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

metacat/src/edu/ucsb/nceas/metacat/replication/ReplicationService.java @ 8810

-            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.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;
-            leinfelder
+import java.security.PrivateKey;
 import java.security.cert.X509Certificate;
-            leinfelder
+import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
-            leinfelder
+import java.sql.Timestamp;
-            slaughter
+import java.util.ArrayList;
 import java.util.Arrays;
-            leinfelder
+import java.util.Calendar;
-            tao
+import java.util.Date;
-            leinfelder
+import java.util.HashMap;
-            leinfelder
+import java.util.Hashtable;
-            slaughter
+import java.util.List;
-            leinfelder
+import java.util.Map;
-            leinfelder
+import java.util.Timer;
 import java.util.Vector;
             daigle
-            leinfelder
+import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
             berkley
-            jones
+import org.apache.commons.io.IOUtils;
-            leinfelder
+import org.apache.http.HttpResponse;
 import org.apache.http.conn.scheme.Scheme;
 import org.apache.http.conn.ssl.SSLSocketFactory;
-            leinfelder
+import org.apache.log4j.Logger;
-            leinfelder
+import org.dataone.client.rest.DefaultHttpMultipartRestClient;
 import org.dataone.client.rest.RestClient;
-            leinfelder
+import org.dataone.client.auth.CertificateManager;
-            slaughter
+import org.dataone.service.types.v1.Identifier;
-            leinfelder
+import org.dataone.service.types.v2.SystemMetadata;
-            leinfelder
+import org.dataone.service.util.DateTimeMarshaller;
-            leinfelder
+import org.dataone.service.util.TypeMarshaller;
-            leinfelder
+import org.jibx.runtime.JiBXException;
-            leinfelder
+import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 import org.xml.sax.XMLReader;
-            daigle
+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;
-            leinfelder
+import edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas;
-            leinfelder
+import edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI;
-            leinfelder
+import edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE;
-            leinfelder
+import edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata;
-            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;
-            slaughter
+import edu.ucsb.nceas.metacat.dataone.SyncAccessPolicy;
-            leinfelder
+import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
-            leinfelder
+import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
-            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;
-            leinfelder
+import edu.ucsb.nceas.metacat.util.ReplicationUtil;
-            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;
-            leinfelder
+import edu.ucsb.nceas.utilities.access.DocInfoHandler;
 import edu.ucsb.nceas.utilities.access.XMLAccessDAO;
             daigle
-            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";
-            leinfelder
+	public static final String FORCEREPLICATEDELETEALL = "forcereplicatedeleteall";
-            daigle
+	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";
             leinfelder
 	private static int CLIENTTIMEOUT = 30000;
             tao
-            daigle
+	public static final String REPLICATION_LOG_FILE_NAME = "metacatreplication.log";
             leinfelder
-            leinfelder
+	private static String DATA_FILE_FLAG = null;
-            daigle
+	public static String METACAT_REPL_ERROR_MSG = null;
 	private static Logger logReplication = Logger.getLogger("ReplicationLogging");
 	private static Logger logMetacat = Logger.getLogger(ReplicationService.class);
             tao
-            leinfelder
+	static {
 		// lookup the client timeout
 		String clientTimeout = null;
 		try {
 			clientTimeout = PropertyService.getProperty("replication.client.timeout");
 			CLIENTTIMEOUT = Integer.parseInt(clientTimeout);
 		} catch (Exception e) {
 			// just use default
 			logReplication.warn("No custom client timeout specified in configuration, using default." + e.getMessage());
+		}
-            leinfelder
+		try {
 			DATA_FILE_FLAG = PropertyService.getProperty("replication.datafileflag");
 		} catch (PropertyNotFoundException e) {
 			logReplication.error("No 'replication.datafileflag' specified in configuration." + e.getMessage());
+		}
             leinfelder
-            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;
+	}
-            leinfelder
+	public 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);
+	}
             leinfelder
-            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
+	public static void handleServerControlRequest(
-            leinfelder
+			Hashtable<String, String[]> params, HttpServletRequest request, HttpServletResponse response) {
-            daigle
+		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;
 		String hub = null;
-            leinfelder
+		Writer out = null;
-            leinfelder
+		boolean showGenerateSystemMetadata = true;
-            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
-            daigle
+				//Get hub value
 				hub = ((String[]) params.get("hub"))[0];
             bojilova
-            leinfelder
+				Calendar cal = Calendar.getInstance();
                 cal.set(1980, 1, 1);
-            daigle
+				String sql = "INSERT INTO xml_replication "
-            leinfelder
+						+ "(server, last_checked, replicate, datareplicate, hub) "
 						+ "VALUES (?,?,?,?,?)";
             daigle
 				pstmt = dbConn.prepareStatement(sql);
 				pstmt.setString(1, server);
-            leinfelder
+				pstmt.setTimestamp(2, new Timestamp(cal.getTimeInMillis()));
 				pstmt.setInt(3, Integer.parseInt(replicate));
 				pstmt.setInt(4, Integer.parseInt(dataReplicate));
-            leinfelder
+				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");
             leinfelder
-            daigle
+				// delete server from server list
 			} else if (subaction.equals("delete")) {
 				server = ((String[]) params.get("server"))[0];
 				pstmt = dbConn.prepareStatement("DELETE FROM xml_replication "
-            leinfelder
+						+ "WHERE server LIKE ?");
 				pstmt.setString(1, server);
-            daigle
+				pstmt.execute();
 				pstmt.close();
 				dbConn.commit();
-            leinfelder
+				out.write("Server " + server + " deleted");
-            daigle
+			} else if (subaction.equals("list")) {
-            leinfelder
+				// nothing special - it's the default behavior
             leinfelder
-            leinfelder
+			} else if (subaction.equals("generatesystemmetadata")) {
 				GenerateSystemMetadata gsm = new GenerateSystemMetadata();
 				int serverLocation = -1;
 				String serverid = ((String[]) params.get("serverid"))[0];
 				serverLocation = Integer.parseInt(serverid);
 				gsm.setServerLocation(serverLocation );
 				gsm.multiThreadUpgrade();
 				out.write("System Metadata generated for server " + serverid);
-            leinfelder
+			} else if (subaction.equals("generateore")) {
 				GenerateORE gore = new GenerateORE();
 				int serverLocation = -1;
 				String serverid = ((String[]) params.get("serverid"))[0];
 				serverLocation = Integer.parseInt(serverid);
 				gore.setServerLocation(serverLocation );
 				gore.upgrade();
 				out.write("Generated ORE maps for server " + serverid);
-            leinfelder
+			} else if (subaction.equals("updatedoi")) {
 				UpdateDOI udoi = new UpdateDOI();
 				int serverLocation = -1;
 				String serverid = ((String[]) params.get("serverid"))[0];
 				serverLocation = Integer.parseInt(serverid);
 				udoi.setServerLocation(serverLocation );
             walker
 				//Get the list of IDs, if any were given
 				String ids = ((String[]) params.get("ids"))[0];
             leinfelder
-            walker
+				//Get the formatId, if one was given
 				String formatIds = ((String[]) params.get("formatIds"))[0];
 				//Allow DOI's to be updated by both ID and formatId
 				if((ids.length() > 0) || (formatIds.length() > 0)){
 					//If at least one ID was given, update their DOI registrations
 					if(ids.length() > 0){
 						String delimeter = " ";
 						String[] idArray = ids.split(delimeter);
 						List<String> idList = Arrays.asList(idArray);
 						udoi.upgradeById(idList);
+					}
 					//If at least one formatId was given, update the DOI registrations
 					if(formatIds.length() > 0){
 						String delimeter = " ";
 						String[] formatIdArray = formatIds.split(delimeter);
 						List<String> formatIdList = Arrays.asList(formatIdArray);
 						udoi.upgradeByFormatId(formatIdList);
+					}
+				}
 				else{
 					udoi.upgrade();
+				}
 				out.write("Updated DOI's for server " + serverid);
-            leinfelder
+			} else if (subaction.equals("removeinvalidreplicas")) {
 				RemoveInvalidReplicas rir = new RemoveInvalidReplicas();
 				int serverLocation = -1;
 				String serverid = ((String[]) params.get("serverid"))[0];
 				serverLocation = Integer.parseInt(serverid);
 				rir.setServerLocation(serverLocation );
 				rir.upgrade();
 				out.write("Removed invalid replicas for server " + serverid);
-            slaughter
+			} else if (subaction.equals("syncaccesspolicy")) {
 				SyncAccessPolicy syncAP = new SyncAccessPolicy();
 				response.setContentType("text/html");
 				out = response.getWriter();
-            leinfelder
+				if (params.containsKey("pid")) {
 					String[] pids = params.get("pid");
 					logMetacat.debug("Attempting to sync access policies for pids: " + pids);
 					ArrayList<String> pidsToSync = new ArrayList<String>(Arrays.asList(pids));
-            slaughter
+					try {
-            leinfelder
+						List<Identifier> syncedPids = syncAP.sync(pidsToSync);
 						out.write("<html><body>Syncing access policies has completed for " + syncedPids.size() + " pids.</body></html>");
-            slaughter
+					} catch (Exception e) {
 						logMetacat.error("Error syncing all access polies: "
 								+ e.getMessage());
 						response.setContentType("text/html");
 						out = response.getWriter();
 						out.write("<html><body>Error syncing access policies</body></html>");
+					}
 				} else {
-            slaughter
+					logMetacat.debug("Request to sync all access policies has been submitted.");
-            slaughter
+					try {
 						syncAP.syncAll();
-            slaughter
+						out.write("<html><body>Request to sync all access policies has been submitted.</body></html>");
-            slaughter
+					} catch (Exception e) {
 						logMetacat.error("Error syncing access policies: "
 								+ e.getMessage());
 						out.write("<html><body>Error syncing access policies: " + e.getMessage() + " </body></html>");
+					}
+				}
-            daigle
+			} else {
             leinfelder
-            leinfelder
+				out.write("<error>Unkonwn subaction</error>");
-            leinfelder
+				return;
+			}
-            leinfelder
+			// hide SM/ORE buttons?
 //			String dataoneConfigured = PropertyService.getProperty("configutil.dataoneConfigured");
 //			if (dataoneConfigured != null) {
 //				showGenerateSystemMetadata = Boolean.parseBoolean(dataoneConfigured);
 //			}
             leinfelder
 			// always list them after processing
 			response.setContentType("text/html");
 			out.write("<html><body><table border=\"1\">");
 			out.write("<tr><td><b>server</b></td>");
 			out.write("<td><b>last_checked</b></td>");
 			out.write("<td><b>replicate</b></td>");
 			out.write("<td><b>datareplicate</b></td>");
 			out.write("<td><b>hub</b></td>");
 			if (showGenerateSystemMetadata) {
-            leinfelder
+				out.write("<td><b>System Metadata</b></td>");
 				out.write("<td><b>ORE Maps</b></td>");
-            leinfelder
+				out.write("<td><b>DOI Registrations</b></td>");
-            leinfelder
+				out.write("<td><b>Invalid Replicas</b></td>");
             leinfelder
-            slaughter
+			out.write("<td><b>Sync Access Policies</b></td>");
-            leinfelder
+			out.write("</tr>");
             tao
-            leinfelder
+			pstmt = dbConn.prepareStatement("SELECT serverid, server, last_checked, replicate, datareplicate, hub FROM xml_replication");
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			boolean tablehasrows = rs.next();
 			while (tablehasrows) {
-            leinfelder
+				String serverId = rs.getString(1);
-            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>");
 				out.write(rs.getString(6) + "</td>");
 				if (showGenerateSystemMetadata) {
-            leinfelder
+					// for SM
-            leinfelder
+					out.write("<td><form action='" + request.getContextPath() + "/admin'>");
-            leinfelder
+					out.write("<input name='serverid' type='hidden' value='" + serverId  + "'/>");
-            leinfelder
+					out.write("<input name='configureType' type='hidden' value='replication'/>");
 					out.write("<input name='action' type='hidden' value='servercontrol'/>");
 					out.write("<input name='subaction' type='hidden' value='generatesystemmetadata'/>");
 					out.write("<input type='submit' value='Generate System Metadata'/>");
 					out.write("</form></td>");
             leinfelder
 					// for ORE maps
 					out.write("<td><form action='" + request.getContextPath() + "/admin'>");
-            leinfelder
+					out.write("<input name='serverid' type='hidden' value='" + serverId + "'/>");
-            leinfelder
+					out.write("<input name='configureType' type='hidden' value='replication'/>");
 					out.write("<input name='action' type='hidden' value='servercontrol'/>");
 					out.write("<input name='subaction' type='hidden' value='generateore'/>");
 					out.write("<input type='submit' value='Generate ORE'/>");
 					out.write("</form></td>");
             leinfelder
-            leinfelder
+					// for DOI updating
 					out.write("<td><form action='" + request.getContextPath() + "/admin'>");
 					out.write("<input name='serverid' type='hidden' value='" + serverId + "'/>");
 					out.write("<input name='configureType' type='hidden' value='replication'/>");
 					out.write("<input name='action' type='hidden' value='servercontrol'/>");
 					out.write("<input name='subaction' type='hidden' value='updatedoi'/>");
-            walker
+					out.write("<label>Update by ID:</label>");
 					out.write("<textarea name='ids'></textarea>");
 					out.write("<label>Update by formatId:</label>");
 					out.write("<textarea name='formatIds'></textarea>");
-            leinfelder
+					out.write("<input type='submit' value='Update DOIs'/>");
 					out.write("</form></td>");
-            leinfelder
+					// for invalid replicas
 					out.write("<td><form action='" + request.getContextPath() + "/admin'>");
 					out.write("<input name='serverid' type='hidden' value='" + serverId + "'/>");
 					out.write("<input name='configureType' type='hidden' value='replication'/>");
 					out.write("<input name='action' type='hidden' value='servercontrol'/>");
 					out.write("<input name='subaction' type='hidden' value='removeinvalidreplicas'/>");
 					String disabled = "";
 					if (Integer.valueOf(serverId) == 1) {
 						disabled = "disabled='true'";
+					}
 					out.write("<input type='submit' value='Remove Invalid Replicas' " + disabled + " />");
 					out.write("</form></td>");
             leinfelder
-            slaughter
+				// for syncing access policies (MN -> CN)
 				out.write("<td><form action='" + request.getContextPath() + "/admin'>");
 				out.write("<input name='serverid' type='hidden' value='" + serverId + "'/>");
 				out.write("<input name='configureType' type='hidden' value='replication'/>");
 				out.write("<input name='action' type='hidden' value='servercontrol'/>");
 				out.write("<input name='subaction' type='hidden' value='syncaccesspolicy'/>");
 				out.write("<input type='submit' value='Sync access policies'/>");
 				out.write("</form></td>");
-            leinfelder
+				out.write("</tr>");
 				tablehasrows = rs.next();
             daigle
-            leinfelder
+			out.write("</table></body></html>");
-            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
+	/**
-            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
+			// strip out the system metadata portion
 			String systemMetadataXML = ReplicationUtil.getSystemMetadataContent(docInfoStr);
 			docInfoStr = ReplicationUtil.getContentWithoutSystemMetadata(docInfoStr);
-            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");
             leinfelder
 			// process system metadata
-            tao
+			SystemMetadata sysMeta = null;
-            leinfelder
+			if (systemMetadataXML != null) {
-            tao
+				sysMeta =
-            leinfelder
+					TypeMarshaller.unmarshalTypeFromStream(
 							SystemMetadata.class,
 							new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
 				// need the guid-to-docid mapping
-            leinfelder
+				boolean mappingExists = true;
-            leinfelder
+		      	mappingExists = IdentifierManager.getInstance().mappingExists(sysMeta.getIdentifier().getValue());
-            leinfelder
+		      	if (!mappingExists) {
 		      		IdentifierManager.getInstance().createMapping(sysMeta.getIdentifier().getValue(), docid);
+		      	}
-            leinfelder
+				// save the system metadata
 				HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
             tao
             leinfelder
             berkley
-            leinfelder
+			// dates
 			String createdDateString = docinfoHash.get("date_created");
 			String updatedDateString = docinfoHash.get("date_updated");
-            leinfelder
+			Date createdDate = DateTimeMarshaller.deserializeDateToUTC(createdDateString);
 			Date updatedDate = DateTimeMarshaller.deserializeDateToUTC(updatedDateString);
             leinfelder
-            daigle
+			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
-            leinfelder
+			DocumentImplWrapper wrapper = new DocumentImplWrapper(parserBase, false, 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
+				if(sysMeta != null) {
 					// submit for indexing. When the doc writing process fails, the index process will fail as well. But this failure
 					// will not interrupt the process.
 					try {
 						MetacatSolrIndex.getInstance().submit(sysMeta.getIdentifier(), sysMeta, null, true);
 					} catch (Exception ee) {
 						logReplication.warn("ReplicationService.handleForceReplicateRequest - couldn't index the doc since "+ee.getMessage());
+					}
+				}
-            leinfelder
+				//process extra access rules before dealing with the write exception (doc exist already)
 				try {
 		        	// check if we had a guid -> docid mapping
 		        	String docidNoRev = DocumentUtil.getDocIdFromAccessionNumber(docid);
 		        	int rev = DocumentUtil.getRevisionFromAccessionNumber(docid);
-            leinfelder
+		        	IdentifierManager.getInstance().getGUID(docidNoRev, rev);
-            leinfelder
+		        	// no need to create the mapping if we have it
 		        } catch (McdbDocNotFoundException mcdbe) {
 		        	// create mapping if we don't
 		        	IdentifierManager.getInstance().createMapping(docid, docid);
+		        }
-            daigle
+		        Vector<XMLAccessDAO> accessControlList = dih.getAccessControlList();
 		        if (accessControlList != null) {
 		        	AccessControlForSingleFile acfsf = new AccessControlForSingleFile(docid);
 		        	for (XMLAccessDAO xmlAccessDAO : accessControlList) {
-            leinfelder
+		        		try {
 			        		if (!acfsf.accessControlExists(xmlAccessDAO)) {
 			        			acfsf.insertPermissions(xmlAccessDAO);
 								logReplication.info("ReplicationService.handleForceReplicateRequest - document " + docid
 										+ " permissions added to DB");
+			        		}
 		        		} catch (PermOrderException poe) {
 		        			// this is problematic, but should not prevent us from replicating
 		        			// see https://redmine.dataone.org/issues/2583
 		        			String msg = "Could not insert access control for: " + docid + " Message: " + poe.getMessage();
 		        			logMetacat.error(msg, poe);
 		        			logReplication.error(msg, poe);
             daigle
+		            }
+		        }
             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(), request.getHeader("User-Agent"), 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,
-            leinfelder
+			HttpServletRequest request, boolean removeAll) {
-            daigle
+		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);
-            leinfelder
+			DocumentImpl.delete(docid, null, null, server, removeAll);
-            daigle
+			logReplication.info("ReplicationService.handleForceReplicateDeleteRequest - document " + docid + " was successfully deleted ");
-            leinfelder
+			EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), REPLICATIONUSER, docid,
-            daigle
+					"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
+			{
-            leinfelder
+//				dbaction = "update";
 				dbaction = null;
             daigle
             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
-            leinfelder
+			// strip out the system metadata portion
 		    String systemMetadataXML = ReplicationUtil.getSystemMetadataContent(docInfoStr);
 		   	docInfoStr = ReplicationUtil.getContentWithoutSystemMetadata(docInfoStr);
-            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");
             leinfelder
 			String createdDateString = docinfoHash.get("date_created");
 			String updatedDateString = docinfoHash.get("date_updated");
-            leinfelder
+			Date createdDate = DateTimeMarshaller.deserializeDateToUTC(createdDateString);
 			Date updatedDate = DateTimeMarshaller.deserializeDateToUTC(updatedDateString);
             leinfelder
-            daigle
+			logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - docHomeServer of datafile: " + docHomeServer);
-            leinfelder
+			// in case we have a write exception, we still want to track access and sysmeta
 			Exception writeException = null;
 			// do we need the object content?
 			if (dbaction != null && (dbaction.equals("insert") || dbaction.equals("update"))) {
-            daigle
+				//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");
-            leinfelder
+				InputStream inputStream = getURLStream(url);
-            leinfelder
+				//register data file into xml_documents table and write data file
-            daigle
+				//into file system
 				try {
-            leinfelder
+					DocumentImpl.writeDataFileInReplication(inputStream,
-            leinfelder
+							datafilePath, docName, docType, docid, null, docHomeServer,
-            daigle
+							server, DocumentImpl.DOCUMENTTABLE, false, createdDate,
 							updatedDate);
 				} catch (Exception e) {
 					writeException = e;
+				}
+			}
             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);
 			// process system metadata
 	        if (systemMetadataXML != null) {
 	      	  SystemMetadata sysMeta =
 	      		TypeMarshaller.unmarshalTypeFromStream(
 	      				  SystemMetadata.class,
 	      				  new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
 	      	  // need the guid-to-docid mapping
 	      	  boolean mappingExists = true;
-            leinfelder
+	      	  mappingExists = IdentifierManager.getInstance().mappingExists(sysMeta.getIdentifier().getValue());
-            leinfelder
+	      	  if (!mappingExists) {
 	      		  IdentifierManager.getInstance().createMapping(sysMeta.getIdentifier().getValue(), docid);
+	      	  }
 	      	  // save the system metadata
 	      	  HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
-            leinfelder
+	      	  // submit for indexing
-            leinfelder
+              MetacatSolrIndex.getInstance().submit(sysMeta.getIdentifier(), sysMeta, null, true);
             leinfelder
 	        // process the access control
-            leinfelder
+	        try {
 	        	// check if we had a guid -> docid mapping
 	        	String docidNoRev = DocumentUtil.getDocIdFromAccessionNumber(docid);
-            leinfelder
+	        	int rev = DocumentUtil.getRevisionFromAccessionNumber(docid);
 	        	IdentifierManager.getInstance().getGUID(docidNoRev, rev);
-            leinfelder
+	        	// no need to create the mapping if we have it
 	        } catch (McdbDocNotFoundException mcdbe) {
 	        	// create mapping if we don't
 	        	IdentifierManager.getInstance().createMapping(docid, docid);
+	        }
-            leinfelder
+	        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");
+	        		}
+	            }
+	        }
 	        // throw the write exception now -- this happens when access changes on an object
 			if (writeException != null) {
 				throw writeException;
+			}
             daigle
-            leinfelder
+			logReplication.info("ReplicationService.handleForceReplicateDataFileRequest - datafile " + docid + " added to DB with "
 					+ "action " + dbaction);
 			EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), REPLICATIONUSER,
 					docid, dbaction);
-            daigle
+		} catch (Exception e) {
-            leinfelder
+			e.printStackTrace();
 			logMetacat.error("ReplicationService.handleForceReplicateDataFileRequest - " + ReplicationService.METACAT_REPL_ERROR_MSG, e);
-            daigle
+			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];
             tao
-            daigle
+		try {
-            leinfelder
+			// get docinfo as XML string
 			String docinfoXML = getDocumentInfo(docid);
             leinfelder
-            leinfelder
+			// get a writer for sending back to response
-            daigle
+			response.setContentType("text/xml");
-            leinfelder
+			Writer out = response.getWriter();
-            leinfelder
+			out.write(docinfoXML);
-            leinfelder
+			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
-            leinfelder
+	public static Hashtable<String, String> getDocumentInfoMap(String docid)
 			throws HandlerException, AccessControlException, JiBXException,
 			IOException, McdbException, SAXException {
 		// Try get docid info from remote server
 		DocInfoHandler dih = new DocInfoHandler();
 		XMLReader docinfoParser = ReplicationHandler.initParser(dih);
 		String docInfoStr = getDocumentInfo(docid);
 		// strip out the system metadata portion
 		String systemMetadataXML = ReplicationUtil.getSystemMetadataContent(docInfoStr);
 		docInfoStr = ReplicationUtil.getContentWithoutSystemMetadata(docInfoStr);
 		docinfoParser.parse(new InputSource(new StringReader(docInfoStr)));
 		Hashtable<String, String> docinfoHash = dih.getDocInfo();
 		return docinfoHash;
+	}
-            leinfelder
+	/**
-            leinfelder
+	 * Gets a docInfo XML snippet for the replication API
 	 * @param docid
 	 * @return
 	 * @throws AccessControlException
 	 * @throws JiBXException
 	 * @throws IOException
 	 * @throws McdbException
 	 */
 	public static String getDocumentInfo(String docid) throws AccessControlException, JiBXException, IOException, McdbException {
 		StringBuffer sb = new StringBuffer();
 		DocumentImpl doc = new DocumentImpl(docid);
 		sb.append("<documentinfo><docid>").append(docid);
 		sb.append("</docid>");
 		try {
 			// serialize the System Metadata as XML for docinfo
 			String guid = IdentifierManager.getInstance().getGUID(doc.getDocID(), doc.getRev());
 			SystemMetadata systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);
 			ByteArrayOutputStream baos = new ByteArrayOutputStream();
 			TypeMarshaller.marshalTypeToOutputStream(systemMetadata, baos);
 			String systemMetadataXML = baos.toString("UTF-8");
 			sb.append("<systemMetadata>");
 			sb.append(systemMetadataXML);
 			sb.append("</systemMetadata>");
 		} catch(McdbDocNotFoundException e) {
 		  logMetacat.warn("No SystemMetadata found for: " + docid);
+		}
 		Calendar created = Calendar.getInstance();
 		created.setTime(doc.getCreateDate());
 		Calendar updated = Calendar.getInstance();
 		updated.setTime(doc.getUpdateDate());
-            leinfelder
+		sb.append("<docname><![CDATA[").append(doc.getDocname());
 		sb.append("]]></docname><doctype>").append(doc.getDoctype());
-            leinfelder
+		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(DateTimeMarshaller.serializeDateToUTC(doc.getCreateDate()));
 		sb.append("</date_created>");
 		sb.append("<date_updated>");
 		sb.append(DateTimeMarshaller.serializeDateToUTC(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>");
 		sb.append("<accessControl>");
 		AccessControlForSingleFile acfsf = new AccessControlForSingleFile(docid);
 		sb.append(acfsf.getAccessString());
 		sb.append("</accessControl>");
 		sb.append("</documentinfo>");
 		return sb.toString();
+	}
 	/**
-            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
+				// submit for indexing
-            leinfelder
+                MetacatSolrIndex.getInstance().submit(sysMeta.getIdentifier(), sysMeta, null, true);
             leinfelder
 			logReplication.info("ReplicationService.handleForceReplicateSystemMetadataRequest - processed guid: " + guid);
-            leinfelder
+			EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), 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
-            jones
+		} catch (Exception e) {
-            daigle
+			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);
-            jones
+		} finally {
 		    IOUtils.closeQuietly(fin);
+		}
             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;
-            jones
+		FileOutputStream fos = null;
-            jones
+		InputStream is = null;
 		OutputStream outputStream = 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) {
-            jones
+				fos = new FileOutputStream(documentPath);
-            jones
+				is = di.toXml(fos, null, null, true);
-            jones
+				fos.close();
-            jones
+				is.close();
             daigle
             tao
-            leinfelder
+			// read the file from disk and send it to outputstream
-            jones
+			outputStream = response.getOutputStream();
 			is = di.readFromFileSystem(outputStream, null, null, documentPath);
 			is.close();
 			outputStream.close();
             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();
-            leinfelder
+		} catch (Exception e) {
 			logReplication
 			.error("ReplicationService.handleGetDocumentRequest - General exception encountered."
 					+ "handlGetDocumentRequest for file: "
 					+ documentPath
 					+ " : "
 					+ e.getMessage());
 			// e.printStackTrace(System.out);
 			errorMsg = e.getMessage();
-            jones
+		} finally {
-            jones
+            IOUtils.closeQuietly(fos);
-            jones
+            IOUtils.closeQuietly(is);
             IOUtils.closeQuietly(outputStream);
             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();
             leinfelder
-            daigle
+			// 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
-            leinfelder
+			out.append("<?xml version=\"1.0\"?><replication>");
 			out.append("<server>")
-            daigle
+					.append(MetacatUtil.getLocalReplicationServerName());
 			//doclist.append(util.getProperty("replicationpath"));
-            leinfelder
+			out.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
-            jones
+			StringBuffer delsql = new StringBuffer();
-            leinfelder
+			delsql.append("SELECT t1.docid FROM xml_revisions t1 LEFT JOIN xml_documents t2 on t1.docid = t2.docid WHERE t2.docid IS NULL ");
             jones
-            daigle
+			// 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)) {
-            jones
+				delsql.append("and t1.server_location = 1");
             daigle
 			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
-            leinfelder
+							out.append("<updatedDocument>");
 							out.append("<docid>").append(rs.getString(1));
 							out.append("</docid><rev>" + rs.getInt(2));
 							out.append("</rev>");
 							out.append("</updatedDocument>");
-            daigle
+						}//if
 						else {
 							//for data file document, in datafile attributes
 							//we put "datafile" value there
-            leinfelder
+							out.append("<updatedDocument>");
 							out.append("<docid>").append(rs.getString(1));
 							out.append("</docid><rev>" + rs.getInt(2));
 							out.append("</rev>");
 							out.append("<datafile>");
 							out.append(DATA_FILE_FLAG);
 							out.append("</datafile>");
 							out.append("</updatedDocument>");
-            daigle
+						}//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
-            leinfelder
+							out.append("<updatedDocument>");
 							out.append("<docid>" + rs.getString(1));
 							out.append("</docid><rev>" + rs.getInt(2));
 							out.append("</rev>");
 							out.append("</updatedDocument>");
-            daigle
+						} 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
-            leinfelder
+				out.append("<deletedDocument><docid>").append(rs.getString(1));
 				out.append("</docid><rev></rev></deletedDocument>");
-            daigle
+				//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);
-            leinfelder
+				out.append("<updatedDocument>");
 				out.append("<docid>").append(v.elementAt(0));
 				out.append("</docid><rev>");
 				out.append(v.elementAt(1));
 				out.append("</rev>");
 				out.append("</updatedDocument>");
             daigle
 			// add revision doc list
-            leinfelder
+			out.append(prepareRevisionDoc(dbConn, revisionSql.toString(),
-            daigle
+					replicateData));
             tao
-            leinfelder
+			out.append("</updates></replication>");
 			logReplication.info("ReplicationService.handleUpdateRequest - done writing to output stream.");
-            daigle
+			pstmt.close();
 			//conn.close();
             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();
-            leinfelder
+		logReplication.warn("Processing replication revision for documents");
-            leinfelder
+		while (rs.next()) {
-            daigle
+			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) {
-            leinfelder
+				logMetacat.debug("SKipping data file because data replication is not configured");
-            daigle
+				// do nothing
 			} else {
-            leinfelder
+				String docid = rs.getString(1);
 				int rev = rs.getInt(2);
 				logMetacat.debug("Processing replication revision for docid: " + docid + "." + rev);
             tao
-            daigle
+				revDocList.append("<revisionDocument>");
-            leinfelder
+				revDocList.append("<docid>").append(docid);
 				revDocList.append("</docid><rev>").append(rev);
-            daigle
+				revDocList.append("</rev>");
 				// data file
 				if (recordDoctype.equals("BIN")) {
 					revDocList.append("<datafile>");
-            leinfelder
+					revDocList.append(DATA_FILE_FLAG);
-            daigle
+					revDocList.append("</datafile>");
+				}
 				revDocList.append("</revisionDocument>");
             tao
-            daigle
+			}//else
+		}
 		//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) {
             leinfelder
-            leinfelder
+		// use standard format -- the receiving end wants this too
 		String dateString = DateTimeMarshaller.serializeDateToUTC(Calendar.getInstance().getTime());
             leinfelder
-            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 "
-            leinfelder
+					+ "xml_replication where serverid = ?");
-            daigle
+			pstmt = dbConn.prepareStatement(sql);
-            leinfelder
+			pstmt.setInt(1, serverCode);
-            daigle
+			//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 "
-            leinfelder
+					+ "WHERE server LIKE ?");
 			pstmt.setString(1, server);
-            daigle
+			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;
+	}
             leinfelder
 	/**
 	 * Returns a Map of serverCode=serverName
 	 * @return Map of server codes to names (URIs)
 	 */
 	public static Map<Integer, String> getServerCodes() throws ServiceException {
 		DBConnection dbConn = null;
 		int serialNumber = -1;
 		PreparedStatement pstmt = null;
 		Map<Integer, String> codes = new HashMap<Integer, String>();
             tao
-            leinfelder
+		try {
 			dbConn = DBConnectionPool.getDBConnection("MetacatReplication.getServerCodes");
 			serialNumber = dbConn.getCheckOutSerialNumber();
 			pstmt = dbConn.prepareStatement("SELECT serverid, server FROM xml_replication ");
 			pstmt.execute();
 			ResultSet rs = pstmt.getResultSet();
 			while (rs.next()) {
 				int serverCode = rs.getInt(1);
 				String server = rs.getString(2);
 				codes.put(serverCode, server);
+			}
 			pstmt.close();
 		} catch (SQLException sqle) {
 			throw new ServiceException("ReplicationService.getServerCodes - "
 					+ "SQL error when getting server map: " + sqle.getMessage());
 		} finally {
 			try {
 				pstmt.close();
 			}//try
 			catch (Exception ee) {
 				logMetacat.error("ReplicationService.getServerCodes - " + ReplicationService.METACAT_REPL_ERROR_MSG);
 				logReplication.error("ReplicationService.getServerCodes - Error in MetacatReplicatio.getServerCodes: "
 						+ ee.getMessage());
 			}//catch
 			finally {
 				DBConnectionPool.returnDBConnection(dbConn, serialNumber);
 			}//finally
 		}//finally
 		return codes;
+	}
-            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 "
-            leinfelder
+					+ "WHERE docid LIKE ? ");
 			pstmt.setString(1, docId);
-            daigle
+			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
 	 */
-            leinfelder
+	public static String getURLContent(URL u) throws Exception {
-            daigle
+		char istreamChar;
 		int istreamInt;
-            leinfelder
+		// get the response content
-            leinfelder
+		InputStream input = getURLStream(u);
-            leinfelder
+		logReplication.info("ReplicationService.getURLContent - After getting response from: " + 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();
+	}
             leinfelder
 	/**
-            leinfelder
+	 * This method returns the InputStream after opening a url
 	 * @param u the url to return the content from
 	 * @return a InputStream representing the content of the url
 	 * @throws java.io.IOException
 	 */
-            leinfelder
+	public static InputStream getURLStream(URL u) throws Exception {
-            leinfelder
+	    logReplication.info("Getting url stream from " + u.toString());
 		logReplication.info("ReplicationService.getURLStream - Before sending request to: " + u.toString());
 		// use httpclient to set up SSL
-            leinfelder
+		DefaultHttpMultipartRestClient client = getSSLClient();
-            leinfelder
+		// get the response content
-            leinfelder
+		InputStream input = client.doGetRequest(u.toString(), CLIENTTIMEOUT);
-            leinfelder
+		logReplication.info("ReplicationService.getURLStream - After getting response from: " + u.toString());
 		return input;
+	}
 	/**
-            leinfelder
+	 * Sets up an HttpClient with SSL connection.
 	 * Sends client certificate to the server when doing the request.
 	 * @return
 	 */
-            leinfelder
+	private static DefaultHttpMultipartRestClient getSSLClient() {
 		DefaultHttpMultipartRestClient client = new DefaultHttpMultipartRestClient();
             leinfelder
 		// set up this server's client identity
 		String subject = null;
 		try {
-            leinfelder
+			// TODO: should there be alternative ways to get the key and certificate?
-            leinfelder
+			String certificateFile = PropertyService.getProperty("replication.certificate.file");
 	    	String keyFile = PropertyService.getProperty("replication.privatekey.file");
 			String keyPassword = PropertyService.getProperty("replication.privatekey.password");
 			X509Certificate certificate = CertificateManager.getInstance().loadCertificateFromFile(certificateFile);
 			PrivateKey privateKey = CertificateManager.getInstance().loadPrivateKeyFromFile(keyFile, keyPassword);
-            leinfelder
+			subject = CertificateManager.getInstance().getSubjectDN(certificate);
-            leinfelder
+			CertificateManager.getInstance().registerCertificate(subject, certificate, privateKey);
-            leinfelder
+		} catch (Exception e) {
 			// this is pretty much required for replication communication
-            leinfelder
+			logReplication.warn("Could not find server's client certificate/private key: " + e.getMessage());
             leinfelder
             leinfelder
 		// set the configured timeout
-            leinfelder
+		//client.setTimeouts(CLIENTTIMEOUT);
             leinfelder
-            leinfelder
+		SSLSocketFactory socketFactory = null;
 		try {
 			socketFactory = CertificateManager.getInstance().getSSLSocketFactory(subject);
 		} catch (FileNotFoundException e) {
 			// these are somewhat expected for anonymous client use
 			logReplication.warn("Could not set up SSL connection for client - likely because the certificate could not be located: " + e.getMessage());
 		} catch (Exception e) {
 			// this is likely more severe
 			logReplication.warn("Funky SSL going on: " + e.getClass() + ":: " + e.getMessage());
+		}
 		try {
 			//443 is the default port, this value is overridden if explicitly set in the URL
 			Scheme sch = new Scheme("https", 443, socketFactory);
 			client.getHttpClient().getConnectionManager().getSchemeRegistry().register(sch);
 		} catch (Exception e) {
 			// this is likely more severe
 			logReplication.error("Failed to set up SSL connection for client. Continuing. " + e.getClass() + ":: " + e.getMessage(), e);
+		}
 		return client;
+	}
             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 "
-            leinfelder
+					+ "xml_replication where server like ? ");
 			pstmt.setString(1, server);
-            daigle
+			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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