Metacat

/**

 *  '$RCSfile$'

 *  Copyright: 2000 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *

 *   '$Author: $'

 *     '$Date: 2009-06-13 15:28:13 +0300  $'

 *

 * 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;

import java.io.ByteArrayOutputStream;

import java.io.File;

import java.io.FileNotFoundException;

import java.io.FileOutputStream;

import java.io.IOException;

import java.io.InputStream;

import java.io.OutputStream;

import java.io.PrintWriter;

import java.sql.SQLException;

import java.util.*;

import java.text.DateFormat;

import javax.servlet.ServletContext;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import org.apache.commons.io.IOUtils;

import org.apache.log4j.Logger;

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;

import org.dataone.service.exceptions.UnsupportedType;

import org.dataone.service.mn.MemberNodeCrud;

import org.dataone.service.types.*;

import org.jibx.runtime.BindingDirectory;

import org.jibx.runtime.IBindingFactory;

import org.jibx.runtime.IMarshallingContext;

import org.jibx.runtime.IUnmarshallingContext;

import org.jibx.runtime.JiBXException;

import com.gc.iotools.stream.is.InputStreamFromOutputStream;

import edu.ucsb.nceas.metacat.AccessionNumberException;

import edu.ucsb.nceas.metacat.MetacatResultSet;

import edu.ucsb.nceas.metacat.MetacatResultSet.Document;

import edu.ucsb.nceas.metacat.DocumentImpl;

import edu.ucsb.nceas.metacat.EventLog;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.McdbException;

import edu.ucsb.nceas.metacat.MetacatHandler;

import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;

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

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

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

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

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

import edu.ucsb.nceas.utilities.ParseLSIDException;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

/**

 * 

 * Implements DataONE MemberNode CRUD API for Metacat. 

 * 

 * @author Matthew Jones

 */

public class CrudService implements MemberNodeCrud {

    /*private ServletContext servletContext;

    private HttpServletRequest request;

    private HttpServletResponse response;*/

    private static CrudService crudService = null;

    private MetacatHandler handler;

    private Hashtable<String, String[]> params;

    Logger logMetacat = null;

    private String metacatUrl;

    /**

     * singleton accessor

     */

    public static CrudService getInstance()

    {

      if(crudService == null)

      {

        crudService = new CrudService();

      }

      return crudService;

    }

    /**

     * Initializes new instance by setting servlet context,request and response.

     * TODO: remove dependency on Servlet infrastructure

     * TODO: Make this a real service, and make it a Singleton

     */

    public CrudService() {

    //change crud service into a singleton.  dont pass servlet data structures here

        logMetacat = Logger.getLogger(CrudService.class);

        try

        {

            String server = PropertyService.getProperty("server.name");

            String port = PropertyService.getProperty("server.httpPort");

            String context = PropertyService.getProperty("application.context");

            metacatUrl = "http://" + server + ":" + port + "/" + context;

            logMetacat.debug("Initializing CrudService with url " + metacatUrl);

        }

        catch(Exception e)

        {

            logMetacat.error("Could not find servlet url in CrudService: " + e.getMessage());

            e.printStackTrace();

            throw new RuntimeException("Error getting servlet url in CrudService: " + e.getMessage());

        }

        /*this.servletContext = servletContext;

        this.request = request;

        this.response = response;*/

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

        handler = new MetacatHandler(new Timer());

    }

    /**

     * return the context url CrudService is using.

     */

    public String getContextUrl()

    {

        return metacatUrl;

    }

    /**

     * set the params for this service from an HttpServletRequest param list

     */

    public void setParamsFromRequest(HttpServletRequest request)

    {

        Enumeration paramlist = request.getParameterNames();

        while (paramlist.hasMoreElements()) {

            String name = (String) paramlist.nextElement();

            String[] value = (String[])request.getParameterValues(name);

            params.put(name, value);

        }

    }

    /**

     * set the parameter values needed for this request

     */

    public void setParameter(String name, String[] value)

    {

        params.put(name, value);

    }

    public Identifier create(AuthToken token, Identifier guid, 

            InputStream object, SystemMetadata sysmeta) throws InvalidToken, 

            ServiceFailure, NotAuthorized, IdentifierNotUnique, UnsupportedType, 

            InsufficientResources, InvalidSystemMetadata, NotImplemented {

        logMetacat.debug("Starting CrudService.create()...");

        // authenticate & get user info

        SessionData sessionData = getSessionData(token);

        String username = sessionData.getUserName();

        String[] groups = sessionData.getGroupNames();

        // verify that guid == SystemMetadata.getIdentifier()

        logMetacat.debug("Comparing guid|sysmeta_guid: " + guid.getValue() + "|" + sysmeta.getIdentifier().getValue());

        if (!guid.getValue().equals(sysmeta.getIdentifier().getValue())) {

            throw new InvalidSystemMetadata("1180", 

                "GUID in method call does not match GUID in system metadata.");

        }

        logMetacat.debug("Checking if identifier exists...");

        // Check that the identifier does not already exist

        IdentifierManager im = IdentifierManager.getInstance();

        if (im.identifierExists(guid.getValue())) {

            throw new IdentifierNotUnique("1120", 

                "GUID is already in use by an existing object.");

        }

        // Check if we are handling metadata or data

        boolean isScienceMetadata = isScienceMetadata(sysmeta);

        if (isScienceMetadata) {

            // CASE METADATA:

            try {

                this.insertDocument(object, guid, sessionData);

            } catch (IOException e) {

                String msg = "Could not create string from XML stream: " +

                    " " + e.getMessage();

                logMetacat.debug(msg);

                throw new ServiceFailure("1190", msg);

            }

        } else {

            // DEFAULT CASE: DATA (needs to be checked and completed)

            insertDataObject(object, guid, sessionData);

        }

        // For Metadata and Data, insert the system metadata into the object store too

        insertSystemMetadata(sysmeta, sessionData);

        logMetacat.debug("Returning from CrudService.create()");

        return guid;

    }

    /**

     * update an existing object with a new object.  Change the system metadata

     * to reflect the changes and update it as well.

     */

    public Identifier update(AuthToken token, Identifier guid, 

            InputStream object, Identifier obsoletedGuid, SystemMetadata sysmeta) 

            throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique, 

            UnsupportedType, InsufficientResources, NotFound, InvalidSystemMetadata, 

            NotImplemented {

        try

        {

            SessionData sessionData = getSessionData(token);

            //find the old systemmetadata (sm.old) document id (the one linked to obsoletedGuid)

            SystemMetadata sm = getSystemMetadata(token, obsoletedGuid);

            //change sm.old's obsoletedBy field 

            List l = sm.getObsoletedByList();

            l.add(guid);

            sm.setObsoletedByList(l);

            //update sm.old

            updateSystemMetadata(sm, sessionData);

            //change the obsoletes field of the new systemMetadata (sm.new) to point to the id of the old one

            sysmeta.addObsolete(obsoletedGuid);

            //insert sm.new

            insertSystemMetadata(sysmeta, sessionData);

            boolean isScienceMetadata = isScienceMetadata(sysmeta);

            if(isScienceMetadata)

            {

                //update the doc

                updateDocument(object, obsoletedGuid, guid, sessionData);

            }

            else

            {

                //update a data file, not xml

                insertDataObject(object, guid, sessionData);

            }

            return guid;

        }

        catch(Exception e)

        {

            throw new ServiceFailure("1030", "Error updating document in CrudService: " + e.getMessage());

        }

    }

    /**

     * set the permission on the document

     * @param token

     * @param principal

     * @param permission

     * @param permissionType

     * @param permissionOrder

     * @return

     */

    public void setAccess(AuthToken token, Identifier id, String principal, String permission,

            String permissionType, String permissionOrder)

      throws ServiceFailure

    {

        try

        {

            IdentifierManager im = IdentifierManager.getInstance();

            String docid = im.getLocalId(id.getValue());

            final SessionData sessionData = getSessionData(token);

            String permNum = "0";

            if(permission == "read")

            {

                permNum = "4";

            }

            else if(permission == "write")

            {

                permNum = "6";

            }

            handler.setAccess(metacatUrl, sessionData.getUserName(), docid, 

                    principal, permNum, permissionType, permissionOrder);

        }

        catch(Exception e)

        {

            throw new ServiceFailure("1000", "Could not set access on the document with id " + id.getValue());

        }

    }

    /**

     *  Retrieve the list of objects present on the MN that match the calling 

     *  parameters. This method is required to support the process of Member 

     *  Node synchronization. At a minimum, this method should be able to 

     *  return a list of objects that match:

     *  startTime <= SystemMetadata.dateSysMetadataModified

     *  but is expected to also support date range (by also specifying endTime), 

     *  and should also support slicing of the matching set of records by 

     *  indicating the starting index of the response (where 0 is the index 

     *  of the first item) and the count of elements to be returned.

     *  

     *  If startTime or endTime is null, the query is not restricted by that parameter.

     *  

     * @see http://mule1.dataone.org/ArchitectureDocs/mn_api_replication.html#MN_replication.listObjects

     * @param token

     * @param startTime

     * @param endTime

     * @param objectFormat

     * @param replicaStatus

     * @param start

     * @param count

     * @return ObjectList

     * @throws NotAuthorized

     * @throws InvalidRequest

     * @throws NotImplemented

     * @throws ServiceFailure

     * @throws InvalidToken

     */

    public ObjectList listObjects(AuthToken token, Date startTime, Date endTime, 

        ObjectFormat objectFormat, boolean replicaStatus, int start, int count)

      throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken

    {

      ObjectList ol = new ObjectList();

      final SessionData sessionData = getSessionData(token);

      try

      {

          params.clear();

          params.put("returndoctype", new String[] {"http://dataone.org/service/types/SystemMetadata/0.1"});

          params.put("qformat", new String[] {"xml"});

          params.put("returnfield", new String[] {"size", "originMemberNode", 

                  "identifier", "objectFormat", "dateSysMetadataModified", "checksum"});

          params.put("anyfield", new String[] {"%"});

          MetacatResultSet rs = handler.query(metacatUrl, params, sessionData.getUserName(), 

                  sessionData.getGroupNames(), sessionData.getId());

          List docs = rs.getDocuments();

          if(count == 1000)

          {

              count = docs.size();

          }

          for(int i=start; i<count; i++)

          {

              //get the document from the results

              Document d = (Document)docs.get(i);

              ObjectFormat returnedObjectFormat = ObjectFormat.convert(d.getField("objectFormat"));

              if(objectFormat != null && !objectFormat.toString().trim().equals(returnedObjectFormat.toString().trim()))

              { //make sure the objectFormat is the one specified

                  continue;

              }

              Date dateSysMetadataModified = parseDate(d.getField("dateSysMetadataModified"));

              int startDateComparison = 0;

              int endDateComparison = 0;

              if(startTime != null)

              {

                  startDateComparison = dateSysMetadataModified.compareTo(startTime);

              }

              if(endTime != null)

              {

                  endDateComparison = dateSysMetadataModified.compareTo(endTime);

              }

              if(startDateComparison < 0 || endDateComparison > 0)

              { //this date falls outside of the startTime and endTime params, so

                //skip it

                  continue;                  

              }

              ObjectInfo info = new ObjectInfo();

              //add the fields to the info object

              Checksum cs = new Checksum();

              cs.setValue(d.getField("checksum"));

              info.setChecksum(cs);

              info.setDateSysMetadataModified(dateSysMetadataModified);

              Identifier id = new Identifier();

              id.setValue(d.getField("identifier"));

              info.setIdentifier(id);

              info.setObjectFormat(returnedObjectFormat);

              info.setSize(new Long(d.getField("size").trim()).longValue());

              //add the ObjectInfo to the ObjectList

              ol.addObjectInfo(info);

              //System.out.println(d.toString());

          }

      }

      catch(Exception e)

      {

          e.printStackTrace();

          throw new ServiceFailure("1580", "Error retrieving ObjectList: " + e.getMessage());

      }

      return ol;

    }

    /**

     * Call listObjects with the default values for replicaStatus (true), start (0),

     * and count (1000).

     * @param token

     * @param startTime

     * @param endTime

     * @param objectFormat

     * @return

     * @throws NotAuthorized

     * @throws InvalidRequest

     * @throws NotImplemented

     * @throws ServiceFailure

     * @throws InvalidToken

     */

    public ObjectList listObjects(AuthToken token, Date startTime, Date endTime, 

        ObjectFormat objectFormat)

      throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken

    {

       return listObjects(token, startTime, endTime, objectFormat, true, 0, 1000);

    }

    /**

     * Delete a document.  NOT IMPLEMENTED

     */

    public Identifier delete(AuthToken token, Identifier guid)

            throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

            NotImplemented {

        throw new NotImplemented("1000", "This method not yet implemented.");

    }

    /**

     * describe a document.  NOT IMPLEMENTED

     */

    public DescribeResponse describe(AuthToken token, Identifier guid)

            throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

            NotImplemented {

        throw new NotImplemented("1000", "This method not yet implemented.");

    }

    /**

     * get a document with a specified guid.

     */

    public InputStream get(AuthToken token, Identifier guid)

            throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

            NotImplemented {

        // Retrieve the session information from the AuthToken

        // If the session is expired, then the user is 'public'

        final SessionData sessionData = getSessionData(token);

        // Look up the localId for this global identifier

        IdentifierManager im = IdentifierManager.getInstance();

        try {

            final String localId = im.getLocalId(guid.getValue());

            final InputStreamFromOutputStream<String> objectStream = 

                new InputStreamFromOutputStream<String>() {

                @Override

                public String produce(final OutputStream dataSink) throws Exception {

                    try {

                        handler.readFromMetacat(metacatUrl, null, 

                                dataSink, localId, "xml",

                                sessionData.getUserName(), 

                                sessionData.getGroupNames(), true, params);

                    } catch (PropertyNotFoundException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (ClassNotFoundException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (IOException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (SQLException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (McdbException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (ParseLSIDException e) {

                        throw new NotFound("1020", e.getMessage());

                    } catch (InsufficientKarmaException e) {

                        throw new NotAuthorized("1000", "Not authorized for get().");

                    }

                    return "Completed";

                }

            };

            return objectStream;

        } catch (McdbDocNotFoundException e) {

            throw new NotFound("1020", e.getMessage());

        }

    }

    /**

     * get the checksum for a document.  NOT IMPLEMENTED

     */

    public Checksum getChecksum(AuthToken token, Identifier guid)

            throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

            InvalidRequest, NotImplemented {

        throw new NotImplemented("1000", "This method not yet implemented.");

    }

    /**

     * get the checksum for a document.  NOT IMPLEMENTED

     */

    public Checksum getChecksum(AuthToken token, Identifier guid, 

            String checksumAlgorithm) throws InvalidToken, ServiceFailure, 

            NotAuthorized, NotFound, InvalidRequest, NotImplemented {

        throw new NotImplemented("1000", "This method not yet implemented.");

    }

    /**

     * get log records.  NOT IMPLEMENTED

     */

    public LogRecordSet getLogRecords(AuthToken token, Date fromDate, Date toDate)

            throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest, 

            NotImplemented {

        throw new NotImplemented("1000", "This method not yet implemented.");

    }

    /**

     * get the system metadata for a document with a specified guid.

     */

    public SystemMetadata getSystemMetadata(AuthToken token, Identifier guid)

            throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, 

            InvalidRequest, NotImplemented {

        logMetacat.debug("CrudService.getSystemMetadata - for guid: " + guid.getValue());

        // Retrieve the session information from the AuthToken

        // If the session is expired, then the user is 'public'

        final SessionData sessionData = getSessionData(token);

        // TODO: Check access control rules

        try {

            IdentifierManager im = IdentifierManager.getInstance();

            final String localId = im.getSystemMetadataId(guid.getValue());

            // Read system metadata from metacat's db

            final InputStreamFromOutputStream<String> objectStream = 

                new InputStreamFromOutputStream<String>() {

                @Override

                public String produce(final OutputStream dataSink) throws Exception {

                    try {

                        handler.readFromMetacat(metacatUrl, null, 

                                dataSink, localId, "xml",

                                sessionData.getUserName(), 

                                sessionData.getGroupNames(), true, params);

                    } catch (PropertyNotFoundException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (ClassNotFoundException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (IOException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (SQLException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (McdbException e) {

                        throw new ServiceFailure("1030", e.getMessage());

                    } catch (ParseLSIDException e) {

                        throw new NotFound("1020", e.getMessage());

                    } catch (InsufficientKarmaException e) {

                        throw new NotAuthorized("1000", "Not authorized for get().");

                    }

                    return "Completed";

                }

            };

            // Deserialize the xml to create a SystemMetadata object

            SystemMetadata sysmeta = deserializeSystemMetadata(objectStream);

            return sysmeta;

        } catch (McdbDocNotFoundException e) {

            //e.printStackTrace();

            throw new NotFound("1000", e.getMessage());

        }                

    }

    /**

     * parse the date in the systemMetadata

     * @param s

     * @return

     * @throws Exception

     */

    private Date parseDate(String s)

      throws Exception

    {

        Date d = null;

        int tIndex = s.indexOf("T");

        int zIndex = s.indexOf("Z");

        if(tIndex != -1 && zIndex != -1)

        { //parse a date that looks like 2010-05-18T21:12:54.362Z

            //System.out.println("original date: " + s);

            String date = s.substring(0, tIndex);

            String year = date.substring(0, date.indexOf("-"));

            String month = date.substring(date.indexOf("-") + 1, date.lastIndexOf("-"));

            String day = date.substring(date.lastIndexOf("-") + 1, date.length());

            /*System.out.println("date: " + "year: " + new Integer(year).intValue() + 

                    " month: " + new Integer(month).intValue() + " day: " + 

                    new Integer(day).intValue());

            */

            String time = s.substring(tIndex + 1, zIndex);

            String hour = time.substring(0, time.indexOf(":"));

            String minute = time.substring(time.indexOf(":") + 1, time.lastIndexOf(":"));

            String seconds = "00";

            String milliseconds = "00";

            if(time.indexOf(".") != -1)

            {

                seconds = time.substring(time.lastIndexOf(":") + 1, time.indexOf("."));

                milliseconds = time.substring(time.indexOf(".") + 1, time.length());

            }

            /*System.out.println("time: " + "hour: " + new Integer(hour).intValue() + 

                    " minute: " + new Integer(minute).intValue() + " seconds: " + 

                    new Integer(seconds).intValue() + " milli: " + 

                    new Integer(milliseconds).intValue());*/

            //d = DateFormat.getDateTimeInstance().parse(date + " " + time);

            Calendar c = Calendar.getInstance(TimeZone.getTimeZone("GMT-0"));

            c.set(new Integer(year).intValue(), new Integer(month).intValue() - 1, 

                  new Integer(day).intValue(), new Integer(hour).intValue(), 

                  new Integer(minute).intValue(), new Integer(seconds).intValue());

            c.set(Calendar.MILLISECOND, new Integer(milliseconds).intValue());

            d = new Date(c.getTimeInMillis());

            //System.out.println("d: " + d);

            return d;

        }

        else

        {  //if it's not in the expected format, try the formatter

            return DateFormat.getDateTimeInstance().parse(s);

        }

    }

    /*

     * Look up the information on the session using the token provided in

     * the AuthToken.  The Session should have all relevant user information.

     * If the session has expired or is invalid, the 'public' session will

     * be returned, giving the user anonymous access.

     */

    private static SessionData getSessionData(AuthToken token) {

        SessionData sessionData = null;

        String sessionId = "PUBLIC";

        if (token != null) {

            sessionId = token.getToken();

        }

        // if the session id is registered in SessionService, get the

        // SessionData for it. Otherwise, use the public session.

        if (SessionService.isSessionRegistered(sessionId)) {

            sessionData = SessionService.getRegisteredSession(sessionId);

        } else {

            sessionData = SessionService.getPublicSession();

        }

        return sessionData;

    }

    /** 

     * Determine if a given object should be treated as an XML science metadata

     * object. 

     * 

     * TODO: This test should be externalized in a configuration dictionary rather than being hardcoded.

     * 

     * @param sysmeta the SystemMetadata describig the object

     * @return true if the object should be treated as science metadata

     */

    private boolean isScienceMetadata(SystemMetadata sysmeta) {

        boolean scimeta = false;

        switch (sysmeta.getObjectFormat()) {

            case EML_2_1_0: scimeta = true; break;

            case EML_2_0_1: scimeta = true; break;

            case EML_2_0_0: scimeta = true; break;

            case FGDC_STD_001_1_1999: scimeta = true; break;

            case FGDC_STD_001_1998: scimeta = true; break;

            case NCML_2_2: scimeta = true; break;

        }

        return scimeta;

    }

    /**

     * insert a data doc

     * @param object

     * @param guid

     * @param sessionData

     * @throws ServiceFailure

     */

    private void insertDataObject(InputStream object, Identifier guid, 

            SessionData sessionData) throws ServiceFailure {

        String username = sessionData.getUserName();

        String[] groups = sessionData.getGroupNames();

        // generate guid/localId pair for object

        logMetacat.debug("Generating a guid/localId mapping");

        IdentifierManager im = IdentifierManager.getInstance();

        String localId = im.generateLocalId(guid.getValue(), 1);

        try {

            logMetacat.debug("Case DATA: starting to write to disk.");

            if (DocumentImpl.getDataFileLockGrant(localId)) {

                // Save the data file to disk using "localId" as the name

                try {

                    String datafilepath = PropertyService.getProperty("application.datafilepath");

                    File dataDirectory = new File(datafilepath);

                    dataDirectory.mkdirs();

                    File newFile = writeStreamToFile(dataDirectory, localId, object);

                    // TODO: Check that the file size matches SystemMetadata

                    //                        long size = newFile.length();

                    //                        if (size == 0) {

                    //                            throw new IOException("Uploaded file is 0 bytes!");

                    //                        }

                    // Register the file in the database (which generates an exception

                    // if the localId is not acceptable or other untoward things happen

                    try {

                        logMetacat.debug("Registering document...");

                        System.out.println("inserting data object: localId: " + localId);

                        DocumentImpl.registerDocument(localId, "BIN", localId,

                                username, groups);

                        logMetacat.debug("Registration step completed.");

                    } catch (SQLException e) {

                        //newFile.delete();

                        logMetacat.debug("SQLE: " + e.getMessage());

                        e.printStackTrace(System.out);

                        throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());

                    } catch (AccessionNumberException e) {

                        //newFile.delete();

                        logMetacat.debug("ANE: " + e.getMessage());

                        e.printStackTrace(System.out);

                        throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());

                    } catch (Exception e) {

                        //newFile.delete();

                        logMetacat.debug("Exception: " + e.getMessage());

                        e.printStackTrace(System.out);

                        throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());

                    }

                    logMetacat.debug("Logging the creation event.");

                    EventLog.getInstance().log(metacatUrl,

                            username, localId, "create");

                    // Schedule replication for this data file

                    logMetacat.debug("Scheduling replication.");

                    ForceReplicationHandler frh = new ForceReplicationHandler(

                            localId, "insert", false, null);

                } catch (PropertyNotFoundException e) {

                    throw new ServiceFailure("1190", "Could not lock file for writing:" + e.getMessage());

                }

            }

        } catch (Exception e) {

            // Could not get a lock on the document, so we can not update the file now

            throw new ServiceFailure("1190", "Failed to lock file: " + e.getMessage());

        }

    }

    /**

     * write a file to a stream

     * @param dir

     * @param fileName

     * @param data

     * @return

     * @throws ServiceFailure

     */

    private File writeStreamToFile(File dir, String fileName, InputStream data) 

        throws ServiceFailure {

        File newFile = new File(dir, fileName);

        logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath());

        try {

            if (newFile.createNewFile()) {

                // write data stream to desired file

                OutputStream os = new FileOutputStream(newFile);

                long length = IOUtils.copyLarge(data, os);

                os.flush();

                os.close();

            } else {

                logMetacat.debug("File creation failed, or file already exists.");

                throw new ServiceFailure("1190", "File already exists: " + fileName);

            }

        } catch (FileNotFoundException e) {

            logMetacat.debug("FNF: " + e.getMessage());

            throw new ServiceFailure("1190", "File not found: " + fileName + " " 

                    + e.getMessage());

        } catch (IOException e) {

            logMetacat.debug("IOE: " + e.getMessage());

            throw new ServiceFailure("1190", "File was not written: " + fileName 

                    + " " + e.getMessage());

        }

        return newFile;

    }

    /**

     * insert a systemMetadata doc

     */

    private void insertSystemMetadata(SystemMetadata sysmeta, SessionData sessionData) 

        throws ServiceFailure {

        logMetacat.debug("Starting to insert SystemMetadata...");

        // generate guid/localId pair for sysmeta

        Identifier sysMetaGuid = new Identifier();

        sysMetaGuid.setValue(DocumentUtil.generateDocumentId(1));

        sysmeta.setDateSysMetadataModified(new Date());

        String xml = new String(serializeSystemMetadata(sysmeta).toByteArray());

        String localId = insertDocument(xml, sysMetaGuid, sessionData);

        //insert the system metadata doc id into the identifiers table to 

        //link it to the data or metadata document

        IdentifierManager.getInstance().createSystemMetadataMapping(sysmeta.getIdentifier().getValue(), sysMetaGuid.getValue());

    }

    /**

     * update a systemMetadata doc

     */

    private void updateSystemMetadata(SystemMetadata sm, SessionData sessionData)

      throws ServiceFailure

    {

        try

        {

            String smId = IdentifierManager.getInstance().getSystemMetadataId(sm.getIdentifier().getValue());

            sm.setDateSysMetadataModified(new Date());

            String xml = new String(serializeSystemMetadata(sm).toByteArray());

            Identifier id = new Identifier();

            id.setValue(smId);

            String localId = updateDocument(xml, id, null, sessionData);

            IdentifierManager.getInstance().updateSystemMetadataMapping(sm.getIdentifier().getValue(), localId);

        }

        catch(Exception e)

        {

            throw new ServiceFailure("1030", "Error updating system metadata: " + e.getMessage());

        }

    }

    /**

     * insert a document

     * NOTE: this method shouldn't be used from the update or create() methods.  

     * we shouldn't be putting the science metadata or data objects into memory.

     */

    private String insertDocument(String xml, Identifier guid, SessionData sessionData)

        throws ServiceFailure

    {

        return insertOrUpdateDocument(xml, guid, sessionData, "insert");

    }

    /**

     * insert a document from a stream

     */

    private String insertDocument(InputStream is, Identifier guid, SessionData sessionData)

      throws IOException, ServiceFailure

    {

        //HACK: change this eventually.  we should not be converting the stream to a string

        String xml = IOUtils.toString(is);

        return insertDocument(xml, guid, sessionData);

    }