it.infn.ct.R_portlet.java Source code

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Here is the source code for it.infn.ct.R_portlet.java

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/**************************************************************************
Copyright (c) 2011:
Istituto Nazionale di Fisica Nucleare (INFN), Italy
Consorzio COMETA (COMETA), Italy
    
See http://www.infn.it and and http://www.consorzio-cometa.it for details on
the copyright holders.
    
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
    
http://www.apache.org/licenses/LICENSE-2.0
    
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
    
@author <a href="mailto:riccardo.bruno@ct.infn.it">Riccardo Brunor</a>(COMETA)
****************************************************************************/
package it.infn.ct;

// Import generic java libraries
import java.io.*;
import java.util.Iterator;
import java.util.List;
import java.util.Calendar;
import java.text.SimpleDateFormat;

// Importing portlet libraries
import javax.portlet.*;

// Importing liferay libraries
import com.liferay.portal.theme.ThemeDisplay;
import com.liferay.portal.kernel.util.WebKeys;
import com.liferay.portal.model.User;

// Importing Apache libraries
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.fileupload.*;
import org.apache.commons.fileupload.disk.DiskFileItemFactory;
import org.apache.commons.fileupload.portlet.PortletFileUpload;

// Importing GridEngine Job libraries 
import it.infn.ct.GridEngine.Job.*;
import it.infn.ct.GridEngine.Job.MultiInfrastructureJobSubmission;

//
// This is the class that overrides the GenericPortlet class methods
// You can create your own portlet just customizing the code skeleton
// available below. It provides mainly a working example on:
//    1) How to manage combination of Actions/Views
//    2) How to manage portlet preferences and help
//    3) How to show information using the Log object
//    4) How to execute a distributed application with GridEngine
//
public class R_portlet extends GenericPortlet {

    // AppLogger class (No customizations needed)
    // Although developers can use System.out.println to watch their own console outputs
    // the use of Java logs is highly recommended.
    // Java Log object offers different output levels to show information:
    //    trace
    //    debug
    //    info
    //    warn
    //    error
    //    fatal
    // All of them accept a String as parameter containing the proper message to show.
    // AppLogger class uses  LogLevel eunerated type to express the log level verbosity
    // the setLogLevel method allows the portlet to print-out all logs types equal
    // or below the given log level accordingly to the priority:
    //       trace,debug,info,warn,erro,fatal
    private enum LogLevels {
        trace, debug, info, warn, error, fatal
    }

    // The AppLogger class wraps the apache.common Log object allowing the user to
    // enable/disable log accordingly to a given loglevel; the higher is the level 
    // more verbose will be the produced output
    private class AppLogger {
        // Values associated 
        private static final int TRACE_LEVEL = 6;
        private static final int DEBUG_LEVEL = 5;
        private static final int INFO_LEVEL = 4;
        private static final int WARN_LEVEL = 3;
        private static final int ERROR_LEVEL = 2;
        private static final int FATAL_LEVEL = 1;
        private static final int UNKNOWN_LEVEL = 0;

        private Log _log;
        private int logLevel = AppLogger.INFO_LEVEL;

        public void setLogLevel(String level) {
            switch (LogLevels.valueOf(level)) {
            case trace:
                logLevel = AppLogger.TRACE_LEVEL;
                break;
            case debug:
                logLevel = AppLogger.DEBUG_LEVEL;
                break;
            case info:
                logLevel = AppLogger.INFO_LEVEL;
                break;
            case warn:
                logLevel = AppLogger.WARN_LEVEL;
                break;
            case error:
                logLevel = AppLogger.ERROR_LEVEL;
                break;
            case fatal:
                logLevel = AppLogger.FATAL_LEVEL;
                break;
            default:
                logLevel = AppLogger.UNKNOWN_LEVEL;
            }
        }

        public AppLogger(Class cname) {
            _log = LogFactory.getLog(cname);
        }

        public void trace(String s) {
            if (_log.isTraceEnabled() && logLevel >= AppLogger.TRACE_LEVEL)
                _log.trace(s);
        }

        public void debug(String s) {
            if (_log.isDebugEnabled() && logLevel >= AppLogger.DEBUG_LEVEL)
                _log.trace(s);
        }

        public void info(String s) {
            if (_log.isInfoEnabled() && logLevel >= AppLogger.INFO_LEVEL)
                _log.info(s);
        }

        public void warn(String s) {
            if (_log.isWarnEnabled() && logLevel >= AppLogger.WARN_LEVEL)
                _log.warn(s);
        }

        public void error(String s) {
            if (_log.isErrorEnabled() && logLevel >= AppLogger.ERROR_LEVEL)
                _log.error(s);
        }

        public void fatal(String s) {
            if (_log.isFatalEnabled() && logLevel >= AppLogger.FATAL_LEVEL)
                _log.fatal(s);
        }
    } // AppLogger

    // Instantiate the logger object
    AppLogger _log = new AppLogger(R_portlet.class);

    // This portlet uses Aciont/Views enumerations in order to 
    // manage the different portlet modes and the corresponding 
    // view to display
    // You may override the current values with your own business
    // logic best identifiers and manage them through: jsp and java code
    // The jsp parameter PortletStatus will be the responsible of
    // portlet mode switching. This parameter will be read by
    // the processAction method who will select the proper view mode
    // registering again into 'PortletStatus' renderResponse parameter
    // the next view mode.
    // The default prortlet mode by default is: ACTION_INPUT (see ProcessAction)
    private enum Actions {
        ACTION_INPUT // Called before to show the INPUT view
        , ACTION_SUBMIT // Called after the user press the submit button
        , ACTION_PILOT // The user wants to modify the selected pilot script
    }

    private enum Views {
        VIEW_INPUT // View containing application input fields
        , VIEW_SUBMIT // View reporting the job submission
        , VIEW_PILOT // Shows the pilot script and makes it editable
    }

    // Infrastructure information class stores the required information
    // to submit a job into a given e-Infrastructure.
    class Info_Infrastructure {
        String enableInfrastructure;
        String nameInfrastructure;
        String acronymInfrastructure;
        String bdiiHost;
        String wmsHosts;
        String pxServerHost;
        String pxServerPort;
        String pxServerSecure;
        String pxRobotId;
        String pxRobotVO;
        String pxRobotRole;
        String pxRobotRenewalFlag;
        String softwareTags;

        Info_Infrastructure() {
            enableInfrastructure = nameInfrastructure = acronymInfrastructure = bdiiHost = wmsHosts = pxServerHost = pxServerPort = pxServerSecure = pxRobotId = pxRobotVO = pxRobotRole = pxRobotRenewalFlag = softwareTags = "";
        }

        // Dump the content of infrastructure
        String dumpInfrastructure() {
            String dump = LS + "    enableInfrastructure : '" + enableInfrastructure + "'" + LS
                    + "    nameInfrastructure   : '" + nameInfrastructure + "'" + LS
                    + "    acronymInfrastructure: '" + acronymInfrastructure + "'" + LS
                    + "    bdiiHost             : '" + bdiiHost + "'" + LS + "    wmsHosts             : '"
                    + wmsHosts + "'" + LS + "    pxServerHost         : '" + pxServerHost + "'" + LS
                    + "    pxServerPort         : '" + pxServerPort + "'" + LS + "    pxRobotId            : '"
                    + pxRobotId + "'" + LS + "    pxRobotRole          : '" + pxRobotRole + "'" + LS
                    + "    pxRobotVO            : '" + pxRobotVO + "'" + LS + "    softwareTags         : '"
                    + softwareTags + "'" + LS;
            return dump;
        }
    }

    // The init values will be read form portlet.xml from <init-param> xml tag
    // This tag will be useful to setup defaults values for your own portlet
    class App_Init {
        String portletVersion;
        String logLevel;
        String numInfrastructures;
        Info_Infrastructure[] infoInfra;
        String pxUserProxy;
        String sciGwyAppId;
        String sciGwyUserTrackingDB_Hostname;
        String sciGwyUserTrackingDB_Username;
        String sciGwyUserTrackingDB_Password;
        String sciGwyUserTrackingDB_Database;
        String jobRequirements;
        String pilotScript;

        public App_Init() {
            portletVersion = logLevel = numInfrastructures = pxUserProxy = sciGwyAppId = sciGwyUserTrackingDB_Hostname = sciGwyUserTrackingDB_Username = sciGwyUserTrackingDB_Password = sciGwyUserTrackingDB_Database = jobRequirements = pilotScript = "";
            // Initialize Info Infrastructure
            infoInfra = null;
        }
    } // App_Init

    // Instanciate the App_Init object
    App_Init appInit = new App_Init();

    // This object is used to store the values of portlet preferences
    // The init method will initialize their values with corresponding init_*
    // variables when the portlet first starts (see init_Preferences var).
    // Please notice that not all init_* variables have a corresponding pref_* value
    class App_Preferences {
        String logLevel;
        String numInfrastructures;
        Info_Infrastructure[] infoInfra;
        String pxUserProxy;
        String sciGwyAppId;
        String jobRequirements;
        String pilotScript;

        // This values ranges from 1 to numInfrastructures
        // It is used by the preference edit pane to scroll
        // among inserted infrastructures
        int paneInfrastucture;
        int inumInfrastructures;

        public App_Preferences() {
            logLevel = pxUserProxy = sciGwyAppId = jobRequirements = pilotScript = "";

            // Initialize Info Infrastructure
            infoInfra = null;

            // Initialize the paneInfrastructure;
            paneInfrastucture = 0;
        } // App_Preferences

        // Set the number of infrastructures
        public void setNumInfrastructures(String numInfras) {
            numInfrastructures = numInfras;
            inumInfrastructures = Integer.parseInt(numInfras);
        } // setNumInfrastructures
          // Returns the number of infrastructures

        public int getNumInfrastructures() {
            return inumInfrastructures;
        } // getNumInfrastructure

        public int getCurrInfrastructure() {
            return paneInfrastucture;
        } // getCurrInfrastructure

        public void switchNextInfrastructure() {
            if (inumInfrastructures > 0) {
                paneInfrastucture++;
                if (paneInfrastucture > inumInfrastructures)
                    paneInfrastucture = 1;
            }
        } // switchNextInfrastructure

        public void switchPreviousInfrastructure() {
            if (inumInfrastructures > 0) {
                paneInfrastucture--;
                if (paneInfrastucture <= 0)
                    paneInfrastucture = inumInfrastructures;
            }
        } // switchPreviousInfrastructure
          // Delete the current infrastructure shifting left the array

        public void delCurrInfrastructure() {
            // It is not possible to have zero Infrastructures
            if (inumInfrastructures > 1) {
                // Shift left the Infrastructure preferences
                for (int i = paneInfrastucture; i <= inumInfrastructures - 1; i++) {
                    infoInfra[i - 1].enableInfrastructure = infoInfra[i].enableInfrastructure;
                    infoInfra[i - 1].nameInfrastructure = infoInfra[i].nameInfrastructure;
                    infoInfra[i - 1].acronymInfrastructure = infoInfra[i].acronymInfrastructure;
                    infoInfra[i - 1].bdiiHost = infoInfra[i].bdiiHost;
                    infoInfra[i - 1].wmsHosts = infoInfra[i].wmsHosts;
                    infoInfra[i - 1].pxServerHost = infoInfra[i].pxServerHost;
                    infoInfra[i - 1].pxServerPort = infoInfra[i].pxServerPort;
                    infoInfra[i - 1].pxServerSecure = infoInfra[i].pxServerSecure;
                    infoInfra[i - 1].pxRobotId = infoInfra[i].pxRobotId;
                    infoInfra[i - 1].pxRobotVO = infoInfra[i].pxRobotVO;
                    infoInfra[i - 1].pxRobotRole = infoInfra[i].pxRobotRole;
                    infoInfra[i - 1].pxRobotRenewalFlag = infoInfra[i].pxRobotRenewalFlag;
                    infoInfra[i - 1].softwareTags = infoInfra[i].softwareTags;
                }
                // The removed infrastructure is the last in the array
                if (inumInfrastructures == paneInfrastucture)
                    paneInfrastucture--;
                // Now reduce the number of insfrastructures
                setNumInfrastructures("" + (--inumInfrastructures));
            }
        } // delCurrInfrastructure
          // Adds a new infrastructure

        public void addNewInfrastructure() {
            setNumInfrastructures("" + (++inumInfrastructures));
            // Create the new array
            Info_Infrastructure[] new_infoInfrastructure = new Info_Infrastructure[inumInfrastructures];
            // Copy all values from old the old array
            for (int i = 0; i < inumInfrastructures - 1; i++) {
                Info_Infrastructure new_infoInfra = new Info_Infrastructure();
                new_infoInfra.enableInfrastructure = infoInfra[i].enableInfrastructure;
                new_infoInfra.nameInfrastructure = infoInfra[i].nameInfrastructure;
                new_infoInfra.acronymInfrastructure = infoInfra[i].acronymInfrastructure;
                new_infoInfra.bdiiHost = infoInfra[i].bdiiHost;
                new_infoInfra.wmsHosts = infoInfra[i].wmsHosts;
                new_infoInfra.pxServerHost = infoInfra[i].pxServerHost;
                new_infoInfra.pxServerPort = infoInfra[i].pxServerPort;
                new_infoInfra.pxServerSecure = infoInfra[i].pxServerSecure;
                new_infoInfra.pxRobotId = infoInfra[i].pxRobotId;
                new_infoInfra.pxRobotVO = infoInfra[i].pxRobotVO;
                new_infoInfra.pxRobotRole = infoInfra[i].pxRobotRole;
                new_infoInfra.pxRobotRenewalFlag = infoInfra[i].pxRobotRenewalFlag;
                new_infoInfra.softwareTags = infoInfra[i].softwareTags;
                new_infoInfrastructure[i] = new_infoInfra;
            } // Copy infrastructure settings
              // Last infrastructure remaining
            Info_Infrastructure new_infoInfra = new Info_Infrastructure();
            new_infoInfra.enableInfrastructure = "yes/no";
            new_infoInfra.nameInfrastructure = "Infrastructure name";
            new_infoInfra.acronymInfrastructure = "Infrastructure acronym";
            new_infoInfra.bdiiHost = "BDII host";
            new_infoInfra.wmsHosts = "WMS host";
            new_infoInfra.pxServerHost = "Robot proxy server host";
            new_infoInfra.pxServerPort = "Robot proxy server port";
            new_infoInfra.pxServerSecure = "Robot proxy server secure flag";
            new_infoInfra.pxRobotId = "Robot proxy id";
            new_infoInfra.pxRobotVO = "Robot proxy VO";
            new_infoInfra.pxRobotRole = "Robot proxy Role";
            new_infoInfra.pxRobotRenewalFlag = "Robot proxy renewal flag";
            new_infoInfra.softwareTags = "Software tags";
            new_infoInfrastructure[inumInfrastructures - 1] = new_infoInfra;
            // Link the new array of infrastructures
            infoInfra = new_infoInfrastructure;
            // Point to the new infrastructure
            paneInfrastucture = inumInfrastructures;
        } // addNewInfrastructure

        // Makes a dump of a given infrastructure
        String dumpInfrastructure(int numInfrastructure) {
            String dump = "";
            if (getNumInfrastructures() > 0) {
                dump = LS + "Infrastructure #" + numInfrastructure;
                dump += LS + infoInfra[numInfrastructure - 1].dumpInfrastructure();

            }
            return dump;
        } // dumpInfrastructure
          // Makes a dump of all infrastructures

        String dumpInfrastructures() {
            String dump = "";
            for (int i = 0; i < getNumInfrastructures(); i++) {
                int j = i + 1;
                dump += dumpInfrastructure(j);
            } // for all infrastructures
            return dump;
        } // dumpInfrastructures        
          // Makes a dump of all preferences

        String dumpPreferences() {
            String dump = LS + "Preference values:" + LS + "------------------" + LS + "pref_logLevel          : '"
                    + logLevel + "'" + LS + "pref_sciGwyAppId       : '" + sciGwyAppId + "'" + LS
                    + "pref_numInfrastructures: '" + numInfrastructures + "'" + LS + "pref_currInfrastructure: '"
                    + getCurrInfrastructure() + "'" + LS + dumpInfrastructures() + LS + "pref_jobRequirements   : '"
                    + jobRequirements + "'" + LS + "pref_pilotScript       : '" + pilotScript + "'" + LS
                    + "pref_pxUserProxy       : '" + pxUserProxy + "'" + LS;
            return dump;
        } // dumpPreferences
    } // App_Preferences

    // Instanciate the App_Preferences object
    App_Preferences appPreferences = new App_Preferences();

    //
    // Application input values
    //
    // Job submission values are collected inside a single object
    class App_Input {
        // Applicatoin inputs
        String inputFileName; // Filename for application input file
        String inputFileText; // Text for application input file 
        String jobIdentifier; // User' given job identifier                

        // Each inputSandobox file must be declared below
        // This variable contains the content of an uploaded file
        String inputSandbox_inputFile;

        // Some user level information
        // must be stored as well
        String username;
        String timestamp;

        public App_Input() {
            inputFileName = inputFileText = jobIdentifier = inputSandbox_inputFile = username = timestamp = "";
        }
    } // App_Input

    // Liferay user data
    // Classes below are used by this portlet code to get information
    // about the current user
    public ThemeDisplay themeDisplay; // Liferay' ThemeDisplay variable
    public User user; // From ThemeDisplay get User data
    public String username; // From User data the username        

    // Liferay portlet data        
    PortletSession portletSession; // PorteltSession
    PortletContext portletContext; // PortletContext
    public String appServerPath; // This variable stores the absolute path of the Web applications

    // Other misc valuse
    // (!) Pay attention that altough the use of the LS variable
    //     the replaceAll("\n","") has to be used 
    public String LS = System.getProperty("line.separator");

    // Users must have separated inputSandbox files
    // these file will be generated into /tmp directory
    // and prefixed with the format <timestamp>_<user>_*
    // The timestamp format is:
    public static final String tsFormat = "yyyyMMddHHmmss";

    //
    // Portlet Methods
    // 

    //
    // init
    //
    // The init method will be called when installing the portlet for the first time 
    // This is the right time to get default values from WEBINF/portlet.xml file
    // Those values will be assigned into parameters the first time the processAction
    // will be called thanks to the appPreferences object
    //
    @Override
    public void init() throws PortletException {
        // Load default values from portlet.xml              
        appInit.portletVersion = "" + getInitParameter("portletVersion");
        appInit.logLevel = "" + getInitParameter("logLevel");
        appInit.numInfrastructures = "" + getInitParameter("numInfrastructures");
        int numInfra = Integer.parseInt(appInit.numInfrastructures);
        _log.info("Number of infrastructures: '" + numInfra + "'");
        if (numInfra > 0)
            appInit.infoInfra = new Info_Infrastructure[numInfra];
        for (int i = 0; i < numInfra; i++) {
            int j = i + 1;
            appInit.infoInfra[i] = new Info_Infrastructure();
            appInit.infoInfra[i].enableInfrastructure = "" + getInitParameter(j + "_enableInfrastructure");
            appInit.infoInfra[i].nameInfrastructure = "" + getInitParameter(j + "_nameInfrastructure");
            appInit.infoInfra[i].acronymInfrastructure = "" + getInitParameter(j + "_acronymInfrastructure");
            appInit.infoInfra[i].bdiiHost = "" + getInitParameter(j + "_bdiiHost");
            appInit.infoInfra[i].wmsHosts = "" + getInitParameter(j + "_wmsHosts");
            appInit.infoInfra[i].pxServerHost = "" + getInitParameter(j + "_pxServerHost");
            appInit.infoInfra[i].pxServerPort = "" + getInitParameter(j + "_pxServerPort");
            appInit.infoInfra[i].pxServerSecure = "" + getInitParameter(j + "_pxServerSecure");
            appInit.infoInfra[i].pxRobotId = "" + getInitParameter(j + "_pxRobotId");
            appInit.infoInfra[i].pxRobotVO = "" + getInitParameter(j + "_pxRobotVO");
            appInit.infoInfra[i].pxRobotRole = "" + getInitParameter(j + "_pxRobotRole");
            appInit.infoInfra[i].pxRobotRenewalFlag = "" + getInitParameter(j + "_pxRobotRenewalFlag");
            appInit.infoInfra[i].softwareTags = "" + getInitParameter(j + "_softwareTags");
        }
        appInit.pxUserProxy = "" + getInitParameter("pxUserProxy");
        appInit.sciGwyAppId = "" + getInitParameter("sciGwyAppId");
        appInit.sciGwyUserTrackingDB_Hostname = "" + getInitParameter("sciGwyUserTrackingDB_Hostname");
        appInit.sciGwyUserTrackingDB_Username = "" + getInitParameter("sciGwyUserTrackingDB_Username");
        appInit.sciGwyUserTrackingDB_Password = "" + getInitParameter("sciGwyUserTrackingDB_Password");
        appInit.sciGwyUserTrackingDB_Database = "" + getInitParameter("sciGwyUserTrackingDB_Database");
        appInit.jobRequirements = "" + getInitParameter("jobRequirements");
        // WARNING: Although the pilot script field is considered here it is not
        // Possible to specify a bash script code inside thie init_pilotScript
        // xml field. The content of pilot script must be inserted manually upon
        // the portlet installation through its configuration pane.        
        appInit.pilotScript = "" + getInitParameter("pilotScript");
        appInit.pilotScript = appInit.pilotScript.replaceAll("\r", "");

        // Assigns the log level      
        _log.setLogLevel(appInit.logLevel);

        // Get information about all infrastructures
        String infrastructuresInfrormations = "";
        for (int i = 0; i < numInfra; i++) {
            int j = i + 1;
            infrastructuresInfrormations += LS + "Infrastructure #" + j + LS + "  enableInfrastructure  : '"
                    + appInit.infoInfra[i].enableInfrastructure + "'" + LS + "  nameInfrastructures   : '"
                    + appInit.infoInfra[i].nameInfrastructure + "'" + LS + "  acronymInfrastructures: '"
                    + appInit.infoInfra[i].acronymInfrastructure + "'" + LS + "  bdiiHost              : '"
                    + appInit.infoInfra[i].bdiiHost + "'" + LS + "  wmsHosts              : '"
                    + appInit.infoInfra[i].wmsHosts + "'" + LS + "  pxServerHost          : '"
                    + appInit.infoInfra[i].pxServerHost + "'" + LS + "  pxServerPort          : '"
                    + appInit.infoInfra[i].pxServerPort + "'" + LS + "  pxServerSecure        : '"
                    + appInit.infoInfra[i].pxServerSecure + "'" + LS + "  pxRobotId             : '"
                    + appInit.infoInfra[i].pxRobotId + "'" + LS + "  pxRobotVO             : '"
                    + appInit.infoInfra[i].pxRobotVO + "'" + LS + "  pxRobotRole           : '"
                    + appInit.infoInfra[i].pxRobotRole + "'" + LS + "  pxRobotRenewalFlag    : '"
                    + appInit.infoInfra[i].pxRobotRenewalFlag + "'" + LS + "  softwareTags          : '"
                    + appInit.infoInfra[i].softwareTags + "'" + LS;
        }
        // Show loaded values into log
        _log.info(LS + "Loading default values " + LS + "-----------------------" + LS
                + "portletVersion               : '" + appInit.portletVersion + "'" + LS
                + "logLevel                     : '" + appInit.logLevel + "'" + LS
                + "numInfrastructures           : '" + appInit.numInfrastructures + "'" + LS
                + infrastructuresInfrormations + LS + "pxUserProxy                  : '" + appInit.pxUserProxy + "'"
                + LS + "sciGwyAppId                  : '" + appInit.sciGwyAppId + "'" + LS
                + "sciGwyUserTrackingDB_Hostname: '" + appInit.sciGwyUserTrackingDB_Hostname + "'" + LS
                + "sciGwyUserTrackingDB_Username: '" + appInit.sciGwyUserTrackingDB_Username + "'" + LS
                + "sciGwyUserTrackingDB_Password: '" + appInit.sciGwyUserTrackingDB_Password + "'" + LS
                + "sciGwyUserTrackingDB_Database: '" + appInit.sciGwyUserTrackingDB_Database + "'" + LS
                + "jobRequirements              : '" + appInit.jobRequirements + "'" + LS
                + "pilotScript                  : '" + appInit.pilotScript + "'" + LS + LS
                + "!WARNING: Although the pilot script field is considered into the portlet.xml" + LS
                + "it is not possible to specify a bash script code inside the init_pilotScript" + LS
                + "xml' field. The content of the pilot script must be inserted manually upon" + LS
                + "the portlet installation through its configuration pane." + LS);
    } // init

    //
    // processAction
    //
    // This method allows the portlet to process an action request; this method is normally
    // called upon each user interaction (a submit button inside a jsp' <form statement)
    //
    @Override
    public void processAction(ActionRequest request, ActionResponse response) throws PortletException, IOException {
        _log.info("calling processAction ...");

        // Determine the username
        themeDisplay = (ThemeDisplay) request.getAttribute(WebKeys.THEME_DISPLAY);
        user = themeDisplay.getUser();
        username = user.getScreenName();
        _log.info("User: '" + user + "'");

        // Determine the application pathname                
        portletSession = request.getPortletSession();
        portletContext = portletSession.getPortletContext();
        appServerPath = portletContext.getRealPath("/");
        _log.info("Web Application path: '" + appServerPath + "'");

        // Determine the current portlet mode and forward this state to the response
        // Accordingly to JSRs168/286 the standard portlet modes are:
        // VIEW, EDIT, HELP
        PortletMode mode = request.getPortletMode();
        response.setPortletMode(request.getPortletMode());

        // Switch among different portlet modes: VIEW, EDIT, HELP
        // Custom modes are not covered by this template
        if (mode.equals(PortletMode.VIEW)) {
            // The VIEW mode is the normal portlet mode where normal portlet
            // content will be shown to the user
            _log.info("Portlet mode: VIEW");

            // The actionStatus value will be taken from the calling jsp file
            // through the 'PortletStatus' parameter; the corresponding
            // VIEW mode will be stored registering the portlet status
            // as render parameter. See the call to setRenderParameter
            // If the actionStatus parameter is null or empty the default
            // action will be the ACTION_INPUT (input form)
            // This happens the first time the portlet is shown
            // The PortletStatus variable is managed by jsp and this java code
            String actionStatus = request.getParameter("PortletStatus");
            // Assigns the default ACTION
            if (null == actionStatus || actionStatus.equals(""))
                actionStatus = "" + Actions.ACTION_INPUT;

            // Different actions will be performed accordingly to the
            // different possible statuses
            switch (Actions.valueOf(actionStatus)) {
            case ACTION_INPUT:
                _log.info("Got action: 'ACTION_INPUT'");

                // Assign the correct view
                response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT);
                break;
            case ACTION_PILOT:
                _log.info("Got action: 'ACTION_PILOT'");
                // Stores the new pilot script
                String pilotScript = request.getParameter("pilotScript");
                pilotScript.replaceAll("\r", "");
                storeString(appServerPath + "WEB-INF/job/" + appPreferences.pilotScript, pilotScript);
                // Assign the correct view
                response.setPortletMode(PortletMode.EDIT);
                break;
            case ACTION_SUBMIT:
                _log.info("Got action: 'ACTION_SUBMIT'");

                // Get current preference values
                getPreferences(request, null);

                // Create the appInput object
                App_Input appInput = new App_Input();

                // Stores the user submitting the job
                appInput.username = username;

                // Determine the submissionTimeStamp                    
                SimpleDateFormat dateFormat = new SimpleDateFormat(tsFormat);
                String timestamp = dateFormat.format(Calendar.getInstance().getTime());
                appInput.timestamp = timestamp;

                // Process input fields and files to upload
                getInputForm(request, appInput);

                // Following files have to be updated with
                // values taken from textareas or from uploaded files:
                // input_file.txt
                updateFiles(appInput);

                // Submit the job
                submitJob(appInput);

                // Send the jobIdentifier and assign the correct view                    
                response.setRenderParameter("PortletStatus", "" + Views.VIEW_SUBMIT);
                response.setRenderParameter("jobIdentifier", "" + appInput.jobIdentifier);
                break;
            default:
                _log.info("Unhandled action: '" + actionStatus + "'");
                response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT);
            }
        } else if (mode.equals(PortletMode.HELP)) {
            // The HELP mode used to give portlet usage HELP to the user
            // This code will be called after the call to doHelp method                         
            _log.info("Portlet mode: HELP");
        } else if (mode.equals(PortletMode.EDIT)) {
            // The EDIT mode is used to view/setup portlet preferences
            // This code will be called after the user sends the actionURL 
            // generated by the doEdit method 
            // The code below just stores new preference values or
            // reacts to the preference settings changes
            _log.info("Portlet mode: EDIT");

            // New application preferences will takem from edit.jsp            
            String newpref_logLevel = "" + request.getParameter("pref_logLevel");
            String newpref_sciGwyAppId = "" + request.getParameter("pref_sciGwyAppId");

            // Retrieve the current ifnrstructure in preference
            int numInfrastructures = appPreferences.getNumInfrastructures();
            int currInfra = appPreferences.getCurrInfrastructure();

            _log.info(LS + "Number of infrastructures: '" + numInfrastructures + "'" + LS
                    + "currentInfrastructure:     '" + currInfra + "'" + LS);

            // Take care of the preference action (Infrastructure preferences)
            // <,>,+,- buttons
            String pref_action = "" + request.getParameter("pref_action");
            _log.info("pref_action: '" + pref_action + "'");

            // Reacts to the Infrastructure change and
            // Determine the next view mode (return to the input pane)                        
            if (pref_action.equalsIgnoreCase("next")) {
                appPreferences.switchNextInfrastructure();
                _log.info(
                        "Got next infrastructure action; switching to: '" + appPreferences.paneInfrastucture + "'");
            } else if (pref_action.equalsIgnoreCase("previous")) {
                appPreferences.switchPreviousInfrastructure();
                _log.info(
                        "Got prev infrastructure action; switching to: '" + appPreferences.paneInfrastucture + "'");
            } else if (pref_action.equalsIgnoreCase("add")) {
                appPreferences.addNewInfrastructure();
                storePreferences(request);
                _log.info("Got add infrastructure action; current infrastrucure is now: '"
                        + appPreferences.paneInfrastucture + "'");
                return;
            } else if (pref_action.equalsIgnoreCase("remove")) {
                appPreferences.delCurrInfrastructure();
                storePreferences(request);
                _log.info("Got remove infrastructure action; current infrastrucure is now: '"
                        + appPreferences.paneInfrastucture + "' and infrastructures: '"
                        + appPreferences.numInfrastructures + "'");
                return;
            } else if (pref_action.equalsIgnoreCase("done")) {
                // None of the above actions selected; return to the VIEW mode
                response.setPortletMode(PortletMode.VIEW);
                response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT);
                return;
            } else if (pref_action.equalsIgnoreCase("viewPilot")) {
                int i = currInfra - 1;
                // None of the above actions selected; return to the VIEW mode
                response.setPortletMode(PortletMode.VIEW);
                response.setRenderParameter("PortletStatus", "" + Views.VIEW_PILOT);
                response.setRenderParameter("pilotScript",
                        updateString(appServerPath + "WEB-INF/job/" + appPreferences.pilotScript));
                return;
            } else {
                // No other special actions to do ...
            }

            // Take the values of the current infrastructure
            // Current infrastructure pane held by appPreferences.paneInfrastucture value
            Info_Infrastructure newpref_infraInfo = new Info_Infrastructure();
            if (appPreferences.getCurrInfrastructure() > 0) {
                newpref_infraInfo.enableInfrastructure = "" + request.getParameter("pref_enableInfrastructure");
                newpref_infraInfo.nameInfrastructure = "" + request.getParameter("pref_nameInfrastructure");
                newpref_infraInfo.acronymInfrastructure = "" + request.getParameter("pref_acronymInfrastructure");
                newpref_infraInfo.bdiiHost = "" + request.getParameter("pref_bdiiHost");
                newpref_infraInfo.wmsHosts = "" + request.getParameter("pref_wmsHosts");
                newpref_infraInfo.pxServerHost = "" + request.getParameter("pref_pxServerHost");
                newpref_infraInfo.pxServerPort = "" + request.getParameter("pref_pxServerPort");
                newpref_infraInfo.pxServerSecure = "" + request.getParameter("pref_pxServerSecure");
                newpref_infraInfo.pxRobotId = "" + request.getParameter("pref_pxRobotId");
                newpref_infraInfo.pxRobotVO = "" + request.getParameter("pref_pxRobotVO");
                newpref_infraInfo.pxRobotRole = "" + request.getParameter("pref_pxRobotRole");
                newpref_infraInfo.pxRobotRenewalFlag = "" + request.getParameter("pref_pxRobotRenewalFlag");
                newpref_infraInfo.softwareTags = "" + request.getParameter("pref_softwareTags");
            } // Setup current infrastructure 

            // Other application preferences                                     
            String newpref_jobRequirements = "" + request.getParameter("pref_jobRequirements");
            String newpref_pilotScript = "" + request.getParameter("pref_pilotScript");
            String newpref_pxUserProxy = "" + request.getParameter("pref_pxUserProxy");

            // Cleanup the pilot script from dangerous \r characters
            newpref_pilotScript = newpref_pilotScript.replaceAll("\r", "");

            // Show preference values changes
            String infrastructuresInformations = "";
            if (currInfra > 0) {
                // Current preference values
                String pref_enableInfrastructure = appPreferences.infoInfra[currInfra - 1].enableInfrastructure;
                String pref_nameInfrastructure = appPreferences.infoInfra[currInfra - 1].nameInfrastructure;
                String pref_acronymInfrastructure = appPreferences.infoInfra[currInfra - 1].acronymInfrastructure;
                String pref_bdiiHost = appPreferences.infoInfra[currInfra - 1].bdiiHost;
                String pref_wmsHosts = appPreferences.infoInfra[currInfra - 1].wmsHosts;
                String pref_pxServerHost = appPreferences.infoInfra[currInfra - 1].pxServerHost;
                String pref_pxServerPort = appPreferences.infoInfra[currInfra - 1].pxServerPort;
                String pref_pxServerSecure = appPreferences.infoInfra[currInfra - 1].pxServerSecure;
                String pref_pxRobotId = appPreferences.infoInfra[currInfra - 1].pxRobotId;
                String pref_pxRobotVO = appPreferences.infoInfra[currInfra - 1].pxRobotVO;
                String pref_pxRobotRole = appPreferences.infoInfra[currInfra - 1].pxRobotRole;
                String pref_pxRobotRenewalFlag = appPreferences.infoInfra[currInfra - 1].pxRobotRenewalFlag;
                String pref_softwareTags = appPreferences.infoInfra[currInfra - 1].softwareTags;
                // New preference values
                String newpref_enableInfrastructure = newpref_infraInfo.enableInfrastructure;
                String newpref_nameInfrastructure = newpref_infraInfo.nameInfrastructure;
                String newpref_acronymInfrastructure = newpref_infraInfo.acronymInfrastructure;
                String newpref_bdiiHost = newpref_infraInfo.bdiiHost;
                String newpref_wmsHosts = newpref_infraInfo.wmsHosts;
                String newpref_pxServerHost = newpref_infraInfo.pxServerHost;
                String newpref_pxServerPort = newpref_infraInfo.pxServerPort;
                String newpref_pxServerSecure = newpref_infraInfo.pxServerSecure;
                String newpref_pxRobotId = newpref_infraInfo.pxRobotId;
                String newpref_pxRobotVO = newpref_infraInfo.pxRobotVO;
                String newpref_pxRobotRole = newpref_infraInfo.pxRobotRole;
                String newpref_pxRobotRenewalFlag = newpref_infraInfo.pxRobotRenewalFlag;
                String newpref_softwareTags = newpref_infraInfo.softwareTags;

                // Prepare the Log string with changes
                infrastructuresInformations += LS + "Infrastructure #" + appPreferences.paneInfrastucture + LS
                        + "  enableInfrastructure       : '" + pref_enableInfrastructure + "' -> '"
                        + newpref_enableInfrastructure + "'" + LS + "  nameInfrastructures        : '"
                        + pref_nameInfrastructure + "' -> '" + newpref_nameInfrastructure + "'" + LS
                        + "  acronymInfrastructures     : '" + pref_acronymInfrastructure + "' -> '"
                        + newpref_acronymInfrastructure + "'" + LS + "  bdiiHost                   : '"
                        + pref_bdiiHost + "' -> '" + newpref_bdiiHost + "'" + LS
                        + "  wmsHosts                   : '" + pref_wmsHosts + "' -> '" + newpref_wmsHosts + "'"
                        + LS + "  pxServerHost               : '" + pref_pxServerHost + "' -> '"
                        + newpref_pxServerHost + "'" + LS + "  pxServerPort               : '" + pref_pxServerPort
                        + "' -> '" + newpref_pxServerPort + "'" + LS + "  pxServerSecure             : '"
                        + pref_pxServerSecure + "' -> '" + newpref_pxServerSecure + "'" + LS
                        + "  pxRobotId                  : '" + pref_pxRobotId + "' -> '" + newpref_pxRobotId + "'"
                        + LS + "  pxRobotVO                  : '" + pref_pxRobotVO + "' -> '" + newpref_pxRobotVO
                        + "'" + LS + "  pxRobotRole                : '" + pref_pxRobotRole + "' -> '"
                        + newpref_pxRobotRole + "'" + LS + "  pxRobotRenewalFlag         : '"
                        + pref_pxRobotRenewalFlag + "' -> '" + newpref_pxRobotRenewalFlag + "'" + LS
                        + "  softwareTags               : '" + pref_softwareTags + "' -> '" + newpref_softwareTags
                        + "'" + LS;
                // Assigns new values
                appPreferences.infoInfra[currInfra - 1].enableInfrastructure = newpref_enableInfrastructure;
                appPreferences.infoInfra[currInfra - 1].nameInfrastructure = newpref_nameInfrastructure;
                appPreferences.infoInfra[currInfra - 1].acronymInfrastructure = newpref_acronymInfrastructure;
                appPreferences.infoInfra[currInfra - 1].bdiiHost = newpref_bdiiHost;
                appPreferences.infoInfra[currInfra - 1].wmsHosts = newpref_wmsHosts;
                appPreferences.infoInfra[currInfra - 1].pxServerHost = newpref_pxServerHost;
                appPreferences.infoInfra[currInfra - 1].pxServerPort = newpref_pxServerPort;
                appPreferences.infoInfra[currInfra - 1].pxServerSecure = newpref_pxServerSecure;
                appPreferences.infoInfra[currInfra - 1].pxRobotId = newpref_pxRobotId;
                appPreferences.infoInfra[currInfra - 1].pxRobotVO = newpref_pxRobotVO;
                appPreferences.infoInfra[currInfra - 1].pxRobotRole = newpref_pxRobotRole;
                appPreferences.infoInfra[currInfra - 1].pxRobotRenewalFlag = newpref_pxRobotRenewalFlag;
                appPreferences.infoInfra[currInfra - 1].softwareTags = newpref_softwareTags;
            } // for each Infrastructure
            _log.info(LS + "variable name          : 'Old Value' -> 'New value'" + LS
                    + "---------------------------------------------------" + LS + "pref_logLevel          : '"
                    + appPreferences.logLevel + "' -> '" + newpref_logLevel + "'" + LS
                    + "pref_SciGwyAppId       : '" + appPreferences.sciGwyAppId + "' -> '" + newpref_sciGwyAppId
                    + "'" + LS + "pref_numInfrastructures: '" + appPreferences.numInfrastructures + "' -> '"
                    + numInfrastructures + "'" + LS + infrastructuresInformations + LS
                    + "pref_jobRequirements   : '" + appPreferences.jobRequirements + "' -> '"
                    + newpref_jobRequirements + "'" + LS + "pref_pilotScript       : '" + appPreferences.pilotScript
                    + "' -> '" + newpref_pilotScript + "'" + LS + "pref_pxUserProxy       : '"
                    + appPreferences.pxUserProxy + "' -> '" + newpref_pxUserProxy + "'" + LS);

            // Assign the new variable to the preference object
            appPreferences.logLevel = newpref_logLevel;
            appPreferences.sciGwyAppId = newpref_sciGwyAppId;
            appPreferences.pxUserProxy = newpref_pxUserProxy;
            appPreferences.jobRequirements = newpref_jobRequirements;
            appPreferences.pilotScript = newpref_pilotScript;
            appPreferences.pxUserProxy = newpref_pxUserProxy;

            // Store new preferences
            storePreferences(request);
        } else {
            // Unsupported portlet modes come here
            _log.warn("Custom portlet mode: '" + mode.toString() + "'");
        }
    } // processAction

    //
    // Store preferences
    //
    // Uses the appPreference object settings to store Application parameters
    //
    void storePreferences(ActionRequest request) throws PortletException, IOException {
        // The code below stores all the portlet preference values
        PortletPreferences prefs = request.getPreferences();
        int nunInfrastructures = appPreferences.getNumInfrastructures();
        if (prefs != null) {
            prefs.setValue("pref_logLevel", appPreferences.logLevel);
            prefs.setValue("pref_sciGwyAppId", appPreferences.sciGwyAppId);
            prefs.setValue("pref_numInfrastructures", appPreferences.numInfrastructures);
            for (int i = 0; i < nunInfrastructures; i++) {
                int j = i + 1;
                prefs.setValue("pref_" + j + "_enableInfrastructure",
                        appPreferences.infoInfra[i].enableInfrastructure);
                prefs.setValue("pref_" + j + "_nameInfrastructure", appPreferences.infoInfra[i].nameInfrastructure);
                prefs.setValue("pref_" + j + "_acronymInfrastructure",
                        appPreferences.infoInfra[i].acronymInfrastructure);
                prefs.setValue("pref_" + j + "_bdiiHost", appPreferences.infoInfra[i].bdiiHost);
                prefs.setValue("pref_" + j + "_wmsHosts", appPreferences.infoInfra[i].wmsHosts);
                prefs.setValue("pref_" + j + "_pxServerHost", appPreferences.infoInfra[i].pxServerHost);
                prefs.setValue("pref_" + j + "_pxServerPort", appPreferences.infoInfra[i].pxServerPort);
                prefs.setValue("pref_" + j + "_pxServerSecure", appPreferences.infoInfra[i].pxServerSecure);
                prefs.setValue("pref_" + j + "_pxRobotId", appPreferences.infoInfra[i].pxRobotId);
                prefs.setValue("pref_" + j + "_pxRobotVO", appPreferences.infoInfra[i].pxRobotVO);
                prefs.setValue("pref_" + j + "_pxRobotRole", appPreferences.infoInfra[i].pxRobotRole);
                prefs.setValue("pref_" + j + "_pxRobotRenewalFlag", appPreferences.infoInfra[i].pxRobotRenewalFlag);
                prefs.setValue("pref_" + j + "_softwareTags", appPreferences.infoInfra[i].softwareTags);
            }
            prefs.setValue("pref_jobRequirements", appPreferences.jobRequirements);
            prefs.setValue("pref_pilotScript", appPreferences.pilotScript);
            prefs.setValue("pref_pxUserProxy", appPreferences.pxUserProxy);
            prefs.store();
        } // pref !=null
    } // storePreferences                                          

    //
    // Method responsible to show portlet content to the user accordingly to the current view mode
    //
    @Override
    protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException {
        _log.info("calling doView ...");
        response.setContentType("text/html");

        // Determine the application pathname                
        portletSession = request.getPortletSession();
        portletContext = portletSession.getPortletContext();
        appServerPath = portletContext.getRealPath("/");
        _log.info("Web Application path: '" + appServerPath + "'");

        // Switch among supported views; the currentView is determined by the
        // portlet render parameter value stored into PortletStatus identifier
        // this value has been assigned by the actionStatus or it will be 
        // null in case the doView method will be called without a
        // previous processAction call; in such a case the default VIEW_INPIUT
        // will be selected.
        //The PortletStatus variable is managed by jsp and this java code
        String currentView = request.getParameter("PortletStatus");
        if (null == currentView || currentView.equals(""))
            currentView = "" + Views.VIEW_INPUT;

        // Different actions will be performed accordingly to the
        // different possible view modes
        switch (Views.valueOf(currentView)) {
        // The following code is responsible to call the proper jsp file
        // that will provide the correct portlet interface
        case VIEW_INPUT: {
            _log.info("VIEW_INPUT Selected ...");
            PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/input.jsp");
            dispatcher.include(request, response);
        }
            break;
        case VIEW_PILOT: {
            _log.info("VIEW_PILOT Selected ...");
            String pilotScript = request.getParameter("pilotScript");
            request.setAttribute("pilotScript", pilotScript);
            PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/viewPilot.jsp");
            dispatcher.include(request, response);
        }
            break;
        case VIEW_SUBMIT: {
            _log.info("VIEW_SUBMIT Selected ...");
            String jobIdentifier = request.getParameter("jobIdentifier");
            request.setAttribute("jobIdentifier", jobIdentifier);
            PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/submit.jsp");
            dispatcher.include(request, response);
        }
            break;
        default:
            _log.info("Unknown view mode: " + currentView.toString());
        } // switch            
    } // doView

    //
    // doEdit
    //
    // This methods prepares an actionURL that will be used by edit.jsp file into a <input ...> form
    // As soon the user press the action button the processAction will be called and the portlet mode
    // will be set as EDIT.
    @Override
    public void doEdit(RenderRequest request, RenderResponse response) throws PortletException, IOException {
        response.setContentType("text/html");

        // Get current preference values
        getPreferences(null, request);

        // Get the current infrastructure and the number of infrastructure
        int currInfra = appPreferences.getCurrInfrastructure();
        int numInfrastructures = appPreferences.getNumInfrastructures();

        // ActionURL and the current preference value will be passed to the edit.jsp
        PortletURL pref_actionURL = response.createActionURL();
        request.setAttribute("pref_actionURL", pref_actionURL.toString());
        // Send preference values
        request.setAttribute("pref_logLevel", appPreferences.logLevel);
        request.setAttribute("pref_sciGwyAppId", appPreferences.sciGwyAppId);
        request.setAttribute("pref_numInfrastructures", appPreferences.numInfrastructures);
        request.setAttribute("pref_currInfrastructure", "" + appPreferences.paneInfrastucture);
        // Send Infrastructure specific data
        if (currInfra > 0 && currInfra <= numInfrastructures) {
            request.setAttribute("pref_enableInfrastructure",
                    appPreferences.infoInfra[currInfra - 1].enableInfrastructure);
            request.setAttribute("pref_nameInfrastructure",
                    appPreferences.infoInfra[currInfra - 1].nameInfrastructure);
            request.setAttribute("pref_acronymInfrastructure",
                    appPreferences.infoInfra[currInfra - 1].acronymInfrastructure);
            request.setAttribute("pref_bdiiHost", appPreferences.infoInfra[currInfra - 1].bdiiHost);
            request.setAttribute("pref_wmsHosts", appPreferences.infoInfra[currInfra - 1].wmsHosts);
            request.setAttribute("pref_pxServerHost", appPreferences.infoInfra[currInfra - 1].pxServerHost);
            request.setAttribute("pref_pxServerPort", appPreferences.infoInfra[currInfra - 1].pxServerPort);
            request.setAttribute("pref_pxServerSecure", appPreferences.infoInfra[currInfra - 1].pxServerSecure);
            request.setAttribute("pref_pxRobotId", appPreferences.infoInfra[currInfra - 1].pxRobotId);
            request.setAttribute("pref_pxRobotVO", appPreferences.infoInfra[currInfra - 1].pxRobotVO);
            request.setAttribute("pref_pxRobotRole", appPreferences.infoInfra[currInfra - 1].pxRobotRole);
            request.setAttribute("pref_pxRobotRenewalFlag",
                    appPreferences.infoInfra[currInfra - 1].pxRobotRenewalFlag);
            request.setAttribute("pref_softwareTags", appPreferences.infoInfra[currInfra - 1].softwareTags);
        } // if paneInfrastructure > 0
        request.setAttribute("pref_jobRequirements", appPreferences.jobRequirements);
        request.setAttribute("pref_pilotScript", appPreferences.pilotScript);
        request.setAttribute("pref_pxUserProxy", appPreferences.pxUserProxy);

        // The edit.jsp will be the responsible to show/edit the current preference values
        PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/edit.jsp");
        dispatcher.include(request, response);
    } // doEdit

    //
    // doHelp
    //
    // This method just calls the jsp responsible to show the portlet information
    @Override
    public void doHelp(RenderRequest request, RenderResponse response) throws PortletException, IOException {
        response.setContentType("text/html");
        request.setAttribute("portletVersion", appInit.portletVersion);
        PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/help.jsp");
        dispatcher.include(request, response);
    } // doHelp

    //
    // updateString
    //
    // This method takes as input a filename and will transfer its
    // content inside a String variable
    private String updateString(String file) throws IOException {
        String line;
        StringBuilder stringBuilder = new StringBuilder();
        BufferedReader reader = new BufferedReader(new FileReader(file));
        while ((line = reader.readLine()) != null) {
            stringBuilder.append(line);
            stringBuilder.append(LS);
        }
        return stringBuilder.toString();
    }

    //
    // storeString
    //
    // This method will transfer the content of a given String into
    // a given filename
    private void storeString(String fileName, String fileContent) throws IOException {
        BufferedWriter writer = new BufferedWriter(new FileWriter(fileName));
        writer.write(fileContent);
        writer.close();
    }

    //
    // getInputForm
    //
    // The use of upload file controls needs the use of "multipart/form-data"
    // form type. With this kind of input form it is necessary to process 
    // each item of the action request manually
    //
    // All form' input items are identified by the 'name' input property
    // inside the jsp file
    private enum inputControlsIds {
        file_inputFile // Input file textarea 
        , inputFile // Input file input file
        , JobIdentifier // User defined Job identifier
    };

    //
    // getInputForm (method)
    //
    void getInputForm(ActionRequest request, App_Input appInput) {
        if (PortletFileUpload.isMultipartContent(request))
            try {
                FileItemFactory factory = new DiskFileItemFactory();
                PortletFileUpload upload = new PortletFileUpload(factory);
                List items = upload.parseRequest(request);
                File repositoryPath = new File("/tmp");
                DiskFileItemFactory diskFileItemFactory = new DiskFileItemFactory();
                diskFileItemFactory.setRepository(repositoryPath);
                Iterator iter = items.iterator();
                String logstring = "";
                while (iter.hasNext()) {
                    FileItem item = (FileItem) iter.next();
                    String fieldName = item.getFieldName();
                    String fileName = item.getName();
                    String contentType = item.getContentType();
                    boolean isInMemory = item.isInMemory();
                    long sizeInBytes = item.getSize();
                    // Prepare a log string with field list
                    logstring += LS + "field name: '" + fieldName + "' - '" + item.getString() + "'";
                    switch (inputControlsIds.valueOf(fieldName)) {
                    case file_inputFile:
                        appInput.inputFileName = item.getString();
                        processInputFile(item, appInput);
                        break;
                    case inputFile:
                        appInput.inputFileText = item.getString();
                        break;
                    case JobIdentifier:
                        appInput.jobIdentifier = item.getString();
                        break;
                    default:
                        _log.warn("Unhandled input field: '" + fieldName + "' - '" + item.getString() + "'");
                    } // switch fieldName                                                   
                } // while iter.hasNext()   
                _log.info(LS + "Reporting" + LS + "---------" + LS + logstring + LS);
            } // try
            catch (Exception e) {
                _log.info("Caught exception while processing files to upload: '" + e.toString() + "'");
            }
        // The input form do not use the "multipart/form-data" 
        else {
            // Retrieve from the input form the given application values
            appInput.inputFileName = (String) request.getParameter("file_inputFile");
            appInput.inputFileText = (String) request.getParameter("inputFile");
            appInput.jobIdentifier = (String) request.getParameter("JobIdentifier");
        } // ! isMultipartContent

        // Show into the log the taken inputs
        _log.info(LS + "Taken input parameters:" + LS + "-----------------------" + LS + "inputFileName: '"
                + appInput.inputFileName + "'" + LS + "inputFileText: '" + appInput.inputFileText + "'" + LS
                + "jobIdentifier: '" + appInput.jobIdentifier + "'" + LS);
    } // getInputForm 

    //
    // processInputFile
    //
    // This method is called when the user specifies a input file to upload
    // the file will be saved first into /tmp directory and then its content
    // stored into the corresponding String variable
    // Before to submit the job the String value will be stored in the 
    // proper job inputSandbox file
    void processInputFile(FileItem item, App_Input appInput) {
        // Determin the filename
        String fileName = item.getName();
        if (!fileName.equals("")) {
            // Determine the fieldName
            String fieldName = item.getFieldName();

            // Create a filename for the uploaded file
            String theNewFileName = "/tmp/" + appInput.timestamp + "_" + appInput.username + "_" + fileName;
            File uploadedFile = new File(theNewFileName);
            _log.info("Uploading file: '" + fileName + "' into '" + theNewFileName + "'");
            try {
                item.write(uploadedFile);
            } catch (Exception e) {
                _log.error("Caught exception while uploading file: 'file_inputFile'");
            }
            // File content has to be inserted into a String variables:
            //   inputFileName -> inputFileText
            try {
                if (fieldName.equals("file_inputFile"))
                    appInput.inputFileText = updateString(theNewFileName);
                // Other params can be added as below ...
                //else if(fieldName.equals("..."))
                //   ...=updateString(theNewFileName);
                else { // Never happens
                }
            } catch (Exception e) {
                _log.error("Caught exception while processing strings: '" + e.toString() + "'");
            }
        } // if
    } // processInputFile

    //
    // updateFiles
    //
    // Before to submit the job this method creates the inputSandbox files
    // starting from users' input fields (textareas or uploaded files)
    void updateFiles(App_Input appInput) {
        // First of all remomve all possible ^Ms from Strings
        appInput.inputFileText = appInput.inputFileText.replaceAll("\r", "");
        // Now save string content into files
        // This must be done for each input sandbox file
        try {
            appInput.inputSandbox_inputFile = "/tmp/" + appInput.timestamp + "_" + appInput.username
                    + "_input_file.txt";
            FileWriter fwInput = new FileWriter(appInput.inputSandbox_inputFile);
            BufferedWriter bwInput = new BufferedWriter(fwInput);
            bwInput.write(appInput.inputFileText);
            bwInput.close();
        } catch (Exception e) {
            _log.error("Caught exception while creating inputSandbox files");
        }
    } // updateFiles

    //
    // getPreferences
    //
    // This method retrieves current portlet preference values and it can
    // be called by both processAction or doView methods
    private void getPreferences(ActionRequest actionRequest, RenderRequest renderRequest) {
        _log.info("Calling: getPreferences ...");
        PortletPreferences prefs = null;
        if (null != actionRequest)
            prefs = actionRequest.getPreferences();
        else if (null != renderRequest)
            prefs = renderRequest.getPreferences();
        else
            _log.warn("Both render request and action request are null");

        if (null != prefs) {
            appPreferences.logLevel = "" + prefs.getValue("pref_logLevel", appInit.logLevel);
            appPreferences.sciGwyAppId = "" + prefs.getValue("pref_sciGwyAppId", appInit.sciGwyAppId);
            appPreferences.setNumInfrastructures(
                    "" + prefs.getValue("pref_numInfrastructures", appInit.numInfrastructures));
            // Now retrieves the infrastructures information
            int numInfras = appPreferences.getNumInfrastructures();
            _log.debug(LS + ">>>>>>>>>>> numInfras: '" + numInfras + "'" + LS);

            // Allocate the array only if it is not initialized yet
            if (appPreferences.infoInfra == null) {
                appPreferences.infoInfra = new Info_Infrastructure[numInfras];
                appPreferences.paneInfrastucture = 1; // Initialize the edit pane number
            }
            // For each infrastructure
            // The preference name is indexed with the infrastructure number: 1,2,...
            String infrastructuresInfrormations = "";
            for (int i = 0; i < numInfras; i++) {
                int j = i + 1;
                // Allocate the Info_Infrastructure class onlt if it is not initialized yet
                if (null == appPreferences.infoInfra[i]) {
                    appPreferences.infoInfra[i] = new Info_Infrastructure();
                }
                appPreferences.infoInfra[i].enableInfrastructure = ""
                        + prefs.getValue("pref_" + j + "_enableInfrastructure",
                                (i < Integer.parseInt(appInit.numInfrastructures)
                                        ? appInit.infoInfra[i].enableInfrastructure
                                        : "yes/no"));
                appPreferences.infoInfra[i].nameInfrastructure = ""
                        + prefs.getValue("pref_" + j + "_nameInfrastructure",
                                (i < Integer.parseInt(appInit.numInfrastructures)
                                        ? appInit.infoInfra[i].nameInfrastructure
                                        : "Name infrastructure"));
                appPreferences.infoInfra[i].acronymInfrastructure = ""
                        + prefs.getValue("pref_" + j + "_acronymInfrastructure",
                                (i < Integer.parseInt(appInit.numInfrastructures)
                                        ? appInit.infoInfra[i].acronymInfrastructure
                                        : "Acronym infrastructure"));
                appPreferences.infoInfra[i].bdiiHost = "" + prefs.getValue("pref_" + j + "_bdiiHost",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].bdiiHost
                                : "BDII host"));
                appPreferences.infoInfra[i].wmsHosts = "" + prefs.getValue("pref_" + j + "_wmsHosts",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].wmsHosts
                                : "WMS host"));
                appPreferences.infoInfra[i].pxServerHost = "" + prefs.getValue("pref_" + j + "_pxServerHost",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].pxServerHost
                                : "Proxy server host"));
                appPreferences.infoInfra[i].pxServerPort = "" + prefs.getValue("pref_" + j + "_pxServerPort",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].pxServerPort
                                : "Proxy server port"));
                appPreferences.infoInfra[i].pxServerSecure = "" + prefs.getValue("pref_" + j + "_pxServerSecure",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].pxServerSecure
                                : "Proxy server secure connection flag"));
                appPreferences.infoInfra[i].pxRobotId = "" + prefs.getValue("pref_" + j + "_pxRobotId",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].pxRobotId
                                : "Proxy server robot identifier"));
                appPreferences.infoInfra[i].pxRobotVO = "" + prefs.getValue("pref_" + j + "_pxRobotVO",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].pxRobotVO
                                : "Proxy server robot VO"));
                appPreferences.infoInfra[i].pxRobotRole = "" + prefs.getValue("pref_" + j + "_pxRobotRole",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].pxRobotRole
                                : "Proxy server robot role"));
                appPreferences.infoInfra[i].pxRobotRenewalFlag = ""
                        + prefs.getValue("pref_" + j + "_pxRobotRenewalFlag",
                                (i < Integer.parseInt(appInit.numInfrastructures)
                                        ? appInit.infoInfra[i].pxRobotRenewalFlag
                                        : "Proxy server renewal"));
                appPreferences.infoInfra[i].softwareTags = "" + prefs.getValue("pref_" + j + "_softwareTags",
                        (i < Integer.parseInt(appInit.numInfrastructures) ? appInit.infoInfra[i].softwareTags
                                : "Software tags"));
            } // for each Infrastructure                           
            appPreferences.jobRequirements = "" + prefs.getValue("pref_jobRequirements", appInit.jobRequirements);
            appPreferences.pilotScript = "" + prefs.getValue("pref_pilotScript", appInit.pilotScript);
            appPreferences.pxUserProxy = "" + prefs.getValue("pref_pxUserProxy", appInit.pxUserProxy);

            // Assigns the log level      
            _log.setLogLevel(appPreferences.logLevel);

            // Show preference values into log
            _log.info(appPreferences.dumpPreferences());
        } // if
    } // getPreferences

    //
    // submitJob
    //
    // This method sends the job into the distributed infrastructure using
    // the GridEngine methods.
    void submitJob(App_Input appInput) {
        // Get the number of configured Infrastructures
        int numInfras = appPreferences.getNumInfrastructures();
        if (numInfras > 0) {
            //
            // Initialize the GridEngine Multi Infrastructure Job Submission object
            //
            MultiInfrastructureJobSubmission miJobSubmission = new MultiInfrastructureJobSubmission();
            //
            // Determine the number of infrastructures
            //
            int numEnabledInfrastructures = 0;
            for (int i = 0; i < numInfras; i++)
                if (appPreferences.infoInfra[i].enableInfrastructure.equalsIgnoreCase("yes"))
                    numEnabledInfrastructures++;
            _log.info("Enabled infrastructures: '" + numEnabledInfrastructures + "'");

            // Initialize the array of GridEngine' infrastructure objects
            InfrastructureInfo infrastructures[] = new InfrastructureInfo[numEnabledInfrastructures];
            // For each infrastructure

            for (int i = 0, h = 0; i < numInfras; i++) {
                int j = i + 1;
                // For each enabled infrastructure ... 
                if (appPreferences.infoInfra[i].enableInfrastructure.equalsIgnoreCase("yes")) {

                    // Take care of the adaptor/wms list
                    // GridEngine supports a list of WMSes/adaptors as an array of strinigs
                    // while the AppPreferences uses a ';' separated list of entries
                    // Following code makes the necessary conversion
                    String wmsHostList[] = null;
                    if (null != appPreferences.infoInfra[i].wmsHosts
                            && !appPreferences.infoInfra[i].wmsHosts.equals("")) {
                        wmsHostList = appPreferences.infoInfra[i].wmsHosts.split(";");
                        String showWMSList = LS + "wmsHostList" + LS + "-----------";
                        for (int k = 0; k < wmsHostList.length; k++)
                            showWMSList += LS + wmsHostList[k];
                        if (null != _log)
                            _log.info(showWMSList);
                    } // if wmsList 

                    // Multi-infrastructure support
                    // Different Infrastructure objects can be created accordingly to the 
                    // requested infrastructure type specified into the acronymInfrastructure
                    // field. Each infrastructure maps its specific values accordingly to
                    // several field mappings shown below on each infrastructure case
                    if (appPreferences.infoInfra[i].acronymInfrastructure.equalsIgnoreCase("unicore")) {
                        // Multi-infrastructure support (field mapping)
                        // UNICORE infrastructure requires to specify:
                        // * Keystore file -> bdiiHost first  field of the given ';' separated string
                        // * Password      -> bdiiHost second field of the given ';' separated string
                        // * JSAGA adaptor -> wmsHosts
                        String unicoreItems[] = appPreferences.infoInfra[i].bdiiHost.split(";");
                        int numUnicoreItems = unicoreItems.length;
                        String keyStore = "";
                        String password = "";
                        if (numUnicoreItems > 0)
                            keyStore = unicoreItems[0].trim();
                        if (numUnicoreItems > 1)
                            password = unicoreItems[1].trim();

                        // Build the GridEngine' infrastructure object and assign it to the infrastructures array
                        infrastructures[h++] = new InfrastructureInfo(
                                appPreferences.infoInfra[i].acronymInfrastructure, "unicore", keyStore, password,
                                wmsHostList);
                        if (_log != null)
                            _log.info("Unicore infrastructure: " + LS + " keyStore:      '" + keyStore + "'" + LS
                                    + " password:      '" + password + "'" + LS + " JSAGA adaptor: '" + wmsHostList
                                    + "'");
                    } else if (appPreferences.infoInfra[i].acronymInfrastructure.equalsIgnoreCase("garuda")) {
                        // Multi-infrastructure support (field mapping)
                        // GARUDA infrastructure requires to specify:
                        // * VO Group         -> pxRobotVO
                        // * VO Role          -> pxRobotRole
                        // * JSAGA adaptor    -> wmsHosts
                        // * Robot proxy Host -- pxServerHost
                        // * Robot proxy Port -- pxServerPort
                        // * Robot proxy Id   -- pxRobotId

                        // Build the GridEngine' infrastructure object and assign it to the infrastructures array
                        infrastructures[h++] = new InfrastructureInfo(
                                appPreferences.infoInfra[i].acronymInfrastructure, "wsgram", wmsHostList,
                                appPreferences.infoInfra[i].pxServerHost, appPreferences.infoInfra[i].pxServerPort,
                                appPreferences.infoInfra[i].pxRobotId, appPreferences.infoInfra[i].pxRobotVO,
                                appPreferences.infoInfra[i].pxRobotRole);
                        if (_log != null)
                            _log.info("GARUDA infrastructure: " + LS + " pxServerHost:  '"
                                    + appPreferences.infoInfra[i].pxServerHost + "'" + LS + " pxServerPort:  '"
                                    + appPreferences.infoInfra[i].pxServerPort + "'" + LS + " pxRobotId:     '"
                                    + appPreferences.infoInfra[i].pxRobotId + "'" + LS + " VO Group:      '"
                                    + appPreferences.infoInfra[i].pxRobotVO + "'" + LS + " VO Role:       '"
                                    + appPreferences.infoInfra[i].pxRobotRole + "'" + LS + " JSAGA adaptor: '"
                                    + wmsHostList + "'");
                    } else if (appPreferences.infoInfra[i].acronymInfrastructure.equalsIgnoreCase("ourgrid")) {
                        // Multi-infrastructure support (field mapping)
                        // OURGRID infrastructure requires to specify:
                        // * Username      -> bdiiHost first  field of the given ';' separated string
                        // * Password      -> bdiiHost second field of the given ';' separated string
                        // * JSAGA adaptor -> wmsHosts
                        String ourgridItems[] = appPreferences.infoInfra[i].bdiiHost.split(";");
                        int numOurGridItems = ourgridItems.length;
                        String username = "";
                        String password = "";
                        if (numOurGridItems > 0)
                            username = ourgridItems[0].trim();
                        if (numOurGridItems > 1)
                            password = ourgridItems[1].trim();

                        // Build the GridEngine' infrastructure object and assign it to the infrastructures array
                        infrastructures[h++] = new InfrastructureInfo(
                                appPreferences.infoInfra[i].acronymInfrastructure, "ourgrid", username, password,
                                wmsHostList);
                        if (_log != null)
                            _log.info("OURGRID infrastructure: " + LS + " username:      '" + username + "'" + LS
                                    + " password:      '" + password + "'" + LS + " JSAGA adaptor: '" + wmsHostList
                                    + "'");

                    } else {
                        // Multi-infrastructure support (no matching cases)
                        // If the acronym does not match to a specific infrastructure type
                        // the preference fields will be interpreted as gLite middleware settings

                        // Build the GridEngine' infrastructure object and assign it to the infrastructures array
                        // (!)Not yet used values:
                        //    pxServerSecure
                        //    pxRobotRenewalFlag
                        //    pxUserProxy                
                        infrastructures[h++] = new InfrastructureInfo(
                                appPreferences.infoInfra[i].acronymInfrastructure,
                                appPreferences.infoInfra[i].bdiiHost, wmsHostList,
                                appPreferences.infoInfra[i].pxServerHost, appPreferences.infoInfra[i].pxServerPort,
                                appPreferences.infoInfra[i].pxRobotId, appPreferences.infoInfra[i].pxRobotVO,
                                appPreferences.infoInfra[i].pxRobotRole, appPreferences.infoInfra[i].softwareTags);
                    }
                    // Shows the added infrastructure
                    if (_log != null)
                        _log.info(LS + appPreferences.infoInfra[i].dumpInfrastructure());
                } // Add enabled infrastructure
                else {
                    if (_log != null)
                        _log.info(LS + "Disabled infrastructure: " + LS
                                + appPreferences.infoInfra[i].dumpInfrastructure());
                }
            } // for each infrastructure

            for (int iEn = 0; iEn < infrastructures.length; iEn++)
                miJobSubmission.addInfrastructure(infrastructures[iEn]);
            //
            // Configure the job properties
            //
            // (!) Job level unused preference values
            //     pxUserProxy
            //     pxRobotRenewalFlag
            //

            // Application Id
            int applicationId = Integer.parseInt(appPreferences.sciGwyAppId);

            // UserTrakingDatabase                          
            String hostUTDB = appInit.sciGwyUserTrackingDB_Hostname; // Grid Engine' UserTraking database host
            // Data below should not used by portlets
            //String  unameUTDB=appInit.sciGwyUserTrackingDB_Username; // Username
            //String passwdUTDB=appInit.sciGwyUserTrackingDB_Password; // Password
            //String dbnameUTDB=appInit.sciGwyUserTrackingDB_Database; // Database

            // Job details
            String executable = "/bin/sh"; // Application executable
            String arguments = appPreferences.pilotScript // executable' argument: pilot_script.sh
                    + " '" + appInput.jobIdentifier + "'" // User job identifier
                    + " '" + appInput.username + "'" // User name
            ; // 
            String outputPath = "/tmp/"; // Output Path
            String outputFile = ".R-Output.txt"; // Distributed application standard output
            String errorFile = ".R-Error.txt"; // Distrubuted application standard error
            String appFile = "R-Files.tar.gz"; // Hostname output files (created by the pilot script)

            // InputSandbox (string with comma separated list of file names)
            String inputSandbox = appServerPath + "WEB-INF/job/" + appPreferences.pilotScript // pilot script
                    + "," + appInput.inputSandbox_inputFile // input file
            ;
            // OutputSandbox (string with comma separated list of file names)
            String outputSandbox = appFile + ",README.txt"; // Output file

            // Take care of job requirements
            // More requirements can be specified in the preference value 'jobRequirements'
            // separating each requirement by the ';' character
            String jdlRequirements[] = appPreferences.jobRequirements.split(";");
            int numRequirements = 0;
            for (int i = 0; i < jdlRequirements.length; i++) {
                if (!jdlRequirements[i].equals("")) {
                    jdlRequirements[numRequirements] = "JDLRequirements=(" + jdlRequirements[i] + ")";
                    numRequirements++;
                }
                _log.info("Requirement[" + i + "]='" + jdlRequirements[i] + "'");
            } // for each jobRequirement

            // Other job initialization settings
            miJobSubmission.setExecutable(executable); // Specify the executeable
            miJobSubmission.setArguments(arguments); // Specify the application' arguments
            miJobSubmission.setOutputPath(outputPath); // Specify the output directory 
            miJobSubmission.setOutputFiles(outputSandbox); // Setup output files (OutputSandbox)
            miJobSubmission.setJobOutput(outputFile); // Specify the std-outputr file
            miJobSubmission.setJobError(errorFile); // Specify the std-error file
            if (null != inputSandbox // Setup input files (InputSandbox) avoiding empty inputSandboxes
                    && inputSandbox.length() > 0)
                miJobSubmission.setInputFiles(inputSandbox);

            // Submit Job
            miJobSubmission.submitJobAsync(miJobSubmission.getInfrastructure(), username, hostUTDB, applicationId,
                    appInput.jobIdentifier);

            // Show log
            // View jobSubmission details in the log
            _log.info(LS + "JobSent" + LS + "-------" + LS + "Executable    : '" + executable + "'" + LS
                    + "Arguments     : '" + arguments + "'" + LS + "Output path   : '" + outputPath + "'" + LS
                    + "Output sandbox: '" + outputSandbox + "'" + LS + "Ouput file    : '" + outputFile + "'" + LS
                    + "Error file    : '" + errorFile + "'" + LS + "Input sandbox : '" + inputSandbox + "'" + LS); // _log.info        

        } // numInfra > 0
        else {
            _log.warn(LS + "There are no infrastructures configured; impossible to send any job" + LS
                    + "Configure the application preferences in order to setup at least" + LS + "an infrastructure."
                    + LS);
        } // numInfra == 0                     
    } // submitJob
} // R_portlet