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/**
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* '$RCSfile$'
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* Copyright: 2000-2011 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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*
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* '$Author$'
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* '$Date$'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat.dataone;
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6226
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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6174
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import java.io.InputStream;
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6241
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cjones
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import java.io.OutputStream;
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32 |
6226
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cjones
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import java.sql.SQLException;
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33 |
6225
|
leinfelder
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import java.util.ArrayList;
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34 |
6186
|
leinfelder
|
import java.util.Calendar;
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35 |
6174
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cjones
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import java.util.Date;
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36 |
6226
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cjones
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import java.util.Hashtable;
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37 |
6194
|
leinfelder
|
import java.util.List;
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38 |
6226
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cjones
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import java.util.Timer;
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39 |
6186
|
leinfelder
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import java.util.Vector;
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6174
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cjones
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41 |
6542
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leinfelder
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import javax.servlet.http.HttpServletRequest;
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6226
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cjones
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6542
|
leinfelder
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6241
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cjones
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import org.apache.commons.io.IOUtils;
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6186
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leinfelder
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import org.apache.log4j.Logger;
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6865
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cjones
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import org.dataone.client.CNode;
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import org.dataone.client.D1Client;
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48 |
6241
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cjones
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import org.dataone.client.ObjectFormatCache;
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49 |
6371
|
leinfelder
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import org.dataone.service.util.Constants;
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6241
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cjones
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import org.dataone.service.exceptions.IdentifierNotUnique;
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51 |
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import org.dataone.service.exceptions.InsufficientResources;
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6174
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cjones
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import org.dataone.service.exceptions.InvalidRequest;
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6241
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cjones
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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6174
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cjones
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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6241
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import org.dataone.service.exceptions.UnsupportedType;
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6366
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leinfelder
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import org.dataone.service.types.v1.AccessPolicy;
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61 |
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import org.dataone.service.types.v1.AccessRule;
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6803
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leinfelder
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import org.dataone.service.types.v1.DescribeResponse;
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6366
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leinfelder
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import org.dataone.service.types.v1.Event;
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import org.dataone.service.types.v1.Identifier;
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65 |
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import org.dataone.service.types.v1.Group;
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import org.dataone.service.types.v1.Log;
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import org.dataone.service.types.v1.LogEntry;
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6865
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import org.dataone.service.types.v1.Node;
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leinfelder
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import org.dataone.service.types.v1.NodeReference;
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6865
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cjones
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import org.dataone.service.types.v1.NodeType;
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import org.dataone.service.types.v1.ObjectFormat;
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import org.dataone.service.types.v1.Permission;
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import org.dataone.service.types.v1.Person;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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6532
|
leinfelder
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import org.dataone.service.types.v1.SubjectInfo;
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6366
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leinfelder
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import org.dataone.service.types.v1.SubjectList;
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import org.dataone.service.types.v1.SystemMetadata;
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6445
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leinfelder
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import org.dataone.service.types.v1.util.ChecksumUtil;
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6174
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cjones
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6241
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cjones
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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6186
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leinfelder
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import edu.ucsb.nceas.metacat.EventLog;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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6194
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leinfelder
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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6226
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cjones
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import edu.ucsb.nceas.metacat.MetacatHandler;
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6803
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leinfelder
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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6447
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leinfelder
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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6226
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cjones
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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6241
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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;
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6254
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cjones
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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6226
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cjones
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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6186
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leinfelder
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6174
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cjones
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public abstract class D1NodeService {
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6227
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cjones
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private static Logger logMetacat = Logger.getLogger(D1NodeService.class);
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6186
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leinfelder
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6542
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leinfelder
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/** For logging the operations */
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protected HttpServletRequest request;
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cjones
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6226
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/* reference to the metacat handler */
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6389
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leinfelder
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protected MetacatHandler handler;
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6174
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6226
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/* parameters set in the incoming request */
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private Hashtable<String, String[]> params;
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6241
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cjones
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/**
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* Constructor - used to set the metacatUrl from a subclass extending D1NodeService
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*
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* @param metacatUrl - the URL of the metacat service, including the ending /d1
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*/
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6542
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public D1NodeService(HttpServletRequest request) {
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this.request = request;
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}
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6241
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cjones
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/**
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6803
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leinfelder
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* This method provides a lighter weight mechanism than
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* getSystemMetadata() for a client to determine basic
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* properties of the referenced object.
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - the identifier of the object to be described
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*
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* @return describeResponse - A set of values providing a basic description
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* of the object.
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*
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* @throws InvalidToken
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* @throws ServiceFailure
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* @throws NotAuthorized
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* @throws NotFound
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* @throws NotImplemented
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* @throws InvalidRequest
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*/
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public DescribeResponse describe(Session session, Identifier pid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
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// get system metadata and construct the describe response
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SystemMetadata sysmeta = getSystemMetadata(session, pid);
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DescribeResponse describeResponse =
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new DescribeResponse(sysmeta.getFormatId(), sysmeta.getSize(),
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sysmeta.getDateSysMetadataModified(),
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sysmeta.getChecksum(), sysmeta.getSerialVersion());
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return describeResponse;
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}
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149 |
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/**
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* Low level, "are you alive" operation. A valid ping response is
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151 |
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* indicated by a HTTP status of 200.
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*
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153 |
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* @return true if the service is alive
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*
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* @throws NotImplemented
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156 |
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* @throws ServiceFailure
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157 |
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* @throws InsufficientResources
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158 |
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*/
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159 |
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public Date ping()
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160 |
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throws NotImplemented, ServiceFailure, InsufficientResources {
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161 |
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162 |
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// test if we can get a database connection
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163 |
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int serialNumber = -1;
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164 |
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DBConnection dbConn = null;
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165 |
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try {
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166 |
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dbConn = DBConnectionPool.getDBConnection("MNodeService.ping");
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167 |
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serialNumber = dbConn.getCheckOutSerialNumber();
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168 |
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} catch (SQLException e) {
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169 |
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ServiceFailure sf = new ServiceFailure("", e.getMessage());
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170 |
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sf.initCause(e);
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throw sf;
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172 |
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} finally {
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173 |
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// Return the database connection
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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175 |
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}
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176 |
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177 |
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return Calendar.getInstance().getTime();
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178 |
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}
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179 |
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|
180 |
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/**
|
181 |
6241
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cjones
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* Adds a new object to the Node, where the object is either a data
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182 |
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* object or a science metadata object. This method is called by clients
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183 |
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* to create new data objects on Member Nodes or internally for Coordinating
|
184 |
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* Nodes
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185 |
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*
|
186 |
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* @param session - the Session object containing the credentials for the Subject
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187 |
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* @param pid - The object identifier to be created
|
188 |
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* @param object - the object bytes
|
189 |
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* @param sysmeta - the system metadata that describes the object
|
190 |
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*
|
191 |
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* @return pid - the object identifier created
|
192 |
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*
|
193 |
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* @throws InvalidToken
|
194 |
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* @throws ServiceFailure
|
195 |
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* @throws NotAuthorized
|
196 |
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* @throws IdentifierNotUnique
|
197 |
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* @throws UnsupportedType
|
198 |
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* @throws InsufficientResources
|
199 |
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* @throws InvalidSystemMetadata
|
200 |
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* @throws NotImplemented
|
201 |
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* @throws InvalidRequest
|
202 |
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*/
|
203 |
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public Identifier create(Session session, Identifier pid, InputStream object,
|
204 |
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SystemMetadata sysmeta)
|
205 |
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throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
206 |
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UnsupportedType, InsufficientResources, InvalidSystemMetadata,
|
207 |
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NotImplemented, InvalidRequest {
|
208 |
6174
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cjones
|
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209 |
6241
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cjones
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Identifier resultPid = null;
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210 |
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String localId = null;
|
211 |
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boolean allowed = false;
|
212 |
|
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|
213 |
6530
|
leinfelder
|
// check for null session
|
214 |
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if (session == null) {
|
215 |
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throw new InvalidToken("4894", "Session is required to WRITE to the Node.");
|
216 |
|
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}
|
217 |
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Subject subject = session.getSubject();
|
218 |
|
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|
219 |
6688
|
leinfelder
|
Subject publicSubject = new Subject();
|
220 |
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publicSubject.setValue(Constants.SUBJECT_PUBLIC);
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221 |
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// be sure the user is authenticated for create()
|
222 |
6518
|
leinfelder
|
if (subject == null || subject.getValue() == null ||
|
223 |
6688
|
leinfelder
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subject.equals(publicSubject) ) {
|
224 |
6241
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cjones
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throw new NotAuthorized("1100", "The provided identity does not have " +
|
225 |
6518
|
leinfelder
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"permission to WRITE to the Node.");
|
226 |
6241
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cjones
|
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227 |
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}
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228 |
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|
229 |
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// verify that pid == SystemMetadata.getIdentifier()
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logMetacat.debug("Comparing pid|sysmeta_pid: " +
|
231 |
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pid.getValue() + "|" + sysmeta.getIdentifier().getValue());
|
232 |
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if (!pid.getValue().equals(sysmeta.getIdentifier().getValue())) {
|
233 |
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throw new InvalidSystemMetadata("1180",
|
234 |
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"The supplied system metadata is invalid. " +
|
235 |
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"The identifier " + pid.getValue() + " does not match identifier" +
|
236 |
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"in the system metadata identified by " +
|
237 |
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sysmeta.getIdentifier().getValue() + ".");
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238 |
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|
239 |
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}
|
240 |
|
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|
241 |
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logMetacat.debug("Checking if identifier exists...");
|
242 |
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// Check that the identifier does not already exist
|
243 |
6278
|
leinfelder
|
if (IdentifierManager.getInstance().identifierExists(pid.getValue())) {
|
244 |
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throw new IdentifierNotUnique("1120",
|
245 |
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"The requested identifier " + pid.getValue() +
|
246 |
|
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" is already used by another object and" +
|
247 |
|
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"therefore can not be used for this object. Clients should choose" +
|
248 |
|
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"a new identifier that is unique and retry the operation or " +
|
249 |
6518
|
leinfelder
|
"use CN.reserveIdentifier() to reserve one.");
|
250 |
6337
|
leinfelder
|
|
251 |
6241
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cjones
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}
|
252 |
6518
|
leinfelder
|
|
253 |
6522
|
leinfelder
|
// check that we are not attempting to subvert versioning
|
254 |
|
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if (sysmeta.getObsoletes() != null && sysmeta.getObsoletes().getValue() != null) {
|
255 |
|
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throw new InvalidSystemMetadata("1180",
|
256 |
|
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"The supplied system metadata is invalid. " +
|
257 |
|
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"The obsoletes field cannot have a value when creating entries.");
|
258 |
|
|
}
|
259 |
|
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if (sysmeta.getObsoletedBy() != null && sysmeta.getObsoletedBy().getValue() != null) {
|
260 |
|
|
throw new InvalidSystemMetadata("1180",
|
261 |
|
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"The supplied system metadata is invalid. " +
|
262 |
|
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"The obsoletedBy field cannot have a value when creating entries.");
|
263 |
|
|
}
|
264 |
|
|
|
265 |
6596
|
leinfelder
|
// TODO: this probably needs to be refined more
|
266 |
6241
|
cjones
|
try {
|
267 |
|
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allowed = isAuthorized(session, pid, Permission.WRITE);
|
268 |
|
|
|
269 |
|
|
} catch (NotFound e) {
|
270 |
|
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// The identifier doesn't exist, writing should be fine.
|
271 |
|
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allowed = true;
|
272 |
|
|
}
|
273 |
|
|
|
274 |
6445
|
leinfelder
|
// verify checksum, only if we can reset the inputstream
|
275 |
|
|
if (object.markSupported()) {
|
276 |
|
|
String checksumAlgorithm = sysmeta.getChecksum().getAlgorithm();
|
277 |
|
|
String checksumValue = sysmeta.getChecksum().getValue();
|
278 |
|
|
try {
|
279 |
|
|
String computedChecksumValue = ChecksumUtil.checksum(object, checksumAlgorithm).getValue();
|
280 |
|
|
// it's very important that we don't consume the stream
|
281 |
|
|
object.reset();
|
282 |
|
|
if (!computedChecksumValue.equals(checksumValue)) {
|
283 |
|
|
throw new InvalidSystemMetadata("4896", "Checksum given does not match that of the object");
|
284 |
|
|
}
|
285 |
|
|
} catch (Exception e) {
|
286 |
|
|
String msg = "Error verifying checksum values";
|
287 |
|
|
logMetacat.error(msg, e);
|
288 |
|
|
throw new ServiceFailure("1190", msg + ": " + e.getMessage());
|
289 |
|
|
}
|
290 |
|
|
} else {
|
291 |
|
|
logMetacat.warn("mark is not supported on the object's input stream - cannot verify checksum without consuming stream");
|
292 |
|
|
}
|
293 |
|
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|
294 |
6241
|
cjones
|
// we have the go ahead
|
295 |
|
|
if ( allowed ) {
|
296 |
|
|
|
297 |
|
|
// Science metadata (XML) or science data object?
|
298 |
|
|
// TODO: there are cases where certain object formats are science metadata
|
299 |
|
|
// but are not XML (netCDF ...). Handle this.
|
300 |
|
|
if ( isScienceMetadata(sysmeta) ) {
|
301 |
|
|
|
302 |
|
|
// CASE METADATA:
|
303 |
|
|
String objectAsXML = "";
|
304 |
|
|
try {
|
305 |
|
|
objectAsXML = IOUtils.toString(object, "UTF-8");
|
306 |
|
|
localId = insertOrUpdateDocument(objectAsXML, pid, session, "insert");
|
307 |
|
|
//localId = im.getLocalId(pid.getValue());
|
308 |
|
|
|
309 |
|
|
} catch (IOException e) {
|
310 |
|
|
String msg = "The Node is unable to create the object. " +
|
311 |
|
|
"There was a problem converting the object to XML";
|
312 |
|
|
logMetacat.info(msg);
|
313 |
|
|
throw new ServiceFailure("1190", msg + ": " + e.getMessage());
|
314 |
|
|
|
315 |
|
|
}
|
316 |
|
|
|
317 |
6302
|
leinfelder
|
} else {
|
318 |
|
|
|
319 |
|
|
// DEFAULT CASE: DATA (needs to be checked and completed)
|
320 |
|
|
localId = insertDataObject(object, pid, session);
|
321 |
|
|
}
|
322 |
|
|
|
323 |
6241
|
cjones
|
}
|
324 |
6313
|
leinfelder
|
|
325 |
|
|
// save the sysmeta
|
326 |
6468
|
leinfelder
|
try {
|
327 |
6572
|
cjones
|
// lock and unlock of the pid happens in the subclass
|
328 |
6468
|
leinfelder
|
HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);
|
329 |
6572
|
cjones
|
|
330 |
6468
|
leinfelder
|
} catch (Exception e) {
|
331 |
6495
|
leinfelder
|
logMetacat.error("Problem creating system metadata: " + pid.getValue(), e);
|
332 |
6468
|
leinfelder
|
throw new ServiceFailure("1190", e.getMessage());
|
333 |
|
|
}
|
334 |
6302
|
leinfelder
|
|
335 |
6241
|
cjones
|
// setting the resulting identifier failed
|
336 |
6302
|
leinfelder
|
if (localId == null ) {
|
337 |
|
|
throw new ServiceFailure("1190", "The Node is unable to create the object. ");
|
338 |
6241
|
cjones
|
}
|
339 |
6313
|
leinfelder
|
|
340 |
6302
|
leinfelder
|
resultPid = pid;
|
341 |
|
|
|
342 |
6241
|
cjones
|
return resultPid;
|
343 |
|
|
}
|
344 |
|
|
|
345 |
6227
|
cjones
|
/**
|
346 |
|
|
* Return the log records associated with a given event between the start and
|
347 |
|
|
* end dates listed given a particular Subject listed in the Session
|
348 |
|
|
*
|
349 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
350 |
|
|
* @param fromDate - the start date of the desired log records
|
351 |
|
|
* @param toDate - the end date of the desired log records
|
352 |
|
|
* @param event - restrict log records of a specific event type
|
353 |
|
|
* @param start - zero based offset from the first record in the
|
354 |
|
|
* set of matching log records. Used to assist with
|
355 |
|
|
* paging the response.
|
356 |
|
|
* @param count - maximum number of log records to return in the response.
|
357 |
|
|
* Used to assist with paging the response.
|
358 |
|
|
*
|
359 |
|
|
* @return the desired log records
|
360 |
|
|
*
|
361 |
|
|
* @throws InvalidToken
|
362 |
|
|
* @throws ServiceFailure
|
363 |
|
|
* @throws NotAuthorized
|
364 |
|
|
* @throws InvalidRequest
|
365 |
|
|
* @throws NotImplemented
|
366 |
|
|
*/
|
367 |
|
|
public Log getLogRecords(Session session, Date fromDate, Date toDate,
|
368 |
6179
|
cjones
|
Event event, Integer start, Integer count) throws InvalidToken, ServiceFailure,
|
369 |
6227
|
cjones
|
NotAuthorized, InvalidRequest, NotImplemented {
|
370 |
6174
|
cjones
|
|
371 |
6186
|
leinfelder
|
|
372 |
6227
|
cjones
|
Log log = new Log();
|
373 |
6321
|
leinfelder
|
List<LogEntry> logs = new Vector<LogEntry>();
|
374 |
6227
|
cjones
|
IdentifierManager im = IdentifierManager.getInstance();
|
375 |
|
|
EventLog el = EventLog.getInstance();
|
376 |
6353
|
cjones
|
if ( fromDate == null ) {
|
377 |
6227
|
cjones
|
logMetacat.debug("setting fromdate from null");
|
378 |
|
|
fromDate = new Date(1);
|
379 |
|
|
}
|
380 |
6353
|
cjones
|
if ( toDate == null ) {
|
381 |
6227
|
cjones
|
logMetacat.debug("setting todate from null");
|
382 |
|
|
toDate = new Date();
|
383 |
|
|
}
|
384 |
6186
|
leinfelder
|
|
385 |
6353
|
cjones
|
if ( start == null ) {
|
386 |
|
|
start = 0;
|
387 |
|
|
|
388 |
|
|
}
|
389 |
|
|
|
390 |
|
|
if ( count == null ) {
|
391 |
|
|
count = 1000;
|
392 |
|
|
|
393 |
|
|
}
|
394 |
|
|
|
395 |
6227
|
cjones
|
logMetacat.debug("fromDate: " + fromDate);
|
396 |
|
|
logMetacat.debug("toDate: " + toDate);
|
397 |
6186
|
leinfelder
|
|
398 |
6227
|
cjones
|
String report = el.getReport(null, null, null, null,
|
399 |
|
|
new java.sql.Timestamp(fromDate.getTime()),
|
400 |
|
|
new java.sql.Timestamp(toDate.getTime()), false);
|
401 |
6186
|
leinfelder
|
|
402 |
6227
|
cjones
|
logMetacat.debug("report: " + report);
|
403 |
6186
|
leinfelder
|
|
404 |
6227
|
cjones
|
String logEntry = "<logEntry>";
|
405 |
|
|
String endLogEntry = "</logEntry>";
|
406 |
|
|
int startIndex = 0;
|
407 |
|
|
int foundIndex = report.indexOf(logEntry, startIndex);
|
408 |
|
|
while (foundIndex != -1) {
|
409 |
|
|
// parse out each entry
|
410 |
|
|
int endEntryIndex = report.indexOf(endLogEntry, foundIndex);
|
411 |
|
|
String entry = report.substring(foundIndex, endEntryIndex);
|
412 |
|
|
logMetacat.debug("entry: " + entry);
|
413 |
|
|
startIndex = endEntryIndex + endLogEntry.length();
|
414 |
|
|
foundIndex = report.indexOf(logEntry, startIndex);
|
415 |
6186
|
leinfelder
|
|
416 |
6227
|
cjones
|
String entryId = getLogEntryField("entryid", entry);
|
417 |
|
|
String ipAddress = getLogEntryField("ipAddress", entry);
|
418 |
|
|
String principal = getLogEntryField("principal", entry);
|
419 |
6542
|
leinfelder
|
String userAgent = getLogEntryField("userAgent", entry);
|
420 |
6227
|
cjones
|
String docid = getLogEntryField("docid", entry);
|
421 |
|
|
String eventS = getLogEntryField("event", entry);
|
422 |
|
|
String dateLogged = getLogEntryField("dateLogged", entry);
|
423 |
6186
|
leinfelder
|
|
424 |
6227
|
cjones
|
LogEntry le = new LogEntry();
|
425 |
6186
|
leinfelder
|
|
426 |
6227
|
cjones
|
Event e = Event.convert(eventS);
|
427 |
|
|
if (e == null) { // skip any events that are not Dataone Crud events
|
428 |
|
|
continue;
|
429 |
|
|
}
|
430 |
|
|
le.setEvent(e);
|
431 |
6754
|
leinfelder
|
le.setEntryId(entryId);
|
432 |
6227
|
cjones
|
Identifier identifier = new Identifier();
|
433 |
|
|
try {
|
434 |
6241
|
cjones
|
logMetacat.debug("converting docid '" + docid + "' to a pid.");
|
435 |
6227
|
cjones
|
if (docid == null || docid.trim().equals("") || docid.trim().equals("null")) {
|
436 |
|
|
continue;
|
437 |
|
|
}
|
438 |
|
|
docid = docid.substring(0, docid.lastIndexOf("."));
|
439 |
|
|
identifier.setValue(im.getGUID(docid, im.getLatestRevForLocalId(docid)));
|
440 |
|
|
} catch (Exception ex) {
|
441 |
6241
|
cjones
|
// try to get the pid, if that doesn't
|
442 |
6227
|
cjones
|
// work, just use the local id
|
443 |
|
|
// throw new ServiceFailure("1030",
|
444 |
6241
|
cjones
|
// "Error getting pid for localId " +
|
445 |
6227
|
cjones
|
// docid + ": " + ex.getMessage());\
|
446 |
6186
|
leinfelder
|
|
447 |
6241
|
cjones
|
// skip it if the pid can't be found
|
448 |
6227
|
cjones
|
continue;
|
449 |
|
|
}
|
450 |
6186
|
leinfelder
|
|
451 |
6227
|
cjones
|
le.setIdentifier(identifier);
|
452 |
|
|
le.setIpAddress(ipAddress);
|
453 |
|
|
Calendar c = Calendar.getInstance();
|
454 |
|
|
String year = dateLogged.substring(0, 4);
|
455 |
|
|
String month = dateLogged.substring(5, 7);
|
456 |
|
|
String date = dateLogged.substring(8, 10);
|
457 |
|
|
logMetacat.debug("year: " + year + " month: " + month + " day: " + date);
|
458 |
|
|
c.set(new Integer(year).intValue(), new Integer(month).intValue(),
|
459 |
|
|
new Integer(date).intValue());
|
460 |
|
|
Date logDate = c.getTime();
|
461 |
|
|
le.setDateLogged(logDate);
|
462 |
|
|
NodeReference memberNode = new NodeReference();
|
463 |
|
|
memberNode.setValue(ipAddress);
|
464 |
6754
|
leinfelder
|
le.setNodeIdentifier(memberNode);
|
465 |
6227
|
cjones
|
Subject princ = new Subject();
|
466 |
|
|
princ.setValue(principal);
|
467 |
|
|
le.setSubject(princ);
|
468 |
6542
|
leinfelder
|
le.setUserAgent(userAgent);
|
469 |
6186
|
leinfelder
|
|
470 |
6321
|
leinfelder
|
// event filtering?
|
471 |
6227
|
cjones
|
if (event == null) {
|
472 |
6321
|
leinfelder
|
logs.add(le);
|
473 |
|
|
} else if (le.getEvent().equals(event)) {
|
474 |
|
|
logs.add(le);
|
475 |
6227
|
cjones
|
}
|
476 |
|
|
}
|
477 |
6321
|
leinfelder
|
|
478 |
|
|
// d1 paging
|
479 |
|
|
int total = logs.size();
|
480 |
|
|
if (start != null && count != null) {
|
481 |
|
|
int toIndex = start + count;
|
482 |
|
|
if (toIndex <= total) {
|
483 |
|
|
logs = new ArrayList<LogEntry>(logs.subList(start, toIndex));
|
484 |
|
|
}
|
485 |
|
|
}
|
486 |
6186
|
leinfelder
|
|
487 |
6227
|
cjones
|
log.setLogEntryList(logs);
|
488 |
6321
|
leinfelder
|
log.setStart(start);
|
489 |
|
|
log.setCount(logs.size());
|
490 |
|
|
log.setTotal(total);
|
491 |
6227
|
cjones
|
logMetacat.info("getLogRecords");
|
492 |
|
|
return log;
|
493 |
|
|
}
|
494 |
6241
|
cjones
|
|
495 |
6227
|
cjones
|
/**
|
496 |
|
|
* Return the object identified by the given object identifier
|
497 |
|
|
*
|
498 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
499 |
|
|
* @param pid - the object identifier for the given object
|
500 |
|
|
*
|
501 |
|
|
* TODO: The D1 Authorization API doesn't provide information on which
|
502 |
|
|
* authentication system the Subject belongs to, and so it's not possible to
|
503 |
|
|
* discern which Person or Group is a valid KNB LDAP DN. Fix this.
|
504 |
|
|
*
|
505 |
|
|
* @return inputStream - the input stream of the given object
|
506 |
|
|
*
|
507 |
|
|
* @throws InvalidToken
|
508 |
|
|
* @throws ServiceFailure
|
509 |
|
|
* @throws NotAuthorized
|
510 |
|
|
* @throws InvalidRequest
|
511 |
|
|
* @throws NotImplemented
|
512 |
|
|
*/
|
513 |
|
|
public InputStream get(Session session, Identifier pid)
|
514 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
515 |
6609
|
cjones
|
NotImplemented {
|
516 |
6226
|
cjones
|
|
517 |
6227
|
cjones
|
InputStream inputStream = null; // bytes to be returned
|
518 |
6226
|
cjones
|
handler = new MetacatHandler(new Timer());
|
519 |
6227
|
cjones
|
boolean allowed = false;
|
520 |
|
|
String localId; // the metacat docid for the pid
|
521 |
6226
|
cjones
|
|
522 |
6227
|
cjones
|
// get the local docid from Metacat
|
523 |
|
|
try {
|
524 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
525 |
|
|
|
526 |
6226
|
cjones
|
} catch (McdbDocNotFoundException e) {
|
527 |
|
|
throw new NotFound("1020", "The object specified by " +
|
528 |
6227
|
cjones
|
pid.getValue() +
|
529 |
6283
|
leinfelder
|
" does not exist at this node.");
|
530 |
6226
|
cjones
|
}
|
531 |
|
|
|
532 |
|
|
// check for authorization
|
533 |
6227
|
cjones
|
allowed = isAuthorized(session, pid, Permission.READ);
|
534 |
|
|
|
535 |
|
|
// if the person is authorized, perform the read
|
536 |
6323
|
leinfelder
|
if (allowed) {
|
537 |
6226
|
cjones
|
try {
|
538 |
6323
|
leinfelder
|
inputStream = handler.read(localId);
|
539 |
|
|
} catch (Exception e) {
|
540 |
6226
|
cjones
|
throw new ServiceFailure("1020", "The object specified by " +
|
541 |
|
|
pid.getValue() +
|
542 |
6323
|
leinfelder
|
"could not be returned due to error: " +
|
543 |
6226
|
cjones
|
e.getMessage());
|
544 |
|
|
}
|
545 |
6227
|
cjones
|
}
|
546 |
6226
|
cjones
|
|
547 |
6227
|
cjones
|
// if we fail to set the input stream
|
548 |
|
|
if ( inputStream == null ) {
|
549 |
6226
|
cjones
|
throw new NotFound("1020", "The object specified by " +
|
550 |
|
|
pid.getValue() +
|
551 |
|
|
"does not exist at this node.");
|
552 |
6227
|
cjones
|
}
|
553 |
|
|
|
554 |
6389
|
leinfelder
|
// log the read event
|
555 |
6532
|
leinfelder
|
String principal = Constants.SUBJECT_PUBLIC;
|
556 |
6421
|
leinfelder
|
if (session != null && session.getSubject() != null) {
|
557 |
6389
|
leinfelder
|
principal = session.getSubject().getValue();
|
558 |
|
|
}
|
559 |
6542
|
leinfelder
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "read");
|
560 |
6389
|
leinfelder
|
|
561 |
6227
|
cjones
|
return inputStream;
|
562 |
|
|
}
|
563 |
6174
|
cjones
|
|
564 |
6227
|
cjones
|
/**
|
565 |
|
|
* Return the system metadata for a given object
|
566 |
|
|
*
|
567 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
568 |
|
|
* @param pid - the object identifier for the given object
|
569 |
|
|
*
|
570 |
|
|
* @return inputStream - the input stream of the given system metadata object
|
571 |
|
|
*
|
572 |
|
|
* @throws InvalidToken
|
573 |
|
|
* @throws ServiceFailure
|
574 |
|
|
* @throws NotAuthorized
|
575 |
|
|
* @throws NotFound
|
576 |
|
|
* @throws InvalidRequest
|
577 |
|
|
* @throws NotImplemented
|
578 |
|
|
*/
|
579 |
|
|
public SystemMetadata getSystemMetadata(Session session, Identifier pid)
|
580 |
6572
|
cjones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
581 |
6609
|
cjones
|
NotImplemented {
|
582 |
6572
|
cjones
|
|
583 |
|
|
if (!isAuthorized(session, pid, Permission.READ)) {
|
584 |
|
|
throw new NotAuthorized("1400", Permission.READ + " not allowed on " + pid.getValue());
|
585 |
|
|
}
|
586 |
|
|
SystemMetadata systemMetadata = null;
|
587 |
|
|
try {
|
588 |
|
|
systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
589 |
|
|
|
590 |
|
|
} catch (Exception e) {
|
591 |
|
|
// convert hazelcast RuntimeException to NotFound
|
592 |
|
|
throw new NotFound("1420", "No record found for: " + pid.getValue());
|
593 |
|
|
|
594 |
|
|
}
|
595 |
6227
|
cjones
|
|
596 |
|
|
return systemMetadata;
|
597 |
6174
|
cjones
|
}
|
598 |
6572
|
cjones
|
|
599 |
6227
|
cjones
|
/**
|
600 |
6865
|
cjones
|
* Test if the user identified by the provided token has administrative authorization
|
601 |
|
|
* for the operation on the specified object.
|
602 |
|
|
*
|
603 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
604 |
|
|
* @param pid - The identifer of the resource for which access is being checked
|
605 |
|
|
* @param operation - The type of operation which is being requested for the given pid
|
606 |
|
|
*
|
607 |
|
|
* @return true if the operation is allowed
|
608 |
|
|
*
|
609 |
|
|
* @throws ServiceFailure
|
610 |
|
|
* @throws InvalidToken
|
611 |
|
|
* @throws NotFound
|
612 |
|
|
* @throws NotAuthorized
|
613 |
|
|
* @throws NotImplemented
|
614 |
|
|
*/
|
615 |
|
|
protected boolean isAdminAuthorized(Session session, Identifier pid,
|
616 |
|
|
Permission permission)
|
617 |
|
|
throws ServiceFailure, InvalidToken, NotFound, NotAuthorized,
|
618 |
|
|
NotImplemented {
|
619 |
|
|
|
620 |
|
|
boolean allowed = false;
|
621 |
|
|
// are we allowed to do this? only CNs and target MNs are allowed
|
622 |
|
|
CNode cn = D1Client.getCN();
|
623 |
|
|
List<Node> nodes = cn.listNodes().getNodeList();
|
624 |
|
|
|
625 |
|
|
if ( nodes == null ) {
|
626 |
|
|
throw new ServiceFailure("4852", "Couldn't get node list.");
|
627 |
|
|
|
628 |
|
|
}
|
629 |
|
|
|
630 |
|
|
// find the node in the node list
|
631 |
|
|
for ( Node node : nodes ) {
|
632 |
|
|
|
633 |
|
|
NodeReference nodeReference = node.getIdentifier();
|
634 |
|
|
logMetacat.debug("In isAdminAuthorized(), Node reference is: " + nodeReference.getValue());
|
635 |
|
|
|
636 |
|
|
Subject subject = session.getSubject();
|
637 |
|
|
|
638 |
|
|
if (node.getType() == NodeType.CN) {
|
639 |
|
|
List<Subject> nodeSubjects = node.getSubjectList();
|
640 |
|
|
|
641 |
|
|
// check if the session subject is in the node subject list
|
642 |
|
|
for (Subject nodeSubject : nodeSubjects) {
|
643 |
|
|
if ( nodeSubject.equals(subject) ) {
|
644 |
|
|
allowed = true; // subject of session == target node subject
|
645 |
|
|
break;
|
646 |
|
|
|
647 |
|
|
}
|
648 |
6874
|
cjones
|
}
|
649 |
6865
|
cjones
|
}
|
650 |
|
|
}
|
651 |
|
|
|
652 |
|
|
|
653 |
|
|
return allowed;
|
654 |
|
|
}
|
655 |
|
|
|
656 |
|
|
/**
|
657 |
6227
|
cjones
|
* Test if the user identified by the provided token has authorization
|
658 |
6865
|
cjones
|
* for the operation on the specified object.
|
659 |
6227
|
cjones
|
*
|
660 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
661 |
|
|
* @param pid - The identifer of the resource for which access is being checked
|
662 |
|
|
* @param operation - The type of operation which is being requested for the given pid
|
663 |
|
|
*
|
664 |
|
|
* @return true if the operation is allowed
|
665 |
|
|
*
|
666 |
|
|
* @throws ServiceFailure
|
667 |
|
|
* @throws InvalidToken
|
668 |
|
|
* @throws NotFound
|
669 |
|
|
* @throws NotAuthorized
|
670 |
|
|
* @throws NotImplemented
|
671 |
|
|
* @throws InvalidRequest
|
672 |
|
|
*/
|
673 |
|
|
public boolean isAuthorized(Session session, Identifier pid, Permission permission)
|
674 |
|
|
throws ServiceFailure, InvalidToken, NotFound, NotAuthorized,
|
675 |
6609
|
cjones
|
NotImplemented {
|
676 |
6174
|
cjones
|
|
677 |
6227
|
cjones
|
boolean allowed = false;
|
678 |
|
|
|
679 |
6816
|
leinfelder
|
// permissions are hierarchical
|
680 |
6830
|
leinfelder
|
List<Permission> expandedPermissions = null;
|
681 |
6816
|
leinfelder
|
|
682 |
|
|
// for the "Verified" symbolic user
|
683 |
|
|
Subject verifiedSubject = new Subject();
|
684 |
|
|
verifiedSubject.setValue(Constants.SUBJECT_VERIFIED_USER);
|
685 |
|
|
|
686 |
6227
|
cjones
|
// get the subjects from the session
|
687 |
|
|
List<Subject> subjects = new ArrayList<Subject>();
|
688 |
6412
|
leinfelder
|
if (session != null) {
|
689 |
|
|
Subject subject = session.getSubject();
|
690 |
|
|
if (subject != null) {
|
691 |
|
|
subjects.add(subject);
|
692 |
|
|
}
|
693 |
6664
|
leinfelder
|
SubjectInfo subjectInfo = session.getSubjectInfo();
|
694 |
|
|
if (subjectInfo != null) {
|
695 |
6816
|
leinfelder
|
// add the equivalent identities
|
696 |
6664
|
leinfelder
|
List<Person> personList = subjectInfo.getPersonList();
|
697 |
6412
|
leinfelder
|
if (personList != null) {
|
698 |
|
|
for (Person p: personList) {
|
699 |
|
|
subjects.add(p.getSubject());
|
700 |
6664
|
leinfelder
|
if (p.getVerified()) {
|
701 |
|
|
// add the verified symbolic user
|
702 |
|
|
if (!subjects.contains(verifiedSubject)) {
|
703 |
|
|
subjects.add(verifiedSubject);
|
704 |
|
|
}
|
705 |
|
|
}
|
706 |
6412
|
leinfelder
|
}
|
707 |
|
|
}
|
708 |
6816
|
leinfelder
|
// add the groups
|
709 |
6664
|
leinfelder
|
List<Group> groupList = subjectInfo.getGroupList();
|
710 |
6412
|
leinfelder
|
if (groupList != null) {
|
711 |
|
|
for (Group g: groupList) {
|
712 |
|
|
subjects.add(g.getSubject());
|
713 |
|
|
}
|
714 |
|
|
}
|
715 |
|
|
}
|
716 |
6664
|
leinfelder
|
// add the authenticated symbolic as a check
|
717 |
|
|
Subject authenticatedSubject = new Subject();
|
718 |
|
|
authenticatedSubject.setValue(Constants.SUBJECT_AUTHENTICATED_USER);
|
719 |
|
|
subjects.add(authenticatedSubject);
|
720 |
|
|
|
721 |
6227
|
cjones
|
}
|
722 |
|
|
|
723 |
6293
|
leinfelder
|
// add public subject
|
724 |
|
|
Subject publicSubject = new Subject();
|
725 |
6532
|
leinfelder
|
publicSubject.setValue(Constants.SUBJECT_PUBLIC);
|
726 |
6293
|
leinfelder
|
subjects.add(publicSubject);
|
727 |
|
|
|
728 |
6227
|
cjones
|
// get the system metadata
|
729 |
6241
|
cjones
|
String pidStr = pid.getValue();
|
730 |
6227
|
cjones
|
SystemMetadata systemMetadata = null;
|
731 |
|
|
try {
|
732 |
6574
|
cjones
|
systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
733 |
|
|
|
734 |
|
|
} catch (Exception e) {
|
735 |
|
|
// convert Hazelcast RuntimeException to NotFound
|
736 |
|
|
logMetacat.error("An error occurred while getting system metadata for identifier " +
|
737 |
|
|
pid.getValue() + ". The error message was: " + e.getMessage());
|
738 |
|
|
throw new NotFound("1800", "No record found for " + pidStr);
|
739 |
|
|
|
740 |
6858
|
cjones
|
}
|
741 |
6596
|
leinfelder
|
|
742 |
|
|
// throw not found if it was not found
|
743 |
|
|
if (systemMetadata == null) {
|
744 |
6652
|
leinfelder
|
throw new NotFound("1800", "No system metadata could be found for given PID: " + pidStr);
|
745 |
6596
|
leinfelder
|
}
|
746 |
6245
|
leinfelder
|
|
747 |
6293
|
leinfelder
|
// do we own it?
|
748 |
|
|
for (Subject s: subjects) {
|
749 |
6688
|
leinfelder
|
allowed = systemMetadata.getRightsHolder().equals(s);
|
750 |
6293
|
leinfelder
|
if (allowed) {
|
751 |
|
|
return allowed;
|
752 |
|
|
}
|
753 |
|
|
}
|
754 |
|
|
|
755 |
|
|
// otherwise check the access rules
|
756 |
6245
|
leinfelder
|
try {
|
757 |
|
|
List<AccessRule> allows = systemMetadata.getAccessPolicy().getAllowList();
|
758 |
6293
|
leinfelder
|
search: // label break
|
759 |
6245
|
leinfelder
|
for (AccessRule accessRule: allows) {
|
760 |
|
|
for (Subject s: subjects) {
|
761 |
6816
|
leinfelder
|
if (accessRule.getSubjectList().contains(s)) {
|
762 |
6830
|
leinfelder
|
for (Permission p: accessRule.getPermissionList()) {
|
763 |
|
|
expandedPermissions = expandPermissions(p);
|
764 |
|
|
allowed = expandedPermissions.contains(permission);
|
765 |
|
|
if (allowed) {
|
766 |
|
|
break search; //label break
|
767 |
|
|
}
|
768 |
6816
|
leinfelder
|
}
|
769 |
|
|
|
770 |
6245
|
leinfelder
|
}
|
771 |
|
|
}
|
772 |
|
|
}
|
773 |
|
|
} catch (Exception e) {
|
774 |
|
|
// catch all for errors - safe side should be to deny the access
|
775 |
|
|
logMetacat.error("Problem checking authorization - defaulting to deny", e);
|
776 |
|
|
allowed = false;
|
777 |
|
|
}
|
778 |
6227
|
cjones
|
|
779 |
6245
|
leinfelder
|
// throw or return?
|
780 |
6227
|
cjones
|
if (!allowed) {
|
781 |
6245
|
leinfelder
|
throw new NotAuthorized("1820", permission + " not allowed on " + pidStr);
|
782 |
6227
|
cjones
|
}
|
783 |
6245
|
leinfelder
|
|
784 |
6227
|
cjones
|
return allowed;
|
785 |
6241
|
cjones
|
|
786 |
6227
|
cjones
|
}
|
787 |
|
|
|
788 |
6256
|
cjones
|
/*
|
789 |
6227
|
cjones
|
* parse a logEntry and get the relevant field from it
|
790 |
|
|
*
|
791 |
|
|
* @param fieldname
|
792 |
|
|
* @param entry
|
793 |
|
|
* @return
|
794 |
|
|
*/
|
795 |
|
|
private String getLogEntryField(String fieldname, String entry) {
|
796 |
|
|
String begin = "<" + fieldname + ">";
|
797 |
|
|
String end = "</" + fieldname + ">";
|
798 |
|
|
// logMetacat.debug("looking for " + begin + " and " + end +
|
799 |
|
|
// " in entry " + entry);
|
800 |
|
|
String s = entry.substring(entry.indexOf(begin) + begin.length(), entry
|
801 |
|
|
.indexOf(end));
|
802 |
|
|
logMetacat.debug("entry " + fieldname + " : " + s);
|
803 |
|
|
return s;
|
804 |
|
|
}
|
805 |
6174
|
cjones
|
|
806 |
6257
|
cjones
|
/**
|
807 |
6241
|
cjones
|
* Determine if a given object should be treated as an XML science metadata
|
808 |
|
|
* object.
|
809 |
|
|
*
|
810 |
|
|
* @param sysmeta - the SystemMetadata describing the object
|
811 |
|
|
* @return true if the object should be treated as science metadata
|
812 |
|
|
*/
|
813 |
6433
|
leinfelder
|
public static boolean isScienceMetadata(SystemMetadata sysmeta) {
|
814 |
6241
|
cjones
|
|
815 |
|
|
ObjectFormat objectFormat = null;
|
816 |
|
|
boolean isScienceMetadata = false;
|
817 |
|
|
|
818 |
|
|
try {
|
819 |
6561
|
leinfelder
|
objectFormat = ObjectFormatCache.getInstance().getFormat(sysmeta.getFormatId());
|
820 |
6433
|
leinfelder
|
if ( objectFormat.getFormatType().equals("METADATA") ) {
|
821 |
6402
|
cjones
|
isScienceMetadata = true;
|
822 |
|
|
|
823 |
|
|
}
|
824 |
6241
|
cjones
|
|
825 |
|
|
} catch (InvalidRequest e) {
|
826 |
|
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
827 |
|
|
sysmeta.getIdentifier().getValue() +
|
828 |
|
|
" is science metadata: " + e.getMessage());
|
829 |
|
|
|
830 |
|
|
} catch (ServiceFailure e) {
|
831 |
|
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
832 |
|
|
sysmeta.getIdentifier().getValue() +
|
833 |
|
|
" is science metadata: " + e.getMessage());
|
834 |
|
|
|
835 |
|
|
} catch (NotFound e) {
|
836 |
|
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
837 |
|
|
sysmeta.getIdentifier().getValue() +
|
838 |
|
|
" is science metadata: " + e.getMessage());
|
839 |
|
|
|
840 |
|
|
} catch (InsufficientResources e) {
|
841 |
|
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
842 |
|
|
sysmeta.getIdentifier().getValue() +
|
843 |
|
|
" is science metadata: " + e.getMessage());
|
844 |
|
|
|
845 |
|
|
} catch (NotImplemented e) {
|
846 |
|
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
847 |
|
|
sysmeta.getIdentifier().getValue() +
|
848 |
|
|
" is science metadata: " + e.getMessage());
|
849 |
|
|
|
850 |
|
|
}
|
851 |
|
|
|
852 |
|
|
return isScienceMetadata;
|
853 |
6226
|
cjones
|
|
854 |
6241
|
cjones
|
}
|
855 |
|
|
|
856 |
|
|
/**
|
857 |
|
|
* Insert or update an XML document into Metacat
|
858 |
|
|
*
|
859 |
|
|
* @param xml - the XML document to insert or update
|
860 |
|
|
* @param pid - the identifier to be used for the resulting object
|
861 |
|
|
*
|
862 |
|
|
* @return localId - the resulting docid of the document created or updated
|
863 |
|
|
*
|
864 |
|
|
*/
|
865 |
6807
|
leinfelder
|
public String insertOrUpdateDocument(String xml, Identifier pid,
|
866 |
6241
|
cjones
|
Session session, String insertOrUpdate)
|
867 |
|
|
throws ServiceFailure {
|
868 |
|
|
|
869 |
|
|
logMetacat.debug("Starting to insert xml document...");
|
870 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
871 |
|
|
|
872 |
|
|
// generate pid/localId pair for sysmeta
|
873 |
|
|
String localId = null;
|
874 |
|
|
|
875 |
|
|
if(insertOrUpdate.equals("insert")) {
|
876 |
|
|
localId = im.generateLocalId(pid.getValue(), 1);
|
877 |
|
|
|
878 |
|
|
} else {
|
879 |
|
|
//localid should already exist in the identifier table, so just find it
|
880 |
|
|
try {
|
881 |
|
|
logMetacat.debug("Updating pid " + pid.getValue());
|
882 |
|
|
logMetacat.debug("looking in identifier table for pid " + pid.getValue());
|
883 |
|
|
|
884 |
|
|
localId = im.getLocalId(pid.getValue());
|
885 |
|
|
|
886 |
|
|
logMetacat.debug("localId: " + localId);
|
887 |
|
|
//increment the revision
|
888 |
|
|
String docid = localId.substring(0, localId.lastIndexOf("."));
|
889 |
|
|
String revS = localId.substring(localId.lastIndexOf(".") + 1, localId.length());
|
890 |
|
|
int rev = new Integer(revS).intValue();
|
891 |
|
|
rev++;
|
892 |
|
|
docid = docid + "." + rev;
|
893 |
|
|
localId = docid;
|
894 |
|
|
logMetacat.debug("incremented localId: " + localId);
|
895 |
|
|
|
896 |
|
|
} catch(McdbDocNotFoundException e) {
|
897 |
|
|
throw new ServiceFailure("1030", "D1NodeService.insertOrUpdateDocument(): " +
|
898 |
|
|
"pid " + pid.getValue() +
|
899 |
|
|
" should have been in the identifier table, but it wasn't: " +
|
900 |
|
|
e.getMessage());
|
901 |
|
|
|
902 |
|
|
}
|
903 |
|
|
|
904 |
|
|
}
|
905 |
|
|
|
906 |
6443
|
leinfelder
|
params = new Hashtable<String, String[]>();
|
907 |
6241
|
cjones
|
String[] action = new String[1];
|
908 |
|
|
action[0] = insertOrUpdate;
|
909 |
|
|
params.put("action", action);
|
910 |
|
|
String[] docid = new String[1];
|
911 |
|
|
docid[0] = localId;
|
912 |
|
|
params.put("docid", docid);
|
913 |
|
|
String[] doctext = new String[1];
|
914 |
|
|
doctext[0] = xml;
|
915 |
|
|
params.put("doctext", doctext);
|
916 |
|
|
|
917 |
6532
|
leinfelder
|
String username = Constants.SUBJECT_PUBLIC;
|
918 |
6241
|
cjones
|
String[] groupnames = null;
|
919 |
6302
|
leinfelder
|
if (session != null ) {
|
920 |
|
|
username = session.getSubject().getValue();
|
921 |
6532
|
leinfelder
|
if (session.getSubjectInfo() != null) {
|
922 |
|
|
List<Group> groupList = session.getSubjectInfo().getGroupList();
|
923 |
6302
|
leinfelder
|
if (groupList != null) {
|
924 |
|
|
groupnames = new String[groupList.size()];
|
925 |
|
|
for (int i = 0; i > groupList.size(); i++ ) {
|
926 |
|
|
groupnames[i] = groupList.get(i).getGroupName();
|
927 |
|
|
}
|
928 |
|
|
}
|
929 |
|
|
}
|
930 |
6241
|
cjones
|
}
|
931 |
|
|
|
932 |
|
|
// do the insert or update action
|
933 |
6443
|
leinfelder
|
handler = new MetacatHandler(new Timer());
|
934 |
6542
|
leinfelder
|
String result = handler.handleInsertOrUpdateAction(request.getRemoteAddr(), request.getHeader("User-Agent"), null,
|
935 |
6241
|
cjones
|
null, params, username, groupnames);
|
936 |
|
|
|
937 |
|
|
if(result.indexOf("<error>") != -1) {
|
938 |
|
|
String detailCode = "";
|
939 |
|
|
if ( insertOrUpdate.equals("insert") ) {
|
940 |
|
|
detailCode = "1190";
|
941 |
|
|
|
942 |
|
|
} else if ( insertOrUpdate.equals("update") ) {
|
943 |
|
|
detailCode = "1310";
|
944 |
|
|
|
945 |
|
|
}
|
946 |
|
|
throw new ServiceFailure(detailCode,
|
947 |
|
|
"Error inserting or updating document: " + result);
|
948 |
|
|
}
|
949 |
|
|
logMetacat.debug("Finsished inserting xml document with id " + localId);
|
950 |
|
|
|
951 |
|
|
return localId;
|
952 |
|
|
}
|
953 |
|
|
|
954 |
|
|
/**
|
955 |
|
|
* Insert a data document
|
956 |
|
|
*
|
957 |
|
|
* @param object
|
958 |
|
|
* @param pid
|
959 |
|
|
* @param sessionData
|
960 |
|
|
* @throws ServiceFailure
|
961 |
|
|
* @returns localId of the data object inserted
|
962 |
|
|
*/
|
963 |
6807
|
leinfelder
|
public String insertDataObject(InputStream object, Identifier pid,
|
964 |
6241
|
cjones
|
Session session) throws ServiceFailure {
|
965 |
|
|
|
966 |
6532
|
leinfelder
|
String username = Constants.SUBJECT_PUBLIC;
|
967 |
6241
|
cjones
|
String[] groupnames = null;
|
968 |
6302
|
leinfelder
|
if (session != null ) {
|
969 |
|
|
username = session.getSubject().getValue();
|
970 |
6532
|
leinfelder
|
if (session.getSubjectInfo() != null) {
|
971 |
|
|
List<Group> groupList = session.getSubjectInfo().getGroupList();
|
972 |
6302
|
leinfelder
|
if (groupList != null) {
|
973 |
|
|
groupnames = new String[groupList.size()];
|
974 |
|
|
for (int i = 0; i > groupList.size(); i++ ) {
|
975 |
|
|
groupnames[i] = groupList.get(i).getGroupName();
|
976 |
|
|
}
|
977 |
|
|
}
|
978 |
|
|
}
|
979 |
6241
|
cjones
|
}
|
980 |
|
|
|
981 |
|
|
// generate pid/localId pair for object
|
982 |
|
|
logMetacat.debug("Generating a pid/localId mapping");
|
983 |
|
|
IdentifierManager im = IdentifierManager.getInstance();
|
984 |
|
|
String localId = im.generateLocalId(pid.getValue(), 1);
|
985 |
6719
|
leinfelder
|
|
986 |
|
|
// Save the data file to disk using "localId" as the name
|
987 |
|
|
String datafilepath = null;
|
988 |
|
|
try {
|
989 |
|
|
datafilepath = PropertyService.getProperty("application.datafilepath");
|
990 |
|
|
} catch (PropertyNotFoundException e) {
|
991 |
|
|
ServiceFailure sf = new ServiceFailure("1190", "Lookup data file path" + e.getMessage());
|
992 |
|
|
sf.initCause(e);
|
993 |
|
|
throw sf;
|
994 |
|
|
}
|
995 |
|
|
boolean locked = false;
|
996 |
|
|
try {
|
997 |
|
|
locked = DocumentImpl.getDataFileLockGrant(localId);
|
998 |
|
|
} catch (Exception e) {
|
999 |
|
|
ServiceFailure sf = new ServiceFailure("1190", "Could not lock file for writing:" + e.getMessage());
|
1000 |
|
|
sf.initCause(e);
|
1001 |
|
|
throw sf;
|
1002 |
|
|
}
|
1003 |
|
|
|
1004 |
|
|
logMetacat.debug("Case DATA: starting to write to disk.");
|
1005 |
|
|
if (locked) {
|
1006 |
|
|
|
1007 |
6241
|
cjones
|
File dataDirectory = new File(datafilepath);
|
1008 |
|
|
dataDirectory.mkdirs();
|
1009 |
|
|
|
1010 |
|
|
File newFile = writeStreamToFile(dataDirectory, localId, object);
|
1011 |
|
|
|
1012 |
|
|
// TODO: Check that the file size matches SystemMetadata
|
1013 |
|
|
// long size = newFile.length();
|
1014 |
|
|
// if (size == 0) {
|
1015 |
|
|
// throw new IOException("Uploaded file is 0 bytes!");
|
1016 |
|
|
// }
|
1017 |
|
|
|
1018 |
|
|
// Register the file in the database (which generates an exception
|
1019 |
|
|
// if the localId is not acceptable or other untoward things happen
|
1020 |
|
|
try {
|
1021 |
|
|
logMetacat.debug("Registering document...");
|
1022 |
|
|
DocumentImpl.registerDocument(localId, "BIN", localId,
|
1023 |
|
|
username, groupnames);
|
1024 |
|
|
logMetacat.debug("Registration step completed.");
|
1025 |
|
|
|
1026 |
|
|
} catch (SQLException e) {
|
1027 |
|
|
//newFile.delete();
|
1028 |
|
|
logMetacat.debug("SQLE: " + e.getMessage());
|
1029 |
|
|
e.printStackTrace(System.out);
|
1030 |
|
|
throw new ServiceFailure("1190", "Registration failed: " +
|
1031 |
|
|
e.getMessage());
|
1032 |
|
|
|
1033 |
|
|
} catch (AccessionNumberException e) {
|
1034 |
|
|
//newFile.delete();
|
1035 |
|
|
logMetacat.debug("ANE: " + e.getMessage());
|
1036 |
|
|
e.printStackTrace(System.out);
|
1037 |
|
|
throw new ServiceFailure("1190", "Registration failed: " +
|
1038 |
|
|
e.getMessage());
|
1039 |
|
|
|
1040 |
|
|
} catch (Exception e) {
|
1041 |
|
|
//newFile.delete();
|
1042 |
|
|
logMetacat.debug("Exception: " + e.getMessage());
|
1043 |
|
|
e.printStackTrace(System.out);
|
1044 |
|
|
throw new ServiceFailure("1190", "Registration failed: " +
|
1045 |
|
|
e.getMessage());
|
1046 |
|
|
}
|
1047 |
|
|
|
1048 |
|
|
logMetacat.debug("Logging the creation event.");
|
1049 |
6542
|
leinfelder
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, "create");
|
1050 |
6241
|
cjones
|
|
1051 |
|
|
// Schedule replication for this data file
|
1052 |
|
|
logMetacat.debug("Scheduling replication.");
|
1053 |
|
|
ForceReplicationHandler frh = new ForceReplicationHandler(
|
1054 |
|
|
localId, "create", false, null);
|
1055 |
6719
|
leinfelder
|
}
|
1056 |
|
|
|
1057 |
|
|
return localId;
|
1058 |
6241
|
cjones
|
|
1059 |
|
|
}
|
1060 |
6255
|
cjones
|
|
1061 |
6256
|
cjones
|
/**
|
1062 |
|
|
* Insert a systemMetadata document and return its localId
|
1063 |
|
|
*/
|
1064 |
6807
|
leinfelder
|
public void insertSystemMetadata(SystemMetadata sysmeta)
|
1065 |
6572
|
cjones
|
throws ServiceFailure {
|
1066 |
|
|
|
1067 |
|
|
logMetacat.debug("Starting to insert SystemMetadata...");
|
1068 |
|
|
sysmeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
1069 |
|
|
logMetacat.debug("Inserting new system metadata with modified date " +
|
1070 |
|
|
sysmeta.getDateSysMetadataModified());
|
1071 |
|
|
|
1072 |
|
|
//insert the system metadata
|
1073 |
|
|
try {
|
1074 |
|
|
// note: the calling subclass handles the map hazelcast lock/unlock
|
1075 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);
|
1076 |
|
|
|
1077 |
|
|
} catch (Exception e) {
|
1078 |
|
|
throw new ServiceFailure("1190", e.getMessage());
|
1079 |
|
|
|
1080 |
|
|
}
|
1081 |
6256
|
cjones
|
}
|
1082 |
|
|
|
1083 |
|
|
/**
|
1084 |
6255
|
cjones
|
* Update a systemMetadata document
|
1085 |
|
|
*
|
1086 |
|
|
* @param sysMeta - the system metadata object in the system to update
|
1087 |
|
|
*/
|
1088 |
6858
|
cjones
|
protected void updateSystemMetadata(SystemMetadata sysMeta)
|
1089 |
|
|
throws ServiceFailure {
|
1090 |
|
|
|
1091 |
|
|
logMetacat.debug("D1NodeService.updateSystemMetadata() called.");
|
1092 |
|
|
sysMeta.setDateSysMetadataModified(new Date());
|
1093 |
|
|
try {
|
1094 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().lock(sysMeta.getIdentifier());
|
1095 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
|
1096 |
|
|
|
1097 |
|
|
} catch (Exception e) {
|
1098 |
|
|
throw new ServiceFailure("4862", e.getMessage());
|
1099 |
|
|
|
1100 |
|
|
} finally {
|
1101 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().unlock(sysMeta.getIdentifier());
|
1102 |
|
|
|
1103 |
|
|
}
|
1104 |
|
|
|
1105 |
|
|
}
|
1106 |
6816
|
leinfelder
|
|
1107 |
|
|
/**
|
1108 |
|
|
* Given a Permission, returns a list of all permissions that it encompasses
|
1109 |
|
|
* Permissions are hierarchical so that WRITE also allows READ.
|
1110 |
|
|
* @param permission
|
1111 |
|
|
* @return list of included Permissions for the given permission
|
1112 |
|
|
*/
|
1113 |
|
|
protected List<Permission> expandPermissions(Permission permission) {
|
1114 |
|
|
List<Permission> expandedPermissions = new ArrayList<Permission>();
|
1115 |
|
|
if (permission.equals(Permission.READ)) {
|
1116 |
|
|
expandedPermissions.add(Permission.READ);
|
1117 |
|
|
}
|
1118 |
|
|
if (permission.equals(Permission.WRITE)) {
|
1119 |
|
|
expandedPermissions.add(Permission.READ);
|
1120 |
|
|
expandedPermissions.add(Permission.WRITE);
|
1121 |
|
|
}
|
1122 |
|
|
if (permission.equals(Permission.CHANGE_PERMISSION)) {
|
1123 |
|
|
expandedPermissions.add(Permission.READ);
|
1124 |
|
|
expandedPermissions.add(Permission.WRITE);
|
1125 |
|
|
expandedPermissions.add(Permission.CHANGE_PERMISSION);
|
1126 |
|
|
}
|
1127 |
|
|
return expandedPermissions;
|
1128 |
|
|
}
|
1129 |
6255
|
cjones
|
|
1130 |
|
|
/*
|
1131 |
6241
|
cjones
|
* Write a stream to a file
|
1132 |
|
|
*
|
1133 |
|
|
* @param dir - the directory to write to
|
1134 |
|
|
* @param fileName - the file name to write to
|
1135 |
|
|
* @param data - the object bytes as an input stream
|
1136 |
|
|
*
|
1137 |
|
|
* @return newFile - the new file created
|
1138 |
|
|
*
|
1139 |
|
|
* @throws ServiceFailure
|
1140 |
|
|
*/
|
1141 |
|
|
private File writeStreamToFile(File dir, String fileName, InputStream data)
|
1142 |
|
|
throws ServiceFailure {
|
1143 |
|
|
|
1144 |
|
|
File newFile = new File(dir, fileName);
|
1145 |
|
|
logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath());
|
1146 |
|
|
|
1147 |
|
|
try {
|
1148 |
|
|
if (newFile.createNewFile()) {
|
1149 |
|
|
// write data stream to desired file
|
1150 |
|
|
OutputStream os = new FileOutputStream(newFile);
|
1151 |
|
|
long length = IOUtils.copyLarge(data, os);
|
1152 |
|
|
os.flush();
|
1153 |
|
|
os.close();
|
1154 |
|
|
} else {
|
1155 |
|
|
logMetacat.debug("File creation failed, or file already exists.");
|
1156 |
|
|
throw new ServiceFailure("1190", "File already exists: " + fileName);
|
1157 |
|
|
}
|
1158 |
|
|
} catch (FileNotFoundException e) {
|
1159 |
|
|
logMetacat.debug("FNF: " + e.getMessage());
|
1160 |
|
|
throw new ServiceFailure("1190", "File not found: " + fileName + " "
|
1161 |
|
|
+ e.getMessage());
|
1162 |
|
|
} catch (IOException e) {
|
1163 |
|
|
logMetacat.debug("IOE: " + e.getMessage());
|
1164 |
|
|
throw new ServiceFailure("1190", "File was not written: " + fileName
|
1165 |
|
|
+ " " + e.getMessage());
|
1166 |
|
|
}
|
1167 |
|
|
|
1168 |
|
|
return newFile;
|
1169 |
|
|
}
|
1170 |
|
|
|
1171 |
|
|
}
|