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

metacat/src/edu/ucsb/nceas/metacat/dataone/MNodeService.java @ 8509

-            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;
 import java.io.FileOutputStream;
-            cjones
+import java.io.IOException;
-            cjones
+import java.io.InputStream;
-            leinfelder
+import java.io.InputStreamReader;
-            leinfelder
+import java.io.OutputStreamWriter;
-            leinfelder
+import java.io.UnsupportedEncodingException;
-            leinfelder
+import java.io.Writer;
-            leinfelder
+import java.math.BigInteger;
-            leinfelder
+import java.net.URISyntaxException;
-            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;
-            leinfelder
+import org.apache.commons.beanutils.BeanUtils;
-            cjones
+import org.apache.commons.io.IOUtils;
-            cjones
+import org.apache.log4j.Logger;
-            cjones
+import org.dataone.client.CNode;
-            leinfelder
+import org.dataone.client.D1Client;
 import org.dataone.client.MNode;
-            leinfelder
+import org.dataone.client.ObjectFormatCache;
-            leinfelder
+import org.dataone.client.auth.CertificateManager;
-            leinfelder
+import org.dataone.client.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.v1.MNCore;
 import org.dataone.service.mn.tier1.v1.MNRead;
 import org.dataone.service.mn.tier2.v1.MNAuthorization;
 import org.dataone.service.mn.tier3.v1.MNStorage;
 import org.dataone.service.mn.tier4.v1.MNReplication;
-            leinfelder
+import org.dataone.service.mn.v1.MNQuery;
-            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;
 import org.dataone.service.types.v1.Log;
 import org.dataone.service.types.v1.LogEntry;
 import org.dataone.service.types.v1.MonitorInfo;
 import org.dataone.service.types.v1.MonitorList;
 import org.dataone.service.types.v1.Node;
-            cjones
+import org.dataone.service.types.v1.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.v1.ObjectFormat;
-            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;
-            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;
 import org.dataone.service.types.v1.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.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;
             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.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.SystemUtil;
-            cjones
+import edu.ucsb.nceas.utilities.PropertyNotFoundException;
-            leinfelder
+import edu.ucsb.nceas.utilities.XMLUtilities;
-            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()
  * MNReplication.replicate()
+ *
-            cjones
+ */
-            cjones
+public class MNodeService extends D1NodeService
-            leinfelder
+    implements MNAuthorization, MNCore, MNRead, MNReplication, MNStorage, MNQuery {
             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:";
             leinfelder
 	/* the logger instance */
-            jones
+    private Logger logMetacat = null;
             cjones
     /* A reference to a remote Memeber Node */
     private MNode mn;
     /* 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
-            leinfelder
+    	// only admin of  the MN or the CN is allowed a full delete
         boolean allowed = false;
-            leinfelder
+        allowed = isAdminAuthorized(session);
             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 {
             cjones
-            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
         // 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.");
             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?
         allowed = isAuthorized(session, pid, Permission.WRITE);
         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);
-            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());
+            }
             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
                 String objectAsXML = "";
                 try {
                     objectAsXML = IOUtils.toString(object, "UTF-8");
-            leinfelder
+                    // give the old pid so we can calculate the new local id
                     localId = insertOrUpdateDocument(objectAsXML, 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);
             jones
-            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 (EZIDException e) {
                 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
-            cjones
+        // check for null session
-            leinfelder
+        if (session == null) {
-            cjones
+          throw new InvalidToken("1110", "Session is required to WRITE to the Node.");
             leinfelder
-            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);
-            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.");
+        }
-            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 (EZIDException 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 {
-            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();
         // get from the membernode
         // TODO: switch credentials for the server retrieval?
         this.mn = D1Client.getMN(sourceNode);
         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
             cjones
-            cjones
+            // no local replica, get a replica
-            cjones
+            if ( object == null ) {
-            cjones
+                // session should be null to use the default certificate
                 // location set in the Certificate manager
                 object = mn.getReplica(thisNodeSession, pid);
-            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
             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;
         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
     public ObjectList listObjects(Session session, Date startTime, Date endTime, ObjectFormatIdentifier objectFormatId, Boolean replicaStatus, Integer start,
             Integer count) throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken {
             cjones
-            jones
+        ObjectList objectList = null;
             leinfelder
-            jones
+        try {
-            leinfelder
+        	// safeguard against large requests
             if (count == null || count > MAXIMUM_DB_RECORD_COUNT) {
             	count = MAXIMUM_DB_RECORD_COUNT;
+            }
-            jones
+            objectList = IdentifierManager.getInstance().querySystemMetadata(startTime, endTime, objectFormatId, replicaStatus, start, count);
         } catch (Exception e) {
             throw new ServiceFailure("1580", "Error querying system metadata: " + e.getMessage());
+        }
             leinfelder
-            jones
+        return objectList;
             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;
-            jones
+        String mnCoreServiceVersion = null;
         String mnReadServiceVersion = null;
         String mnAuthorizationServiceVersion = null;
         String mnStorageServiceVersion = null;
         String mnReplicationServiceVersion = null;
             cjones
-            jones
+        boolean nodeSynchronize = false;
         boolean nodeReplicate = false;
         boolean mnCoreServiceAvailable = false;
         boolean mnReadServiceAvailable = false;
         boolean mnAuthorizationServiceAvailable = false;
         boolean mnStorageServiceAvailable = false;
         boolean mnReplicationServiceAvailable = false;
             cjones
-            jones
+        try {
             // get the properties of the node based on configuration information
-            jones
+            nodeName = PropertyService.getProperty("dataone.nodeName");
-            cjones
+            nodeId = PropertyService.getProperty("dataone.nodeId");
-            jones
+            subject = PropertyService.getProperty("dataone.subject");
-            cjones
+            contactSubject = PropertyService.getProperty("dataone.contactSubject");
-            jones
+            nodeDesc = PropertyService.getProperty("dataone.nodeDescription");
-            jones
+            nodeTypeString = PropertyService.getProperty("dataone.nodeType");
             nodeType = NodeType.convert(nodeTypeString);
-            jones
+            nodeSynchronize = new Boolean(PropertyService.getProperty("dataone.nodeSynchronize")).booleanValue();
             nodeReplicate = new Boolean(PropertyService.getProperty("dataone.nodeReplicate")).booleanValue();
             mnCoreServiceVersion = PropertyService.getProperty("dataone.mnCore.serviceVersion");
             mnReadServiceVersion = PropertyService.getProperty("dataone.mnRead.serviceVersion");
             mnAuthorizationServiceVersion = PropertyService.getProperty("dataone.mnAuthorization.serviceVersion");
             mnStorageServiceVersion = PropertyService.getProperty("dataone.mnStorage.serviceVersion");
             mnReplicationServiceVersion = PropertyService.getProperty("dataone.mnReplication.serviceVersion");
             mnCoreServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnCore.serviceAvailable")).booleanValue();
             mnReadServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnRead.serviceAvailable")).booleanValue();
             mnAuthorizationServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnAuthorization.serviceAvailable")).booleanValue();
             mnStorageServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnStorage.serviceAvailable")).booleanValue();
             mnReplicationServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnReplication.serviceAvailable")).booleanValue();
-            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
-            jones
+            Service sMNCore = new Service();
             sMNCore.setName("MNCore");
             sMNCore.setVersion(mnCoreServiceVersion);
             sMNCore.setAvailable(mnCoreServiceAvailable);
             jones
-            jones
+            Service sMNRead = new Service();
             sMNRead.setName("MNRead");
             sMNRead.setVersion(mnReadServiceVersion);
             sMNRead.setAvailable(mnReadServiceAvailable);
             jones
-            jones
+            Service sMNAuthorization = new Service();
             sMNAuthorization.setName("MNAuthorization");
             sMNAuthorization.setVersion(mnAuthorizationServiceVersion);
             sMNAuthorization.setAvailable(mnAuthorizationServiceAvailable);
             jones
-            jones
+            Service sMNStorage = new Service();
             sMNStorage.setName("MNStorage");
             sMNStorage.setVersion(mnStorageServiceVersion);
             sMNStorage.setAvailable(mnStorageServiceAvailable);
             jones
-            jones
+            Service sMNReplication = new Service();
             sMNReplication.setName("MNReplication");
             sMNReplication.setVersion(mnReplicationServiceVersion);
             sMNReplication.setAvailable(mnReplicationServiceAvailable);
             jones
-            jones
+            services.addService(sMNRead);
             services.addService(sMNCore);
             services.addService(sMNAuthorization);
             services.addService(sMNStorage);
             services.addService(sMNReplication);
             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
-            jones
+    /**
      * Returns the number of operations that have been serviced by the node
      * over time periods of one and 24 hours.
+     *
      * @param session - the Session object containing the credentials for the Subject
      * @param period - An ISO8601 compatible DateTime range specifying the time
      *                 range for which to return operation statistics.
      * @param requestor - Limit to operations performed by given requestor identity.
      * @param event -  Enumerated value indicating the type of event being examined
      * @param format - Limit to events involving objects of the specified format
+     *
      * @return the desired log records
+     *
      * @throws InvalidToken
      * @throws ServiceFailure
      * @throws NotAuthorized
      * @throws InvalidRequest
      * @throws NotImplemented
      */
-            cjones
+    public MonitorList getOperationStatistics(Session session, Date startTime,
         Date endTime, Subject requestor, Event event, ObjectFormatIdentifier formatId)
         throws NotImplemented, ServiceFailure, NotAuthorized, InsufficientResources, UnsupportedType {
             cjones
-            jones
+        MonitorList monitorList = new MonitorList();
             cjones
-            jones
+        try {
             cjones
-            jones
+            // get log records first
-            leinfelder
+            Log logs = getLogRecords(session, startTime, endTime, event, null, 0, null);
             cjones
-            jones
+            // TODO: aggregate by day or hour -- needs clarification
             int count = 1;
             for (LogEntry logEntry : logs.getLogEntryList()) {
                 Identifier pid = logEntry.getIdentifier();
                 Date logDate = logEntry.getDateLogged();
                 // if we are filtering by format
                 if (formatId != null) {
-            leinfelder
+                    SystemMetadata sysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
-            leinfelder
+                    if (!sysmeta.getFormatId().getValue().equals(formatId.getValue())) {
-            jones
+                        // does not match
                         continue;
+                    }
+                }
                 MonitorInfo item = new MonitorInfo();
                 item.setCount(count);
                 item.setDate(new java.sql.Date(logDate.getTime()));
                 monitorList.addMonitorInfo(item);
             cjones
             jones
         } catch (Exception e) {
             e.printStackTrace();
             throw new ServiceFailure("2081", "Could not retrieve statistics: " + e.getMessage());
+        }
             cjones
-            jones
+        return monitorList;
             cjones
             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
             jones
         // TODO: update the CN URL below when the CNRead.SynchronizationFailed
         // method is changed to include the URL as a parameter
-            cjones
+        logMetacat.debug("Synchronization for the object identified by " +
                 pid.getValue() + " failed from " + syncFailed.getNodeId() +
                 " 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)
-            leinfelder
+        throws NotAuthorized, NotImplemented, ServiceFailure, InvalidToken {
             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) {
-            cjones
+            throw new ServiceFailure("2181", "The object specified by " +
                     pid.getValue() + " does not exist at this node.");
             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) {
             throw new ServiceFailure("2181", "Could not determine if node is authorized: "
                     + 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) {
-            cjones
+                throw new ServiceFailure("1020", "The object specified by " +
                     pid.getValue() + "could not be returned due to error: " + e.getMessage());
             jones
+        }
             cjones
-            jones
+        // if we fail to set the input stream
         if (inputStream == null) {
-            cjones
+            throw new ServiceFailure("2181", "The object specified by " +
                 pid.getValue() + "does not exist at this 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;
+    }
-            cjones
+    /**
-            cjones
+     * A method to notify the Member Node that the authoritative copy of
-            cjones
+     * system metadata on the Coordinating Nodes has changed.
+     *
      * @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 {
-            cjones
+        // cannot be called by public
         if (session == null) {
         	throw new InvalidToken("2183", "No session was provided.");
+        }
-            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);
+        }
         // compare what we have locally to what is sent in the change notification
         try {
-            leinfelder
+            currentLocalSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
         } catch (RuntimeException e) {
-            cjones
+            String msg = "SystemMetadata for pid " + pid.getValue() +
-            leinfelder
+              " couldn't be updated because it couldn't be found locally: " +
-            cjones
+              e.getMessage();
-            leinfelder
+            logMetacat.error(msg);
             ServiceFailure sf = new ServiceFailure("1333", msg);
             sf.initCause(e);
             throw sf;
             cjones
         if (currentLocalSysMeta.getSerialVersion().longValue() < serialVersion ) {
             try {
                 newSysMeta = cn.getSystemMetadata(null, pid);
             } catch (NotFound e) {
                 // huh? you just said you had it
-            leinfelder
+            	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);
                 sf.initCause(e);
                 throw sf;
             cjones
             leinfelder
-            cjones
+            // update the local copy of system metadata for the pid
             try {
-            leinfelder
+                HazelcastService.getInstance().getSystemMetadataMap().put(newSysMeta.getIdentifier(), newSysMeta);
-            cjones
+                logMetacat.info("Updated local copy of system metadata for pid " +
                     pid.getValue() + " after change notification from the CN.");
-            leinfelder
+            } catch (RuntimeException e) {
-            cjones
+                String msg = "SystemMetadata for pid " + pid.getValue() +
-            leinfelder
+                  " couldn't be updated: " +
-            cjones
+                  e.getMessage();
-            leinfelder
+                logMetacat.error(msg);
                 ServiceFailure sf = new ServiceFailure("1333", msg);
                 sf.initCause(e);
                 throw sf;
             cjones
             leinfelder
             // submit for indexing
             try {
 				MetacatSolrIndex.getInstance().submit(newSysMeta.getIdentifier(), newSysMeta, null);
 			} catch (Exception e) {
                 logMetacat.error("Could not submit changed systemMetadata for indexing, pid: " + newSysMeta.getIdentifier().getValue(), e);
+			}
             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
 	@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
 	@Override
 	public boolean isAuthorized(Identifier pid, Permission permission)
 			throws ServiceFailure, InvalidRequest, InvalidToken, NotFound,
 			NotAuthorized, NotImplemented {
 		return isAuthorized(null, pid, permission);
+	}
 	@Override
 	public boolean systemMetadataChanged(Identifier pid, long serialVersion, Date dateSysMetaLastModified)
 			throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
 			InvalidRequest {
 		return systemMetadataChanged(null, pid, serialVersion, dateSysMetaLastModified);
+	}
 	@Override
 	public Log getLogRecords(Date fromDate, Date toDate, Event event, String pidFilter,
 			Integer start, Integer count) throws InvalidRequest, InvalidToken,
 			NotAuthorized, NotImplemented, ServiceFailure {
 		return getLogRecords(null, fromDate, toDate, event, pidFilter, start, count);
+	}
 	@Override
 	public DescribeResponse describe(Identifier pid) throws InvalidToken,
 			NotAuthorized, NotImplemented, ServiceFailure, NotFound {
 		return describe(null, pid);
+	}
 	@Override
 	public InputStream get(Identifier pid) throws InvalidToken, NotAuthorized,
 			NotImplemented, ServiceFailure, NotFound, InsufficientResources {
 		return get(null, pid);
+	}
 	@Override
 	public Checksum getChecksum(Identifier pid, String algorithm)
 			throws InvalidRequest, InvalidToken, NotAuthorized, NotImplemented,
 			ServiceFailure, NotFound {
 		return getChecksum(null, pid, algorithm);
+	}
 	@Override
 	public SystemMetadata getSystemMetadata(Identifier pid)
 			throws InvalidToken, NotAuthorized, NotImplemented, ServiceFailure,
 			NotFound {
 		return getSystemMetadata(null, pid);
+	}
 	@Override
 	public ObjectList listObjects(Date startTime, Date endTime,
 			ObjectFormatIdentifier objectFormatId, Boolean replicaStatus, Integer start,
 			Integer count) throws InvalidRequest, InvalidToken, NotAuthorized,
 			NotImplemented, ServiceFailure {
 		return listObjects(null, startTime, endTime, objectFormatId, replicaStatus, start, count);
+	}
 	@Override
 	public boolean synchronizationFailed(SynchronizationFailed syncFailed)
 			throws InvalidToken, NotAuthorized, NotImplemented, ServiceFailure {
 		return synchronizationFailed(null, syncFailed);
+	}
 	@Override
 	public InputStream getReplica(Identifier pid) throws InvalidToken,
 			NotAuthorized, NotImplemented, ServiceFailure, NotFound,
 			InsufficientResources {
 		return getReplica(null, pid);
+	}
 	@Override
 	public boolean replicate(SystemMetadata sysmeta, NodeReference sourceNode)
 			throws NotImplemented, ServiceFailure, NotAuthorized,
 			InvalidRequest, InvalidToken, InsufficientResources,
 			UnsupportedType {
 		return replicate(null, sysmeta, sourceNode);
+	}
 	@Override
 	public Identifier create(Identifier pid, InputStream object,
 			SystemMetadata sysmeta) throws IdentifierNotUnique,
 			InsufficientResources, InvalidRequest, InvalidSystemMetadata,
 			InvalidToken, NotAuthorized, NotImplemented, ServiceFailure,
 			UnsupportedType {
 		return create(null, pid, object, sysmeta);
+	}
 	@Override
 	public Identifier delete(Identifier pid) throws InvalidToken,
 			ServiceFailure, NotAuthorized, NotFound, NotImplemented {
 		return delete(null, pid);
+	}
 	@Override
-            leinfelder
+	public Identifier generateIdentifier(String scheme, String fragment)
-            leinfelder
+			throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
 			InvalidRequest {
-            leinfelder
+		return generateIdentifier(null, scheme, fragment);
             leinfelder
 	@Override
 	public Identifier update(Identifier pid, InputStream object,
 			Identifier newPid, SystemMetadata sysmeta) throws IdentifierNotUnique,
 			InsufficientResources, InvalidRequest, InvalidSystemMetadata,
 			InvalidToken, NotAuthorized, NotImplemented, ServiceFailure,
 			UnsupportedType, NotFound {
 		return update(null, pid, object, newPid, sysmeta);
+	}
             leinfelder
 	@Override
 	public QueryEngineDescription getQueryEngineDescription(String engine)
 			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
 	public QueryEngineList listQueryEngines() throws InvalidToken,
 			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
 	public InputStream query(String engine, String query) throws InvalidToken,
 			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
+	 */
-            leinfelder
+	public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata {
             leinfelder
             leinfelder
 		// get the original SM
 		SystemMetadata originalSystemMetadata = this.getSystemMetadata(session, originalIdentifier);
 		// make copy of it
 		SystemMetadata sysmeta = new SystemMetadata();
 		try {
 			BeanUtils.copyProperties(sysmeta, originalSystemMetadata);
 		} 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);
 		// get the bytes
 		InputStream inputStream = this.get(session, originalIdentifier);
 		// 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);
 				// TODO: ensure all data package objects allow public read
 				// 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 {
 					BeanUtils.copyProperties(oreSysMeta, originalOreSysMeta);
 				} 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()));
 				// 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);
 					// should be done generating the ORE here
 				} 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;
             leinfelder
 		return newIdentifier;
+	}
             leinfelder
 	/**
-            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:*+resourceMap:*+id:\"" + pid + "\"";;
 			if (includeObsolete) {
 				query = "fl=id,resourceMap&wt=xml&q=resourceMap:*+id:\"" + pid + "\"";
+			}
-            leinfelder
+			InputStream results = this.query("solr", query);
 			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
+	 * Packages the given package in a Bagit collection for download
 	 * @param pid
 	 * @throws NotImplemented
 	 * @throws NotFound
 	 * @throws NotAuthorized
 	 * @throws ServiceFailure
 	 * @throws InvalidToken
 	 */
-            leinfelder
+	public InputStream getPackage(Session session, Identifier pid) throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
-            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
 			// 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);
 							//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
 				packagePids.add(pid);
             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
+			// track the pid-to-file mapping
 			StringBuffer pidMapping = new StringBuffer();
             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
-            walker
+			File pidMappingFile = new File(tempDir, "pid-mapping.txt");
-            leinfelder
+			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
-            walker
+			for(int i=tempFiles.size()-1; i>=0; i--){
 				File tf = new File(tempFiles.get(i).getPath());
-            leinfelder
+				tf.delete();
+			}
             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
 	/**
 	 * Get a rendered view of the object identified by pid.
 	 * Uses the registered format given by the format parameter.
 	 * Typically, this is structured HTML that can be styled with CSS.
 	 * @param session
 	 * @param pid
 	 * @param format
 	 * @return
 	 * @throws InvalidToken
 	 * @throws ServiceFailure
 	 * @throws NotAuthorized
 	 * @throws NotFound
 	 * @throws NotImplemented
 	 */
-            leinfelder
+	public InputStream getView(Session session, Identifier pid, String format) throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
-            leinfelder
+		InputStream resultInputStream = null;
 		SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
 		InputStream object = this.get(session, pid);
 		try {
 			// can only transform metadata, really
-            leinfelder
+			ObjectFormat objectFormat = ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId());
-            leinfelder
+			if (objectFormat.getFormatType().equals("METADATA")) {
 				// transform
 				DBTransform transformer = new DBTransform();
 	            String documentContent = IOUtils.toString(object, "UTF-8");
 	            String sourceType = objectFormat.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[]>();
-            leinfelder
+	            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()});
-            leinfelder
+	            transformer.transformXMLDocument(
 	                    documentContent ,
 	                    sourceType,
 	                    targetType ,
 	                    format,
 	                    writer,
 	                    params,
 	                    null //sessionid
 	                    );
 	            // finally, get the HTML back
 	            resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
 	            ((ContentTypeByteArrayInputStream) resultInputStream).setContentType("text/html");
 			} else {
 				// just return the raw bytes
 				resultInputStream = object;
+			}
 		} catch (IOException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (PropertyNotFoundException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (SQLException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
 		} catch (ClassNotFoundException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
+		}
 		return resultInputStream;
             leinfelder
             cjones
             cjones

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