Metacat

/**

 *  '$RCSfile$'

 *    Purpose: A Class that implements a metadata catalog as a java Servlet

 *  Copyright: 2006 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Matt Jones, Dan Higgins, Jivka Bojilova, Chad Berkley, Matthew Perry

 *

 *   '$Author: tao $'

 *     '$Date: 2016-03-23 15:57:25 -0700 (Wed, 23 Mar 2016) $'

 * '$Revision: 9583 $'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat;

import java.io.IOException;

import java.io.OutputStreamWriter;

import java.io.PrintWriter;

import java.io.Writer;

import java.sql.PreparedStatement;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.sql.Timestamp;

import java.util.Enumeration;

import java.util.Hashtable;

import java.util.Timer;

import java.util.Vector;

import javax.servlet.ServletConfig;

import javax.servlet.ServletContext;

import javax.servlet.ServletException;

import javax.servlet.ServletOutputStream;

import javax.servlet.http.HttpServlet;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import javax.servlet.http.HttpSession;

import org.apache.commons.lang.StringEscapeUtils;

import org.apache.log4j.Logger;

import org.apache.log4j.PropertyConfigurator;

import edu.ucsb.nceas.metacat.common.query.EnabledQueryEngines;

import edu.ucsb.nceas.metacat.database.DBConnection;

import edu.ucsb.nceas.metacat.database.DBConnectionPool;

import edu.ucsb.nceas.metacat.database.DatabaseService;

import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;

import edu.ucsb.nceas.metacat.plugin.MetacatHandlerPlugin;

import edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager;

import edu.ucsb.nceas.metacat.properties.PropertyService;

import edu.ucsb.nceas.metacat.properties.SkinPropertyService;

import edu.ucsb.nceas.metacat.replication.ReplicationService;

import edu.ucsb.nceas.metacat.service.ServiceService;

import edu.ucsb.nceas.metacat.service.SessionService;

import edu.ucsb.nceas.metacat.service.XMLSchemaService;

import edu.ucsb.nceas.metacat.shared.BaseException;

import edu.ucsb.nceas.metacat.shared.HandlerException;

import edu.ucsb.nceas.metacat.shared.MetacatUtilException;

import edu.ucsb.nceas.metacat.shared.ServiceException;

import edu.ucsb.nceas.metacat.spatial.SpatialHarvester;

import edu.ucsb.nceas.metacat.util.AuthUtil;

import edu.ucsb.nceas.metacat.util.ConfigurationUtil;

import edu.ucsb.nceas.metacat.util.DocumentUtil;

import edu.ucsb.nceas.metacat.util.ErrorSendingErrorException;

import edu.ucsb.nceas.metacat.util.RequestUtil;

import edu.ucsb.nceas.metacat.util.ResponseUtil;

import edu.ucsb.nceas.metacat.util.SessionData;

import edu.ucsb.nceas.metacat.util.SystemUtil;

import edu.ucsb.nceas.metacat.workflow.WorkflowSchedulerClient;

import edu.ucsb.nceas.utilities.FileUtil;

import edu.ucsb.nceas.utilities.GeneralPropertyException;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

import edu.ucsb.nceas.utilities.UtilException;

/**

 * A metadata catalog server implemented as a Java Servlet

 *

 * Valid actions are:

 * 

 * action=login

 *     username

 *     password

 *     qformat

 * action=logout

 *     qformat

 * action=query -- query the values of all elements and attributes and return a result set of nodes

 *     meta_file_id --

 *     returndoctype --

 *     filterdoctype --

 *     returnfield --

 *     owner --

 *     site --

 *     operator --

 *     casesensitive --

 *     searchmode --

 *     anyfield --

 * action=spatial_query -- run a spatial query.  these queries may include any of the

 *                         queries supported by the WFS / WMS standards

 *     xmax --

 *     ymax --

 *     xmin --

 *     ymin --

 *     skin --

 *     pagesize --

 *     pagestart --

 * action=squery -- structured query (see pathquery.dtd)

 *     query --

 *     pagesize --

 *     pagestart --

 * action=export -- export a zip format for data packadge

 *     docid -- 

 * action=read -- read any metadata/data file from Metacat and from Internet

 *     archiveEntryName --

 *     docid --

 *     qformat --

 *     metadatadocid --

 * action=readinlinedata -- read inline data only

 *     inlinedataid

 * action=insert -- insert an XML document into the database store

 *     qformat -- 

 *     docid --

 *     doctext --

 *     dtdtext --

 * action=insertmultipart -- insert an xml document into the database using multipart encoding

 *     qformat -- 

 *     docid --

 * action=update -- update an XML document that is in the database store

 *     qformat -- 

 *     docid --

 *     doctext --

 *     dtdtext --

 * action=delete -- delete an XML document from the database store

 *     docid --

 * action=validate -- validate the xml contained in valtext

 *     valtext --

 *     docid --

 * action=setaccess -- change access permissions for a user on a document.

 *     docid --

 *     principal --

 *     permission --

 *     permType --

 *     permOrder --

 * action=getaccesscontrol -- retrieve acl info for Metacat document

 *     docid -- 

 * action=getprincipals -- retrieve a list of principals in XML

 * action=getalldocids -- retrieves a list of all docids registered with the system

 *     scope --

 * action=getlastdocid --

 *     scope --

 *     username --

 * action=isregistered -- checks to see if the provided docid is registered

 *     docid --

 * action=getrevisionanddoctype -- get a document's revision and doctype from database 

 *     docid --

 * action=getversion -- 

 * action=getdoctypes -- retrieve all doctypes (publicID) 

 * action=getdtdschema -- retrieve a DTD or Schema file

 *     doctype --

 * action=getlog -- get a report of events that have occurred in the system

 *     ipAddress --  filter on one or more IP addresses>

 *     principal -- filter on one or more principals (LDAP DN syntax)

 *     docid -- filter on one or more document identifiers (with revision)

 *     event -- filter on event type (e.g., read, insert, update, delete)

 *     start -- filter out events before the start date-time

 *     end -- filter out events before the end date-time

 * action=getloggedinuserinfo -- get user info for the currently logged in user

 *     ipAddress --  filter on one or more IP addresses>

 *     principal -- filter on one or more principals (LDAP DN syntax)

 *     docid -- filter on one or more document identifiers (with revision)

 *     event -- filter on event type (e.g., read, insert, update, delete)

 *     start -- filter out events before the start date-time

 *     end -- filter out events before the end date-time

 * action=shrink -- Shrink the database connection pool size if it has grown and 

 *                  extra connections are no longer being used.

 * action=buildindex --

 *     docid --

 * action=refreshServices --

 * action=scheduleWorkflow -- Schedule a workflow to be run.  Scheduling a workflow 

 *                            registers it with the scheduling engine and creates a row

 *                            in the scheduled_job table.  Note that this may be 

 *                            extracted into a separate servlet.

 *     delay -- The amount of time from now before the workflow should be run.  The 

 *              delay can be expressed in number of seconds, minutes, hours and days, 

 *              for instance 30s, 2h, etc.

 *     starttime -- The time that the workflow should first run.  If both are provided

 *                  this takes precedence over delay.  The time should be expressed as: 

 *                  MM/dd/yyyy HH:mm:ss with the timezone assumed to be that of the OS.

 *     endtime -- The time when the workflow should end. The time should be expressed as: 

 *                  MM/dd/yyyy HH:mm:ss with the timezone assumed to be that of the OS.

 *     intervalvalue -- The numeric value of the interval between runs

 *     intervalunit -- The unit of the interval between runs.  Can be s, m, h, d for 

 *                     seconds, minutes, hours and days respectively

 *     workflowid -- The lsid of the workflow that we want to schedule.  This workflow

 *                   must already exist in the database.

 *     karid -- The karid for the workflow that we want to schedule.

 *     workflowname -- The name of the workflow.

 *     forwardto -- If provided, forward to this page when processing is done.

 *     qformat -- If provided, render results using the stylesheets associated with

 *                this skin.  Default is xml.

 * action=unscheduleWorkflow -- Unschedule a workflow.  Unscheduling a workflow 

 *                            removes it from the scheduling engine and changes the 

 *                            status in the scheduled_job table to " unscheduled.  Note 

 *                            that this may be extracted into a separate servlet.

 *     workflowjobname -- The job ID for the workflow run that we want to unschedule.  This

 *                      is held in the database as scheduled_job.name

 *     forwardto -- If provided, forward to this page when processing is done.

 *     qformat -- If provided, render results using the stylesheets associated with

 *                this skin.  Default is xml.

 * action=rescheduleWorkflow -- Unschedule a workflow.  Rescheduling a workflow 

 *                            registers it with the scheduling engine and changes the 

 *                            status in the scheduled_job table to " scheduled.  Note 

 *                            that this may be extracted into a separate servlet.

 *     workflowjobname -- The job ID for the workflow run that we want to reschedule.  This

 *                      is held in the database as scheduled_job.name

 *     forwardto -- If provided, forward to this page when processing is done.

 *     qformat -- If provided, render results using the stylesheets associated with

 *                this skin.  Default is xml.

 * action=deleteScheduledWorkflow -- Delete a workflow.  Deleting a workflow 

 *                            removes it from the scheduling engine and changes the 

 *                            status in the scheduled_job table to " deleted.  Note 

 *                            that this may be extracted into a separate servlet.

 *     workflowjobname -- The job ID for the workflow run that we want to delete.  This

 *                      is held in the database as scheduled_job.name

 *     forwardto -- If provided, forward to this page when processing is done.

 *     qformat -- If provided, render results using the stylesheets associated with

 *                this skin.  Default is xml.

 * action=reindex -- rebuild the solr index for the specified pids.

 *     pid -- the id of the document which will be rebuilt slor index.

 * action=reindexall -- rebuild the solr index for all objects in the systemmetadata table.

 *     

 * Here are some of the common parameters for actions

 *     doctype -- document type list returned by the query (publicID) 

 *     qformat=xml -- display resultset from query in XML 

 *     qformat=html -- display resultset from query in HTML 

 *     qformat=zip -- zip resultset from query

 *     docid=34 -- display the document with the document ID number 34 

 *     doctext -- XML text of the document to load into the database 

 *     acltext -- XML access text for a document to load into the database 

 *     dtdtext -- XML DTD text for a new DTD to load into Metacat XML Catalog 

 *     query -- actual query text (to go with 'action=query' or 'action=squery')

 *     valtext -- XML text to be validated 

 *     scope --can limit the query by the scope of the id

 *     docid --the docid to check

 *     datadoc -- data document name (id)

 */

public class MetaCatServlet extends HttpServlet {

	private static final long serialVersionUID = 1L;

	private Timer timer = null;

    private static boolean _firstHalfInitialized = false;

    private static boolean _fullyInitialized = false;

    private MetacatHandler handler = null;

    // Constants -- these should be final in a servlet

    public static final String SCHEMALOCATIONKEYWORD = ":schemaLocation";

    public static final String NONAMESPACELOCATION = ":noNamespaceSchemaLocation";

    public static final String EML2KEYWORD = ":eml";

    private static final String FALSE = "false";

    private static final String TRUE  = "true";

    private static String LOG_CONFIG_NAME = null;

    public static final String APPLICATION_NAME = "metacat";

	public static final String DEFAULT_ENCODING = "UTF-8";

    /**

     * Initialize the servlet by creating appropriate database connections

     */

    public void init(ServletConfig config) throws ServletException {

    	Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

    	try {

    		if(_firstHalfInitialized) {

    			return;

    		}

            super.init(config);

            ServletContext context = config.getServletContext();

            context.setAttribute("APPLICATION_NAME", APPLICATION_NAME);

            ServiceService serviceService = ServiceService.getInstance(context);

            logMetacat.debug("MetaCatServlet.init - ServiceService singleton created " + serviceService);

            // Initialize the properties file

            String dirPath = ServiceService.getRealConfigDir();

            LOG_CONFIG_NAME = dirPath + "/log4j.properties";

            PropertyConfigurator.configureAndWatch(LOG_CONFIG_NAME);

            // Register preliminary services

            ServiceService.registerService("PropertyService", PropertyService.getInstance(context));         

            ServiceService.registerService("SkinPropertyService", SkinPropertyService.getInstance());

            ServiceService.registerService("SessionService", SessionService.getInstance()); 

            // Check to see if the user has requested to bypass configuration 

            // (dev option) and check see if metacat has been configured.

    		// If both are false then stop the initialization

            if (!ConfigurationUtil.bypassConfiguration() && !ConfigurationUtil.isMetacatConfigured()) {

            	return;

            }  

            _firstHalfInitialized = true;

            initSecondHalf(context);

    	} catch (ServiceException se) {

        	String errorMessage = 

        		"Service problem while intializing MetaCat Servlet: " + se.getMessage();

            logMetacat.error("MetaCatServlet.init - " + errorMessage);

            throw new ServletException(errorMessage);

        } catch (MetacatUtilException mue) {

        	String errorMessage = "Metacat utility problem while intializing MetaCat Servlet: " 

        		+ mue.getMessage();

            logMetacat.error("MetaCatServlet.init - " + errorMessage);

            throw new ServletException(errorMessage);

        } 

    }

	/**

	 * Initialize the remainder of the servlet. This is the part that can only

	 * be initialized after metacat properties have been configured

	 * 

	 * @param context

	 *            the servlet context of MetaCatServlet

	 */

	public void initSecondHalf(ServletContext context) throws ServletException {

		Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

		try {			

			ServiceService.registerService("DatabaseService", DatabaseService.getInstance());

			// initialize DBConnection pool

			DBConnectionPool connPool = DBConnectionPool.getInstance();

			logMetacat.debug("MetaCatServlet.initSecondHalf - DBConnection pool initialized: " + connPool.toString());

			// register the XML schema service

			ServiceService.registerService("XMLSchemaService", XMLSchemaService.getInstance());

			// check if eml201 document were corrected or not. if not, correct eml201 documents.

			// Before Metacat 1.8.1, metacat uses tag RELEASE_EML_2_0_1_UPDATE_6 as eml

			// schema, which accidentily points to wrong version of eml-resource.xsd.

			String correctedEML201Doc = PropertyService.getProperty("document.eml201DocumentCorrected");

			if (correctedEML201Doc != null && correctedEML201Doc.equals(FALSE)) {

				logMetacat.info("MetaCatServlet.initSecondHalf - Start to correct eml201 documents");

				EML201DocumentCorrector correct = new EML201DocumentCorrector();

				boolean success = correct.run();

				if (success) {

					PropertyService.setProperty("document.eml201DocumentCorrected", TRUE);

				}

				logMetacat.info("MetaCatServlet.initSecondHalf - Finish to correct eml201 documents");

			}

			// Index the paths specified in the metacat.properties

			checkIndexPaths();

			// initiate the indexing Queue

			IndexingQueue.getInstance();

			// start the IndexingThread if indexingTimerTaskTime more than 0.

			// It will index all the documents not yet indexed in the database

			int indexingTimerTaskTime = Integer.parseInt(PropertyService

					.getProperty("database.indexingTimerTaskTime"));

			int delayTime = Integer.parseInt(PropertyService

					.getProperty("database.indexingInitialDelay"));

			if (indexingTimerTaskTime > 0) {

				timer = new Timer();

				timer.schedule(new IndexingTimerTask(), delayTime, indexingTimerTaskTime);

			}

			/*

			 * If spatial option is turned on and set to regenerate the spatial

			 * cache on restart, trigger the harvester regeneratation method

			 */

			if (PropertyService.getProperty("spatial.runSpatialOption").equals("true") && 

					PropertyService.getProperty("spatial.regenerateCacheOnRestart").equals("true")) {

				// Begin timer

				long before = System.currentTimeMillis();

				// if either the point or polygon shape files do not exist, then regenerate the entire spatial cache

				// this may be expensive with many documents		

				SpatialHarvester sh = new SpatialHarvester();

				sh.regenerate();

				sh.destroy();

				// After running the first time, we want to to set

				// regenerateCacheOnRestart to false

				// so that it does not regenerate the cache every time tomcat is

				// restarted

				PropertyService.setProperty("spatial.regenerateCacheOnRestart", "false");

				// End timer

				long after = System.currentTimeMillis();

				logMetacat.info("MetaCatServlet.initSecondHalf - Spatial Harvester Time  " 

						+ (after - before) + "ms");

			} else {

				logMetacat.info("MetaCatServlet.initSecondHalf - Spatial cache is not set to regenerate on restart");

			}

			// Set up the replication log file by setting the "replication.logfile.name" 

			// system property and reconfiguring the log4j property configurator.

			String replicationLogPath = PropertyService.getProperty("replication.logdir") 

				+ FileUtil.getFS() + ReplicationService.REPLICATION_LOG_FILE_NAME;				

			if (FileUtil.getFileStatus(replicationLogPath) == FileUtil.DOES_NOT_EXIST) {

				FileUtil.createFile(replicationLogPath);

			}

			if (FileUtil.getFileStatus(replicationLogPath) < FileUtil.EXISTS_READ_WRITABLE) {

				logMetacat.error("MetaCatServlet.initSecondHalf - Replication log file: " + replicationLogPath 

						+ " does not exist read/writable.");

			}

			System.setProperty("replication.logfile.name", replicationLogPath);			

			PropertyConfigurator.configureAndWatch(LOG_CONFIG_NAME);

			SessionService.getInstance().unRegisterAllSessions();

	         //Initialize Metacat Handler

            handler = new MetacatHandler(timer);

			handler.set_sitemapScheduled(false);

			// initialize the plugins

			MetacatHandlerPluginManager.getInstance();

			// initialize the HazelcastService

			ServiceService.registerService("HazelcastService", HazelcastService.getInstance());

			_fullyInitialized = true;

			logMetacat.warn("MetaCatServlet.initSecondHalf - Metacat (" + MetacatVersion.getVersionID()

					+ ") initialized.");

		} catch (SQLException e) {

			String errorMessage = "SQL problem while intializing MetaCat Servlet: "

					+ e.getMessage();

			logMetacat.error("MetaCatServlet.initSecondHalf - " + errorMessage);

			throw new ServletException(errorMessage);

		} catch (IOException ie) {

			String errorMessage = "IO problem while intializing MetaCat Servlet: "

					+ ie.getMessage();

			logMetacat.error("MetaCatServlet.initSecondHalf - " + errorMessage);

			throw new ServletException(errorMessage);

		} catch (GeneralPropertyException gpe) {

			String errorMessage = "Could not retrieve property while intializing MetaCat Servlet: "

					+ gpe.getMessage();

			logMetacat.error("MetaCatServlet.initSecondHalf - " + errorMessage);

			throw new ServletException(errorMessage);

		} catch (ServiceException se) {

			String errorMessage = "Service problem while intializing MetaCat Servlet: "

				+ se.getMessage();

			logMetacat.error("MetaCatServlet.initSecondHalf - " + errorMessage);

			throw new ServletException(errorMessage);

		} catch (UtilException ue) {

        	String errorMessage = "Utility problem while intializing MetaCat Servlet: " 

        		+ ue.getMessage();

            logMetacat.error("MetaCatServlet.initSecondHalf - " + errorMessage);

            throw new ServletException(errorMessage);

        } 

	}

    /**

	 * Close all db connections from the pool

	 */

    public void destroy() {

    	Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

    	ServiceService.stopAllServices();

        // Close all db connection

        logMetacat.warn("MetaCatServlet.destroy - Destroying MetacatServlet");

        timer.cancel();

        IndexingQueue.getInstance().setMetacatRunning(false);

        DBConnectionPool.release();

    }

    /** Handle "GET" method requests from HTTP clients */

    public void doGet(HttpServletRequest request, HttpServletResponse response)

    throws ServletException, IOException {

        // Process the data and send back the response

        handleGetOrPost(request, response);

    }

    /** Handle "POST" method requests from HTTP clients */

    public void doPost(HttpServletRequest request, HttpServletResponse response)

    throws ServletException, IOException {

        // Process the data and send back the response

        handleGetOrPost(request, response);

    }

    /**

	 * Index the paths specified in the metacat.properties

	 */

    private void checkIndexPaths() {

    	Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

    	logMetacat.debug("MetaCatServlet.checkIndexPaths - starting....");

    	if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {

    		logMetacat.info("MetaCatServlet.checkIndexPaths - the pathquery is disabled and it does nothing for checking path_index");

            return;

        }

    	logMetacat.debug("MetaCatServlet.checkIndexPaths - after checking is the pathquery enabled or not...");

        Vector<String> pathsForIndexing = null;

        try {  

        	pathsForIndexing = SystemUtil.getPathsForIndexing();

        }

        catch (MetacatUtilException ue) {

        	pathsForIndexing = null;

            logMetacat.error("MetaCatServlet.checkIndexPaths - not find index paths.  Setting " 

            		+ "pathsForIndexing to null: " + ue.getMessage());

        }

        if (pathsForIndexing != null && !pathsForIndexing.isEmpty()) {

            logMetacat.debug("MetaCatServlet.checkIndexPaths - Indexing paths specified in metacat.properties....");

            DBConnection conn = null;

            int serialNumber = -1;

            PreparedStatement pstmt = null;

            PreparedStatement pstmt1 = null;

            ResultSet rs = null;

            for (String pathIndex : pathsForIndexing) {

                logMetacat.debug("MetaCatServlet.checkIndexPaths - Checking if '" + pathIndex  + "' is indexed.... ");

                try {

                    //check out DBConnection

                    conn = DBConnectionPool.

                            getDBConnection("MetaCatServlet.checkIndexPaths");

                    serialNumber = conn.getCheckOutSerialNumber();

                    pstmt = conn.prepareStatement(

                            "SELECT * FROM xml_path_index " + "WHERE path = ?");

                    pstmt.setString(1, pathIndex);

                    pstmt.execute();

                    rs = pstmt.getResultSet();

                    if (!rs.next()) {

                        logMetacat.debug("MetaCatServlet.checkIndexPaths - not indexed yet.");

                        rs.close();

                        pstmt.close();

                        conn.increaseUsageCount(1);

                        logMetacat.debug("MetaCatServlet.checkIndexPaths - Inserting following path in xml_path_index: "

                                + pathIndex);

                        if(pathIndex.indexOf("@")<0){

                            pstmt = conn.prepareStatement("SELECT DISTINCT n.docid, "

                                    + "n.nodedata, n.nodedatanumerical, n.nodedatadate, n.parentnodeid"

                                    + " FROM xml_nodes n, xml_index i WHERE"

                                    + " i.path = ? and n.parentnodeid=i.nodeid and"

                                    + " n.nodetype LIKE 'TEXT' order by n.parentnodeid");

                        } else {

                            pstmt = conn.prepareStatement("SELECT DISTINCT n.docid, "

                                    + "n.nodedata, n.nodedatanumerical, n.nodedatadate, n.parentnodeid"

                                    + " FROM xml_nodes n, xml_index i WHERE"

                                    + " i.path = ? and n.nodeid=i.nodeid and"

                                    + " n.nodetype LIKE 'ATTRIBUTE' order by n.parentnodeid");

                        }

                        pstmt.setString(1, pathIndex);

                        pstmt.execute();

                        rs = pstmt.getResultSet();

                        int count = 0;

                        logMetacat.debug("MetaCatServlet.checkIndexPaths - Executed the select statement for: "

                                + pathIndex);

                        try {

                            while (rs.next()) {

                                String docid = rs.getString(1);

                                String nodedata = rs.getString(2);

                                float nodedatanumerical = rs.getFloat(3);

                                Timestamp nodedatadate = rs.getTimestamp(4);

                                int parentnodeid = rs.getInt(5);

                                if (!nodedata.trim().equals("")) {

                                    pstmt1 = conn.prepareStatement(

                                            "INSERT INTO xml_path_index"

                                            + " (docid, path, nodedata, "

                                            + "nodedatanumerical, nodedatadate, parentnodeid)"

                                            + " VALUES (?, ?, ?, ?, ?, ?)");

                                    pstmt1.setString(1, docid);

                                    pstmt1.setString(2, pathIndex);

                                    pstmt1.setString(3, nodedata);

                                    pstmt1.setFloat(4, nodedatanumerical);

                                    pstmt1.setTimestamp(5, nodedatadate);

                                    pstmt1.setInt(6, parentnodeid);

                                    pstmt1.execute();

                                    pstmt1.close();

                                    count++;

                                }

                            }

                        } catch (Exception e) {

                            logMetacat.error("MetaCatServlet.checkIndexPaths - Exception:" + e.getMessage());

                            e.printStackTrace();

                        }

                        rs.close();

                        pstmt.close();

                        conn.increaseUsageCount(1);

                        logMetacat.info("MetaCatServlet.checkIndexPaths - Indexed " + count + " records from xml_nodes for '"

                                + pathIndex + "'");

                    } else {

                        logMetacat.debug("MetaCatServlet.checkIndexPaths - already indexed.");

                    }

                    rs.close();

                    pstmt.close();

                    conn.increaseUsageCount(1);

                } catch (Exception e) {

                    logMetacat.error("MetaCatServlet.checkIndexPaths - Error in MetaCatServlet.checkIndexPaths: "

                            + e.getMessage());

                }finally {

                    //check in DBonnection

                    DBConnectionPool.returnDBConnection(conn, serialNumber);

                }

            }

            logMetacat.debug("MetaCatServlet.checkIndexPaths - Path Indexing Completed");

        }

    }

    /**

	 * Control servlet response depending on the action parameter specified

	 */

	@SuppressWarnings("unchecked")

	private void handleGetOrPost(HttpServletRequest request,

			HttpServletResponse response) throws ServletException, IOException {

		Logger logMetacat = Logger.getLogger(MetaCatServlet.class);

		String requestEncoding = request.getCharacterEncoding();

		if (requestEncoding == null) {

			logMetacat.debug("null requestEncoding, setting to application default: " + DEFAULT_ENCODING);

			request.setCharacterEncoding(DEFAULT_ENCODING);

		}

		logMetacat.debug("requestEncoding: " + requestEncoding);

		// Update the last update time for this user if they are not new

		HttpSession httpSession = request.getSession(false);

		if (httpSession != null) {

		    SessionService.getInstance().touchSession(httpSession.getId());

		}

		// Each time metacat is called, check to see if metacat has been 

		// configured. If not then forward to the administration servlet

		if (!ConfigurationUtil.isMetacatConfigured()) {

			try {

				RequestUtil.forwardRequest(request, response, "/admin?action=configure", null);

				return;

			} catch (MetacatUtilException mue) {

				logMetacat.error("MetacatServlet.handleGetOrPost - utility error when forwarding to " + 

						"configuration screen: " + mue.getMessage());

				throw new ServletException("MetacatServlet.handleGetOrPost - utility error when forwarding to " + 

						"configuration screen: " + mue.getMessage());

			}

		}

		// if we get here, metacat is configured.  If we have not completed the 

		// second half of the initialization, do so now.  This allows us to initially

		// configure metacat without a restart.

		logMetacat.info("MetacatServlet.handleGetOrPost - the _fullyInitailzied value is "+_fullyInitialized);

		if (!_fullyInitialized) {

			initSecondHalf(request.getSession().getServletContext());

		}

		/*

		 * logMetacat.debug("Connection pool size: "

		 * +connPool.getSizeOfDBConnectionPool(),10); logMetacat.debug("Free

		 * DBConnection number: "

		 */

		// If all DBConnection in the pool are free and DBConnection pool

		// size is greater than initial value, shrink the connection pool

		// size to initial value

		DBConnectionPool.shrinkDBConnectionPoolSize();

		// Debug message to print out the method which have a busy DBConnection

		try {

			@SuppressWarnings("unused")

			DBConnectionPool pool = DBConnectionPool.getInstance();

//			pool.printMethodNameHavingBusyDBConnection();

		} catch (SQLException e) {

			logMetacat.error("MetaCatServlet.handleGetOrPost - Error in MetacatServlet.handleGetOrPost: " + e.getMessage());

			e.printStackTrace();

		}

		try {

			String ctype = request.getContentType();

			if (ctype != null && ctype.startsWith("multipart/form-data")) {

			    if(isReadOnly(response)) {

			        return;

			    }

				handler.handleMultipartForm(request, response);

				return;

			} 

			String name = null;

			String[] value = null;

			String[] docid = new String[3];

			Hashtable<String, String[]> params = new Hashtable<String, String[]>();

			// Check if this is a simple read request that doesn't use the

			// "action" syntax

			// These URLs are of the form:

			// http://localhost:8180/metacat/metacat/docid/skinname

			// e.g., http://localhost:8180/metacat/metacat/test.1.1/knb

			String pathInfo = request.getPathInfo();

			if (pathInfo != null) {

				String[] path = pathInfo.split("/");

				if (path.length > 1) {

					String docidToRead = path[1];

					String docs[] = new String[1];

					docs[0] = docidToRead;

					logMetacat.debug("MetaCatServlet.handleGetOrPost - READING DOCID FROM PATHINFO: " + docs[0]);

					params.put("docid", docs);

					String skin = null;

					if (path.length > 2) {

						skin = path[2];

						String skins[] = new String[1];

						skins[0] = skin;

						params.put("qformat", skins);

					}

					// attempt to redirect to metacatui (#view/{pid}) if not getting the raw XML

					// see: https://projects.ecoinformatics.org/ecoinfo/issues/6546

					if (!skin.equals("xml")) {

						String uiContext = PropertyService.getProperty("ui.context");

						String docidNoRev = DocumentUtil.getDocIdFromAccessionNumber(docidToRead);

						int rev = DocumentUtil.getRevisionFromAccessionNumber(docidToRead);

						String pid = null;

						try {

							pid = IdentifierManager.getInstance().getGUID(docidNoRev, rev);

							response.sendRedirect(SystemUtil.getServerURL() + "/" + uiContext + "/#view/" + pid );

							return;

						} catch (McdbDocNotFoundException nfe) {

							logMetacat.warn("Could not locate PID for docid: " + docidToRead, nfe);

						}

					}

					// otherwise carry on as usual

					handler.handleReadAction(params, request, response, "public", null, null);

					return;

				}

			}

			Enumeration<String> paramlist = 

				(Enumeration<String>) request.getParameterNames();

			while (paramlist.hasMoreElements()) {

				name = paramlist.nextElement();

				value = request.getParameterValues(name);

				// Decode the docid and mouse click information

				// THIS IS OBSOLETE -- I THINK -- REMOVE THIS BLOCK

				// 4/12/2007d

				// MBJ

				if (name.endsWith(".y")) {

					docid[0] = name.substring(0, name.length() - 2);

					params.put("docid", docid);

					name = "ypos";

				}

				if (name.endsWith(".x")) {

					name = "xpos";

				}

				params.put(name, value);

			}

			// handle param is emptpy

			if (params.isEmpty() || params == null) {

				return;

			}

			// if the user clicked on the input images, decode which image

			// was clicked then set the action.

			if (params.get("action") == null) {

				PrintWriter out = response.getWriter();

				response.setContentType("text/xml");

				out.println("<?xml version=\"1.0\"?>");

				out.println("<error>");

				out.println("Action not specified");

				out.println("</error>");

				out.close();

				return;

			}

			String action = (params.get("action"))[0];

			logMetacat.info("MetaCatServlet.handleGetOrPost - Action is: " + action);

			// This block handles session management for the servlet

			// by looking up the current session information for all actions

			// other than "login" and "logout"

			String userName = null;

			String password = null;

			String[] groupNames = null;

			String sessionId = null;

			name = null;

			// handle login action

			if (action.equals("login")) {

				//PrintWriter out = response.getWriter();

				Writer out = new OutputStreamWriter(response.getOutputStream(), DEFAULT_ENCODING);

				handler.handleLoginAction(out, params, request, response);

				out.close();

				// handle logout action

			} else if (action.equals("logout")) {

				Writer out = new OutputStreamWriter(response.getOutputStream(), DEFAULT_ENCODING);

				handler.handleLogoutAction(out, params, request, response);

				out.close();

				// handle session validate request

			} else if (action.equals("validatesession")) {

				Writer out = new OutputStreamWriter(response.getOutputStream(), DEFAULT_ENCODING);

				String idToValidate = null;

				String idsToValidate[] = params.get("sessionid");

				if (idsToValidate != null) {

					idToValidate = idsToValidate[0];

				} else {

					// use the sessionid from the cookie

					SessionData sessionData = RequestUtil.getSessionData(request);

					if (sessionData != null) {

						idToValidate = sessionData.getId();

					}

				}

				SessionService.getInstance().validateSession(out, response, idToValidate);

				out.close();

				// aware of session expiration on every request

			} else {

				SessionData sessionData = RequestUtil.getSessionData(request);

				if (sessionData != null) {

					userName = sessionData.getUserName();

					password = sessionData.getPassword();

					groupNames = sessionData.getGroupNames();

					sessionId = sessionData.getId();

				}

				logMetacat.info("MetaCatServlet.handleGetOrPost - The user is : " + userName);

			}

			// Now that we know the session is valid, we can delegate the

			// request to a particular action handler

			if (action.equals("query")) {

		        Writer out = new OutputStreamWriter(response.getOutputStream(), DEFAULT_ENCODING);

				handler.handleQuery(out, params, response, userName, groupNames, sessionId);

				out.close();

			} else if (action.equals("squery")) {

				Writer out = new OutputStreamWriter(response.getOutputStream(), DEFAULT_ENCODING);

				if (params.containsKey("query")) {

					handler.handleSQuery(out, params, response, userName, groupNames, sessionId);

					out.close();

				} else {

					out.write("Illegal action squery without \"query\" parameter");

					out.close();

				}

			} else if (action.trim().equals("spatial_query")) {

				logMetacat

						.debug("MetaCatServlet.handleGetOrPost - ******************* SPATIAL QUERY ********************");

				Writer out = new OutputStreamWriter(response.getOutputStream(), DEFAULT_ENCODING);

				handler.handleSpatialQuery(out, params, response, userName, groupNames, sessionId);

				out.close();

			} else if (action.trim().equals("dataquery")) {

				logMetacat.debug("MetaCatServlet.handleGetOrPost - ******************* DATA QUERY ********************");

				handler.handleDataquery(params, response, sessionId);

			} else if (action.trim().equals("editcart")) {

				logMetacat.debug("MetaCatServlet.handleGetOrPost - ******************* EDIT CART ********************");

				handler.handleEditCart(params, response, sessionId);

			} else if (action.equals("export")) {

				handler.handleExportAction(params, response, userName, groupNames, password);

			} else if (action.equals("read")) {

				if (params.get("archiveEntryName") != null) {

					ArchiveHandler.getInstance().readArchiveEntry(params, request,

							response, userName, password, groupNames);

				} else {

					handler.handleReadAction(params, request, response, userName, password,

							groupNames);

				}

			} else if (action.equals("readinlinedata")) {

				handler.handleReadInlineDataAction(params, request, response, userName, password,

						groupNames);

			} else if (action.equals("insert") || action.equals("update")) {

			    if(isReadOnly(response)) {

                    return;

                }

				PrintWriter out = response.getWriter();

				if ((userName != null) && !userName.equals("public")) {