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5282
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jones
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/**
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* '$RCSfile$'
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* Copyright: 2010 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: jones $'
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* '$Date: 2010-02-03 17:58:12 -0900 (Wed, 03 Feb 2010) $'
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* '$Revision: 5211 $'
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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;
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6384
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cjones
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import java.math.BigInteger;
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5282
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jones
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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5895
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berkley
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import java.sql.Timestamp;
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32 |
6107
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leinfelder
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.Vector;
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5282
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jones
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import org.apache.log4j.Logger;
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39 |
8810
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leinfelder
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import org.dataone.client.v2.formats.ObjectFormatCache;
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7010
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cjones
|
import org.dataone.service.exceptions.BaseException;
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6904
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cjones
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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42 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.AccessPolicy;
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43 |
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Checksum;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.ObjectFormatIdentifier;
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import org.dataone.service.types.v1.ObjectInfo;
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import org.dataone.service.types.v1.ObjectList;
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import org.dataone.service.types.v1.Permission;
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import org.dataone.service.types.v1.Replica;
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import org.dataone.service.types.v1.ReplicationPolicy;
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import org.dataone.service.types.v1.ReplicationStatus;
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import org.dataone.service.types.v1.Subject;
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9230
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tao
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import org.dataone.service.types.v2.MediaType;
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import org.dataone.service.types.v2.MediaTypeProperty;
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8810
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leinfelder
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import org.dataone.service.types.v2.SystemMetadata;
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5282
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jones
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6108
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leinfelder
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import edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess;
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5282
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jones
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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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7438
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leinfelder
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import edu.ucsb.nceas.metacat.database.DatabaseService;
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9119
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tao
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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5887
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berkley
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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6108
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leinfelder
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import edu.ucsb.nceas.metacat.shared.AccessException;
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6299
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leinfelder
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import edu.ucsb.nceas.metacat.shared.ServiceException;
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5286
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jones
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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6299
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leinfelder
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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7475
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leinfelder
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import edu.ucsb.nceas.utilities.access.AccessControlInterface;
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import edu.ucsb.nceas.utilities.access.XMLAccessDAO;
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5282
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jones
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/**
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* Manage the relationship between Metacat local identifiers (LocalIDs) that are
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6099
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leinfelder
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* codified as the (docid, rev) pair with globally unique string identifiers
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5282
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jones
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* (GUIDs) that are opaque strings. This class provides methods to manage these
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* identifiers, and to search for and look up LocalIDs based on their GUID and
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* vice versa. IdentifierManager is a singleton.
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*
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* @author Matthew Jones
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*/
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public class IdentifierManager {
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5334
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berkley
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public static final String TYPE_SYSTEM_METADATA = "systemmetadata";
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public static final String TYPE_IDENTIFIER = "identifier";
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5282
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jones
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/**
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* The single instance of the manager that is always returned.
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*/
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private static IdentifierManager self = null;
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6099
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leinfelder
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private Logger logMetacat = Logger.getLogger(IdentifierManager.class);
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5282
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jones
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/**
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* A private constructor that initializes the class when getInstance() is
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* called.
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*/
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6099
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leinfelder
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private IdentifierManager() {}
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5282
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jones
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/**
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* Return the single instance of the manager after initializing it if it
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* wasn't previously initialized.
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*
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* @return the single IdentifierManager instance
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*/
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public static IdentifierManager getInstance()
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{
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if (self == null) {
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self = new IdentifierManager();
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}
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return self;
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}
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9230
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tao
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/*public SystemMetadata asSystemMetadata(Date dateUploaded, String rightsHolder,
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6097
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leinfelder
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String checksum, String checksumAlgorithm, String originMemberNode,
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String authoritativeMemberNode, Date dateModified, String submitter,
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6561
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leinfelder
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String guid, String fmtidStr, BigInteger size, BigInteger serialVersion) {
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6097
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leinfelder
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SystemMetadata sysMeta = new SystemMetadata();
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Identifier sysMetaId = new Identifier();
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sysMetaId.setValue(guid);
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sysMeta.setIdentifier(sysMetaId);
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sysMeta.setDateUploaded(dateUploaded);
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Subject rightsHolderSubject = new Subject();
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rightsHolderSubject.setValue(rightsHolder);
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sysMeta.setRightsHolder(rightsHolderSubject);
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Checksum checksumObject = new Checksum();
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checksumObject.setValue(checksum);
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6397
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leinfelder
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checksumObject.setAlgorithm(checksumAlgorithm);
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6097
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leinfelder
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sysMeta.setChecksum(checksumObject);
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NodeReference omn = new NodeReference();
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omn.setValue(originMemberNode);
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sysMeta.setOriginMemberNode(omn);
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NodeReference amn = new NodeReference();
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amn.setValue(authoritativeMemberNode);
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sysMeta.setAuthoritativeMemberNode(amn);
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sysMeta.setDateSysMetadataModified(dateModified);
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Subject submitterSubject = new Subject();
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submitterSubject.setValue(submitter);
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sysMeta.setSubmitter(submitterSubject);
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7010
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cjones
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ObjectFormatIdentifier fmtid = null;
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6124
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cjones
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try {
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7010
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cjones
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ObjectFormatIdentifier formatId = new ObjectFormatIdentifier();
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formatId.setValue(fmtidStr);
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fmtid = ObjectFormatCache.getInstance().getFormat(formatId).getFormatId();
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6561
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leinfelder
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sysMeta.setFormatId(fmtid);
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7010
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cjones
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} catch (BaseException nfe) {
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logMetacat.error("The objectFormat " + fmtidStr +
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6384
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cjones
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" is not registered. Setting the default format id.");
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7010
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cjones
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fmtid = new ObjectFormatIdentifier();
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fmtid.setValue("application/octet-stream");
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sysMeta.setFormatId(fmtid);
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6124
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cjones
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}
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6097
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leinfelder
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sysMeta.setSize(size);
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6561
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leinfelder
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sysMeta.setSerialVersion(serialVersion);
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6097
|
leinfelder
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return sysMeta;
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9230
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tao
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}*/
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159 |
6097
|
leinfelder
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160 |
5282
|
jones
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/**
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161 |
5895
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berkley
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* return a hash of all of the info that is in the systemmetadata table
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162 |
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* @param localId
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* @return
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*/
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165 |
9230
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tao
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/*public Hashtable<String, String> getSystemMetadataInfo(String localId)
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166 |
5895
|
berkley
|
throws McdbDocNotFoundException
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167 |
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{
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168 |
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try
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169 |
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{
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170 |
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AccessionNumber acc = new AccessionNumber(localId, "NONE");
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localId = acc.getDocid();
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}
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catch(Exception e)
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{
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//do nothing. just try the localId as it is
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}
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177 |
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Hashtable<String, String> h = new Hashtable<String, String>();
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178 |
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String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
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179 |
5944
|
berkley
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"origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size " +
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180 |
5895
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berkley
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"from systemmetadata where docid = ?";
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181 |
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DBConnection dbConn = null;
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182 |
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int serialNumber = -1;
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183 |
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try
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184 |
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{
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185 |
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// Get a database connection from the pool
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186 |
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");
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187 |
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serialNumber = dbConn.getCheckOutSerialNumber();
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188 |
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189 |
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// Execute the insert statement
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190 |
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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191 |
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stmt.setString(1, localId);
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192 |
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ResultSet rs = stmt.executeQuery();
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193 |
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if (rs.next())
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194 |
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{
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195 |
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String guid = rs.getString(1);
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196 |
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Timestamp dateUploaded = rs.getTimestamp(2);
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197 |
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String rightsHolder = rs.getString(3);
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198 |
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String checksum = rs.getString(4);
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199 |
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String checksumAlgorithm = rs.getString(5);
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200 |
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String originMemberNode = rs.getString(6);
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201 |
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String authoritativeMemberNode = rs.getString(7);
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202 |
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Timestamp dateModified = rs.getTimestamp(8);
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203 |
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String submitter = rs.getString(9);
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204 |
5917
|
berkley
|
String objectFormat = rs.getString(10);
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205 |
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long size = new Long(rs.getString(11)).longValue();
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206 |
5895
|
berkley
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207 |
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h.put("guid", guid);
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208 |
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h.put("date_uploaded", new Long(dateUploaded.getTime()).toString());
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209 |
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h.put("rights_holder", rightsHolder);
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210 |
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h.put("checksum", checksum);
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211 |
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h.put("checksum_algorithm", checksumAlgorithm);
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212 |
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h.put("origin_member_node", originMemberNode);
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213 |
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h.put("authoritative_member_node", authoritativeMemberNode);
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214 |
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h.put("date_modified", new Long(dateModified.getTime()).toString());
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215 |
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h.put("submitter", submitter);
|
216 |
5917
|
berkley
|
h.put("object_format", objectFormat);
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217 |
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h.put("size", new Long(size).toString());
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218 |
5895
|
berkley
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219 |
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stmt.close();
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220 |
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}
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221 |
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else
|
222 |
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{
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223 |
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stmt.close();
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224 |
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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225 |
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throw new McdbDocNotFoundException("2Could not find document " + localId);
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226 |
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}
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227 |
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228 |
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}
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229 |
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catch (SQLException e)
|
230 |
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{
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231 |
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e.printStackTrace();
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232 |
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logMetacat.error("Error while getting system metadata info for localid " + localId + " : "
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233 |
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+ e.getMessage());
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234 |
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}
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235 |
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finally
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236 |
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{
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237 |
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// Return database connection to the pool
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238 |
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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239 |
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}
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240 |
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return h;
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241 |
9230
|
tao
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}*/
|
242 |
5895
|
berkley
|
|
243 |
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/**
|
244 |
6097
|
leinfelder
|
* return a hash of all of the info that is in the systemmetadata table
|
245 |
6099
|
leinfelder
|
* @param guid
|
246 |
6097
|
leinfelder
|
* @return
|
247 |
6108
|
leinfelder
|
* @throws McdbDocNotFoundException
|
248 |
6097
|
leinfelder
|
*/
|
249 |
6099
|
leinfelder
|
public SystemMetadata getSystemMetadata(String guid)
|
250 |
6097
|
leinfelder
|
throws McdbDocNotFoundException
|
251 |
|
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{
|
252 |
6099
|
leinfelder
|
|
253 |
6097
|
leinfelder
|
SystemMetadata sysMeta = new SystemMetadata();
|
254 |
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String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
|
255 |
6375
|
leinfelder
|
"origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size, " +
|
256 |
9230
|
tao
|
"replication_allowed, number_replicas, obsoletes, obsoleted_by, serial_version, archived, series_id, file_name, media_type " +
|
257 |
6099
|
leinfelder
|
"from systemmetadata where guid = ?";
|
258 |
6097
|
leinfelder
|
DBConnection dbConn = null;
|
259 |
|
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int serialNumber = -1;
|
260 |
6533
|
cjones
|
Boolean replicationAllowed = new Boolean(false);
|
261 |
|
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BigInteger numberOfReplicas = new BigInteger("-1");
|
262 |
6561
|
leinfelder
|
BigInteger serialVersion = new BigInteger("-1");
|
263 |
7428
|
leinfelder
|
Boolean archived = new Boolean(false);
|
264 |
6561
|
leinfelder
|
|
265 |
6097
|
leinfelder
|
try
|
266 |
|
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{
|
267 |
|
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// Get a database connection from the pool
|
268 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getSystemMetadata");
|
269 |
|
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serialNumber = dbConn.getCheckOutSerialNumber();
|
270 |
|
|
|
271 |
|
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// Execute the statement
|
272 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
273 |
6099
|
leinfelder
|
stmt.setString(1, guid);
|
274 |
6097
|
leinfelder
|
ResultSet rs = stmt.executeQuery();
|
275 |
|
|
if (rs.next())
|
276 |
|
|
{
|
277 |
|
|
Timestamp dateUploaded = rs.getTimestamp(2);
|
278 |
|
|
String rightsHolder = rs.getString(3);
|
279 |
|
|
String checksum = rs.getString(4);
|
280 |
|
|
String checksumAlgorithm = rs.getString(5);
|
281 |
|
|
String originMemberNode = rs.getString(6);
|
282 |
|
|
String authoritativeMemberNode = rs.getString(7);
|
283 |
|
|
Timestamp dateModified = rs.getTimestamp(8);
|
284 |
|
|
String submitter = rs.getString(9);
|
285 |
6296
|
cjones
|
String fmtidStr = rs.getString(10);
|
286 |
6384
|
cjones
|
BigInteger size = new BigInteger(rs.getString(11));
|
287 |
6535
|
cjones
|
replicationAllowed = new Boolean(rs.getBoolean(12));
|
288 |
6533
|
cjones
|
numberOfReplicas = new BigInteger(rs.getString(13));
|
289 |
|
|
String obsoletes = rs.getString(14);
|
290 |
|
|
String obsoletedBy = rs.getString(15);
|
291 |
6561
|
leinfelder
|
serialVersion = new BigInteger(rs.getString(16));
|
292 |
7428
|
leinfelder
|
archived = new Boolean(rs.getBoolean(17));
|
293 |
9038
|
tao
|
String series_id = rs.getString(18);
|
294 |
9230
|
tao
|
String file_name = rs.getString(19);
|
295 |
|
|
String media_type = rs.getString(20);
|
296 |
6375
|
leinfelder
|
|
297 |
6097
|
leinfelder
|
Identifier sysMetaId = new Identifier();
|
298 |
|
|
sysMetaId.setValue(guid);
|
299 |
|
|
sysMeta.setIdentifier(sysMetaId);
|
300 |
6561
|
leinfelder
|
sysMeta.setSerialVersion(serialVersion);
|
301 |
6097
|
leinfelder
|
sysMeta.setDateUploaded(dateUploaded);
|
302 |
|
|
Subject rightsHolderSubject = new Subject();
|
303 |
|
|
rightsHolderSubject.setValue(rightsHolder);
|
304 |
|
|
sysMeta.setRightsHolder(rightsHolderSubject);
|
305 |
|
|
Checksum checksumObject = new Checksum();
|
306 |
|
|
checksumObject.setValue(checksum);
|
307 |
6397
|
leinfelder
|
checksumObject.setAlgorithm(checksumAlgorithm);
|
308 |
6097
|
leinfelder
|
sysMeta.setChecksum(checksumObject);
|
309 |
6519
|
leinfelder
|
if (originMemberNode != null) {
|
310 |
|
|
NodeReference omn = new NodeReference();
|
311 |
|
|
omn.setValue(originMemberNode);
|
312 |
|
|
sysMeta.setOriginMemberNode(omn);
|
313 |
|
|
}
|
314 |
|
|
if (authoritativeMemberNode != null) {
|
315 |
|
|
NodeReference amn = new NodeReference();
|
316 |
|
|
amn.setValue(authoritativeMemberNode);
|
317 |
|
|
sysMeta.setAuthoritativeMemberNode(amn);
|
318 |
|
|
}
|
319 |
6097
|
leinfelder
|
sysMeta.setDateSysMetadataModified(dateModified);
|
320 |
7639
|
leinfelder
|
if (submitter != null) {
|
321 |
|
|
Subject submitterSubject = new Subject();
|
322 |
|
|
submitterSubject.setValue(submitter);
|
323 |
|
|
sysMeta.setSubmitter(submitterSubject);
|
324 |
|
|
}
|
325 |
7023
|
leinfelder
|
ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier();
|
326 |
|
|
fmtid.setValue(fmtidStr);
|
327 |
|
|
sysMeta.setFormatId(fmtid);
|
328 |
6097
|
leinfelder
|
sysMeta.setSize(size);
|
329 |
6423
|
leinfelder
|
if (obsoletes != null) {
|
330 |
|
|
Identifier obsoletesId = new Identifier();
|
331 |
|
|
obsoletesId.setValue(obsoletes);
|
332 |
|
|
sysMeta.setObsoletes(obsoletesId);
|
333 |
|
|
}
|
334 |
|
|
if (obsoletedBy != null) {
|
335 |
|
|
Identifier obsoletedById = new Identifier();
|
336 |
|
|
obsoletedById.setValue(obsoletedBy);
|
337 |
|
|
sysMeta.setObsoletedBy(obsoletedById);
|
338 |
|
|
}
|
339 |
7428
|
leinfelder
|
sysMeta.setArchived(archived);
|
340 |
9038
|
tao
|
if(series_id != null) {
|
341 |
|
|
Identifier seriesId = new Identifier();
|
342 |
|
|
seriesId.setValue(series_id);
|
343 |
|
|
sysMeta.setSeriesId(seriesId);
|
344 |
|
|
}
|
345 |
9230
|
tao
|
if(file_name != null ) {
|
346 |
|
|
sysMeta.setFileName(file_name);
|
347 |
|
|
}
|
348 |
|
|
|
349 |
|
|
if(media_type != null ) {
|
350 |
|
|
MediaType mediaType = new MediaType();
|
351 |
|
|
mediaType.setName(media_type);
|
352 |
|
|
// get media type properties from another table.
|
353 |
|
|
String mediaTypePropertyQuery = "select name, value from smmediatypeproperties where guid = ?";
|
354 |
|
|
PreparedStatement stmt2 = dbConn.prepareStatement(mediaTypePropertyQuery);
|
355 |
|
|
stmt2.setString(1, guid);
|
356 |
|
|
ResultSet rs2 = stmt2.executeQuery();
|
357 |
|
|
while (rs2.next()) {
|
358 |
|
|
String name = rs2.getString(1);
|
359 |
|
|
String value = rs2.getString(2);
|
360 |
|
|
MediaTypeProperty property = new MediaTypeProperty();
|
361 |
|
|
property.setName(name);
|
362 |
|
|
property.setValue(value);
|
363 |
|
|
mediaType.addProperty(property);
|
364 |
|
|
}
|
365 |
|
|
sysMeta.setMediaType(mediaType);
|
366 |
|
|
rs2.close();
|
367 |
|
|
stmt2.close();
|
368 |
|
|
}
|
369 |
6097
|
leinfelder
|
stmt.close();
|
370 |
|
|
}
|
371 |
|
|
else
|
372 |
|
|
{
|
373 |
|
|
stmt.close();
|
374 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
375 |
6099
|
leinfelder
|
throw new McdbDocNotFoundException("Could not find " + guid);
|
376 |
6097
|
leinfelder
|
}
|
377 |
|
|
|
378 |
|
|
}
|
379 |
|
|
catch (SQLException e)
|
380 |
|
|
{
|
381 |
|
|
e.printStackTrace();
|
382 |
6099
|
leinfelder
|
logMetacat.error("Error while getting system metadata for guid " + guid + " : "
|
383 |
6097
|
leinfelder
|
+ e.getMessage());
|
384 |
|
|
}
|
385 |
|
|
finally
|
386 |
|
|
{
|
387 |
|
|
// Return database connection to the pool
|
388 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
389 |
|
|
}
|
390 |
6377
|
leinfelder
|
|
391 |
6533
|
cjones
|
// populate the replication policy
|
392 |
6107
|
leinfelder
|
ReplicationPolicy replicationPolicy = new ReplicationPolicy();
|
393 |
6533
|
cjones
|
if ( numberOfReplicas != null && numberOfReplicas.intValue() != -1 ) {
|
394 |
|
|
replicationPolicy.setNumberReplicas(numberOfReplicas.intValue());
|
395 |
|
|
|
396 |
|
|
}
|
397 |
|
|
|
398 |
|
|
if ( replicationAllowed != null ) {
|
399 |
|
|
replicationPolicy.setReplicationAllowed(replicationAllowed);
|
400 |
|
|
|
401 |
|
|
}
|
402 |
6107
|
leinfelder
|
replicationPolicy.setBlockedMemberNodeList(getReplicationPolicy(guid, "blocked"));
|
403 |
|
|
replicationPolicy.setPreferredMemberNodeList(getReplicationPolicy(guid, "preferred"));
|
404 |
6533
|
cjones
|
sysMeta.setReplicationPolicy(replicationPolicy);
|
405 |
6107
|
leinfelder
|
|
406 |
6533
|
cjones
|
// look up replication status
|
407 |
|
|
sysMeta.setReplicaList(getReplicationStatus(guid));
|
408 |
6108
|
leinfelder
|
|
409 |
6533
|
cjones
|
// look up access policy
|
410 |
|
|
try {
|
411 |
|
|
sysMeta.setAccessPolicy(getAccessPolicy(guid));
|
412 |
|
|
} catch (AccessException e) {
|
413 |
|
|
throw new McdbDocNotFoundException(e);
|
414 |
|
|
}
|
415 |
6107
|
leinfelder
|
|
416 |
6097
|
leinfelder
|
return sysMeta;
|
417 |
|
|
}
|
418 |
|
|
|
419 |
|
|
|
420 |
6107
|
leinfelder
|
private List<NodeReference> getReplicationPolicy(String guid, String policy)
|
421 |
|
|
throws McdbDocNotFoundException {
|
422 |
|
|
|
423 |
|
|
List<NodeReference> nodes = new ArrayList<NodeReference>();
|
424 |
|
|
String sql = "select guid, policy, member_node " +
|
425 |
7392
|
leinfelder
|
"from smReplicationPolicy where guid = ? and policy = ?";
|
426 |
6107
|
leinfelder
|
DBConnection dbConn = null;
|
427 |
|
|
int serialNumber = -1;
|
428 |
|
|
try {
|
429 |
|
|
// Get a database connection from the pool
|
430 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicationPolicy");
|
431 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
432 |
|
|
|
433 |
|
|
// Execute the statement
|
434 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
435 |
|
|
stmt.setString(1, guid);
|
436 |
|
|
stmt.setString(2, policy);
|
437 |
|
|
ResultSet rs = stmt.executeQuery();
|
438 |
|
|
while (rs.next())
|
439 |
|
|
{
|
440 |
|
|
String memberNode = rs.getString(3);
|
441 |
|
|
NodeReference node = new NodeReference();
|
442 |
|
|
node.setValue(memberNode);
|
443 |
|
|
nodes.add(node);
|
444 |
|
|
|
445 |
|
|
}
|
446 |
|
|
stmt.close();
|
447 |
|
|
|
448 |
|
|
} catch (SQLException e) {
|
449 |
|
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
450 |
|
|
}
|
451 |
|
|
finally {
|
452 |
|
|
// Return database connection to the pool
|
453 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
454 |
|
|
}
|
455 |
|
|
|
456 |
|
|
return nodes;
|
457 |
|
|
}
|
458 |
6097
|
leinfelder
|
|
459 |
6107
|
leinfelder
|
private List<Replica> getReplicationStatus(String guid) throws McdbDocNotFoundException {
|
460 |
|
|
|
461 |
|
|
List<Replica> replicas = new ArrayList<Replica>();
|
462 |
|
|
String sql = "select guid, member_node, status, date_verified " +
|
463 |
7392
|
leinfelder
|
"from smReplicationStatus where guid = ?";
|
464 |
6107
|
leinfelder
|
DBConnection dbConn = null;
|
465 |
|
|
int serialNumber = -1;
|
466 |
|
|
try {
|
467 |
|
|
// Get a database connection from the pool
|
468 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicas");
|
469 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
470 |
|
|
|
471 |
|
|
// Execute the statement
|
472 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
473 |
|
|
stmt.setString(1, guid);
|
474 |
|
|
ResultSet rs = stmt.executeQuery();
|
475 |
|
|
while (rs.next())
|
476 |
|
|
{
|
477 |
|
|
String memberNode = rs.getString(2);
|
478 |
|
|
String status = rs.getString(3);
|
479 |
7399
|
cjones
|
java.sql.Timestamp verified = rs.getTimestamp(4);
|
480 |
6107
|
leinfelder
|
|
481 |
|
|
Replica replica = new Replica();
|
482 |
|
|
NodeReference node = new NodeReference();
|
483 |
|
|
node.setValue(memberNode);
|
484 |
|
|
replica.setReplicaMemberNode(node);
|
485 |
6454
|
leinfelder
|
replica.setReplicationStatus(ReplicationStatus.valueOf(status));
|
486 |
6107
|
leinfelder
|
replica.setReplicaVerified(new Date(verified.getTime()));
|
487 |
|
|
replicas.add(replica);
|
488 |
|
|
}
|
489 |
|
|
stmt.close();
|
490 |
|
|
|
491 |
|
|
} catch (SQLException e) {
|
492 |
|
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
493 |
|
|
}
|
494 |
|
|
finally {
|
495 |
|
|
// Return database connection to the pool
|
496 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
497 |
|
|
}
|
498 |
|
|
|
499 |
|
|
return replicas;
|
500 |
|
|
}
|
501 |
|
|
|
502 |
5378
|
berkley
|
|
503 |
|
|
/**
|
504 |
|
|
* return the newest rev for a given localId
|
505 |
|
|
* @param localId
|
506 |
|
|
* @return
|
507 |
|
|
*/
|
508 |
|
|
public int getLatestRevForLocalId(String localId)
|
509 |
|
|
throws McdbDocNotFoundException
|
510 |
|
|
{
|
511 |
5798
|
berkley
|
try
|
512 |
|
|
{
|
513 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NONE");
|
514 |
|
|
localId = acc.getDocid();
|
515 |
|
|
}
|
516 |
|
|
catch(Exception e)
|
517 |
|
|
{
|
518 |
|
|
//do nothing. just try the localId as it is
|
519 |
|
|
}
|
520 |
5378
|
berkley
|
int rev = 0;
|
521 |
6595
|
leinfelder
|
String sql = "select rev from xml_documents where docid like ? ";
|
522 |
5378
|
berkley
|
DBConnection dbConn = null;
|
523 |
|
|
int serialNumber = -1;
|
524 |
|
|
try
|
525 |
|
|
{
|
526 |
|
|
// Get a database connection from the pool
|
527 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLatestRevForLocalId");
|
528 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
529 |
|
|
|
530 |
|
|
// Execute the insert statement
|
531 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
532 |
6595
|
leinfelder
|
stmt.setString(1, localId);
|
533 |
5378
|
berkley
|
ResultSet rs = stmt.executeQuery();
|
534 |
|
|
if (rs.next())
|
535 |
|
|
{
|
536 |
|
|
rev = rs.getInt(1);
|
537 |
|
|
stmt.close();
|
538 |
|
|
}
|
539 |
|
|
else
|
540 |
|
|
{
|
541 |
|
|
stmt.close();
|
542 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
543 |
5798
|
berkley
|
throw new McdbDocNotFoundException("While trying to get the latest rev, could not find document " + localId);
|
544 |
5378
|
berkley
|
}
|
545 |
|
|
}
|
546 |
|
|
catch (SQLException e)
|
547 |
|
|
{
|
548 |
|
|
logMetacat.error("Error while looking up the guid: "
|
549 |
|
|
+ e.getMessage());
|
550 |
|
|
}
|
551 |
|
|
finally
|
552 |
|
|
{
|
553 |
|
|
// Return database connection to the pool
|
554 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
555 |
|
|
}
|
556 |
|
|
return rev;
|
557 |
|
|
}
|
558 |
|
|
|
559 |
|
|
/**
|
560 |
5377
|
berkley
|
* return all local ids in the object store that do not have associated
|
561 |
6099
|
leinfelder
|
* system metadata
|
562 |
5377
|
berkley
|
*/
|
563 |
7168
|
leinfelder
|
public List<String> getLocalIdsWithNoSystemMetadata(boolean includeRevisions, int serverLocation)
|
564 |
5377
|
berkley
|
{
|
565 |
|
|
Vector<String> ids = new Vector<String>();
|
566 |
6099
|
leinfelder
|
String sql = "select docid, rev from xml_documents " +
|
567 |
|
|
"where docid not in " +
|
568 |
6720
|
leinfelder
|
"(select docid from identifier where guid in (select guid from systemmetadata))";
|
569 |
7168
|
leinfelder
|
if (serverLocation > 0) {
|
570 |
|
|
sql = sql + " and server_location = ? ";
|
571 |
|
|
}
|
572 |
6704
|
leinfelder
|
|
573 |
6745
|
leinfelder
|
String revisionSql = "select docid, rev from xml_revisions " +
|
574 |
6704
|
leinfelder
|
"where docid not in " +
|
575 |
6720
|
leinfelder
|
"(select docid from identifier where guid in (select guid from systemmetadata))";
|
576 |
7168
|
leinfelder
|
if (serverLocation > 0) {
|
577 |
|
|
revisionSql = revisionSql + " and server_location = ? ";
|
578 |
|
|
}
|
579 |
6704
|
leinfelder
|
|
580 |
|
|
if (includeRevisions) {
|
581 |
|
|
sql = sql + " UNION ALL " + revisionSql;
|
582 |
|
|
}
|
583 |
|
|
|
584 |
5377
|
berkley
|
DBConnection dbConn = null;
|
585 |
|
|
int serialNumber = -1;
|
586 |
|
|
try
|
587 |
|
|
{
|
588 |
|
|
// Get a database connection from the pool
|
589 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");
|
590 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
591 |
|
|
|
592 |
|
|
// Execute the insert statement
|
593 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
594 |
7168
|
leinfelder
|
// set params based on what we have in the query string
|
595 |
|
|
if (serverLocation > 0) {
|
596 |
|
|
stmt.setInt(1, serverLocation);
|
597 |
|
|
if (includeRevisions) {
|
598 |
|
|
stmt.setInt(2, serverLocation);
|
599 |
|
|
}
|
600 |
|
|
}
|
601 |
5377
|
berkley
|
ResultSet rs = stmt.executeQuery();
|
602 |
|
|
while (rs.next())
|
603 |
|
|
{
|
604 |
|
|
String localid = rs.getString(1);
|
605 |
5798
|
berkley
|
String rev = rs.getString(2);
|
606 |
|
|
localid += "." + rev;
|
607 |
6099
|
leinfelder
|
logMetacat.debug("id to add SM for: " + localid);
|
608 |
5377
|
berkley
|
ids.add(localid);
|
609 |
|
|
}
|
610 |
|
|
stmt.close();
|
611 |
|
|
}
|
612 |
|
|
catch (SQLException e)
|
613 |
|
|
{
|
614 |
|
|
logMetacat.error("Error while looking up the guid: "
|
615 |
|
|
+ e.getMessage());
|
616 |
|
|
}
|
617 |
|
|
finally
|
618 |
|
|
{
|
619 |
|
|
// Return database connection to the pool
|
620 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
621 |
|
|
}
|
622 |
|
|
|
623 |
|
|
return ids;
|
624 |
|
|
}
|
625 |
|
|
|
626 |
|
|
/**
|
627 |
|
|
* return a listing of all local ids in the object store
|
628 |
|
|
* @return a list of all local ids in metacat
|
629 |
|
|
*/
|
630 |
|
|
public List<String> getAllLocalIds()
|
631 |
6416
|
rnahf
|
// seems to be an unnecessary and restrictive throw -rnahf 13-Sep-2011
|
632 |
|
|
// throws Exception
|
633 |
5377
|
berkley
|
{
|
634 |
|
|
Vector<String> ids = new Vector<String>();
|
635 |
|
|
String sql = "select docid from xml_documents";
|
636 |
|
|
DBConnection dbConn = null;
|
637 |
|
|
int serialNumber = -1;
|
638 |
|
|
try
|
639 |
|
|
{
|
640 |
|
|
// Get a database connection from the pool
|
641 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");
|
642 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
643 |
|
|
|
644 |
|
|
// Execute the insert statement
|
645 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
646 |
|
|
ResultSet rs = stmt.executeQuery();
|
647 |
|
|
while (rs.next())
|
648 |
|
|
{
|
649 |
|
|
String localid = rs.getString(1);
|
650 |
|
|
ids.add(localid);
|
651 |
|
|
}
|
652 |
|
|
stmt.close();
|
653 |
|
|
}
|
654 |
|
|
catch (SQLException e)
|
655 |
|
|
{
|
656 |
|
|
logMetacat.error("Error while looking up the guid: "
|
657 |
|
|
+ e.getMessage());
|
658 |
|
|
}
|
659 |
|
|
finally
|
660 |
|
|
{
|
661 |
|
|
// Return database connection to the pool
|
662 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
663 |
|
|
}
|
664 |
|
|
return ids;
|
665 |
|
|
}
|
666 |
|
|
|
667 |
6416
|
rnahf
|
|
668 |
6118
|
leinfelder
|
/**
|
669 |
6416
|
rnahf
|
* return a listing of all guids in the object store
|
670 |
|
|
* @return a list of all GUIDs in metacat
|
671 |
|
|
*/
|
672 |
7187
|
leinfelder
|
public List<String> getAllSystemMetadataGUIDs()
|
673 |
6416
|
rnahf
|
{
|
674 |
|
|
Vector<String> guids = new Vector<String>();
|
675 |
7187
|
leinfelder
|
String sql = "select guid from systemmetadata";
|
676 |
6416
|
rnahf
|
DBConnection dbConn = null;
|
677 |
|
|
int serialNumber = -1;
|
678 |
|
|
try
|
679 |
|
|
{
|
680 |
|
|
// Get a database connection from the pool
|
681 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllGUIDs");
|
682 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
683 |
|
|
|
684 |
|
|
// Execute the insert statement
|
685 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
686 |
|
|
ResultSet rs = stmt.executeQuery();
|
687 |
|
|
while (rs.next())
|
688 |
|
|
{
|
689 |
|
|
String guid = rs.getString(1);
|
690 |
|
|
guids.add(guid);
|
691 |
|
|
}
|
692 |
|
|
stmt.close();
|
693 |
|
|
}
|
694 |
|
|
catch (SQLException e)
|
695 |
|
|
{
|
696 |
|
|
logMetacat.error("Error while retrieving the guid: "
|
697 |
|
|
+ e.getMessage());
|
698 |
|
|
}
|
699 |
|
|
finally
|
700 |
|
|
{
|
701 |
|
|
// Return database connection to the pool
|
702 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
703 |
|
|
}
|
704 |
|
|
return guids;
|
705 |
|
|
}
|
706 |
|
|
|
707 |
|
|
|
708 |
|
|
|
709 |
|
|
/**
|
710 |
6118
|
leinfelder
|
* returns a list of system metadata-only guids since the given date
|
711 |
|
|
* @return a list of system ids in metacat that do not correspond to objects
|
712 |
|
|
* TODO: need to check which server they are on
|
713 |
|
|
*/
|
714 |
|
|
public List<String> getUpdatedSystemMetadataIds(Date since)
|
715 |
|
|
throws Exception
|
716 |
|
|
{
|
717 |
|
|
List<String> ids = new Vector<String>();
|
718 |
|
|
String sql =
|
719 |
|
|
"select guid from " + TYPE_SYSTEM_METADATA +
|
720 |
|
|
" where guid not in " +
|
721 |
|
|
" (select guid from " + TYPE_IDENTIFIER + ") " +
|
722 |
|
|
" and date_modified > ?";
|
723 |
|
|
DBConnection dbConn = null;
|
724 |
|
|
int serialNumber = -1;
|
725 |
|
|
try
|
726 |
|
|
{
|
727 |
|
|
// Get a database connection from the pool
|
728 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getUpdatedSystemMetadataIds");
|
729 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
730 |
6099
|
leinfelder
|
|
731 |
6118
|
leinfelder
|
// Execute the insert statement
|
732 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
733 |
|
|
stmt.setDate(1, new java.sql.Date(since.getTime()));
|
734 |
|
|
ResultSet rs = stmt.executeQuery();
|
735 |
|
|
while (rs.next())
|
736 |
|
|
{
|
737 |
|
|
String guid = rs.getString(1);
|
738 |
|
|
ids.add(guid);
|
739 |
|
|
}
|
740 |
|
|
stmt.close();
|
741 |
|
|
}
|
742 |
|
|
catch (SQLException e)
|
743 |
|
|
{
|
744 |
|
|
logMetacat.error("Error while looking up the updated guids: "
|
745 |
|
|
+ e.getMessage());
|
746 |
|
|
}
|
747 |
|
|
finally
|
748 |
|
|
{
|
749 |
|
|
// Return database connection to the pool
|
750 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
751 |
|
|
}
|
752 |
|
|
return ids;
|
753 |
|
|
}
|
754 |
5282
|
jones
|
|
755 |
6459
|
leinfelder
|
/**
|
756 |
|
|
* returns a list of system metadata-only guids since the given date
|
757 |
|
|
* @return a list of system ids in metacat that do not correspond to objects
|
758 |
|
|
* TODO: need to check which server they are on
|
759 |
|
|
*/
|
760 |
|
|
public Date getLastModifiedDate() throws Exception {
|
761 |
|
|
Date maxDate = null;
|
762 |
6118
|
leinfelder
|
|
763 |
6459
|
leinfelder
|
List<String> ids = new Vector<String>();
|
764 |
|
|
String sql =
|
765 |
|
|
"select max(date_modified) from " + TYPE_SYSTEM_METADATA;
|
766 |
|
|
DBConnection dbConn = null;
|
767 |
|
|
int serialNumber = -1;
|
768 |
|
|
try
|
769 |
|
|
{
|
770 |
|
|
// Get a database connection from the pool
|
771 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLastModifiedDate");
|
772 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
773 |
|
|
|
774 |
|
|
// Execute the insert statement
|
775 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
776 |
|
|
ResultSet rs = stmt.executeQuery();
|
777 |
|
|
if (rs.next()) {
|
778 |
|
|
maxDate = rs.getDate(1);
|
779 |
|
|
}
|
780 |
|
|
stmt.close();
|
781 |
|
|
}
|
782 |
|
|
catch (SQLException e)
|
783 |
|
|
{
|
784 |
|
|
logMetacat.error("Error while looking up the latest update date: "
|
785 |
|
|
+ e.getMessage());
|
786 |
|
|
}
|
787 |
|
|
finally
|
788 |
|
|
{
|
789 |
|
|
// Return database connection to the pool
|
790 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
791 |
|
|
}
|
792 |
|
|
return maxDate;
|
793 |
|
|
}
|
794 |
|
|
|
795 |
6118
|
leinfelder
|
|
796 |
5282
|
jones
|
/**
|
797 |
|
|
* Determine if an identifier exists already, returning true if so.
|
798 |
7045
|
leinfelder
|
* NOTE: looks in the identifier and system metadata table for a match
|
799 |
|
|
* (in that order)
|
800 |
5282
|
jones
|
*
|
801 |
|
|
* @param guid the global identifier to look up
|
802 |
|
|
* @return boolean true if the identifier exists
|
803 |
|
|
*/
|
804 |
9017
|
tao
|
public boolean identifierExists(String guid) throws SQLException
|
805 |
5282
|
jones
|
{
|
806 |
|
|
boolean idExists = false;
|
807 |
|
|
try {
|
808 |
|
|
String id = getLocalId(guid);
|
809 |
|
|
if (id != null) {
|
810 |
|
|
idExists = true;
|
811 |
|
|
}
|
812 |
|
|
} catch (McdbDocNotFoundException e) {
|
813 |
6123
|
leinfelder
|
// try system metadata only
|
814 |
9017
|
tao
|
//this will check if the guid field on the system metadata table has the id
|
815 |
9030
|
tao
|
idExists = systemMetadataPIDExists(guid);
|
816 |
9017
|
tao
|
if(!idExists) {
|
817 |
|
|
//if the guid field of the system metadata table doesn't have the id,
|
818 |
|
|
//we will check if the serial_id field of the system metadata table has it
|
819 |
|
|
idExists=systemMetadataSIDExists(guid);
|
820 |
|
|
}
|
821 |
|
|
|
822 |
5282
|
jones
|
}
|
823 |
|
|
return idExists;
|
824 |
|
|
}
|
825 |
|
|
|
826 |
|
|
/**
|
827 |
7045
|
leinfelder
|
* Determine if an identifier mapping exists already,
|
828 |
|
|
* returning true if so.
|
829 |
5282
|
jones
|
*
|
830 |
7045
|
leinfelder
|
* @param guid the global identifier to look up
|
831 |
|
|
* @return boolean true if the identifier exists
|
832 |
|
|
*/
|
833 |
9024
|
tao
|
public boolean mappingExists(String guid) throws SQLException
|
834 |
7045
|
leinfelder
|
{
|
835 |
|
|
boolean idExists = false;
|
836 |
|
|
try {
|
837 |
|
|
String id = getLocalId(guid);
|
838 |
|
|
if (id != null) {
|
839 |
|
|
idExists = true;
|
840 |
|
|
}
|
841 |
|
|
} catch (McdbDocNotFoundException e) {
|
842 |
|
|
// nope!
|
843 |
|
|
}
|
844 |
|
|
return idExists;
|
845 |
|
|
}
|
846 |
|
|
|
847 |
|
|
/**
|
848 |
|
|
*
|
849 |
5453
|
berkley
|
* @param guid
|
850 |
|
|
* @param rev
|
851 |
|
|
* @return
|
852 |
|
|
*/
|
853 |
|
|
public String generateLocalId(String guid, int rev)
|
854 |
|
|
{
|
855 |
|
|
return generateLocalId(guid, rev, false);
|
856 |
|
|
}
|
857 |
5286
|
jones
|
|
858 |
|
|
/**
|
859 |
|
|
* Given a global identifier (guid), create a suitable local identifier that
|
860 |
|
|
* follows Metacat's docid semantics and format (scope.id.rev), and create
|
861 |
|
|
* a mapping between these two identifiers. This effectively reserves both
|
862 |
|
|
* the global and the local identifier, as they will now be present in the
|
863 |
7070
|
leinfelder
|
* identifier mapping table.
|
864 |
|
|
*
|
865 |
|
|
* REMOVED feature: If the incoming guid has the syntax of a
|
866 |
5286
|
jones
|
* Metacat docid (scope.id.rev), then simply use it.
|
867 |
7070
|
leinfelder
|
* WHY: because "test.1.001" becomes "test.1.1" which is not correct for DataONE
|
868 |
|
|
* identifier use (those revision numbers are just chartacters and should not be interpreted)
|
869 |
5286
|
jones
|
*
|
870 |
|
|
* @param guid the global string identifier
|
871 |
|
|
* @param rev the revision number to be used in the localId
|
872 |
|
|
* @return String containing the localId to be used for Metacat operations
|
873 |
|
|
*/
|
874 |
5453
|
berkley
|
public String generateLocalId(String guid, int rev, boolean isSystemMetadata)
|
875 |
5286
|
jones
|
{
|
876 |
|
|
String localId = "";
|
877 |
|
|
boolean conformsToDocidFormat = false;
|
878 |
|
|
|
879 |
7070
|
leinfelder
|
// BRL -- do not allow Metacat-conforming IDs to be used:
|
880 |
|
|
// test.1.001 becomes test.1.1 which is NOT correct for DataONE identifiers
|
881 |
5286
|
jones
|
// Check if the guid passed in is already in docid (scope.id.rev) format
|
882 |
7070
|
leinfelder
|
// try {
|
883 |
|
|
// AccessionNumber acc = new AccessionNumber(guid, "NONE");
|
884 |
|
|
// if (new Integer(acc.getRev()).intValue() > 0) {
|
885 |
|
|
// conformsToDocidFormat = true;
|
886 |
|
|
// }
|
887 |
|
|
// } catch (NumberFormatException e) {
|
888 |
|
|
// // No action needed, simply detecting invalid AccessionNumbers
|
889 |
|
|
// } catch (AccessionNumberException e) {
|
890 |
|
|
// // No action needed, simply detecting invalid AccessionNumbers
|
891 |
|
|
// } catch (SQLException e) {
|
892 |
|
|
// // No action needed, simply detecting invalid AccessionNumbers
|
893 |
|
|
// }
|
894 |
5286
|
jones
|
|
895 |
|
|
if (conformsToDocidFormat) {
|
896 |
|
|
// if it conforms, use it for both guid and localId
|
897 |
|
|
localId = guid;
|
898 |
|
|
} else {
|
899 |
|
|
// if not, then generate a new unique localId
|
900 |
|
|
localId = DocumentUtil.generateDocumentId(rev);
|
901 |
|
|
}
|
902 |
|
|
|
903 |
|
|
// Register this new pair in the identifier mapping table
|
904 |
6099
|
leinfelder
|
logMetacat.debug("creating mapping in generateLocalId");
|
905 |
5453
|
berkley
|
if(!isSystemMetadata)
|
906 |
|
|
{ //don't do this if we're generating for system metadata
|
907 |
|
|
createMapping(guid, localId);
|
908 |
|
|
}
|
909 |
5286
|
jones
|
|
910 |
|
|
return localId;
|
911 |
|
|
}
|
912 |
5322
|
berkley
|
|
913 |
|
|
/**
|
914 |
|
|
* given a local identifer, look up the guid. Throw McdbDocNotFoundException
|
915 |
5452
|
berkley
|
* if the docid, rev is not found in the identifiers or systemmetadata tables
|
916 |
5322
|
berkley
|
*
|
917 |
|
|
* @param docid the docid to look up
|
918 |
|
|
* @param rev the revision of the docid to look up
|
919 |
|
|
* @return String containing the mapped guid
|
920 |
|
|
* @throws McdbDocNotFoundException if the docid, rev is not found
|
921 |
|
|
*/
|
922 |
|
|
public String getGUID(String docid, int rev)
|
923 |
|
|
throws McdbDocNotFoundException
|
924 |
|
|
{
|
925 |
6099
|
leinfelder
|
logMetacat.debug("getting guid for " + docid);
|
926 |
5322
|
berkley
|
String query = "select guid from identifier where docid = ? and rev = ?";
|
927 |
|
|
String guid = null;
|
928 |
|
|
|
929 |
|
|
DBConnection dbConn = null;
|
930 |
|
|
int serialNumber = -1;
|
931 |
|
|
try {
|
932 |
|
|
// Get a database connection from the pool
|
933 |
5377
|
berkley
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getGUID");
|
934 |
5322
|
berkley
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
935 |
|
|
|
936 |
|
|
// Execute the insert statement
|
937 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
938 |
|
|
stmt.setString(1, docid);
|
939 |
|
|
stmt.setInt(2, rev);
|
940 |
|
|
ResultSet rs = stmt.executeQuery();
|
941 |
5451
|
berkley
|
if (rs.next())
|
942 |
|
|
{
|
943 |
5322
|
berkley
|
guid = rs.getString(1);
|
944 |
5451
|
berkley
|
}
|
945 |
|
|
else
|
946 |
|
|
{
|
947 |
6104
|
leinfelder
|
throw new McdbDocNotFoundException("No guid registered for docid " + docid + "." + rev);
|
948 |
5322
|
berkley
|
}
|
949 |
5451
|
berkley
|
|
950 |
5322
|
berkley
|
} catch (SQLException e) {
|
951 |
|
|
logMetacat.error("Error while looking up the guid: "
|
952 |
|
|
+ e.getMessage());
|
953 |
|
|
} finally {
|
954 |
|
|
// Return database connection to the pool
|
955 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
956 |
|
|
}
|
957 |
|
|
|
958 |
|
|
return guid;
|
959 |
|
|
}
|
960 |
5333
|
berkley
|
|
961 |
9015
|
tao
|
/**
|
962 |
|
|
* Get the pid of the head (current) version of objects match the specified sid.
|
963 |
9119
|
tao
|
* 1. locate all candidate chain-ends for S1:
|
964 |
|
|
* determined by: seriesId == S1 AND (obsoletedBy == null OR obsoletedBy.seriesId != S1) // these are the type1 and type2 ends
|
965 |
|
|
* If obsoletedBy is missing, we generally consider it a type 2 end except:
|
966 |
|
|
* there is another object in the chain (has the same series id) that obsoletes the missing object.
|
967 |
|
|
* 2. if only 1 candidate chain-end, return it as the HEAD
|
968 |
|
|
* 3. otherwise return the one in the chain with the latest dateUploaded value.
|
969 |
9015
|
tao
|
* @param sid specified sid which should match.
|
970 |
|
|
* @return the pid of the head version. The null will be returned if there is no pid found.
|
971 |
9016
|
tao
|
* @throws SQLException
|
972 |
9015
|
tao
|
*/
|
973 |
9016
|
tao
|
public Identifier getHeadPID(Identifier sid) throws SQLException {
|
974 |
9015
|
tao
|
Identifier pid = null;
|
975 |
|
|
if(sid != null && sid.getValue() != null && !sid.getValue().trim().equals("")) {
|
976 |
|
|
logMetacat.debug("getting pid of the head version for matching the sid: " + sid.getValue());
|
977 |
9119
|
tao
|
String sql = "select guid from systemMetadata where series_id = ? order by date_uploaded DESC";
|
978 |
9015
|
tao
|
DBConnection dbConn = null;
|
979 |
|
|
int serialNumber = -1;
|
980 |
9119
|
tao
|
int endsCount = 0;
|
981 |
|
|
boolean hasError = false;
|
982 |
9015
|
tao
|
try {
|
983 |
|
|
// Get a database connection from the pool
|
984 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getHeadPID");
|
985 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
986 |
|
|
// Execute the insert statement
|
987 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
988 |
|
|
stmt.setString(1, sid.getValue());
|
989 |
|
|
ResultSet rs = stmt.executeQuery();
|
990 |
9119
|
tao
|
boolean hasNext = rs.next();
|
991 |
|
|
boolean first = true;
|
992 |
|
|
Identifier firstOne = new Identifier();//since the sql using the desc order, the first one has the latest upload date.
|
993 |
|
|
if (hasNext)
|
994 |
9015
|
tao
|
{
|
995 |
9119
|
tao
|
while(hasNext) {
|
996 |
|
|
String guidStr = rs.getString(1);
|
997 |
|
|
Identifier guid = new Identifier();
|
998 |
|
|
guid.setValue(guidStr);
|
999 |
|
|
if(first) {
|
1000 |
|
|
firstOne = guid;
|
1001 |
|
|
first =false;
|
1002 |
|
|
}
|
1003 |
|
|
SystemMetadata sysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(guid);
|
1004 |
|
|
if(sysmeta.getObsoletedBy() == null) {
|
1005 |
|
|
//type 1 end
|
1006 |
9128
|
tao
|
logMetacat.debug(""+guidStr+" is a type 1 end for sid "+sid.getValue());
|
1007 |
9119
|
tao
|
pid = guid;
|
1008 |
|
|
endsCount++;
|
1009 |
|
|
} else {
|
1010 |
|
|
Identifier obsoletedBy = sysmeta.getObsoletedBy();
|
1011 |
|
|
SystemMetadata obsoletedBySysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletedBy);
|
1012 |
|
|
if(obsoletedBySysmeta != null) {
|
1013 |
|
|
Identifier sidInObsoletedBy = obsoletedBySysmeta.getSeriesId();
|
1014 |
|
|
if(sidInObsoletedBy == null|| !sidInObsoletedBy.equals(sid)) {
|
1015 |
|
|
// type 2 end
|
1016 |
9128
|
tao
|
logMetacat.debug(""+guidStr+" is a type 2 end for sid "+sid.getValue());
|
1017 |
9119
|
tao
|
pid = guid;
|
1018 |
|
|
endsCount++;
|
1019 |
|
|
}
|
1020 |
|
|
} else {
|
1021 |
|
|
//obsoletedBySysmeta doesn't exist; it means the object is missing
|
1022 |
|
|
//generally, we consider it we generally consider it a type 2 end except:
|
1023 |
|
|
//there is another object in the chain (has the same series id) that obsoletes the missing object.
|
1024 |
|
|
String sql2 = "select guid from systemMetadata where obsoletes = ? and series_id = ?";
|
1025 |
|
|
PreparedStatement stmt2 = dbConn.prepareStatement(sql2);
|
1026 |
|
|
stmt2.setString(1, obsoletedBy.getValue());
|
1027 |
|
|
stmt2.setString(2, sid.getValue());
|
1028 |
|
|
ResultSet result = stmt2.executeQuery();
|
1029 |
|
|
boolean next = result.next();
|
1030 |
|
|
int count = 0;
|
1031 |
|
|
while(next) {
|
1032 |
|
|
count++;
|
1033 |
|
|
next = result.next();
|
1034 |
|
|
}
|
1035 |
|
|
if(count == 0) {
|
1036 |
|
|
//the exception (another object in the chain (has the same series id) that obsoletes the missing object) doesn't exist
|
1037 |
|
|
// it is a type 2 end
|
1038 |
9128
|
tao
|
logMetacat.debug(""+guidStr+" is a type 2 end for sid "+sid.getValue());
|
1039 |
9119
|
tao
|
pid = guid;
|
1040 |
|
|
endsCount++;
|
1041 |
|
|
} else if (count ==1) {
|
1042 |
|
|
// it is not end, do nothing;
|
1043 |
|
|
} else {
|
1044 |
|
|
// something is wrong - there are more than one objects obsolete the missing object!
|
1045 |
|
|
hasError = true;
|
1046 |
|
|
break;
|
1047 |
|
|
}
|
1048 |
|
|
}
|
1049 |
|
|
}
|
1050 |
|
|
hasNext = rs.next();
|
1051 |
|
|
}
|
1052 |
|
|
if(endsCount == 1) {
|
1053 |
|
|
//it has one end and it is an ideal chain. We already assign the guid to the pid. So do nothing.
|
1054 |
9128
|
tao
|
logMetacat.info("It is an ideal for sid "+sid.getValue());
|
1055 |
9119
|
tao
|
}
|
1056 |
|
|
if(hasError || endsCount >1) {
|
1057 |
|
|
// it is not an ideal chain, use the one with latest upload date(the first one in the result set since we have the desc order)
|
1058 |
9128
|
tao
|
logMetacat.info("It is NOT an ideal for sid "+sid.getValue());
|
1059 |
9119
|
tao
|
pid = firstOne;
|
1060 |
|
|
}
|
1061 |
9026
|
tao
|
} else {
|
1062 |
9119
|
tao
|
//it is not a sid or at least we don't have anything to match it.
|
1063 |
|
|
//do nothing, so null will be returned
|
1064 |
9026
|
tao
|
}
|
1065 |
9015
|
tao
|
|
1066 |
|
|
} catch (SQLException e) {
|
1067 |
|
|
logMetacat.error("Error while get the head pid for the sid "+sid.getValue()+" : "
|
1068 |
|
|
+ e.getMessage());
|
1069 |
9016
|
tao
|
throw e;
|
1070 |
9015
|
tao
|
} finally {
|
1071 |
|
|
// Return database connection to the pool
|
1072 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1073 |
|
|
}
|
1074 |
|
|
}
|
1075 |
|
|
return pid;
|
1076 |
|
|
}
|
1077 |
|
|
|
1078 |
9016
|
tao
|
/**
|
1079 |
9032
|
tao
|
* Check if the specified sid object exists on the serial id field on the system metadata table
|
1080 |
|
|
* @param sid
|
1081 |
|
|
* @return true if it exists; false otherwise.
|
1082 |
|
|
* @throws SQLException
|
1083 |
|
|
*/
|
1084 |
|
|
public boolean systemMetadataSIDExists(Identifier sid) throws SQLException {
|
1085 |
|
|
if (sid != null && sid.getValue() != null && !sid.getValue().trim().equals("")) {
|
1086 |
|
|
return systemMetadataSIDExists(sid.getValue());
|
1087 |
|
|
} else {
|
1088 |
|
|
return false;
|
1089 |
|
|
}
|
1090 |
|
|
}
|
1091 |
|
|
|
1092 |
|
|
/**
|
1093 |
9016
|
tao
|
* Check if the specified sid exists on the serial id field on the system metadata table
|
1094 |
|
|
* @param id
|
1095 |
|
|
* @return true if it exists; false otherwise.
|
1096 |
|
|
*/
|
1097 |
9017
|
tao
|
public boolean systemMetadataSIDExists(String sid) throws SQLException {
|
1098 |
9016
|
tao
|
boolean exists = false;
|
1099 |
9032
|
tao
|
logMetacat.debug("Check if the sid: " + sid +" exists on the series_id field of the system metadata table.");
|
1100 |
9016
|
tao
|
if(sid != null && !sid.trim().equals("")) {
|
1101 |
|
|
String sql = "select guid from systemMetadata where series_id = ?";
|
1102 |
|
|
DBConnection dbConn = null;
|
1103 |
|
|
int serialNumber = -1;
|
1104 |
|
|
try {
|
1105 |
|
|
// Get a database connection from the pool
|
1106 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.serialIdExists");
|
1107 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1108 |
|
|
// Execute the insert statement
|
1109 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
1110 |
|
|
stmt.setString(1, sid);
|
1111 |
|
|
ResultSet rs = stmt.executeQuery();
|
1112 |
|
|
if (rs.next())
|
1113 |
|
|
{
|
1114 |
|
|
exists = true;
|
1115 |
|
|
}
|
1116 |
|
|
|
1117 |
|
|
} catch (SQLException e) {
|
1118 |
|
|
logMetacat.error("Error while checking if the sid "+sid+" exists on the series_id field of the system metadata table: "
|
1119 |
|
|
+ e.getMessage());
|
1120 |
|
|
throw e;
|
1121 |
|
|
} finally {
|
1122 |
|
|
// Return database connection to the pool
|
1123 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1124 |
|
|
}
|
1125 |
|
|
}
|
1126 |
|
|
return exists;
|
1127 |
|
|
}
|
1128 |
|
|
|
1129 |
9032
|
tao
|
/**
|
1130 |
|
|
* Determine if the specified identifier object exists or not.
|
1131 |
|
|
* @param pid - the specified identifier
|
1132 |
|
|
* @return true if it is exists.
|
1133 |
|
|
* @throws SQLException
|
1134 |
|
|
* @throws NullPointerException
|
1135 |
|
|
*/
|
1136 |
|
|
public boolean systemMetadataPIDExists(Identifier pid) throws SQLException {
|
1137 |
|
|
if (pid != null && pid.getValue() != null && !pid.getValue().trim().equals("")) {
|
1138 |
|
|
return systemMetadataPIDExists(pid.getValue());
|
1139 |
|
|
} else {
|
1140 |
|
|
return false;
|
1141 |
|
|
}
|
1142 |
|
|
}
|
1143 |
|
|
|
1144 |
9030
|
tao
|
public boolean systemMetadataPIDExists(String guid) throws SQLException {
|
1145 |
6123
|
leinfelder
|
logMetacat.debug("looking up system metadata for guid " + guid);
|
1146 |
|
|
boolean exists = false;
|
1147 |
6337
|
leinfelder
|
String query = "select guid from systemmetadata where guid = ?";
|
1148 |
6123
|
leinfelder
|
DBConnection dbConn = null;
|
1149 |
|
|
int serialNumber = -1;
|
1150 |
9032
|
tao
|
if(guid != null && !guid.trim().equals("")) {
|
1151 |
|
|
try {
|
1152 |
|
|
// Get a database connection from the pool
|
1153 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.systemMetadataExisits");
|
1154 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1155 |
6123
|
leinfelder
|
|
1156 |
9032
|
tao
|
// Execute the insert statement
|
1157 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1158 |
|
|
stmt.setString(1, guid);
|
1159 |
|
|
ResultSet rs = stmt.executeQuery();
|
1160 |
|
|
if (rs.next()) {
|
1161 |
|
|
exists = true;
|
1162 |
|
|
}
|
1163 |
6123
|
leinfelder
|
|
1164 |
9032
|
tao
|
} catch (SQLException e) {
|
1165 |
|
|
logMetacat.error("Error while looking up the system metadata: "
|
1166 |
|
|
+ e.getMessage());
|
1167 |
|
|
throw e;
|
1168 |
|
|
} finally {
|
1169 |
|
|
// Return database connection to the pool
|
1170 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1171 |
|
|
}
|
1172 |
6123
|
leinfelder
|
}
|
1173 |
|
|
return exists;
|
1174 |
|
|
}
|
1175 |
|
|
|
1176 |
5333
|
berkley
|
/**
|
1177 |
5887
|
berkley
|
* creates a system metadata mapping and adds additional fields from sysmeta
|
1178 |
|
|
* to the table for quick searching.
|
1179 |
|
|
*
|
1180 |
|
|
* @param guid the id to insert
|
1181 |
|
|
* @param localId the systemMetadata object to get the local id for
|
1182 |
6108
|
leinfelder
|
* @throws McdbDocNotFoundException
|
1183 |
6892
|
cjones
|
* @throws SQLException
|
1184 |
6904
|
cjones
|
* @throws InvalidSystemMetadata
|
1185 |
5887
|
berkley
|
*/
|
1186 |
7188
|
leinfelder
|
public void insertOrUpdateSystemMetadata(SystemMetadata sysmeta)
|
1187 |
6904
|
cjones
|
throws McdbDocNotFoundException, SQLException, InvalidSystemMetadata {
|
1188 |
6277
|
leinfelder
|
String guid = sysmeta.getIdentifier().getValue();
|
1189 |
7188
|
leinfelder
|
|
1190 |
|
|
// Get a database connection from the pool
|
1191 |
|
|
DBConnection dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadata");
|
1192 |
|
|
int serialNumber = dbConn.getCheckOutSerialNumber();
|
1193 |
6892
|
cjones
|
|
1194 |
7188
|
leinfelder
|
try {
|
1195 |
|
|
// use a single transaction for it all
|
1196 |
|
|
dbConn.setAutoCommit(false);
|
1197 |
|
|
|
1198 |
|
|
// insert the record if needed
|
1199 |
9030
|
tao
|
if (!IdentifierManager.getInstance().systemMetadataPIDExists(guid)) {
|
1200 |
7188
|
leinfelder
|
insertSystemMetadata(guid, dbConn);
|
1201 |
|
|
}
|
1202 |
|
|
// update with the values
|
1203 |
|
|
updateSystemMetadata(sysmeta, dbConn);
|
1204 |
|
|
|
1205 |
|
|
// commit if we got here with no errors
|
1206 |
|
|
dbConn.commit();
|
1207 |
|
|
} catch (Exception e) {
|
1208 |
|
|
e.printStackTrace();
|
1209 |
|
|
logMetacat.error("Error while creating " + TYPE_SYSTEM_METADATA + " record: " + guid, e );
|
1210 |
|
|
dbConn.rollback();
|
1211 |
9220
|
tao
|
throw new SQLException("Can't save system metadata "+e.getMessage());
|
1212 |
7188
|
leinfelder
|
} finally {
|
1213 |
|
|
// Return database connection to the pool
|
1214 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1215 |
|
|
}
|
1216 |
|
|
|
1217 |
|
|
|
1218 |
5887
|
berkley
|
}
|
1219 |
6099
|
leinfelder
|
|
1220 |
5887
|
berkley
|
|
1221 |
|
|
/**
|
1222 |
6079
|
leinfelder
|
* update a mapping
|
1223 |
|
|
* @param guid
|
1224 |
|
|
* @param localId
|
1225 |
|
|
*/
|
1226 |
|
|
public void updateMapping(String guid, String localId)
|
1227 |
|
|
{
|
1228 |
|
|
|
1229 |
6099
|
leinfelder
|
logMetacat.debug("$$$$$$$$$$$$$$ updating mapping table");
|
1230 |
5350
|
berkley
|
int serialNumber = -1;
|
1231 |
|
|
DBConnection dbConn = null;
|
1232 |
|
|
try {
|
1233 |
|
|
// Parse the localId into scope and rev parts
|
1234 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
1235 |
|
|
String docid = acc.getDocid();
|
1236 |
|
|
int rev = 1;
|
1237 |
|
|
if(acc.getRev() != null)
|
1238 |
|
|
{
|
1239 |
|
|
rev = (new Integer(acc.getRev()).intValue());
|
1240 |
|
|
}
|
1241 |
|
|
|
1242 |
|
|
// Get a database connection from the pool
|
1243 |
|
|
dbConn =
|
1244 |
6079
|
leinfelder
|
DBConnectionPool.getDBConnection("IdentifierManager.updateMapping");
|
1245 |
5350
|
berkley
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1246 |
|
|
|
1247 |
6099
|
leinfelder
|
// Execute the update statement
|
1248 |
6595
|
leinfelder
|
String query = "update " + TYPE_IDENTIFIER + " set (docid, rev) = (?, ?) where guid = ?";
|
1249 |
5350
|
berkley
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1250 |
|
|
stmt.setString(1, docid);
|
1251 |
|
|
stmt.setInt(2, rev);
|
1252 |
6595
|
leinfelder
|
stmt.setString(3, guid);
|
1253 |
5350
|
berkley
|
int rows = stmt.executeUpdate();
|
1254 |
|
|
|
1255 |
|
|
stmt.close();
|
1256 |
|
|
} catch (SQLException e) {
|
1257 |
|
|
e.printStackTrace();
|
1258 |
6079
|
leinfelder
|
logMetacat.error("SQL error while updating a mapping identifier: "
|
1259 |
5350
|
berkley
|
+ e.getMessage());
|
1260 |
|
|
} catch (NumberFormatException e) {
|
1261 |
|
|
e.printStackTrace();
|
1262 |
6079
|
leinfelder
|
logMetacat.error("NumberFormat error while updating a mapping identifier: "
|
1263 |
5350
|
berkley
|
+ e.getMessage());
|
1264 |
|
|
} catch (AccessionNumberException e) {
|
1265 |
|
|
e.printStackTrace();
|
1266 |
6079
|
leinfelder
|
logMetacat.error("AccessionNumber error while updating a mapping identifier: "
|
1267 |
5350
|
berkley
|
+ e.getMessage());
|
1268 |
|
|
} finally {
|
1269 |
|
|
// Return database connection to the pool
|
1270 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1271 |
|
|
}
|
1272 |
6099
|
leinfelder
|
logMetacat.debug("done updating mapping");
|
1273 |
5350
|
berkley
|
}
|
1274 |
6099
|
leinfelder
|
|
1275 |
|
|
private void updateSystemMetadataFields(long dateUploaded, String rightsHolder,
|
1276 |
6892
|
cjones
|
String checksum, String checksumAlgorithm, String originMemberNode,
|
1277 |
|
|
String authoritativeMemberNode, long modifiedDate, String submitter,
|
1278 |
|
|
String guid, String objectFormat, BigInteger size, boolean archived,
|
1279 |
|
|
boolean replicationAllowed, int numberReplicas, String obsoletes,
|
1280 |
9230
|
tao
|
String obsoletedBy, BigInteger serialVersion, String seriesId,
|
1281 |
|
|
String fileName, MediaType mediaType, DBConnection dbConn) throws SQLException {
|
1282 |
|
|
PreparedStatement stmt = null;
|
1283 |
|
|
PreparedStatement stmt2 = null;
|
1284 |
|
|
try {
|
1285 |
|
|
dbConn.setAutoCommit(false);
|
1286 |
|
|
// Execute the insert statement
|
1287 |
|
|
String query = "update " + TYPE_SYSTEM_METADATA +
|
1288 |
|
|
" set (date_uploaded, rights_holder, checksum, checksum_algorithm, " +
|
1289 |
|
|
"origin_member_node, authoritive_member_node, date_modified, " +
|
1290 |
|
|
"submitter, object_format, size, archived, replication_allowed, number_replicas, " +
|
1291 |
9231
|
tao
|
"obsoletes, obsoleted_by, serial_version, series_id, file_name, media_type) " +
|
1292 |
9230
|
tao
|
"= (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,?,?) where guid = ?";
|
1293 |
|
|
stmt = dbConn.prepareStatement(query);
|
1294 |
|
|
|
1295 |
|
|
//data values
|
1296 |
|
|
stmt.setTimestamp(1, new java.sql.Timestamp(dateUploaded));
|
1297 |
|
|
stmt.setString(2, rightsHolder);
|
1298 |
|
|
stmt.setString(3, checksum);
|
1299 |
|
|
stmt.setString(4, checksumAlgorithm);
|
1300 |
|
|
stmt.setString(5, originMemberNode);
|
1301 |
|
|
stmt.setString(6, authoritativeMemberNode);
|
1302 |
|
|
stmt.setTimestamp(7, new java.sql.Timestamp(modifiedDate));
|
1303 |
|
|
stmt.setString(8, submitter);
|
1304 |
|
|
stmt.setString(9, objectFormat);
|
1305 |
|
|
stmt.setString(10, size.toString());
|
1306 |
|
|
stmt.setBoolean(11, archived);
|
1307 |
|
|
stmt.setBoolean(12, replicationAllowed);
|
1308 |
|
|
stmt.setInt(13, numberReplicas);
|
1309 |
|
|
stmt.setString(14, obsoletes);
|
1310 |
|
|
stmt.setString(15, obsoletedBy);
|
1311 |
|
|
stmt.setString(16, serialVersion.toString());
|
1312 |
|
|
stmt.setString(17, seriesId);
|
1313 |
|
|
stmt.setString(18, fileName);
|
1314 |
|
|
if (mediaType == null) {
|
1315 |
|
|
stmt.setString(19, null);
|
1316 |
|
|
} else {
|
1317 |
|
|
stmt.setString(19, mediaType.getName());
|
1318 |
|
|
}
|
1319 |
|
|
//where clause
|
1320 |
|
|
stmt.setString(20, guid);
|
1321 |
|
|
logMetacat.debug("stmt: " + stmt.toString());
|
1322 |
|
|
//execute
|
1323 |
|
|
int rows = stmt.executeUpdate();
|
1324 |
|
|
|
1325 |
|
|
//insert media type properties into another table
|
1326 |
|
|
if(mediaType != null && mediaType.getPropertyList() != null) {
|
1327 |
|
|
String sql2 = "insert into smmediatypeproperties " +
|
1328 |
|
|
"(guid, name, value) " + "values (?, ?, ?)";
|
1329 |
|
|
stmt2 = dbConn.prepareStatement(sql2);
|
1330 |
|
|
for(MediaTypeProperty item : mediaType.getPropertyList()) {
|
1331 |
|
|
if(item != null) {
|
1332 |
|
|
String name = item.getName();
|
1333 |
|
|
String value = item.getValue();
|
1334 |
|
|
stmt2.setString(1, guid);
|
1335 |
|
|
stmt2.setString(2, name);
|
1336 |
|
|
stmt2.setString(3, value);
|
1337 |
|
|
logMetacat.debug("insert media type properties query: " + stmt2.toString());
|
1338 |
|
|
int row =stmt2.executeUpdate();
|
1339 |
|
|
}
|
1340 |
|
|
|
1341 |
|
|
}
|
1342 |
|
|
}
|
1343 |
|
|
dbConn.commit();
|
1344 |
|
|
dbConn.setAutoCommit(true);
|
1345 |
|
|
} catch (Exception e) {
|
1346 |
|
|
dbConn.rollback();
|
1347 |
|
|
dbConn.setAutoCommit(true);
|
1348 |
|
|
throw new SQLException(e.getMessage());
|
1349 |
|
|
} finally {
|
1350 |
|
|
if(stmt != null) {
|
1351 |
|
|
stmt.close();
|
1352 |
|
|
}
|
1353 |
|
|
if(stmt2 != null) {
|
1354 |
|
|
stmt2.close();
|
1355 |
|
|
}
|
1356 |
|
|
}
|
1357 |
6892
|
cjones
|
|
1358 |
7188
|
leinfelder
|
|
1359 |
|
|
}
|
1360 |
|
|
|
1361 |
|
|
private void insertReplicationPolicy(String guid, String policy, List<String> memberNodes, DBConnection dbConn) throws SQLException
|
1362 |
|
|
{
|
1363 |
|
|
|
1364 |
|
|
// remove existing values first
|
1365 |
7392
|
leinfelder
|
String delete = "delete from smReplicationPolicy " +
|
1366 |
7188
|
leinfelder
|
"where guid = ? and policy = ?";
|
1367 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
1368 |
|
|
//data values
|
1369 |
|
|
stmt.setString(1, guid);
|
1370 |
|
|
stmt.setString(2, policy);
|
1371 |
|
|
//execute
|
1372 |
|
|
int deletedCount = stmt.executeUpdate();
|
1373 |
|
|
stmt.close();
|
1374 |
5957
|
berkley
|
|
1375 |
7188
|
leinfelder
|
for (String memberNode: memberNodes) {
|
1376 |
5887
|
berkley
|
// Execute the insert statement
|
1377 |
7392
|
leinfelder
|
String insert = "insert into smReplicationPolicy " +
|
1378 |
7188
|
leinfelder
|
"(guid, policy, member_node) " +
|
1379 |
|
|
"values (?, ?, ?)";
|
1380 |
|
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1381 |
5887
|
berkley
|
|
1382 |
|
|
//data values
|
1383 |
7188
|
leinfelder
|
insertStatement.setString(1, guid);
|
1384 |
|
|
insertStatement.setString(2, policy);
|
1385 |
|
|
insertStatement.setString(3, memberNode);
|
1386 |
|
|
|
1387 |
7392
|
leinfelder
|
logMetacat.debug("smReplicationPolicy sql: " + insertStatement.toString());
|
1388 |
6375
|
leinfelder
|
|
1389 |
5887
|
berkley
|
//execute
|
1390 |
7188
|
leinfelder
|
int rows = insertStatement.executeUpdate();
|
1391 |
|
|
insertStatement.close();
|
1392 |
5887
|
berkley
|
}
|
1393 |
7188
|
leinfelder
|
|
1394 |
5887
|
berkley
|
}
|
1395 |
|
|
|
1396 |
7188
|
leinfelder
|
private void insertReplicationStatus(String guid, List<Replica> replicas, DBConnection dbConn) throws SQLException {
|
1397 |
|
|
|
1398 |
|
|
// remove existing values first
|
1399 |
7392
|
leinfelder
|
String delete = "delete from smReplicationStatus " +
|
1400 |
7188
|
leinfelder
|
"where guid = ?";
|
1401 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
1402 |
|
|
//data values
|
1403 |
|
|
stmt.setString(1, guid);
|
1404 |
|
|
//execute
|
1405 |
|
|
int deletedCount = stmt.executeUpdate();
|
1406 |
|
|
stmt.close();
|
1407 |
6107
|
leinfelder
|
|
1408 |
7188
|
leinfelder
|
if (replicas != null) {
|
1409 |
|
|
for (Replica replica: replicas) {
|
1410 |
6107
|
leinfelder
|
// Execute the insert statement
|
1411 |
7392
|
leinfelder
|
String insert = "insert into smReplicationStatus " +
|
1412 |
7188
|
leinfelder
|
"(guid, member_node, status, date_verified) " +
|
1413 |
|
|
"values (?, ?, ?, ?)";
|
1414 |
6107
|
leinfelder
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1415 |
|
|
|
1416 |
|
|
//data values
|
1417 |
7188
|
leinfelder
|
String memberNode = replica.getReplicaMemberNode().getValue();
|
1418 |
|
|
String status = replica.getReplicationStatus().toString();
|
1419 |
7399
|
cjones
|
java.sql.Timestamp sqlDate = new java.sql.Timestamp(replica.getReplicaVerified().getTime());
|
1420 |
6107
|
leinfelder
|
insertStatement.setString(1, guid);
|
1421 |
7188
|
leinfelder
|
insertStatement.setString(2, memberNode);
|
1422 |
|
|
insertStatement.setString(3, status);
|
1423 |
7399
|
cjones
|
insertStatement.setTimestamp(4, sqlDate);
|
1424 |
7188
|
leinfelder
|
|
1425 |
7392
|
leinfelder
|
logMetacat.debug("smReplicationStatus sql: " + insertStatement.toString());
|
1426 |
7102
|
leinfelder
|
|
1427 |
6107
|
leinfelder
|
//execute
|
1428 |
|
|
int rows = insertStatement.executeUpdate();
|
1429 |
|
|
insertStatement.close();
|
1430 |
|
|
}
|
1431 |
|
|
}
|
1432 |
7188
|
leinfelder
|
|
1433 |
6107
|
leinfelder
|
}
|
1434 |
|
|
|
1435 |
5334
|
berkley
|
/**
|
1436 |
5887
|
berkley
|
* Insert the system metadata fields into the db
|
1437 |
|
|
* @param sm
|
1438 |
6108
|
leinfelder
|
* @throws McdbDocNotFoundException
|
1439 |
6892
|
cjones
|
* @throws SQLException
|
1440 |
6904
|
cjones
|
* @throws InvalidSystemMetadata
|
1441 |
7188
|
leinfelder
|
* @throws AccessException
|
1442 |
5887
|
berkley
|
*/
|
1443 |
7188
|
leinfelder
|
public void updateSystemMetadata(SystemMetadata sm, DBConnection dbConn)
|
1444 |
|
|
throws McdbDocNotFoundException, SQLException, InvalidSystemMetadata, AccessException {
|
1445 |
6107
|
leinfelder
|
|
1446 |
6892
|
cjones
|
Boolean replicationAllowed = false;
|
1447 |
|
|
Integer numberReplicas = -1;
|
1448 |
6107
|
leinfelder
|
ReplicationPolicy replicationPolicy = sm.getReplicationPolicy();
|
1449 |
|
|
if (replicationPolicy != null) {
|
1450 |
|
|
replicationAllowed = replicationPolicy.getReplicationAllowed();
|
1451 |
|
|
numberReplicas = replicationPolicy.getNumberReplicas();
|
1452 |
|
|
replicationAllowed = replicationAllowed == null ? false: replicationAllowed;
|
1453 |
|
|
numberReplicas = numberReplicas == null ? -1: numberReplicas;
|
1454 |
|
|
}
|
1455 |
6904
|
cjones
|
|
1456 |
6107
|
leinfelder
|
// the main systemMetadata fields
|
1457 |
6892
|
cjones
|
updateSystemMetadataFields(
|
1458 |
6311
|
leinfelder
|
sm.getDateUploaded() == null ? null: sm.getDateUploaded().getTime(),
|
1459 |
|
|
sm.getRightsHolder() == null ? null: sm.getRightsHolder().getValue(),
|
1460 |
|
|
sm.getChecksum() == null ? null: sm.getChecksum().getValue(),
|
1461 |
6397
|
leinfelder
|
sm.getChecksum() == null ? null: sm.getChecksum().getAlgorithm(),
|
1462 |
6311
|
leinfelder
|
sm.getOriginMemberNode() == null ? null: sm.getOriginMemberNode().getValue(),
|
1463 |
|
|
sm.getAuthoritativeMemberNode() == null ? null: sm.getAuthoritativeMemberNode().getValue(),
|
1464 |
|
|
sm.getDateSysMetadataModified() == null ? null: sm.getDateSysMetadataModified().getTime(),
|
1465 |
|
|
sm.getSubmitter() == null ? null: sm.getSubmitter().getValue(),
|
1466 |
6904
|
cjones
|
sm.getIdentifier().getValue(),
|
1467 |
|
|
sm.getFormatId() == null ? null: sm.getFormatId().getValue(),
|
1468 |
|
|
sm.getSize(),
|
1469 |
|
|
sm.getArchived() == null ? false: sm.getArchived(),
|
1470 |
|
|
replicationAllowed,
|
1471 |
|
|
numberReplicas,
|
1472 |
|
|
sm.getObsoletes() == null ? null:sm.getObsoletes().getValue(),
|
1473 |
|
|
sm.getObsoletedBy() == null ? null: sm.getObsoletedBy().getValue(),
|
1474 |
7188
|
leinfelder
|
sm.getSerialVersion(),
|
1475 |
8810
|
leinfelder
|
sm.getSeriesId() == null ? null: sm.getSeriesId().getValue(),
|
1476 |
9230
|
tao
|
sm.getFileName() == null ? null: sm.getFileName(),
|
1477 |
|
|
sm.getMediaType() == null ? null: sm.getMediaType(),
|
1478 |
7188
|
leinfelder
|
dbConn
|
1479 |
6561
|
leinfelder
|
);
|
1480 |
6097
|
leinfelder
|
|
1481 |
|
|
String guid = sm.getIdentifier().getValue();
|
1482 |
|
|
|
1483 |
6107
|
leinfelder
|
// save replication policies
|
1484 |
|
|
if (replicationPolicy != null) {
|
1485 |
|
|
List<String> nodes = null;
|
1486 |
|
|
String policy = null;
|
1487 |
|
|
|
1488 |
6494
|
leinfelder
|
// check for null
|
1489 |
|
|
if (replicationPolicy.getBlockedMemberNodeList() != null) {
|
1490 |
|
|
nodes = new ArrayList<String>();
|
1491 |
|
|
policy = "blocked";
|
1492 |
|
|
for (NodeReference node: replicationPolicy.getBlockedMemberNodeList()) {
|
1493 |
|
|
nodes.add(node.getValue());
|
1494 |
|
|
}
|
1495 |
7188
|
leinfelder
|
this.insertReplicationPolicy(guid, policy, nodes, dbConn);
|
1496 |
6107
|
leinfelder
|
}
|
1497 |
|
|
|
1498 |
6494
|
leinfelder
|
if (replicationPolicy.getPreferredMemberNodeList() != null) {
|
1499 |
|
|
nodes = new ArrayList<String>();
|
1500 |
|
|
policy = "preferred";
|
1501 |
|
|
for (NodeReference node: replicationPolicy.getPreferredMemberNodeList()) {
|
1502 |
|
|
nodes.add(node.getValue());
|
1503 |
|
|
}
|
1504 |
7188
|
leinfelder
|
this.insertReplicationPolicy(guid, policy, nodes, dbConn);
|
1505 |
6107
|
leinfelder
|
}
|
1506 |
|
|
}
|
1507 |
6097
|
leinfelder
|
|
1508 |
6107
|
leinfelder
|
// save replica information
|
1509 |
7188
|
leinfelder
|
this.insertReplicationStatus(guid, sm.getReplicaList(), dbConn);
|
1510 |
6107
|
leinfelder
|
|
1511 |
6108
|
leinfelder
|
// save access policy
|
1512 |
|
|
AccessPolicy accessPolicy = sm.getAccessPolicy();
|
1513 |
|
|
if (accessPolicy != null) {
|
1514 |
7188
|
leinfelder
|
this.insertAccessPolicy(guid, accessPolicy);
|
1515 |
6108
|
leinfelder
|
}
|
1516 |
5887
|
berkley
|
}
|
1517 |
|
|
|
1518 |
|
|
/**
|
1519 |
6108
|
leinfelder
|
* Creates Metacat access rules and inserts them
|
1520 |
|
|
* @param accessPolicy
|
1521 |
|
|
* @throws McdbDocNotFoundException
|
1522 |
|
|
* @throws AccessException
|
1523 |
|
|
*/
|
1524 |
|
|
private void insertAccessPolicy(String guid, AccessPolicy accessPolicy) throws McdbDocNotFoundException, AccessException {
|
1525 |
|
|
|
1526 |
6744
|
leinfelder
|
// check for the existing permOrder so that we remain compatible with it (DataONE does not care)
|
1527 |
|
|
XMLAccessAccess accessController = new XMLAccessAccess();
|
1528 |
|
|
String existingPermOrder = AccessControlInterface.ALLOWFIRST;
|
1529 |
|
|
Vector<XMLAccessDAO> existingAccess = accessController.getXMLAccessForDoc(guid);
|
1530 |
|
|
if (existingAccess != null && existingAccess.size() > 0) {
|
1531 |
|
|
existingPermOrder = existingAccess.get(0).getPermOrder();
|
1532 |
|
|
}
|
1533 |
|
|
|
1534 |
6108
|
leinfelder
|
List<XMLAccessDAO> accessDAOs = new ArrayList<XMLAccessDAO>();
|
1535 |
|
|
for (AccessRule accessRule: accessPolicy.getAllowList()) {
|
1536 |
|
|
List<Subject> subjects = accessRule.getSubjectList();
|
1537 |
|
|
List<Permission> permissions = accessRule.getPermissionList();
|
1538 |
|
|
for (Subject subject: subjects) {
|
1539 |
6122
|
leinfelder
|
XMLAccessDAO accessDAO = new XMLAccessDAO();
|
1540 |
|
|
accessDAO.setPrincipalName(subject.getValue());
|
1541 |
|
|
accessDAO.setGuid(guid);
|
1542 |
|
|
accessDAO.setPermType(AccessControlInterface.ALLOW);
|
1543 |
6744
|
leinfelder
|
accessDAO.setPermOrder(existingPermOrder);
|
1544 |
|
|
if (permissions != null) {
|
1545 |
|
|
for (Permission permission: permissions) {
|
1546 |
|
|
Long metacatPermission = new Long(convertPermission(permission));
|
1547 |
|
|
accessDAO.addPermission(metacatPermission);
|
1548 |
|
|
}
|
1549 |
6122
|
leinfelder
|
}
|
1550 |
|
|
accessDAOs.add(accessDAO);
|
1551 |
6108
|
leinfelder
|
}
|
1552 |
|
|
}
|
1553 |
|
|
|
1554 |
|
|
|
1555 |
6744
|
leinfelder
|
// remove all existing allow records
|
1556 |
|
|
accessController.deleteXMLAccessForDoc(guid, AccessControlInterface.ALLOW);
|
1557 |
|
|
// add the ones we can for this guid
|
1558 |
|
|
accessController.insertAccess(guid, accessDAOs);
|
1559 |
6108
|
leinfelder
|
|
1560 |
6744
|
leinfelder
|
|
1561 |
6108
|
leinfelder
|
}
|
1562 |
|
|
|
1563 |
|
|
/**
|
1564 |
|
|
* Lookup access policy from Metacat
|
1565 |
|
|
* @param guid
|
1566 |
|
|
* @return
|
1567 |
|
|
* @throws McdbDocNotFoundException
|
1568 |
|
|
* @throws AccessException
|
1569 |
|
|
*/
|
1570 |
6720
|
leinfelder
|
public AccessPolicy getAccessPolicy(String guid) throws McdbDocNotFoundException, AccessException {
|
1571 |
6450
|
leinfelder
|
AccessPolicy accessPolicy = new AccessPolicy();
|
1572 |
|
|
|
1573 |
6122
|
leinfelder
|
// use GUID to look up the access
|
1574 |
6744
|
leinfelder
|
XMLAccessAccess accessController = new XMLAccessAccess();
|
1575 |
6720
|
leinfelder
|
List<XMLAccessDAO> accessDAOs = accessController.getXMLAccessForDoc(guid);
|
1576 |
|
|
|
1577 |
6108
|
leinfelder
|
for (XMLAccessDAO accessDAO: accessDAOs) {
|
1578 |
6744
|
leinfelder
|
// only add allow rule
|
1579 |
|
|
if (accessDAO.getPermType().equals(AccessControlInterface.ALLOW)) {
|
1580 |
|
|
AccessRule accessRule = new AccessRule();
|
1581 |
|
|
List <Permission> permissions = convertPermission(accessDAO.getPermission().intValue());
|
1582 |
7088
|
leinfelder
|
// cannot include if we have no permissions
|
1583 |
|
|
if (permissions == null || permissions.isEmpty()) {
|
1584 |
|
|
logMetacat.warn("skipping empty access rule permissions for " + guid);
|
1585 |
|
|
continue;
|
1586 |
|
|
}
|
1587 |
6744
|
leinfelder
|
accessRule.setPermissionList(permissions);
|
1588 |
|
|
Subject subject = new Subject();
|
1589 |
|
|
subject.setValue(accessDAO.getPrincipalName());
|
1590 |
|
|
accessRule.addSubject(subject);
|
1591 |
|
|
accessPolicy.addAllow(accessRule);
|
1592 |
|
|
}
|
1593 |
6108
|
leinfelder
|
}
|
1594 |
|
|
return accessPolicy;
|
1595 |
|
|
}
|
1596 |
|
|
|
1597 |
|
|
public int convertPermission(Permission permission) {
|
1598 |
|
|
if (permission.equals(Permission.READ)) {
|
1599 |
|
|
return AccessControlInterface.READ;
|
1600 |
|
|
}
|
1601 |
|
|
if (permission.equals(Permission.WRITE)) {
|
1602 |
|
|
return AccessControlInterface.WRITE;
|
1603 |
|
|
}
|
1604 |
|
|
if (permission.equals(Permission.CHANGE_PERMISSION)) {
|
1605 |
|
|
return AccessControlInterface.CHMOD;
|
1606 |
|
|
}
|
1607 |
|
|
return -1;
|
1608 |
|
|
}
|
1609 |
|
|
|
1610 |
6722
|
leinfelder
|
public List<Permission> convertPermission(int permission) {
|
1611 |
6744
|
leinfelder
|
|
1612 |
6722
|
leinfelder
|
List<Permission> permissions = new ArrayList<Permission>();
|
1613 |
6744
|
leinfelder
|
if (permission == AccessControlInterface.ALL) {
|
1614 |
6722
|
leinfelder
|
permissions.add(Permission.READ);
|
1615 |
|
|
permissions.add(Permission.WRITE);
|
1616 |
6744
|
leinfelder
|
permissions.add(Permission.CHANGE_PERMISSION);
|
1617 |
6722
|
leinfelder
|
return permissions;
|
1618 |
6108
|
leinfelder
|
}
|
1619 |
6744
|
leinfelder
|
|
1620 |
|
|
if ((permission & AccessControlInterface.CHMOD) == AccessControlInterface.CHMOD) {
|
1621 |
6722
|
leinfelder
|
permissions.add(Permission.CHANGE_PERMISSION);
|
1622 |
6108
|
leinfelder
|
}
|
1623 |
6744
|
leinfelder
|
if ((permission & AccessControlInterface.READ) == AccessControlInterface.READ) {
|
1624 |
6722
|
leinfelder
|
permissions.add(Permission.READ);
|
1625 |
6744
|
leinfelder
|
}
|
1626 |
|
|
if ((permission & AccessControlInterface.WRITE) == AccessControlInterface.WRITE) {
|
1627 |
6722
|
leinfelder
|
permissions.add(Permission.WRITE);
|
1628 |
6720
|
leinfelder
|
}
|
1629 |
6744
|
leinfelder
|
|
1630 |
|
|
return permissions;
|
1631 |
6108
|
leinfelder
|
}
|
1632 |
|
|
|
1633 |
|
|
/**
|
1634 |
6099
|
leinfelder
|
* Lookup a localId given the GUID. If
|
1635 |
|
|
* the identifier is not found, throw an exception.
|
1636 |
|
|
*
|
1637 |
|
|
* @param guid the global identifier to look up
|
1638 |
|
|
* @return String containing the corresponding LocalId
|
1639 |
|
|
* @throws McdbDocNotFoundException if the identifier is not found
|
1640 |
5334
|
berkley
|
*/
|
1641 |
9024
|
tao
|
public String getLocalId(String guid) throws McdbDocNotFoundException, SQLException {
|
1642 |
5334
|
berkley
|
|
1643 |
|
|
String db_guid = "";
|
1644 |
|
|
String docid = "";
|
1645 |
|
|
int rev = 0;
|
1646 |
|
|
|
1647 |
6099
|
leinfelder
|
String query = "select guid, docid, rev from " + TYPE_IDENTIFIER + " where guid = ?";
|
1648 |
5334
|
berkley
|
|
1649 |
|
|
DBConnection dbConn = null;
|
1650 |
5333
|
berkley
|
int serialNumber = -1;
|
1651 |
5334
|
berkley
|
try {
|
1652 |
|
|
// Get a database connection from the pool
|
1653 |
|
|
dbConn = DBConnectionPool.getDBConnection("Identifier.getLocalId");
|
1654 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1655 |
|
|
|
1656 |
|
|
// Execute the insert statement
|
1657 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1658 |
|
|
stmt.setString(1, guid);
|
1659 |
|
|
ResultSet rs = stmt.executeQuery();
|
1660 |
|
|
if (rs.next()) {
|
1661 |
|
|
db_guid = rs.getString(1);
|
1662 |
|
|
docid = rs.getString(2);
|
1663 |
|
|
rev = rs.getInt(3);
|
1664 |
|
|
assert(db_guid.equals(guid));
|
1665 |
|
|
} else {
|
1666 |
|
|
throw new McdbDocNotFoundException("Document not found:" + guid);
|
1667 |
|
|
}
|
1668 |
|
|
stmt.close();
|
1669 |
|
|
} catch (SQLException e) {
|
1670 |
|
|
logMetacat.error("Error while looking up the local identifier: "
|
1671 |
|
|
+ e.getMessage());
|
1672 |
9024
|
tao
|
throw e;
|
1673 |
5334
|
berkley
|
} finally {
|
1674 |
|
|
// Return database connection to the pool
|
1675 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1676 |
|
|
}
|
1677 |
|
|
return docid + "." + rev;
|
1678 |
|
|
}
|
1679 |
|
|
|
1680 |
5377
|
berkley
|
/**
|
1681 |
5895
|
berkley
|
* query the systemmetadata table based on the given parameters
|
1682 |
|
|
* @param startTime
|
1683 |
|
|
* @param endTime
|
1684 |
|
|
* @param objectFormat
|
1685 |
9249
|
tao
|
* @param nodeId
|
1686 |
5895
|
berkley
|
* @param start
|
1687 |
|
|
* @param count
|
1688 |
|
|
* @return ObjectList
|
1689 |
6299
|
leinfelder
|
* @throws SQLException
|
1690 |
|
|
* @throws ServiceException
|
1691 |
|
|
* @throws PropertyNotFoundException
|
1692 |
5895
|
berkley
|
*/
|
1693 |
6836
|
cjones
|
public ObjectList querySystemMetadata(Date startTime, Date endTime,
|
1694 |
9249
|
tao
|
ObjectFormatIdentifier objectFormatId, NodeReference nodeId,
|
1695 |
9072
|
tao
|
int start, int count, Identifier identifier, boolean isSID)
|
1696 |
6836
|
cjones
|
throws SQLException, PropertyNotFoundException, ServiceException {
|
1697 |
5895
|
berkley
|
ObjectList ol = new ObjectList();
|
1698 |
5943
|
berkley
|
DBConnection dbConn = null;
|
1699 |
|
|
int serialNumber = -1;
|
1700 |
6836
|
cjones
|
|
1701 |
6299
|
leinfelder
|
try {
|
1702 |
7452
|
leinfelder
|
String fieldSql = "select guid, date_uploaded, rights_holder, checksum, "
|
1703 |
6836
|
cjones
|
+ "checksum_algorithm, origin_member_node, authoritive_member_node, "
|
1704 |
|
|
+ "date_modified, submitter, object_format, size from systemmetadata";
|
1705 |
7410
|
leinfelder
|
|
1706 |
|
|
// handle special case quickly
|
1707 |
|
|
String countSql = "select count(guid) from systemmetadata";
|
1708 |
7452
|
leinfelder
|
|
1709 |
|
|
// the clause
|
1710 |
|
|
String whereClauseSql = "";
|
1711 |
6836
|
cjones
|
|
1712 |
5895
|
berkley
|
boolean f1 = false;
|
1713 |
|
|
boolean f2 = false;
|
1714 |
|
|
boolean f3 = false;
|
1715 |
9072
|
tao
|
boolean f4 = false;
|
1716 |
6836
|
cjones
|
|
1717 |
9072
|
tao
|
|
1718 |
6299
|
leinfelder
|
if (startTime != null) {
|
1719 |
7452
|
leinfelder
|
whereClauseSql += " where systemmetadata.date_modified >= ?";
|
1720 |
5895
|
berkley
|
f1 = true;
|
1721 |
|
|
}
|
1722 |
6836
|
cjones
|
|
1723 |
6299
|
leinfelder
|
if (endTime != null) {
|
1724 |
|
|
if (!f1) {
|
1725 |
7452
|
leinfelder
|
whereClauseSql += " where systemmetadata.date_modified < ?";
|
1726 |
6836
|
cjones
|
} else {
|
1727 |
7452
|
leinfelder
|
whereClauseSql += " and systemmetadata.date_modified < ?";
|
1728 |
5917
|
berkley
|
}
|
1729 |
5895
|
berkley
|
f2 = true;
|
1730 |
|
|
}
|
1731 |
6836
|
cjones
|
|
1732 |
6337
|
leinfelder
|
if (objectFormatId != null) {
|
1733 |
6299
|
leinfelder
|
if (!f1 && !f2) {
|
1734 |
7452
|
leinfelder
|
whereClauseSql += " where object_format = ?";
|
1735 |
6836
|
cjones
|
} else {
|
1736 |
7452
|
leinfelder
|
whereClauseSql += " and object_format = ?";
|
1737 |
5917
|
berkley
|
}
|
1738 |
5895
|
berkley
|
f3 = true;
|
1739 |
|
|
}
|
1740 |
9072
|
tao
|
|
1741 |
|
|
if(identifier != null && identifier.getValue() != null && !identifier.getValue().equals("")) {
|
1742 |
|
|
if (!f1 && !f2 && !f3 ) {
|
1743 |
|
|
if(isSID) {
|
1744 |
|
|
whereClauseSql += " where series_id = ?";
|
1745 |
|
|
} else {
|
1746 |
|
|
whereClauseSql += " where guid = ?";
|
1747 |
|
|
}
|
1748 |
|
|
|
1749 |
|
|
} else {
|
1750 |
|
|
if(isSID) {
|
1751 |
|
|
whereClauseSql += " and series_id = ?";
|
1752 |
|
|
} else {
|
1753 |
|
|
whereClauseSql += " and guid = ?";
|
1754 |
|
|
}
|
1755 |
|
|
}
|
1756 |
|
|
f4 = true;
|
1757 |
|
|
}
|
1758 |
6836
|
cjones
|
|
1759 |
9249
|
tao
|
/*if (!replicaStatus) {
|
1760 |
7030
|
cjones
|
String currentNodeId = PropertyService.getInstance().getProperty("dataone.nodeId");
|
1761 |
9072
|
tao
|
if (!f1 && !f2 && !f3 && !f4) {
|
1762 |
7462
|
leinfelder
|
whereClauseSql += " where authoritive_member_node = '" +
|
1763 |
6836
|
cjones
|
currentNodeId.trim() + "'";
|
1764 |
|
|
} else {
|
1765 |
7462
|
leinfelder
|
whereClauseSql += " and authoritive_member_node = '" +
|
1766 |
6836
|
cjones
|
currentNodeId.trim() + "'";
|
1767 |
5917
|
berkley
|
}
|
1768 |
9249
|
tao
|
}*/
|
1769 |
|
|
|
1770 |
|
|
if (nodeId != null && nodeId.getValue() != null && !nodeId.getValue().trim().equals("")) {
|
1771 |
|
|
if (!f1 && !f2 && !f3 && !f4) {
|
1772 |
|
|
whereClauseSql += " where authoritive_member_node = '" +
|
1773 |
|
|
nodeId.getValue().trim() + "'";
|
1774 |
|
|
} else {
|
1775 |
|
|
whereClauseSql += " and authoritive_member_node = '" +
|
1776 |
|
|
nodeId.getValue().trim() + "'";
|
1777 |
|
|
}
|
1778 |
5895
|
berkley
|
}
|
1779 |
9072
|
tao
|
|
1780 |
|
|
|
1781 |
7452
|
leinfelder
|
// connection
|
1782 |
5943
|
berkley
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.querySystemMetadata");
|
1783 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1784 |
6836
|
cjones
|
|
1785 |
7452
|
leinfelder
|
// the field query
|
1786 |
|
|
String orderBySql = " order by guid ";
|
1787 |
|
|
String fieldQuery = fieldSql + whereClauseSql + orderBySql;
|
1788 |
|
|
String finalQuery = DatabaseService.getInstance().getDBAdapter().getPagedQuery(fieldQuery, start, count);
|
1789 |
|
|
PreparedStatement fieldStmt = dbConn.prepareStatement(finalQuery);
|
1790 |
|
|
|
1791 |
|
|
// construct the count query and statment
|
1792 |
|
|
String countQuery = countSql + whereClauseSql;
|
1793 |
|
|
PreparedStatement countStmt = dbConn.prepareStatement(countQuery);
|
1794 |
|
|
|
1795 |
9072
|
tao
|
if (f1 && f2 && f3 && f4) {
|
1796 |
7452
|
leinfelder
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1797 |
|
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1798 |
|
|
fieldStmt.setString(3, objectFormatId.getValue());
|
1799 |
9072
|
tao
|
fieldStmt.setString(4, identifier.getValue());
|
1800 |
7452
|
leinfelder
|
// count
|
1801 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1802 |
|
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1803 |
|
|
countStmt.setString(3, objectFormatId.getValue());
|
1804 |
9072
|
tao
|
countStmt.setString(4, identifier.getValue());
|
1805 |
|
|
} if (f1 && f2 && f3 && !f4) {
|
1806 |
7452
|
leinfelder
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1807 |
|
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1808 |
9072
|
tao
|
fieldStmt.setString(3, objectFormatId.getValue());
|
1809 |
7452
|
leinfelder
|
// count
|
1810 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1811 |
|
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1812 |
9072
|
tao
|
countStmt.setString(3, objectFormatId.getValue());
|
1813 |
|
|
} else if (f1 && f2 && !f3 && f4) {
|
1814 |
7452
|
leinfelder
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1815 |
9072
|
tao
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1816 |
|
|
fieldStmt.setString(3, identifier.getValue());
|
1817 |
|
|
// count
|
1818 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1819 |
|
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1820 |
|
|
countStmt.setString(3, identifier.getValue());
|
1821 |
|
|
} else if (f1 && f2 && !f3 && !f4) {
|
1822 |
|
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1823 |
|
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1824 |
|
|
// count
|
1825 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1826 |
|
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1827 |
|
|
} else if (f1 && !f2 && f3 && f4) {
|
1828 |
|
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1829 |
7452
|
leinfelder
|
fieldStmt.setString(2, objectFormatId.getValue());
|
1830 |
9072
|
tao
|
fieldStmt.setString(3, identifier.getValue());
|
1831 |
7452
|
leinfelder
|
// count
|
1832 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1833 |
|
|
countStmt.setString(2, objectFormatId.getValue());
|
1834 |
9072
|
tao
|
countStmt.setString(3, identifier.getValue());
|
1835 |
|
|
} else if (f1 && !f2 && f3 && !f4) {
|
1836 |
7452
|
leinfelder
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1837 |
9072
|
tao
|
fieldStmt.setString(2, objectFormatId.getValue());
|
1838 |
7452
|
leinfelder
|
// count
|
1839 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1840 |
9072
|
tao
|
countStmt.setString(2, objectFormatId.getValue());
|
1841 |
|
|
} else if (f1 && !f2 && !f3 && f4) {
|
1842 |
|
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1843 |
|
|
fieldStmt.setString(2, identifier.getValue());
|
1844 |
|
|
// count
|
1845 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1846 |
|
|
countStmt.setString(2, identifier.getValue());
|
1847 |
|
|
} else if (f1 && !f2 && !f3 && !f4) {
|
1848 |
|
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1849 |
|
|
// count
|
1850 |
|
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1851 |
|
|
} else if (!f1 && f2 && f3 && f4) {
|
1852 |
7452
|
leinfelder
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1853 |
|
|
fieldStmt.setString(2, objectFormatId.getValue());
|
1854 |
9072
|
tao
|
fieldStmt.setString(3, identifier.getValue());
|
1855 |
7452
|
leinfelder
|
// count
|
1856 |
|
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1857 |
|
|
countStmt.setString(2, objectFormatId.getValue());
|
1858 |
9072
|
tao
|
countStmt.setString(3, identifier.getValue());
|
1859 |
|
|
} else if (!f1 && f2 && f3 && !f4) {
|
1860 |
|
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1861 |
|
|
fieldStmt.setString(2, objectFormatId.getValue());
|
1862 |
|
|
// count
|
1863 |
|
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1864 |
|
|
countStmt.setString(2, objectFormatId.getValue());
|
1865 |
|
|
} else if (!f1 && !f2 && f3 && f4) {
|
1866 |
7452
|
leinfelder
|
fieldStmt.setString(1, objectFormatId.getValue());
|
1867 |
9072
|
tao
|
fieldStmt.setString(2, identifier.getValue());
|
1868 |
7452
|
leinfelder
|
// count
|
1869 |
|
|
countStmt.setString(1, objectFormatId.getValue());
|
1870 |
9072
|
tao
|
countStmt.setString(2, identifier.getValue());
|
1871 |
|
|
} else if (!f1 && !f2 && f3 && !f4) {
|
1872 |
|
|
fieldStmt.setString(1, objectFormatId.getValue());
|
1873 |
|
|
// count
|
1874 |
|
|
countStmt.setString(1, objectFormatId.getValue());
|
1875 |
|
|
} else if (!f1 && f2 && !f3 && f4) {
|
1876 |
7452
|
leinfelder
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1877 |
9072
|
tao
|
fieldStmt.setString(2, identifier.getValue());
|
1878 |
7452
|
leinfelder
|
// count
|
1879 |
|
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1880 |
9072
|
tao
|
countStmt.setString(2, identifier.getValue());
|
1881 |
|
|
} else if (!f1 && f2 && !f3 && !f4) {
|
1882 |
|
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1883 |
|
|
// count
|
1884 |
|
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1885 |
|
|
} else if (!f1 && !f2 && !f3 && f4) {
|
1886 |
|
|
fieldStmt.setString(1, identifier.getValue());
|
1887 |
|
|
// count
|
1888 |
|
|
countStmt.setString(1, identifier.getValue());
|
1889 |
|
|
} else if (!f1 && !f2 && !f3 && !f4) {
|
1890 |
|
|
//do nothing
|
1891 |
5895
|
berkley
|
}
|
1892 |
6836
|
cjones
|
|
1893 |
7461
|
leinfelder
|
logMetacat.debug("list objects fieldStmt: " + fieldStmt.toString());
|
1894 |
|
|
|
1895 |
|
|
logMetacat.debug("list objects countStmt: " + countStmt.toString());
|
1896 |
|
|
|
1897 |
7452
|
leinfelder
|
// get the total object count no matter what
|
1898 |
|
|
int total = 0;
|
1899 |
|
|
ResultSet totalResult = countStmt.executeQuery();
|
1900 |
|
|
if (totalResult.next()) {
|
1901 |
|
|
total = totalResult.getInt(1);
|
1902 |
5895
|
berkley
|
}
|
1903 |
7438
|
leinfelder
|
|
1904 |
7461
|
leinfelder
|
logMetacat.debug("list objects total: " + total);
|
1905 |
|
|
|
1906 |
7452
|
leinfelder
|
// set the totals
|
1907 |
|
|
ol.setStart(start);
|
1908 |
|
|
ol.setCount(count);
|
1909 |
|
|
ol.setTotal(total);
|
1910 |
|
|
|
1911 |
|
|
// retrieve the actual records if requested
|
1912 |
|
|
if (count != 0) {
|
1913 |
|
|
|
1914 |
|
|
ResultSet rs = fieldStmt.executeQuery();
|
1915 |
7410
|
leinfelder
|
while (rs.next()) {
|
1916 |
7438
|
leinfelder
|
|
1917 |
7410
|
leinfelder
|
String guid = rs.getString(1);
|
1918 |
7461
|
leinfelder
|
logMetacat.debug("query found object with guid " + guid);
|
1919 |
7410
|
leinfelder
|
// Timestamp dateUploaded = rs.getTimestamp(2);
|
1920 |
|
|
// String rightsHolder = rs.getString(3);
|
1921 |
|
|
String checksum = rs.getString(4);
|
1922 |
|
|
String checksumAlgorithm = rs.getString(5);
|
1923 |
|
|
// String originMemberNode = rs.getString(6);
|
1924 |
|
|
// String authoritiveMemberNode = rs.getString(7);
|
1925 |
|
|
Timestamp dateModified = rs.getTimestamp(8);
|
1926 |
|
|
// String submitter = rs.getString(9);
|
1927 |
|
|
String fmtidStr = rs.getString(10);
|
1928 |
|
|
String sz = rs.getString(11);
|
1929 |
|
|
BigInteger size = new BigInteger("0");
|
1930 |
|
|
|
1931 |
|
|
if (sz != null && !sz.trim().equals("")) {
|
1932 |
|
|
size = new BigInteger(rs.getString(11));
|
1933 |
|
|
}
|
1934 |
|
|
|
1935 |
|
|
ObjectInfo oi = new ObjectInfo();
|
1936 |
|
|
|
1937 |
|
|
Identifier id = new Identifier();
|
1938 |
|
|
id.setValue(guid);
|
1939 |
|
|
oi.setIdentifier(id);
|
1940 |
|
|
|
1941 |
|
|
if (dateModified != null) {
|
1942 |
|
|
oi.setDateSysMetadataModified(dateModified);
|
1943 |
|
|
}
|
1944 |
|
|
|
1945 |
|
|
Checksum cs = new Checksum();
|
1946 |
|
|
cs.setValue(checksum);
|
1947 |
|
|
try {
|
1948 |
|
|
// cs.setAlgorithm(ChecksumAlgorithm.valueOf(checksumAlgorithm));
|
1949 |
|
|
cs.setAlgorithm(checksumAlgorithm);
|
1950 |
|
|
} catch (Exception e) {
|
1951 |
|
|
logMetacat.error("could not parse checksum algorithm", e);
|
1952 |
|
|
continue;
|
1953 |
|
|
}
|
1954 |
|
|
oi.setChecksum(cs);
|
1955 |
|
|
|
1956 |
|
|
// set the format type
|
1957 |
|
|
ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier();
|
1958 |
|
|
fmtid.setValue(fmtidStr);
|
1959 |
|
|
oi.setFormatId(fmtid);
|
1960 |
|
|
|
1961 |
|
|
oi.setSize(size);
|
1962 |
|
|
|
1963 |
7438
|
leinfelder
|
ol.addObjectInfo(oi);
|
1964 |
|
|
|
1965 |
7410
|
leinfelder
|
}
|
1966 |
7452
|
leinfelder
|
|
1967 |
7461
|
leinfelder
|
logMetacat.debug("list objects count: " + ol.sizeObjectInfoList());
|
1968 |
|
|
|
1969 |
7452
|
leinfelder
|
// set the actual count retrieved
|
1970 |
|
|
ol.setCount(ol.sizeObjectInfoList());
|
1971 |
7410
|
leinfelder
|
|
1972 |
|
|
}
|
1973 |
|
|
|
1974 |
5895
|
berkley
|
}
|
1975 |
6836
|
cjones
|
|
1976 |
6299
|
leinfelder
|
finally {
|
1977 |
5943
|
berkley
|
// Return database connection to the pool
|
1978 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1979 |
|
|
}
|
1980 |
6836
|
cjones
|
|
1981 |
5895
|
berkley
|
return ol;
|
1982 |
|
|
}
|
1983 |
|
|
|
1984 |
|
|
/**
|
1985 |
6099
|
leinfelder
|
* create a mapping in the identifier table
|
1986 |
5377
|
berkley
|
* @param guid
|
1987 |
|
|
* @param localId
|
1988 |
|
|
*/
|
1989 |
6099
|
leinfelder
|
public void createMapping(String guid, String localId)
|
1990 |
5453
|
berkley
|
{
|
1991 |
5334
|
berkley
|
|
1992 |
|
|
int serialNumber = -1;
|
1993 |
5333
|
berkley
|
DBConnection dbConn = null;
|
1994 |
|
|
try {
|
1995 |
|
|
|
1996 |
|
|
// Parse the localId into scope and rev parts
|
1997 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
1998 |
|
|
String docid = acc.getDocid();
|
1999 |
5344
|
berkley
|
int rev = 1;
|
2000 |
6099
|
leinfelder
|
if (acc.getRev() != null) {
|
2001 |
5344
|
berkley
|
rev = (new Integer(acc.getRev()).intValue());
|
2002 |
|
|
}
|
2003 |
5333
|
berkley
|
|
2004 |
|
|
// Get a database connection from the pool
|
2005 |
6099
|
leinfelder
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
2006 |
5333
|
berkley
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
2007 |
|
|
|
2008 |
|
|
// Execute the insert statement
|
2009 |
6099
|
leinfelder
|
String query = "insert into " + TYPE_IDENTIFIER + " (guid, docid, rev) values (?, ?, ?)";
|
2010 |
5333
|
berkley
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
2011 |
|
|
stmt.setString(1, guid);
|
2012 |
|
|
stmt.setString(2, docid);
|
2013 |
|
|
stmt.setInt(3, rev);
|
2014 |
6099
|
leinfelder
|
logMetacat.debug("mapping query: " + stmt.toString());
|
2015 |
5333
|
berkley
|
int rows = stmt.executeUpdate();
|
2016 |
|
|
|
2017 |
|
|
stmt.close();
|
2018 |
|
|
} catch (SQLException e) {
|
2019 |
5344
|
berkley
|
e.printStackTrace();
|
2020 |
6099
|
leinfelder
|
logMetacat.error("createGenericMapping: SQL error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
2021 |
5333
|
berkley
|
+ e.getMessage());
|
2022 |
|
|
} catch (NumberFormatException e) {
|
2023 |
5344
|
berkley
|
e.printStackTrace();
|
2024 |
6099
|
leinfelder
|
logMetacat.error("createGenericMapping: NumberFormat error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
2025 |
5333
|
berkley
|
+ e.getMessage());
|
2026 |
|
|
} catch (AccessionNumberException e) {
|
2027 |
5344
|
berkley
|
e.printStackTrace();
|
2028 |
6099
|
leinfelder
|
logMetacat.error("createGenericMapping: AccessionNumber error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
2029 |
5333
|
berkley
|
+ e.getMessage());
|
2030 |
|
|
} finally {
|
2031 |
|
|
// Return database connection to the pool
|
2032 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
2033 |
|
|
}
|
2034 |
|
|
}
|
2035 |
6099
|
leinfelder
|
|
2036 |
|
|
/**
|
2037 |
7017
|
leinfelder
|
* remove a mapping in the identifier table
|
2038 |
|
|
* @param guid
|
2039 |
|
|
* @param localId
|
2040 |
|
|
*/
|
2041 |
|
|
public void removeMapping(String guid, String localId)
|
2042 |
|
|
{
|
2043 |
|
|
|
2044 |
|
|
int serialNumber = -1;
|
2045 |
|
|
DBConnection dbConn = null;
|
2046 |
|
|
try {
|
2047 |
|
|
|
2048 |
|
|
// Parse the localId into scope and rev parts
|
2049 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
2050 |
|
|
String docid = acc.getDocid();
|
2051 |
|
|
int rev = 1;
|
2052 |
|
|
if (acc.getRev() != null) {
|
2053 |
|
|
rev = (new Integer(acc.getRev()).intValue());
|
2054 |
|
|
}
|
2055 |
|
|
|
2056 |
|
|
// Get a database connection from the pool
|
2057 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.removeMapping");
|
2058 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
2059 |
|
|
|
2060 |
|
|
// Execute the insert statement
|
2061 |
|
|
String query = "DELETE FROM " + TYPE_IDENTIFIER + " WHERE guid = ? AND docid = ? AND rev = ?";
|
2062 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
2063 |
|
|
stmt.setString(1, guid);
|
2064 |
|
|
stmt.setString(2, docid);
|
2065 |
|
|
stmt.setInt(3, rev);
|
2066 |
|
|
logMetacat.debug("remove mapping query: " + stmt.toString());
|
2067 |
|
|
int rows = stmt.executeUpdate();
|
2068 |
|
|
|
2069 |
|
|
stmt.close();
|
2070 |
|
|
} catch (SQLException e) {
|
2071 |
|
|
e.printStackTrace();
|
2072 |
|
|
logMetacat.error("removeMapping: SQL error while removing a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
2073 |
|
|
+ e.getMessage());
|
2074 |
|
|
} catch (NumberFormatException e) {
|
2075 |
|
|
e.printStackTrace();
|
2076 |
|
|
logMetacat.error("removeMapping: NumberFormat error while removing a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
2077 |
|
|
+ e.getMessage());
|
2078 |
|
|
} catch (AccessionNumberException e) {
|
2079 |
|
|
e.printStackTrace();
|
2080 |
|
|
logMetacat.error("removeMapping: AccessionNumber error while removing a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
2081 |
|
|
+ e.getMessage());
|
2082 |
|
|
} finally {
|
2083 |
|
|
// Return database connection to the pool
|
2084 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
2085 |
|
|
}
|
2086 |
|
|
}
|
2087 |
|
|
|
2088 |
|
|
/**
|
2089 |
6099
|
leinfelder
|
* create the systemmetadata record
|
2090 |
|
|
* @param guid
|
2091 |
7188
|
leinfelder
|
* @param dbConn
|
2092 |
|
|
* @throws SQLException
|
2093 |
6099
|
leinfelder
|
*/
|
2094 |
7188
|
leinfelder
|
private void insertSystemMetadata(String guid, DBConnection dbConn) throws SQLException
|
2095 |
6099
|
leinfelder
|
{
|
2096 |
|
|
|
2097 |
7188
|
leinfelder
|
// Execute the insert statement
|
2098 |
|
|
String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid) values (?)";
|
2099 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
2100 |
|
|
stmt.setString(1, guid);
|
2101 |
|
|
logMetacat.debug("system metadata query: " + stmt.toString());
|
2102 |
|
|
int rows = stmt.executeUpdate();
|
2103 |
6099
|
leinfelder
|
|
2104 |
7188
|
leinfelder
|
stmt.close();
|
2105 |
|
|
|
2106 |
6099
|
leinfelder
|
}
|
2107 |
6277
|
leinfelder
|
|
2108 |
8852
|
tao
|
public boolean deleteSystemMetadata(String guid)
|
2109 |
6277
|
leinfelder
|
{
|
2110 |
8852
|
tao
|
boolean success = false;
|
2111 |
6277
|
leinfelder
|
int serialNumber = -1;
|
2112 |
|
|
DBConnection dbConn = null;
|
2113 |
6648
|
leinfelder
|
String query = null;
|
2114 |
|
|
PreparedStatement stmt = null;
|
2115 |
|
|
int rows = 0;
|
2116 |
6277
|
leinfelder
|
try {
|
2117 |
|
|
|
2118 |
8852
|
tao
|
// Get a database connection from the pool
|
2119 |
6648
|
leinfelder
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.deleteSystemMetadata");
|
2120 |
6277
|
leinfelder
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
2121 |
8852
|
tao
|
dbConn.setAutoCommit(false);
|
2122 |
|
|
|
2123 |
7392
|
leinfelder
|
// remove the smReplicationPolicy
|
2124 |
|
|
query = "delete from smReplicationPolicy " +
|
2125 |
6648
|
leinfelder
|
"where guid = ?";
|
2126 |
|
|
stmt = dbConn.prepareStatement(query);
|
2127 |
|
|
stmt.setString(1, guid);
|
2128 |
7392
|
leinfelder
|
logMetacat.debug("delete smReplicationPolicy: " + stmt.toString());
|
2129 |
6648
|
leinfelder
|
rows = stmt.executeUpdate();
|
2130 |
|
|
stmt.close();
|
2131 |
|
|
|
2132 |
7392
|
leinfelder
|
// remove the smReplicationStatus
|
2133 |
|
|
query = "delete from smReplicationStatus " +
|
2134 |
6648
|
leinfelder
|
"where guid = ?";
|
2135 |
|
|
stmt = dbConn.prepareStatement(query);
|
2136 |
|
|
stmt.setString(1, guid);
|
2137 |
7392
|
leinfelder
|
logMetacat.debug("delete smReplicationStatus: " + stmt.toString());
|
2138 |
6648
|
leinfelder
|
rows = stmt.executeUpdate();
|
2139 |
|
|
stmt.close();
|
2140 |
|
|
|
2141 |
9230
|
tao
|
// remove the smmediatypeproperties
|
2142 |
|
|
query = "delete from smmediatypeproperties " +
|
2143 |
|
|
"where guid = ?";
|
2144 |
|
|
stmt = dbConn.prepareStatement(query);
|
2145 |
|
|
stmt.setString(1, guid);
|
2146 |
|
|
logMetacat.debug("delete smmediatypeproperties: " + stmt.toString());
|
2147 |
|
|
rows = stmt.executeUpdate();
|
2148 |
|
|
stmt.close();
|
2149 |
|
|
|
2150 |
8852
|
tao
|
// remove main system metadata entry
|
2151 |
|
|
query = "delete from " + TYPE_SYSTEM_METADATA + " where guid = ? ";
|
2152 |
|
|
stmt = dbConn.prepareStatement(query);
|
2153 |
|
|
stmt.setString(1, guid);
|
2154 |
|
|
logMetacat.debug("delete system metadata: " + stmt.toString());
|
2155 |
|
|
rows = stmt.executeUpdate();
|
2156 |
|
|
stmt.close();
|
2157 |
|
|
|
2158 |
|
|
dbConn.commit();
|
2159 |
|
|
dbConn.setAutoCommit(true);
|
2160 |
|
|
success = true;
|
2161 |
6744
|
leinfelder
|
// TODO: remove the access?
|
2162 |
6648
|
leinfelder
|
// Metacat keeps "deleted" documents so we should not remove access rules.
|
2163 |
|
|
|
2164 |
6277
|
leinfelder
|
} catch (Exception e) {
|
2165 |
|
|
e.printStackTrace();
|
2166 |
|
|
logMetacat.error("Error while deleting " + TYPE_SYSTEM_METADATA + " record: " + guid, e );
|
2167 |
6648
|
leinfelder
|
try {
|
2168 |
|
|
dbConn.rollback();
|
2169 |
|
|
} catch (SQLException sqle) {
|
2170 |
|
|
logMetacat.error("Error while rolling back delete for record: " + guid, sqle );
|
2171 |
|
|
}
|
2172 |
6277
|
leinfelder
|
} finally {
|
2173 |
|
|
// Return database connection to the pool
|
2174 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
2175 |
|
|
}
|
2176 |
8852
|
tao
|
return success;
|
2177 |
6277
|
leinfelder
|
}
|
2178 |
6862
|
leinfelder
|
|
2179 |
|
|
public void updateAuthoritativeMemberNodeId(String existingMemberNodeId, String newMemberNodeId)
|
2180 |
|
|
{
|
2181 |
|
|
DBConnection dbConn = null;
|
2182 |
|
|
int serialNumber = -1;
|
2183 |
|
|
|
2184 |
|
|
try {
|
2185 |
|
|
// Get a database connection from the pool
|
2186 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.updateAuthoritativeMemberNodeId");
|
2187 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
2188 |
|
|
|
2189 |
|
|
// Execute the insert statement
|
2190 |
|
|
String query = "update " + TYPE_SYSTEM_METADATA +
|
2191 |
|
|
" set authoritive_member_node = ? " +
|
2192 |
|
|
" where authoritive_member_node = ?";
|
2193 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
2194 |
|
|
|
2195 |
|
|
//data values
|
2196 |
|
|
stmt.setString(1, newMemberNodeId);
|
2197 |
|
|
stmt.setString(2, existingMemberNodeId);
|
2198 |
|
|
|
2199 |
|
|
logMetacat.debug("stmt: " + stmt.toString());
|
2200 |
|
|
//execute
|
2201 |
|
|
int rows = stmt.executeUpdate();
|
2202 |
|
|
|
2203 |
|
|
stmt.close();
|
2204 |
|
|
} catch (SQLException e) {
|
2205 |
|
|
e.printStackTrace();
|
2206 |
|
|
logMetacat.error("updateSystemMetadataFields: SQL error while updating system metadata: "
|
2207 |
|
|
+ e.getMessage());
|
2208 |
|
|
} catch (NumberFormatException e) {
|
2209 |
|
|
e.printStackTrace();
|
2210 |
|
|
logMetacat.error("updateSystemMetadataFields: NumberFormat error while updating system metadata: "
|
2211 |
|
|
+ e.getMessage());
|
2212 |
|
|
} finally {
|
2213 |
|
|
// Return database connection to the pool
|
2214 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
2215 |
|
|
}
|
2216 |
|
|
}
|
2217 |
5282
|
jones
|
}
|