/src/edu/ucsb/nceas/metacat/dataone/MNodeService.java - Annotate - Metacat - Ecoinformatics Redmine

metacat/src/edu/ucsb/nceas/metacat/dataone/MNodeService.java @ 9493

-            cjones
+/**
  *  '$RCSfile$'
  *  Copyright: 2000-2011 Regents of the University of California and the
  *              National Center for Ecological Analysis and Synthesis
+ *
  *   '$Author:  $'
  *     '$Date:  $'
+ *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation; either version 2 of the License, or
  * (at your option) any later version.
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
+ *
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  */
 package edu.ucsb.nceas.metacat.dataone;
-            leinfelder
+import java.io.ByteArrayInputStream;
-            leinfelder
+import java.io.ByteArrayOutputStream;
-            leinfelder
+import java.io.File;
-            leinfelder
+import java.io.FileInputStream;
-            leinfelder
+import java.io.FileOutputStream;
-            cjones
+import java.io.IOException;
-            cjones
+import java.io.InputStream;
-            leinfelder
+import java.io.InputStreamReader;
-            leinfelder
+import java.io.OutputStreamWriter;
-            walker
+import java.io.StringReader;
-            leinfelder
+import java.io.UnsupportedEncodingException;
-            leinfelder
+import java.io.Writer;
-            leinfelder
+import java.math.BigInteger;
-            leinfelder
+import java.net.URISyntaxException;
-            walker
+import java.nio.charset.Charset;
-            cjones
+import java.security.NoSuchAlgorithmException;
-            leinfelder
+import java.sql.SQLException;
-            leinfelder
+import java.util.ArrayList;
-            leinfelder
+import java.util.Calendar;
-            cjones
+import java.util.Date;
-            walker
+import java.util.HashMap;
-            tao
+import java.util.HashSet;
-            leinfelder
+import java.util.Hashtable;
-            cjones
+import java.util.List;
-            leinfelder
+import java.util.Map;
-            leinfelder
+import java.util.Set;
-            leinfelder
+import java.util.Timer;
-            leinfelder
+import java.util.UUID;
-            leinfelder
+import java.util.Vector;
             cjones
-            leinfelder
+import javax.servlet.http.HttpServletRequest;
-            walker
+import javax.xml.transform.Result;
 import javax.xml.transform.Source;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
             leinfelder
-            cjones
+import org.apache.commons.io.IOUtils;
-            cjones
+import org.apache.log4j.Logger;
-            leinfelder
+import org.dataone.client.v2.CNode;
 import org.dataone.client.v2.itk.D1Client;
 import org.dataone.client.v2.MNode;
 import org.dataone.client.v2.formats.ObjectFormatCache;
-            leinfelder
+import org.dataone.client.auth.CertificateManager;
-            leinfelder
+import org.dataone.client.v2.formats.ObjectFormatInfo;
-            leinfelder
+import org.dataone.configuration.Settings;
-            leinfelder
+import org.dataone.ore.ResourceMapFactory;
-            cjones
+import org.dataone.service.exceptions.BaseException;
-            cjones
+import org.dataone.service.exceptions.IdentifierNotUnique;
 import org.dataone.service.exceptions.InsufficientResources;
 import org.dataone.service.exceptions.InvalidRequest;
 import org.dataone.service.exceptions.InvalidSystemMetadata;
 import org.dataone.service.exceptions.InvalidToken;
 import org.dataone.service.exceptions.NotAuthorized;
 import org.dataone.service.exceptions.NotFound;
 import org.dataone.service.exceptions.NotImplemented;
 import org.dataone.service.exceptions.ServiceFailure;
-            leinfelder
+import org.dataone.service.exceptions.SynchronizationFailed;
-            cjones
+import org.dataone.service.exceptions.UnsupportedType;
-            leinfelder
+import org.dataone.service.mn.tier1.v2.MNCore;
 import org.dataone.service.mn.tier1.v2.MNRead;
 import org.dataone.service.mn.tier2.v2.MNAuthorization;
 import org.dataone.service.mn.tier3.v2.MNStorage;
 import org.dataone.service.mn.tier4.v2.MNReplication;
 import org.dataone.service.mn.v2.MNPackage;
 import org.dataone.service.mn.v2.MNQuery;
 import org.dataone.service.mn.v2.MNView;
-            leinfelder
+import org.dataone.service.types.v1.AccessRule;
-            leinfelder
+import org.dataone.service.types.v1.Checksum;
-            leinfelder
+import org.dataone.service.types.v1.DescribeResponse;
-            leinfelder
+import org.dataone.service.types.v1.Event;
 import org.dataone.service.types.v1.Identifier;
-            leinfelder
+import org.dataone.service.types.v2.Log;
 import org.dataone.service.types.v2.LogEntry;
 import org.dataone.service.types.v2.OptionList;
-            leinfelder
+import org.dataone.service.types.v1.MonitorInfo;
 import org.dataone.service.types.v1.MonitorList;
-            leinfelder
+import org.dataone.service.types.v2.Node;
 import org.dataone.service.types.v2.NodeList;
-            leinfelder
+import org.dataone.service.types.v1.NodeReference;
 import org.dataone.service.types.v1.NodeState;
 import org.dataone.service.types.v1.NodeType;
-            leinfelder
+import org.dataone.service.types.v2.ObjectFormat;
-            tao
+import org.dataone.service.types.v1.Group;
-            leinfelder
+import org.dataone.service.types.v1.ObjectFormatIdentifier;
 import org.dataone.service.types.v1.ObjectList;
 import org.dataone.service.types.v1.Permission;
 import org.dataone.service.types.v1.Ping;
-            tao
+import org.dataone.service.types.v1.Replica;
-            cjones
+import org.dataone.service.types.v1.ReplicationStatus;
-            leinfelder
+import org.dataone.service.types.v1.Schedule;
 import org.dataone.service.types.v1.Service;
 import org.dataone.service.types.v1.Services;
 import org.dataone.service.types.v1.Session;
 import org.dataone.service.types.v1.Subject;
 import org.dataone.service.types.v1.Synchronization;
-            leinfelder
+import org.dataone.service.types.v2.SystemMetadata;
-            leinfelder
+import org.dataone.service.types.v1.util.AuthUtils;
-            leinfelder
+import org.dataone.service.types.v1.util.ChecksumUtil;
-            leinfelder
+import org.dataone.service.types.v1_1.QueryEngineDescription;
 import org.dataone.service.types.v1_1.QueryEngineList;
-            leinfelder
+import org.dataone.service.types.v1_1.QueryField;
-            jones
+import org.dataone.service.util.Constants;
-            leinfelder
+import org.dataone.service.util.TypeMarshaller;
-            leinfelder
+import org.dspace.foresite.OREException;
 import org.dspace.foresite.OREParserException;
 import org.dspace.foresite.ORESerialiserException;
 import org.dspace.foresite.ResourceMap;
-            walker
+import org.ecoinformatics.datamanager.parser.DataPackage;
 import org.ecoinformatics.datamanager.parser.Entity;
 import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
 import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;
-            walker
+import org.w3c.dom.Document;
             cjones
-            leinfelder
+import edu.ucsb.nceas.ezid.EZIDException;
-            leinfelder
+import edu.ucsb.nceas.metacat.DBQuery;
-            leinfelder
+import edu.ucsb.nceas.metacat.DBTransform;
-            cjones
+import edu.ucsb.nceas.metacat.EventLog;
-            cjones
+import edu.ucsb.nceas.metacat.IdentifierManager;
-            cjones
+import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
-            leinfelder
+import edu.ucsb.nceas.metacat.MetaCatServlet;
-            leinfelder
+import edu.ucsb.nceas.metacat.MetacatHandler;
-            tao
+import edu.ucsb.nceas.metacat.ReadOnlyChecker;
-            tao
+import edu.ucsb.nceas.metacat.common.query.EnabledQueryEngines;
-            leinfelder
+import edu.ucsb.nceas.metacat.common.query.stream.ContentTypeByteArrayInputStream;
-            leinfelder
+import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
-            tao
+import edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler;
-            tao
+import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
-            cjones
+import edu.ucsb.nceas.metacat.properties.PropertyService;
-            leinfelder
+import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
-            leinfelder
+import edu.ucsb.nceas.metacat.util.DeleteOnCloseFileInputStream;
-            leinfelder
+import edu.ucsb.nceas.metacat.util.DocumentUtil;
-            leinfelder
+import edu.ucsb.nceas.metacat.util.SkinUtil;
-            leinfelder
+import edu.ucsb.nceas.metacat.util.SystemUtil;
-            cjones
+import edu.ucsb.nceas.utilities.PropertyNotFoundException;
-            leinfelder
+import edu.ucsb.nceas.utilities.XMLUtilities;
-            leinfelder
+import edu.ucsb.nceas.utilities.export.HtmlToPdf;
-            leinfelder
+import gov.loc.repository.bagit.Bag;
 import gov.loc.repository.bagit.BagFactory;
 import gov.loc.repository.bagit.writer.impl.ZipWriter;
             cjones
-            cjones
+/**
  * Represents Metacat's implementation of the DataONE Member Node
  * service API. Methods implement the various MN* interfaces, and methods common
  * to both Member Node and Coordinating Node interfaces are found in the
  * D1NodeService base class.
             cjones
  * Implements:
  * MNCore.ping()
  * MNCore.getLogRecords()
  * MNCore.getObjectStatistics()
  * MNCore.getOperationStatistics()
  * MNCore.getStatus()
  * MNCore.getCapabilities()
  * MNRead.get()
  * MNRead.getSystemMetadata()
  * MNRead.describe()
  * MNRead.getChecksum()
  * MNRead.listObjects()
  * MNRead.synchronizationFailed()
  * MNAuthorization.isAuthorized()
  * MNAuthorization.setAccessPolicy()
  * MNStorage.create()
  * MNStorage.update()
  * MNStorage.delete()
-            tao
+ * MNStorage.updateSystemMetadata()
-            cjones
+ * MNReplication.replicate()
+ *
-            cjones
+ */
-            cjones
+public class MNodeService extends D1NodeService
-            leinfelder
+    implements MNAuthorization, MNCore, MNRead, MNReplication, MNStorage, MNQuery, MNView, MNPackage {
             cjones
-            tao
+    //private static final String PATHQUERY = "pathquery";
-            leinfelder
+	public static final String UUID_SCHEME = "UUID";
 	public static final String DOI_SCHEME = "DOI";
-            leinfelder
+	private static final String UUID_PREFIX = "urn:uuid:";
             walker
 	private static String XPATH_EML_ID = "/eml:eml/@packageId";
             leinfelder
 	/* the logger instance */
-            jones
+    private Logger logMetacat = null;
             cjones
     /* A reference to a remote Memeber Node */
-            tao
+    //private MNode mn;
             cjones
     /* A reference to a Coordinating Node */
     private CNode cn;
             cjones
             cjones
-            jones
+    /**
      * Singleton accessor to get an instance of MNodeService.
+     *
      * @return instance - the instance of MNodeService
      */
-            leinfelder
+    public static MNodeService getInstance(HttpServletRequest request) {
         return new MNodeService(request);
             cjones
-            jones
+    /**
      * Constructor, private for singleton access
      */
-            leinfelder
+    private MNodeService(HttpServletRequest request) {
         super(request);
-            jones
+        logMetacat = Logger.getLogger(MNodeService.class);
             leinfelder
         // set the Member Node certificate file location
         CertificateManager.getInstance().setCertificateLocation(Settings.getConfiguration().getString("D1Client.certificate.file"));
             cjones
             jones
     /**
      * Deletes an object from the Member Node, where the object is either a
      * data object or a science metadata object.
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param pid - The object identifier to be deleted
+     *
      * @return pid - the identifier of the object used for the deletion
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws NotFound
      * @throws NotImplemented
      * @throws InvalidRequest
      */
     @Override
     public Identifier delete(Session session, Identifier pid)
-            cjones
+        throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
             jones
-            tao
+        if(isReadOnlyMode()) {
-            tao
+            throw new ServiceFailure("2902", ReadOnlyChecker.DATAONEERROR);
             tao
-            leinfelder
+    	// only admin of  the MN or the CN is allowed a full delete
         boolean allowed = false;
-            leinfelder
+        allowed = isAdminAuthorized(session);
             tao
-            tao
+        String serviceFailureCode = "2902";
         Identifier sid = getPIDForSID(pid, serviceFailureCode);
         if(sid != null) {
             pid = sid;
+        }
-            tao
+        //check if it is the authoritative member node
         if(!allowed) {
             allowed = isAuthoritativeMNodeAdmin(session, pid);
+        }
-            leinfelder
+        if (!allowed) {
-            cjones
+            throw new NotAuthorized("1320", "The provided identity does not have " + "permission to delete objects on the Node.");
             leinfelder
-            leinfelder
+    	// defer to superclass implementation
         return super.delete(session, pid);
             cjones
-            jones
+    /**
      * Updates an existing object by creating a new object identified by
      * newPid on the Member Node which explicitly obsoletes the object
      * identified by pid through appropriate changes to the SystemMetadata
      * of pid and newPid
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param pid - The identifier of the object to be updated
      * @param object - the new object bytes
      * @param sysmeta - the new system metadata describing the object
+     *
      * @return newPid - the identifier of the new object
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws NotFound
      * @throws NotImplemented
      * @throws IdentifierNotUnique
      * @throws UnsupportedType
      * @throws InsufficientResources
      * @throws InvalidSystemMetadata
      * @throws InvalidRequest
      */
     @Override
-            cjones
+    public Identifier update(Session session, Identifier pid, InputStream object,
         Identifier newPid, SystemMetadata sysmeta)
         throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
         UnsupportedType, InsufficientResources, NotFound,
         InvalidSystemMetadata, NotImplemented, InvalidRequest {
             tao
         if(isReadOnlyMode()) {
-            tao
+            throw new ServiceFailure("1310", ReadOnlyChecker.DATAONEERROR);
             tao
             cjones
-            tao
+        //transform a sid to a pid if it is applicable
         String serviceFailureCode = "1310";
         Identifier sid = getPIDForSID(pid, serviceFailureCode);
         if(sid != null) {
             pid = sid;
+        }
-            jones
+        String localId = null;
         boolean allowed = false;
         boolean isScienceMetadata = false;
             leinfelder
         if (session == null) {
         	throw new InvalidToken("1210", "No session has been provided");
+        }
-            jones
+        Subject subject = session.getSubject();
-            leinfelder
+        // verify the pid is valid format
-            leinfelder
+        if (!isValidIdentifier(pid)) {
-            leinfelder
+        	throw new InvalidRequest("1202", "The provided identifier is invalid.");
             jones
             tao
         // verify the new pid is valid format
         if (!isValidIdentifier(newPid)) {
             throw new InvalidRequest("1202", "The provided identifier is invalid.");
+        }
         // make sure that the newPid doesn't exists
         boolean idExists = true;
         try {
             idExists = IdentifierManager.getInstance().identifierExists(newPid.getValue());
         } catch (SQLException e) {
             throw new ServiceFailure("1310",
                                     "The requested identifier " + newPid.getValue() +
                                     " couldn't be determined if it is unique since : "+e.getMessage());
+        }
         if (idExists) {
                 throw new IdentifierNotUnique("1220",
                           "The requested identifier " + newPid.getValue() +
                           " is already used by another object and" +
                           "therefore can not be used for this object. Clients should choose" +
                           "a new identifier that is unique and retry the operation or " +
                           "use CN.reserveIdentifier() to reserve one.");
+        }
             jones
         // check for the existing identifier
         try {
             localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
             cjones
-            jones
+        } catch (McdbDocNotFoundException e) {
-            cjones
+            throw new InvalidRequest("1202", "The object with the provided " +
                 "identifier was not found.");
-            tao
+        } catch (SQLException ee) {
             throw new ServiceFailure("1310", "The object with the provided " +
                     "identifier "+pid.getValue()+" can't be identified since - "+ee.getMessage());
             jones
             leinfelder
-            leinfelder
+        // set the originating node
         NodeReference originMemberNode = this.getCapabilities().getIdentifier();
         sysmeta.setOriginMemberNode(originMemberNode);
-            leinfelder
+        // set the submitter to match the certificate
         sysmeta.setSubmitter(subject);
-            leinfelder
+        // set the dates
         Date now = Calendar.getInstance().getTime();
-            cjones
+        sysmeta.setDateSysMetadataModified(now);
         sysmeta.setDateUploaded(now);
             leinfelder
         // make sure serial version is set to something
         BigInteger serialVersion = sysmeta.getSerialVersion();
         if (serialVersion == null) {
         	sysmeta.setSerialVersion(BigInteger.ZERO);
+        }
             jones
         // does the subject have WRITE ( == update) priveleges on the pid?
-            tao
+        //allowed = isAuthorized(session, pid, Permission.WRITE);
         //CN having the permission is allowed; user with the write permission and calling on the authoritative node is allowed.
         allowed = allowUpdating(session, pid, Permission.WRITE);
-            jones
+        if (allowed) {
             leinfelder
         	// check quality of SM
         	if (sysmeta.getObsoletedBy() != null) {
         		throw new InvalidSystemMetadata("1300", "Cannot include obsoletedBy when updating object");
+        	}
         	if (sysmeta.getObsoletes() != null && !sysmeta.getObsoletes().getValue().equals(pid.getValue())) {
         		throw new InvalidSystemMetadata("1300", "The identifier provided in obsoletes does not match old Identifier");
+        	}
             jones
             // get the existing system metadata for the object
             SystemMetadata existingSysMeta = getSystemMetadata(session, pid);
-            tao
+            //System.out.println("the archive is "+existingSysMeta.getArchived());
             //Base on documentation, we can't update an archived object:
             //The update operation MUST fail with Exceptions.InvalidRequest on objects that have the Types.SystemMetadata.archived property set to true.
             if(existingSysMeta.getArchived() != null && existingSysMeta.getArchived()) {
                 throw new InvalidRequest("1202","An archived object"+pid.getValue()+" can't be updated");
+            }
             jones
-            leinfelder
+            // check for previous update
             // see: https://redmine.dataone.org/issues/3336
             Identifier existingObsoletedBy = existingSysMeta.getObsoletedBy();
             if (existingObsoletedBy != null) {
             	throw new InvalidRequest("1202",
             			"The previous identifier has already been made obsolete by: " + existingObsoletedBy.getValue());
+            }
-            tao
+            //check the sid in the system metadata. If it exists, it should be non-exist or match the old sid in the previous system metadata.
             Identifier sidInSys = sysmeta.getSeriesId();
             if(sidInSys != null) {
-            tao
+                if (!isValidIdentifier(sidInSys)) {
                     throw new InvalidSystemMetadata("1300", "The provided series id in the system metadata is invalid.");
+                }
-            tao
+                Identifier previousSid = existingSysMeta.getSeriesId();
                 if(previousSid != null) {
                     // there is a previous sid, if the new sid doesn't match it, the new sid should be non-existing.
-            tao
+                    if(!sidInSys.getValue().equals(previousSid.getValue())) {
-            tao
+                        try {
                             idExists = IdentifierManager.getInstance().identifierExists(sidInSys.getValue());
                         } catch (SQLException e) {
                             throw new ServiceFailure("1310",
                                                     "The requested identifier " + sidInSys.getValue() +
                                                     " couldn't be determined if it is unique since : "+e.getMessage());
+                        }
                         if(idExists) {
                             throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata doesn't match the previous series id "
                                                             +previousSid.getValue()+", so it should NOT exist. However, it was used by another object.");
+                        }
+                    }
                 } else {
                     // there is no previous sid, the new sid should be non-existing.
                     try {
                         idExists = IdentifierManager.getInstance().identifierExists(sidInSys.getValue());
                     } catch (SQLException e) {
                         throw new ServiceFailure("1310",
                                                 "The requested identifier " + sidInSys.getValue() +
                                                 " couldn't be determined if it is unique since : "+e.getMessage());
+                    }
                     if(idExists) {
                         throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata should NOT exist since the previous series id is null."
                                                         +"However, it was used by another object.");
+                    }
+                }
-            tao
+                //the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario)
                 if(sidInSys.getValue().equals(newPid.getValue())) {
                     throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata shouldn't have the same value of the pid.");
+                }
             tao
             jones
             isScienceMetadata = isScienceMetadata(sysmeta);
             // do we have XML metadata or a data object?
             if (isScienceMetadata) {
                 // update the science metadata XML document
                 // TODO: handle non-XML metadata/data documents (like netCDF)
                 // TODO: don't put objects into memory using stream to string
-            tao
+                //String objectAsXML = "";
-            jones
+                try {
-            tao
+                    //objectAsXML = IOUtils.toString(object, "UTF-8");
             walker
-            tao
+                    localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update");
-            jones
+                    // register the newPid and the generated localId
                     if (newPid != null) {
                         IdentifierManager.getInstance().createMapping(newPid.getValue(), localId);
+                    }
                 } catch (IOException e) {
                     String msg = "The Node is unable to create the object. " + "There was a problem converting the object to XML";
                     logMetacat.info(msg);
                     throw new ServiceFailure("1310", msg + ": " + e.getMessage());
+                }
             } else {
                 // update the data object
                 localId = insertDataObject(object, newPid, session);
+            }
             leinfelder
             // add the newPid to the obsoletedBy list for the existing sysmeta
             existingSysMeta.setObsoletedBy(newPid);
-            tao
+            //increase version
             BigInteger current = existingSysMeta.getSerialVersion();
             //System.out.println("the current version is "+current);
             current = current.add(BigInteger.ONE);
             //System.out.println("the new current version is "+current);
             existingSysMeta.setSerialVersion(current);
-            leinfelder
+            // then update the existing system metadata
             updateSystemMetadata(existingSysMeta);
             // prep the new system metadata, add pid to the affected lists
             sysmeta.setObsoletes(pid);
             //sysmeta.addDerivedFrom(pid);
-            jones
+            // and insert the new system metadata
             insertSystemMetadata(sysmeta);
             // log the update event
-            leinfelder
+            EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), subject.getValue(), localId, Event.UPDATE.toString());
             leinfelder
             // attempt to register the identifier - it checks if it is a doi
             try {
-            leinfelder
+    			DOIService.getInstance().registerDOI(sysmeta);
-            leinfelder
+    		} catch (Exception e) {
-            leinfelder
+                throw new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
+    		}
             jones
         } else {
             throw new NotAuthorized("1200", "The provided identity does not have " + "permission to UPDATE the object identified by " + pid.getValue()
                     + " on the Member Node.");
+        }
         return newPid;
             cjones
             cjones
-            jones
+    public Identifier create(Session session, Identifier pid, InputStream object, SystemMetadata sysmeta) throws InvalidToken, ServiceFailure, NotAuthorized,
             IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, InvalidRequest {
             cjones
-            tao
+        if(isReadOnlyMode()) {
-            tao
+            throw new ServiceFailure("1190", ReadOnlyChecker.DATAONEERROR);
             tao
-            cjones
+        // check for null session
-            leinfelder
+        if (session == null) {
-            cjones
+          throw new InvalidToken("1110", "Session is required to WRITE to the Node.");
             leinfelder
-            tao
+        // verify the pid is valid format
         if (!isValidIdentifier(pid)) {
             throw new InvalidRequest("1102", "The provided identifier is invalid.");
+        }
-            leinfelder
+        // set the submitter to match the certificate
         sysmeta.setSubmitter(session.getSubject());
-            leinfelder
+        // set the originating node
         NodeReference originMemberNode = this.getCapabilities().getIdentifier();
         sysmeta.setOriginMemberNode(originMemberNode);
             leinfelder
         // if no authoritative MN, set it to the same
         if (sysmeta.getAuthoritativeMemberNode() == null) {
         	sysmeta.setAuthoritativeMemberNode(originMemberNode);
+        }
-            cjones
+        sysmeta.setArchived(false);
-            leinfelder
+        // set the dates
         Date now = Calendar.getInstance().getTime();
-            cjones
+        sysmeta.setDateSysMetadataModified(now);
         sysmeta.setDateUploaded(now);
             leinfelder
         // set the serial version
         sysmeta.setSerialVersion(BigInteger.ZERO);
             cjones
         // check that we are not attempting to subvert versioning
         if (sysmeta.getObsoletes() != null && sysmeta.getObsoletes().getValue() != null) {
             throw new InvalidSystemMetadata("1180",
               "The supplied system metadata is invalid. " +
               "The obsoletes field cannot have a value when creating entries.");
+        }
             leinfelder
-            cjones
+        if (sysmeta.getObsoletedBy() != null && sysmeta.getObsoletedBy().getValue() != null) {
             throw new InvalidSystemMetadata("1180",
               "The supplied system metadata is invalid. " +
               "The obsoletedBy field cannot have a value when creating entries.");
+        }
             tao
         // verify the sid in the system metadata
         Identifier sid = sysmeta.getSeriesId();
         boolean idExists = false;
         if(sid != null) {
             if (!isValidIdentifier(sid)) {
                 throw new InvalidSystemMetadata("1180", "The provided series id is invalid.");
+            }
             try {
                 idExists = IdentifierManager.getInstance().identifierExists(sid.getValue());
             } catch (SQLException e) {
                 throw new ServiceFailure("1190",
                                         "The series identifier " + sid.getValue() +
                                         " in the system metadata couldn't be determined if it is unique since : "+e.getMessage());
+            }
             if (idExists) {
                     throw new InvalidSystemMetadata("1180",
                               "The series identifier " + sid.getValue() +
                               " is already used by another object and" +
                               "therefore can not be used for this object. Clients should choose" +
                               "a new identifier that is unique and retry the operation or " +
                               "use CN.reserveIdentifier() to reserve one.");
+            }
             //the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario )
             if(sid.getValue().equals(pid.getValue())) {
                 throw new InvalidSystemMetadata("1180", "The series id "+sid.getValue()+" in the system metadata shouldn't have the same value of the pid.");
+            }
+        }
             cjones
-            leinfelder
+        // call the shared impl
-            leinfelder
+        Identifier resultPid = super.create(session, pid, object, sysmeta);
         // attempt to register the identifier - it checks if it is a doi
         try {
-            leinfelder
+			DOIService.getInstance().registerDOI(sysmeta);
-            leinfelder
+		} catch (Exception e) {
-            leinfelder
+			ServiceFailure sf = new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
 			sf.initCause(e);
             throw sf;
             leinfelder
         // return
 		return resultPid ;
             jones
             cjones
-            jones
+    /**
      * Called by a Coordinating Node to request that the Member Node create a
      * copy of the specified object by retrieving it from another Member
      * Node and storing it locally so that it can be made accessible to
      * the DataONE system.
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param sysmeta - Copy of the CN held system metadata for the object
      * @param sourceNode - A reference to node from which the content should be
      *                     retrieved. The reference should be resolved by
      *                     checking the CN node registry.
+     *
      * @return true if the replication succeeds
+     *
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws NotImplemented
      * @throws UnsupportedType
      * @throws InsufficientResources
      * @throws InvalidRequest
      */
     @Override
-            cjones
+    public boolean replicate(Session session, SystemMetadata sysmeta,
             NodeReference sourceNode) throws NotImplemented, ServiceFailure,
             NotAuthorized, InvalidRequest, InsufficientResources,
             UnsupportedType {
-            tao
+        /*if(isReadOnlyMode()) {
-            tao
+            throw new InvalidRequest("2153", "The Metacat member node is on the read-only mode and your request can't be fulfiled. Please try again later.");
-            tao
+        }*/
             cjones
-            cjones
+        if (session != null && sysmeta != null && sourceNode != null) {
             logMetacat.info("MNodeService.replicate() called with parameters: \n" +
                             "\tSession.Subject      = "                           +
                             session.getSubject().getValue() + "\n"                +
-            cjones
+                            "\tidentifier           = "                           +
                             sysmeta.getIdentifier().getValue()                    +
-            cjones
+                            "\n" + "\tSource NodeReference ="                     +
                             sourceNode.getValue());
+        }
-            jones
+        boolean result = false;
-            cjones
+        String nodeIdStr = null;
-            cjones
+        NodeReference nodeId = null;
             cjones
-            cjones
+        // get the referenced object
         Identifier pid = sysmeta.getIdentifier();
-            tao
+        // verify the pid is valid format
         if (!isValidIdentifier(pid)) {
             throw new InvalidRequest("2153", "The provided identifier in the system metadata is invalid.");
+        }
             cjones
         // get from the membernode
         // TODO: switch credentials for the server retrieval?
         this.cn = D1Client.getCN();
         InputStream object = null;
         Session thisNodeSession = null;
         SystemMetadata localSystemMetadata = null;
         BaseException failure = null;
-            cjones
+        String localId = null;
-            cjones
+        // TODO: check credentials
         // cannot be called by public
-            leinfelder
+        if (session == null || session.getSubject() == null) {
-            cjones
+            String msg = "No session was provided to replicate identifier " +
             sysmeta.getIdentifier().getValue();
-            tao
+            logMetacat.error(msg);
-            cjones
+            throw new NotAuthorized("2152", msg);
             cjones
-            cjones
+        // get the local node id
         try {
-            cjones
+            nodeIdStr = PropertyService.getProperty("dataone.nodeId");
-            cjones
+            nodeId = new NodeReference();
             nodeId.setValue(nodeIdStr);
             cjones
-            cjones
+        } catch (PropertyNotFoundException e1) {
-            cjones
+            String msg = "Couldn't get dataone.nodeId property: " + e1.getMessage();
-            cjones
+            failure = new ServiceFailure("2151", msg);
-            tao
+            //setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
-            cjones
+            logMetacat.error(msg);
-            tao
+            //return true;
             throw new ServiceFailure("2151", msg);
             cjones
             cjones
             cjones
             jones
         try {
-            cjones
+            // do we already have a replica?
             try {
-            cjones
+                localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
-            cjones
+                // if we have a local id, get the local object
                 try {
                     object = MetacatHandler.read(localId);
                 } catch (Exception e) {
-            leinfelder
+                	// NOTE: we may already know about this ID because it could be a data file described by a metadata file
                 	// https://redmine.dataone.org/issues/2572
                 	// TODO: fix this so that we don't prevent ourselves from getting replicas
-            cjones
+                    // let the CN know that the replication failed
-            leinfelder
+                	logMetacat.warn("Object content not found on this node despite having localId: " + localId);
                 	String msg = "Can't read the object bytes properly, replica is invalid.";
                     ServiceFailure serviceFailure = new ServiceFailure("2151", msg);
-            leinfelder
+                    setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, serviceFailure);
                     logMetacat.warn(msg);
-            cjones
+                    throw serviceFailure;
+                }
-            cjones
+            } catch (McdbDocNotFoundException e) {
-            cjones
+                logMetacat.info("No replica found. Continuing.");
             cjones
-            tao
+            } catch (SQLException ee) {
                 throw new ServiceFailure("2151", "Couldn't identify the local id of the object with the specified identifier "
                                         +pid.getValue()+" since - "+ee.getMessage());
             cjones
-            cjones
+            // no local replica, get a replica
-            cjones
+            if ( object == null ) {
-            tao
+                /*boolean success = true;
-            tao
+                try {
                     //use the v2 ping api to connect the source node
                     mn.ping();
                 } catch (Exception e) {
                     success = false;
-            tao
+                }*/
                 D1NodeVersionChecker checker = new D1NodeVersionChecker(sourceNode);
                 String nodeVersion = checker.getVersion("MNRead");
                 if(nodeVersion != null && nodeVersion.equals(D1NodeVersionChecker.V1)) {
                     //The source node is a v1 node, we use the v1 api
-            tao
+                    org.dataone.client.v1.MNode mNodeV1 =  org.dataone.client.v1.itk.D1Client.getMN(sourceNode);
-            tao
+                    object = mNodeV1.getReplica(thisNodeSession, pid);
                 } else if (nodeVersion != null && nodeVersion.equals(D1NodeVersionChecker.V2)){
-            tao
+                 // session should be null to use the default certificate
                     // location set in the Certificate manager
-            tao
+                    MNode mn = D1Client.getMN(sourceNode);
-            tao
+                    object = mn.getReplica(thisNodeSession, pid);
-            tao
+                } else {
                     throw new ServiceFailure("2151", "The version of MNRead service is "+nodeVersion+" in the source node "+sourceNode.getValue()+" and it is supported. Please check the information in the cn");
             tao
-            cjones
+                logMetacat.info("MNodeService.getReplica() called for identifier "
-            cjones
+                                + pid.getValue());
+            }
-            cjones
+        } catch (InvalidToken e) {
             String msg = "Could not retrieve object to replicate (InvalidToken): "+ e.getMessage();
             failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
             cjones
-            jones
+        } catch (NotFound e) {
-            cjones
+            String msg = "Could not retrieve object to replicate (NotFound): "+ e.getMessage();
             failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
             cjones
-            tao
+        } catch (NotAuthorized e) {
             String msg = "Could not retrieve object to replicate (NotAuthorized): "+ e.getMessage();
             failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
         } catch (NotImplemented e) {
             String msg = "Could not retrieve object to replicate (mn.getReplica NotImplemented): "+ e.getMessage();
             failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
         } catch (ServiceFailure e) {
             String msg = "Could not retrieve object to replicate (ServiceFailure): "+ e.getMessage();
             failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
         } catch (InsufficientResources e) {
             String msg = "Could not retrieve object to replicate (InsufficientResources): "+ e.getMessage();
             failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
             jones
-            leinfelder
+        // verify checksum on the object, if supported
         if (object.markSupported()) {
-            cjones
+            Checksum givenChecksum = sysmeta.getChecksum();
             Checksum computedChecksum = null;
             try {
-            leinfelder
+                computedChecksum = ChecksumUtil.checksum(object, givenChecksum.getAlgorithm());
-            cjones
+                object.reset();
             cjones
-            cjones
+            } catch (Exception e) {
-            leinfelder
+                String msg = "Error computing checksum on replica: " + e.getMessage();
-            leinfelder
+                logMetacat.error(msg);
-            cjones
+                ServiceFailure sf = new ServiceFailure("2151", msg);
                 sf.initCause(e);
-            tao
+                setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, sf);
-            cjones
+                throw sf;
+            }
-            cjones
+            if (!givenChecksum.getValue().equals(computedChecksum.getValue())) {
-            leinfelder
+                logMetacat.error("Given    checksum for " + pid.getValue() +
-            cjones
+                    "is " + givenChecksum.getValue());
-            leinfelder
+                logMetacat.error("Computed checksum for " + pid.getValue() +
-            cjones
+                    "is " + computedChecksum.getValue());
-            tao
+                String msg = "Computed checksum does not match declared checksum";
                 failure = new ServiceFailure("2151", msg);
                 setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
                 throw new ServiceFailure("2151", msg);
             cjones
             leinfelder
             cjones
-            jones
+        // add it to local store
         Identifier retPid;
         try {
-            leinfelder
+            // skip the MN.create -- this mutates the system metadata and we don't want it to
-            cjones
+            if ( localId == null ) {
-            leinfelder
+                // TODO: this will fail if we already "know" about the identifier
             	// FIXME: see https://redmine.dataone.org/issues/2572
-            cjones
+                retPid = super.create(session, pid, object, sysmeta);
                 result = (retPid.getValue().equals(pid.getValue()));
+            }
             cjones
-            leinfelder
+        } catch (Exception e) {
-            leinfelder
+            String msg = "Could not save object to local store (" + e.getClass().getName() + "): " + e.getMessage();
-            leinfelder
+            failure = new ServiceFailure("2151", msg);
             setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
             logMetacat.error(msg);
             throw new ServiceFailure("2151", msg);
             jones
-            cjones
+        // finish by setting the replication status
         setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.COMPLETED, null);
-            jones
+        return result;
             cjones
             tao
     /*
      * If the given node supports v2 replication.
      */
     private boolean supportV2Replication(Node node) throws InvalidRequest {
         return supportVersionReplication(node, "v2");
+    }
     /*
      * If the given node support the the given version replication. Return true if it does.
      */
     private boolean supportVersionReplication(Node node, String version) throws InvalidRequest{
         boolean support = false;
         if(node == null) {
             throw new InvalidRequest("2153", "There is no capacity information about the node in the replicate.");
         } else {
             Services services = node.getServices();
             if(services == null) {
                 throw new InvalidRequest("2153", "Can't get replica from a node which doesn't have the replicate service.");
             } else {
                List<Service> list = services.getServiceList();
                if(list == null) {
                    throw new InvalidRequest("2153", "Can't get replica from a node which doesn't have the replicate service.");
                } else {
                    for(Service service : list) {
                        if(service != null && service.getName() != null && service.getName().equals("MNReplication") &&
                                service.getVersion() != null && service.getVersion().equalsIgnoreCase(version) && service.getAvailable() == true ) {
                            support = true;
+                       }
+                   }
+               }
+            }
+        }
         return support;
+    }
             cjones
-            jones
+    /**
      * Return the object identified by the given object identifier
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param pid - the object identifier for the given object
+     *
      * @return inputStream - the input stream of the given object
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws InvalidRequest
      * @throws NotImplemented
      */
     @Override
-            cjones
+    public InputStream get(Session session, Identifier pid)
     throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
             cjones
-            jones
+        return super.get(session, pid);
             cjones
             cjones
             cjones
-            jones
+    /**
      * Returns a Checksum for the specified object using an accepted hashing algorithm
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param pid - the object identifier for the given object
      * @param algorithm -  the name of an algorithm that will be used to compute
      *                     a checksum of the bytes of the object
+     *
      * @return checksum - the checksum of the given object
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws NotFound
      * @throws InvalidRequest
      * @throws NotImplemented
      */
     @Override
-            cjones
+    public Checksum getChecksum(Session session, Identifier pid, String algorithm)
         throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
         InvalidRequest, NotImplemented {
             cjones
-            jones
+        Checksum checksum = null;
-            tao
+        String serviceFailure = "1410";
         String notFound = "1420";
         //Checkum only handles the pid, not sid
         checkV1SystemMetaPidExist(pid, serviceFailure, "The checksum for the object specified by "+pid.getValue()+" couldn't be returned ",  notFound,
                 "The object specified by "+pid.getValue()+" does not exist at this node.");
-            jones
+        InputStream inputStream = get(session, pid);
-            cjones
+        try {
-            jones
+            checksum = ChecksumUtil.checksum(inputStream, algorithm);
         } catch (NoSuchAlgorithmException e) {
             throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
                     + e.getMessage());
-            cjones
+        } catch (IOException e) {
-            jones
+            throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
                     + e.getMessage());
             cjones
             cjones
-            jones
+        if (checksum == null) {
             throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned.");
+        }
             cjones
-            jones
+        return checksum;
             cjones
             cjones
-            jones
+    /**
      * Return the system metadata for a given object
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param pid - the object identifier for the given object
+     *
      * @return inputStream - the input stream of the given system metadata object
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws NotFound
      * @throws InvalidRequest
      * @throws NotImplemented
      */
     @Override
-            cjones
+    public SystemMetadata getSystemMetadata(Session session, Identifier pid)
         throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
         NotImplemented {
             leinfelder
-            jones
+        return super.getSystemMetadata(session, pid);
+    }
             leinfelder
-            jones
+    /**
      * Retrieve the list of objects present on the MN that match the calling parameters
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param startTime - Specifies the beginning of the time range from which
      *                    to return object (>=)
      * @param endTime - Specifies the beginning of the time range from which
      *                  to return object (>=)
      * @param objectFormat - Restrict results to the specified object format
      * @param replicaStatus - Indicates if replicated objects should be returned in the list
      * @param start - The zero-based index of the first value, relative to the
      *                first record of the resultset that matches the parameters.
      * @param count - The maximum number of entries that should be returned in
      *                the response. The Member Node may return less entries
      *                than specified in this value.
+     *
      * @return objectList - the list of objects matching the criteria
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws InvalidRequest
      * @throws NotImplemented
      */
     @Override
-            leinfelder
+    public ObjectList listObjects(Session session, Date startTime, Date endTime, ObjectFormatIdentifier objectFormatId, Identifier identifier, Boolean replicaStatus, Integer start,
-            jones
+            Integer count) throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken {
-            tao
+        NodeReference nodeId = null;
         if(!replicaStatus) {
             //not include those objects whose authoritative node is not this mn
             nodeId = new NodeReference();
             try {
                 String currentNodeId = PropertyService.getInstance().getProperty("dataone.nodeId"); // return only pids for which this mn
                 nodeId.setValue(currentNodeId);
             } catch(Exception e) {
                 throw new ServiceFailure("1580", e.getMessage());
+            }
+        }
         return super.listObjects(session, startTime, endTime, objectFormatId, identifier, nodeId, start, count);
             cjones
             cjones
-            jones
+    /**
-            jones
+     * Return a description of the node's capabilities and services.
             jones
      * @return node - the technical capabilities of the Member Node
+     *
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws InvalidRequest
      * @throws NotImplemented
      */
     @Override
-            cjones
+    public Node getCapabilities()
         throws NotImplemented, ServiceFailure {
             cjones
-            jones
+        String nodeName = null;
         String nodeId = null;
-            jones
+        String subject = null;
-            cjones
+        String contactSubject = null;
-            jones
+        String nodeDesc = null;
-            jones
+        String nodeTypeString = null;
         NodeType nodeType = null;
-            tao
+        List<String> mnCoreServiceVersions = null;
         List<String> mnReadServiceVersions = null;
         List<String> mnAuthorizationServiceVersions = null;
         List<String> mnStorageServiceVersions = null;
         List<String> mnReplicationServiceVersions = null;
             cjones
-            jones
+        boolean nodeSynchronize = false;
         boolean nodeReplicate = false;
-            tao
+        List<String> mnCoreServiceAvailables = null;
         List<String> mnReadServiceAvailables = null;
         List<String> mnAuthorizationServiceAvailables = null;
         List<String> mnStorageServiceAvailables = null;
         List<String> mnReplicationServiceAvailables = null;
             cjones
-            jones
+        try {
             // get the properties of the node based on configuration information
-            tao
+            nodeName = Settings.getConfiguration().getString("dataone.nodeName");
             nodeId = Settings.getConfiguration().getString("dataone.nodeId");
             subject = Settings.getConfiguration().getString("dataone.subject");
             contactSubject = Settings.getConfiguration().getString("dataone.contactSubject");
             nodeDesc = Settings.getConfiguration().getString("dataone.nodeDescription");
             nodeTypeString = Settings.getConfiguration().getString("dataone.nodeType");
-            jones
+            nodeType = NodeType.convert(nodeTypeString);
-            tao
+            nodeSynchronize = new Boolean(Settings.getConfiguration().getString("dataone.nodeSynchronize")).booleanValue();
             nodeReplicate = new Boolean(Settings.getConfiguration().getString("dataone.nodeReplicate")).booleanValue();
             jones
-            jones
+            // Set the properties of the node based on configuration information and
             // calls to current status methods
-            leinfelder
+            String serviceName = SystemUtil.getSecureContextURL() + "/" + PropertyService.getProperty("dataone.serviceName");
-            jones
+            Node node = new Node();
-            leinfelder
+            node.setBaseURL(serviceName + "/" + nodeTypeString);
-            jones
+            node.setDescription(nodeDesc);
             jones
-            jones
+            // set the node's health information
             node.setState(NodeState.UP);
             // set the ping response to the current value
             Ping canPing = new Ping();
             canPing.setSuccess(false);
             try {
-            leinfelder
+            	Date pingDate = ping();
                 canPing.setSuccess(pingDate != null);
             } catch (BaseException e) {
-            jones
+                e.printStackTrace();
-            leinfelder
+                // guess it can't be pinged
             jones
             cjones
-            jones
+            node.setPing(canPing);
             jones
-            jones
+            NodeReference identifier = new NodeReference();
             identifier.setValue(nodeId);
             node.setIdentifier(identifier);
-            jones
+            Subject s = new Subject();
             s.setValue(subject);
             node.addSubject(s);
-            cjones
+            Subject contact = new Subject();
             contact.setValue(contactSubject);
             node.addContactSubject(contact);
-            jones
+            node.setName(nodeName);
             node.setReplicate(nodeReplicate);
             node.setSynchronize(nodeSynchronize);
             jones
-            jones
+            // services: MNAuthorization, MNCore, MNRead, MNReplication, MNStorage
             Services services = new Services();
             jones
-            tao
+            mnCoreServiceVersions = Settings.getConfiguration().getList("dataone.mnCore.serviceVersion");
             mnCoreServiceAvailables = Settings.getConfiguration().getList("dataone.mnCore.serviceAvailable");
             if(mnCoreServiceVersions != null && mnCoreServiceAvailables != null && mnCoreServiceVersions.size() == mnCoreServiceAvailables.size()) {
                 for(int i=0; i<mnCoreServiceVersions.size(); i++) {
                     String version = mnCoreServiceVersions.get(i);
                     boolean available = new Boolean(mnCoreServiceAvailables.get(i)).booleanValue();
                     Service sMNCore = new Service();
                     sMNCore.setName("MNCore");
                     sMNCore.setVersion(version);
                     sMNCore.setAvailable(available);
                     services.addService(sMNCore);
+                }
+            }
             mnReadServiceVersions = Settings.getConfiguration().getList("dataone.mnRead.serviceVersion");
             mnReadServiceAvailables = Settings.getConfiguration().getList("dataone.mnRead.serviceAvailable");
             if(mnReadServiceVersions != null && mnReadServiceAvailables != null && mnReadServiceVersions.size()==mnReadServiceAvailables.size()) {
                 for(int i=0; i<mnReadServiceVersions.size(); i++) {
                     String version = mnReadServiceVersions.get(i);
                     boolean available = new Boolean(mnReadServiceAvailables.get(i)).booleanValue();
                     Service sMNRead = new Service();
                     sMNRead.setName("MNRead");
                     sMNRead.setVersion(version);
                     sMNRead.setAvailable(available);
                     services.addService(sMNRead);
+                }
+            }
             mnAuthorizationServiceVersions = Settings.getConfiguration().getList("dataone.mnAuthorization.serviceVersion");
             mnAuthorizationServiceAvailables = Settings.getConfiguration().getList("dataone.mnAuthorization.serviceAvailable");
             if(mnAuthorizationServiceVersions != null && mnAuthorizationServiceAvailables != null && mnAuthorizationServiceVersions.size()==mnAuthorizationServiceAvailables.size()) {
                 for(int i=0; i<mnAuthorizationServiceVersions.size(); i++) {
                     String version = mnAuthorizationServiceVersions.get(i);
                     boolean available = new Boolean(mnAuthorizationServiceAvailables.get(i)).booleanValue();
                     Service sMNAuthorization = new Service();
                     sMNAuthorization.setName("MNAuthorization");
                     sMNAuthorization.setVersion(version);
                     sMNAuthorization.setAvailable(available);
                     services.addService(sMNAuthorization);
+                }
+            }
             mnStorageServiceVersions = Settings.getConfiguration().getList("dataone.mnStorage.serviceVersion");
             mnStorageServiceAvailables = Settings.getConfiguration().getList("dataone.mnStorage.serviceAvailable");
             if(mnStorageServiceVersions != null && mnStorageServiceAvailables != null && mnStorageServiceVersions.size() == mnStorageServiceAvailables.size()) {
                 for(int i=0; i<mnStorageServiceVersions.size(); i++) {
                     String version = mnStorageServiceVersions.get(i);
                     boolean available = new Boolean(mnStorageServiceAvailables.get(i)).booleanValue();
                     Service sMNStorage = new Service();
                     sMNStorage.setName("MNStorage");
                     sMNStorage.setVersion(version);
                     sMNStorage.setAvailable(available);
                     services.addService(sMNStorage);
+                }
+            }
             mnReplicationServiceVersions = Settings.getConfiguration().getList("dataone.mnReplication.serviceVersion");
             mnReplicationServiceAvailables = Settings.getConfiguration().getList("dataone.mnReplication.serviceAvailable");
             if(mnReplicationServiceVersions != null && mnReplicationServiceAvailables != null && mnReplicationServiceVersions.size() == mnReplicationServiceAvailables.size()) {
                 for (int i=0; i<mnReplicationServiceVersions.size(); i++) {
                     String version = mnReplicationServiceVersions.get(i);
                     boolean available = new Boolean(mnReplicationServiceAvailables.get(i)).booleanValue();
                     Service sMNReplication = new Service();
                     sMNReplication.setName("MNReplication");
                     sMNReplication.setVersion(version);
                     sMNReplication.setAvailable(available);
                     services.addService(sMNReplication);
+                }
+            }
-            jones
+            node.setServices(services);
             jones
-            jones
+            // Set the schedule for synchronization
             Synchronization synchronization = new Synchronization();
             Schedule schedule = new Schedule();
             Date now = new Date();
-            leinfelder
+            schedule.setYear(PropertyService.getProperty("dataone.nodeSynchronization.schedule.year"));
             schedule.setMon(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mon"));
             schedule.setMday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mday"));
             schedule.setWday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.wday"));
             schedule.setHour(PropertyService.getProperty("dataone.nodeSynchronization.schedule.hour"));
             schedule.setMin(PropertyService.getProperty("dataone.nodeSynchronization.schedule.min"));
             schedule.setSec(PropertyService.getProperty("dataone.nodeSynchronization.schedule.sec"));
-            jones
+            synchronization.setSchedule(schedule);
             synchronization.setLastHarvested(now);
             synchronization.setLastCompleteHarvest(now);
             node.setSynchronization(synchronization);
             jones
-            jones
+            node.setType(nodeType);
             return node;
             jones
-            jones
+        } catch (PropertyNotFoundException pnfe) {
             String msg = "MNodeService.getCapabilities(): " + "property not found: " + pnfe.getMessage();
             logMetacat.error(msg);
             throw new ServiceFailure("2162", msg);
+        }
             cjones
             cjones
             leinfelder
             cjones
-            jones
+    /**
      * A callback method used by a CN to indicate to a MN that it cannot
      * complete synchronization of the science metadata identified by pid.  Log
      * the event in the metacat event log.
+     *
      * @param session
      * @param syncFailed
+     *
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws NotImplemented
      */
     @Override
-            leinfelder
+    public boolean synchronizationFailed(Session session, SynchronizationFailed syncFailed)
-            cjones
+        throws NotImplemented, ServiceFailure, NotAuthorized {
             cjones
-            jones
+        String localId;
-            cjones
+        Identifier pid;
         if ( syncFailed.getPid() != null ) {
             pid = new Identifier();
             pid.setValue(syncFailed.getPid());
             boolean allowed;
             //are we allowed? only CNs
             try {
-            leinfelder
+                allowed = isAdminAuthorized(session);
-            cjones
+                if ( !allowed ){
                     throw new NotAuthorized("2162",
                             "Not allowed to call synchronizationFailed() on this node.");
+                }
             } catch (InvalidToken e) {
                 throw new NotAuthorized("2162",
                         "Not allowed to call synchronizationFailed() on this node.");
             leinfelder
             cjones
         } else {
             throw new ServiceFailure("2161", "The identifier cannot be null.");
+        }
-            jones
+        try {
-            cjones
+            localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
-            jones
+        } catch (McdbDocNotFoundException e) {
-            cjones
+            throw new ServiceFailure("2161", "The identifier specified by " +
                     syncFailed.getPid() + " was not found on this node.");
             cjones
-            tao
+        } catch (SQLException e) {
             throw new ServiceFailure("2161", "Couldn't identify the local id of the identifier specified by " +
                     syncFailed.getPid() + " since "+e.getMessage());
             jones
         // TODO: update the CN URL below when the CNRead.SynchronizationFailed
         // method is changed to include the URL as a parameter
-            rnahf
+        logMetacat.warn("Synchronization for the object identified by " +
-            cjones
+                pid.getValue() + " failed from " + syncFailed.getNodeId() +
-            rnahf
+                " with message: " + syncFailed.getDescription() +
                 ". Logging the event to the Metacat EventLog as a 'syncFailed' event.");
-            jones
+        // TODO: use the event type enum when the SYNCHRONIZATION_FAILED event is added
-            leinfelder
+        String principal = Constants.SUBJECT_PUBLIC;
-            leinfelder
+        if (session != null && session.getSubject() != null) {
-            cjones
+          principal = session.getSubject().getValue();
             leinfelder
         try {
-            cjones
+          EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "synchronization_failed");
-            leinfelder
+        } catch (Exception e) {
-            cjones
+            throw new ServiceFailure("2161", "Could not log the error for: " + pid.getValue());
             leinfelder
-            jones
+        //EventLog.getInstance().log("CN URL WILL GO HERE",
         //  session.getSubject().getValue(), localId, Event.SYNCHRONIZATION_FAILED);
-            leinfelder
+        return true;
             cjones
             cjones
-            jones
+    /**
      * Essentially a get() but with different logging behavior
      */
     @Override
-            cjones
+    public InputStream getReplica(Session session, Identifier pid)
-            tao
+        throws NotAuthorized, NotImplemented, ServiceFailure, InvalidToken, NotFound {
             cjones
-            cjones
+        logMetacat.info("MNodeService.getReplica() called.");
-            leinfelder
+        // cannot be called by public
         if (session == null) {
         	throw new InvalidToken("2183", "No session was provided.");
+        }
-            cjones
+        logMetacat.info("MNodeService.getReplica() called with parameters: \n" +
              "\tSession.Subject      = " + session.getSubject().getValue() + "\n" +
              "\tIdentifier           = " + pid.getValue());
-            jones
+        InputStream inputStream = null; // bytes to be returned
         handler = new MetacatHandler(new Timer());
         boolean allowed = false;
         String localId; // the metacat docid for the pid
             cjones
-            jones
+        // get the local docid from Metacat
         try {
             localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
         } catch (McdbDocNotFoundException e) {
-            tao
+            throw new NotFound("2185", "The object specified by " +
-            cjones
+                    pid.getValue() + " does not exist at this node.");
-            tao
+        } catch (SQLException e) {
             throw new ServiceFailure("2181", "The local id of the object specified by " +
                     pid.getValue() + " couldn't be identified since "+e.getMessage());
             jones
             cjones
-            leinfelder
+        Subject targetNodeSubject = session.getSubject();
             leinfelder
-            leinfelder
+        // check for authorization to replicate, null session to act as this source MN
-            cjones
+        try {
-            leinfelder
+            allowed = D1Client.getCN().isNodeAuthorized(null, targetNodeSubject, pid);
-            cjones
+        } catch (InvalidToken e1) {
             throw new ServiceFailure("2181", "Could not determine if node is authorized: "
                 + e1.getMessage());
         } catch (NotFound e1) {
-            tao
+            throw new NotFound("2185", "Could not find the object "+pid.getValue()+" in this node - "
-            cjones
+                    + e1.getMessage());
             cjones
-            cjones
+        } catch (InvalidRequest e1) {
             throw new ServiceFailure("2181", "Could not determine if node is authorized: "
                     + e1.getMessage());
+        }
-            cjones
+        logMetacat.info("Called D1Client.isNodeAuthorized(). Allowed = " + allowed +
             " for identifier " + pid.getValue());
-            jones
+        // if the person is authorized, perform the read
         if (allowed) {
             try {
-            jones
+                inputStream = MetacatHandler.read(localId);
-            jones
+            } catch (Exception e) {
-            tao
+                throw new ServiceFailure("2181", "The object specified by " +
-            cjones
+                    pid.getValue() + "could not be returned due to error: " + e.getMessage());
             jones
-            tao
+        } else {
             throw new NotAuthorized("2182", "The pid "+pid.getValue()+" is not authorized to be read by the client.");
             jones
             cjones
-            jones
+        // if we fail to set the input stream
         if (inputStream == null) {
-            cjones
+            throw new ServiceFailure("2181", "The object specified by " +
-            tao
+                pid.getValue() + " can't be returned from the node.");
             jones
         // log the replica event
         String principal = null;
         if (session.getSubject() != null) {
             principal = session.getSubject().getValue();
+        }
-            cjones
+        EventLog.getInstance().log(request.getRemoteAddr(),
             request.getHeader("User-Agent"), principal, localId, "replicate");
             jones
         return inputStream;
+    }
             tao
-            cjones
+    /**
-            cjones
+     * A method to notify the Member Node that the authoritative copy of
-            cjones
+     * system metadata on the Coordinating Nodes has changed.
             tao
-            cjones
+     * @param session   Session information that contains the identity of the
      *                  calling user as retrieved from the X.509 certificate
      *                  which must be traceable to the CILogon service.
      * @param serialVersion   The serialVersion of the system metadata
      * @param dateSysMetaLastModified  The time stamp for when the system metadata was changed
      * @throws NotImplemented
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws InvalidRequest
      * @throws InvalidToken
      */
-            leinfelder
+    public boolean systemMetadataChanged(Session session, Identifier pid,
-            cjones
+        long serialVersion, Date dateSysMetaLastModified)
         throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest,
         InvalidToken {
-            tao
+        boolean needCheckAuthoriativeNode = true;
         return systemMetadataChanged(needCheckAuthoriativeNode, session, pid,serialVersion, dateSysMetaLastModified);
+    }
     /**
      * A method to notify the Member Node that the authoritative copy of
      * system metadata on the Coordinating Nodes has changed.
      * @param needCheckAuthoriativeNode  this is for the dataone version 2. In the
      * version 2, there are two scenarios:
      * 1. If the node is the authoritative node, it only accepts serial version and replica list.
      * 2. If the node is a replica, it accepts everything.
      * For the v1, api, the parameter should be false.
      * @param session   Session information that contains the identity of the
      *                  calling user as retrieved from the X.509 certificate
      *                  which must be traceable to the CILogon service.
      * @param serialVersion   The serialVersion of the system metadata
      * @param dateSysMetaLastModified  The time stamp for when the system metadata was changed
      * @throws NotImplemented
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws InvalidRequest
      * @throws InvalidToken
      */
     public boolean systemMetadataChanged(boolean needCheckAuthoriativeNode, Session session, Identifier pid,
         long serialVersion, Date dateSysMetaLastModified)
         throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest,
         InvalidToken {
             cjones
-            tao
+        /*if(isReadOnlyMode()) {
-            tao
+            throw new InvalidRequest("1334", "The Metacat member node is on the read-only mode and your request can't be fulfiled. Please try again later.");
-            tao
+        }*/
-            cjones
+        // cannot be called by public
         if (session == null) {
-            tao
+        	throw new InvalidToken("1332", "No session was provided.");
             cjones
-            tao
+        String serviceFailureCode = "1333";
         Identifier sid = getPIDForSID(pid, serviceFailureCode);
         if(sid != null) {
             pid = sid;
+        }
-            cjones
+        SystemMetadata currentLocalSysMeta = null;
         SystemMetadata newSysMeta = null;
         CNode cn = D1Client.getCN();
         NodeList nodeList = null;
         Subject callingSubject = null;
         boolean allowed = false;
         // are we allowed to call this?
         callingSubject = session.getSubject();
         nodeList = cn.listNodes();
         for(Node node : nodeList.getNodeList()) {
             // must be a CN
             if ( node.getType().equals(NodeType.CN)) {
                List<Subject> subjectList = node.getSubjectList();
                // the calling subject must be in the subject list
                if ( subjectList.contains(callingSubject)) {
                    allowed = true;
+               }
+            }
+        }
         if (!allowed ) {
             String msg = "The subject identified by " + callingSubject.getValue() +
               " is not authorized to call this service.";
             throw new NotAuthorized("1331", msg);
+        }
         try {
-            tao
+            HazelcastService.getInstance().getSystemMetadataMap().lock(pid);
             cjones
-            tao
+            // compare what we have locally to what is sent in the change notification
-            cjones
+            try {
-            tao
+                currentLocalSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
             } catch (RuntimeException e) {
                 String msg = "SystemMetadata for pid " + pid.getValue() +
                   " couldn't be updated because it couldn't be found locally: " +
                   e.getMessage();
-            leinfelder
+                logMetacat.error(msg);
-            tao
+                ServiceFailure sf = new ServiceFailure("1333", msg);
-            leinfelder
+                sf.initCause(e);
-            tao
+                throw sf;
             cjones
             leinfelder
-            tao
+            if(currentLocalSysMeta == null) {
                 throw new InvalidRequest("1334", "We can't find the system metadata in the node for the id "+pid.getValue());
+            }
-            tao
+            if (currentLocalSysMeta.getSerialVersion().longValue() <= serialVersion ) {
-            tao
+                try {
                     newSysMeta = cn.getSystemMetadata(null, pid);
                 } catch (NotFound e) {
                     // huh? you just said you had it
                 	String msg = "On updating the local copy of system metadata " +
                     "for pid " + pid.getValue() +", the CN reports it is not found." +
                     " The error message was: " + e.getMessage();
                     logMetacat.error(msg);
                     //ServiceFailure sf = new ServiceFailure("1333", msg);
                     InvalidRequest sf = new InvalidRequest("1334", msg);
                     sf.initCause(e);
                     throw sf;
             tao
             tao
                 //check about the sid in the system metadata
                 Identifier newSID = newSysMeta.getSeriesId();
                 if(newSID != null) {
                     if (!isValidIdentifier(newSID)) {
                         throw new InvalidRequest("1334", "The series identifier in the new system metadata is invalid.");
+                    }
                     Identifier currentSID = currentLocalSysMeta.getSeriesId();
                     if( currentSID != null && currentSID.getValue() != null) {
                         if(!newSID.getValue().equals(currentSID.getValue())) {
                             //newSID doesn't match the currentSID. The newSID shouldn't be used.
                             try {
                                 if(IdentifierManager.getInstance().identifierExists(newSID.getValue())) {
                                     throw new InvalidRequest("1334", "The series identifier "+newSID.getValue()+" in the new system metadata has been used by another object.");
+                                }
                             } catch (SQLException sql) {
                                 throw new ServiceFailure("1333", "Couldn't determine if the SID "+newSID.getValue()+" in the system metadata exists in the node since "+sql.getMessage());
+                            }
+                        }
                     } else {
                         //newSID shouldn't be used
-            tao
+                        try {
                             if(IdentifierManager.getInstance().identifierExists(newSID.getValue())) {
                                 throw new InvalidRequest("1334", "The series identifier "+newSID.getValue()+" in the new system metadata has been used by another object.");
+                            }
                         } catch (SQLException sql) {
                             throw new ServiceFailure("1333", "Couldn't determine if the SID "+newSID.getValue()+" in the system metadata exists in the node since "+sql.getMessage());
+                        }
+                    }
             tao
                 // update the local copy of system metadata for the pid
                 try {
                     if(needCheckAuthoriativeNode) {
                         //this is for the v2 api.
                         if(isAuthoritativeNode(pid)) {
                             //this is the authoritative node, so we only accept replica and serial version
-            tao
+                            logMetacat.debug("MNodeService.systemMetadataChanged - this is the authoritative node for the pid "+pid.getValue());
-            tao
+                            List<Replica> replicas = newSysMeta.getReplicaList();
                             newSysMeta = currentLocalSysMeta;
                             newSysMeta.setSerialVersion(new BigInteger((new Long(serialVersion)).toString()));
                             newSysMeta.setReplicaList(replicas);
-            tao
+                        } else {
                             //we need to archive the object in the replica node
                             logMetacat.debug("MNodeService.systemMetadataChanged - this is NOT the authoritative node for the pid "+pid.getValue());
                             logMetacat.debug("MNodeService.systemMetadataChanged - the new value of archive is "+newSysMeta.getArchived()+" for the pid "+pid.getValue());
                             logMetacat.debug("MNodeService.systemMetadataChanged - the local value of archive is "+currentLocalSysMeta.getArchived()+" for the pid "+pid.getValue());
                             if (newSysMeta.getArchived() != null && newSysMeta.getArchived() == true  &&
                                     ((currentLocalSysMeta.getArchived() != null && currentLocalSysMeta.getArchived() == false ) || currentLocalSysMeta.getArchived() == null)){
                                 logMetacat.debug("MNodeService.systemMetadataChanged - start to archive object "+pid.getValue());
                                 boolean logArchive = false;
                                 boolean needUpdateModificationDate = false;
                                 try {
                                     archiveObject(logArchive, session, pid, newSysMeta, needUpdateModificationDate);
                                 } catch (NotFound e) {
                                     throw new InvalidRequest("1334", "Can't find the pid "+pid.getValue()+" for archive.");
+                                }
-            tao
+                            } else if((newSysMeta.getArchived() == null || newSysMeta.getArchived() == false) && (currentLocalSysMeta.getArchived() != null && currentLocalSysMeta.getArchived() == true )) {
                                 throw new InvalidRequest("1334", "The pid "+pid.getValue()+" has been archived and it can't be reset to false.");
             tao
             tao
+                    }
-            tao
+                    HazelcastService.getInstance().getSystemMetadataMap().put(newSysMeta.getIdentifier(), newSysMeta);
                     logMetacat.info("Updated local copy of system metadata for pid " +
                         pid.getValue() + " after change notification from the CN.");
                     // TODO: consider inspecting the change for archive
                     // see: https://projects.ecoinformatics.org/ecoinfo/issues/6417
     //                if (newSysMeta.getArchived() != null && newSysMeta.getArchived().booleanValue()) {
     //                	try {
     //						this.archive(session, newSysMeta.getIdentifier());
     //					} catch (NotFound e) {
     //						// do we care? nothing to do about it now
     //						logMetacat.error(e.getMessage(), e);
     //					}
     //                }
                 } catch (RuntimeException e) {
                     String msg = "SystemMetadata for pid " + pid.getValue() +
                       " couldn't be updated: " +
                       e.getMessage();
                     logMetacat.error(msg);
                     ServiceFailure sf = new ServiceFailure("1333", msg);
                     sf.initCause(e);
                     throw sf;
             tao
             cjones
-            tao
+                try {
                     String localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
                     EventLog.getInstance().log(request.getRemoteAddr(),
                             request.getHeader("User-Agent"), session.getSubject().getValue(),
                             localId, "updateSystemMetadata");
                 } catch (Exception e) {
                     // do nothing, no localId to log with
                     logMetacat.warn("MNodeService.systemMetadataChanged - Could not log 'updateSystemMetadata' event because no localId was found for pid: " + pid.getValue());
+                }
             tao
             cjones
-            tao
+        } finally {
             HazelcastService.getInstance().getSystemMetadataMap().unlock(pid);
+        }
-            tao
+        if (currentLocalSysMeta.getSerialVersion().longValue() <= serialVersion ) {
-            leinfelder
+            // attempt to re-register the identifier (it checks if it is a doi)
             try {
-            tao
+                DOIService.getInstance().registerDOI(newSysMeta);
             } catch (Exception e) {
                 logMetacat.warn("Could not [re]register DOI: " + e.getMessage(), e);
+            }
             leinfelder
-            leinfelder
+            // submit for indexing
             try {
-            tao
+                MetacatSolrIndex.getInstance().submit(newSysMeta.getIdentifier(), newSysMeta, null, true);
             } catch (Exception e) {
-            leinfelder
+                logMetacat.error("Could not submit changed systemMetadata for indexing, pid: " + newSysMeta.getIdentifier().getValue(), e);
             tao
             cjones
-            leinfelder
+        return true;
             cjones
-            cjones
+    /*
      * Set the replication status for the object on the Coordinating Node
+     *
      * @param session - the session for the this target node
      * @param pid - the identifier of the object being updated
      * @param nodeId - the identifier of this target node
      * @param status - the replication status to set
      * @param failure - the exception to include, if any
      */
     private void setReplicationStatus(Session session, Identifier pid,
         NodeReference nodeId, ReplicationStatus status, BaseException failure)
         throws ServiceFailure, NotImplemented, NotAuthorized,
         InvalidRequest {
         // call the CN as the MN to set the replication status
         try {
             this.cn = D1Client.getCN();
             this.cn.setReplicationStatus(session, pid, nodeId,
                     status, failure);
         } catch (InvalidToken e) {
-            leinfelder
+        	String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (InvalidToken): " + e.getMessage();
             logMetacat.error(msg);
         	throw new ServiceFailure("2151",
                     msg);
             cjones
         } catch (NotFound e) {
-            leinfelder
+        	String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (NotFound): " + e.getMessage();
             logMetacat.error(msg);
         	throw new ServiceFailure("2151",
                     msg);
             cjones
+        }
+    }
             leinfelder
     private SystemMetadata makePublicIfNot(SystemMetadata sysmeta, Identifier pid) throws ServiceFailure, InvalidToken, NotFound, NotImplemented, InvalidRequest {
     	// check if it is publicly readable
 		boolean isPublic = false;
 		Subject publicSubject = new Subject();
 		publicSubject.setValue(Constants.SUBJECT_PUBLIC);
 		Session publicSession = new Session();
 		publicSession.setSubject(publicSubject);
 		AccessRule publicRule = new AccessRule();
 		publicRule.addPermission(Permission.READ);
 		publicRule.addSubject(publicSubject);
 		// see if we need to add the rule
 		try {
 			isPublic = this.isAuthorized(publicSession, pid, Permission.READ);
 		} catch (NotAuthorized na) {
 			// well, certainly not authorized for public read!
+		}
 		if (!isPublic) {
 			sysmeta.getAccessPolicy().addAllow(publicRule);
+		}
 		return sysmeta;
+    }
             leinfelder
 	@Override
-            leinfelder
+	public Identifier generateIdentifier(Session session, String scheme, String fragment)
-            leinfelder
+			throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
 			InvalidRequest {
             leinfelder
-            leinfelder
+		// check for null session
         if (session == null) {
           throw new InvalidToken("2190", "Session is required to generate an Identifier at this Node.");
+        }
-            leinfelder
+		Identifier identifier = new Identifier();
             leinfelder
-            leinfelder
+		// handle different schemes
 		if (scheme.equalsIgnoreCase(UUID_SCHEME)) {
 			// UUID
 			UUID uuid = UUID.randomUUID();
             identifier.setValue(UUID_PREFIX + uuid.toString());
 		} else if (scheme.equalsIgnoreCase(DOI_SCHEME)) {
-            leinfelder
+			// generate a DOI
-            leinfelder
+			try {
-            leinfelder
+				identifier = DOIService.getInstance().generateDOI();
-            leinfelder
+			} catch (EZIDException e) {
-            leinfelder
+				ServiceFailure sf = new ServiceFailure("2191", "Could not generate DOI: " + e.getMessage());
 				sf.initCause(e);
 				throw sf;
             leinfelder
-            leinfelder
+		} else {
 			// default if we don't know the scheme
 			if (fragment != null) {
 				// for now, just autogen with fragment
 				String autogenId = DocumentUtil.generateDocumentId(fragment, 0);
 				identifier.setValue(autogenId);
 			} else {
 				// autogen with no fragment
 				String autogenId = DocumentUtil.generateDocumentId(0);
 				identifier.setValue(autogenId);
+			}
             leinfelder
-            leinfelder
+		// TODO: reserve the identifier with the CN. We can only do this when
 		// 1) the MN is part of a CN cluster
 		// 2) the request is from an authenticated user
 		return identifier;
             leinfelder
             leinfelder
             leinfelder
             leinfelder
 	@Override
-            leinfelder
+	public QueryEngineDescription getQueryEngineDescription(Session session, String engine)
-            leinfelder
+			throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
 			NotFound {
-            tao
+	    if(engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
-            tao
+	        if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
                 throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
+            }
-            tao
+	        QueryEngineDescription qed = new QueryEngineDescription();
-            tao
+	        qed.setName(EnabledQueryEngines.PATHQUERYENGINE);
-            tao
+	        qed.setQueryEngineVersion("1.0");
 	        qed.addAdditionalInfo("This is the traditional structured query for Metacat");
 	        Vector<String> pathsForIndexing = null;
 	        try {
 	            pathsForIndexing = SystemUtil.getPathsForIndexing();
 	        } catch (MetacatUtilException e) {
 	            logMetacat.warn("Could not get index paths", e);
+	        }
 	        for (String fieldName: pathsForIndexing) {
 	            QueryField field = new QueryField();
 	            field.addDescription("Indexed field for path '" + fieldName + "'");
 	            field.setName(fieldName);
 	            field.setReturnable(true);
 	            field.setSearchable(true);
 	            field.setSortable(false);
 	            // TODO: determine type and multivaluedness
 	            field.setType(String.class.getName());
 	            //field.setMultivalued(true);
 	            qed.addQueryField(field);
+	        }
 	        return qed;
-            tao
+	    } else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
-            tao
+	        if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
-            tao
+                throw new NotImplemented("0000", "MNodeService.getQueryEngineDescription - the query engine "+engine +" hasn't been implemented or has been disabled.");
             tao
-            tao
+	        try {
-            tao
+	            QueryEngineDescription qed = MetacatSolrEngineDescriptionHandler.getInstance().getQueryEngineDescritpion();
-            tao
+	            return qed;
 	        } catch (Exception e) {
 	            e.printStackTrace();
 	            throw new ServiceFailure("Solr server error", e.getMessage());
+	        }
 	    } else {
 	        throw new NotFound("404", "The Metacat member node can't find the query engine - "+engine);
+	    }
             leinfelder
 	@Override
-            leinfelder
+	public QueryEngineList listQueryEngines(Session session) throws InvalidToken,
-            leinfelder
+			ServiceFailure, NotAuthorized, NotImplemented {
 		QueryEngineList qel = new QueryEngineList();
-            tao
+		//qel.addQueryEngine(EnabledQueryEngines.PATHQUERYENGINE);
 		//qel.addQueryEngine(EnabledQueryEngines.SOLRENGINE);
 		List<String> enables = EnabledQueryEngines.getInstance().getEnabled();
-            tao
+		for(String name : enables) {
 		    qel.addQueryEngine(name);
             tao
-            leinfelder
+		return qel;
+	}
 	@Override
-            leinfelder
+	public InputStream query(Session session, String engine, String query) throws InvalidToken,
-            leinfelder
+			ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented,
 			NotFound {
-            tao
+	    String user = Constants.SUBJECT_PUBLIC;
         String[] groups= null;
-            tao
+        Set<Subject> subjects = null;
-            tao
+        if (session != null) {
             user = session.getSubject().getValue();
-            tao
+            subjects = AuthUtils.authorizedClientSubjects(session);
-            tao
+            if (subjects != null) {
                 List<String> groupList = new ArrayList<String>();
                 for (Subject subject: subjects) {
                     groupList.add(subject.getValue());
+                }
                 groups = groupList.toArray(new String[0]);
+            }
-            tao
+        } else {
             //add the public user subject to the set
             Subject subject = new Subject();
             subject.setValue(Constants.SUBJECT_PUBLIC);
-            leinfelder
+            subjects = new HashSet<Subject>();
-            tao
+            subjects.add(subject);
             tao
-            tao
+        //System.out.println("====== user is "+user);
         //System.out.println("====== groups are "+groups);
-            tao
+		if (engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
-            tao
+		    if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
                 throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
+            }
-            leinfelder
+			try {
 				DBQuery queryobj = new DBQuery();
             tao
-            leinfelder
+				String results = queryobj.performPathquery(query, user, groups);
-            leinfelder
+				ContentTypeByteArrayInputStream ctbais = new ContentTypeByteArrayInputStream(results.getBytes(MetaCatServlet.DEFAULT_ENCODING));
 				ctbais.setContentType("text/xml");
 				return ctbais;
             leinfelder
 			} catch (Exception e) {
-            leinfelder
+				throw new ServiceFailure("Pathquery error", e.getMessage());
             leinfelder
-            tao
+		} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
-            tao
+		    if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
-            tao
+		        throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
             tao
-            tao
+		    logMetacat.info("The query is ==================================== \n"+query);
-            tao
+		    try {
             tao
-            tao
+                return MetacatSolrIndex.getInstance().query(query, subjects);
-            tao
+            } catch (Exception e) {
                 // TODO Auto-generated catch block
                 throw new ServiceFailure("Solr server error", e.getMessage());
+            }
             leinfelder
 		return null;
+	}
             leinfelder
 	/**
 	 * Given an existing Science Metadata PID, this method mints a DOI
 	 * and updates the original object "publishing" the update with the DOI.
 	 * This includes updating the ORE map that describes the Science Metadata+data.
 	 * TODO: ensure all referenced objects allow public read
+	 *
 	 * @see https://projects.ecoinformatics.org/ecoinfo/issues/6014
+	 *
 	 * @param originalIdentifier
 	 * @param request
-            leinfelder
+	 * @throws InvalidRequest
 	 * @throws NotImplemented
 	 * @throws NotAuthorized
 	 * @throws ServiceFailure
 	 * @throws InvalidToken
-            leinfelder
+	 * @throws NotFound
-            leinfelder
+	 * @throws InvalidSystemMetadata
 	 * @throws InsufficientResources
 	 * @throws UnsupportedType
 	 * @throws IdentifierNotUnique
-            leinfelder
+	 */
-            walker
+	public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken,
 	ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique,
 	UnsupportedType, InsufficientResources, InvalidSystemMetadata, IOException {
             leinfelder
-            tao
+	    String serviceFailureCode = "1030";
 	    Identifier sid = getPIDForSID(originalIdentifier, serviceFailureCode);
 	    if(sid != null) {
 	        originalIdentifier = sid;
+	    }
-            leinfelder
+		// get the original SM
 		SystemMetadata originalSystemMetadata = this.getSystemMetadata(session, originalIdentifier);
-            leinfelder
+		// make copy of it using the marshaller to ensure DEEP copy
 		SystemMetadata sysmeta = null;
-            leinfelder
+		try {
-            leinfelder
+			ByteArrayOutputStream baos = new ByteArrayOutputStream();
 			TypeMarshaller.marshalTypeToOutputStream(originalSystemMetadata, baos);
 			sysmeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
-            leinfelder
+		} catch (Exception e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
+		}
-            leinfelder
+		// mint a DOI for the new revision
 		Identifier newIdentifier = this.generateIdentifier(session, MNodeService.DOI_SCHEME, null);
             leinfelder
 		// set new metadata values
-            leinfelder
+		sysmeta.setIdentifier(newIdentifier);
 		sysmeta.setObsoletes(originalIdentifier);
 		sysmeta.setObsoletedBy(null);
-            leinfelder
+		// ensure it is publicly readable
 		sysmeta = makePublicIfNot(sysmeta, originalIdentifier);
-            walker
+		//Get the bytes
 		InputStream inputStream = null;
 		boolean isScienceMetadata = isScienceMetadata(sysmeta);
 		//If it's a science metadata doc, we want to update the packageId first
 		if(isScienceMetadata){
 			InputStream originalObject = this.get(session, originalIdentifier);
 			//Edit the science metadata with the new package Id (EML)
 			inputStream = editScienceMetadata(session, originalObject, originalIdentifier, newIdentifier);
+		}
 		else{
 			inputStream = this.get(session, originalIdentifier);
+		}
             leinfelder
 		// update the object
-            leinfelder
+		this.update(session, originalIdentifier, inputStream, newIdentifier, sysmeta);
             leinfelder
-            leinfelder
+		// update ORE that references the scimeta
-            leinfelder
+		// first try the naive method, then check the SOLR index
-            leinfelder
+		try {
-            leinfelder
+			String localId = IdentifierManager.getInstance().getLocalId(originalIdentifier.getValue());
             leinfelder
-            leinfelder
+			Identifier potentialOreIdentifier = new Identifier();
 			potentialOreIdentifier.setValue(SystemMetadataFactory.RESOURCE_MAP_PREFIX + localId);
             leinfelder
-            leinfelder
+			InputStream oreInputStream = null;
 			try {
 				oreInputStream = this.get(session, potentialOreIdentifier);
 			} catch (NotFound nf) {
 				// this is probably okay for many sci meta data docs
 				logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
-            leinfelder
+				// try the SOLR index
-            leinfelder
+				List<Identifier> potentialOreIdentifiers = this.lookupOreFor(originalIdentifier, false);
-            leinfelder
+				if (potentialOreIdentifiers != null) {
 					potentialOreIdentifier = potentialOreIdentifiers.get(0);
 					try {
 						oreInputStream = this.get(session, potentialOreIdentifier);
 					} catch (NotFound nf2) {
 						// this is probably okay for many sci meta data docs
 						logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
+					}
+				}
             leinfelder
 			if (oreInputStream != null) {
 				Identifier newOreIdentifier = MNodeService.getInstance(request).generateIdentifier(session, MNodeService.UUID_SCHEME, null);
 				Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
 				Map<Identifier, List<Identifier>> sciMetaMap = resourceMapStructure.get(potentialOreIdentifier);
 				List<Identifier> dataIdentifiers = sciMetaMap.get(originalIdentifier);
             leinfelder
-            leinfelder
+				// reconstruct the ORE with the new identifiers
 				sciMetaMap.remove(originalIdentifier);
 				sciMetaMap.put(newIdentifier, dataIdentifiers);
 				ResourceMap resourceMap = ResourceMapFactory.getInstance().createResourceMap(newOreIdentifier, sciMetaMap);
 				String resourceMapString = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);
 				// get the original ORE SM and update the values
-            leinfelder
+				SystemMetadata originalOreSysMeta = this.getSystemMetadata(session, potentialOreIdentifier);
 				SystemMetadata oreSysMeta = new SystemMetadata();
 				try {
-            leinfelder
+					ByteArrayOutputStream baos = new ByteArrayOutputStream();
 					TypeMarshaller.marshalTypeToOutputStream(originalOreSysMeta, baos);
 					oreSysMeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
-            leinfelder
+				} catch (Exception e) {
 					// report as service failure
 					ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 					sf.initCause(e);
 					throw sf;
+				}
-            leinfelder
+				oreSysMeta.setIdentifier(newOreIdentifier);
 				oreSysMeta.setObsoletes(potentialOreIdentifier);
 				oreSysMeta.setObsoletedBy(null);
 				oreSysMeta.setSize(BigInteger.valueOf(resourceMapString.getBytes("UTF-8").length));
 				oreSysMeta.setChecksum(ChecksumUtil.checksum(resourceMapString.getBytes("UTF-8"), oreSysMeta.getChecksum().getAlgorithm()));
-            leinfelder
+				// ensure ORE is publicly readable
-            leinfelder
+				oreSysMeta = makePublicIfNot(oreSysMeta, potentialOreIdentifier);
             leinfelder
 				// ensure all data objects allow public read
 				List<String> pidsToSync = new ArrayList<String>();
 				for (Identifier dataId: dataIdentifiers) {
 					SystemMetadata dataSysMeta = this.getSystemMetadata(session, dataId);
 					dataSysMeta = makePublicIfNot(dataSysMeta, dataId);
 					this.updateSystemMetadata(dataSysMeta);
 					pidsToSync.add(dataId.getValue());
+				}
 				SyncAccessPolicy sap = new SyncAccessPolicy();
 				try {
 					sap.sync(pidsToSync);
 				} catch (Exception e) {
 					// ignore
 					logMetacat.warn("Error attempting to sync access for data objects when publishing package");
+				}
-            leinfelder
+				// save the updated ORE
 				this.update(
 						session,
 						potentialOreIdentifier,
 						new ByteArrayInputStream(resourceMapString.getBytes("UTF-8")),
 						newOreIdentifier,
 						oreSysMeta);
-            leinfelder
+			} else {
 				// create a new ORE for them
 				// https://projects.ecoinformatics.org/ecoinfo/issues/6194
 				try {
 					// find the local id for the NEW package.
 					String newLocalId = IdentifierManager.getInstance().getLocalId(newIdentifier.getValue());
 					@SuppressWarnings("unused")
 					SystemMetadata extraSysMeta = SystemMetadataFactory.createSystemMetadata(newLocalId, true, false);
-            leinfelder
+					// should be done generating the ORE here, and the same permissions were used from the metadata object
             leinfelder
 				} catch (Exception e) {
 					// oops, guess there was a problem - no package for you
 					logMetacat.error("Could not generate new ORE for published object: " + newIdentifier.getValue(), e);
+				}
             leinfelder
 		} catch (McdbDocNotFoundException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (UnsupportedEncodingException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (OREException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (URISyntaxException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (OREParserException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (ORESerialiserException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (NoSuchAlgorithmException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
-            tao
+		} catch (SQLException e) {
             // report as service failure
             ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
             sf.initCause(e);
             throw sf;
+        }
             leinfelder
 		return newIdentifier;
+	}
             leinfelder
 	/**
-            walker
+	   * Update a science metadata document with its new Identifier
+	   *
 	   * @param session - the Session object containing the credentials for the Subject
 	   * @param object - the InputStream for the XML object to be edited
 	   * @param pid - the Identifier of the XML object to be updated
 	   * @param newPid = the new Identifier to give to the modified XML doc
+	   *
 	   * @return newObject - The InputStream for the modified XML object
+	   *
 	   * @throws ServiceFailure
 	   * @throws IOException
 	   * @throws UnsupportedEncodingException
 	   * @throws InvalidToken
 	   * @throws NotAuthorized
 	   * @throws NotFound
 	   * @throws NotImplemented
 	   */
 	  public InputStream editScienceMetadata(Session session, InputStream object, Identifier pid, Identifier newPid)
 	  	throws ServiceFailure, IOException, UnsupportedEncodingException, InvalidToken, NotAuthorized, NotFound, NotImplemented {
 		logMetacat.debug("D1NodeService.editScienceMetadata() called.");
 		 InputStream newObject = null;
 	    try{
 	    	//Get the root node of the XML document
 	    	byte[] xmlBytes  = IOUtils.toByteArray(object);
 	        String xmlStr = new String(xmlBytes, "UTF-8");
 	    	Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new StringReader(xmlStr));
 		    org.w3c.dom.Node docNode = doc.getDocumentElement();
 		    //Get the system metadata for this object
 		    SystemMetadata sysMeta = null;
 		    try{
 		    	sysMeta = getSystemMetadata(session, pid);
 		    } catch(NotAuthorized e){
 		    	throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
 		    			"This session is not authorized to access the system metadata for " +
 		    			pid.getValue() + " : " + e.getMessage());
 		    } catch(NotFound e){
 		    	throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
 		    			"Could not find the system metadata for " +
 		    			pid.getValue() + " : " + e.getMessage());
+		    }
 		    //Get the formatId
 	        ObjectFormatIdentifier objFormatId = sysMeta.getFormatId();
 	        String formatId = objFormatId.getValue();
 	    	//For all EML formats
 	        if(formatId.indexOf("eml") == 0){
 	        	//Update or add the id attribute
 	    	    XMLUtilities.addAttributeNodeToDOMTree(docNode, XPATH_EML_ID, newPid.getValue());
+	        }
 	        //The modified object InputStream
 		    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
 		    Source xmlSource = new DOMSource(docNode);
 		    Result outputTarget = new StreamResult(outputStream);
 		    TransformerFactory.newInstance().newTransformer().transform(xmlSource, outputTarget);
 		    newObject = new ByteArrayInputStream(outputStream.toByteArray());
 	    } catch(TransformerException e) {
 	    	throw new ServiceFailure("1030", "MNNodeService.editScienceMetadata(): " +
 	                "Could not update the ID in the XML document for " +
 	                "pid " + pid.getValue() +" : " + e.getMessage());
 	    } catch(IOException e){
 	    	throw new ServiceFailure("1030", "MNNodeService.editScienceMetadata(): " +
 	                "Could not update the ID in the XML document for " +
 	                "pid " + pid.getValue() +" : " + e.getMessage());
+	    }
 	    return newObject;
+	  }
 	/**
-            leinfelder
+	 * Determines if we already have registered an ORE map for this package
 	 * NOTE: uses a solr query to locate OREs for the object
 	 * @param guid of the EML/packaging object
 	 * @return list of resource map identifiers for the given pid
 	 */
-            leinfelder
+	public List<Identifier> lookupOreFor(Identifier guid, boolean includeObsolete) {
-            leinfelder
+		// Search for the ORE if we can find it
 		String pid = guid.getValue();
 		List<Identifier> retList = null;
 		try {
-            leinfelder
+			String query = "fl=id,resourceMap&wt=xml&q=-obsoletedBy:[* TO *]+resourceMap:[* TO *]+id:\"" + pid + "\"";
-            leinfelder
+			if (includeObsolete) {
-            leinfelder
+				query = "fl=id,resourceMap&wt=xml&q=resourceMap:[* TO *]+id:\"" + pid + "\"";
             leinfelder
-            leinfelder
+			InputStream results = this.query(null, "solr", query);
-            leinfelder
+			org.w3c.dom.Node rootNode = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new InputStreamReader(results, "UTF-8"));
 			//String resultString = XMLUtilities.getDOMTreeAsString(rootNode);
 			org.w3c.dom.NodeList nodeList = XMLUtilities.getNodeListWithXPath(rootNode, "//arr[@name=\"resourceMap\"]/str");
 			if (nodeList != null && nodeList.getLength() > 0) {
 				retList = new ArrayList<Identifier>();
 				for (int i = 0; i < nodeList.getLength(); i++) {
 					String found = nodeList.item(i).getFirstChild().getNodeValue();
 					Identifier oreId = new Identifier();
 					oreId.setValue(found);
 					retList.add(oreId);
+				}
+			}
 		} catch (Exception e) {
 			logMetacat.error("Error checking for resourceMap[s] on pid " + pid + ". " + e.getMessage(), e);
+		}
 		return retList;
+	}
             leinfelder
 	@Override
 	public InputStream getPackage(Session session, ObjectFormatIdentifier formatId,
 			Identifier pid) throws InvalidToken, ServiceFailure,
 			NotAuthorized, InvalidRequest, NotImplemented, NotFound {
-            tao
+	    if(formatId == null) {
 	        throw new InvalidRequest("2873", "The format type can't be null in the getpackage method.");
-            tao
+	    } else if(!formatId.getValue().equals("application/bagit-097")) {
-            tao
+	        throw new NotImplemented("", "The format "+formatId.getValue()+" is not supported in the getpackage method");
+	    }
-            tao
+	    String serviceFailureCode = "2871";
 	    Identifier sid = getPIDForSID(pid, serviceFailureCode);
 	    if(sid != null) {
 	        pid = sid;
+	    }
-            leinfelder
+		InputStream bagInputStream = null;
 		BagFactory bagFactory = new BagFactory();
 		Bag bag = bagFactory.createBag();
 		// track the temp files we use so we can delete them when finished
 		List<File> tempFiles = new ArrayList<File>();
 		// the pids to include in the package
 		List<Identifier> packagePids = new ArrayList<Identifier>();
-            leinfelder
+		// catch non-D1 service errors and throw as ServiceFailures
 		try {
-            walker
+			//Create a map of dataone ids and file names
 			Map<Identifier, String> fileNames = new HashMap<Identifier, String>();
             leinfelder
-            leinfelder
+			// track the pid-to-file mapping
 			StringBuffer pidMapping = new StringBuffer();
-            leinfelder
+			// find the package contents
 			SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
-            leinfelder
+			if (ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId()).getFormatType().equals("RESOURCE")) {
-            walker
+				//Get the resource map as a map of Identifiers
-            leinfelder
+				InputStream oreInputStream = this.get(session, pid);
 				Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
 				packagePids.addAll(resourceMapStructure.keySet());
-            walker
+				//Loop through each object in this resource map
-            leinfelder
+				for (Map<Identifier, List<Identifier>> entries: resourceMapStructure.values()) {
-            walker
+					//Loop through each metadata object in this entry
 					Set<Identifier> metadataIdentifiers = entries.keySet();
 					for(Identifier metadataID: metadataIdentifiers){
 						try{
 							//Get the system metadata for this metadata object
 							SystemMetadata metadataSysMeta = this.getSystemMetadata(session, metadataID);
-            leinfelder
+							// include user-friendly metadata
 							if (ObjectFormatCache.getInstance().getFormat(metadataSysMeta.getFormatId()).getFormatType().equals("METADATA")) {
 								InputStream metadataStream = this.get(session, metadataID);
 								try {
 									// transform
 						            String format = "default";
 									DBTransform transformer = new DBTransform();
 						            String documentContent = IOUtils.toString(metadataStream, "UTF-8");
 						            String sourceType = metadataSysMeta.getFormatId().getValue();
 						            String targetType = "-//W3C//HTML//EN";
 						            ByteArrayOutputStream baos = new ByteArrayOutputStream();
 						            Writer writer = new OutputStreamWriter(baos , "UTF-8");
 						            // TODO: include more params?
 						            Hashtable<String, String[]> params = new Hashtable<String, String[]>();
 						            String localId = null;
 									try {
 										localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
 									} catch (McdbDocNotFoundException e) {
 										throw new NotFound("1020", e.getMessage());
+									}
 									params.put("qformat", new String[] {format});
 						            params.put("docid", new String[] {localId});
 						            params.put("pid", new String[] {pid.getValue()});
 						            params.put("displaymodule", new String[] {"printall"});
 						            transformer.transformXMLDocument(
 						                    documentContent ,
 						                    sourceType,
 						                    targetType ,
 						                    format,
 						                    writer,
 						                    params,
 						                    null //sessionid
 						                    );
 						            // finally, get the HTML back
 						            ContentTypeByteArrayInputStream resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
 						            // write to temp file with correct css path
 						            File tmpDir = File.createTempFile("package_", "_dir");
 						            tmpDir.delete();
 						            tmpDir.mkdir();
 						            File htmlFile = File.createTempFile("metadata", ".html", tmpDir);
 						            File cssDir = new File(tmpDir, format);
 						            cssDir.mkdir();
 						            File cssFile = new File(tmpDir, format + "/" + format + ".css");
 						            String pdfFileName = metadataID.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-METADATA.pdf";
 						            File pdfFile = new File(tmpDir, pdfFileName);
 						            //File pdfFile = File.createTempFile("metadata", ".pdf", tmpDir);
 						            // put the CSS file in place for the html to find it
 						            String originalCssPath = SystemUtil.getContextDir() + "/style/skins/" + format + "/" + format + ".css";
 						            IOUtils.copy(new FileInputStream(originalCssPath), new FileOutputStream(cssFile));
 						            // write the HTML file
 						            IOUtils.copy(resultInputStream, new FileOutputStream(htmlFile));
 						            // convert to PDF
 						            HtmlToPdf.export(htmlFile.getAbsolutePath(), pdfFile.getAbsolutePath());
 						            //add to the package
 						            bag.addFileToPayload(pdfFile);
 									pidMapping.append(metadataID.getValue() + " (pdf)" +  "\t" + "data/" + pdfFile.getName() + "\n");
 						            // mark for clean up after we are done
 									htmlFile.delete();
 									cssFile.delete();
 									cssDir.delete();
 						            tempFiles.add(tmpDir);
 									tempFiles.add(pdfFile); // delete this first later on
 								} catch (Exception e) {
 									logMetacat.warn("Could not transform metadata", e);
+								}
+							}
-            walker
+							//If this is in eml format, extract the filename and GUID from each entity in its package
 							if (metadataSysMeta.getFormatId().getValue().startsWith("eml://")) {
 								//Get the package
 								DataPackageParserInterface parser = new Eml200DataPackageParser();
 								InputStream emlStream = this.get(session, metadataID);
 								parser.parse(emlStream);
 								DataPackage dataPackage = parser.getDataPackage();
 								//Get all the entities in this package and loop through each to extract its ID and file name
 								Entity[] entities = dataPackage.getEntityList();
 								for(Entity entity: entities){
 									try{
 										//Get the file name from the metadata
 										String fileNameFromMetadata = entity.getName();
 										//Get the ecogrid URL from the metadata
 										String ecogridIdentifier = entity.getEntityIdentifier();
 										//Parse the ecogrid URL to get the local id
 										String idFromMetadata = DocumentUtil.getAccessionNumberFromEcogridIdentifier(ecogridIdentifier);
 										//Get the docid and rev pair
 										String docid = DocumentUtil.getDocIdFromString(idFromMetadata);
 										String rev = DocumentUtil.getRevisionStringFromString(idFromMetadata);
 										//Get the GUID
 										String guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(rev));
 										Identifier dataIdentifier = new Identifier();
 										dataIdentifier.setValue(guid);
 										//Add the GUID to our GUID & file name map
 										fileNames.put(dataIdentifier, fileNameFromMetadata);
+									}
 									catch(Exception e){
 										//Prevent just one entity error
 										e.printStackTrace();
 										logMetacat.debug(e.getMessage(), e);
+									}
+								}
+							}
+						}
 						catch(Exception e){
 							//Catch errors that would prevent package download
 							logMetacat.debug(e.toString());
+						}
+					}
-            leinfelder
+					packagePids.addAll(entries.keySet());
 					for (List<Identifier> dataPids: entries.values()) {
 						packagePids.addAll(dataPids);
+					}
             leinfelder
-            leinfelder
+			} else {
 				// just the lone pid in this package
-            tao
+				//packagePids.add(pid);
 			    //throw an invalid request exception
 			    throw new InvalidRequest("", "The given pid "+pid.getValue()+" is not a package id (resource map id). Please use a package id instead.");
             leinfelder
             walker
-            walker
+			//Create a temp file, then delete it and make a directory with that name
 			File tempDir = File.createTempFile("temp", Long.toString(System.nanoTime()));
 			tempDir.delete();
 			tempDir = new File(tempDir.getPath() + "_dir");
 			tempDir.mkdir();
-            walker
+			tempFiles.add(tempDir);
-            leinfelder
+			File pidMappingFile = new File(tempDir, "pid-mapping.txt");
             walker
-            leinfelder
+			// loop through the package contents
 			for (Identifier entryPid: packagePids) {
-            walker
+				//Get the system metadata for each item
-            walker
+				SystemMetadata entrySysMeta = this.getSystemMetadata(session, entryPid);
             walker
 				String objectFormatType = ObjectFormatCache.getInstance().getFormat(entrySysMeta.getFormatId()).getFormatType();
-            walker
+				String fileName = null;
             walker
-            walker
+				//TODO: Be more specific of what characters to replace. Make sure periods arent replaced for the filename from metadata
 				//Our default file name is just the ID + format type (e.g. walker.1.1-DATA)
 				fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + objectFormatType;
 				if(fileNames.containsKey(entryPid)){
 					//Let's use the file name and extension from the metadata is we have it
 					fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + fileNames.get(entryPid).replaceAll("[^a-zA-Z0-9\\-\\.]", "_");
+				}
 				else{
 					//If we couldn't find a given file name, use the system metadata extension
 					String extension = ObjectFormatInfo.instance().getExtension(entrySysMeta.getFormatId().getValue());
 					fileName += extension;
+				}
-            walker
+		        //Create a new file for this item and add to the list
-            walker
+				File tempFile = new File(tempDir, fileName);
-            leinfelder
+				tempFiles.add(tempFile);
             walker
 				InputStream entryInputStream = this.get(session, entryPid);
-            leinfelder
+				IOUtils.copy(entryInputStream, new FileOutputStream(tempFile));
 				bag.addFileToPayload(tempFile);
 				pidMapping.append(entryPid.getValue() + "\t" + "data/" + tempFile.getName() + "\n");
+			}
 			//add the the pid to data file map
 			IOUtils.write(pidMapping.toString(), new FileOutputStream(pidMappingFile));
 			bag.addFileAsTag(pidMappingFile);
-            leinfelder
+			tempFiles.add(pidMappingFile);
-            leinfelder
+			bag = bag.makeComplete();
             leinfelder
-            walker
+			///Now create the zip file
-            walker
+			//Use the pid as the file name prefix, replacing all non-word characters
 			String zipName = pid.getValue().replaceAll("\\W", "_");
             leinfelder
-            walker
+			File bagFile = new File(tempDir, zipName+".zip");
-            leinfelder
+			bag.setFile(bagFile);
-            leinfelder
+			ZipWriter zipWriter = new ZipWriter(bagFactory);
-            leinfelder
+			bag.write(zipWriter, bagFile);
 			bagFile = bag.getFile();
-            leinfelder
+			// use custom FIS that will delete the file when closed
 			bagInputStream = new DeleteOnCloseFileInputStream(bagFile);
 			// also mark for deletion on shutdown in case the stream is never closed
 			bagFile.deleteOnExit();
-            walker
+			tempFiles.add(bagFile);
             leinfelder
-            leinfelder
+			// clean up other temp files
-            leinfelder
+			for (int i=tempFiles.size()-1; i>=0; i--){
 				tempFiles.get(i).delete();
             leinfelder
             walker
-            leinfelder
+		} catch (IOException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (OREException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (URISyntaxException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (OREParserException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
             leinfelder
 		return bagInputStream;
             leinfelder
             tao
 	 /**
 	   * Archives an object, where the object is either a
 	   * data object or a science metadata object.
+	   *
 	   * @param session - the Session object containing the credentials for the Subject
 	   * @param pid - The object identifier to be archived
+	   *
 	   * @return pid - the identifier of the object used for the archiving
+	   *
 	   * @throws InvalidToken
 	   * @throws ServiceFailure
 	   * @throws NotAuthorized
 	   * @throws NotFound
 	   * @throws NotImplemented
 	   * @throws InvalidRequest
 	   */
 	  public Identifier archive(Session session, Identifier pid)
 	      throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
-            tao
+	      if(isReadOnlyMode()) {
-            tao
+	            throw new ServiceFailure("2912", ReadOnlyChecker.DATAONEERROR);
             tao
-            tao
+	      boolean allowed = false;
 	      // do we have a valid pid?
 	      if (pid == null || pid.getValue().trim().equals("")) {
 	          throw new ServiceFailure("1350", "The provided identifier was invalid.");
+	      }
 	      String serviceFailureCode = "1350";
 	      Identifier sid = getPIDForSID(pid, serviceFailureCode);
 	      if(sid != null) {
 	          pid = sid;
+	      }
 	      // does the subject have archive (a D1 CHANGE_PERMISSION level) privileges on the pid?
 	      try {
 	            allowed = isAuthorized(session, pid, Permission.CHANGE_PERMISSION);
 	        } catch (InvalidRequest e) {
 	          throw new ServiceFailure("1350", e.getDescription());
+	        }
 	      if (allowed) {
 	         try {
 	             HazelcastService.getInstance().getSystemMetadataMap().lock(pid);
 	             logMetacat.debug("MNodeService.archive - lock the identifier "+pid.getValue()+" in the system metadata map.");
 	             SystemMetadata sysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
-            tao
+	             boolean needModifyDate = true;
-            tao
+	             boolean logArchive = true;
 	             super.archiveObject(logArchive, session, pid, sysmeta, needModifyDate);
-            tao
+	         } finally {
 	             HazelcastService.getInstance().getSystemMetadataMap().unlock(pid);
 	             logMetacat.debug("MNodeService.archive - unlock the identifier "+pid.getValue()+" in the system metadata map.");
+	         }
 	      } else {
 	          throw new NotAuthorized("1320", "The provided identity does not have " + "permission to archive the object on the Node.");
+	      }
 	      return pid;
+	  }
             tao
 	/**
 	 * Update the system metadata of the specified pid.
 	 */
-            tao
+	@Override
 	public boolean updateSystemMetadata(Session session, Identifier pid,
             SystemMetadata sysmeta) throws NotImplemented, NotAuthorized,
             ServiceFailure, InvalidRequest, InvalidSystemMetadata, InvalidToken {
             tao
 	  if(isReadOnlyMode()) {
-            tao
+            throw new ServiceFailure("4868",  ReadOnlyChecker.DATAONEERROR);
             tao
-            tao
+	 if(sysmeta == null) {
-            tao
+	     throw  new InvalidRequest("4869", "The system metadata object should NOT be null in the updateSystemMetadata request.");
             tao
-            tao
+	 if(pid == null || pid.getValue() == null) {
-            tao
+         throw new InvalidRequest("4869", "Please specify the id in the updateSystemMetadata request ") ;
             tao
      if (session == null) {
          //TODO: many of the thrown exceptions do not use the correct error codes
          //check these against the docs and correct them
          throw new NotAuthorized("4861", "No Session - could not authorize for updating system metadata." +
                  "  If you are not logged in, please do so and retry the request.");
      } else {
          try {
              //Following session can do the change:
-            tao
+           //- Authoritative Member Node (we can use isNodeAdmin since we checked isAuthoritativeNode )
-            tao
+             //- Owner of object (coved by the userHasPermission method)
              //- user subjects with the change permission
              //Note: Coordinating Node can not because MN is authoritative
-            tao
+             /*if(!isAuthoritativeNode(pid)) {
                 throw  new InvalidRequest("4863", "Client can only call updateSystemMetadata request on the authoritative memember node.");
+             }
-            tao
+             if(!isNodeAdmin(session) && !userHasPermission(session, pid, Permission.CHANGE_PERMISSION)) {
                  throw new NotAuthorized("4861", "The client -"+ session.getSubject().getValue()+ "is not authorized for updating the system metadata of the object "+pid.getValue());
-            tao
+             }*/
              if(!allowUpdating(session, pid, Permission.CHANGE_PERMISSION)) {
                  throw new NotAuthorized("4861", "The client -"+ session.getSubject().getValue()+ "is not authorized for updating the system metadata of the object "+pid.getValue());
             tao
          } catch (NotFound e) {
-            tao
+             throw new InvalidRequest("4869", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
             tao
+     }
-            tao
+      //update the system metadata locally
       boolean success = false;
       try {
           HazelcastService.getInstance().getSystemMetadataMap().lock(pid);
           SystemMetadata currentSysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
           if(currentSysmeta == null) {
-            tao
+              throw  new InvalidRequest("4869", "We can't find the current system metadata on the member node for the id "+pid.getValue());
             tao
           Date currentModiDate = currentSysmeta.getDateSysMetadataModified();
           Date commingModiDate = sysmeta.getDateSysMetadataModified();
           if(commingModiDate == null) {
-            tao
+              throw  new InvalidRequest("4869", "The system metadata modification date can't be null.");
             tao
           if(currentModiDate != null && commingModiDate.getTime() != currentModiDate.getTime()) {
-            tao
+              throw new InvalidRequest("4869", "Your system metadata modification date is "+commingModiDate.toString()+
-            tao
+                      ". It doesn't match our current system metadata modification date in the member node - "+currentModiDate.toString()+
                       ". Please check if you have got the newest version of the system metadata before the modification.");
+          }
           boolean needUpdateModificationDate = true;
-            tao
+          boolean fromCN = false;
           success = updateSystemMetadata(session, pid, sysmeta, needUpdateModificationDate, currentSysmeta, fromCN);
-            tao
+      } finally {
           HazelcastService.getInstance().getSystemMetadataMap().unlock(pid);
+      }
             tao
       if(success) {
-            tao
+          //TODO
-            tao
+          //notify the cns the synchornize the new system metadata.
-            tao
+          this.cn = D1Client.getCN();
           try {
-            tao
+              if(this.cn == null)  {
                   logMetacat.warn("updateSystemMetadata - can't get the instance of the CN. So the system metadata in CN can't be updated.");
               } else {
                   this.cn.synchronize(null, pid);
+              }
-            tao
+          } catch (BaseException e) {
               e.printStackTrace();
               logMetacat.error("It is a DataONEBaseException and its detail code is "+e.getDetail_code() +" and its code is "+e.getCode());
               logMetacat.error("Can't update the systemmetadata of pid "+pid.getValue()+" in CNs since "+e.getMessage());
-            tao
+          } catch (Exception e) {
-            tao
+              e.printStackTrace();
-            tao
+              logMetacat.error("Can't update the systemmetadata of pid "+pid.getValue()+" in CNs since "+e.getMessage());
+          }
             leinfelder
           // attempt to re-register the identifier (it checks if it is a doi)
           try {
         	  DOIService.getInstance().registerDOI(sysmeta);
           } catch (Exception e) {
   			logMetacat.warn("Could not [re]register DOI: " + e.getMessage(), e);
+          }
             tao
       return success;
+    }
             tao
 	/*
      * Determine if the current node is the authoritative node for the given pid.
      */
-            tao
+    protected boolean isAuthoritativeNode(Identifier pid) throws InvalidRequest {
-            tao
+        boolean isAuthoritativeNode = false;
         if(pid != null && pid.getValue() != null) {
             SystemMetadata sys = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
             if(sys != null) {
                 NodeReference node = sys.getAuthoritativeMemberNode();
                 if(node != null) {
                     String nodeValue = node.getValue();
                     logMetacat.debug("The authoritative node for id "+pid.getValue()+" is "+nodeValue);
                     //System.out.println("The authoritative node for id "+pid.getValue()+" is "+nodeValue);
                     String currentNodeId = Settings.getConfiguration().getString("dataone.nodeId");
                     logMetacat.debug("The node id in metacat.properties is "+currentNodeId);
                     //System.out.println("The node id in metacat.properties is "+currentNodeId);
                     if(currentNodeId != null && !currentNodeId.trim().equals("") && currentNodeId.equals(nodeValue)) {
                         logMetacat.debug("They are matching");
                         //System.out.println("They are matching");
                         isAuthoritativeNode = true;
+                    }
-            tao
+                } else {
                     throw new InvalidRequest("4869", "Coudn't find the authoritative member node in the system metadata associated with the pid "+pid.getValue());
             tao
-            tao
+            } else {
                 throw new InvalidRequest("4869", "Coudn't find the system metadata associated with the pid "+pid.getValue());
             tao
-            tao
+        } else {
             throw new InvalidRequest("4869", "The request pid is null");
             tao
         return isAuthoritativeNode;
+    }
             cjones
-            tao
+    /*
      * Rules are:
      * 1. If the session has an cn object, it is allowed.
      * 2. If it is not a cn object, the client should have approperate permission and it should also happen on the authorative node.
      */
-            tao
+    private boolean allowUpdating(Session session, Identifier pid, Permission permission) throws NotAuthorized, NotFound, InvalidRequest {
-            tao
+        boolean allow = false;
         if(isCNAdmin (session)) {
             allow = true;
         } else {
             if(isAuthoritativeNode(pid)) {
                 if(userHasPermission(session, pid, permission)) {
                     allow = true;
                 } else {
                     allow = false;
+                }
             } else {
                 throw new NotAuthorized("4861", "Client can only call the request on the authoritative memember node.");
+            }
+        }
         return allow;
+    }
-            tao
+    /**
      * Check if the metacat is in the read-only mode.
      * @return true if it is; otherwise false.
      */
     protected boolean isReadOnlyMode() {
         boolean readOnly = false;
         ReadOnlyChecker checker = new ReadOnlyChecker();
         readOnly = checker.isReadOnly();
         return readOnly;
+    }
             cjones

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