/*
 * #%L
 * Netarchivesuite - deploy
 * %%
 * Copyright (C) 2005 - 2018 The Royal Danish Library, 
 *             the National Library of France and the Austrian National Library.
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation, either version 2.1 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 Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU General Lesser Public
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/lgpl-2.1.html>.
 * #L%
 */
package dk.netarkivet.deploy;

import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Map.Entry;

import org.dom4j.Element;

import dk.netarkivet.common.exceptions.IOFailure;

/**
 * A LinuxMachine is the instance of the abstract machine class, which runs the operating system Linux or another Unix
 * dependent operation system. This class only contains the operating system specific functions.
 */
public class LinuxMachine extends Machine {

        public static final String HERITRIX_1_CLASSNAME = "org.archive.crawler.Heritrix";

        protected LinkedHashMap<String, String> bundles = new LinkedHashMap<>();
        protected LinkedHashMap<String, String> certificates = new LinkedHashMap<String, String>();

        /**
     * The constructor. Starts by initialising the parent abstract class, then sets the operating system dependent
     * variables.
     *
     * @param subTreeRoot The XML root element.
     * @param parentSettings The Settings to be inherited from the PhysicalLocation, where this machine is placed.
     * @param param The machine parameters to be inherited from the PhysicalLocation.
     * @param netarchiveSuiteSource The name of the NetarchiveSuite package file. Must end with '.zip'.
     * @param securityPolicy The security policy file, to be copied into machine directory.
     * @param dbFile The name of the database file.
     * @param arcdbFile The name of the archive file.
     * @param resetDir Whether the temporary directory should be reset.
     * @param externalJarFolder The folder containing the external jar library files.
     * @param logoFile user specific logo png file.
     * @param menulogoFile user specific menulogo png file.
     * @param deployConfiguration The general deployment configuration.
     */
    public LinuxMachine(Element subTreeRoot, XmlStructure parentSettings, Parameters param,
            String netarchiveSuiteSource, File slf4JConfig, File securityPolicy, File dbFile,
            File arcdbFile, boolean resetDir, File externalJarFolder, File logoFile, File menulogoFile,
            DeployConfiguration deployConfiguration) {
        super(subTreeRoot, parentSettings, param, netarchiveSuiteSource, slf4JConfig, securityPolicy, dbFile,
                arcdbFile, resetDir, externalJarFolder, logoFile, menulogoFile);
        // set operating system
        operatingSystem = Constants.OPERATING_SYSTEM_LINUX_ATTRIBUTE;
        scriptExtension = Constants.SCRIPT_EXTENSION_LINUX;

        String[] bundlesArr;
        String[] certificatesArr;
        String srcStr;
        String dstStr;
        int idx;
        for (Application app : applications) {
            if (app.isBundledHarvester()) {
                bundlesArr = app.getSettingsValues(Constants.SETTINGS_HARVEST_HERITRIX3_BUNDLE_LEAF);
                if ((bundlesArr == null || bundlesArr.length == 0)
                        && deployConfiguration.getDefaultBundlerZip() != null) {
                    bundlesArr = new String[] { deployConfiguration.getDefaultBundlerZip().getAbsolutePath() };
                } else if ((bundlesArr == null || bundlesArr.length == 0 || bundlesArr[0].length()==0)
                        && deployConfiguration.getDefaultBundlerZip() == null) {
                    throw new IllegalArgumentException("A Heritrix bundler needs to be defined for H3 controllers, "
                            + "either directly in the deploy configuration or from the command line with the -B option.");
                }
                certificatesArr = app.getSettingsValues(Constants.SETTINGS_HARVEST_HERITRIX3_CERTIFICATE_LEAF);
                if (bundlesArr != null && bundlesArr.length > 0 && certificatesArr != null) {
                    for (int i = 0; i < bundlesArr.length; ++i) {
                        srcStr = bundlesArr[i];
                        if (!bundles.containsKey(srcStr)) {
                            idx = srcStr.lastIndexOf('/');
                            if (idx != -1) {
                                dstStr = srcStr.substring(idx + 1);
                            } else {
                                dstStr = srcStr;
                            }
                            dstStr = machineParameters.getInstallDirValue() + "/" + getEnvironmentName() + "/" + dstStr;
                            bundles.put(srcStr, dstStr);
                            System.out.println(srcStr + " -> " + dstStr);
                        }
                    }
                    for (int i = 0; i < certificatesArr.length; ++i) {
                        srcStr = certificatesArr[i];
                        if (!certificates.containsKey(srcStr)) {
                            idx = srcStr.lastIndexOf('/');
                            if (idx != -1) {
                                dstStr = srcStr.substring(idx + 1);
                            } else {
                                dstStr = srcStr;
                            }
                            dstStr = machineParameters.getInstallDirValue() + "/" + getEnvironmentName() + "/" + dstStr;
                            certificates.put(srcStr, dstStr);
                            System.out.println(srcStr + " -> " + dstStr);
                        }
                    }
                    XmlStructure appSettings = app.getSettings();
                    Element heritrixBundleElement =
                            appSettings.getSubChild(Constants.SETTINGS_HARVEST_HERITRIX3_BUNDLE_LEAF);
                    if (heritrixBundleElement == null) {
                        appSettings.getSubChild(Constants.SETTINGS_HERITRIX3_BRANCH).addElement("bundle");
                        heritrixBundleElement =
                                appSettings.getSubChild(Constants.SETTINGS_HARVEST_HERITRIX3_BUNDLE_LEAF);
                        heritrixBundleElement.setText((String)bundles.values().toArray()[0]);
                    } else {
                        heritrixBundleElement.setText(bundles.get(heritrixBundleElement.getText()));
                    }
                    Element h3KeystoreElement = appSettings
                            .getSubChild(Constants.SETTINGS_HARVEST_HERITRIX3_CERTIFICATE_LEAF);
                    if (h3KeystoreElement != null) {
                        String h3KeystoreName = certificates.get(h3KeystoreElement.getText());
                        if (h3KeystoreName != null) {
                            h3KeystoreElement.setText(h3KeystoreName);
                        }
                    }
                }
            }
        }
    }

    protected static final class osInstallScriptTpl {
        protected static final String[] mainScript = {
            // echo copying null.zip to:kb-test-adm-001.kb.dk
            "echo copying ${netarchiveSuiteFileName} to:${name}",
            // scp null.zip dev@kb-test-adm-001.kb.dk:/home/dev
            "scp ${netarchiveSuiteFileName} ${machineUserLogin}:${installDirValue}",
            // echo deleting dev@kb-test-adm-001.kb.dk:/home/dev/TEST/lib
            "echo deleting ${machineUserLogin}:${installDirValue}/${environmentName}/lib",
            // ssh dev@kb-test-adm-001.kb.dk rm -rf /home/dev/TEST/lib
            "ssh ${machineUserLogin} \"rm -rf ${installDirValue}/${environmentName}/lib\"",
            // echo unzipping null.zip at:kb-test-adm-001.kb.dk
            "echo unzipping ${netarchiveSuiteFileName} at:${name}",
            // ssh dev@kb-test-adm-001.kb.dk unzip -q -o /home/dev/null.zip -d /home/dev/TEST
            "ssh ${machineUserLogin} \"unzip -q -o ${installDirValue}/${netarchiveSuiteFileName} -d ${installDirValue}/${environmentName}\"",
            // update Logos.
            "${osUpdateLogos}",
            // create other directories.
            "${osInstallScriptCreateDir}",
            // echo preparing for copying of settings and scripts
            "echo preparing for copying of settings and scripts",
            // For overriding jmxremote.password give user all rights.
            // ssh machine: "if [ -e conf/jmxremote.password ];
            // then chmod u+rwx conf/jmxremote.password; fi; "
            "ssh ${machineUserLogin} \" cd ~; if [ -e ${installDirValue}/${environmentName}/conf/jmxremote.password ]; then chmod u+rwx ${installDirValue}/${environmentName}/conf/jmxremote.password; fi; \"",
            // For overriding jmxremote.access give user all rights.
            // ssh machine: "if [ -e conf/jmxremote.access ];
            // then chmod u+rwx conf/jmxremote.access; fi; "
            "ssh ${machineUserLogin} \" cd ~; if [ -e ${installDirValue}/${environmentName}/conf/jmxremote.access ]; then chmod u+rwx ${installDirValue}/${environmentName}/conf/jmxremote.access; fi; \"",
            // echo copying settings and scripts
            "echo copying settings and scripts",
            // scp -r kb-test-adm-001.kb.dk/* dev@kb-test-adm-001.kb.dk:/home/dev/TEST/conf/
            "scp -r ${name}/* ${machineUserLogin}:${installDirValue}/${environmentName}/conf/",
            // INSTALL EXTERNAL JAR FILES.
            "${osInstallExternalJarFiles}",
            // APPLY HARVEST DEFINITION DATABASE!
            "${osInstallDatabase}",
            // APPLY ARCHIVE DATABASE!
            "${osInstallArchiveDatabase}",
            // echo make scripts executable
            "echo make scripts executable",
            // Allow only user to be able to deal with these files
            // (go=-rwx,u=+rwx) = 700.
            // ssh dev@kb-test-adm-001.kb.dk "chmod 700 /home/dev/TEST/conf/*.sh "
            "ssh ${machineUserLogin} \"chmod 700 ${installDirValue}/${environmentName}/conf/*.sh \"",
            // HANDLE JMXREMOTE PASSWORD AND ACCESS FILE.
            "${JMXremoteFilesCommand}",
            // END OF SCRIPT
            "${heritrix3Files}"
        };
        protected static final String scpFile = "scp ${srcFileName} ${machineUserLogin}:${dstFileName}";
    }

    @Override
    protected String osInstallScript() {
        Map<String, String> env = new HashMap<String, String>();
        StringBuilder sb = new StringBuilder();
        Iterator<Entry<String, String>> iter;
        String tmpStr;
        env.put("machineUserLogin", machineUserLogin());
        iter = bundles.entrySet().iterator();
        Entry<String, String> entry;
        while (iter.hasNext()) {
                entry = iter.next();
                env.put("srcFileName", entry.getKey());
            env.put("dstFileName", entry.getValue());
            tmpStr = Template.untemplate(osInstallScriptTpl.scpFile, env, true);
            if (sb.length() > 0) {
                sb.append("\n");
            }
            sb.append(tmpStr);
        }
        iter = certificates.entrySet().iterator();
        while (iter.hasNext()) {
                entry = iter.next();
                env.put("srcFileName", entry.getKey());
            env.put("dstFileName", entry.getValue());
            tmpStr = Template.untemplate(osInstallScriptTpl.scpFile, env, true);
            if (sb.length() > 0) {
                sb.append("\n");
            }
            sb.append(tmpStr);
        }

        env.clear();
        env.put("netarchiveSuiteFileName", netarchiveSuiteFileName);
        env.put("name", hostname);
        env.put("machineUserLogin", machineUserLogin());
        env.put("installDirValue", machineParameters.getInstallDirValue());
        env.put("environmentName", getEnvironmentName());
        env.put("osUpdateLogos", osUpdateLogos());
        env.put("osInstallScriptCreateDir", osInstallScriptCreateDir());
        env.put("osInstallExternalJarFiles", osInstallExternalJarFiles());
        env.put("osInstallDatabase", osInstallDatabase());
        env.put("osInstallArchiveDatabase", osInstallArchiveDatabase());
        env.put("JMXremoteFilesCommand", getJMXremoteFilesCommand());
        env.put("heritrix3Files", sb.toString());
        String str = Template.untemplate(osInstallScriptTpl.mainScript, env, true, "\n");
        return str;
    }

    protected static final class osKillScriptTpl {
        protected static final String[] mainScript = {
            "ssh ${machineUserLogin} \". /etc/profile; ${installDirValue}/${environmentName}/conf/killall.sh\";"
        };
    }

    @Override
    protected String osKillScript() {
        Map<String, String> env = new HashMap<String, String>();
        env.put("machineUserLogin", machineUserLogin());
        env.put("environmentName", getEnvironmentName());
        env.put("installDirValue", machineParameters.getInstallDirValue());
        String str = Template.untemplate(osKillScriptTpl.mainScript, env, true, "\n");
        return str;
    }

    protected static final class osStartScriptTpl {
        protected static final String[] mainScript = {
            "ssh ${machineUserLogin} \". /etc/profile;. ~/.bash_profile; ${installDirValue}/${environmentName}/conf/startall.sh; sleep 5; cat ${installDirValue}/${environmentName}/*.log\""
        };
    }

    /**
     * Creates the operation system specific starting script for this machine.
     * <p>
     * pseudo code: - ssh maclogin ". /etc/profile; conf/startall.sh; sleep 5; cat install/*.log"
     * <p>
     * where: maclogin = login for machine (username@machine). conf = path to /conf directory. install = path to install
     * directory.
     *
     * @return Operation system specific part of the startscript.
     */
    @Override
    protected String osStartScript() {
        Map<String, String> env = new HashMap<String, String>();
        env.put("machineUserLogin", machineUserLogin());
        env.put("environmentName", getEnvironmentName());
        env.put("installDirValue", machineParameters.getInstallDirValue());
        String str = Template.untemplate(osStartScriptTpl.mainScript, env, true, "\n");
        return str;
    }

    @Override
    protected String getInstallDirPath() {
        return machineParameters.getInstallDirValue() + Constants.SLASH + getEnvironmentName();
    }

    @Override
    protected String getConfDirPath() {
        return getInstallDirPath() + Constants.CONF_DIR_LINUX;
    }

    /**
     * Creates the local path to the lib dir.
     *
     * @return The path to the lib dir for ssh.
     */
    protected String getLocalLibDirPath() {
        return Constants.LIB_DIR_LINUX;
    }

    /**
     * This function creates the script to kill all applications on this machine. The scripts calls all the kill script
     * for each application. It also runs the script for killing any external database.
     * <p>
     * pseudo code: - echo Killing all applications at machine: mac - if [ -e ./kill_app.sh ] - ./kill_app.sh - fi - ...
     * <p>
     * where: mac = machine name. app = application name. ... = the same for other applications.
     *
     * @param directory The directory for this machine (use global variable?).
     * @throws IOFailure If an error occurred during the creation of the local killall script.
     */
    @Override
    protected void createOSLocalKillAllScript(File directory) throws IOFailure {
        // create the kill all script file
        File killAllScript = new File(directory, Constants.SCRIPT_NAME_KILL_ALL + scriptExtension);
        try {
            // Initialise script
            PrintWriter killPrinter = new PrintWriter(killAllScript, getTargetEncoding());
            try {
                killPrinter.println(ScriptConstants.ECHO_KILL_ALL_APPS + Constants.COLON + Constants.SPACE
                        + Constants.APOSTROPHE + hostname + Constants.APOSTROPHE);
                killPrinter.println(ScriptConstants.BIN_BASH_COMMENT);
                killPrinter.println(ScriptConstants.CD + Constants.SPACE + getConfDirPath());
                // insert path to kill script for all applications
                for (Application app : applications) {
                    // Constructing filename
                    String appScript = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_LOCAL_KILL
                            + app.getIdentification() + scriptExtension;
                    // check if file exists
                    killPrinter.println(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE + appScript + Constants.SPACE
                            + ScriptConstants.LINUX_THEN + Constants.SPACE);
                    killPrinter.println(ScriptConstants.MULTI_SPACE_6 + appScript);
                    killPrinter.println(ScriptConstants.FI);
                }

                // kill the harvest database, if any, after the applications
                killPrinter.print(callKillHarvestDatabase());
                // kill the admin database, if any, after the applications
                killPrinter.print(callKillArchiveDatabase());
            } finally {
                // close script
                killPrinter.close();
            }
        } catch (IOException e) {
            String msg = "Problems creating local kill all script. ";
            log.error(msg, e);
            throw new IOFailure(msg, e);
        }
    }

    /**
     * This function creates the script to start all applications on this machine. The scripts calls all the start
     * script for each application. It also runs the script for starting any external database.
     * <p>
     * pseudo code: - echo Starting all applications at machine: mac - if [ -e ./start_app.sh ] - ./start_app.sh - fi -
     * ...
     * <p>
     * where: mac = machine name. app = application name. ... = the same for other applications.
     *
     * @param directory The directory for this machine (use global variable?).
     * @throws IOFailure If an error occurred during the creation of the local startall script.
     */
    @Override
    protected void createOSLocalStartAllScript(File directory) throws IOFailure {
        // create the start all script file
        File startAllScript = new File(directory, Constants.SCRIPT_NAME_START_ALL + scriptExtension);
        try {
            // Initialise script
            PrintWriter startPrinter = new PrintWriter(startAllScript, getTargetEncoding());
            try {
                startPrinter.println(ScriptConstants.BIN_BASH_COMMENT);
                startPrinter.println(ScriptConstants.CD + Constants.SPACE + getConfDirPath());

                // start the harvest database, if any, before the applications.
                startPrinter.print(callStartHarvestDatabase());
                // start the admin database, if any, before the applications.
                startPrinter.print(callStartArchiveDatabase());

                startPrinter.println(ScriptConstants.ECHO_START_ALL_APPS + Constants.COLON + Constants.SPACE
                        + Constants.APOSTROPHE + hostname + Constants.APOSTROPHE);

                // insert path to start script for each applications
                for (Application app : applications) {
                    // make name of file
                    String appScript = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_LOCAL_START
                            + app.getIdentification() + scriptExtension;
                    // check if file exists
                    startPrinter.println(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE + appScript + Constants.SPACE
                            + ScriptConstants.LINUX_THEN + Constants.SPACE);
                    startPrinter.println(ScriptConstants.MULTI_SPACE_6 + appScript);
                    startPrinter.println(ScriptConstants.FI);
                }
            } finally {
                // close script
                startPrinter.close();
            }
        } catch (IOException e) {
            String msg = "Problems creating local start all script. ";
            log.trace(msg, e);
            throw new IOFailure(msg, e);
        }
    }

    /**
     * Creates the kill scripts for all the applications.
     * <p>
     * The script starts by finding all running processes of the application. If it finds any processes, it kills them.
     * <p>
     * The kill_app.sh should have the following structure:
     * <p>
     * - echo Killing linux application. - #!/bin/bash - PIDS = $(ps -wwfe | grep fullapp | grep -v grep | grep
     * path\settings_app.xml | awk "{print \\$2}") - if [ -n "$PIDS" ]; then - kill -9 $PIDS; - fi
     * <p>
     * Also, if a heritrix process is started, the following is added: - PIDS = $(ps -wwfe | grep heritrix | grep -v
     * grep | grep path\settings_app.xml | awk "{print \\$2}") - if [ -n "$PIDS" ]; then - kill -9 $PIDS; - fi
     * <p>
     * where: path = the path to the ./conf directory. fullapp = the full application name with class path. app = the id
     * of the application (name + instanceId). heritrix = the heritrix class path.
     *
     * @param directory The directory for this machine (use global variable?).
     * @throws IOFailure If an error occured during the creation of the kill application script file.
     */
    @Override
    protected void createApplicationKillScripts(File directory) throws IOFailure {
        // go through all applications and create their kill script
        for (Application app : applications) {
            File appKillScript = new File(directory, Constants.SCRIPT_NAME_LOCAL_KILL + app.getIdentification()
                    + scriptExtension);
            try {
                // make print writer for writing to file
                PrintWriter appPrint = new PrintWriter(appKillScript, getTargetEncoding());
                try {
                    // echo Killing linux application.
                    appPrint.println(ScriptConstants.ECHO_KILL_LINUX_APPLICATION + Constants.COLON + Constants.SPACE
                            + app.getIdentification());
                    // #!/bin/bash
                    appPrint.println(ScriptConstants.BIN_BASH_COMMENT);

                    // First try an ordinary kill, wait 2 seconds. Then test,
                    // if process is still around. If it is make a hard kill
                    // (-9)

                    // PIDS = $(ps -wwfe | grep fullapp | grep -v grep | grep
                    // path\settings_app.xml | awk "{print \\$2}")
                    appPrint.println(ScriptConstants.getLinuxPIDS(app.getTotalName(), getConfDirPath(),
                            app.getIdentification()));
                    // if [ -n "$PIDS" ]; then
                    appPrint.println(ScriptConstants.LINUX_IF_N_EXIST + Constants.SPACE + Constants.QUOTE_MARK
                            + ScriptConstants.PIDS + Constants.QUOTE_MARK + Constants.SPACE
                            + ScriptConstants.LINUX_N_THEN);

                    appPrint.println(ScriptConstants.KILL_PIDS + Constants.SEMICOLON);
                    // fi
                    appPrint.println(ScriptConstants.FI);
                    appPrint.println();
                    appPrint.println(ScriptConstants.SLEEP_2);

                    appPrint.println();
                    // Set PIDS
                    appPrint.println(ScriptConstants.getLinuxPIDS(app.getTotalName(), getConfDirPath(),
                            app.getIdentification()));
                    // IF
                    appPrint.println(ScriptConstants.LINUX_IF_N_EXIST + Constants.SPACE + Constants.QUOTE_MARK
                            + ScriptConstants.PIDS + Constants.QUOTE_MARK + Constants.SPACE
                            + ScriptConstants.LINUX_N_THEN);

                    // kill -9 $PIDS;
                    appPrint.println(ScriptConstants.KILL_9_PIDS + Constants.SEMICOLON);
                    // fi
                    appPrint.println(ScriptConstants.FI);

                    // If the application contains a heritrix instance,
                    // then make script for killing the heritrix process.
                    String[] heritrixJmxPort = app.getSettingsValues(Constants.SETTINGS_HARVEST_HERITRIX_JMX_PORT);
                    if (heritrixJmxPort != null && heritrixJmxPort.length > 0) {
                        // log if more than one jmx port defined for heritrix.
                        if (heritrixJmxPort.length > 1) {
                            log.trace(heritrixJmxPort.length + " number of jmx-ports for a heritrix " + "harvester.");
                        }
                        appPrint.println();
                        // - PIDS = $(ps -wwfe | grep heritrix | grep -v grep
                        // | grep path\settings_app.xml | awk "{print \\$2}")
                        appPrint.println(ScriptConstants.getLinuxPIDS(HERITRIX_1_CLASSNAME, getConfDirPath(),
                                app.getIdentification()));
                        // - if [ -n "$PIDS" ]; then
                        appPrint.println(ScriptConstants.LINUX_IF_N_EXIST + Constants.SPACE + Constants.QUOTE_MARK
                                + ScriptConstants.PIDS + Constants.QUOTE_MARK + Constants.SPACE
                                + ScriptConstants.LINUX_N_THEN);
                        // first make a ordinary kill, wait 2 seconds, then make a
                        // hard kill -9
                        appPrint.println(ScriptConstants.KILL_PIDS + Constants.SEMICOLON);
                        // - fi
                        appPrint.println(ScriptConstants.FI);
                        appPrint.println();
                        // wait 2 seconds
                        appPrint.println(ScriptConstants.SLEEP_2);
                        appPrint.println();
                        // See if Process is still around
                        appPrint.println(ScriptConstants.getLinuxPIDS(HERITRIX_1_CLASSNAME, getConfDirPath(),
                                app.getIdentification()));
                        // if still around
                        appPrint.println(ScriptConstants.LINUX_IF_N_EXIST + Constants.SPACE + Constants.QUOTE_MARK
                                + ScriptConstants.PIDS + Constants.QUOTE_MARK + Constants.SPACE
                                + ScriptConstants.LINUX_N_THEN);
                        // - kill -9 $PIDS;
                        appPrint.println(ScriptConstants.KILL_9_PIDS + Constants.SEMICOLON);
                        // - fi
                        appPrint.println(ScriptConstants.FI);
                    }
                } finally {
                    // close file
                    appPrint.close();
                }
            } catch (IOException e) {
                String msg = "Problems creating application kill script: ";
                log.error(msg, e);
                throw new IOFailure(msg, e);
            }
        }
    }

    /**
     * Creates the start scripts for all the applications.
     * <p>
     * The application should only be started, if it is not running already. The script starts by finding all running
     * processes of the application. If any processes are found, a new application should not be started. Otherwise
     * start the application.
     * <p>
     * The start_app.sh should have the following structure:
     * <p>
     * - echo Starting linux application: app - cd path - #!/bin/bash - PIDS = $(ps -wwfe | grep fullapp | grep -v grep
     * | grep path\settings_app.xml | awk "{print \\$2}") - if [ -n "$PIDS" ]; then - echo Application already running.
     * - else - export CLASSPATH = cp:$CLASSPATH; - JAVA - fi
     * <p>
     * where: path = the path to the install directory. fullapp = the full name application with java path. app = the
     * name of the application. cp = the classpaths for the application. JAVA = the command to run the java application.
     *
     * @param directory The directory for this machine (use global variable?).
     * @throws IOFailure If an error occurred during the creation of the start application script file.
     */
    @Override
    protected void createApplicationStartScripts(File directory) throws IOFailure {
        // go through all applications and create their start script
        for (Application app : applications) {
            if (app.getTotalName().contains("GUI")) {
                 createHarvestDatabaseUpdateScript(directory, true);
            }
            File appStartScript = new File(directory, Constants.SCRIPT_NAME_LOCAL_START + app.getIdentification()
                    + scriptExtension);
            try {
                // make print writer for writing to file
                PrintWriter appPrint = new PrintWriter(appStartScript, getTargetEncoding());
                try {
                    // #!/bin/bash
                    appPrint.println(ScriptConstants.ECHO_START_LINUX_APP + Constants.COLON + Constants.SPACE
                            + app.getIdentification());
                    // cd path
                    appPrint.println(ScriptConstants.CD + Constants.SPACE + app.installPathLinux());
                    // PIDS = $(ps -wwfe | grep fullapp | grep -v grep | grep
                    // path\settings_app.xml | awk "{print \\$2}")
                    appPrint.println(ScriptConstants.getLinuxPIDS(app.getTotalName(), getConfDirPath(),
                            app.getIdentification()));
                    // if [ -n "$PIDS" ]; then
                    appPrint.println(ScriptConstants.LINUX_IF_N_EXIST + Constants.SPACE + Constants.QUOTE_MARK
                            + ScriptConstants.PIDS + Constants.QUOTE_MARK + Constants.SPACE
                            + ScriptConstants.LINUX_N_THEN);
                    // echo Application already running.
                    appPrint.println(ScriptConstants.ECHO_APP_ALREADY_RUNNING);
                    // else
                    appPrint.println(ScriptConstants.ELSE);
                    // export CLASSPATH = cp;
                    appPrint.println(ScriptConstants.MULTI_SPACE_4 + ScriptConstants.EXPORT_CLASSPATH
                            + osGetClassPath(app) + ScriptConstants.VALUE_OF_CLASSPATH + Constants.SEMICOLON);
                    // JAVA
                    String securityManagement = "";
                    if (app.getTotalName().contains(ScriptConstants.BITARCHIVE_APPLICATION_NAME)) {
                        securityManagement = Constants.SPACE + Constants.DASH + ScriptConstants.OPTION_SECURITY_MANAGER
                                + Constants.SPACE + Constants.DASH + ScriptConstants.OPTION_SECURITY_POLICY
                                + getConfDirPath() + Constants.SECURITY_POLICY_FILE_NAME;
                    }
                    appPrint.println(ScriptConstants.MULTI_SPACE_4
                            + ScriptConstants.JAVA
                            + Constants.SPACE
                            + app.getMachineParameters().writeJavaOptions()
                            + Constants.SPACE
                            + Constants.DASH
                            + ScriptConstants.OPTION_SETTINGS
                            + getConfDirPath()
                            + Constants.PREFIX_SETTINGS
                            + app.getIdentification()
                            + Constants.EXTENSION_XML_FILES

                            // TODO check to see if inheritedSlf4jConfigFile is not null
                            + Constants.SPACE + Constants.DASH + ScriptConstants.OPTION_LOGBACK_CONFIG
                            + getConfDirPath() + Constants.LOGBACK_PREFIX + app.getIdentification()
                            + Constants.EXTENSION_XML_FILES

                            + securityManagement

                            + Constants.SPACE + app.getTotalName() + Constants.SPACE + ScriptConstants.LINUX_DEV_NULL
                            + Constants.SPACE + Constants.SCRIPT_NAME_LOCAL_START + app.getIdentification()
                            + Constants.EXTENSION_LOG_FILES + Constants.SPACE
                            + ScriptConstants.LINUX_ERROR_MESSAGE_TO_1);
                    // fi
                    appPrint.println(ScriptConstants.FI);
                } finally {
                    // close file
                    appPrint.close();
                }
            } catch (IOException e) {
                String msg = "Problems creating application start script. ";
                log.trace(msg, e);
                throw new IOFailure(msg, e);
            }
        }
    }

    @Override
    protected String osGetClassPath(Application app) {
        StringBuilder res = new StringBuilder();
        // get all the classpaths
        for (Element cp : app.getMachineParameters().getClassPaths()) {
            res.append(getInstallDirPath() + Constants.SLASH + cp.getText().trim() + Constants.COLON);
        }
        return res.toString();
    }

    @Override
    protected String osInstallDatabase() {
        StringBuilder res = new StringBuilder();

        String databaseDir = machineParameters.getHarvestDatabaseDirValue();
        // Do not install if no proper database directory.
        if (databaseDir == null || databaseDir.isEmpty()) {
            return Constants.EMPTY;
        }

        // copy to final destination if database argument.
        if (databaseFile != null) {
            // echo Copying database
            res.append(ScriptConstants.ECHO_COPYING_DATABASE);
            res.append(Constants.NEWLINE);
            // scp database.jar user@machine:dbDir/db
            res.append(ScriptConstants.SCP + Constants.SPACE);
            res.append(databaseFile.getPath());
            res.append(Constants.SPACE);
            res.append(machineUserLogin());
            res.append(Constants.COLON);
            res.append(getInstallDirPath());
            res.append(Constants.SLASH);
            res.append(Constants.HARVEST_DATABASE_BASE_PATH);
            res.append(Constants.NEWLINE);
        }
        // unzip database.
        res.append(ScriptConstants.ECHO_UNZIPPING_DATABASE);
        res.append(Constants.NEWLINE);
        // ssh user@machine "
        // cd dir; if [ -d databaseDir ]; then echo ;
        // else mkdir databaseDir; fi; if [ $(ls -A databaseDir) ];
        // then echo ERROR MESSAGE: DIR NOT EMPTY;
        // else unzip -q -o dbDir/db -d databaseDir/.; fi; exit;
        // "
        res.append(ScriptConstants.SSH + Constants.SPACE);
        res.append(machineUserLogin());
        res.append(Constants.SPACE + Constants.QUOTE_MARK + ScriptConstants.CD + Constants.SPACE);
        res.append(getInstallDirPath());
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.LINUX_IF_DIR_EXIST + Constants.SPACE);
        res.append(databaseDir);
        res.append(Constants.SPACE + ScriptConstants.LINUX_THEN + Constants.SPACE + ScriptConstants.ECHO
                + Constants.SPACE);
        res.append(ScriptConstants.DATABASE_ERROR_PROMPT_DIR_NOT_EMPTY);
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.ELSE + Constants.SPACE
                + ScriptConstants.LINUX_UNZIP_COMMAND + Constants.SPACE);
        res.append(Constants.HARVEST_DATABASE_BASE_PATH);
        res.append(Constants.SPACE + ScriptConstants.SCRIPT_DIR + Constants.SPACE);
        res.append(databaseDir);
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.FI + Constants.SEMICOLON + Constants.SPACE
                + ScriptConstants.EXIT + Constants.SEMICOLON + Constants.SPACE + Constants.QUOTE_MARK);
        res.append(Constants.NEWLINE);

        return res.toString();
    }

    @Override
    protected String osInstallExternalJarFiles() {
        if (jarFolder == null) {
            return Constants.EMPTY;
        }

        StringBuilder res = new StringBuilder();

        // Comment about copying files.
        res.append(ScriptConstants.ECHO_INSTALLING_EXTERNAL_JAR_FILES);
        res.append(Constants.NEWLINE);
        // if [ -d folder ]; then scp folder machine:installdir/external; fi;
        res.append(ScriptConstants.LINUX_IF_DIR_EXIST + Constants.SPACE);
        res.append(jarFolder.getPath());
        res.append(Constants.SPACE + ScriptConstants.LINUX_THEN + Constants.SPACE + ScriptConstants.SCP
                + Constants.SPACE + ScriptConstants.DASH_R + Constants.SPACE);
        res.append(jarFolder.getPath());
        res.append(Constants.SPACE);
        res.append(machineUserLogin());
        res.append(Constants.COLON);
        res.append(getInstallDirPath());
        res.append(Constants.SLASH + Constants.EXTERNAL_JAR_DIRECTORY + Constants.SEMICOLON + Constants.SPACE
                + ScriptConstants.FI + Constants.SEMICOLON);
        res.append(Constants.NEWLINE);

        return res.toString();
    }

    @Override
    protected String osInstallArchiveDatabase() {
        String adminDatabaseDir = machineParameters.getArchiveDatabaseDirValue();
        // Do not install if no proper archive database directory.
        if (adminDatabaseDir == null || adminDatabaseDir.isEmpty()) {
            return Constants.EMPTY;
        }

        // Initialise the StringBuilder containing the resulting script.
        StringBuilder res = new StringBuilder();

        // copy to final destination if database argument.
        if (arcDatabaseFile != null) {
            // echo Copying database
            res.append(ScriptConstants.ECHO_COPYING_ARCHIVE_DATABASE);
            res.append(Constants.NEWLINE);
            // scp database.jar user@machine:dbDir/bpdb
            res.append(ScriptConstants.SCP + Constants.SPACE);
            res.append(arcDatabaseFile.getPath());
            res.append(Constants.SPACE);
            res.append(machineUserLogin());
            res.append(Constants.COLON);
            res.append(getInstallDirPath());
            res.append(Constants.SLASH);
            // Now the two databases are in different directories
            res.append(Constants.ARCHIVE_DATABASE_BASE_PATH);
            res.append(Constants.NEWLINE);
        }
        // unzip database.
        res.append(ScriptConstants.ECHO_UNZIPPING_ARCHIVE_DATABASE);
        res.append(Constants.NEWLINE);
        // ssh user@machine "
        // cd dir; if [ -d bpDatabaseDir ]; then echo ;
        // else mkdir bpDatabaseDir; fi; if [ $(ls -A bpDatabaseDir) ];
        // then echo ERROR MESSAGE: DIR NOT EMPTY;
        // else unzip -q -o dbDir/bpdb -d databaseDir/.; fi; exit;
        // "
        res.append(ScriptConstants.SSH + Constants.SPACE);
        res.append(machineUserLogin());
        res.append(Constants.SPACE + Constants.QUOTE_MARK + ScriptConstants.CD + Constants.SPACE);
        res.append(getInstallDirPath());
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.LINUX_IF_DIR_EXIST + Constants.SPACE);
        res.append(adminDatabaseDir);
        res.append(Constants.SPACE + ScriptConstants.LINUX_THEN + Constants.SPACE + ScriptConstants.ECHO
                + Constants.SPACE);
        res.append(ScriptConstants.DATABASE_ERROR_PROMPT_DIR_NOT_EMPTY);
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.ELSE + Constants.SPACE
                + ScriptConstants.LINUX_UNZIP_COMMAND + Constants.SPACE);
        res.append(Constants.ARCHIVE_DATABASE_BASE_PATH);
        res.append(Constants.SPACE + ScriptConstants.SCRIPT_DIR + Constants.SPACE);
        res.append(adminDatabaseDir);
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.FI + Constants.SEMICOLON + Constants.SPACE
                + ScriptConstants.EXIT + Constants.SEMICOLON + Constants.SPACE + Constants.QUOTE_MARK);
        res.append(Constants.NEWLINE);

        return res.toString();
    }

    /**
     * Creates the specified directories in the deploy-configuration file.
     * <p>
     * Structure - ssh login cd path; DIRS; CLEANDIR; exit;
     * <p>
     * where: login = username@machine. path = path to install directory. DIRS = the way to create directories. CLEANDIR
     * = the command to clean the tempDir (if chosen as optional)
     * <p>
     * The install creation of DIR has the following structure for directory dir: if [ ! -d dir ]; then mkdir dir; fi;
     *
     * @return The script for creating the directories.
     */
    @Override
    protected String osInstallScriptCreateDir() {
        StringBuilder res = new StringBuilder();
        res.append(ScriptConstants.ECHO_CREATING_DIRECTORIES);
        res.append(Constants.NEWLINE);
        res.append(ScriptConstants.SSH + Constants.SPACE);
        res.append(machineUserLogin());
        res.append(Constants.SPACE + Constants.QUOTE_MARK + ScriptConstants.CD + Constants.SPACE);
        res.append(getInstallDirPath());
        res.append(Constants.SEMICOLON + Constants.SPACE);

        // go through all directories.
        String dir;

        // get archive.bitpresevation.baseDir directory.
        dir = settings.getLeafValue(Constants.SETTINGS_ARCHIVE_BP_BASEDIR_LEAF);
        if (dir != null && !dir.isEmpty() && !dir.equalsIgnoreCase(Constants.DOT)) {
            res.append(createPathToDir(dir));
            res.append(scriptCreateDir(dir, false));
        }

        // get archive.arcrepository.baseDir directory.
        dir = settings.getLeafValue(Constants.SETTINGS_ARCHIVE_ARC_BASEDIR_LEAF);
        if (dir != null && !dir.isEmpty() && !dir.equalsIgnoreCase(Constants.DOT)) {
            res.append(scriptCreateDir(dir, false));
        }

        // get tempDir directory.
        dir = settings.getLeafValue(Constants.SETTINGS_TEMPDIR_LEAF);
        if (dir != null && !dir.isEmpty() && !dir.equalsIgnoreCase(Constants.DOT)) {
            res.append(createPathToDir(dir));
            res.append(scriptCreateDir(dir, resetTempDir));
        }

        // get the application specific directories.
        res.append(getAppDirectories());

        res.append(ScriptConstants.EXIT + Constants.SEMICOLON + Constants.SPACE + Constants.QUOTE_MARK
                + Constants.NEWLINE);

        return res.toString();
    }

    @Override
    protected String scriptCreateDir(String dir, boolean clean) {
        StringBuilder res = new StringBuilder();
        res.append(ScriptConstants.LINUX_IF_NOT_DIR_EXIST + Constants.SPACE);
        res.append(dir);
        res.append(Constants.SPACE + ScriptConstants.LINUX_THEN + Constants.SPACE + ScriptConstants.MKDIR
                + Constants.SPACE);
        res.append(dir);
        if (clean) {
            res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.ELSE_REMOVE + Constants.SPACE);
            res.append(dir);
            res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.MKDIR + Constants.SPACE);
            res.append(dir);
        }
        res.append(Constants.SEMICOLON + Constants.SPACE + ScriptConstants.FI + Constants.SEMICOLON + Constants.SPACE);

        return res.toString();
    }

    /**
     * Function for creating the directories along the path until the end directory. Does not create the end directory.
     *
     * @param dir The path to the directory.
     * @return The script for creating the directory.
     */
    protected String createPathToDir(String dir) {
        StringBuilder res = new StringBuilder();

        String[] pathDirs = dir.split(Constants.REGEX_SLASH_CHARACTER);
        StringBuilder path = new StringBuilder();

        // only make directories along path to last directory,
        // don't create end directory.
        for (int i = 0; i < pathDirs.length - 1; i++) {
            // don't make directory of empty path.
            if (!pathDirs[i].isEmpty()) {
                path.append(pathDirs[i]);
                res.append(scriptCreateDir(path.toString(), false));
            }
            path.append(Constants.SLASH);
        }

        return res.toString();
    }

    @Override
    protected String getAppDirectories() {
        StringBuilder res = new StringBuilder();
        String[] dirs;

        for (Application app : applications) {
            // get archive.fileDir directories.
            dirs = app.getSettingsValues(Constants.SETTINGS_BITARCHIVE_BASEFILEDIR_LEAF);
            if (dirs != null && dirs.length > 0) {
                for (String dir : dirs) {
                    res.append(createPathToDir(dir));
                    res.append(scriptCreateDir(dir, false));
                    for (String subdir : Constants.BASEFILEDIR_SUBDIRECTORIES) {
                        res.append(scriptCreateDir(dir + Constants.SLASH + subdir, false));
                    }
                }
            }

            // get harvester.harvesting.serverDir directories.
            dirs = app.getSettingsValues(Constants.SETTINGS_HARVEST_SERVERDIR_LEAF);
            if (dirs != null && dirs.length > 0) {
                for (String dir : dirs) {
                    res.append(createPathToDir(dir));
                    res.append(scriptCreateDir(dir, false));
                }
            }

            // get the viewerproxy.baseDir directories.
            dirs = app.getSettingsValues(Constants.SETTINGS_VIEWERPROXY_BASEDIR_LEAF);
            if (dirs != null && dirs.length > 0) {
                for (String dir : dirs) {
                    res.append(createPathToDir(dir));
                    res.append(scriptCreateDir(dir, false));
                }
            }

            // get the common.tempDir directories. But only those,
            // which are not the same as the machine common.tempDir.
            dirs = app.getSettingsValues(Constants.SETTINGS_TEMPDIR_LEAF);
            if (dirs != null && dirs.length > 0) {
                String machineDir = settings.getLeafValue(Constants.SETTINGS_TEMPDIR_LEAF);
                for (String dir : dirs) {
                    // Don't make machine temp dir twice.
                    if (!dir.equals(machineDir)) {
                        res.append(createPathToDir(dir));
                        res.append(scriptCreateDir(dir, resetTempDir));
                    }
                }
            }
        }

        return res.toString();
    }

    /**
     * Dummy function on linux machine. This is only used for windows machines!
     *
     * @param dir The directory to put the file.
     */
    @Override
    protected void createInstallDirScript(File dir) {
        // Do nothing. Dummy function on linux machine.
    }

    @Override
    protected String changeFileDirPathForSecurity(String path) {
        path += Constants.SLASH + Constants.SECURITY_FILE_DIR_TAG + Constants.SLASH;
        return path.replace(Constants.SLASH, ScriptConstants.SECURITY_DIR_SEPARATOR);
    }

    @Override
    protected String getJMXremoteFilesCommand() {
        String accessFilePath;
        String passwordFilePath;
        String[] options;

        // retrieve the access file path.
        options = settings.getLeafValues(Constants.SETTINGS_COMMON_JMX_ACCESSFILE);

        // extract the path, if any. Else set default.
        if (options.length == 0) {
            accessFilePath = Constants.JMX_ACCESS_FILE_PATH_DEFAULT;
        } else {
            accessFilePath = options[0];
            // warn if more than one access file is defined.
            if (options.length > 1) {
                log.debug(Constants.MSG_WARN_TOO_MANY_JMXREMOTE_FILE_PATHS);
            }
        }

        // retrieve the password file path.
        options = settings.getLeafValues(Constants.SETTINGS_COMMON_JMX_PASSWORDFILE);

        // extract the path, if any. Else set default.
        if (options.length == 0) {
            passwordFilePath = Constants.JMX_PASSWORD_FILE_PATH_DEFAULT;
        } else {
            passwordFilePath = options[0];
            // warn if more than one access file is defined.
            if (options.length > 1) {
                log.debug(Constants.MSG_WARN_TOO_MANY_JMXREMOTE_FILE_PATHS);
            }
        }

        // initialise the resulting command string.
        StringBuilder res = new StringBuilder();

        // echo make password files readonly
        res.append(ScriptConstants.ECHO_MAKE_PASSWORD_FILES);
        res.append(Constants.NEWLINE);

        // IF NOT DEFAULT PATHS, THEN MAKE SCRIPT TO MOVE THE FILES.
        if (!accessFilePath.equals(Constants.JMX_ACCESS_FILE_PATH_DEFAULT)) {
            // ssh dev@kb-test-adm-001.kb.dk "mv -f
            // installpath/conf/jmxremote.access installpath/accessFilePath"
            res.append(ScriptConstants.SSH + Constants.SPACE);
            res.append(machineUserLogin());
            res.append(Constants.SPACE + Constants.QUOTE_MARK);
            res.append(ScriptConstants.LINUX_FORCE_MOVE);
            res.append(Constants.SPACE);
            res.append(getInstallDirPath());
            res.append(Constants.SLASH);
            res.append(Constants.JMX_ACCESS_FILE_PATH_DEFAULT);
            res.append(Constants.SPACE);
            res.append(getInstallDirPath());
            res.append(Constants.SLASH);
            res.append(accessFilePath);
            res.append(Constants.QUOTE_MARK);
            res.append(Constants.NEWLINE);
        }

        if (!passwordFilePath.equals(Constants.JMX_PASSWORD_FILE_PATH_DEFAULT)) {
            // ssh dev@kb-test-adm-001.kb.dk "mv -f
            // installpath/conf/jmxremote.access installpath/accessFilePath"
            res.append(ScriptConstants.SSH + Constants.SPACE);
            res.append(machineUserLogin());
            res.append(Constants.SPACE + Constants.QUOTE_MARK);
            res.append(ScriptConstants.LINUX_FORCE_MOVE);
            res.append(Constants.SPACE);
            res.append(getInstallDirPath());
            res.append(Constants.SLASH);
            res.append(Constants.JMX_PASSWORD_FILE_PATH_DEFAULT);
            res.append(Constants.SPACE);
            res.append(getInstallDirPath());
            res.append(Constants.SLASH);
            res.append(passwordFilePath);
            res.append(Constants.QUOTE_MARK);
            res.append(Constants.NEWLINE);
        }

        // Allow only user to be able to only read jmxremote.password
        // (a=-rwx,u=+r) = 400.
        // ssh dev@kb-test-adm-001.kb.dk "chmod 400
        // /home/dev/TEST/conf/jmxremote.password"
        res.append(ScriptConstants.SSH + Constants.SPACE);
        res.append(machineUserLogin());
        res.append(Constants.SPACE + Constants.QUOTE_MARK + ScriptConstants.LINUX_USER_400 + Constants.SPACE);
        res.append(getInstallDirPath());
        res.append(Constants.SLASH);
        res.append(passwordFilePath);
        res.append(Constants.QUOTE_MARK);
        res.append(Constants.NEWLINE);
        // ssh dev@kb-test-adm-001.kb.dk "chmod 400
        // /home/dev/TEST/conf/jmxremote.access"
        res.append(ScriptConstants.SSH + Constants.SPACE);
        res.append(machineUserLogin());
        res.append(Constants.SPACE + Constants.QUOTE_MARK + ScriptConstants.LINUX_USER_400 + Constants.SPACE);
        res.append(getInstallDirPath());
        res.append(Constants.SLASH);
        res.append(accessFilePath);
        res.append(Constants.QUOTE_MARK);
        res.append(Constants.NEWLINE);

        return res.toString();
    }

    /**
     * Creates script for restarting all the applications on a machine. This script should start by killing all the
     * existing processes, and then starting them again.
     * <p>
     * First the killall scripts is called, then wait for 5 seconds for the applications to be fully terminated, and
     * finally the startall script is called.
     *
     * @param dir The directory where the script file will be placed.
     * @throws IOFailure If the restart script cannot be created.
     */
    @Override
    protected void createRestartScript(File dir) throws IOFailure {
        try {
            // initialise the script file.
            File restartScript = new File(dir, Constants.SCRIPT_NAME_RESTART + scriptExtension);

            // make print writer for writing to file
            PrintWriter restartPrint = new PrintWriter(restartScript, getTargetEncoding());
            try {
                // init, go to directory
                restartPrint.println(ScriptConstants.BIN_BASH_COMMENT);
                restartPrint.println(ScriptConstants.CD + Constants.SPACE + getConfDirPath());

                // call killall script.
                restartPrint.print(Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_KILL_ALL + scriptExtension);
                restartPrint.print(Constants.NEWLINE);

                // call wait script.
                restartPrint.print(ScriptConstants.SLEEP);
                restartPrint.print(Constants.SPACE);
                restartPrint.print(Constants.WAIT_TIME_DURING_RESTART);
                restartPrint.print(Constants.NEWLINE);

                // call startall script.
                restartPrint.print(Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_START_ALL + scriptExtension);
                restartPrint.print(Constants.NEWLINE);
            } finally {
                // close file
                restartPrint.close();
            }
        } catch (IOException e) {
            // Log the error and throw an IOFailure.
            log.trace(Constants.MSG_ERROR_RESTART_FILE, e);
            throw new IOFailure(Constants.MSG_ERROR_RESTART_FILE, e);
        }
    }

    /**
     * Creates a script for starting the archive database on a given machine. This is only created if the
     * &lt;globalArchiveDatabaseDir&gt; parameter is defined on the machine level.
     * <p>
     * <br/>
     * &gt; #!/bin/bash <br/>
     * &gt; cd InstallDir <br/>
     * &gt; java -cp 'DB-CLASSPATH' org.apache.derby.drda.NetworkServerControl start < /dev/null >
     * start_external_database.log 2>&1 &
     *
     * @param dir The directory where the script will be placed.
     * @throws IOFailure If the script cannot be written.
     */
    @Override
    protected void createArchiveDatabaseStartScript(File dir) throws IOFailure {

        // Ignore if no archive database directory has been defined.
        String dbDir = machineParameters.getArchiveDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return;
        }

        try {
            // initialise the script file.
            File startArcDBScript = new File(dir, Constants.SCRIPT_NAME_ADMIN_DB_START + scriptExtension);

            // retrieve the port
            String port = settings.getLeafValue(Constants.SETTINGS_ARCHIVE_DATABASE_PORT);

            // make print writer for writing to file
            PrintWriter startDBPrint = new PrintWriter(startArcDBScript, getTargetEncoding());
            try {
                // - #!/bin/bash
                startDBPrint.println(ScriptConstants.BIN_BASH_COMMENT);
                // - cd InstallDir
                startDBPrint.print(ScriptConstants.CD + Constants.SPACE);
                startDBPrint.println(getInstallDirPath());
                // - java -Dderby.system.home=$INSTALLDIR/archivedatabasedir
                // -cp 'DB-CLASSPATH'
                // org.apache.derby.drda.NetworkServerControl start
                // < /dev/null > start_external_database.log 2>&1 &
                startDBPrint.print(ScriptConstants.JAVA + Constants.SPACE);
                // FIXME: Incomplete implementation of NAS-2030
                // startDBPrint.print("-Dderby.system.home="
                // + getInstallDirPath() + Constants.SLASH
                // + dbDir
                // + Constants.SPACE);

                startDBPrint.print(machineParameters.writeJavaOptions());
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(ScriptConstants.JAVA_CLASSPATH);
                startDBPrint.print(Constants.SPACE + getDbClasspaths());
                startDBPrint.print(ScriptConstants.DERBY_ACCESS_METHOD);
                // insert the PORT if any specified.
                if (port != null && !port.isEmpty()) {
                    startDBPrint.print(Constants.SPACE);
                    startDBPrint.print(ScriptConstants.DATABASE_PORT_ARGUMENT);
                    startDBPrint.print(Constants.SPACE);
                    startDBPrint.print(port);
                }
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(ScriptConstants.DERBY_COMMAND_START);
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(ScriptConstants.LINUX_DEV_NULL);
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(Constants.SCRIPT_NAME_ADMIN_DB_START);
                startDBPrint.print(Constants.EXTENSION_LOG_FILES);
                startDBPrint.print(Constants.SPACE);
                startDBPrint.println(ScriptConstants.LINUX_ERROR_MESSAGE_TO_1);
            } finally {
                // close file
                startDBPrint.close();
            }
        } catch (IOException e) {
            // Log the error and throw an IOFailure.
            log.trace(Constants.MSG_ERROR_DB_START_FILE, e);
            throw new IOFailure(Constants.MSG_ERROR_DB_START_FILE, e);
        }
    }

    /**
     * Method for generating the command for running the external_admin_database_start script. This should be called
     * before the application on the machines have been started.
     * <p>
     * <br/>
     * &gt; echo Starting external database <br/>
     * &gt; if [ -e ./start_external_admin_database.sh ]; then <br/>
     * &gt; ./start_external_admin_database.sh & <br/>
     * &gt; sleep 5 <br/>
     * &gt; fi
     *
     * @return The command for running external_admin_database_start script.
     */
    protected String callStartArchiveDatabase() {
        // Ignore if no archive database directory has been defined.
        String dbDir = machineParameters.getArchiveDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return "";
        }

        // Constructing filename
        String appScript = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_ADMIN_DB_START + scriptExtension;

        StringBuilder res = new StringBuilder();
        // echo Starting external database
        res.append(ScriptConstants.ECHO_START_EXTERNAL_ADMIN_DATABASE);
        res.append(Constants.NEWLINE);
        // if [ -e ./start_external_database.sh ]; then
        res.append(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE);
        res.append(appScript + Constants.SPACE + ScriptConstants.LINUX_THEN);
        res.append(Constants.NEWLINE);
        // ./start_external_database.sh
        res.append(ScriptConstants.MULTI_SPACE_6 + appScript);
        res.append(ScriptConstants.LINUX_RUN_BACKGROUND + Constants.NEWLINE);
        // sleep 5
        res.append(ScriptConstants.MULTI_SPACE_6 + ScriptConstants.SLEEP_5);
        res.append(Constants.NEWLINE);
        // fi
        res.append(ScriptConstants.FI + Constants.NEWLINE);

        return res.toString();
    }

    /**
     * Creates a script for killing the archive database on a given machine. This is only created if the
     * &lt;globalArchiveDatabaseDir&gt; parameter is defined on the machine level.
     * <p>
     * The output is appended to the log, thus the '>>' instead of the standard '>' when redirecting the output.
     * <p>
     * <br/>
     * &gt; #!/bin/bash <br/>
     * &gt; cd InstallDir <br/>
     * &gt; java -cp 'DB-CLASSPATH' org.apache.derby.drda.NetworkServerControl shutdown < /dev/null >>
     * start_external_database.log 2>&1 &
     * <p>
     * <br/>
     * where 'PORT' is in the setting: settings.archive.admin.database.port
     *
     * @param dir The directory where the script will be placed.
     * @throws IOFailure If the script cannot be created.
     */
    @Override
    protected void createArchiveDatabaseKillScript(File dir) throws IOFailure {
        // Ignore if no archive database directory has been defined.
        String dbDir = machineParameters.getArchiveDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return;
        }

        try {
            // initialise the script file.
            File killArcDBScript = new File(dir, Constants.SCRIPT_NAME_ADMIN_DB_KILL + scriptExtension);

            // retrieve the port for the database.
            String port = settings.getLeafValue(Constants.SETTINGS_ARCHIVE_DATABASE_PORT);

            // make print writer for writing to file
            PrintWriter killDBPrint = new PrintWriter(killArcDBScript, getTargetEncoding());
            try {
                // - #!/bin/bash
                killDBPrint.println(ScriptConstants.BIN_BASH_COMMENT);

                // - cd InstallDir
                killDBPrint.print(ScriptConstants.CD + Constants.SPACE);
                killDBPrint.println(getInstallDirPath());
                // - java -cp 'DB-CLASSPATH'
                // org.apache.derby.drda.NetworkServerControl shutdown
                // < /dev/null >> start_external_database.log 2>&1 &
                killDBPrint.print(ScriptConstants.JAVA + Constants.SPACE);
                killDBPrint.print(ScriptConstants.JAVA_CLASSPATH);
                killDBPrint.print(Constants.SPACE + getDbClasspaths());
                killDBPrint.print(ScriptConstants.DERBY_ACCESS_METHOD);
                // insert the PORT if any specified.
                if (port != null && !port.isEmpty()) {
                    killDBPrint.print(Constants.SPACE);
                    killDBPrint.print(ScriptConstants.DATABASE_PORT_ARGUMENT);
                    killDBPrint.print(Constants.SPACE);
                    killDBPrint.print(port);
                }
                killDBPrint.print(Constants.SPACE);
                killDBPrint.print(ScriptConstants.DERBY_COMMAND_KILL);
                killDBPrint.print(Constants.SPACE);
                killDBPrint.print(ScriptConstants.LINUX_DEV_NULL);
                killDBPrint.print(Constants.GREATER_THAN);
                killDBPrint.print(Constants.SPACE);
                killDBPrint.print(Constants.SCRIPT_NAME_ADMIN_DB_START);
                killDBPrint.print(Constants.EXTENSION_LOG_FILES);
                killDBPrint.print(Constants.SPACE);
                killDBPrint.println(ScriptConstants.LINUX_ERROR_MESSAGE_TO_1);
            } finally {
                // close file
                killDBPrint.close();
            }
        } catch (IOException e) {
            // Log the error and throw an IOFailure.
            log.trace(Constants.MSG_ERROR_DB_KILL_FILE, e);
            throw new IOFailure(Constants.MSG_ERROR_DB_KILL_FILE, e);
        }
    }

    /**
     * Method for generating the command for running the external_database_kill script. This should be called when the
     * application on the machines have been killed.
     * <p>
     * <br/>
     * &gt; echo Killing external database <br/>
     * &gt; if [ -e ./kill_external_database.sh ]; then <br/>
     * &gt; ./kill_external_database.sh <br/>
     * &gt; fi
     *
     * @return The command for running external_database_kill script.
     */
    protected String callKillArchiveDatabase() {
        // Ignore if no archive database directory has been defined.
        String dbDir = machineParameters.getArchiveDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return "";
        }

        // Constructing filename
        String appScript = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_ADMIN_DB_KILL + scriptExtension;

        StringBuilder res = new StringBuilder();
        // echo Killing external database
        res.append(ScriptConstants.ECHO_KILL_EXTERNAL_ADMIN_DATABASE);
        res.append(Constants.NEWLINE);
        // if [ -e ./kill_external_database.sh ]; then
        res.append(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE);
        res.append(appScript + Constants.SPACE + ScriptConstants.LINUX_THEN);
        res.append(Constants.NEWLINE);
        // ./kill_external_database.sh
        res.append(ScriptConstants.MULTI_SPACE_6 + appScript);
        res.append(Constants.NEWLINE);
        // fi
        res.append(ScriptConstants.FI + Constants.NEWLINE);

        return res.toString();
    }

    /**
     * Creates a script for starting the harvest database on a given machine. This is only created if the
     * &lt;deployHarvestDatabaseDir&gt; parameter is defined on the machine level.
     * <p>
     * <br/>
     * &gt; #!/bin/bash <br/>
     * &gt; cd InstallDir <br/>
     * &gt; java -cp 'DB-CLASSPATH' org.apache.derby.drda.NetworkServerControl start < /dev/null >
     * start_external_harvest_database.log 2>&1 &
     *
     * @param dir The directory where the script will be placed.
     * @throws IOFailure If the script cannot be written.
     */
    @Override
    protected void createHarvestDatabaseStartScript(File dir) throws IOFailure {
        // Ignore if no harvest database directory has been defined.
        String dbDir = machineParameters.getHarvestDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return;
        }

        try {
            // initialise the script file.
            File startHarvestDBScript = new File(dir, Constants.SCRIPT_NAME_HARVEST_DB_START + scriptExtension);

            // retrieve the port
            String port = settings.getLeafValue(Constants.SETTINGS_HARVEST_DATABASE_PORT);

            // make print writer for writing to file
            PrintWriter startDBPrint = new PrintWriter(startHarvestDBScript, getTargetEncoding());
            try {
                // - #!/bin/bash
                startDBPrint.println(ScriptConstants.BIN_BASH_COMMENT);
                // - cd InstallDir
                startDBPrint.print(ScriptConstants.CD + Constants.SPACE);
                startDBPrint.println(getInstallDirPath());
                // - java -cp 'DB-CLASSPATH'
                // org.apache.derby.drda.NetworkServerControl start
                // < /dev/null > start_external_harvest_database.log 2>&1 &
                startDBPrint.print(ScriptConstants.JAVA + Constants.SPACE);
                // FIXME: Incomplete implementation of NAS-2030
                // startDBPrint.print("-Dderby.system.home="
                // + getInstallDirPath() + Constants.SLASH
                // + dbDir
                // + Constants.SPACE);

                startDBPrint.print(machineParameters.writeJavaOptions());
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(ScriptConstants.JAVA_CLASSPATH);
                startDBPrint.print(Constants.SPACE + getDbClasspaths());
                startDBPrint.print(ScriptConstants.DERBY_ACCESS_METHOD);
                // insert the PORT if any specified.
                if (port != null && !port.isEmpty()) {
                    startDBPrint.print(Constants.SPACE);
                    startDBPrint.print(ScriptConstants.DATABASE_PORT_ARGUMENT);
                    startDBPrint.print(Constants.SPACE);
                    startDBPrint.print(port);
                }
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(ScriptConstants.DERBY_COMMAND_START);
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(ScriptConstants.LINUX_DEV_NULL);
                startDBPrint.print(Constants.SPACE);
                startDBPrint.print(Constants.SCRIPT_NAME_HARVEST_DB_START);
                startDBPrint.print(Constants.EXTENSION_LOG_FILES);
                startDBPrint.print(Constants.SPACE);
                startDBPrint.println(ScriptConstants.LINUX_ERROR_MESSAGE_TO_1);
            } finally {
                // close file
                startDBPrint.close();
            }
        } catch (IOException e) {
            // Log the error and throw an IOFailure.
            log.trace(Constants.MSG_ERROR_DB_START_FILE, e);
            throw new IOFailure(Constants.MSG_ERROR_DB_START_FILE, e);
        }
    }

    /**
     * Method for generating the command for running the external_harvest_database_start script. This should be called
     * before the application on the machines have been started.
     * <p>
     * <br/>
     * &gt; echo Starting external harvest database <br/>
     * &gt; if [ -e ./start_external_harvest_database.sh ]; then <br/>
     * &gt; ./start_external_harvest_database.sh & <br/>
     * &gt; sleep 5 <br/>
     * &gt; fi
     *
     * @return The command for running external_harvest_database_start script.
     */
    protected String callStartHarvestDatabase() {
        // Ignore if no archive database directory has been defined.
        String dbDir = machineParameters.getHarvestDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return "";
        }

        // Constructing filename
        String appScript = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_HARVEST_DB_START + scriptExtension;

        //String app2Script = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_HARVEST_DB_UPDATE + scriptExtension;
        ;

        StringBuilder res = new StringBuilder();
        // echo Starting external harvest database
        res.append(ScriptConstants.ECHO_START_EXTERNAL_HARVEST_DATABASE);
        res.append(Constants.NEWLINE);
        // if [ -e ./start_external_harvest_database.sh ]; then
        res.append(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE);
        res.append(appScript + Constants.SPACE + ScriptConstants.LINUX_THEN);
        res.append(Constants.NEWLINE);
        // ./start_external_harvest_database.sh
        res.append(ScriptConstants.MULTI_SPACE_6 + appScript);
        res.append(ScriptConstants.LINUX_RUN_BACKGROUND + Constants.NEWLINE);
        // sleep 5
        res.append(ScriptConstants.MULTI_SPACE_6 + ScriptConstants.SLEEP_5);
        // fi
        res.append(Constants.NEWLINE + ScriptConstants.FI);
        res.append(Constants.NEWLINE);
        // echo Updating external harvest database
        //res.append(ScriptConstants.ECHO_UPDATE_EXTERNAL_HARVEST_DATABASE);
        //res.append(Constants.NEWLINE);
        // if [ -e ./start_external_harvest_database.sh ]; then
        //res.append(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE);
        //res.append(app2Script + Constants.SPACE + ScriptConstants.LINUX_THEN);
        //res.append(Constants.NEWLINE);
        //res.append(ScriptConstants.MULTI_SPACE_6 + app2Script);
        //res.append(Constants.NEWLINE);
        //fi
        //res.append(ScriptConstants.FI + Constants.NEWLINE);

        return res.toString();
    }

    /**
     * Creates a script for killing the harvest database on a given machine. This is only created if the
     * &lt;globalHarvestDatabaseDir&gt; parameter is defined on the machine level.
     * <p>
     * The output is appended to the log, thus the '>>' instead of the standard '>' when redirecting the output.
     * <p>
     * <br/>
     * &gt; #!/bin/bash <br/>
     * &gt; cd InstallDir <br/>
     * &gt; java -cp 'DB-CLASSPATH' org.apache.derby.drda.NetworkServerControl shutdown < /dev/null >>
     * start_external_harvest_database.log 2>&1 &
     * <p>
     * <br/>
     * where 'PORT' is in the setting: settings.common.database.port
     *
     * @param dir The directory where the script will be placed.
     * @throws IOFailure If the script cannot be created.
     */
    @Override
    protected void createHarvestDatabaseKillScript(File dir) throws IOFailure {
        // Ignore if no harvest database directory has been defined.
        String dbDir = machineParameters.getHarvestDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return;
        }

        try {
            // initialise the script file.
            File killHarvestDBScript = new File(dir, Constants.SCRIPT_NAME_HARVEST_DB_KILL + scriptExtension);

            // retrieve the port for the database.
            String port = settings.getLeafValue(Constants.SETTINGS_HARVEST_DATABASE_PORT);

            // make print writer for writing to file
            PrintWriter killDBPrint = new PrintWriter(killHarvestDBScript, getTargetEncoding());
            try {
                // - #!/bin/bash
                killDBPrint.println(ScriptConstants.BIN_BASH_COMMENT);

                // - cd InstallDir
                killDBPrint.print(ScriptConstants.CD + Constants.SPACE);
                killDBPrint.println(getInstallDirPath());
                // - java -cp 'DB-CLASSPATH'
                // org.apache.derby.drda.NetworkServerControl shutdown
                // < /dev/null >> start_external_harvest_database.log 2>&1 &
                killDBPrint.print(ScriptConstants.JAVA + Constants.SPACE);
                killDBPrint.print(ScriptConstants.JAVA_CLASSPATH);
                killDBPrint.print(Constants.SPACE + getDbClasspaths());
                killDBPrint.print(ScriptConstants.DERBY_ACCESS_METHOD);
                // insert the PORT if any specified.
                if (port != null && !port.isEmpty()) {
                    killDBPrint.print(Constants.SPACE);
                    killDBPrint.print(ScriptConstants.DATABASE_PORT_ARGUMENT);
                    killDBPrint.print(Constants.SPACE);
                    killDBPrint.print(port);
                }
                killDBPrint.print(Constants.SPACE);
                killDBPrint.print(ScriptConstants.DERBY_COMMAND_KILL);
                killDBPrint.print(Constants.SPACE);
                killDBPrint.print(ScriptConstants.LINUX_DEV_NULL);
                killDBPrint.print(Constants.GREATER_THAN);
                killDBPrint.print(Constants.SPACE);
                killDBPrint.print(Constants.SCRIPT_NAME_HARVEST_DB_START);
                killDBPrint.print(Constants.EXTENSION_LOG_FILES);
                killDBPrint.print(Constants.SPACE);
                killDBPrint.println(ScriptConstants.LINUX_ERROR_MESSAGE_TO_1);
            } finally {
                // close file
                killDBPrint.close();
            }
        } catch (IOException e) {
            // Log the error and throw an IOFailure.
            log.trace(Constants.MSG_ERROR_DB_KILL_FILE, e);
            throw new IOFailure(Constants.MSG_ERROR_DB_KILL_FILE, e);
        }
    }

    /**
     * Method for generating the command for running the external_database_kill script. This should be called when the
     * application on the machines have been killed.
     * <p>
     * <br/>
     * &gt; echo Killing external harvest database <br/>
     * &gt; if [ -e ./kill_external_harvest_database.sh ]; then <br/>
     * &gt; ./kill_external_harvest_database.sh <br/>
     * &gt; fi
     *
     * @return The command for running external_harvest_database_kill script.
     */
    protected String callKillHarvestDatabase() {
        // Ignore if no harvest database directory has been defined.
        String dbDir = machineParameters.getHarvestDatabaseDirValue();
        if (dbDir.isEmpty()) {
            return "";
        }

        // Constructing filename
        String appScript = Constants.DOT + Constants.SLASH + Constants.SCRIPT_NAME_HARVEST_DB_KILL + scriptExtension;

        StringBuilder res = new StringBuilder();
        // echo Killing external harvest database
        res.append(ScriptConstants.ECHO_KILL_EXTERNAL_HARVEST_DATABASE);
        res.append(Constants.NEWLINE);
        // if [ -e ./kill_external_harvest_database.sh ]; then
        res.append(ScriptConstants.LINUX_IF_EXIST + Constants.SPACE);
        res.append(appScript + Constants.SPACE + ScriptConstants.LINUX_THEN);
        res.append(Constants.NEWLINE);
        // ./kill_external_harvest_database.sh
        res.append(ScriptConstants.MULTI_SPACE_6 + appScript);
        res.append(Constants.NEWLINE);
        // fi
        res.append(ScriptConstants.FI + Constants.NEWLINE);

        return res.toString();
    }

    /**
     * Method for combining the classpaths for the database access. <br/>
     * E.g. /home/test/NAS/lib/db/derby.jar:/home/test/NAS/lib/db/derbynet.jar
     *
     * @return The combined classpaths for accessing the database.
     */
    private String getDbClasspaths() {
        StringBuilder res = new StringBuilder();

        for (int i = 0; i < ScriptConstants.DERBY_ACCESS_CLASSPATH.length; i++) {
            // ignore colon at the first classpath.
            if (i != 0) {
                res.append(Constants.COLON);
            }
            res.append(getInstallDirPath() + Constants.SLASH);
            res.append(ScriptConstants.DERBY_ACCESS_CLASSPATH[i]);
        }
        res.append(Constants.SPACE);
        return res.toString();
    }

    @Override
    protected void createHarvestDatabaseUpdateScript(File dir, boolean forceCreate) {
        // Ignore if no harvest database directory has been defined or this isn't a harvest server app.
        String dbDir = machineParameters.getHarvestDatabaseDirValue();
        if (dbDir.isEmpty() && !forceCreate) {
            return;
        }

        try {
            // initialise the script file.
            File updateHarvestDBScript = new File(dir, Constants.SCRIPT_NAME_HARVEST_DB_UPDATE + scriptExtension);

            File updateHarvestDBSettingsFile = new File(dir, Constants.SETTINGS_PREFIX
                    + Constants.SCRIPT_NAME_HARVEST_DB_UPDATE + Constants.EXTENSION_XML_FILES);
            PrintWriter updateDBSettings = new PrintWriter(updateHarvestDBSettingsFile, getTargetEncoding());
            updateDBSettings.println(settings.getXML());
            updateDBSettings.close();

            // make print writer for writing to file
            PrintWriter updateDBPrint = new PrintWriter(updateHarvestDBScript, getTargetEncoding());
            try {
                // - #!/bin/bash
                updateDBPrint.println(ScriptConstants.BIN_BASH_COMMENT);

                // - cd InstallDir
                updateDBPrint.print(ScriptConstants.CD + Constants.SPACE);
                updateDBPrint.println(getInstallDirPath());

                // - java -cp
                // org.apache.derby.drda.NetworkServerControl shutdown
                // < /dev/null >> start_external_harvest_database.log 2>&1 &

                updateDBPrint.print(ScriptConstants.EXPORT_CLASSPATH);
                updateDBPrint.print(getHarvestServerClasspath() + getHarvesterCoreClasspath() + ScriptConstants.NEWLINE);

                updateDBPrint.print(ScriptConstants.JAVA + Constants.SPACE + "-" + ScriptConstants.OPTION_SETTINGS
                        + getConfDirPath() + updateHarvestDBSettingsFile.getName() + Constants.SPACE);
                updateDBPrint.print(ScriptConstants.HARVEST_DATABASE_UPDATE_APP);

                updateDBPrint.print(Constants.SPACE);
                updateDBPrint.print(ScriptConstants.LINUX_DEV_NULL);
                updateDBPrint.print(Constants.GREATER_THAN);
                updateDBPrint.print(Constants.SPACE);
                updateDBPrint.print(Constants.SCRIPT_NAME_HARVEST_DB_UPDATE);
                updateDBPrint.print(Constants.EXTENSION_LOG_FILES);
                updateDBPrint.print(Constants.SPACE);
                updateDBPrint.println(ScriptConstants.LINUX_ERROR_MESSAGE_TO_1);
            } finally {
                // close file
                updateDBPrint.close();
            }
        } catch (IOException e) {
            // Log the error and throw an IOFailure.
            log.trace(Constants.MSG_ERROR_DB_KILL_FILE, e);
            throw new IOFailure(Constants.MSG_ERROR_DB_KILL_FILE, e);
        }
    }

    private String getDefaultMachineClasspath() {
        StringBuilder res = new StringBuilder();
        // get all the classpaths
        for (Element cp : machineParameters.getClassPaths()) {
            res.append(getInstallDirPath() + Constants.SLASH + cp.getText().trim() + Constants.COLON);
        }
        return res.toString();
    }

    private String getHarvestServerClasspath() {
        return getDefaultMachineClasspath() +
                getInstallDirPath() + Constants.SLASH + "lib/netarchivesuite-harvest-scheduler.jar" + Constants.COLON;
    }

    private String getHarvesterCoreClasspath() {
        return getDefaultMachineClasspath() +
                getInstallDirPath() + Constants.SLASH + "lib/netarchivesuite-harvester-core.jar" + Constants.COLON;
    }


    @Override
    protected String getLibDirPath() {
        return getInstallDirPath() + Constants.LIB_DIR_LINUX;
    }

        @Override
        protected String osUpdateLogos() {
                if (logoFile == null && menulogoFile == null) {
                        return "";
                }
                
                StringBuilder res = new StringBuilder();
                
        res.append(ScriptConstants.ECHO_CHANGING_LOGOS);
        res.append(Constants.NEWLINE);

        if (logoFile != null) {
                res = updateLogofileInWarFiles(res, logoFile, Constants.DEFAULT_LOGO_FILENAME);         
        }
        
        if (menulogoFile != null) {
                res = updateLogofileInWarFiles(res, menulogoFile, Constants.DEFAULT_MENULOGO_FILENAME);         
        }
        
        return res.toString();
        }

}