/src/edu/ucsb/nceas/metacat/replication/ReplicationService.java - Annotate - Metacat - Ecoinformatics Redmine

metacat/src/edu/ucsb/nceas/metacat/replication/ReplicationService.java @ 6490

-            berkley
+/**
  *  '$RCSfile$'
  *    Purpose: A Class that implements replication for metacat
  *  Copyright: 2000 Regents of the University of California and the
  *             National Center for Ecological Analysis and Synthesis
  *    Authors: Chad Berkley
+ *
  *   '$Author$'
  *     '$Date$'
  * '$Revision$'
             jones
  * 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
-            berkley
+ */
-            daigle
+package edu.ucsb.nceas.metacat.replication;
             berkley
-            leinfelder
+import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
-            leinfelder
+import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-            leinfelder
+import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
 import java.io.StringReader;
 import java.io.Writer;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.text.SimpleDateFormat;
-            tao
+import java.util.Date;
-            leinfelder
+import java.util.Hashtable;
-            leinfelder
+import java.util.List;
-            leinfelder
+import java.util.Timer;
 import java.util.Vector;
             daigle
-            leinfelder
+import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
             berkley
-            leinfelder
+import org.apache.log4j.Logger;
-            leinfelder
+import org.dataone.service.types.v1.SystemMetadata;
-            leinfelder
+import org.dataone.service.util.TypeMarshaller;
-            leinfelder
+import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 import org.xml.sax.XMLReader;
-            daigle
+import edu.ucsb.nceas.metacat.DocInfoHandler;
 import edu.ucsb.nceas.metacat.DocumentImpl;
 import edu.ucsb.nceas.metacat.DocumentImplWrapper;
 import edu.ucsb.nceas.metacat.EventLog;
-            leinfelder
+import edu.ucsb.nceas.metacat.IdentifierManager;
 import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
-            daigle
+import edu.ucsb.nceas.metacat.McdbException;
-            daigle
+import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;
-            daigle
+import edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile;
-            daigle
+import edu.ucsb.nceas.metacat.accesscontrol.PermOrderException;
-            daigle
+import edu.ucsb.nceas.metacat.accesscontrol.XMLAccessDAO;
-            cjones
+import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
-            daigle
+import edu.ucsb.nceas.metacat.database.DBConnection;
 import edu.ucsb.nceas.metacat.database.DBConnectionPool;
 import edu.ucsb.nceas.metacat.database.DatabaseService;
-            leinfelder
+import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
-            daigle
+import edu.ucsb.nceas.metacat.properties.PropertyService;
-            daigle
+import edu.ucsb.nceas.metacat.shared.BaseService;
 import edu.ucsb.nceas.metacat.shared.HandlerException;
 import edu.ucsb.nceas.metacat.shared.ServiceException;
-            daigle
+import edu.ucsb.nceas.metacat.util.DocumentUtil;
-            daigle
+import edu.ucsb.nceas.metacat.util.MetacatUtil;
-            daigle
+import edu.ucsb.nceas.metacat.util.SystemUtil;
-            daigle
+import edu.ucsb.nceas.utilities.FileUtil;
-            daigle
+import edu.ucsb.nceas.utilities.GeneralPropertyException;
-            daigle
+import edu.ucsb.nceas.utilities.PropertyNotFoundException;
-            daigle
+public class ReplicationService extends BaseService {
             daigle
-            daigle
+	private static ReplicationService replicationService = null;
             sgarg
-            daigle
+	private long timeInterval;
 	private Date firstTime;
 	private boolean timedReplicationIsOn = false;
 	Timer replicationDaemon;
 	private static Vector<String> fileLocks = new Vector<String>();
 //	private Thread lockThread = null;
 	public static final String FORCEREPLICATEDELETE = "forcereplicatedelete";
 	private static String TIMEREPLICATION = "replication.timedreplication";
 	private static String TIMEREPLICATIONINTERVAl ="replication.timedreplicationinterval";
 	private static String FIRSTTIME = "replication.firsttimedreplication";
 	private static final int TIMEINTERVALLIMIT = 7200000;
 	public static final String REPLICATIONUSER = "replication";
             tao
-            daigle
+	public static final String REPLICATION_LOG_FILE_NAME = "metacatreplication.log";
 	public static String METACAT_REPL_ERROR_MSG = null;
 	private static Logger logReplication = Logger.getLogger("ReplicationLogging");
 	private static Logger logMetacat = Logger.getLogger(ReplicationService.class);
             tao
-            daigle
+	private ReplicationService() throws ServiceException {
 		_serviceName = "ReplicationService";
 		initialize();
+	}
 	private void initialize() throws ServiceException {
 		// initialize db connections to handle any update requests
 		// deltaT = util.getProperty("replication.deltaT");
 		// the default deltaT can be set from metacat.properties
 		// create a thread to do the delta-T check but don't execute it yet
 		replicationDaemon = new Timer(true);
 		try {
 			String replLogFile = PropertyService.getProperty("replication.logdir")
 				+ FileUtil.getFS() + REPLICATION_LOG_FILE_NAME;
 			METACAT_REPL_ERROR_MSG = "An error occurred in replication.  Please see the " +
 				"replication log at: " + replLogFile;
 			String timedRepIsOnStr =
 				PropertyService.getProperty("replication.timedreplication");
 			timedReplicationIsOn = (new Boolean(timedRepIsOnStr)).booleanValue();
 			logReplication.info("ReplicationService.initialize - The timed replication on is" + timedReplicationIsOn);
             berkley
-            daigle
+			String timeIntervalStr =
 				PropertyService.getProperty("replication.timedreplicationinterval");
 			timeInterval = (new Long(timeIntervalStr)).longValue();
 			logReplication.info("ReplicationService.initialize - The timed replication time Interval is " + timeInterval);
             tao
-            daigle
+			String firstTimeStr =
 				PropertyService.getProperty("replication.firsttimedreplication");
 			logReplication.info("ReplicationService.initialize - first replication time form property is " + firstTimeStr);
 			firstTime = ReplicationHandler.combinateCurrentDateAndGivenTime(firstTimeStr);
             tao
-            daigle
+			logReplication.info("ReplicationService.initialize - After combine current time, the real first time is "
 					+ firstTime.toString() + " minisec");
             tao
-            daigle
+			// set up time replication if it is on
 			if (timedReplicationIsOn) {
 				replicationDaemon.scheduleAtFixedRate(new ReplicationHandler(),
 						firstTime, timeInterval);
 				logReplication.info("ReplicationService.initialize - deltaT handler started with rate="
 						+ timeInterval + " mini seconds at " + firstTime.toString());
+			}
             tao
-            daigle
+		} catch (PropertyNotFoundException pnfe) {
 			throw new ServiceException(
 					"ReplicationService.initialize - Property error while instantiating "
 							+ "replication service: " + pnfe.getMessage());
 		} catch (HandlerException he) {
 			throw new ServiceException(
 					"ReplicationService.initialize - Handler error while instantiating "
 							+ "replication service" + he.getMessage());
+		}
+	}
             tao
-            daigle
+	/**
 	 * Get the single instance of SessionService.
+	 *
 	 * @return the single instance of SessionService
 	 */
 	public static ReplicationService getInstance() throws ServiceException {
 		if (replicationService == null) {
 			replicationService = new ReplicationService();
+		}
 		return replicationService;
+	}
             tao
-            daigle
+	public boolean refreshable() {
 		return true;
+	}
             tao
-            daigle
+	protected void doRefresh() throws ServiceException {
 		return;
+	}
 	public void stop() throws ServiceException{
+	}
             bojilova
-            daigle
+	public void stopReplication() throws ServiceException {
 	      //stop the replication server
 	      replicationDaemon.cancel();
 	      replicationDaemon = new Timer(true);
 	      timedReplicationIsOn = false;
 	      try {
 	    	  PropertyService.setProperty("replication.timedreplication", (new Boolean(timedReplicationIsOn)).toString());
 	      } catch (GeneralPropertyException gpe) {
 	    	  logReplication.warn("ReplicationService.stopReplication - Could not set replication.timedreplication property: " + gpe.getMessage());
+	      }
             daigle
-            daigle
+	      logReplication.info("ReplicationService.stopReplication - deltaT handler stopped");
 		return;
+	}
 	protected void startReplication(Hashtable<String, String[]> params) throws ServiceException {
             tao
-            daigle
+	       String firstTimeStr = "";
 	      //start the replication server
 	       if ( params.containsKey("rate") ) {
 	        timeInterval = new Long(
 	               new String(((String[])params.get("rate"))[0])).longValue();
 	        if(timeInterval < TIMEINTERVALLIMIT) {
 	            //deltaT<30 is a timing mess!
 	            timeInterval = TIMEINTERVALLIMIT;
 	            throw new ServiceException("Replication deltaT rate cannot be less than "+
 	                    TIMEINTERVALLIMIT + " millisecs and system automatically setup the rate to "+TIMEINTERVALLIMIT);
+	        }
 	      } else {
 	        timeInterval = TIMEINTERVALLIMIT ;
+	      }
 	      logReplication.info("ReplicationService.startReplication - New rate is: " + timeInterval + " mini seconds.");
 	      if ( params.containsKey("firsttime"))
+	      {
 	         firstTimeStr = ((String[])params.get("firsttime"))[0];
 	         try
+	         {
 	           firstTime = ReplicationHandler.combinateCurrentDateAndGivenTime(firstTimeStr);
 	           logReplication.info("ReplicationService.startReplication - The first time setting is "+firstTime.toString());
+	         }
 	         catch (HandlerException e)
+	         {
 	            throw new ServiceException(e.getMessage());
+	         }
 	         logReplication.warn("After combine current time, the real first time is "
 	                                  +firstTime.toString()+" minisec");
+	      }
 	      else
+	      {
 	    	  logMetacat.error("ReplicationService.startReplication - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 	          logReplication.error("ReplicationService.startReplication - You should specify the first time " +
 	                                  "to start a time replication");
 	          return;
+	      }
 	      timedReplicationIsOn = true;
 	      try {
 	      // save settings to property file
 	      PropertyService.setProperty(TIMEREPLICATION, (new Boolean(timedReplicationIsOn)).toString());
 	      // note we couldn't use firstTime object because it has date info
 	      // we only need time info such as 10:00 PM
 	      PropertyService.setProperty(FIRSTTIME, firstTimeStr);
 	      PropertyService.setProperty(TIMEREPLICATIONINTERVAl, (new Long(timeInterval)).toString());
 	      } catch (GeneralPropertyException gpe) {
 	    	  logReplication.warn("ReplicationService.startReplication - Could not set property: " + gpe.getMessage());
+	      }
 	      replicationDaemon.cancel();
 	      replicationDaemon = new Timer(true);
 	      replicationDaemon.scheduleAtFixedRate(new ReplicationHandler(), firstTime,
 	                                            timeInterval);
 	      logReplication.info("ReplicationService.startReplication - deltaT handler started with rate=" +
 	                                    timeInterval + " milliseconds at " +firstTime.toString());
             bojilova
             daigle
 	public void runOnce() throws ServiceException {
 	      //updates this server exactly once
 	      replicationDaemon.schedule(new ReplicationHandler(), 0);
+	}
             tao
-            daigle
+	/**
 	 * This method can add, delete and list the servers currently included in
 	 * xml_replication.
 	 * action           subaction            other needed params
 	 * ---------------------------------------------------------
 	 * servercontrol    add                  server
 	 * servercontrol    delete               server
 	 * servercontrol    list
 	 */
-            leinfelder
+	protected static void handleServerControlRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response) {
 		String subaction = ((String[]) params.get("subaction"))[0];
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
 		String replicate = null;
 		String server = null;
 		String dataReplicate = null;
-            leinfelder
+		String systemMetadataReplicate = null;
-            daigle
+		String hub = null;
-            leinfelder
+		Writer out = null;
-            daigle
+		try {
-            leinfelder
+			response.setContentType("text/xml");
 			out = response.getWriter();
-            daigle
+			//conn = util.openDBConnection();
 			dbConn = DBConnectionPool
 					.getDBConnection("MetacatReplication.handleServerControlRequest");
 			serialNumber = dbConn.getCheckOutSerialNumber();
             bojilova
-            daigle
+			// add server to server list
 			if (subaction.equals("add")) {
 				replicate = ((String[]) params.get("replicate"))[0];
 				server = ((String[]) params.get("server"))[0];
             tao
-            daigle
+				//Get data replication value
 				dataReplicate = ((String[]) params.get("datareplicate"))[0];
-            leinfelder
+				//Get system metadata replication value
 				systemMetadataReplicate = ((String[]) params.get("systemmetadatareplicate"))[0];
-            daigle
+				//Get hub value
 				hub = ((String[]) params.get("hub"))[0];
             bojilova
-            jones
+				String toDateSql = DatabaseService.getInstance().getDBAdapter().toDate("01/01/1980","MM/DD/YYYY");
-            daigle
+				String sql = "INSERT INTO xml_replication "
-            leinfelder
+						+ "(server, last_checked, replicate, datareplicate, systemmetadatareplicate, hub) "
 						+ "VALUES (?," + toDateSql + ",?,?,?,?)";
             daigle
 				pstmt = dbConn.prepareStatement(sql);
 				pstmt.setString(1, server);
 				pstmt.setInt(2, Integer.parseInt(replicate));
 				pstmt.setInt(3, Integer.parseInt(dataReplicate));
-            leinfelder
+				pstmt.setInt(4, Integer.parseInt(systemMetadataReplicate));
 				pstmt.setInt(5, Integer.parseInt(hub));
             daigle
 				String sqlReport = "XMLAccessAccess.getXMLAccessForDoc - SQL: " + sql;
 				sqlReport += " [" + server + "," + replicate +
 					"," + dataReplicate + "," + hub + "]";
 				logMetacat.info(sqlReport);
-            daigle
+				pstmt.execute();
 				pstmt.close();
 				dbConn.commit();
-            leinfelder
+				out.write("Server " + server + " added");
-            daigle
+				response.setContentType("text/html");
-            leinfelder
+				out.write("<html><body><table border=\"1\">");
-            leinfelder
+				out.write("<tr><td><b>server</b></td>");
 				out.write("<td><b>last_checked</b></td>");
 				out.write("<td><b>replicate</b></td>");
-            leinfelder
+				out.write("<td><b>datareplicate</b></td>");
-            leinfelder
+				out.write("<td><b>systemmetadatareplicate</b></td>");
-            leinfelder
+				out.write("<td><b>hub</b></td></tr>");
-            leinfelder
+				pstmt = dbConn.prepareStatement("SELECT serverid, server, last_checked, replicate, datareplicate, systemmetadatareplicate, hub FROM xml_replication");
-            daigle
+				//increase dbconnection usage
 				dbConn.increaseUsageCount(1);
             tao
-            daigle
+				pstmt.execute();
 				ResultSet rs = pstmt.getResultSet();
 				boolean tablehasrows = rs.next();
 				while (tablehasrows) {
-            leinfelder
+					out.write("<tr><td>" + rs.getString(2) + "</td><td>");
 					out.write(rs.getString(3) + "</td><td>");
 					out.write(rs.getString(4) + "</td><td>");
 					out.write(rs.getString(5) + "</td><td>");
-            leinfelder
+					out.write(rs.getString(6) + "</td><td>");
 					out.write(rs.getString(7) + "</td></tr>");
             bojilova
-            daigle
+					tablehasrows = rs.next();
+				}
-            leinfelder
+				out.write("</table></body></html>");
             bojilova
-            daigle
+				// download certificate with the public key on this server
 				// and import it as a trusted certificate
 				String certURL = ((String[]) params.get("certificate"))[0];
-            daigle
+				if (certURL != null && !certURL.equals("")) {
 					downloadCertificate(certURL);
+				}
             bojilova
-            daigle
+				// delete server from server list
 			} else if (subaction.equals("delete")) {
 				server = ((String[]) params.get("server"))[0];
 				pstmt = dbConn.prepareStatement("DELETE FROM xml_replication "
 						+ "WHERE server LIKE '" + server + "'");
 				pstmt.execute();
 				pstmt.close();
 				dbConn.commit();
-            leinfelder
+				out.write("Server " + server + " deleted");
-            daigle
+				response.setContentType("text/html");
-            leinfelder
+				out.write("<html><body><table border=\"1\">");
-            leinfelder
+				out.write("<tr><td><b>server</b></td>");
 				out.write("<td><b>last_checked</b></td>");
 				out.write("<td><b>replicate</b></td>");
-            leinfelder
+				out.write("<td><b>datareplicate</b></td>");
-            leinfelder
+				out.write("<td><b>systemmetadatareplicate</b></td>");
-            leinfelder
+				out.write("<td><b>hub</b></td></tr>");
             bojilova
-            leinfelder
+				pstmt = dbConn.prepareStatement("SELECT serverid, server, last_checked, replicate, datareplicate, systemmetadatareplicate, hub FROM xml_replication");
-            daigle
+				//increase dbconnection usage
 				dbConn.increaseUsageCount(1);
 				pstmt.execute();
 				ResultSet rs = pstmt.getResultSet();
 				boolean tablehasrows = rs.next();
 				while (tablehasrows) {
-            leinfelder
+					out.write("<tr><td>" + rs.getString(2) + "</td><td>");
 					out.write(rs.getString(3) + "</td><td>");
 					out.write(rs.getString(4) + "</td><td>");
 					out.write(rs.getString(5) + "</td><td>");
-            leinfelder
+					out.write(rs.getString(6) + "</td><td>");
 					out.write(rs.getString(7) + "</td></tr>");
-            daigle
+					tablehasrows = rs.next();
+				}
-            leinfelder
+				out.write("</table></body></html>");
             bojilova
-            daigle
+				// list servers in server list
 			} else if (subaction.equals("list")) {
 				response.setContentType("text/html");
-            leinfelder
+				out.write("<html><body><table border=\"1\">");
-            leinfelder
+				out.write("<tr><td><b>server</b></td>");
 				out.write("<td><b>last_checked</b></td>");
 				out.write("<td><b>replicate</b></td>");
-            leinfelder
+				out.write("<td><b>datareplicate</b></td>");
-            leinfelder
+				out.write("<td><b>systemmetadatareplicate</b></td>");
-            leinfelder
+				out.write("<td><b>hub</b></td></tr>");
-            leinfelder
+				pstmt = dbConn.prepareStatement("SELECT serverid, server, last_checked, replicate, datareplicate, systemmetadatareplicate, hub FROM xml_replication");
-            daigle
+				pstmt.execute();
 				ResultSet rs = pstmt.getResultSet();
 				boolean tablehasrows = rs.next();
 				while (tablehasrows) {
-            leinfelder
+					out.write("<tr><td>" + rs.getString(2) + "</td><td>");
 					out.write(rs.getString(3) + "</td><td>");
 					out.write(rs.getString(4) + "</td><td>");
 					out.write(rs.getString(5) + "</td><td>");
-            leinfelder
+					out.write(rs.getString(6) + "</td><td>");
 					out.write(rs.getString(7) + "</td></tr>");
-            daigle
+					tablehasrows = rs.next();
+				}
-            leinfelder
+				out.write("</table></body></html>");
-            daigle
+			} else {
             tao
-            leinfelder
+				out.write("<error>Unkonwn subaction</error>");
             tao
             daigle
 			pstmt.close();
 			//conn.close();
             tao
-            daigle
+		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleServerControlRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleServerControlRequest - Error in "
 					+ "MetacatReplication.handleServerControlRequest " + e.getMessage());
 			e.printStackTrace(System.out);
 		} finally {
 			try {
 				pstmt.close();
 			}//try
 			catch (SQLException ee) {
 				logMetacat.error("ReplicationService.handleServerControlRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.handleServerControlRequest - Error in MetacatReplication.handleServerControlRequest to close pstmt "
 						+ ee.getMessage());
 			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
-            leinfelder
+			if (out != null) {
 				try {
 					out.close();
 				} catch (IOException e) {
 					logMetacat.error(e.getMessage(), e);
+				}
+			}
-            daigle
+		}//finally
             tao
             daigle
             tao
-            daigle
+	// download certificate with the public key from certURL and
-            daigle
+	// upload it onto this server; it then must be imported as a
 	// trusted certificate
-            daigle
+	private static void downloadCertificate(String certURL) throws FileNotFoundException,
-            daigle
+			IOException, MalformedURLException, PropertyNotFoundException {
             daigle
-            daigle
+		// the path to be uploaded to
-            daigle
+		String certPath = SystemUtil.getContextDir();
             tao
-            daigle
+		// get filename from the URL of the certificate
 		String filename = certURL;
 		int slash = Math.max(filename.lastIndexOf('/'), filename.lastIndexOf('\\'));
 		if (slash > -1) {
 			filename = filename.substring(slash + 1);
+		}
             tao
-            daigle
+		// open file output strem to write the input into it
 		File f = new File(certPath, filename);
 		synchronized (f) {
 			try {
 				if (f.exists()) {
 					throw new IOException("File already exist: " + f.getCanonicalFile());
 					// if ( f.exists() && !f.canWrite() ) {
 					// throw new IOException("Not writable: " +
 					// f.getCanonicalFile());
+				}
 			} catch (SecurityException se) {
 				// if a security manager exists,
 				// its checkRead method is called for f.exist()
 				// or checkWrite method is called for f.canWrite()
 				throw se;
+			}
             tao
-            daigle
+			// create a buffered byte output stream
 			// that uses a default-sized output buffer
 			FileOutputStream fos = new FileOutputStream(f);
 			BufferedOutputStream out = new BufferedOutputStream(fos);
             bojilova
-            daigle
+			// this should be http url
 			URL url = new URL(certURL);
 			BufferedInputStream bis = null;
 			try {
 				bis = new BufferedInputStream(url.openStream());
 				byte[] buf = new byte[4 * 1024]; // 4K buffer
 				int b = bis.read(buf);
 				while (b != -1) {
 					out.write(buf, 0, b);
 					b = bis.read(buf);
+				}
 			} finally {
 				if (bis != null)
 					bis.close();
+			}
 			// the input and the output streams must be closed
 			bis.close();
 			out.flush();
 			out.close();
 			fos.close();
 		} // end of synchronized(f)
+	}
             tao
-            daigle
+	/**
-            daigle
+	 * when a forcereplication request comes in, local host sends a read request
 	 * to the requesting server (remote server) for the specified docid. Then
 	 * store it in local database.
 	 */
-            leinfelder
+	protected static void handleForceReplicateRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response,
 			HttpServletRequest request) {
 		String server = ((String[]) params.get("server"))[0]; // the server that
 		String docid = ((String[]) params.get("docid"))[0]; // sent the document
 		String dbaction = "UPDATE"; // the default action is UPDATE
 		//    boolean override = false;
 		//    int serverCode = 1;
 		DBConnection dbConn = null;
 		int serialNumber = -1;
-            berkley
+		String docName = null;
             tao
-            daigle
+		try {
 			//if the url contains a dbaction then the default action is overridden
 			if (params.containsKey("dbaction")) {
 				dbaction = ((String[]) params.get("dbaction"))[0];
 				//serverCode = MetacatReplication.getServerCode(server);
 				//override = true; //we are now overriding the default action
+			}
 			logReplication.info("ReplicationService.handleForceReplicateRequest - Force replication request from: " + server);
 			logReplication.info("ReplicationService.handleForceReplicateRequest - Force replication docid: " + docid);
 			logReplication.info("ReplicationService.handleForceReplicateRequest - Force replication action: " + dbaction);
 			// sending back read request to remote server
 			URL u = new URL("https://" + server + "?server="
 					+ MetacatUtil.getLocalReplicationServerName() + "&action=read&docid="
 					+ docid);
 			String xmldoc = ReplicationService.getURLContent(u);
             tao
-            daigle
+			// get the document info from server
 			URL docinfourl = new URL("https://" + server + "?server="
 					+ MetacatUtil.getLocalReplicationServerName()
 					+ "&action=getdocumentinfo&docid=" + docid);
             berkley
             tao
-            daigle
+			String docInfoStr = ReplicationService.getURLContent(docinfourl);
             leinfelder
-            daigle
+			//dih is the parser for the docinfo xml format
 			DocInfoHandler dih = new DocInfoHandler();
 			XMLReader docinfoParser = ReplicationHandler.initParser(dih);
 			docinfoParser.parse(new InputSource(new StringReader(docInfoStr)));
 			//      Hashtable<String,Vector<AccessControlForSingleFile>> docinfoHash = dih.getDocInfo();
 			Hashtable<String, String> docinfoHash = dih.getDocInfo();
             leinfelder
-            daigle
+			// Get home server of this docid
 			String homeServer = (String) docinfoHash.get("home_server");
             berkley
-            leinfelder
+        	// replicate doc contents
-            daigle
+			String createdDate = (String) docinfoHash.get("date_created");
 			String updatedDate = (String) docinfoHash.get("date_updated");
 			logReplication.info("ReplicationService.handleForceReplicateRequest - homeServer: " + homeServer);
 			// Get Document type
 			String docType = (String) docinfoHash.get("doctype");
 			logReplication.info("ReplicationService.handleForceReplicateRequest - docType: " + docType);
 			String parserBase = null;
 			// this for eml2 and we need user eml2 parser
 			if (docType != null
 					&& (docType.trim()).equals(DocumentImpl.EML2_0_0NAMESPACE)) {
 				logReplication.warn("ReplicationService.handleForceReplicateRequest - This is an eml200 document!");
 				parserBase = DocumentImpl.EML200;
 			} else if (docType != null
 					&& (docType.trim()).equals(DocumentImpl.EML2_0_1NAMESPACE)) {
 				logReplication.warn("ReplicationService.handleForceReplicateRequest - This is an eml2.0.1 document!");
 				parserBase = DocumentImpl.EML200;
 			} else if (docType != null
 					&& (docType.trim()).equals(DocumentImpl.EML2_1_0NAMESPACE)) {
 				logReplication.warn("ReplicationService.handleForceReplicateRequest - This is an eml2.1.0 document!");
 				parserBase = DocumentImpl.EML210;
-            leinfelder
+			} else if (docType != null
 					&& (docType.trim()).equals(DocumentImpl.EML2_1_1NAMESPACE)) {
 				logReplication.warn("ReplicationService.handleForceReplicateRequest - This is an eml2.1.1 document!");
 				parserBase = DocumentImpl.EML210;
             daigle
 			logReplication.warn("ReplicationService.handleForceReplicateRequest - The parserBase is: " + parserBase);
             tao
-            daigle
+			// Get DBConnection from pool
 			dbConn = DBConnectionPool
 					.getDBConnection("MetacatReplication.handleForceReplicateRequest");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			// write the document to local database
 			DocumentImplWrapper wrapper = new DocumentImplWrapper(parserBase, false);
-            leinfelder
+			//try this independently so we can set access even if the update action is invalid (i.e docid has not changed)
-            daigle
+			try {
-            daigle
+				wrapper.writeReplication(dbConn, xmldoc, null, null,
-            leinfelder
+						dbaction, docid, null, null, homeServer, server, createdDate,
-            daigle
+						updatedDate);
-            daigle
+			} finally {
             tao
-            daigle
+				//process extra access rules before dealing with the write exception (doc exist already)
 		        Vector<XMLAccessDAO> accessControlList = dih.getAccessControlList();
 		        if (accessControlList != null) {
 		        	AccessControlForSingleFile acfsf = new AccessControlForSingleFile(docid);
 		        	for (XMLAccessDAO xmlAccessDAO : accessControlList) {
 		        		if (!acfsf.accessControlExists(xmlAccessDAO)) {
 		        			acfsf.insertPermissions(xmlAccessDAO);
 							logReplication.info("ReplicationService.handleForceReplicateRequest - document " + docid
 									+ " permissions added to DB");
+		        		}
+		            }
+		        }
             leinfelder
 		        // process the real owner and updater
 				String user = (String) docinfoHash.get("user_owner");
 				String updated = (String) docinfoHash.get("user_updated");
 		        updateUserOwner(dbConn, docid, user, updated);
             tao
-            daigle
+				logReplication.info("ReplicationService.handleForceReplicateRequest - document " + docid + " added to DB with "
 						+ "action " + dbaction);
             berkley
-            leinfelder
+				EventLog.getInstance().log(request.getRemoteAddr(), REPLICATIONUSER, docid, dbaction);
             daigle
-            daigle
+		} catch (SQLException sqle) {
-            daigle
+			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
-            daigle
+			logReplication.error("ReplicationService.handleForceReplicateRequest - SQL error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + sqle.getMessage());
 		} catch (MalformedURLException mue) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - URL error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + mue.getMessage());
 		} catch (SAXException se) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - SAX parsing error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + se.getMessage());
 		} catch (HandlerException he) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - Handler error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + he.getMessage());
 		} catch (IOException ioe) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - I/O error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + ioe.getMessage());
 		} catch (PermOrderException poe) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - Permissions order error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + poe.getMessage());
 		} catch (AccessControlException ace) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - Permissions order error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + ace.getMessage());
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - General error when adding doc " + docid +
 					" to DB with action " + dbaction + ": " + e.getMessage());
 		} finally {
-            daigle
+			// Return the checked out DBConnection
 			DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 		}//finally
+	}
             tao
-            daigle
+	/*
 	 * when a forcereplication delete request comes in, local host will delete this
 	 * document
 	 */
-            leinfelder
+	protected static void handleForceReplicateDeleteRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response,
 			HttpServletRequest request) {
 		String server = ((String[]) params.get("server"))[0]; // the server that
 		String docid = ((String[]) params.get("docid"))[0]; // sent the document
 		try {
 			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - force replication delete request from " + server);
 			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - force replication delete docid " + docid);
 			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - Force replication delete request from: " + server);
 			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - Force replication delete docid: " + docid);
 			DocumentImpl.delete(docid, null, null, server);
 			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - document " + docid + " was successfully deleted ");
 			EventLog.getInstance().log(request.getRemoteAddr(), REPLICATIONUSER, docid,
 					"delete");
 			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - document " + docid + " was successfully deleted ");
-            cjones
+		} catch (McdbDocNotFoundException e) {
 			logMetacat.error("ReplicationService.handleForceReplicateDeleteRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("document " + docid
 					+ " failed to delete because " + e.getMessage());
 			logReplication.error("ReplicationService.handleForceReplicateDeleteRequest - error: " + e.getMessage());
 		} catch (InsufficientKarmaException e) {
 			logMetacat.error("ReplicationService.handleForceReplicateDeleteRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("document " + docid
 					+ " failed to delete because " + e.getMessage());
 			logReplication.error("ReplicationService.handleForceReplicateDeleteRequest - error: " + e.getMessage());
 		} catch (SQLException e) {
 			logMetacat.error("ReplicationService.handleForceReplicateDeleteRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("document " + docid
 					+ " failed to delete because " + e.getMessage());
 			logReplication.error("ReplicationService.handleForceReplicateDeleteRequest - error: " + e.getMessage());
-            daigle
+		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleForceReplicateDeleteRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("document " + docid
 					+ " failed to delete because " + e.getMessage());
 			logReplication.error("ReplicationService.handleForceReplicateDeleteRequest - error: " + e.getMessage());
             tao
-            daigle
+		}//catch
             tao
             daigle
             tao
-            daigle
+	/**
 	 * when a forcereplication data file request comes in, local host sends a
 	 * readdata request to the requesting server (remote server) for the specified
 	 * docid. Then store it in local database and file system
 	 */
 	protected static void handleForceReplicateDataFileRequest(Hashtable<String, String[]> params,
 			HttpServletRequest request) {
             tao
-            daigle
+		//make sure there is some parameters
 		if (params.isEmpty()) {
 			return;
+		}
 		// Get remote server
 		String server = ((String[]) params.get("server"))[0];
 		// the docid should include rev number
 		String docid = ((String[]) params.get("docid"))[0];
 		// Make sure there is a docid and server
 		if (docid == null || server == null || server.equals("")) {
 			logMetacat.error("ReplicationService.handleForceReplicateDataFileRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateDataFileRequest - Didn't specify docid or server for replication");
 			return;
+		}
             tao
-            daigle
+		// Overide or not
 		//    boolean override = false;
 		// dbaction - update or insert
 		String dbaction = null;
             tao
-            daigle
+		try {
 			//docid was switch to two parts uinque code and rev
 			//String uniqueCode=MetacatUtil.getDocIdFromString(docid);
 			//int rev=MetacatUtil.getVersionFromString(docid);
 			if (params.containsKey("dbaction")) {
 				dbaction = ((String[]) params.get("dbaction"))[0];
 			} else//default value is update
+			{
 				dbaction = "update";
+			}
             tao
-            daigle
+			logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - Force replication request from: " + server);
 			logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - Force replication docid: " + docid);
 			logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - Force replication action: " + dbaction);
 			// get the document info from server
 			URL docinfourl = new URL("https://" + server + "?server="
 					+ MetacatUtil.getLocalReplicationServerName()
 					+ "&action=getdocumentinfo&docid=" + docid);
             tao
-            daigle
+			String docInfoStr = ReplicationService.getURLContent(docinfourl);
             leinfelder
-            daigle
+			//dih is the parser for the docinfo xml format
 			DocInfoHandler dih = new DocInfoHandler();
 			XMLReader docinfoParser = ReplicationHandler.initParser(dih);
 			docinfoParser.parse(new InputSource(new StringReader(docInfoStr)));
 			Hashtable<String, String> docinfoHash = dih.getDocInfo();
             leinfelder
-            daigle
+			String docName = (String) docinfoHash.get("docname");
             tao
-            daigle
+			String docType = (String) docinfoHash.get("doctype");
             tao
-            daigle
+			String docHomeServer = (String) docinfoHash.get("home_server");
             tao
-            daigle
+			String createdDate = (String) docinfoHash.get("date_created");
             tao
-            daigle
+			String updatedDate = (String) docinfoHash.get("date_updated");
 			logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - docHomeServer of datafile: " + docHomeServer);
 			if (dbaction.equals("insert") || dbaction.equals("update")) {
 				//Get data file and store it into local file system.
 				// sending back readdata request to server
 				URL url = new URL("https://" + server + "?server="
 						+ MetacatUtil.getLocalReplicationServerName()
 						+ "&action=readdata&docid=" + docid);
 				String datafilePath = PropertyService
 						.getProperty("application.datafilepath");
 				Exception writeException = null;
 				//register data file into xml_documents table and wite data file
 				//into file system
 				try {
 					DocumentImpl.writeDataFileInReplication(url.openStream(),
-            leinfelder
+							datafilePath, docName, docType, docid, null, docHomeServer,
-            daigle
+							server, DocumentImpl.DOCUMENTTABLE, false, createdDate,
 							updatedDate);
 				} catch (Exception e) {
 					writeException = e;
+				}
             daigle
-            leinfelder
+				// process the real owner and updater
 				DBConnection dbConn = DBConnectionPool.getDBConnection("ReplicationService.handleForceDataFileRequest");
 		        int serialNumber = dbConn.getCheckOutSerialNumber();
 		        dbConn.setAutoCommit(false);
 				String user = (String) docinfoHash.get("user_owner");
 				String updated = (String) docinfoHash.get("user_updated");
 		        updateUserOwner(dbConn, docid, user, updated);
 		        DBConnectionPool.returnDBConnection(dbConn, serialNumber);
-            daigle
+		        Vector<XMLAccessDAO> accessControlList = dih.getAccessControlList();
 		        if (accessControlList != null) {
 		        	AccessControlForSingleFile acfsf = new AccessControlForSingleFile(docid);
 		        	for (XMLAccessDAO xmlAccessDAO : accessControlList) {
 		        		if (!acfsf.accessControlExists(xmlAccessDAO)) {
 		        			acfsf.insertPermissions(xmlAccessDAO);
 							logReplication.info("ReplicationService.handleForceReplicateRequest - document " + docid
-            daigle
+									+ " permissions added to DB");
             daigle
+		            }
+		        }
             daigle
 				if (writeException != null) {
 					throw writeException;
+				}
 				logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - datafile " + docid + " added to DB with "
 						+ "action " + dbaction);
 				EventLog.getInstance().log(request.getRemoteAddr(), REPLICATIONUSER,
 						docid, dbaction);
+			}
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleForceReplicateDataFileRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleForceReplicateDataFileRequest - Datafile " + docid
 					+ " failed to added to DB with " + "action " + dbaction + " because "
 					+ e.getMessage());
 			logReplication.error("ReplicationService.handleForceReplicateDataFileRequest - ERROR in MetacatReplication.handleForceDataFileReplicate"
 					+ "Request(): " + e.getMessage());
             leinfelder
             daigle
             tao
-            daigle
+	/**
 	 * Grants or denies a lock to a requesting host.
 	 * The servlet parameters of interrest are:
 	 * docid: the docid of the file the lock is being requested for
 	 * currentdate: the timestamp of the document on the remote server
+	 *
 	 */
-            leinfelder
+	protected static void handleGetLockRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response) {
             tao
-            daigle
+		try {
             tao
-            daigle
+			String docid = ((String[]) params.get("docid"))[0];
 			String remoteRev = ((String[]) params.get("updaterev"))[0];
 			DocumentImpl requestDoc = new DocumentImpl(docid);
 			logReplication.info("ReplicationService.handleGetLockRequest - lock request for " + docid);
 			int localRevInt = requestDoc.getRev();
 			int remoteRevInt = Integer.parseInt(remoteRev);
             tao
-            leinfelder
+			// get a writer for sending back to response
 			response.setContentType("text/xml");
 			Writer out = response.getWriter();
-            daigle
+			if (remoteRevInt >= localRevInt) {
 				if (!fileLocks.contains(docid)) { //grant the lock if it is not already locked
 					fileLocks.add(0, docid); //insert at the beginning of the queue Vector
 					//send a message back to the the remote host authorizing the insert
-            leinfelder
+					out.write("<lockgranted><docid>" + docid
-            daigle
+									+ "</docid></lockgranted>");
 					//          lockThread = new Thread(this);
 					//          lockThread.setPriority(Thread.MIN_PRIORITY);
 					//          lockThread.start();
 					logReplication.info("ReplicationService.handleGetLockRequest - lock granted for " + docid);
 				} else { //deny the lock
-            leinfelder
+					out.write("<filelocked><docid>" + docid + "</docid></filelocked>");
-            daigle
+					logReplication.info("ReplicationService.handleGetLockRequest - lock denied for " + docid
 							+ "reason: file already locked");
+				}
 			} else {//deny the lock.
-            leinfelder
+				out.write("<outdatedfile><docid>" + docid + "</docid></filelocked>");
-            daigle
+				logReplication.info("ReplicationService.handleGetLockRequest - lock denied for " + docid
 						+ "reason: client has outdated file");
+			}
-            leinfelder
+			out.close();
-            daigle
+			//conn.close();
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleGetLockRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetLockRequest - error requesting file lock from MetacatReplication."
 					+ "handleGetLockRequest: " + e.getMessage());
 			e.printStackTrace(System.out);
+		}
+	}
             tao
-            daigle
+	/**
 	 * Sends all of the xml_documents information encoded in xml to a requestor
 	 * the format is:
 	 * <!ELEMENT documentinfo (docid, docname, doctype, doctitle, user_owner,
 	 *                  user_updated, home_server, public_access, rev)/>
 	 * all of the subelements of document info are #PCDATA
 	 */
-            leinfelder
+	protected static void handleGetDocumentInfoRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response) {
 		String docid = ((String[]) (params.get("docid")))[0];
 		StringBuffer sb = new StringBuffer();
             tao
-            daigle
+		try {
 			DocumentImpl doc = new DocumentImpl(docid);
 			sb.append("<documentinfo><docid>").append(docid);
-            berkley
+			sb.append("</docid>");
 			sb.append("<docname>").append(doc.getDocname());
-            daigle
+			sb.append("</docname><doctype>").append(doc.getDoctype());
 			sb.append("</doctype>");
 			sb.append("<user_owner>").append(doc.getUserowner());
 			sb.append("</user_owner><user_updated>").append(doc.getUserupdated());
 			sb.append("</user_updated>");
 			sb.append("<date_created>");
 			sb.append(doc.getCreateDate());
 			sb.append("</date_created>");
 			sb.append("<date_updated>");
 			sb.append(doc.getUpdateDate());
 			sb.append("</date_updated>");
 			sb.append("<home_server>");
 			sb.append(doc.getDocHomeServer());
 			sb.append("</home_server>");
 			sb.append("<public_access>").append(doc.getPublicaccess());
 			sb.append("</public_access><rev>").append(doc.getRev());
 			sb.append("</rev>");
             tao
-            daigle
+			sb.append("<accessControl>");
             daigle
 			AccessControlForSingleFile acfsf = new AccessControlForSingleFile(docid);
 			sb.append(acfsf.getAccessString());
-            daigle
+			sb.append("</accessControl>");
             tao
-            daigle
+			sb.append("</documentinfo>");
-            leinfelder
+			// get a writer for sending back to response
-            daigle
+			response.setContentType("text/xml");
-            leinfelder
+			Writer out = response.getWriter();
 			out.write(sb.toString());
 			out.close();
             tao
-            daigle
+		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleGetDocumentInfoRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetDocumentInfoRequest - error in metacatReplication.handlegetdocumentinforequest "
 					+ "for doc: " + docid + " : " + e.getMessage());
+		}
             tao
             daigle
             leinfelder
 	/**
 	 * Sends System Metadata as XML
 	 */
 	protected static void handleGetSystemMetadataRequest(
 			Hashtable<String, String[]> params, HttpServletResponse response) {
 		String guid = ((String[]) (params.get("guid")))[0];
 		String systemMetadataXML = null;
 		try {
 			// serialize the System Metadata as XML
 			SystemMetadata systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);
 			ByteArrayOutputStream baos = new ByteArrayOutputStream();
-            leinfelder
+			TypeMarshaller.marshalTypeToOutputStream(systemMetadata, baos);
-            leinfelder
+			systemMetadataXML = baos.toString("UTF-8");
 			// get a writer for sending back to response
 			response.setContentType("text/xml");
 			Writer out = response.getWriter();
 			out.write(systemMetadataXML);
 			out.close();
             tao
-            leinfelder
+		} catch (Exception e) {
 			String msg = "ReplicationService.handleGetSystemMetadataRequest for guid: " + guid + " : " + e.getMessage();
 			logMetacat.error(msg);
 			logReplication.error(msg);
+		}
+	}
             leinfelder
 	/**
 	 * when a forcereplication request comes in, local host sends a read request
 	 * to the requesting server (remote server) for the specified docid. Then
 	 * store it in local database.
 	 */
 	protected static void handleForceReplicateSystemMetadataRequest(
 			Hashtable<String, String[]> params, HttpServletResponse response,
 			HttpServletRequest request) {
 		String server = ((String[]) params.get("server"))[0]; // the server that
 		String guid = ((String[]) params.get("guid"))[0]; // sent the document
 		try {
 			logReplication.info("ReplicationService.handleForceReplicateSystemMetadataRequest - Force replication system metadata request from: " + server);
 			// get the system metadata from server
 			URL docinfourl = new URL("https://" + server + "?server="
 					+ MetacatUtil.getLocalReplicationServerName()
 					+ "&action=getsystemmetadata&guid=" + guid);
 			String systemMetadataXML = ReplicationService.getURLContent(docinfourl);
 			// process system metadata
 			if (systemMetadataXML != null) {
 				SystemMetadata sysMeta =
-            leinfelder
+					TypeMarshaller.unmarshalTypeFromStream(
-            leinfelder
+							SystemMetadata.class,
 							new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
-            leinfelder
+				HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
             leinfelder
 			logReplication.info("ReplicationService.handleForceReplicateSystemMetadataRequest - processed guid: " + guid);
 			EventLog.getInstance().log(request.getRemoteAddr(), REPLICATIONUSER, guid, "systemMetadata");
             leinfelder
-            leinfelder
+		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleForceReplicateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG, e);
 			logReplication.error("ReplicationService.handleForceReplicateRequest - General error when processing guid: " + guid, e);
+		}
+	}
-            daigle
+	/**
 	 * Sends a datafile to a remote host
 	 */
 	protected static void handleGetDataFileRequest(OutputStream outPut,
 			Hashtable<String, String[]> params, HttpServletResponse response)
             tao
             daigle
 		// File path for data file
 		String filepath;
 		// Request docid
 		String docId = ((String[]) (params.get("docid")))[0];
 		//check if the doicd is null
 		if (docId == null) {
 			logMetacat.error("ReplicationService.handleGetDataFileRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetDataFileRequest - Didn't specify docid for replication");
 			return;
+		}
             tao
-            daigle
+		//try to open a https stream to test if the request server's public key
 		//in the key store, this is security issue
 		try {
 			filepath = PropertyService.getProperty("application.datafilepath");
 			String server = params.get("server")[0];
 			URL u = new URL("https://" + server + "?server="
 					+ MetacatUtil.getLocalReplicationServerName() + "&action=test");
 			String test = ReplicationService.getURLContent(u);
 			//couldn't pass the test
 			if (test.indexOf("successfully") == -1) {
 				//response.setContentType("text/xml");
 				//outPut.println("<error>Couldn't pass the trust test</error>");
 				logMetacat.error("ReplicationService.handleGetDataFileRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.handleGetDataFileRequest - Couldn't pass the trust test");
 				return;
+			}
 		}//try
 		catch (Exception ee) {
 			return;
 		}//catch
             tao
-            daigle
+		if (!filepath.endsWith("/")) {
 			filepath += "/";
+		}
 		// Get file aboslute file name
 		String filename = filepath + docId;
             tao
-            daigle
+		//MIME type
 		String contentType = null;
 		if (filename.endsWith(".xml")) {
 			contentType = "text/xml";
 		} else if (filename.endsWith(".css")) {
 			contentType = "text/css";
 		} else if (filename.endsWith(".dtd")) {
 			contentType = "text/plain";
 		} else if (filename.endsWith(".xsd")) {
 			contentType = "text/xml";
 		} else if (filename.endsWith("/")) {
 			contentType = "text/html";
 		} else {
 			File f = new File(filename);
 			if (f.isDirectory()) {
 				contentType = "text/html";
 			} else {
 				contentType = "application/octet-stream";
+			}
+		}
             tao
-            daigle
+		// Set the mime type
 		response.setContentType(contentType);
             tao
-            daigle
+		// Get the content of the file
 		FileInputStream fin = null;
 		try {
 			// FileInputStream to metacat
 			fin = new FileInputStream(filename);
 			// 4K buffer
 			byte[] buf = new byte[4 * 1024];
 			// Read data from file input stream to byte array
 			int b = fin.read(buf);
 			// Write to outStream from byte array
 			while (b != -1) {
 				outPut.write(buf, 0, b);
 				b = fin.read(buf);
+			}
 			// close file input stream
 			fin.close();
             tao
-            daigle
+		}//try
 		catch (Exception e) {
 			logMetacat.error("ReplicationService.handleGetDataFileRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetDataFileRequest - error getting data file from MetacatReplication."
 					+ "handlGetDataFileRequest " + e.getMessage());
 			e.printStackTrace(System.out);
 		}//catch
             tao
             daigle
 	/**
-            daigle
+	 * Sends a document to a remote host
 	 */
-            leinfelder
+	protected static void handleGetDocumentRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response) {
             tao
-            daigle
+		String urlString = null;
 		String documentPath = null;
-            leinfelder
+		String errorMsg = null;
-            daigle
+		try {
 			// try to open a https stream to test if the request server's public
 			// key
 			// in the key store, this is security issue
 			String server = params.get("server")[0];
 			urlString = "https://" + server + "?server="
 					+ MetacatUtil.getLocalReplicationServerName() + "&action=test";
 			URL u = new URL(urlString);
-            daigle
+			String test = ReplicationService.getURLContent(u);
-            daigle
+			// couldn't pass the test
 			if (test.indexOf("successfully") == -1) {
 				response.setContentType("text/xml");
-            leinfelder
+				Writer out = response.getWriter();
 				out.write("<error>Couldn't pass the trust test " + test + " </error>");
-            daigle
+				out.close();
 				return;
+			}
             tao
-            daigle
+			String docid = params.get("docid")[0];
-            daigle
+			logReplication.debug("ReplicationService.handleGetDocumentRequest - MetacatReplication.handleGetDocumentRequest for docid: "
 					+ docid);
-            daigle
+			DocumentImpl di = new DocumentImpl(docid);
             tao
-            daigle
+			String documentDir = PropertyService
 					.getProperty("application.documentfilepath");
-            daigle
+			documentPath = documentDir + FileUtil.getFS() + docid;
             daigle
-            daigle
+			// if the document does not exist on disk, read it from db and write
 			// it to disk.
 			if (FileUtil.getFileStatus(documentPath) == FileUtil.DOES_NOT_EXIST
 					|| FileUtil.getFileSize(documentPath) == 0) {
-            leinfelder
+				FileOutputStream fos = new FileOutputStream(documentPath);
 				di.toXml(fos, null, null, true);
             daigle
             tao
-            leinfelder
+			// read the file from disk and send it to outputstream
 			OutputStream outputStream = response.getOutputStream();
 			di.readFromFileSystem(outputStream, null, null, documentPath);
             tao
-            daigle
+			logReplication.info("ReplicationService.handleGetDocumentRequest - document " + docid + " sent");
             daigle
-            leinfelder
+			// return to avoid continuing to the error reporting section at the end
 			return;
-            daigle
+		} catch (MalformedURLException mue) {
-            daigle
+			logMetacat.error("ReplicationService.handleGetDocumentRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetDocumentRequest - Url error when getting document from MetacatReplication."
-            daigle
+					+ "handlGetDocumentRequest for url: " + urlString + " : "
 					+ mue.getMessage());
 			// e.printStackTrace(System.out);
             leinfelder
-            daigle
+		} catch (IOException ioe) {
-            daigle
+			logMetacat.error("ReplicationService.handleGetDocumentRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetDocumentRequest - I/O error when getting document from MetacatReplication."
 					+ "handlGetDocumentRequest for file: " + documentPath + " : "
 					+ ioe.getMessage());
-            leinfelder
+			errorMsg = ioe.getMessage();
-            daigle
+		} catch (PropertyNotFoundException pnfe) {
-            daigle
+			logMetacat.error("ReplicationService.handleGetDocumentRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication
 					.error("ReplicationService.handleGetDocumentRequest - Error getting property when getting document from MetacatReplication."
 							+ "handlGetDocumentRequest for file: "
 							+ documentPath
 							+ " : "
 							+ pnfe.getMessage());
-            daigle
+			// e.printStackTrace(System.out);
-            leinfelder
+			errorMsg = pnfe.getMessage();
-            daigle
+		} catch (McdbException me) {
-            daigle
+			logReplication
 					.error("ReplicationService.handleGetDocumentRequest - Document implementation error  getting property when getting document from MetacatReplication."
 							+ "handlGetDocumentRequest for file: "
 							+ documentPath
 							+ " : "
 							+ me.getMessage());
-            daigle
+			// e.printStackTrace(System.out);
-            leinfelder
+			errorMsg = me.getMessage();
             daigle
             leinfelder
 		// report any errors if we got here
 		response.setContentType("text/xml");
 		Writer out = null;
 		try {
 			response.getWriter();
 			out = response.getWriter();
 			out.write("<error>" + errorMsg + "</error>");
 		} catch (Exception e) {
 			logMetacat.error(e.getMessage(), e);
 		} finally {
 			try {
 				out.close();
 			} catch (IOException e) {
 				logMetacat.error(e.getMessage(), e);
+			}
+		}
             daigle
+	}
-            daigle
+	/**
-            daigle
+	 * Sends a list of all of the documents on this sever along with their
 	 * revision numbers. The format is: <!ELEMENT replication (server, updates)>
 	 * <!ELEMENT server (#PCDATA)> <!ELEMENT updates ((updatedDocument |
 	 * deleteDocument | revisionDocument)*)> <!ELEMENT updatedDocument (docid,
 	 * rev, datafile*)> <!ELEMENT deletedDocument (docid, rev)> <!ELEMENT
 	 * revisionDocument (docid, rev, datafile*)> <!ELEMENT docid (#PCDATA)>
 	 * <!ELEMENT rev (#PCDATA)> <!ELEMENT datafile (#PCDATA)> note that the rev
 	 * in deletedDocument is always empty. I just left it in there to make the
 	 * parser implementation easier.
 	 */
-            leinfelder
+	protected static void handleUpdateRequest(Hashtable<String, String[]> params,
-            daigle
+			HttpServletResponse response) {
 		// Checked out DBConnection
 		DBConnection dbConn = null;
 		// DBConenction serial number when checked it out
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
 		// Server list to store server info of xml_replication table
 		ReplicationServerList serverList = null;
             leinfelder
 		// a writer for response
 		Writer out = null;
             tao
-            daigle
+		try {
-            leinfelder
+			// get writer, TODO: encoding?
 			response.setContentType("text/xml");
 			out = response.getWriter();
-            daigle
+			// Check out a DBConnection from pool
 			dbConn = DBConnectionPool
 					.getDBConnection("MetacatReplication.handleUpdateRequest");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			// Create a server list from xml_replication table
 			serverList = new ReplicationServerList();
             tao
-            daigle
+			// Get remote server name from param
 			String server = ((String[]) params.get("server"))[0];
 			// If no servr name in param, return a error
 			if (server == null || server.equals("")) {
-            leinfelder
+				out.write("<error>Request didn't specify server name</error>");
-            daigle
+				out.close();
 				return;
 			}//if
             tao
-            daigle
+			//try to open a https stream to test if the request server's public key
 			//in the key store, this is security issue
-            berkley
+			String testUrl = "https://" + server + "?server="
-            berkley
+            + MetacatUtil.getLocalReplicationServerName() + "&action=test";
-            berkley
+			logReplication.info("Running trust test: " + testUrl);
 			URL u = new URL(testUrl);
-            daigle
+			String test = ReplicationService.getURLContent(u);
-            berkley
+			logReplication.info("Ouput from test is '" + test + "'");
-            daigle
+			//couldn't pass the test
 			if (test.indexOf("successfully") == -1) {
-            berkley
+			    logReplication.error("Trust test failed.");
-            leinfelder
+				out.write("<error>Couldn't pass the trust test</error>");
-            daigle
+				out.close();
 				return;
+			}
-            berkley
+			logReplication.info("Trust test succeeded.");
             tao
-            daigle
+			// Check if local host configure to replicate xml documents to remote
 			// server. If not send back a error message
 			if (!serverList.getReplicationValue(server)) {
-            leinfelder
+				out.write("<error>Configuration not allow to replicate document to you</error>");
-            daigle
+				out.close();
 				return;
 			}//if
             tao
-            daigle
+			// Store the sql command
 			StringBuffer docsql = new StringBuffer();
 			StringBuffer revisionSql = new StringBuffer();
 			// Stroe the docid list
 			StringBuffer doclist = new StringBuffer();
 			// Store the deleted docid list
 			StringBuffer delsql = new StringBuffer();
 			// Store the data set file
 			Vector<Vector<String>> packageFiles = new Vector<Vector<String>>();
             tao
-            daigle
+			// Append local server's name and replication servlet to doclist
 			doclist.append("<?xml version=\"1.0\"?><replication>");
 			doclist.append("<server>")
 					.append(MetacatUtil.getLocalReplicationServerName());
 			//doclist.append(util.getProperty("replicationpath"));
 			doclist.append("</server><updates>");
             tao
-            daigle
+			// Get correct docid that reside on this server according the requesting
 			// server's replicate and data replicate value in xml_replication table
-            jones
+			docsql.append(DatabaseService.getInstance().getDBAdapter().getReplicationDocumentListSQL());
-            daigle
+			//docsql.append("select docid, rev, doctype from xml_documents where (docid not in (select a.docid from xml_documents a, xml_revisions b where a.docid=b.docid and a.rev<=b.rev)) ");
 			revisionSql.append("select docid, rev, doctype from xml_revisions ");
 			// If the localhost is not a hub to the remote server, only replicate
 			// the docid' which home server is local host (server_location =1)
 			if (!serverList.getHubValue(server)) {
 				String serverLocationDoc = " and a.server_location = 1";
 				String serverLocationRev = "where server_location = 1";
 				docsql.append(serverLocationDoc);
 				revisionSql.append(serverLocationRev);
+			}
 			logReplication.info("ReplicationService.handleUpdateRequest - Doc sql: " + docsql.toString());
             tao
-            daigle
+			// Get any deleted documents
 			delsql.append("select distinct docid from ");
 			delsql.append("xml_revisions where docid not in (select docid from ");
 			delsql.append("xml_documents) ");
 			// If the localhost is not a hub to the remote server, only replicate
 			// the docid' which home server is local host (server_location =1)
 			if (!serverList.getHubValue(server)) {
 				delsql.append("and server_location = 1");
+			}
 			logReplication.info("ReplicationService.handleUpdateRequest - Deleted sql: " + delsql.toString());
             tao
-            daigle
+			// Get docid list of local host
 			pstmt = dbConn.prepareStatement(docsql.toString());
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			//If metacat configed to replicate data file
 			//if ((util.getProperty("replicationsenddata")).equals("on"))
 			boolean replicateData = serverList.getDataReplicationValue(server);
 			if (replicateData) {
 				while (tablehasrows) {
 					String recordDoctype = rs.getString(3);
 					Vector<String> packagedoctypes = MetacatUtil
 							.getOptionList(PropertyService
 									.getProperty("xml.packagedoctype"));
 					//if this is a package file, put it at the end
 					//because if a package file is read before all of the files it
 					//refers to are loaded then there is an error
 					if (recordDoctype != null && !packagedoctypes.contains(recordDoctype)) {
 						//If this is not data file
 						if (!recordDoctype.equals("BIN")) {
 							//for non-data file document
 							doclist.append("<updatedDocument>");
 							doclist.append("<docid>").append(rs.getString(1));
 							doclist.append("</docid><rev>").append(rs.getInt(2));
 							doclist.append("</rev>");
 							doclist.append("</updatedDocument>");
 						}//if
 						else {
 							//for data file document, in datafile attributes
 							//we put "datafile" value there
 							doclist.append("<updatedDocument>");
 							doclist.append("<docid>").append(rs.getString(1));
 							doclist.append("</docid><rev>").append(rs.getInt(2));
 							doclist.append("</rev>");
 							doclist.append("<datafile>");
 							doclist.append(PropertyService
 									.getProperty("replication.datafileflag"));
 							doclist.append("</datafile>");
 							doclist.append("</updatedDocument>");
 						}//else
 					}//if packagedoctpes
 					else { //the package files are saved to be put into the xml later.
 						Vector<String> v = new Vector<String>();
 						v.add(rs.getString(1));
 						v.add(String.valueOf(rs.getInt(2)));
 						packageFiles.add(v);
 					}//esle
 					tablehasrows = rs.next();
 				}//while
 			}//if
 			else //metacat was configured not to send data file
+			{
 				while (tablehasrows) {
 					String recordDoctype = rs.getString(3);
 					if (!recordDoctype.equals("BIN")) { //don't replicate data files
 						Vector<String> packagedoctypes = MetacatUtil
 								.getOptionList(PropertyService
 										.getProperty("xml.packagedoctype"));
 						if (recordDoctype != null
 								&& !packagedoctypes.contains(recordDoctype)) { //if this is a package file, put it at the end
 							//because if a package file is read before all of the files it
 							//refers to are loaded then there is an error
 							doclist.append("<updatedDocument>");
 							doclist.append("<docid>").append(rs.getString(1));
 							doclist.append("</docid><rev>").append(rs.getInt(2));
 							doclist.append("</rev>");
 							doclist.append("</updatedDocument>");
 						} else { //the package files are saved to be put into the xml later.
 							Vector<String> v = new Vector<String>();
 							v.add(rs.getString(1));
 							v.add(String.valueOf(rs.getInt(2)));
 							packageFiles.add(v);
+						}
 					}//if
 					tablehasrows = rs.next();
 				}//while
 			}//else
             tao
-            daigle
+			pstmt = dbConn.prepareStatement(delsql.toString());
 			//usage count should increas 1
 			dbConn.increaseUsageCount(1);
             tao
-            daigle
+			pstmt.execute();
 			rs = pstmt.getResultSet();
 			tablehasrows = rs.next();
 			while (tablehasrows) { //handle the deleted documents
 				doclist.append("<deletedDocument><docid>").append(rs.getString(1));
 				doclist.append("</docid><rev></rev></deletedDocument>");
 				//note that rev is always empty for deleted docs
 				tablehasrows = rs.next();
+			}
             tao
-            daigle
+			//now we can put the package files into the xml results
 			for (int i = 0; i < packageFiles.size(); i++) {
 				Vector<String> v = packageFiles.elementAt(i);
 				doclist.append("<updatedDocument>");
 				doclist.append("<docid>").append(v.elementAt(0));
 				doclist.append("</docid><rev>");
 				doclist.append(v.elementAt(1));
 				doclist.append("</rev>");
 				doclist.append("</updatedDocument>");
+			}
 			// add revision doc list
 			doclist.append(prepareRevisionDoc(dbConn, revisionSql.toString(),
 					replicateData));
             leinfelder
-            leinfelder
+			// add the system metadata entries if configured to replicate them
 			boolean replicateSystemMetadata = serverList.getSystemMetadataReplicationValue(server);
 			if (replicateSystemMetadata) {
 				Date since = new Date(System.currentTimeMillis());
 				since = serverList.getLastCheckedDate(server);
 				List<String> systemMetadataEntries =
 					IdentifierManager.getInstance().getUpdatedSystemMetadataIds(since);
 				for (int i = 0; i < systemMetadataEntries.size(); i++) {
 					String guid = systemMetadataEntries.get(i);
 					doclist.append("<updatedSystemMetadata>");
 					doclist.append("<guid>");
 					doclist.append(guid);
 					doclist.append("</guid>");
 					doclist.append("</updatedSystemMetadata>");
+				}
             leinfelder
             tao
-            daigle
+			doclist.append("</updates></replication>");
 			logReplication.info("ReplicationService.handleUpdateRequest - doclist: " + doclist.toString());
 			pstmt.close();
 			//conn.close();
-            leinfelder
+			out.write(doclist.toString());
             tao
-            daigle
+		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleUpdateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleUpdateRequest - error in MetacatReplication." + "handleupdaterequest: "
 					+ e.getMessage());
 			//e.printStackTrace(System.out);
-            leinfelder
+			try {
 				out.write("<error>" + e.getMessage() + "</error>");
 			} catch (IOException e1) {
 				logMetacat.error(e1.getMessage(), e1);
+			}
-            daigle
+		} finally {
 			try {
 				pstmt.close();
 			}//try
 			catch (SQLException ee) {
 				logMetacat.error("ReplicationService.handleUpdateRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.handleUpdateRequest - Error in MetacatReplication."
 						+ "handleUpdaterequest to close pstmt: " + ee.getMessage());
 			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
-            leinfelder
+			try {
 				out.close();
 			} catch (IOException e) {
 				logMetacat.error(e.getMessage(), e);
+			}
-            daigle
+		}//finally
             tao
-            daigle
+	}//handlUpdateRequest
             tao
-            leinfelder
+	/**
+	 *
 	 * @param dbConn connection for doing the update
 	 * @param docid the document id to update
 	 * @param owner the user_owner
 	 * @param updater the user_updated
 	 * @throws SQLException
 	 */
 	public static void updateUserOwner(DBConnection dbConn, String docid, String owner, String updater) throws SQLException {
 		String sql =
 			"UPDATE xml_documents " +
 			"SET user_owner = ?, " +
 			"user_updated = ? " +
 			"WHERE docid = ?;";
 		PreparedStatement pstmt = dbConn.prepareStatement(sql);
 		//usage count should increas 1
 		dbConn.increaseUsageCount(1);
 		docid = DocumentUtil.getSmartDocId(docid);
 		pstmt.setString(1, owner);
 		pstmt.setString(2, updater);
 		pstmt.setString(3, docid);
 		pstmt.execute();
 		pstmt.close();
 		dbConn.commit();
+	}
-            daigle
+	/*
 	 * This method will get the xml string for document in xml_revision
 	 * The schema look like <!ELEMENT revisionDocument (docid, rev, datafile*)>
 	 */
 	private static String prepareRevisionDoc(DBConnection dbConn, String revSql,
 			boolean replicateData) throws Exception {
 		logReplication.warn("ReplicationService.prepareRevisionDoc - The revision document sql is " + revSql);
 		StringBuffer revDocList = new StringBuffer();
 		PreparedStatement pstmt = dbConn.prepareStatement(revSql);
 		//usage count should increas 1
 		dbConn.increaseUsageCount(1);
             tao
-            daigle
+		pstmt.execute();
 		ResultSet rs = pstmt.getResultSet();
 		boolean tablehasrows = rs.next();
 		while (tablehasrows) {
 			String recordDoctype = rs.getString(3);
             tao
-            daigle
+			//If this is data file and it isn't configured to replicate data
 			if (recordDoctype.equals("BIN") && !replicateData) {
 				// do nothing
 				continue;
 			} else {
             tao
-            daigle
+				revDocList.append("<revisionDocument>");
 				revDocList.append("<docid>").append(rs.getString(1));
 				revDocList.append("</docid><rev>").append(rs.getInt(2));
 				revDocList.append("</rev>");
 				// data file
 				if (recordDoctype.equals("BIN")) {
 					revDocList.append("<datafile>");
 					revDocList.append(PropertyService
 							.getProperty("replication.datafileflag"));
 					revDocList.append("</datafile>");
+				}
 				revDocList.append("</revisionDocument>");
             tao
-            daigle
+			}//else
 			tablehasrows = rs.next();
+		}
 		//System.out.println("The revision list is"+ revDocList.toString());
 		return revDocList.toString();
+	}
             tao
-            daigle
+	/**
 	 * Returns the xml_catalog table encoded in xml
 	 */
 	public static String getCatalogXML() {
-            leinfelder
+		return handleGetCatalogRequest(null, null, false);
             daigle
             tao
-            daigle
+	/**
 	 * Sends the contents of the xml_catalog table encoded in xml
 	 * The xml format is:
 	 * <!ELEMENT xml_catalog (row*)>
 	 * <!ELEMENT row (entry_type, source_doctype, target_doctype, public_id,
 	 *                system_id)>
 	 * All of the sub elements of row are #PCDATA
             tao
-            daigle
+	 * If printFlag == false then do not print to out.
 	 */
-            leinfelder
+	protected static String handleGetCatalogRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response,
 			boolean printFlag) {
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
-            leinfelder
+		Writer out = null;
-            daigle
+		try {
-            leinfelder
+			// get writer, TODO: encoding?
-            berkley
+		    if(printFlag)
+		    {
 		        response.setContentType("text/xml");
 		        out = response.getWriter();
+		    }
-            daigle
+			/*conn = MetacatReplication.getDBConnection("MetacatReplication." +
 			                                          "handleGetCatalogRequest");*/
 			dbConn = DBConnectionPool
 					.getDBConnection("MetacatReplication.handleGetCatalogRequest");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			pstmt = dbConn.prepareStatement("select entry_type, "
 					+ "source_doctype, target_doctype, public_id, "
 					+ "system_id from xml_catalog");
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			StringBuffer sb = new StringBuffer();
 			sb.append("<?xml version=\"1.0\"?><xml_catalog>");
 			while (tablehasrows) {
 				sb.append("<row><entry_type>").append(rs.getString(1));
 				sb.append("</entry_type><source_doctype>").append(rs.getString(2));
 				sb.append("</source_doctype><target_doctype>").append(rs.getString(3));
 				sb.append("</target_doctype><public_id>").append(rs.getString(4));
 				// system id may not have server url on front.  Add it if not.
 				String systemID = rs.getString(5);
 				if (!systemID.startsWith("http://")) {
 					systemID = SystemUtil.getContextURL() + systemID;
+				}
 				sb.append("</public_id><system_id>").append(systemID);
 				sb.append("</system_id></row>");
             tao
-            daigle
+				tablehasrows = rs.next();
+			}
 			sb.append("</xml_catalog>");
 			//conn.close();
 			if (printFlag) {
 				response.setContentType("text/xml");
-            leinfelder
+				out.write(sb.toString());
             daigle
 			pstmt.close();
 			return sb.toString();
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.handleGetCatalogRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.handleGetCatalogRequest - error in MetacatReplication.handleGetCatalogRequest:"
 					+ e.getMessage());
 			e.printStackTrace(System.out);
 			if (printFlag) {
-            leinfelder
+				try {
 					out.write("<error>" + e.getMessage() + "</error>");
 				} catch (IOException e1) {
 					logMetacat.error(e1.getMessage(), e1);
+				}
             daigle
 		} finally {
 			try {
 				pstmt.close();
 			}//try
 			catch (SQLException ee) {
 				logMetacat.error("ReplicationService.handleGetCatalogRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.handleGetCatalogRequest - Error in MetacatReplication.handleGetCatalogRequest: "
 						+ ee.getMessage());
 			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
-            leinfelder
+			if (out != null) {
 				try {
 					out.close();
 				} catch (IOException e1) {
 					logMetacat.error(e1.getMessage(), e1);
+				}
+			}
-            daigle
+		}//finally
             tao
-            daigle
+		return null;
+	}
             tao
-            daigle
+	/**
 	 * Sends the current system date to the remote server.  Using this action
 	 * for replication gets rid of any problems with syncronizing clocks
 	 * because a time specific to a document is always kept on its home server.
 	 */
-            leinfelder
+	protected static void handleGetTimeRequest(
-            daigle
+			Hashtable<String, String[]> params, HttpServletResponse response) {
 		SimpleDateFormat formatter = new SimpleDateFormat("MM/dd/yy HH:mm:ss");
 		java.util.Date localtime = new java.util.Date();
 		String dateString = formatter.format(localtime);
             leinfelder
 		// get a writer for sending back to response
-            daigle
+		response.setContentType("text/xml");
-            leinfelder
+		Writer out = null;
 		try {
 			out = response.getWriter();
 			out.write("<timestamp>" + dateString + "</timestamp>");
 			out.close();
 		} catch (IOException e) {
 			logMetacat.error(e.getMessage(), e);
+		}
             daigle
             tao
-            daigle
+	/**
 	 * this method handles the timeout for a file lock.  when a lock is
 	 * granted it is granted for 30 seconds.  When this thread runs out
 	 * it deletes the docid from the queue, thus eliminating the lock.
 	 */
 	public void run() {
 		try {
 			logReplication.info("ReplicationService.run - thread started for docid: "
 					+ (String) fileLocks.elementAt(0));
             tao
-            daigle
+			Thread.sleep(30000); //the lock will expire in 30 seconds
 			logReplication.info("thread for docid: "
 					+ (String) fileLocks.elementAt(fileLocks.size() - 1) + " exiting.");
             tao
-            daigle
+			fileLocks.remove(fileLocks.size() - 1);
 			//fileLocks is treated as a FIFO queue.  If there are more than one lock
 			//in the vector, the first one inserted will be removed.
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.run - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.run - error in file lock thread from "
 					+ "MetacatReplication.run: " + e.getMessage());
+		}
+	}
             tao
-            daigle
+	/**
 	 * Returns the name of a server given a serverCode
 	 * @param serverCode the serverid of the server
 	 * @return the servername or null if the specified serverCode does not
 	 *         exist.
 	 */
 	public static String getServerNameForServerCode(int serverCode) {
 		//System.out.println("serverid: " + serverCode);
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
 		try {
 			dbConn = DBConnectionPool.getDBConnection("MetacatReplication.getServer");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			String sql = new String("select server from "
 					+ "xml_replication where serverid = " + serverCode);
 			pstmt = dbConn.prepareStatement(sql);
 			//System.out.println("getserver sql: " + sql);
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			if (tablehasrows) {
 				//System.out.println("server: " + rs.getString(1));
 				return rs.getString(1);
+			}
             tao
-            daigle
+			//conn.close();
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.getServerNameForServerCode - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.getServerNameForServerCode - Error in MetacatReplication.getServer: " + e.getMessage());
 		} finally {
 			try {
 				pstmt.close();
 			}//try
 			catch (SQLException ee) {
 				logMetacat.error("ReplicationService.getServerNameForServerCode - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.getServerNameForServerCode - Error in MetacactReplication.getserver: "
 						+ ee.getMessage());
 			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//fianlly
 		}//finally
             tao
-            daigle
+		return null;
 		//return null if the server does not exist
+	}
             tao
-            daigle
+	/**
 	 * Returns a server code given a server name
 	 * @param server the name of the server
 	 * @return integer > 0 representing the code of the server, 0 if the server
 	 *  does not exist.
 	 */
 	public static int getServerCodeForServerName(String server) throws ServiceException {
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
 		int serverCode = 0;
             tao
-            daigle
+		try {
             bojilova
-            daigle
+			//conn = util.openDBConnection();
 			dbConn = DBConnectionPool.getDBConnection("MetacatReplication.getServerCode");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			pstmt = dbConn.prepareStatement("SELECT serverid FROM xml_replication "
 					+ "WHERE server LIKE '" + server + "'");
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			if (tablehasrows) {
 				serverCode = rs.getInt(1);
 				pstmt.close();
 				//conn.close();
 				return serverCode;
+			}
             bojilova
-            daigle
+		} catch (SQLException sqle) {
 			throw new ServiceException("ReplicationService.getServerCodeForServerName - "
 					+ "SQL error when getting server code: " + sqle.getMessage());
             tao
-            daigle
+		} finally {
 			try {
 				pstmt.close();
 				//conn.close();
 			}//try
 			catch (Exception ee) {
 				logMetacat.error("ReplicationService.getServerCodeForServerName - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.getServerNameForServerCode - Error in MetacatReplicatio.getServerCode: "
 						+ ee.getMessage());
             bojilova
-            daigle
+			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
 		}//finally
             tao
-            daigle
+		return serverCode;
+	}
             tao
-            daigle
+	/**
 	 * Method to get a host server information for given docid
 	 * @param conn a connection to the database
 	 */
 	public static Hashtable<String, String> getHomeServerInfoForDocId(String docId) {
 		Hashtable<String, String> sl = new Hashtable<String, String>();
 		DBConnection dbConn = null;
 		int serialNumber = -1;
-            daigle
+		docId = DocumentUtil.getDocIdFromString(docId);
-            daigle
+		PreparedStatement pstmt = null;
 		int serverLocation;
 		try {
 			//get conection
 			dbConn = DBConnectionPool.getDBConnection("ReplicationHandler.getHomeServer");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			//get a server location from xml_document table
 			pstmt = dbConn.prepareStatement("select server_location from xml_documents "
 					+ "where docid = ?");
 			pstmt.setString(1, docId);
 			pstmt.execute();
 			ResultSet serverName = pstmt.getResultSet();
 			//get a server location
 			if (serverName.next()) {
 				serverLocation = serverName.getInt(1);
 				pstmt.close();
 			} else {
 				pstmt.close();
 				//ut.returnConnection(conn);
 				return null;
+			}
 			pstmt = dbConn.prepareStatement("select server, last_checked, replicate "
 					+ "from xml_replication where serverid = ?");
 			//increase usage count
 			dbConn.increaseUsageCount(1);
 			pstmt.setInt(1, serverLocation);
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tableHasRows = rs.next();
 			if (tableHasRows) {
             tao
-            daigle
+				String server = rs.getString(1);
 				String last_checked = rs.getString(2);
 				if (!server.equals("localhost")) {
 					sl.put(server, last_checked);
+				}
             tao
-            daigle
+			} else {
 				pstmt.close();
 				//ut.returnConnection(conn);
 				return null;
+			}
 			pstmt.close();
 		} catch (Exception e) {
 			logMetacat.error("ReplicationService.getHomeServerInfoForDocId - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.getHomeServerInfoForDocId - error in replicationHandler.getHomeServer(): "
 					+ e.getMessage());
 		} finally {
 			try {
 				pstmt.close();
 				//ut.returnConnection(conn);
 			} catch (Exception ee) {
 				logMetacat.error("ReplicationService.getHomeServerInfoForDocId - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.getHomeServerInfoForDocId - Eror irn rplicationHandler.getHomeServer() "
 						+ "to close pstmt: " + ee.getMessage());
 			} finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+			}
             tao
-            daigle
+		}//finally
 		return sl;
+	}
             tao
-            daigle
+	/**
 	 * Returns a home server location  given a accnum
 	 * @param accNum , given accNum for a document
+	 *
 	 */
 	public static int getHomeServerCodeForDocId(String accNum) throws ServiceException {
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
 		int serverCode = 1;
-            daigle
+		String docId = DocumentUtil.getDocIdFromString(accNum);
             tao
-            daigle
+		try {
             tao
-            daigle
+			// Get DBConnection
 			dbConn = DBConnectionPool
 					.getDBConnection("ReplicationHandler.getServerLocation");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			pstmt = dbConn.prepareStatement("SELECT server_location FROM xml_documents "
 					+ "WHERE docid LIKE '" + docId + "'");
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			//If a document is find, return the server location for it
 			if (tablehasrows) {
 				serverCode = rs.getInt(1);
 				pstmt.close();
 				//conn.close();
 				return serverCode;
+			}
 			//if couldn't find in xml_documents table, we think server code is 1
 			//(this is new document)
 			else {
 				pstmt.close();
 				//conn.close();
 				return serverCode;
+			}
             tao
-            daigle
+		} catch (SQLException sqle) {
 			throw new ServiceException("ReplicationService.getHomeServerCodeForDocId - "
 					+ "SQL error when getting home server code for docid: " + docId + " : "
 					+ sqle.getMessage());
             tao
-            daigle
+		} finally {
 			try {
 				pstmt.close();
 				//conn.close();
             tao
-            daigle
+			} catch (SQLException sqle) {
 				logMetacat.error("ReplicationService.getHomeServerCodeForDocId - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.getHomeServerCodeForDocId - ReplicationService.getHomeServerCodeForDocId - "
 						+ "SQL error when getting home server code for docid: " + docId + " : "
 						+ sqle.getMessage());
 			} finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
 		}//finally
 		//return serverCode;
+	}
             tao
-            daigle
+	/**
 	 * This method returns the content of a url
 	 * @param u the url to return the content from
 	 * @return a string representing the content of the url
 	 * @throws java.io.IOException
 	 */
 	public static String getURLContent(URL u) throws java.io.IOException {
-            berkley
+	    logReplication.info("Getting url content from " + u.toString());
-            daigle
+		char istreamChar;
 		int istreamInt;
-            berkley
+		logReplication.info("ReplicationService.getURLContent - Before open the stream" + u.toString());
-            daigle
+		InputStream input = u.openStream();
-            berkley
+		logReplication.info("ReplicationService.getURLContent - After open the stream" + u.toString());
-            daigle
+		InputStreamReader istream = new InputStreamReader(input);
 		StringBuffer serverResponse = new StringBuffer();
 		while ((istreamInt = istream.read()) != -1) {
 			istreamChar = (char) istreamInt;
 			serverResponse.append(istreamChar);
+		}
 		istream.close();
 		input.close();
             tao
-            daigle
+		return serverResponse.toString();
+	}
             tao
-            daigle
+//	/**
 //	 * Method for writing replication messages to a log file specified in
 //	 * metacat.properties
 //	 */
 //	public static void replLog(String message) {
 //		try {
 //			FileOutputStream fos = new FileOutputStream(PropertyService
 //					.getProperty("replication.logdir")
 //					+ "/metacatreplication.log", true);
 //			PrintWriter pw = new PrintWriter(fos);
 //			SimpleDateFormat formatter = new SimpleDateFormat("yy-MM-dd HH:mm:ss");
 //			java.util.Date localtime = new java.util.Date();
 //			String dateString = formatter.format(localtime);
 //			dateString += " :: " + message;
 //			// time stamp each entry
 //			pw.println(dateString);
 //			pw.flush();
 //		} catch (Exception e) {
 //			logReplication.error("error writing to replication log from "
 //					+ "MetacatReplication.replLog: " + e.getMessage());
 //			// e.printStackTrace(System.out);
 //		}
 //	}
             tao
-            daigle
+//	/**
 //	 * Method for writing replication messages to a log file specified in
 //	 * metacat.properties
 //	 */
 //	public static void replErrorLog(String message) {
 //		try {
 //			FileOutputStream fos = new FileOutputStream(PropertyService
 //					.getProperty("replication.logdir")
 //					+ "/metacatreplicationerror.log", true);
 //			PrintWriter pw = new PrintWriter(fos);
 //			SimpleDateFormat formatter = new SimpleDateFormat("yy-MM-dd HH:mm:ss");
 //			java.util.Date localtime = new java.util.Date();
 //			String dateString = formatter.format(localtime);
 //			dateString += " :: " + message;
 //			//time stamp each entry
 //			pw.println(dateString);
 //			pw.flush();
 //		} catch (Exception e) {
 //			logReplication.error("error writing to replication error log from "
 //					+ "MetacatReplication.replErrorLog: " + e.getMessage());
 //			//e.printStackTrace(System.out);
 //		}
 //	}
             tao
-            daigle
+	/**
 	 * Returns true if the replicate field for server in xml_replication is 1.
 	 * Returns false otherwise
-            daigle
+	 */
-            daigle
+	public static boolean replToServer(String server) {
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
-            daigle
+		try {
-            daigle
+			dbConn = DBConnectionPool.getDBConnection("MetacatReplication.repltoServer");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			pstmt = dbConn.prepareStatement("select replicate from "
 					+ "xml_replication where server like '" + server + "'");
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			if (tablehasrows) {
 				int i = rs.getInt(1);
 				if (i == 1) {
 					pstmt.close();
 					//conn.close();
 					return true;
 				} else {
 					pstmt.close();
 					//conn.close();
 					return false;
+				}
+			}
 		} catch (SQLException sqle) {
 			logMetacat.error("ReplicationService.replToServer - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 			logReplication.error("ReplicationService.replToServer - SQL error in MetacatReplication.replToServer: "
 					+ sqle.getMessage());
 		} finally {
 			try {
 				pstmt.close();
 				//conn.close();
 			}//try
 			catch (Exception ee) {
 				logMetacat.error("ReplicationService.replToServer - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.replToServer - Error in MetacatReplication.replToServer: "
 						+ ee.getMessage());
 			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
 		}//finally
 		return false;
 		//the default if this server does not exist is to not replicate to it.
             daigle
             tao
             berkley

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