massbank.svn.MSDBUpdateUtil.java Source code

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Here is the source code for massbank.svn.MSDBUpdateUtil.java

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/*******************************************************************************
 *
 * Copyright (C) 2012 MassBank project
 *
 * 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 2 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, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 *
 *******************************************************************************
 *
 * MSDBUpdateUtil.java
 *
 * ver 1.0.4 2013.02.26
 *
 ******************************************************************************/
package massbank.svn;

import java.io.File;
import java.io.IOException;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
import java.net.HttpURLConnection;
import java.util.List;
import java.util.logging.Logger;
import java.lang.StringBuilder;
import java.sql.Statement;
import java.sql.Connection;
import org.apache.commons.io.FileUtils;
import massbank.admin.FileUtil;

public class MSDBUpdateUtil {
    private static final Logger logger = Logger.getLogger("global");

    /**
     *
     */
    public static boolean updateFiles(File srcDir, File destDir, String[] extensions) {
        boolean isUpdated = false;
        if (!srcDir.exists()) {
            return false;
        }
        if (!destDir.exists()) {
            destDir.mkdirs();
        }
        try {
            List<File> srcFileList = (List<File>) FileUtils.listFiles(srcDir, extensions, false);
            List<File> destFileList = (List<File>) FileUtils.listFiles(destDir, extensions, false);
            FileDifference diff = new FileDifference(srcFileList, destFileList);
            String[] addFilePaths = diff.getAddFilePaths();
            String[] delFileNames = diff.getDeleteFileNames();
            if (addFilePaths.length > 0) {
                isUpdated = true;
                for (String path : addFilePaths) {
                    FileUtils.copyFileToDirectory(new File(path), destDir);
                }
            }
            if (delFileNames.length > 0) {
                isUpdated = true;
                for (String name : delFileNames) {
                    String path = destDir.getPath() + File.separator + name;
                    FileUtils.deleteQuietly(new File(path));
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
            return false;
        }
        return isUpdated;
    }

    /**
     *
     */
    public static boolean restoreDatabase(String dbName, String workCopyPath) {
        Connection con1 = SVNUtils.connectDB("");
        if (con1 == null) {
            return false;
        }
        try {
            Statement stmt = con1.createStatement();
            String sql = "CREATE DATABASE IF NOT EXISTS " + dbName;
            stmt.executeUpdate(sql);
            stmt.close();
            con1.close();
        } catch (Exception e) {
            e.printStackTrace();
            return false;
        }
        String dumpFilePath = workCopyPath + File.separator + "other" + File.separator + "massbank_backup.sql";
        File file = new File(dumpFilePath);
        if (!file.exists()) {
            logger.severe("[SVNService] File not found:" + dumpFilePath);
            return false;
        }
        boolean ret = FileUtil.execSqlFile("localhost", dbName, dumpFilePath);
        if (!ret) {
            return false;
        }
        Connection con2 = SVNUtils.connectDB(dbName);
        if (con2 == null) {
            return false;
        }
        try {
            Statement stmt = con2.createStatement();
            String sql1 = "DROP TABLE IF EXISTS PEAK_HEAP";
            stmt.executeUpdate(sql1);
            String sql2 = "CREATE TABLE PEAK_HEAP(INDEX(ID),INDEX(MZ),INDEX(RELATIVE)) "
                    + "ENGINE=HEAP SELECT ID,MZ,RELATIVE FROM PEAK";
            stmt.executeUpdate(sql2);
            stmt.close();
            con2.close();
        } catch (Exception e) {
            e.printStackTrace();
            return false;
        }
        return true;
    }

    /**
     *
     */
    public static boolean updateSubStructData(String serverUrl) {
        boolean ret = true;
        String cgiUrl = serverUrl + "cgi-bin/GenSubstructure.cgi";
        try {
            URL url = new URL(cgiUrl);
            HttpURLConnection con = (HttpURLConnection) url.openConnection();
            con.setConnectTimeout(10 * 1000);
            con.setReadTimeout(60 * 1000);
            BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
            String line = "";
            StringBuilder res = new StringBuilder();
            while ((line = in.readLine()) != null) {
                res.append(line);
            }
            if (res.indexOf("OK") == -1) {
                ret = false;
            }
        } catch (IOException e) {
            e.printStackTrace();
            ret = false;
        }
        return ret;
    }
}