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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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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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30 |
5895
|
berkley
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import java.sql.Timestamp;
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31 |
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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6124
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cjones
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import org.dataone.client.ObjectFormatCache;
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import org.dataone.service.exceptions.NotFound;
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40 |
6108
|
leinfelder
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import org.dataone.service.types.AccessPolicy;
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41 |
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import org.dataone.service.types.AccessRule;
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5895
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berkley
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.ChecksumAlgorithm;
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6107
|
leinfelder
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import org.dataone.service.types.Identifier;
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45 |
6097
|
leinfelder
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import org.dataone.service.types.NodeReference;
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46 |
5895
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berkley
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import org.dataone.service.types.ObjectFormat;
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6124
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cjones
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import org.dataone.service.types.ObjectFormatIdentifier;
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5895
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berkley
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import org.dataone.service.types.ObjectInfo;
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import org.dataone.service.types.ObjectList;
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6108
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leinfelder
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import org.dataone.service.types.Permission;
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51 |
6107
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leinfelder
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import org.dataone.service.types.Replica;
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import org.dataone.service.types.ReplicationPolicy;
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import org.dataone.service.types.ReplicationStatus;
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6097
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leinfelder
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import org.dataone.service.types.Subject;
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5887
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berkley
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import org.dataone.service.types.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.AccessControlInterface;
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import edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess;
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import edu.ucsb.nceas.metacat.accesscontrol.XMLAccessDAO;
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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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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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5286
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jones
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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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
|
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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106 |
6097
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leinfelder
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public SystemMetadata asSystemMetadata(Date dateUploaded, String rightsHolder,
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String checksum, String checksumAlgorithm, String originMemberNode,
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String authoritativeMemberNode, Date dateModified, String submitter,
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String guid, String objectFormat, long size) {
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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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checksumObject.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));
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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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6124
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cjones
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try {
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sysMeta.setObjectFormat(ObjectFormatCache.getFormat(objectFormat));
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} catch (NotFound nfe) {
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logMetacat.error("The objectFormat " + objectFormat +
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" is not registered. Setting the default format.");
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ObjectFormat of = new ObjectFormat();
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ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier();
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fmtid.setValue("application/octet-stream");
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of.setFmtid(fmtid);
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of.setFormatName("Octet Stream");
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sysMeta.setObjectFormat(of);
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}
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6097
|
leinfelder
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sysMeta.setSize(size);
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return sysMeta;
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}
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150 |
5282
|
jones
|
/**
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151 |
5895
|
berkley
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* return a hash of all of the info that is in the systemmetadata table
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* @param localId
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* @return
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*/
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public Hashtable<String, String> getSystemMetadataInfo(String localId)
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throws McdbDocNotFoundException
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{
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try
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{
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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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Hashtable<String, String> h = new Hashtable<String, String>();
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168 |
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String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
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5944
|
berkley
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"origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size " +
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170 |
5895
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berkley
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"from systemmetadata where docid = ?";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try
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{
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");
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serialNumber = dbConn.getCheckOutSerialNumber();
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// Execute the insert statement
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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stmt.setString(1, localId);
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ResultSet rs = stmt.executeQuery();
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if (rs.next())
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{
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185 |
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String guid = rs.getString(1);
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Timestamp dateUploaded = rs.getTimestamp(2);
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String rightsHolder = rs.getString(3);
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String checksum = rs.getString(4);
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String checksumAlgorithm = rs.getString(5);
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190 |
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String originMemberNode = rs.getString(6);
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String authoritativeMemberNode = rs.getString(7);
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192 |
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Timestamp dateModified = rs.getTimestamp(8);
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193 |
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String submitter = rs.getString(9);
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194 |
5917
|
berkley
|
String objectFormat = rs.getString(10);
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195 |
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long size = new Long(rs.getString(11)).longValue();
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196 |
5895
|
berkley
|
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197 |
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h.put("guid", guid);
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198 |
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h.put("date_uploaded", new Long(dateUploaded.getTime()).toString());
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199 |
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h.put("rights_holder", rightsHolder);
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200 |
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h.put("checksum", checksum);
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201 |
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h.put("checksum_algorithm", checksumAlgorithm);
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202 |
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h.put("origin_member_node", originMemberNode);
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203 |
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h.put("authoritative_member_node", authoritativeMemberNode);
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204 |
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h.put("date_modified", new Long(dateModified.getTime()).toString());
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205 |
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h.put("submitter", submitter);
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206 |
5917
|
berkley
|
h.put("object_format", objectFormat);
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207 |
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h.put("size", new Long(size).toString());
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208 |
5895
|
berkley
|
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209 |
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stmt.close();
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210 |
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}
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211 |
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else
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212 |
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{
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213 |
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stmt.close();
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214 |
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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215 |
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throw new McdbDocNotFoundException("2Could not find document " + localId);
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216 |
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}
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217 |
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218 |
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}
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219 |
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catch (SQLException e)
|
220 |
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{
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221 |
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e.printStackTrace();
|
222 |
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logMetacat.error("Error while getting system metadata info for localid " + localId + " : "
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223 |
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+ e.getMessage());
|
224 |
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}
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225 |
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finally
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226 |
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{
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227 |
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// Return database connection to the pool
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228 |
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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229 |
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}
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230 |
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return h;
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231 |
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}
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232 |
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233 |
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/**
|
234 |
6097
|
leinfelder
|
* return a hash of all of the info that is in the systemmetadata table
|
235 |
6099
|
leinfelder
|
* @param guid
|
236 |
6097
|
leinfelder
|
* @return
|
237 |
6108
|
leinfelder
|
* @throws McdbDocNotFoundException
|
238 |
6097
|
leinfelder
|
*/
|
239 |
6099
|
leinfelder
|
public SystemMetadata getSystemMetadata(String guid)
|
240 |
6097
|
leinfelder
|
throws McdbDocNotFoundException
|
241 |
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{
|
242 |
6099
|
leinfelder
|
|
243 |
6097
|
leinfelder
|
SystemMetadata sysMeta = new SystemMetadata();
|
244 |
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String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
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245 |
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"origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size " +
|
246 |
6099
|
leinfelder
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"from systemmetadata where guid = ?";
|
247 |
6097
|
leinfelder
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DBConnection dbConn = null;
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248 |
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int serialNumber = -1;
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249 |
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try
|
250 |
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{
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251 |
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// Get a database connection from the pool
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252 |
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getSystemMetadata");
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253 |
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serialNumber = dbConn.getCheckOutSerialNumber();
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254 |
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255 |
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// Execute the statement
|
256 |
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PreparedStatement stmt = dbConn.prepareStatement(sql);
|
257 |
6099
|
leinfelder
|
stmt.setString(1, guid);
|
258 |
6097
|
leinfelder
|
ResultSet rs = stmt.executeQuery();
|
259 |
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if (rs.next())
|
260 |
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{
|
261 |
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Timestamp dateUploaded = rs.getTimestamp(2);
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262 |
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String rightsHolder = rs.getString(3);
|
263 |
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String checksum = rs.getString(4);
|
264 |
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String checksumAlgorithm = rs.getString(5);
|
265 |
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String originMemberNode = rs.getString(6);
|
266 |
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String authoritativeMemberNode = rs.getString(7);
|
267 |
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Timestamp dateModified = rs.getTimestamp(8);
|
268 |
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String submitter = rs.getString(9);
|
269 |
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String objectFormat = rs.getString(10);
|
270 |
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long size = new Long(rs.getString(11)).longValue();
|
271 |
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|
|
272 |
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Identifier sysMetaId = new Identifier();
|
273 |
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sysMetaId.setValue(guid);
|
274 |
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sysMeta.setIdentifier(sysMetaId);
|
275 |
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sysMeta.setDateUploaded(dateUploaded);
|
276 |
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Subject rightsHolderSubject = new Subject();
|
277 |
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rightsHolderSubject.setValue(rightsHolder);
|
278 |
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sysMeta.setRightsHolder(rightsHolderSubject);
|
279 |
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Checksum checksumObject = new Checksum();
|
280 |
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checksumObject.setValue(checksum);
|
281 |
|
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checksumObject.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));
|
282 |
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sysMeta.setChecksum(checksumObject);
|
283 |
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|
NodeReference omn = new NodeReference();
|
284 |
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omn.setValue(originMemberNode);
|
285 |
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sysMeta.setOriginMemberNode(omn);
|
286 |
|
|
NodeReference amn = new NodeReference();
|
287 |
|
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amn.setValue(authoritativeMemberNode);
|
288 |
|
|
sysMeta.setAuthoritativeMemberNode(amn);
|
289 |
|
|
sysMeta.setDateSysMetadataModified(dateModified);
|
290 |
|
|
Subject submitterSubject = new Subject();
|
291 |
|
|
submitterSubject.setValue(submitter);
|
292 |
|
|
sysMeta.setSubmitter(submitterSubject);
|
293 |
6124
|
cjones
|
try {
|
294 |
|
|
sysMeta.setObjectFormat(ObjectFormatCache.getFormat(objectFormat));
|
295 |
|
|
} catch (NotFound nfe) {
|
296 |
|
|
logMetacat.error("The objectFormat " + objectFormat +
|
297 |
|
|
" is not registered. Setting the default format.");
|
298 |
|
|
ObjectFormat of = new ObjectFormat();
|
299 |
|
|
ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier();
|
300 |
|
|
fmtid.setValue("application/octet-stream");
|
301 |
|
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of.setFmtid(fmtid);
|
302 |
|
|
of.setFormatName("Octet Stream");
|
303 |
|
|
sysMeta.setObjectFormat(of);
|
304 |
|
|
}
|
305 |
6097
|
leinfelder
|
sysMeta.setSize(size);
|
306 |
|
|
|
307 |
|
|
stmt.close();
|
308 |
|
|
}
|
309 |
|
|
else
|
310 |
|
|
{
|
311 |
|
|
stmt.close();
|
312 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
313 |
6099
|
leinfelder
|
throw new McdbDocNotFoundException("Could not find " + guid);
|
314 |
6097
|
leinfelder
|
}
|
315 |
|
|
|
316 |
|
|
}
|
317 |
|
|
catch (SQLException e)
|
318 |
|
|
{
|
319 |
|
|
e.printStackTrace();
|
320 |
6099
|
leinfelder
|
logMetacat.error("Error while getting system metadata for guid " + guid + " : "
|
321 |
6097
|
leinfelder
|
+ e.getMessage());
|
322 |
|
|
}
|
323 |
|
|
finally
|
324 |
|
|
{
|
325 |
|
|
// Return database connection to the pool
|
326 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
327 |
|
|
}
|
328 |
|
|
|
329 |
|
|
// look up provenance information
|
330 |
|
|
sysMeta.setObsoleteList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "obsoletes"));
|
331 |
|
|
sysMeta.setObsoletedByList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "obsoletedBy"));
|
332 |
|
|
sysMeta.setDescribeList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "describes"));
|
333 |
|
|
sysMeta.setDescribedByList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "describedBy"));
|
334 |
|
|
sysMeta.setDerivedFromList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "derivedFrom"));
|
335 |
|
|
|
336 |
6107
|
leinfelder
|
// look up replication policy
|
337 |
|
|
ReplicationPolicy replicationPolicy = new ReplicationPolicy();
|
338 |
|
|
replicationPolicy.setBlockedMemberNodeList(getReplicationPolicy(guid, "blocked"));
|
339 |
|
|
replicationPolicy.setPreferredMemberNodeList(getReplicationPolicy(guid, "preferred"));
|
340 |
|
|
sysMeta.setReplicationPolicy(replicationPolicy);
|
341 |
|
|
|
342 |
|
|
// look up replication status
|
343 |
|
|
sysMeta.setReplicaList(getReplicationStatus(guid));
|
344 |
6108
|
leinfelder
|
|
345 |
|
|
// look up access policy
|
346 |
|
|
try {
|
347 |
|
|
sysMeta.setAccessPolicy(getAccessPolicy(guid));
|
348 |
|
|
} catch (AccessException e) {
|
349 |
|
|
throw new McdbDocNotFoundException(e);
|
350 |
|
|
}
|
351 |
6107
|
leinfelder
|
|
352 |
6097
|
leinfelder
|
return sysMeta;
|
353 |
|
|
}
|
354 |
|
|
|
355 |
|
|
private List<Identifier> getSystemMetadataProvenance(String guid, String relationship)
|
356 |
|
|
throws McdbDocNotFoundException {
|
357 |
|
|
|
358 |
|
|
List<Identifier> identifiers = new ArrayList<Identifier>();
|
359 |
|
|
String sql = "select guid, relationship, target_guid " +
|
360 |
|
|
"from systemMetadataProvenance where guid = ? and relationship = ?";
|
361 |
6107
|
leinfelder
|
DBConnection dbConn = null;
|
362 |
|
|
int serialNumber = -1;
|
363 |
|
|
try {
|
364 |
|
|
// Get a database connection from the pool
|
365 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getSystemMetadataProvenance");
|
366 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
367 |
|
|
|
368 |
|
|
// Execute the statement
|
369 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
370 |
|
|
stmt.setString(1, guid);
|
371 |
|
|
stmt.setString(2, relationship);
|
372 |
|
|
ResultSet rs = stmt.executeQuery();
|
373 |
|
|
while (rs.next())
|
374 |
|
|
{
|
375 |
|
|
String targetGuid = rs.getString(3);
|
376 |
|
|
Identifier id = new Identifier();
|
377 |
|
|
id.setValue(targetGuid);
|
378 |
|
|
identifiers.add(id);
|
379 |
|
|
|
380 |
|
|
}
|
381 |
|
|
stmt.close();
|
382 |
|
|
|
383 |
|
|
}
|
384 |
|
|
catch (SQLException e) {
|
385 |
|
|
logMetacat.error("Error while getting system metadata provenance for guid " + guid, e);
|
386 |
|
|
}
|
387 |
|
|
finally {
|
388 |
|
|
// Return database connection to the pool
|
389 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
390 |
|
|
}
|
391 |
|
|
|
392 |
|
|
return identifiers;
|
393 |
|
|
}
|
394 |
6097
|
leinfelder
|
|
395 |
6107
|
leinfelder
|
private List<NodeReference> getReplicationPolicy(String guid, String policy)
|
396 |
|
|
throws McdbDocNotFoundException {
|
397 |
|
|
|
398 |
|
|
List<NodeReference> nodes = new ArrayList<NodeReference>();
|
399 |
|
|
String sql = "select guid, policy, member_node " +
|
400 |
|
|
"from systemMetadataReplicationPolicy where guid = ? and policy = ?";
|
401 |
|
|
DBConnection dbConn = null;
|
402 |
|
|
int serialNumber = -1;
|
403 |
|
|
try {
|
404 |
|
|
// Get a database connection from the pool
|
405 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicationPolicy");
|
406 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
407 |
|
|
|
408 |
|
|
// Execute the statement
|
409 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
410 |
|
|
stmt.setString(1, guid);
|
411 |
|
|
stmt.setString(2, policy);
|
412 |
|
|
ResultSet rs = stmt.executeQuery();
|
413 |
|
|
while (rs.next())
|
414 |
|
|
{
|
415 |
|
|
String memberNode = rs.getString(3);
|
416 |
|
|
NodeReference node = new NodeReference();
|
417 |
|
|
node.setValue(memberNode);
|
418 |
|
|
nodes.add(node);
|
419 |
|
|
|
420 |
|
|
}
|
421 |
|
|
stmt.close();
|
422 |
|
|
|
423 |
|
|
} catch (SQLException e) {
|
424 |
|
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
425 |
|
|
}
|
426 |
|
|
finally {
|
427 |
|
|
// Return database connection to the pool
|
428 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
429 |
|
|
}
|
430 |
|
|
|
431 |
|
|
return nodes;
|
432 |
|
|
}
|
433 |
6097
|
leinfelder
|
|
434 |
6107
|
leinfelder
|
private List<Replica> getReplicationStatus(String guid) throws McdbDocNotFoundException {
|
435 |
|
|
|
436 |
|
|
List<Replica> replicas = new ArrayList<Replica>();
|
437 |
|
|
String sql = "select guid, member_node, status, date_verified " +
|
438 |
|
|
"from systemMetadataReplicationStatus where guid = ?";
|
439 |
|
|
DBConnection dbConn = null;
|
440 |
|
|
int serialNumber = -1;
|
441 |
|
|
try {
|
442 |
|
|
// Get a database connection from the pool
|
443 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicas");
|
444 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
445 |
|
|
|
446 |
|
|
// Execute the statement
|
447 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
448 |
|
|
stmt.setString(1, guid);
|
449 |
|
|
ResultSet rs = stmt.executeQuery();
|
450 |
|
|
while (rs.next())
|
451 |
|
|
{
|
452 |
|
|
String memberNode = rs.getString(2);
|
453 |
|
|
String status = rs.getString(3);
|
454 |
|
|
java.sql.Date verified = rs.getDate(4);
|
455 |
|
|
|
456 |
|
|
Replica replica = new Replica();
|
457 |
|
|
NodeReference node = new NodeReference();
|
458 |
|
|
node.setValue(memberNode);
|
459 |
|
|
replica.setReplicaMemberNode(node);
|
460 |
|
|
replica.setReplicationStatus(ReplicationStatus.convert(status));
|
461 |
|
|
replica.setReplicaVerified(new Date(verified.getTime()));
|
462 |
|
|
replicas.add(replica);
|
463 |
|
|
}
|
464 |
|
|
stmt.close();
|
465 |
|
|
|
466 |
|
|
} catch (SQLException e) {
|
467 |
|
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
468 |
|
|
}
|
469 |
|
|
finally {
|
470 |
|
|
// Return database connection to the pool
|
471 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
472 |
|
|
}
|
473 |
|
|
|
474 |
|
|
return replicas;
|
475 |
|
|
}
|
476 |
|
|
|
477 |
6097
|
leinfelder
|
/**
|
478 |
5378
|
berkley
|
* return information on the document with localId. These are the fields
|
479 |
|
|
* from the xml_documents table. They can be used to contstruct metadata
|
480 |
|
|
* about the object that is stored.
|
481 |
|
|
* @param localId
|
482 |
|
|
* @return
|
483 |
|
|
* @throws McdbDocNotFoundException
|
484 |
|
|
*/
|
485 |
5441
|
berkley
|
public Hashtable<String, Object> getDocumentInfo(String localId)
|
486 |
5378
|
berkley
|
throws McdbDocNotFoundException
|
487 |
|
|
{
|
488 |
5798
|
berkley
|
try
|
489 |
|
|
{
|
490 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NONE");
|
491 |
|
|
localId = acc.getDocid();
|
492 |
|
|
}
|
493 |
|
|
catch(Exception e)
|
494 |
|
|
{
|
495 |
|
|
//do nothing. just try the localId as it is
|
496 |
|
|
}
|
497 |
5441
|
berkley
|
Hashtable<String, Object> h = new Hashtable<String, Object>();
|
498 |
5378
|
berkley
|
String sql = "select docname, doctype, user_owner, user_updated, " +
|
499 |
|
|
"server_location, rev, date_created, date_updated from " +
|
500 |
|
|
"xml_documents where docid like '" + localId + "'";
|
501 |
|
|
DBConnection dbConn = null;
|
502 |
|
|
int serialNumber = -1;
|
503 |
|
|
try
|
504 |
|
|
{
|
505 |
|
|
// Get a database connection from the pool
|
506 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");
|
507 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
508 |
|
|
|
509 |
|
|
// Execute the insert statement
|
510 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
511 |
|
|
ResultSet rs = stmt.executeQuery();
|
512 |
|
|
if (rs.next())
|
513 |
|
|
{
|
514 |
|
|
String docname = rs.getString(1);
|
515 |
|
|
String doctype = rs.getString(2);
|
516 |
|
|
String user_owner = rs.getString(3);
|
517 |
|
|
String user_updated = rs.getString(4);
|
518 |
|
|
String server_location = rs.getString(5);
|
519 |
|
|
int rev = rs.getInt(6);
|
520 |
|
|
String date_created = rs.getString(7);
|
521 |
|
|
String date_updated = rs.getString(8);
|
522 |
6042
|
cjones
|
h.put("docid", localId);
|
523 |
5378
|
berkley
|
h.put("docname", docname);
|
524 |
|
|
h.put("doctype", doctype);
|
525 |
|
|
h.put("user_owner", user_owner);
|
526 |
|
|
h.put("user_updated", user_updated);
|
527 |
|
|
h.put("server_location", server_location);
|
528 |
|
|
h.put("rev", new Integer(rev).toString());
|
529 |
|
|
h.put("date_created", date_created);
|
530 |
|
|
h.put("date_updated", date_updated);
|
531 |
|
|
|
532 |
|
|
stmt.close();
|
533 |
|
|
}
|
534 |
|
|
else
|
535 |
|
|
{
|
536 |
|
|
stmt.close();
|
537 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
538 |
5798
|
berkley
|
throw new McdbDocNotFoundException("2Could not find document " + localId);
|
539 |
5378
|
berkley
|
}
|
540 |
5441
|
berkley
|
|
541 |
5444
|
berkley
|
String sql2 = "select principal_name, permission, perm_type, perm_order from xml_access " +
|
542 |
5441
|
berkley
|
"where docid like '" + localId + "'";
|
543 |
6099
|
leinfelder
|
logMetacat.debug("executing sql: " + sql2);
|
544 |
5441
|
berkley
|
PreparedStatement stmt2 = dbConn.prepareStatement(sql2);
|
545 |
5442
|
berkley
|
rs = stmt2.executeQuery();
|
546 |
5441
|
berkley
|
Vector accessVector = new Vector();
|
547 |
5445
|
berkley
|
while(rs.next())
|
548 |
5441
|
berkley
|
{
|
549 |
|
|
Hashtable accessHash = new Hashtable();
|
550 |
|
|
String principal_name = rs.getString(1);
|
551 |
|
|
String permission = rs.getString(2);
|
552 |
|
|
String permissionType = rs.getString(3);
|
553 |
|
|
String permissionOrder = rs.getString(4);
|
554 |
|
|
accessHash.put("principal_name", principal_name);
|
555 |
|
|
accessHash.put("permission", permission);
|
556 |
|
|
accessHash.put("permission_type", permissionType);
|
557 |
|
|
accessHash.put("permission_order", permissionOrder);
|
558 |
6099
|
leinfelder
|
logMetacat.debug("accessHash: " + accessHash.toString());
|
559 |
5441
|
berkley
|
accessVector.add(accessHash);
|
560 |
|
|
}
|
561 |
|
|
h.put("access", accessVector);
|
562 |
5378
|
berkley
|
}
|
563 |
|
|
catch (SQLException e)
|
564 |
|
|
{
|
565 |
5444
|
berkley
|
e.printStackTrace();
|
566 |
5378
|
berkley
|
logMetacat.error("Error while getting document info for localid " + localId + " : "
|
567 |
|
|
+ e.getMessage());
|
568 |
|
|
}
|
569 |
|
|
finally
|
570 |
|
|
{
|
571 |
|
|
// Return database connection to the pool
|
572 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
573 |
|
|
}
|
574 |
|
|
return h;
|
575 |
|
|
}
|
576 |
|
|
|
577 |
|
|
/**
|
578 |
|
|
* return the newest rev for a given localId
|
579 |
|
|
* @param localId
|
580 |
|
|
* @return
|
581 |
|
|
*/
|
582 |
|
|
public int getLatestRevForLocalId(String localId)
|
583 |
|
|
throws McdbDocNotFoundException
|
584 |
|
|
{
|
585 |
5798
|
berkley
|
try
|
586 |
|
|
{
|
587 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NONE");
|
588 |
|
|
localId = acc.getDocid();
|
589 |
|
|
}
|
590 |
|
|
catch(Exception e)
|
591 |
|
|
{
|
592 |
|
|
//do nothing. just try the localId as it is
|
593 |
|
|
}
|
594 |
5378
|
berkley
|
int rev = 0;
|
595 |
|
|
String sql = "select rev from xml_documents where docid like '" + localId + "'";
|
596 |
|
|
DBConnection dbConn = null;
|
597 |
|
|
int serialNumber = -1;
|
598 |
|
|
try
|
599 |
|
|
{
|
600 |
|
|
// Get a database connection from the pool
|
601 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLatestRevForLocalId");
|
602 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
603 |
|
|
|
604 |
|
|
// Execute the insert statement
|
605 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
606 |
|
|
ResultSet rs = stmt.executeQuery();
|
607 |
|
|
if (rs.next())
|
608 |
|
|
{
|
609 |
|
|
rev = rs.getInt(1);
|
610 |
|
|
stmt.close();
|
611 |
|
|
}
|
612 |
|
|
else
|
613 |
|
|
{
|
614 |
|
|
stmt.close();
|
615 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
616 |
5798
|
berkley
|
throw new McdbDocNotFoundException("While trying to get the latest rev, could not find document " + localId);
|
617 |
5378
|
berkley
|
}
|
618 |
|
|
}
|
619 |
|
|
catch (SQLException e)
|
620 |
|
|
{
|
621 |
|
|
logMetacat.error("Error while looking up the guid: "
|
622 |
|
|
+ e.getMessage());
|
623 |
|
|
}
|
624 |
|
|
finally
|
625 |
|
|
{
|
626 |
|
|
// Return database connection to the pool
|
627 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
628 |
|
|
}
|
629 |
|
|
return rev;
|
630 |
|
|
}
|
631 |
|
|
|
632 |
|
|
/**
|
633 |
5377
|
berkley
|
* return all local ids in the object store that do not have associated
|
634 |
6099
|
leinfelder
|
* system metadata
|
635 |
5377
|
berkley
|
*/
|
636 |
|
|
public List<String> getLocalIdsWithNoSystemMetadata()
|
637 |
|
|
{
|
638 |
|
|
Vector<String> ids = new Vector<String>();
|
639 |
6099
|
leinfelder
|
String sql = "select docid, rev from xml_documents " +
|
640 |
|
|
"where docid not in " +
|
641 |
|
|
"(select docid from identifier where guid in (select guid from systemmetadata)))";
|
642 |
5377
|
berkley
|
DBConnection dbConn = null;
|
643 |
|
|
int serialNumber = -1;
|
644 |
|
|
try
|
645 |
|
|
{
|
646 |
|
|
// Get a database connection from the pool
|
647 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");
|
648 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
649 |
|
|
|
650 |
|
|
// Execute the insert statement
|
651 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
652 |
|
|
ResultSet rs = stmt.executeQuery();
|
653 |
|
|
while (rs.next())
|
654 |
|
|
{
|
655 |
|
|
String localid = rs.getString(1);
|
656 |
5798
|
berkley
|
String rev = rs.getString(2);
|
657 |
|
|
localid += "." + rev;
|
658 |
6099
|
leinfelder
|
logMetacat.debug("id to add SM for: " + localid);
|
659 |
5377
|
berkley
|
ids.add(localid);
|
660 |
|
|
}
|
661 |
|
|
stmt.close();
|
662 |
|
|
}
|
663 |
|
|
catch (SQLException e)
|
664 |
|
|
{
|
665 |
|
|
logMetacat.error("Error while looking up the guid: "
|
666 |
|
|
+ e.getMessage());
|
667 |
|
|
}
|
668 |
|
|
finally
|
669 |
|
|
{
|
670 |
|
|
// Return database connection to the pool
|
671 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
672 |
|
|
}
|
673 |
|
|
|
674 |
|
|
return ids;
|
675 |
|
|
}
|
676 |
|
|
|
677 |
|
|
/**
|
678 |
|
|
* return a listing of all local ids in the object store
|
679 |
|
|
* @return a list of all local ids in metacat
|
680 |
|
|
*/
|
681 |
|
|
public List<String> getAllLocalIds()
|
682 |
|
|
throws Exception
|
683 |
|
|
{
|
684 |
|
|
Vector<String> ids = new Vector<String>();
|
685 |
|
|
String sql = "select docid from xml_documents";
|
686 |
|
|
DBConnection dbConn = null;
|
687 |
|
|
int serialNumber = -1;
|
688 |
|
|
try
|
689 |
|
|
{
|
690 |
|
|
// Get a database connection from the pool
|
691 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");
|
692 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
693 |
|
|
|
694 |
|
|
// Execute the insert statement
|
695 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
696 |
|
|
ResultSet rs = stmt.executeQuery();
|
697 |
|
|
while (rs.next())
|
698 |
|
|
{
|
699 |
|
|
String localid = rs.getString(1);
|
700 |
|
|
ids.add(localid);
|
701 |
|
|
}
|
702 |
|
|
stmt.close();
|
703 |
|
|
}
|
704 |
|
|
catch (SQLException e)
|
705 |
|
|
{
|
706 |
|
|
logMetacat.error("Error while looking up the guid: "
|
707 |
|
|
+ e.getMessage());
|
708 |
|
|
}
|
709 |
|
|
finally
|
710 |
|
|
{
|
711 |
|
|
// Return database connection to the pool
|
712 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
713 |
|
|
}
|
714 |
|
|
return ids;
|
715 |
|
|
}
|
716 |
|
|
|
717 |
6118
|
leinfelder
|
/**
|
718 |
|
|
* returns a list of system metadata-only guids since the given date
|
719 |
|
|
* @return a list of system ids in metacat that do not correspond to objects
|
720 |
|
|
* TODO: need to check which server they are on
|
721 |
|
|
*/
|
722 |
|
|
public List<String> getUpdatedSystemMetadataIds(Date since)
|
723 |
|
|
throws Exception
|
724 |
|
|
{
|
725 |
|
|
List<String> ids = new Vector<String>();
|
726 |
|
|
String sql =
|
727 |
|
|
"select guid from " + TYPE_SYSTEM_METADATA +
|
728 |
|
|
" where guid not in " +
|
729 |
|
|
" (select guid from " + TYPE_IDENTIFIER + ") " +
|
730 |
|
|
" and date_modified > ?";
|
731 |
|
|
DBConnection dbConn = null;
|
732 |
|
|
int serialNumber = -1;
|
733 |
|
|
try
|
734 |
|
|
{
|
735 |
|
|
// Get a database connection from the pool
|
736 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getUpdatedSystemMetadataIds");
|
737 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
738 |
6099
|
leinfelder
|
|
739 |
6118
|
leinfelder
|
// Execute the insert statement
|
740 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
741 |
|
|
stmt.setDate(1, new java.sql.Date(since.getTime()));
|
742 |
|
|
ResultSet rs = stmt.executeQuery();
|
743 |
|
|
while (rs.next())
|
744 |
|
|
{
|
745 |
|
|
String guid = rs.getString(1);
|
746 |
|
|
ids.add(guid);
|
747 |
|
|
}
|
748 |
|
|
stmt.close();
|
749 |
|
|
}
|
750 |
|
|
catch (SQLException e)
|
751 |
|
|
{
|
752 |
|
|
logMetacat.error("Error while looking up the updated guids: "
|
753 |
|
|
+ e.getMessage());
|
754 |
|
|
}
|
755 |
|
|
finally
|
756 |
|
|
{
|
757 |
|
|
// Return database connection to the pool
|
758 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
759 |
|
|
}
|
760 |
|
|
return ids;
|
761 |
|
|
}
|
762 |
5282
|
jones
|
|
763 |
6118
|
leinfelder
|
|
764 |
|
|
|
765 |
5282
|
jones
|
/**
|
766 |
|
|
* Determine if an identifier exists already, returning true if so.
|
767 |
|
|
*
|
768 |
|
|
* @param guid the global identifier to look up
|
769 |
|
|
* @return boolean true if the identifier exists
|
770 |
|
|
*/
|
771 |
|
|
public boolean identifierExists(String guid)
|
772 |
|
|
{
|
773 |
|
|
boolean idExists = false;
|
774 |
|
|
try {
|
775 |
|
|
String id = getLocalId(guid);
|
776 |
|
|
if (id != null) {
|
777 |
|
|
idExists = true;
|
778 |
|
|
}
|
779 |
|
|
} catch (McdbDocNotFoundException e) {
|
780 |
6123
|
leinfelder
|
// try system metadata only
|
781 |
|
|
try {
|
782 |
|
|
idExists = systemMetadataExisits(guid);
|
783 |
|
|
} catch (McdbDocNotFoundException e2) {
|
784 |
|
|
idExists = false;
|
785 |
|
|
}
|
786 |
5282
|
jones
|
}
|
787 |
|
|
return idExists;
|
788 |
|
|
}
|
789 |
|
|
|
790 |
|
|
/**
|
791 |
|
|
*
|
792 |
5453
|
berkley
|
* @param guid
|
793 |
|
|
* @param rev
|
794 |
|
|
* @return
|
795 |
|
|
*/
|
796 |
|
|
public String generateLocalId(String guid, int rev)
|
797 |
|
|
{
|
798 |
|
|
return generateLocalId(guid, rev, false);
|
799 |
|
|
}
|
800 |
5286
|
jones
|
|
801 |
|
|
/**
|
802 |
|
|
* Given a global identifier (guid), create a suitable local identifier that
|
803 |
|
|
* follows Metacat's docid semantics and format (scope.id.rev), and create
|
804 |
|
|
* a mapping between these two identifiers. This effectively reserves both
|
805 |
|
|
* the global and the local identifier, as they will now be present in the
|
806 |
|
|
* identifier mapping table. If the incoming guid has the syntax of a
|
807 |
|
|
* Metacat docid (scope.id.rev), then simply use it.
|
808 |
|
|
*
|
809 |
|
|
* @param guid the global string identifier
|
810 |
|
|
* @param rev the revision number to be used in the localId
|
811 |
|
|
* @return String containing the localId to be used for Metacat operations
|
812 |
|
|
*/
|
813 |
5453
|
berkley
|
public String generateLocalId(String guid, int rev, boolean isSystemMetadata)
|
814 |
5286
|
jones
|
{
|
815 |
|
|
String localId = "";
|
816 |
|
|
boolean conformsToDocidFormat = false;
|
817 |
|
|
|
818 |
|
|
// Check if the guid passed in is already in docid (scope.id.rev) format
|
819 |
|
|
try {
|
820 |
|
|
AccessionNumber acc = new AccessionNumber(guid, "NONE");
|
821 |
|
|
if (new Integer(acc.getRev()).intValue() > 0) {
|
822 |
|
|
conformsToDocidFormat = true;
|
823 |
|
|
}
|
824 |
|
|
} catch (NumberFormatException e) {
|
825 |
|
|
// No action needed, simply detecting invalid AccessionNumbers
|
826 |
|
|
} catch (AccessionNumberException e) {
|
827 |
|
|
// No action needed, simply detecting invalid AccessionNumbers
|
828 |
|
|
} catch (SQLException e) {
|
829 |
|
|
// No action needed, simply detecting invalid AccessionNumbers
|
830 |
|
|
}
|
831 |
|
|
|
832 |
|
|
if (conformsToDocidFormat) {
|
833 |
|
|
// if it conforms, use it for both guid and localId
|
834 |
|
|
localId = guid;
|
835 |
|
|
} else {
|
836 |
|
|
// if not, then generate a new unique localId
|
837 |
|
|
localId = DocumentUtil.generateDocumentId(rev);
|
838 |
|
|
}
|
839 |
|
|
|
840 |
|
|
// Register this new pair in the identifier mapping table
|
841 |
6099
|
leinfelder
|
logMetacat.debug("creating mapping in generateLocalId");
|
842 |
5453
|
berkley
|
if(!isSystemMetadata)
|
843 |
|
|
{ //don't do this if we're generating for system metadata
|
844 |
|
|
createMapping(guid, localId);
|
845 |
|
|
}
|
846 |
5286
|
jones
|
|
847 |
|
|
return localId;
|
848 |
|
|
}
|
849 |
5322
|
berkley
|
|
850 |
|
|
/**
|
851 |
|
|
* given a local identifer, look up the guid. Throw McdbDocNotFoundException
|
852 |
5452
|
berkley
|
* if the docid, rev is not found in the identifiers or systemmetadata tables
|
853 |
5322
|
berkley
|
*
|
854 |
|
|
* @param docid the docid to look up
|
855 |
|
|
* @param rev the revision of the docid to look up
|
856 |
|
|
* @return String containing the mapped guid
|
857 |
|
|
* @throws McdbDocNotFoundException if the docid, rev is not found
|
858 |
|
|
*/
|
859 |
|
|
public String getGUID(String docid, int rev)
|
860 |
|
|
throws McdbDocNotFoundException
|
861 |
|
|
{
|
862 |
6099
|
leinfelder
|
logMetacat.debug("getting guid for " + docid);
|
863 |
5322
|
berkley
|
String query = "select guid from identifier where docid = ? and rev = ?";
|
864 |
|
|
String guid = null;
|
865 |
|
|
|
866 |
|
|
DBConnection dbConn = null;
|
867 |
|
|
int serialNumber = -1;
|
868 |
|
|
try {
|
869 |
|
|
// Get a database connection from the pool
|
870 |
5377
|
berkley
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getGUID");
|
871 |
5322
|
berkley
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
872 |
|
|
|
873 |
|
|
// Execute the insert statement
|
874 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
875 |
|
|
stmt.setString(1, docid);
|
876 |
|
|
stmt.setInt(2, rev);
|
877 |
|
|
ResultSet rs = stmt.executeQuery();
|
878 |
5451
|
berkley
|
if (rs.next())
|
879 |
|
|
{
|
880 |
5322
|
berkley
|
guid = rs.getString(1);
|
881 |
5451
|
berkley
|
}
|
882 |
|
|
else
|
883 |
|
|
{
|
884 |
6104
|
leinfelder
|
throw new McdbDocNotFoundException("No guid registered for docid " + docid + "." + rev);
|
885 |
5322
|
berkley
|
}
|
886 |
5451
|
berkley
|
|
887 |
5322
|
berkley
|
} catch (SQLException e) {
|
888 |
|
|
logMetacat.error("Error while looking up the guid: "
|
889 |
|
|
+ e.getMessage());
|
890 |
|
|
} finally {
|
891 |
|
|
// Return database connection to the pool
|
892 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
893 |
|
|
}
|
894 |
|
|
|
895 |
|
|
return guid;
|
896 |
|
|
}
|
897 |
5333
|
berkley
|
|
898 |
6123
|
leinfelder
|
public boolean systemMetadataExisits(String guid)
|
899 |
|
|
throws McdbDocNotFoundException {
|
900 |
|
|
logMetacat.debug("looking up system metadata for guid " + guid);
|
901 |
|
|
boolean exists = false;
|
902 |
|
|
String query = "select guid from systemmetadata where guid = ?";
|
903 |
|
|
|
904 |
|
|
DBConnection dbConn = null;
|
905 |
|
|
int serialNumber = -1;
|
906 |
|
|
try {
|
907 |
|
|
// Get a database connection from the pool
|
908 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.systemMetadataExisits");
|
909 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
910 |
|
|
|
911 |
|
|
// Execute the insert statement
|
912 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
913 |
|
|
stmt.setString(1, guid);
|
914 |
|
|
|
915 |
|
|
ResultSet rs = stmt.executeQuery();
|
916 |
|
|
if (rs.next()) {
|
917 |
|
|
exists = true;
|
918 |
|
|
} else {
|
919 |
|
|
throw new McdbDocNotFoundException(
|
920 |
|
|
"No system metadata registered for guid " + guid);
|
921 |
|
|
}
|
922 |
|
|
|
923 |
|
|
} catch (SQLException e) {
|
924 |
|
|
logMetacat.error("Error while looking up the system metadata: "
|
925 |
|
|
+ e.getMessage());
|
926 |
|
|
} finally {
|
927 |
|
|
// Return database connection to the pool
|
928 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
929 |
|
|
}
|
930 |
|
|
|
931 |
|
|
return exists;
|
932 |
|
|
}
|
933 |
|
|
|
934 |
5333
|
berkley
|
/**
|
935 |
5887
|
berkley
|
* creates a system metadata mapping and adds additional fields from sysmeta
|
936 |
|
|
* to the table for quick searching.
|
937 |
|
|
*
|
938 |
|
|
* @param guid the id to insert
|
939 |
|
|
* @param localId the systemMetadata object to get the local id for
|
940 |
6108
|
leinfelder
|
* @throws McdbDocNotFoundException
|
941 |
5887
|
berkley
|
*/
|
942 |
6108
|
leinfelder
|
public void createSystemMetadata(SystemMetadata sysmeta) throws McdbDocNotFoundException
|
943 |
5887
|
berkley
|
{
|
944 |
6099
|
leinfelder
|
insertSystemMetadata(sysmeta.getIdentifier().getValue());
|
945 |
|
|
updateSystemMetadata(sysmeta);
|
946 |
5887
|
berkley
|
}
|
947 |
6099
|
leinfelder
|
|
948 |
5887
|
berkley
|
|
949 |
|
|
/**
|
950 |
6079
|
leinfelder
|
* update a mapping
|
951 |
|
|
* @param guid
|
952 |
|
|
* @param localId
|
953 |
|
|
*/
|
954 |
|
|
public void updateMapping(String guid, String localId)
|
955 |
|
|
{
|
956 |
|
|
|
957 |
6099
|
leinfelder
|
logMetacat.debug("$$$$$$$$$$$$$$ updating mapping table");
|
958 |
5350
|
berkley
|
int serialNumber = -1;
|
959 |
|
|
DBConnection dbConn = null;
|
960 |
|
|
try {
|
961 |
|
|
// Parse the localId into scope and rev parts
|
962 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
963 |
|
|
String docid = acc.getDocid();
|
964 |
|
|
int rev = 1;
|
965 |
|
|
if(acc.getRev() != null)
|
966 |
|
|
{
|
967 |
|
|
rev = (new Integer(acc.getRev()).intValue());
|
968 |
|
|
}
|
969 |
|
|
|
970 |
|
|
// Get a database connection from the pool
|
971 |
|
|
dbConn =
|
972 |
6079
|
leinfelder
|
DBConnectionPool.getDBConnection("IdentifierManager.updateMapping");
|
973 |
5350
|
berkley
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
974 |
|
|
|
975 |
6099
|
leinfelder
|
// Execute the update statement
|
976 |
|
|
String query = "update " + TYPE_IDENTIFIER + " set (docid, rev) = (?, ?) where guid='" + guid + "'";
|
977 |
5350
|
berkley
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
978 |
|
|
stmt.setString(1, docid);
|
979 |
|
|
stmt.setInt(2, rev);
|
980 |
|
|
int rows = stmt.executeUpdate();
|
981 |
|
|
|
982 |
|
|
stmt.close();
|
983 |
|
|
} catch (SQLException e) {
|
984 |
|
|
e.printStackTrace();
|
985 |
6079
|
leinfelder
|
logMetacat.error("SQL error while updating a mapping identifier: "
|
986 |
5350
|
berkley
|
+ e.getMessage());
|
987 |
|
|
} catch (NumberFormatException e) {
|
988 |
|
|
e.printStackTrace();
|
989 |
6079
|
leinfelder
|
logMetacat.error("NumberFormat error while updating a mapping identifier: "
|
990 |
5350
|
berkley
|
+ e.getMessage());
|
991 |
|
|
} catch (AccessionNumberException e) {
|
992 |
|
|
e.printStackTrace();
|
993 |
6079
|
leinfelder
|
logMetacat.error("AccessionNumber error while updating a mapping identifier: "
|
994 |
5350
|
berkley
|
+ e.getMessage());
|
995 |
|
|
} finally {
|
996 |
|
|
// Return database connection to the pool
|
997 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
998 |
|
|
}
|
999 |
6099
|
leinfelder
|
logMetacat.debug("done updating mapping");
|
1000 |
5350
|
berkley
|
}
|
1001 |
6099
|
leinfelder
|
|
1002 |
|
|
private void updateSystemMetadataFields(long dateUploaded, String rightsHolder,
|
1003 |
5887
|
berkley
|
String checksum, String checksumAlgorithm, String originMemberNode,
|
1004 |
5917
|
berkley
|
String authoritativeMemberNode, long modifiedDate, String submitter,
|
1005 |
6107
|
leinfelder
|
String guid, String objectFormat, long size, boolean replicationAllowed,
|
1006 |
|
|
int numberReplicas)
|
1007 |
5887
|
berkley
|
{
|
1008 |
|
|
DBConnection dbConn = null;
|
1009 |
|
|
int serialNumber = -1;
|
1010 |
5957
|
berkley
|
|
1011 |
5887
|
berkley
|
try {
|
1012 |
|
|
// Get a database connection from the pool
|
1013 |
|
|
dbConn =
|
1014 |
|
|
DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
1015 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1016 |
|
|
|
1017 |
|
|
// Execute the insert statement
|
1018 |
|
|
String query = "update " + TYPE_SYSTEM_METADATA +
|
1019 |
|
|
" set (date_uploaded, rights_holder, checksum, checksum_algorithm, " +
|
1020 |
5917
|
berkley
|
"origin_member_node, authoritive_member_node, date_modified, " +
|
1021 |
6107
|
leinfelder
|
"submitter, object_format, size, replication_allowed, number_replicas) " +
|
1022 |
|
|
"= (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) where guid = ?";
|
1023 |
5887
|
berkley
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1024 |
|
|
|
1025 |
|
|
//data values
|
1026 |
|
|
stmt.setTimestamp(1, new java.sql.Timestamp(dateUploaded));
|
1027 |
|
|
stmt.setString(2, rightsHolder);
|
1028 |
|
|
stmt.setString(3, checksum);
|
1029 |
|
|
stmt.setString(4, checksumAlgorithm);
|
1030 |
|
|
stmt.setString(5, originMemberNode);
|
1031 |
|
|
stmt.setString(6, authoritativeMemberNode);
|
1032 |
|
|
stmt.setTimestamp(7, new java.sql.Timestamp(modifiedDate));
|
1033 |
|
|
stmt.setString(8, submitter);
|
1034 |
5917
|
berkley
|
stmt.setString(9, objectFormat);
|
1035 |
|
|
stmt.setString(10, new Long(size).toString());
|
1036 |
6107
|
leinfelder
|
stmt.setBoolean(11, replicationAllowed);
|
1037 |
|
|
stmt.setInt(12, numberReplicas);
|
1038 |
5887
|
berkley
|
//where clause
|
1039 |
6107
|
leinfelder
|
stmt.setString(13, guid);
|
1040 |
6099
|
leinfelder
|
logMetacat.debug("stmt: " + stmt.toString());
|
1041 |
5887
|
berkley
|
//execute
|
1042 |
|
|
int rows = stmt.executeUpdate();
|
1043 |
|
|
|
1044 |
|
|
stmt.close();
|
1045 |
|
|
} catch (SQLException e) {
|
1046 |
|
|
e.printStackTrace();
|
1047 |
5950
|
berkley
|
logMetacat.error("insertAdditionalSystemMetadataFields: SQL error while creating a mapping to the system metadata identifier: "
|
1048 |
5887
|
berkley
|
+ e.getMessage());
|
1049 |
|
|
} catch (NumberFormatException e) {
|
1050 |
|
|
e.printStackTrace();
|
1051 |
5950
|
berkley
|
logMetacat.error("insertAdditionalSystemMetadataFields: NumberFormat error while creating a mapping to the system metadata identifier: "
|
1052 |
5887
|
berkley
|
+ e.getMessage());
|
1053 |
|
|
} finally {
|
1054 |
|
|
// Return database connection to the pool
|
1055 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1056 |
|
|
}
|
1057 |
|
|
}
|
1058 |
|
|
|
1059 |
6097
|
leinfelder
|
private void insertSystemMetadataProvenance(String guid, String relationship, List<String> targetGuids)
|
1060 |
|
|
{
|
1061 |
|
|
DBConnection dbConn = null;
|
1062 |
|
|
int serialNumber = -1;
|
1063 |
|
|
|
1064 |
|
|
try {
|
1065 |
|
|
// Get a database connection from the pool
|
1066 |
|
|
dbConn =
|
1067 |
6107
|
leinfelder
|
DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadataProvenance");
|
1068 |
6097
|
leinfelder
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1069 |
|
|
|
1070 |
|
|
// remove existing values first
|
1071 |
|
|
String delete = "delete from systemMetadataProvenance " +
|
1072 |
|
|
"where guid = ? and relationship = ?";
|
1073 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
1074 |
|
|
//data values
|
1075 |
|
|
stmt.setString(1, guid);
|
1076 |
|
|
stmt.setString(2, relationship);
|
1077 |
|
|
//execute
|
1078 |
|
|
int deletedCount = stmt.executeUpdate();
|
1079 |
|
|
stmt.close();
|
1080 |
|
|
|
1081 |
|
|
for (String targetGuid: targetGuids) {
|
1082 |
|
|
// Execute the insert statement
|
1083 |
|
|
String insert = "insert into systemMetadataProvenance " +
|
1084 |
|
|
"(guid, relationship, target_guid) " +
|
1085 |
|
|
"values (?, ?, ?)";
|
1086 |
|
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1087 |
|
|
|
1088 |
|
|
//data values
|
1089 |
|
|
insertStatement.setString(1, guid);
|
1090 |
|
|
insertStatement.setString(2, relationship);
|
1091 |
|
|
insertStatement.setString(3, targetGuid);
|
1092 |
|
|
//execute
|
1093 |
|
|
int rows = insertStatement.executeUpdate();
|
1094 |
|
|
insertStatement.close();
|
1095 |
|
|
}
|
1096 |
|
|
} catch (SQLException e) {
|
1097 |
|
|
logMetacat.error("SQL error while adding systemMetadataProvenance for: " + guid, e);
|
1098 |
|
|
} finally {
|
1099 |
|
|
// Return database connection to the pool
|
1100 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1101 |
|
|
}
|
1102 |
|
|
}
|
1103 |
|
|
|
1104 |
6107
|
leinfelder
|
private void insertReplicationPolicy(String guid, String policy, List<String> memberNodes)
|
1105 |
|
|
{
|
1106 |
|
|
DBConnection dbConn = null;
|
1107 |
|
|
int serialNumber = -1;
|
1108 |
|
|
|
1109 |
|
|
try {
|
1110 |
|
|
// Get a database connection from the pool
|
1111 |
|
|
dbConn =
|
1112 |
|
|
DBConnectionPool.getDBConnection("IdentifierManager.insertReplicationPolicy");
|
1113 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1114 |
|
|
|
1115 |
|
|
// remove existing values first
|
1116 |
|
|
String delete = "delete from systemMetadataReplicationPolicy " +
|
1117 |
|
|
"where guid = ? and policy = ?";
|
1118 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
1119 |
|
|
//data values
|
1120 |
|
|
stmt.setString(1, guid);
|
1121 |
|
|
stmt.setString(2, policy);
|
1122 |
|
|
//execute
|
1123 |
|
|
int deletedCount = stmt.executeUpdate();
|
1124 |
|
|
stmt.close();
|
1125 |
|
|
|
1126 |
|
|
for (String memberNode: memberNodes) {
|
1127 |
|
|
// Execute the insert statement
|
1128 |
|
|
String insert = "insert into systemMetadataReplicationPolicy " +
|
1129 |
|
|
"(guid, policy, member_node) " +
|
1130 |
|
|
"values (?, ?, ?)";
|
1131 |
|
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1132 |
|
|
|
1133 |
|
|
//data values
|
1134 |
|
|
insertStatement.setString(1, guid);
|
1135 |
|
|
insertStatement.setString(2, policy);
|
1136 |
|
|
insertStatement.setString(3, memberNode);
|
1137 |
|
|
//execute
|
1138 |
|
|
int rows = insertStatement.executeUpdate();
|
1139 |
|
|
insertStatement.close();
|
1140 |
|
|
}
|
1141 |
|
|
} catch (SQLException e) {
|
1142 |
|
|
logMetacat.error("SQL error while adding systemMetadataReplicationPolicy for: " + guid, e);
|
1143 |
|
|
} finally {
|
1144 |
|
|
// Return database connection to the pool
|
1145 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1146 |
|
|
}
|
1147 |
|
|
}
|
1148 |
|
|
|
1149 |
|
|
private void insertReplicationStatus(String guid, List<Replica> replicas) {
|
1150 |
|
|
DBConnection dbConn = null;
|
1151 |
|
|
int serialNumber = -1;
|
1152 |
|
|
|
1153 |
|
|
try {
|
1154 |
|
|
// Get a database connection from the pool
|
1155 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertReplicas");
|
1156 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1157 |
|
|
|
1158 |
|
|
// remove existing values first
|
1159 |
|
|
String delete = "delete from systemMetadataReplicationStatus " +
|
1160 |
|
|
"where guid = ?";
|
1161 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
1162 |
|
|
//data values
|
1163 |
|
|
stmt.setString(1, guid);
|
1164 |
|
|
//execute
|
1165 |
|
|
int deletedCount = stmt.executeUpdate();
|
1166 |
|
|
stmt.close();
|
1167 |
|
|
|
1168 |
|
|
for (Replica replica: replicas) {
|
1169 |
|
|
// Execute the insert statement
|
1170 |
|
|
String insert = "insert into systemMetadataReplicationStatus " +
|
1171 |
|
|
"(guid, member_node, status, date_verified) " +
|
1172 |
|
|
"values (?, ?, ?, ?)";
|
1173 |
|
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1174 |
|
|
|
1175 |
|
|
//data values
|
1176 |
|
|
String memberNode = replica.getReplicaMemberNode().getValue();
|
1177 |
|
|
String status = replica.getReplicationStatus().toString();
|
1178 |
|
|
java.sql.Date sqlDate = new java.sql.Date(replica.getReplicaVerified().getTime());
|
1179 |
|
|
insertStatement.setString(1, guid);
|
1180 |
|
|
insertStatement.setString(2, memberNode);
|
1181 |
|
|
insertStatement.setString(3, status);
|
1182 |
|
|
insertStatement.setDate(4, sqlDate);
|
1183 |
|
|
|
1184 |
|
|
//execute
|
1185 |
|
|
int rows = insertStatement.executeUpdate();
|
1186 |
|
|
insertStatement.close();
|
1187 |
|
|
}
|
1188 |
|
|
} catch (SQLException e) {
|
1189 |
|
|
logMetacat.error("SQL error while adding systemMetadataReplicationStatus for: " + guid, e);
|
1190 |
|
|
} finally {
|
1191 |
|
|
// Return database connection to the pool
|
1192 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1193 |
|
|
}
|
1194 |
|
|
}
|
1195 |
|
|
|
1196 |
5334
|
berkley
|
/**
|
1197 |
5887
|
berkley
|
* Insert the system metadata fields into the db
|
1198 |
|
|
* @param sm
|
1199 |
6108
|
leinfelder
|
* @throws McdbDocNotFoundException
|
1200 |
5887
|
berkley
|
*/
|
1201 |
6108
|
leinfelder
|
public void updateSystemMetadata(SystemMetadata sm) throws McdbDocNotFoundException {
|
1202 |
6107
|
leinfelder
|
|
1203 |
|
|
Boolean replicationAllowed = false;
|
1204 |
|
|
Integer numberReplicas = -1;
|
1205 |
|
|
ReplicationPolicy replicationPolicy = sm.getReplicationPolicy();
|
1206 |
|
|
if (replicationPolicy != null) {
|
1207 |
|
|
replicationAllowed = replicationPolicy.getReplicationAllowed();
|
1208 |
|
|
numberReplicas = replicationPolicy.getNumberReplicas();
|
1209 |
|
|
replicationAllowed = replicationAllowed == null ? false: replicationAllowed;
|
1210 |
|
|
numberReplicas = numberReplicas == null ? -1: numberReplicas;
|
1211 |
|
|
}
|
1212 |
|
|
|
1213 |
|
|
// the main systemMetadata fields
|
1214 |
|
|
updateSystemMetadataFields(
|
1215 |
5887
|
berkley
|
sm.getDateUploaded().getTime(),
|
1216 |
|
|
sm.getRightsHolder().getValue(),
|
1217 |
|
|
sm.getChecksum().getValue(),
|
1218 |
|
|
sm.getChecksum().getAlgorithm().name(),
|
1219 |
|
|
sm.getOriginMemberNode().getValue(),
|
1220 |
|
|
sm.getAuthoritativeMemberNode().getValue(),
|
1221 |
|
|
sm.getDateSysMetadataModified().getTime(),
|
1222 |
|
|
sm.getSubmitter().getValue(),
|
1223 |
5917
|
berkley
|
sm.getIdentifier().getValue(),
|
1224 |
6131
|
cjones
|
sm.getObjectFormat().getFmtid().getValue(),
|
1225 |
6107
|
leinfelder
|
sm.getSize(),
|
1226 |
|
|
replicationAllowed,
|
1227 |
|
|
numberReplicas);
|
1228 |
6097
|
leinfelder
|
|
1229 |
|
|
// add provenance information
|
1230 |
|
|
String guid = sm.getIdentifier().getValue();
|
1231 |
|
|
List<String> targetGuids = null;
|
1232 |
|
|
String relationship = null;
|
1233 |
|
|
|
1234 |
|
|
relationship = "obsoletedBy";
|
1235 |
|
|
targetGuids = new ArrayList<String>();
|
1236 |
|
|
for (Identifier id: sm.getObsoletedByList()) {
|
1237 |
|
|
targetGuids.add(id.getValue());
|
1238 |
|
|
}
|
1239 |
|
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1240 |
|
|
|
1241 |
|
|
relationship = "obsoletes";
|
1242 |
|
|
targetGuids = new ArrayList<String>();
|
1243 |
|
|
for (Identifier id: sm.getObsoleteList()) {
|
1244 |
|
|
targetGuids.add(id.getValue());
|
1245 |
|
|
}
|
1246 |
|
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1247 |
|
|
|
1248 |
|
|
relationship = "describes";
|
1249 |
|
|
targetGuids = new ArrayList<String>();
|
1250 |
|
|
for (Identifier id: sm.getDescribeList()) {
|
1251 |
|
|
targetGuids.add(id.getValue());
|
1252 |
|
|
}
|
1253 |
|
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1254 |
|
|
|
1255 |
|
|
relationship = "describedBy";
|
1256 |
|
|
targetGuids = new ArrayList<String>();
|
1257 |
|
|
for (Identifier id: sm.getDescribedByList()) {
|
1258 |
|
|
targetGuids.add(id.getValue());
|
1259 |
|
|
}
|
1260 |
|
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1261 |
|
|
|
1262 |
|
|
relationship = "derivedFrom";
|
1263 |
|
|
targetGuids = new ArrayList<String>();
|
1264 |
|
|
for (Identifier id: sm.getDerivedFromList()) {
|
1265 |
|
|
targetGuids.add(id.getValue());
|
1266 |
|
|
}
|
1267 |
|
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1268 |
6107
|
leinfelder
|
|
1269 |
|
|
// save replication policies
|
1270 |
|
|
if (replicationPolicy != null) {
|
1271 |
|
|
List<String> nodes = null;
|
1272 |
|
|
String policy = null;
|
1273 |
|
|
|
1274 |
|
|
nodes = new ArrayList<String>();
|
1275 |
|
|
policy = "blocked";
|
1276 |
|
|
for (NodeReference node: replicationPolicy.getBlockedMemberNodeList()) {
|
1277 |
|
|
nodes.add(node.getValue());
|
1278 |
|
|
}
|
1279 |
|
|
this.insertReplicationPolicy(guid, policy, nodes);
|
1280 |
|
|
|
1281 |
|
|
nodes = new ArrayList<String>();
|
1282 |
|
|
policy = "preferred";
|
1283 |
|
|
for (NodeReference node: replicationPolicy.getPreferredMemberNodeList()) {
|
1284 |
|
|
nodes.add(node.getValue());
|
1285 |
|
|
}
|
1286 |
|
|
this.insertReplicationPolicy(guid, policy, nodes);
|
1287 |
|
|
}
|
1288 |
6097
|
leinfelder
|
|
1289 |
6107
|
leinfelder
|
// save replica information
|
1290 |
|
|
this.insertReplicationStatus(guid, sm.getReplicaList());
|
1291 |
|
|
|
1292 |
6108
|
leinfelder
|
// save access policy
|
1293 |
|
|
AccessPolicy accessPolicy = sm.getAccessPolicy();
|
1294 |
|
|
if (accessPolicy != null) {
|
1295 |
|
|
try {
|
1296 |
|
|
this.insertAccessPolicy(guid, accessPolicy);
|
1297 |
|
|
} catch (AccessException e) {
|
1298 |
|
|
throw new McdbDocNotFoundException(e);
|
1299 |
|
|
}
|
1300 |
|
|
}
|
1301 |
5887
|
berkley
|
}
|
1302 |
|
|
|
1303 |
|
|
/**
|
1304 |
6108
|
leinfelder
|
* Creates Metacat access rules and inserts them
|
1305 |
|
|
* @param accessPolicy
|
1306 |
|
|
* @throws McdbDocNotFoundException
|
1307 |
|
|
* @throws AccessException
|
1308 |
|
|
*/
|
1309 |
|
|
private void insertAccessPolicy(String guid, AccessPolicy accessPolicy) throws McdbDocNotFoundException, AccessException {
|
1310 |
|
|
|
1311 |
|
|
List<XMLAccessDAO> accessDAOs = new ArrayList<XMLAccessDAO>();
|
1312 |
|
|
for (AccessRule accessRule: accessPolicy.getAllowList()) {
|
1313 |
|
|
List<Subject> subjects = accessRule.getSubjectList();
|
1314 |
|
|
List<Permission> permissions = accessRule.getPermissionList();
|
1315 |
|
|
for (Subject subject: subjects) {
|
1316 |
6122
|
leinfelder
|
XMLAccessDAO accessDAO = new XMLAccessDAO();
|
1317 |
|
|
accessDAO.setPrincipalName(subject.getValue());
|
1318 |
|
|
accessDAO.setGuid(guid);
|
1319 |
|
|
accessDAO.setPermType(AccessControlInterface.ALLOW);
|
1320 |
|
|
accessDAO.setPermOrder(AccessControlInterface.DENYFIRST);
|
1321 |
|
|
for (Permission permission: permissions) {
|
1322 |
|
|
Long metacatPermission = new Long(convertPermission(permission));
|
1323 |
|
|
accessDAO.addPermission(metacatPermission);
|
1324 |
|
|
}
|
1325 |
|
|
accessDAOs.add(accessDAO);
|
1326 |
6108
|
leinfelder
|
}
|
1327 |
|
|
}
|
1328 |
|
|
|
1329 |
6122
|
leinfelder
|
// use GUID to update
|
1330 |
|
|
XMLAccessAccess accessController = new XMLAccessAccess(true);
|
1331 |
|
|
accessController.replaceAccess(guid, accessDAOs);
|
1332 |
6108
|
leinfelder
|
|
1333 |
|
|
|
1334 |
|
|
}
|
1335 |
|
|
|
1336 |
|
|
/**
|
1337 |
|
|
* Lookup access policy from Metacat
|
1338 |
|
|
* @param guid
|
1339 |
|
|
* @return
|
1340 |
|
|
* @throws McdbDocNotFoundException
|
1341 |
|
|
* @throws AccessException
|
1342 |
|
|
*/
|
1343 |
|
|
private AccessPolicy getAccessPolicy(String guid) throws McdbDocNotFoundException, AccessException {
|
1344 |
6122
|
leinfelder
|
// use GUID to look up the access
|
1345 |
|
|
XMLAccessAccess accessController = new XMLAccessAccess(true);
|
1346 |
|
|
List<XMLAccessDAO> accessDAOs = accessController.getXMLAccessForDoc(guid);
|
1347 |
|
|
AccessRule accessRule = new AccessRule();
|
1348 |
6108
|
leinfelder
|
for (XMLAccessDAO accessDAO: accessDAOs) {
|
1349 |
|
|
Permission permission = convertPermission(accessDAO.getPermission().intValue());
|
1350 |
|
|
accessRule.addPermission(permission);
|
1351 |
|
|
Subject subject = new Subject();
|
1352 |
|
|
subject.setValue(accessDAO.getPrincipalName());
|
1353 |
|
|
accessRule.addSubject(subject);
|
1354 |
|
|
}
|
1355 |
|
|
AccessPolicy accessPolicy = new AccessPolicy();
|
1356 |
|
|
accessPolicy.addAllow(accessRule);
|
1357 |
|
|
return accessPolicy;
|
1358 |
|
|
}
|
1359 |
|
|
|
1360 |
|
|
public int convertPermission(Permission permission) {
|
1361 |
|
|
if (permission.equals(Permission.READ)) {
|
1362 |
|
|
return AccessControlInterface.READ;
|
1363 |
|
|
}
|
1364 |
|
|
if (permission.equals(Permission.WRITE)) {
|
1365 |
|
|
return AccessControlInterface.WRITE;
|
1366 |
|
|
}
|
1367 |
|
|
if (permission.equals(Permission.CHANGE_PERMISSION)) {
|
1368 |
|
|
return AccessControlInterface.CHMOD;
|
1369 |
|
|
}
|
1370 |
|
|
return -1;
|
1371 |
|
|
}
|
1372 |
|
|
|
1373 |
|
|
public Permission convertPermission(int permission) {
|
1374 |
|
|
if (permission == AccessControlInterface.READ) {
|
1375 |
|
|
return Permission.READ;
|
1376 |
|
|
}
|
1377 |
|
|
if (permission == AccessControlInterface.WRITE) {
|
1378 |
|
|
return Permission.WRITE;
|
1379 |
|
|
}
|
1380 |
|
|
if (permission == AccessControlInterface.CHMOD) {
|
1381 |
|
|
return Permission.CHANGE_PERMISSION;
|
1382 |
|
|
}
|
1383 |
|
|
return null;
|
1384 |
|
|
}
|
1385 |
|
|
|
1386 |
|
|
/**
|
1387 |
6099
|
leinfelder
|
* Lookup a localId given the GUID. If
|
1388 |
|
|
* the identifier is not found, throw an exception.
|
1389 |
|
|
*
|
1390 |
|
|
* @param guid the global identifier to look up
|
1391 |
|
|
* @return String containing the corresponding LocalId
|
1392 |
|
|
* @throws McdbDocNotFoundException if the identifier is not found
|
1393 |
5334
|
berkley
|
*/
|
1394 |
6099
|
leinfelder
|
public String getLocalId(String guid) throws McdbDocNotFoundException {
|
1395 |
5334
|
berkley
|
|
1396 |
|
|
String db_guid = "";
|
1397 |
|
|
String docid = "";
|
1398 |
|
|
int rev = 0;
|
1399 |
|
|
|
1400 |
6099
|
leinfelder
|
String query = "select guid, docid, rev from " + TYPE_IDENTIFIER + " where guid = ?";
|
1401 |
5334
|
berkley
|
|
1402 |
|
|
DBConnection dbConn = null;
|
1403 |
5333
|
berkley
|
int serialNumber = -1;
|
1404 |
5334
|
berkley
|
try {
|
1405 |
|
|
// Get a database connection from the pool
|
1406 |
|
|
dbConn = DBConnectionPool.getDBConnection("Identifier.getLocalId");
|
1407 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1408 |
|
|
|
1409 |
|
|
// Execute the insert statement
|
1410 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1411 |
|
|
stmt.setString(1, guid);
|
1412 |
|
|
ResultSet rs = stmt.executeQuery();
|
1413 |
|
|
if (rs.next()) {
|
1414 |
|
|
db_guid = rs.getString(1);
|
1415 |
|
|
docid = rs.getString(2);
|
1416 |
|
|
rev = rs.getInt(3);
|
1417 |
|
|
assert(db_guid.equals(guid));
|
1418 |
|
|
} else {
|
1419 |
|
|
throw new McdbDocNotFoundException("Document not found:" + guid);
|
1420 |
|
|
}
|
1421 |
|
|
stmt.close();
|
1422 |
|
|
} catch (SQLException e) {
|
1423 |
|
|
logMetacat.error("Error while looking up the local identifier: "
|
1424 |
|
|
+ e.getMessage());
|
1425 |
|
|
} finally {
|
1426 |
|
|
// Return database connection to the pool
|
1427 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1428 |
|
|
}
|
1429 |
|
|
return docid + "." + rev;
|
1430 |
|
|
}
|
1431 |
|
|
|
1432 |
5377
|
berkley
|
/**
|
1433 |
5895
|
berkley
|
* query the systemmetadata table based on the given parameters
|
1434 |
|
|
* @param startTime
|
1435 |
|
|
* @param endTime
|
1436 |
|
|
* @param objectFormat
|
1437 |
|
|
* @param replicaStatus
|
1438 |
|
|
* @param start
|
1439 |
|
|
* @param count
|
1440 |
|
|
* @return ObjectList
|
1441 |
|
|
*/
|
1442 |
|
|
public ObjectList querySystemMetadata(Date startTime, Date endTime,
|
1443 |
|
|
ObjectFormat objectFormat, boolean replicaStatus, int start, int count)
|
1444 |
|
|
{
|
1445 |
|
|
ObjectList ol = new ObjectList();
|
1446 |
|
|
int total = 0;
|
1447 |
5943
|
berkley
|
DBConnection dbConn = null;
|
1448 |
|
|
int serialNumber = -1;
|
1449 |
5895
|
berkley
|
|
1450 |
|
|
try
|
1451 |
|
|
{
|
1452 |
|
|
String sql = "select guid, date_uploaded, rights_holder, checksum, " +
|
1453 |
|
|
"checksum_algorithm, origin_member_node, authoritive_member_node, " +
|
1454 |
5917
|
berkley
|
"date_modified, submitter, object_format, size from systemmetadata";
|
1455 |
5895
|
berkley
|
|
1456 |
|
|
boolean f1 = false;
|
1457 |
|
|
boolean f2 = false;
|
1458 |
|
|
boolean f3 = false;
|
1459 |
|
|
|
1460 |
|
|
if(startTime != null)
|
1461 |
|
|
{
|
1462 |
5917
|
berkley
|
sql += " where systemmetadata.date_modified > ?";
|
1463 |
5895
|
berkley
|
f1 = true;
|
1464 |
|
|
}
|
1465 |
|
|
|
1466 |
|
|
if(endTime != null)
|
1467 |
|
|
{
|
1468 |
5917
|
berkley
|
if(!f1)
|
1469 |
|
|
{
|
1470 |
|
|
sql += " where systemmetadata.date_modified < ?";
|
1471 |
|
|
}
|
1472 |
|
|
else
|
1473 |
|
|
{
|
1474 |
|
|
sql += " and systemmetadata.date_modified < ?";
|
1475 |
|
|
}
|
1476 |
5895
|
berkley
|
f2 = true;
|
1477 |
|
|
}
|
1478 |
|
|
|
1479 |
|
|
if(objectFormat != null)
|
1480 |
|
|
{
|
1481 |
5917
|
berkley
|
if(!f1 && !f2)
|
1482 |
|
|
{
|
1483 |
|
|
sql += " where object_format = ?";
|
1484 |
|
|
}
|
1485 |
|
|
else
|
1486 |
|
|
{
|
1487 |
|
|
sql += " and object_format = ?";
|
1488 |
|
|
}
|
1489 |
5895
|
berkley
|
f3 = true;
|
1490 |
|
|
}
|
1491 |
|
|
|
1492 |
|
|
if(replicaStatus)
|
1493 |
|
|
{
|
1494 |
|
|
String currentNodeId = PropertyService.getInstance().getProperty("dataone.memberNodeId");
|
1495 |
5917
|
berkley
|
if(!f1 && !f2 && !f3)
|
1496 |
|
|
{
|
1497 |
|
|
sql += " where authoritive_member_node != '" + currentNodeId.trim() + "'";
|
1498 |
|
|
}
|
1499 |
|
|
else
|
1500 |
|
|
{
|
1501 |
|
|
sql += " and authoritive_member_node != '" + currentNodeId.trim() + "'";
|
1502 |
|
|
}
|
1503 |
5895
|
berkley
|
}
|
1504 |
|
|
|
1505 |
5943
|
berkley
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.querySystemMetadata");
|
1506 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1507 |
5895
|
berkley
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
1508 |
|
|
|
1509 |
|
|
if(f1 && f2 && f3)
|
1510 |
|
|
{
|
1511 |
|
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1512 |
|
|
stmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1513 |
|
|
stmt.setString(3, objectFormat.toString());
|
1514 |
|
|
}
|
1515 |
|
|
else if(f1 && f2 && !f3)
|
1516 |
|
|
{
|
1517 |
|
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1518 |
|
|
stmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1519 |
|
|
}
|
1520 |
|
|
else if(f1 && !f2 && f3)
|
1521 |
|
|
{
|
1522 |
|
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1523 |
|
|
stmt.setString(2, objectFormat.toString());
|
1524 |
|
|
}
|
1525 |
|
|
else if(f1 && !f2 && !f3)
|
1526 |
|
|
{
|
1527 |
|
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1528 |
|
|
}
|
1529 |
|
|
else if(!f1 && f2 && f3)
|
1530 |
|
|
{
|
1531 |
|
|
stmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1532 |
|
|
stmt.setString(2, objectFormat.toString());
|
1533 |
|
|
}
|
1534 |
|
|
else if(!f1 && !f2 && f3)
|
1535 |
|
|
{
|
1536 |
|
|
stmt.setString(1, objectFormat.toString());
|
1537 |
|
|
}
|
1538 |
|
|
else if(!f1 && f2 && !f3)
|
1539 |
|
|
{
|
1540 |
|
|
stmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1541 |
|
|
}
|
1542 |
|
|
|
1543 |
6099
|
leinfelder
|
//logMetacat.debug("LISTOBJECTS QUERY: " + stmt.toString());
|
1544 |
5895
|
berkley
|
|
1545 |
|
|
ResultSet rs = stmt.executeQuery();
|
1546 |
5917
|
berkley
|
for(int i=0; i<start; i++)
|
1547 |
5895
|
berkley
|
{
|
1548 |
5917
|
berkley
|
if(rs.next())
|
1549 |
|
|
{
|
1550 |
|
|
total++;
|
1551 |
|
|
}
|
1552 |
|
|
else
|
1553 |
|
|
{
|
1554 |
|
|
break;
|
1555 |
|
|
}
|
1556 |
5895
|
berkley
|
}
|
1557 |
5917
|
berkley
|
|
1558 |
5895
|
berkley
|
int countIndex = 0;
|
1559 |
|
|
|
1560 |
|
|
while(rs.next())
|
1561 |
|
|
{
|
1562 |
|
|
total++;
|
1563 |
|
|
if(countIndex >= count)
|
1564 |
|
|
{
|
1565 |
|
|
break;
|
1566 |
|
|
}
|
1567 |
|
|
String guid = rs.getString(1);
|
1568 |
6099
|
leinfelder
|
//logMetacat.debug("query found doc with guid " + guid);
|
1569 |
5895
|
berkley
|
//Timestamp dateUploaded = rs.getTimestamp(2);
|
1570 |
|
|
//String rightsHolder = rs.getString(3);
|
1571 |
|
|
String checksum = rs.getString(4);
|
1572 |
|
|
String checksumAlgorithm = rs.getString(5);
|
1573 |
|
|
//String originMemberNode = rs.getString(6);
|
1574 |
|
|
String authoritiveMemberNode = rs.getString(7);
|
1575 |
|
|
Timestamp dateModified = rs.getTimestamp(8);
|
1576 |
|
|
//String submitter = rs.getString(9);
|
1577 |
|
|
String format = rs.getString(10);
|
1578 |
5917
|
berkley
|
String sz = rs.getString(11);
|
1579 |
|
|
long size = 0;
|
1580 |
|
|
if(sz != null && !sz.trim().equals(""))
|
1581 |
|
|
{
|
1582 |
|
|
size = new Long(rs.getString(11)).longValue();
|
1583 |
|
|
}
|
1584 |
5895
|
berkley
|
|
1585 |
|
|
ObjectInfo oi = new ObjectInfo();
|
1586 |
|
|
|
1587 |
|
|
Identifier id = new Identifier();
|
1588 |
|
|
id.setValue(guid);
|
1589 |
|
|
oi.setIdentifier(id);
|
1590 |
|
|
|
1591 |
|
|
oi.setDateSysMetadataModified(new Date(dateModified.getTime()));
|
1592 |
|
|
|
1593 |
|
|
Checksum cs = new Checksum();
|
1594 |
|
|
cs.setValue(checksum);
|
1595 |
5906
|
berkley
|
cs.setAlgorithm(ChecksumAlgorithm.valueOf(checksumAlgorithm));
|
1596 |
5957
|
berkley
|
//cs.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));
|
1597 |
5895
|
berkley
|
oi.setChecksum(cs);
|
1598 |
|
|
|
1599 |
6124
|
cjones
|
ObjectFormat oFormat = ObjectFormatCache.getFormat(format);
|
1600 |
5895
|
berkley
|
if(oFormat != null)
|
1601 |
|
|
{
|
1602 |
|
|
oi.setObjectFormat(oFormat);
|
1603 |
|
|
}
|
1604 |
5906
|
berkley
|
else
|
1605 |
|
|
{ //if there is no object format, just default to text/plain
|
1606 |
6124
|
cjones
|
oi.setObjectFormat(ObjectFormatCache.getFormat("application/octet-stream"));
|
1607 |
5906
|
berkley
|
}
|
1608 |
5917
|
berkley
|
|
1609 |
|
|
oi.setSize(size);
|
1610 |
5895
|
berkley
|
|
1611 |
|
|
ol.addObjectInfo(oi);
|
1612 |
|
|
countIndex++;
|
1613 |
|
|
}
|
1614 |
|
|
|
1615 |
|
|
while(rs.next())
|
1616 |
|
|
{ //expend the resultset to get the total count of possible rows
|
1617 |
|
|
total++;
|
1618 |
|
|
}
|
1619 |
|
|
}
|
1620 |
|
|
catch(Exception e)
|
1621 |
|
|
{
|
1622 |
|
|
e.printStackTrace();
|
1623 |
6099
|
leinfelder
|
logMetacat.error("Error querying system metadata: " + e.getMessage());
|
1624 |
5895
|
berkley
|
}
|
1625 |
5943
|
berkley
|
finally
|
1626 |
|
|
{
|
1627 |
|
|
// Return database connection to the pool
|
1628 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1629 |
|
|
}
|
1630 |
5895
|
berkley
|
|
1631 |
|
|
ol.setStart(start);
|
1632 |
5922
|
berkley
|
ol.setCount(ol.sizeObjectInfoList());
|
1633 |
5895
|
berkley
|
ol.setTotal(total);
|
1634 |
|
|
|
1635 |
|
|
return ol;
|
1636 |
|
|
}
|
1637 |
|
|
|
1638 |
|
|
/**
|
1639 |
6099
|
leinfelder
|
* create a mapping in the identifier table
|
1640 |
5377
|
berkley
|
* @param guid
|
1641 |
|
|
* @param localId
|
1642 |
|
|
*/
|
1643 |
6099
|
leinfelder
|
public void createMapping(String guid, String localId)
|
1644 |
5453
|
berkley
|
{
|
1645 |
5334
|
berkley
|
|
1646 |
|
|
int serialNumber = -1;
|
1647 |
5333
|
berkley
|
DBConnection dbConn = null;
|
1648 |
|
|
try {
|
1649 |
|
|
|
1650 |
|
|
// Parse the localId into scope and rev parts
|
1651 |
|
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
1652 |
|
|
String docid = acc.getDocid();
|
1653 |
5344
|
berkley
|
int rev = 1;
|
1654 |
6099
|
leinfelder
|
if (acc.getRev() != null) {
|
1655 |
5344
|
berkley
|
rev = (new Integer(acc.getRev()).intValue());
|
1656 |
|
|
}
|
1657 |
5333
|
berkley
|
|
1658 |
|
|
// Get a database connection from the pool
|
1659 |
6099
|
leinfelder
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
1660 |
5333
|
berkley
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1661 |
|
|
|
1662 |
|
|
// Execute the insert statement
|
1663 |
6099
|
leinfelder
|
String query = "insert into " + TYPE_IDENTIFIER + " (guid, docid, rev) values (?, ?, ?)";
|
1664 |
5333
|
berkley
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1665 |
|
|
stmt.setString(1, guid);
|
1666 |
|
|
stmt.setString(2, docid);
|
1667 |
|
|
stmt.setInt(3, rev);
|
1668 |
6099
|
leinfelder
|
logMetacat.debug("mapping query: " + stmt.toString());
|
1669 |
5333
|
berkley
|
int rows = stmt.executeUpdate();
|
1670 |
|
|
|
1671 |
|
|
stmt.close();
|
1672 |
|
|
} catch (SQLException e) {
|
1673 |
5344
|
berkley
|
e.printStackTrace();
|
1674 |
6099
|
leinfelder
|
logMetacat.error("createGenericMapping: SQL error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
1675 |
5333
|
berkley
|
+ e.getMessage());
|
1676 |
|
|
} catch (NumberFormatException e) {
|
1677 |
5344
|
berkley
|
e.printStackTrace();
|
1678 |
6099
|
leinfelder
|
logMetacat.error("createGenericMapping: NumberFormat error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
1679 |
5333
|
berkley
|
+ e.getMessage());
|
1680 |
|
|
} catch (AccessionNumberException e) {
|
1681 |
5344
|
berkley
|
e.printStackTrace();
|
1682 |
6099
|
leinfelder
|
logMetacat.error("createGenericMapping: AccessionNumber error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
1683 |
5333
|
berkley
|
+ e.getMessage());
|
1684 |
|
|
} finally {
|
1685 |
|
|
// Return database connection to the pool
|
1686 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1687 |
|
|
}
|
1688 |
|
|
}
|
1689 |
6099
|
leinfelder
|
|
1690 |
|
|
/**
|
1691 |
|
|
* create the systemmetadata record
|
1692 |
|
|
* @param guid
|
1693 |
|
|
*/
|
1694 |
|
|
public void insertSystemMetadata(String guid)
|
1695 |
|
|
{
|
1696 |
|
|
|
1697 |
|
|
int serialNumber = -1;
|
1698 |
|
|
DBConnection dbConn = null;
|
1699 |
|
|
try {
|
1700 |
|
|
|
1701 |
|
|
// Get a database connection from the pool
|
1702 |
|
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadata");
|
1703 |
|
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1704 |
|
|
|
1705 |
|
|
// Execute the insert statement
|
1706 |
|
|
String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid) values (?)";
|
1707 |
|
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1708 |
|
|
stmt.setString(1, guid);
|
1709 |
|
|
logMetacat.debug("system metadata query: " + stmt.toString());
|
1710 |
|
|
int rows = stmt.executeUpdate();
|
1711 |
|
|
|
1712 |
|
|
stmt.close();
|
1713 |
|
|
} catch (Exception e) {
|
1714 |
|
|
e.printStackTrace();
|
1715 |
|
|
logMetacat.error("Error while creating " + TYPE_SYSTEM_METADATA + " record: "
|
1716 |
|
|
+ e.getMessage());
|
1717 |
|
|
} finally {
|
1718 |
|
|
// Return database connection to the pool
|
1719 |
|
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1720 |
|
|
}
|
1721 |
|
|
}
|
1722 |
5282
|
jones
|
}
|