStream is, String minVersion, String maxVersion)
            throws SQLException, IOException, URISyntaxException {

        String sqlContent = readFileAsStringClasspath(is, minVersion, maxVersion);

        if (!sqlContent.isEmpty()) {
            Connection connection = connector.getDataSource().getConnection();
            PreparedStatement ps = connection.prepareStatement(sqlContent);
            ps.executeUpdate();
            connection.close();
        }
    }

    public static String readFileAsStringClasspath(InputStream is, String minVersion, String maxVersion)
            throws java.io.IOException, URISyntaxException {

        DataInputStream in = new DataInputStream(is);
        BufferedReader br = new BufferedReader(new InputStreamReader(in));
        String strLine;
        StringBuilder builder = new StringBuilder();
        boolean reading = false;
        while ((strLine = br.readLine()) != null) {

            if (strLine.startsWith("--")) {

                String version = strLine.replace("--", "");
                reading = (compareVersion(version, minVersion) > 0 && compareVersion(version, maxVersion) <= 0);

                if (reading) {
                    log.info("Loading update for version " + version);
                }

            }

            if (reading) {
                builder.append("\n");
                builder.append(strLine);
            }
        }

        in.close();

        return builder.toString();
    }

    public static int compareVersion(String version1, String version2) {

        String parts1[] = version1.split("-", 2);
        String parts2[] = version2.split("-", 2);

        String tiles1[] = parts1[0].split("\\.");
        String tiles2[] = parts2[0].split("\\.");

        for (int i = 0; i < tiles1.length; i++) {
            int number1 = Integer.parseInt(tiles1[i].trim());
            int number2 = Integer.parseInt(tiles2[i].trim());

            if (number1 != number2) {

                return number1 > number2 ? 1 : -1;

            }

        }

        if (parts1.length > 1) {
            if (parts2.length > 1) {
                return parts1[1].compareTo(parts2[1]);
            } else {
                return -1;
            }
        } else {
            if (parts2.length > 1) {
                return 1;
            }
        }

        return 0;

    }

}