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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.math.BigInteger;
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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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import java.sql.Timestamp;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.HashMap;
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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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import org.apache.log4j.Logger;
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import org.dataone.client.v2.formats.ObjectFormatCache;
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import org.dataone.service.exceptions.BaseException;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.types.v1.AccessPolicy;
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Checksum;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.ObjectFormatIdentifier;
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import org.dataone.service.types.v1.ObjectInfo;
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import org.dataone.service.types.v1.ObjectList;
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import org.dataone.service.types.v1.Permission;
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import org.dataone.service.types.v1.Replica;
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import org.dataone.service.types.v1.ReplicationPolicy;
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import org.dataone.service.types.v1.ReplicationStatus;
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import org.dataone.service.types.v1.Subject;
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import org.dataone.service.types.v2.MediaType;
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import org.dataone.service.types.v2.MediaTypeProperty;
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import org.dataone.service.types.v2.SystemMetadata;
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import edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess;
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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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import edu.ucsb.nceas.metacat.database.DatabaseService;
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.shared.AccessException;
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import edu.ucsb.nceas.metacat.shared.ServiceException;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.access.AccessControlInterface;
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import edu.ucsb.nceas.utilities.access.XMLAccessDAO;
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/**
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* Manage the relationship between Metacat local identifiers (LocalIDs) that are
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* codified as the (docid, rev) pair with globally unique string identifiers
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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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public static final String TYPE_SYSTEM_METADATA = "systemmetadata";
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public static final String TYPE_IDENTIFIER = "identifier";
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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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private Logger logMetacat = Logger.getLogger(IdentifierManager.class);
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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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private IdentifierManager() {}
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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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/*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 fmtidStr, BigInteger size, BigInteger serialVersion) {
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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);
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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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ObjectFormatIdentifier fmtid = null;
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try {
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ObjectFormatIdentifier formatId = new ObjectFormatIdentifier();
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formatId.setValue(fmtidStr);
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fmtid = ObjectFormatCache.getInstance().getFormat(formatId).getFormatId();
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sysMeta.setFormatId(fmtid);
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} catch (BaseException nfe) {
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logMetacat.error("The objectFormat " + fmtidStr +
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" is not registered. Setting the default format id.");
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fmtid = new ObjectFormatIdentifier();
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fmtid.setValue("application/octet-stream");
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sysMeta.setFormatId(fmtid);
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}
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sysMeta.setSize(size);
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sysMeta.setSerialVersion(serialVersion);
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return sysMeta;
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}*/
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/**
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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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String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
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"origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size " +
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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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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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String originMemberNode = rs.getString(6);
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String authoritativeMemberNode = rs.getString(7);
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Timestamp dateModified = rs.getTimestamp(8);
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String submitter = rs.getString(9);
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String objectFormat = rs.getString(10);
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long size = new Long(rs.getString(11)).longValue();
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h.put("guid", guid);
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h.put("date_uploaded", new Long(dateUploaded.getTime()).toString());
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h.put("rights_holder", rightsHolder);
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h.put("checksum", checksum);
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h.put("checksum_algorithm", checksumAlgorithm);
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h.put("origin_member_node", originMemberNode);
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h.put("authoritative_member_node", authoritativeMemberNode);
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h.put("date_modified", new Long(dateModified.getTime()).toString());
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h.put("submitter", submitter);
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h.put("object_format", objectFormat);
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h.put("size", new Long(size).toString());
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stmt.close();
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}
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else
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{
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stmt.close();
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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throw new McdbDocNotFoundException("2Could not find document " + localId);
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}
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}
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catch (SQLException e)
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{
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e.printStackTrace();
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logMetacat.error("Error while getting system metadata info for localid " + localId + " : "
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+ e.getMessage());
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}
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finally
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{
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// Return database connection to the pool
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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}
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return h;
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}*/
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/**
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* return a hash of all of the info that is in the systemmetadata table
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* @param guid
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* @return
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* @throws McdbDocNotFoundException
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*/
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public SystemMetadata getSystemMetadata(String guid)
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throws McdbDocNotFoundException
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{
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SystemMetadata sysMeta = new SystemMetadata();
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String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
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"origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size, " +
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"replication_allowed, number_replicas, obsoletes, obsoleted_by, serial_version, archived, series_id, file_name, media_type " +
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"from systemmetadata where guid = ?";
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DBConnection dbConn = null;
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int serialNumber = -1;
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Boolean replicationAllowed = new Boolean(false);
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BigInteger numberOfReplicas = new BigInteger("-1");
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BigInteger serialVersion = new BigInteger("-1");
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Boolean archived = new Boolean(false);
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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.getSystemMetadata");
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serialNumber = dbConn.getCheckOutSerialNumber();
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// Execute the statement
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PreparedStatement stmt = dbConn.prepareStatement(sql);
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stmt.setString(1, guid);
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ResultSet rs = stmt.executeQuery();
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if (rs.next())
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{
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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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String originMemberNode = rs.getString(6);
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String authoritativeMemberNode = rs.getString(7);
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Timestamp dateModified = rs.getTimestamp(8);
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String submitter = rs.getString(9);
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String fmtidStr = rs.getString(10);
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BigInteger size = new BigInteger(rs.getString(11));
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replicationAllowed = new Boolean(rs.getBoolean(12));
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numberOfReplicas = new BigInteger(rs.getString(13));
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String obsoletes = rs.getString(14);
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String obsoletedBy = rs.getString(15);
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serialVersion = new BigInteger(rs.getString(16));
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archived = new Boolean(rs.getBoolean(17));
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String series_id = rs.getString(18);
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String file_name = rs.getString(19);
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String media_type = rs.getString(20);
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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.setSerialVersion(serialVersion);
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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);
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sysMeta.setChecksum(checksumObject);
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if (originMemberNode != null) {
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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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}
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if (authoritativeMemberNode != null) {
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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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}
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sysMeta.setDateSysMetadataModified(dateModified);
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if (submitter != null) {
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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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}
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ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier();
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fmtid.setValue(fmtidStr);
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sysMeta.setFormatId(fmtid);
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sysMeta.setSize(size);
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if (obsoletes != null) {
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Identifier obsoletesId = new Identifier();
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obsoletesId.setValue(obsoletes);
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sysMeta.setObsoletes(obsoletesId);
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}
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if (obsoletedBy != null) {
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Identifier obsoletedById = new Identifier();
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obsoletedById.setValue(obsoletedBy);
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sysMeta.setObsoletedBy(obsoletedById);
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}
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340
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sysMeta.setArchived(archived);
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341
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if(series_id != null) {
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Identifier seriesId = new Identifier();
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seriesId.setValue(series_id);
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sysMeta.setSeriesId(seriesId);
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345
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}
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346
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if(file_name != null ) {
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347
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sysMeta.setFileName(file_name);
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348
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}
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349
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350
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if(media_type != null ) {
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351
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MediaType mediaType = new MediaType();
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352
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mediaType.setName(media_type);
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353
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// get media type properties from another table.
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354
|
String mediaTypePropertyQuery = "select name, value from smmediatypeproperties where guid = ?";
|
|
355
|
PreparedStatement stmt2 = dbConn.prepareStatement(mediaTypePropertyQuery);
|
|
356
|
stmt2.setString(1, guid);
|
|
357
|
ResultSet rs2 = stmt2.executeQuery();
|
|
358
|
while (rs2.next()) {
|
|
359
|
String name = rs2.getString(1);
|
|
360
|
String value = rs2.getString(2);
|
|
361
|
MediaTypeProperty property = new MediaTypeProperty();
|
|
362
|
property.setName(name);
|
|
363
|
property.setValue(value);
|
|
364
|
mediaType.addProperty(property);
|
|
365
|
}
|
|
366
|
sysMeta.setMediaType(mediaType);
|
|
367
|
rs2.close();
|
|
368
|
stmt2.close();
|
|
369
|
}
|
|
370
|
stmt.close();
|
|
371
|
}
|
|
372
|
else
|
|
373
|
{
|
|
374
|
stmt.close();
|
|
375
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
376
|
throw new McdbDocNotFoundException("Could not find " + guid);
|
|
377
|
}
|
|
378
|
|
|
379
|
}
|
|
380
|
catch (SQLException e)
|
|
381
|
{
|
|
382
|
e.printStackTrace();
|
|
383
|
logMetacat.error("Error while getting system metadata for guid " + guid + " : "
|
|
384
|
+ e.getMessage());
|
|
385
|
}
|
|
386
|
finally
|
|
387
|
{
|
|
388
|
// Return database connection to the pool
|
|
389
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
390
|
}
|
|
391
|
|
|
392
|
// populate the replication policy
|
|
393
|
ReplicationPolicy replicationPolicy = new ReplicationPolicy();
|
|
394
|
if ( numberOfReplicas != null && numberOfReplicas.intValue() != -1 ) {
|
|
395
|
replicationPolicy.setNumberReplicas(numberOfReplicas.intValue());
|
|
396
|
|
|
397
|
}
|
|
398
|
|
|
399
|
if ( replicationAllowed != null ) {
|
|
400
|
replicationPolicy.setReplicationAllowed(replicationAllowed);
|
|
401
|
|
|
402
|
}
|
|
403
|
replicationPolicy.setBlockedMemberNodeList(getReplicationPolicy(guid, "blocked"));
|
|
404
|
replicationPolicy.setPreferredMemberNodeList(getReplicationPolicy(guid, "preferred"));
|
|
405
|
sysMeta.setReplicationPolicy(replicationPolicy);
|
|
406
|
|
|
407
|
// look up replication status
|
|
408
|
sysMeta.setReplicaList(getReplicationStatus(guid));
|
|
409
|
|
|
410
|
// look up access policy
|
|
411
|
try {
|
|
412
|
sysMeta.setAccessPolicy(getAccessPolicy(guid));
|
|
413
|
} catch (AccessException e) {
|
|
414
|
throw new McdbDocNotFoundException(e);
|
|
415
|
}
|
|
416
|
|
|
417
|
return sysMeta;
|
|
418
|
}
|
|
419
|
|
|
420
|
|
|
421
|
private List<NodeReference> getReplicationPolicy(String guid, String policy)
|
|
422
|
throws McdbDocNotFoundException {
|
|
423
|
|
|
424
|
List<NodeReference> nodes = new ArrayList<NodeReference>();
|
|
425
|
String sql = "select guid, policy, member_node " +
|
|
426
|
"from smReplicationPolicy where guid = ? and policy = ? order by policy_id ASC";
|
|
427
|
DBConnection dbConn = null;
|
|
428
|
int serialNumber = -1;
|
|
429
|
try {
|
|
430
|
// Get a database connection from the pool
|
|
431
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicationPolicy");
|
|
432
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
433
|
|
|
434
|
// Execute the statement
|
|
435
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
436
|
stmt.setString(1, guid);
|
|
437
|
stmt.setString(2, policy);
|
|
438
|
ResultSet rs = stmt.executeQuery();
|
|
439
|
while (rs.next())
|
|
440
|
{
|
|
441
|
String memberNode = rs.getString(3);
|
|
442
|
NodeReference node = new NodeReference();
|
|
443
|
node.setValue(memberNode);
|
|
444
|
nodes.add(node);
|
|
445
|
|
|
446
|
}
|
|
447
|
stmt.close();
|
|
448
|
|
|
449
|
} catch (SQLException e) {
|
|
450
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
|
451
|
}
|
|
452
|
finally {
|
|
453
|
// Return database connection to the pool
|
|
454
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
455
|
}
|
|
456
|
|
|
457
|
return nodes;
|
|
458
|
}
|
|
459
|
|
|
460
|
private List<Replica> getReplicationStatus(String guid) throws McdbDocNotFoundException {
|
|
461
|
|
|
462
|
List<Replica> replicas = new ArrayList<Replica>();
|
|
463
|
String sql = "select guid, member_node, status, date_verified " +
|
|
464
|
"from smReplicationStatus where guid = ?";
|
|
465
|
DBConnection dbConn = null;
|
|
466
|
int serialNumber = -1;
|
|
467
|
try {
|
|
468
|
// Get a database connection from the pool
|
|
469
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicas");
|
|
470
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
471
|
|
|
472
|
// Execute the statement
|
|
473
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
474
|
stmt.setString(1, guid);
|
|
475
|
ResultSet rs = stmt.executeQuery();
|
|
476
|
while (rs.next())
|
|
477
|
{
|
|
478
|
String memberNode = rs.getString(2);
|
|
479
|
String status = rs.getString(3);
|
|
480
|
java.sql.Timestamp verified = rs.getTimestamp(4);
|
|
481
|
|
|
482
|
Replica replica = new Replica();
|
|
483
|
NodeReference node = new NodeReference();
|
|
484
|
node.setValue(memberNode);
|
|
485
|
replica.setReplicaMemberNode(node);
|
|
486
|
replica.setReplicationStatus(ReplicationStatus.valueOf(status));
|
|
487
|
replica.setReplicaVerified(new Date(verified.getTime()));
|
|
488
|
replicas.add(replica);
|
|
489
|
}
|
|
490
|
stmt.close();
|
|
491
|
|
|
492
|
} catch (SQLException e) {
|
|
493
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
|
494
|
}
|
|
495
|
finally {
|
|
496
|
// Return database connection to the pool
|
|
497
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
498
|
}
|
|
499
|
|
|
500
|
return replicas;
|
|
501
|
}
|
|
502
|
|
|
503
|
|
|
504
|
/**
|
|
505
|
* return the newest rev for a given localId
|
|
506
|
* @param localId
|
|
507
|
* @return
|
|
508
|
*/
|
|
509
|
public int getLatestRevForLocalId(String localId)
|
|
510
|
throws McdbDocNotFoundException
|
|
511
|
{
|
|
512
|
try
|
|
513
|
{
|
|
514
|
AccessionNumber acc = new AccessionNumber(localId, "NONE");
|
|
515
|
localId = acc.getDocid();
|
|
516
|
}
|
|
517
|
catch(Exception e)
|
|
518
|
{
|
|
519
|
//do nothing. just try the localId as it is
|
|
520
|
}
|
|
521
|
int rev = 0;
|
|
522
|
String sql = "select rev from xml_documents where docid like ? ";
|
|
523
|
DBConnection dbConn = null;
|
|
524
|
int serialNumber = -1;
|
|
525
|
try
|
|
526
|
{
|
|
527
|
// Get a database connection from the pool
|
|
528
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLatestRevForLocalId");
|
|
529
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
530
|
|
|
531
|
// Execute the insert statement
|
|
532
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
533
|
stmt.setString(1, localId);
|
|
534
|
ResultSet rs = stmt.executeQuery();
|
|
535
|
if (rs.next())
|
|
536
|
{
|
|
537
|
rev = rs.getInt(1);
|
|
538
|
stmt.close();
|
|
539
|
}
|
|
540
|
else
|
|
541
|
{
|
|
542
|
stmt.close();
|
|
543
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
544
|
throw new McdbDocNotFoundException("While trying to get the latest rev, could not find document " + localId);
|
|
545
|
}
|
|
546
|
}
|
|
547
|
catch (SQLException e)
|
|
548
|
{
|
|
549
|
logMetacat.error("Error while looking up the guid: "
|
|
550
|
+ e.getMessage());
|
|
551
|
}
|
|
552
|
finally
|
|
553
|
{
|
|
554
|
// Return database connection to the pool
|
|
555
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
556
|
}
|
|
557
|
return rev;
|
|
558
|
}
|
|
559
|
|
|
560
|
/**
|
|
561
|
* return all local ids in the object store that do not have associated
|
|
562
|
* system metadata
|
|
563
|
*/
|
|
564
|
public List<String> getLocalIdsWithNoSystemMetadata(boolean includeRevisions, int serverLocation)
|
|
565
|
{
|
|
566
|
Vector<String> ids = new Vector<String>();
|
|
567
|
String sql = "select docid, rev from xml_documents " +
|
|
568
|
"where docid not in " +
|
|
569
|
"(select docid from identifier where guid in (select guid from systemmetadata))";
|
|
570
|
if (serverLocation > 0) {
|
|
571
|
sql = sql + " and server_location = ? ";
|
|
572
|
}
|
|
573
|
|
|
574
|
String revisionSql = "select docid, rev from xml_revisions " +
|
|
575
|
"where docid not in " +
|
|
576
|
"(select docid from identifier where guid in (select guid from systemmetadata))";
|
|
577
|
if (serverLocation > 0) {
|
|
578
|
revisionSql = revisionSql + " and server_location = ? ";
|
|
579
|
}
|
|
580
|
|
|
581
|
if (includeRevisions) {
|
|
582
|
sql = sql + " UNION ALL " + revisionSql;
|
|
583
|
}
|
|
584
|
|
|
585
|
DBConnection dbConn = null;
|
|
586
|
int serialNumber = -1;
|
|
587
|
try
|
|
588
|
{
|
|
589
|
// Get a database connection from the pool
|
|
590
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");
|
|
591
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
592
|
|
|
593
|
// Execute the insert statement
|
|
594
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
595
|
// set params based on what we have in the query string
|
|
596
|
if (serverLocation > 0) {
|
|
597
|
stmt.setInt(1, serverLocation);
|
|
598
|
if (includeRevisions) {
|
|
599
|
stmt.setInt(2, serverLocation);
|
|
600
|
}
|
|
601
|
}
|
|
602
|
ResultSet rs = stmt.executeQuery();
|
|
603
|
while (rs.next())
|
|
604
|
{
|
|
605
|
String localid = rs.getString(1);
|
|
606
|
String rev = rs.getString(2);
|
|
607
|
localid += "." + rev;
|
|
608
|
logMetacat.debug("id to add SM for: " + localid);
|
|
609
|
ids.add(localid);
|
|
610
|
}
|
|
611
|
stmt.close();
|
|
612
|
}
|
|
613
|
catch (SQLException e)
|
|
614
|
{
|
|
615
|
logMetacat.error("Error while looking up the guid: "
|
|
616
|
+ e.getMessage());
|
|
617
|
}
|
|
618
|
finally
|
|
619
|
{
|
|
620
|
// Return database connection to the pool
|
|
621
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
622
|
}
|
|
623
|
|
|
624
|
return ids;
|
|
625
|
}
|
|
626
|
|
|
627
|
/**
|
|
628
|
* return a listing of all local ids in the object store
|
|
629
|
* @return a list of all local ids in metacat
|
|
630
|
*/
|
|
631
|
public List<String> getAllLocalIds()
|
|
632
|
// seems to be an unnecessary and restrictive throw -rnahf 13-Sep-2011
|
|
633
|
// throws Exception
|
|
634
|
{
|
|
635
|
Vector<String> ids = new Vector<String>();
|
|
636
|
String sql = "select docid from xml_documents";
|
|
637
|
DBConnection dbConn = null;
|
|
638
|
int serialNumber = -1;
|
|
639
|
try
|
|
640
|
{
|
|
641
|
// Get a database connection from the pool
|
|
642
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");
|
|
643
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
644
|
|
|
645
|
// Execute the insert statement
|
|
646
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
647
|
ResultSet rs = stmt.executeQuery();
|
|
648
|
while (rs.next())
|
|
649
|
{
|
|
650
|
String localid = rs.getString(1);
|
|
651
|
ids.add(localid);
|
|
652
|
}
|
|
653
|
stmt.close();
|
|
654
|
}
|
|
655
|
catch (SQLException e)
|
|
656
|
{
|
|
657
|
logMetacat.error("Error while looking up the guid: "
|
|
658
|
+ e.getMessage());
|
|
659
|
}
|
|
660
|
finally
|
|
661
|
{
|
|
662
|
// Return database connection to the pool
|
|
663
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
664
|
}
|
|
665
|
return ids;
|
|
666
|
}
|
|
667
|
|
|
668
|
|
|
669
|
/**
|
|
670
|
* return a listing of all guids in the object store
|
|
671
|
* @return a list of all GUIDs in metacat
|
|
672
|
*/
|
|
673
|
public List<String> getAllSystemMetadataGUIDs()
|
|
674
|
{
|
|
675
|
Vector<String> guids = new Vector<String>();
|
|
676
|
String sql = "select guid from systemmetadata";
|
|
677
|
DBConnection dbConn = null;
|
|
678
|
int serialNumber = -1;
|
|
679
|
try
|
|
680
|
{
|
|
681
|
// Get a database connection from the pool
|
|
682
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllGUIDs");
|
|
683
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
684
|
|
|
685
|
// Execute the insert statement
|
|
686
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
687
|
ResultSet rs = stmt.executeQuery();
|
|
688
|
while (rs.next())
|
|
689
|
{
|
|
690
|
String guid = rs.getString(1);
|
|
691
|
guids.add(guid);
|
|
692
|
}
|
|
693
|
stmt.close();
|
|
694
|
}
|
|
695
|
catch (SQLException e)
|
|
696
|
{
|
|
697
|
logMetacat.error("Error while retrieving the guid: "
|
|
698
|
+ e.getMessage());
|
|
699
|
}
|
|
700
|
finally
|
|
701
|
{
|
|
702
|
// Return database connection to the pool
|
|
703
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
704
|
}
|
|
705
|
return guids;
|
|
706
|
}
|
|
707
|
|
|
708
|
|
|
709
|
|
|
710
|
/**
|
|
711
|
* returns a list of system metadata-only guids since the given date
|
|
712
|
* @return a list of system ids in metacat that do not correspond to objects
|
|
713
|
* TODO: need to check which server they are on
|
|
714
|
*/
|
|
715
|
public List<String> getUpdatedSystemMetadataIds(Date since)
|
|
716
|
throws Exception
|
|
717
|
{
|
|
718
|
List<String> ids = new Vector<String>();
|
|
719
|
String sql =
|
|
720
|
"select guid from " + TYPE_SYSTEM_METADATA +
|
|
721
|
" where guid not in " +
|
|
722
|
" (select guid from " + TYPE_IDENTIFIER + ") " +
|
|
723
|
" and date_modified > ?";
|
|
724
|
DBConnection dbConn = null;
|
|
725
|
int serialNumber = -1;
|
|
726
|
try
|
|
727
|
{
|
|
728
|
// Get a database connection from the pool
|
|
729
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getUpdatedSystemMetadataIds");
|
|
730
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
731
|
|
|
732
|
// Execute the insert statement
|
|
733
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
734
|
stmt.setDate(1, new java.sql.Date(since.getTime()));
|
|
735
|
ResultSet rs = stmt.executeQuery();
|
|
736
|
while (rs.next())
|
|
737
|
{
|
|
738
|
String guid = rs.getString(1);
|
|
739
|
ids.add(guid);
|
|
740
|
}
|
|
741
|
stmt.close();
|
|
742
|
}
|
|
743
|
catch (SQLException e)
|
|
744
|
{
|
|
745
|
logMetacat.error("Error while looking up the updated guids: "
|
|
746
|
+ e.getMessage());
|
|
747
|
}
|
|
748
|
finally
|
|
749
|
{
|
|
750
|
// Return database connection to the pool
|
|
751
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
752
|
}
|
|
753
|
return ids;
|
|
754
|
}
|
|
755
|
|
|
756
|
/**
|
|
757
|
* returns a list of system metadata-only guids since the given date
|
|
758
|
* @return a list of system ids in metacat that do not correspond to objects
|
|
759
|
* TODO: need to check which server they are on
|
|
760
|
*/
|
|
761
|
public Date getLastModifiedDate() throws Exception {
|
|
762
|
Date maxDate = null;
|
|
763
|
|
|
764
|
List<String> ids = new Vector<String>();
|
|
765
|
String sql =
|
|
766
|
"select max(date_modified) from " + TYPE_SYSTEM_METADATA;
|
|
767
|
DBConnection dbConn = null;
|
|
768
|
int serialNumber = -1;
|
|
769
|
try
|
|
770
|
{
|
|
771
|
// Get a database connection from the pool
|
|
772
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLastModifiedDate");
|
|
773
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
774
|
|
|
775
|
// Execute the insert statement
|
|
776
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
|
777
|
ResultSet rs = stmt.executeQuery();
|
|
778
|
if (rs.next()) {
|
|
779
|
maxDate = rs.getDate(1);
|
|
780
|
}
|
|
781
|
stmt.close();
|
|
782
|
}
|
|
783
|
catch (SQLException e)
|
|
784
|
{
|
|
785
|
logMetacat.error("Error while looking up the latest update date: "
|
|
786
|
+ e.getMessage());
|
|
787
|
}
|
|
788
|
finally
|
|
789
|
{
|
|
790
|
// Return database connection to the pool
|
|
791
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
792
|
}
|
|
793
|
return maxDate;
|
|
794
|
}
|
|
795
|
|
|
796
|
|
|
797
|
/**
|
|
798
|
* Determine if an identifier exists already, returning true if so.
|
|
799
|
* NOTE: looks in the identifier and system metadata table for a match
|
|
800
|
* (in that order)
|
|
801
|
*
|
|
802
|
* @param guid the global identifier to look up
|
|
803
|
* @return boolean true if the identifier exists
|
|
804
|
*/
|
|
805
|
public boolean identifierExists(String guid) throws SQLException
|
|
806
|
{
|
|
807
|
boolean idExists = false;
|
|
808
|
try {
|
|
809
|
String id = getLocalId(guid);
|
|
810
|
if (id != null) {
|
|
811
|
idExists = true;
|
|
812
|
}
|
|
813
|
} catch (McdbDocNotFoundException e) {
|
|
814
|
// try system metadata only
|
|
815
|
//this will check if the guid field on the system metadata table has the id
|
|
816
|
idExists = systemMetadataPIDExists(guid);
|
|
817
|
if(!idExists) {
|
|
818
|
//if the guid field of the system metadata table doesn't have the id,
|
|
819
|
//we will check if the serial_id field of the system metadata table has it
|
|
820
|
idExists=systemMetadataSIDExists(guid);
|
|
821
|
}
|
|
822
|
|
|
823
|
}
|
|
824
|
return idExists;
|
|
825
|
}
|
|
826
|
|
|
827
|
/**
|
|
828
|
* Determine if an identifier mapping exists already,
|
|
829
|
* returning true if so.
|
|
830
|
*
|
|
831
|
* @param guid the global identifier to look up
|
|
832
|
* @return boolean true if the identifier exists
|
|
833
|
*/
|
|
834
|
public boolean mappingExists(String guid) throws SQLException
|
|
835
|
{
|
|
836
|
boolean idExists = false;
|
|
837
|
try {
|
|
838
|
String id = getLocalId(guid);
|
|
839
|
if (id != null) {
|
|
840
|
idExists = true;
|
|
841
|
}
|
|
842
|
} catch (McdbDocNotFoundException e) {
|
|
843
|
// nope!
|
|
844
|
}
|
|
845
|
return idExists;
|
|
846
|
}
|
|
847
|
|
|
848
|
/**
|
|
849
|
*
|
|
850
|
* @param guid
|
|
851
|
* @param rev
|
|
852
|
* @return
|
|
853
|
*/
|
|
854
|
public String generateLocalId(String guid, int rev)
|
|
855
|
{
|
|
856
|
return generateLocalId(guid, rev, false);
|
|
857
|
}
|
|
858
|
|
|
859
|
/**
|
|
860
|
* Given a global identifier (guid), create a suitable local identifier that
|
|
861
|
* follows Metacat's docid semantics and format (scope.id.rev), and create
|
|
862
|
* a mapping between these two identifiers. This effectively reserves both
|
|
863
|
* the global and the local identifier, as they will now be present in the
|
|
864
|
* identifier mapping table.
|
|
865
|
*
|
|
866
|
* REMOVED feature: If the incoming guid has the syntax of a
|
|
867
|
* Metacat docid (scope.id.rev), then simply use it.
|
|
868
|
* WHY: because "test.1.001" becomes "test.1.1" which is not correct for DataONE
|
|
869
|
* identifier use (those revision numbers are just chartacters and should not be interpreted)
|
|
870
|
*
|
|
871
|
* @param guid the global string identifier
|
|
872
|
* @param rev the revision number to be used in the localId
|
|
873
|
* @return String containing the localId to be used for Metacat operations
|
|
874
|
*/
|
|
875
|
public String generateLocalId(String guid, int rev, boolean isSystemMetadata)
|
|
876
|
{
|
|
877
|
String localId = "";
|
|
878
|
boolean conformsToDocidFormat = false;
|
|
879
|
|
|
880
|
// BRL -- do not allow Metacat-conforming IDs to be used:
|
|
881
|
// test.1.001 becomes test.1.1 which is NOT correct for DataONE identifiers
|
|
882
|
// Check if the guid passed in is already in docid (scope.id.rev) format
|
|
883
|
// try {
|
|
884
|
// AccessionNumber acc = new AccessionNumber(guid, "NONE");
|
|
885
|
// if (new Integer(acc.getRev()).intValue() > 0) {
|
|
886
|
// conformsToDocidFormat = true;
|
|
887
|
// }
|
|
888
|
// } catch (NumberFormatException e) {
|
|
889
|
// // No action needed, simply detecting invalid AccessionNumbers
|
|
890
|
// } catch (AccessionNumberException e) {
|
|
891
|
// // No action needed, simply detecting invalid AccessionNumbers
|
|
892
|
// } catch (SQLException e) {
|
|
893
|
// // No action needed, simply detecting invalid AccessionNumbers
|
|
894
|
// }
|
|
895
|
|
|
896
|
if (conformsToDocidFormat) {
|
|
897
|
// if it conforms, use it for both guid and localId
|
|
898
|
localId = guid;
|
|
899
|
} else {
|
|
900
|
// if not, then generate a new unique localId
|
|
901
|
localId = DocumentUtil.generateDocumentId(rev);
|
|
902
|
}
|
|
903
|
|
|
904
|
// Register this new pair in the identifier mapping table
|
|
905
|
logMetacat.debug("creating mapping in generateLocalId");
|
|
906
|
if(!isSystemMetadata)
|
|
907
|
{ //don't do this if we're generating for system metadata
|
|
908
|
createMapping(guid, localId);
|
|
909
|
}
|
|
910
|
|
|
911
|
return localId;
|
|
912
|
}
|
|
913
|
|
|
914
|
/**
|
|
915
|
* given a local identifer, look up the guid. Throw McdbDocNotFoundException
|
|
916
|
* if the docid, rev is not found in the identifiers or systemmetadata tables
|
|
917
|
*
|
|
918
|
* @param docid the docid to look up
|
|
919
|
* @param rev the revision of the docid to look up
|
|
920
|
* @return String containing the mapped guid
|
|
921
|
* @throws McdbDocNotFoundException if the docid, rev is not found
|
|
922
|
*/
|
|
923
|
public String getGUID(String docid, int rev)
|
|
924
|
throws McdbDocNotFoundException
|
|
925
|
{
|
|
926
|
logMetacat.debug("getting guid for " + docid);
|
|
927
|
String query = "select guid from identifier where docid = ? and rev = ?";
|
|
928
|
String guid = null;
|
|
929
|
|
|
930
|
DBConnection dbConn = null;
|
|
931
|
int serialNumber = -1;
|
|
932
|
PreparedStatement stmt = null;
|
|
933
|
try {
|
|
934
|
// Get a database connection from the pool
|
|
935
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getGUID");
|
|
936
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
937
|
|
|
938
|
// Execute the insert statement
|
|
939
|
stmt = dbConn.prepareStatement(query);
|
|
940
|
stmt.setString(1, docid);
|
|
941
|
stmt.setInt(2, rev);
|
|
942
|
ResultSet rs = stmt.executeQuery();
|
|
943
|
if (rs.next())
|
|
944
|
{
|
|
945
|
guid = rs.getString(1);
|
|
946
|
}
|
|
947
|
else
|
|
948
|
{
|
|
949
|
throw new McdbDocNotFoundException("No guid registered for docid " + docid + "." + rev);
|
|
950
|
}
|
|
951
|
if(rs != null) {
|
|
952
|
rs.close();
|
|
953
|
}
|
|
954
|
} catch (SQLException e) {
|
|
955
|
logMetacat.error("Error while looking up the guid: "
|
|
956
|
+ e.getMessage());
|
|
957
|
} finally {
|
|
958
|
try {
|
|
959
|
if(stmt != null) {
|
|
960
|
stmt.close();
|
|
961
|
}
|
|
962
|
} catch (Exception e) {
|
|
963
|
logMetacat.warn("Couldn't close the prepared statement since "+e.getMessage());
|
|
964
|
} finally {
|
|
965
|
// Return database connection to the pool
|
|
966
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
967
|
}
|
|
968
|
|
|
969
|
}
|
|
970
|
|
|
971
|
return guid;
|
|
972
|
}
|
|
973
|
|
|
974
|
/**
|
|
975
|
* Get the pid of the head (current) version of objects match the specified sid.
|
|
976
|
* 1. locate all candidate chain-ends for S1:
|
|
977
|
* determined by: seriesId == S1 AND (obsoletedBy == null OR obsoletedBy.seriesId != S1) // these are the type1 and type2 ends
|
|
978
|
* If obsoletedBy is missing, we generally consider it a type 2 end except:
|
|
979
|
* there is another object in the chain (has the same series id) that obsoletes the missing object.
|
|
980
|
* 2. if only 1 candidate chain-end, return it as the HEAD
|
|
981
|
* 3. otherwise return the one in the chain with the latest dateUploaded value.
|
|
982
|
* @param sid specified sid which should match.
|
|
983
|
* @return the pid of the head version. The null will be returned if there is no pid found.
|
|
984
|
* @throws SQLException
|
|
985
|
*/
|
|
986
|
public Identifier getHeadPID(Identifier sid) throws SQLException {
|
|
987
|
Identifier pid = null;
|
|
988
|
if(sid != null && sid.getValue() != null && !sid.getValue().trim().equals("")) {
|
|
989
|
logMetacat.debug("getting pid of the head version for matching the sid: " + sid.getValue());
|
|
990
|
String sql = "select guid, obsoleted_by, obsoletes from systemMetadata where series_id = ? order by date_uploaded DESC";
|
|
991
|
DBConnection dbConn = null;
|
|
992
|
int serialNumber = -1;
|
|
993
|
PreparedStatement stmt = null;
|
|
994
|
PreparedStatement stmt2 = null;
|
|
995
|
ResultSet rs = null;
|
|
996
|
ResultSet result = null;
|
|
997
|
int endsCount = 0;
|
|
998
|
boolean hasError = false;
|
|
999
|
HashMap<String, String> obsoletesIdGuidMap = new HashMap<String, String>();//the key is an obsoletes id, the value is an guid
|
|
1000
|
try {
|
|
1001
|
// Get a database connection from the pool
|
|
1002
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getHeadPID");
|
|
1003
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1004
|
// Execute the insert statement
|
|
1005
|
stmt = dbConn.prepareStatement(sql);
|
|
1006
|
stmt.setString(1, sid.getValue());
|
|
1007
|
rs = stmt.executeQuery();
|
|
1008
|
boolean hasNext = rs.next();
|
|
1009
|
boolean first = true;
|
|
1010
|
Identifier firstOne = new Identifier();//since the sql using the desc order, the first one has the latest upload date.
|
|
1011
|
if (hasNext)
|
|
1012
|
{
|
|
1013
|
while(hasNext) {
|
|
1014
|
String guidStr = rs.getString(1);
|
|
1015
|
String obsoletedByStr = rs.getString(2);
|
|
1016
|
String obsoletesStr = rs.getString(3);
|
|
1017
|
Identifier guid = new Identifier();
|
|
1018
|
guid.setValue(guidStr);
|
|
1019
|
if(obsoletesStr != null && !obsoletesStr.trim().equals("")) {
|
|
1020
|
if(obsoletesIdGuidMap.containsKey(obsoletesStr) && !guidStr.equals(obsoletesIdGuidMap.get(obsoletesStr))) {
|
|
1021
|
logMetacat.error("Both id "+guidStr+" and id "+obsoletesIdGuidMap.get(obsoletesStr)+" obsoletes the id"+obsoletesStr+
|
|
1022
|
". It is illegal. So the head pid maybe is wrong.");
|
|
1023
|
hasError = true;
|
|
1024
|
}
|
|
1025
|
obsoletesIdGuidMap.put(obsoletesStr, guidStr);
|
|
1026
|
}
|
|
1027
|
if(first) {
|
|
1028
|
firstOne = guid;
|
|
1029
|
first =false;
|
|
1030
|
}
|
|
1031
|
//SystemMetadata sysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(guid);
|
|
1032
|
//if(sysmeta.getObsoletedBy() == null) {
|
|
1033
|
if(obsoletedByStr == null || obsoletedByStr.trim().equals("")) {
|
|
1034
|
//type 1 end
|
|
1035
|
logMetacat.debug(""+guidStr+" is a type 1 end for sid "+sid.getValue());
|
|
1036
|
pid = guid;
|
|
1037
|
endsCount++;
|
|
1038
|
} else {
|
|
1039
|
//Identifier obsoletedBy = sysmeta.getObsoletedBy();
|
|
1040
|
Identifier obsoletedBy = new Identifier();
|
|
1041
|
obsoletedBy.setValue(obsoletedByStr);
|
|
1042
|
//SystemMetadata obsoletedBySysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletedBy);
|
|
1043
|
String sql2 = "select series_id, guid from systemMetadata where guid = ? ";
|
|
1044
|
stmt2 = dbConn.prepareStatement(sql2);
|
|
1045
|
stmt2.setString(1, obsoletedByStr);
|
|
1046
|
result = stmt2.executeQuery();
|
|
1047
|
boolean next = result.next();
|
|
1048
|
//if(obsoletedBySysmeta != null) {
|
|
1049
|
if(next) {
|
|
1050
|
logMetacat.debug("The object "+obsoletedBy+" which obsoletes "+guidStr+" does have a system metadata on the table.");
|
|
1051
|
//Identifier sidInObsoletedBy = obsoletedBySysmeta.getSeriesId();
|
|
1052
|
String sidInObsoletedBy = result.getString(1);
|
|
1053
|
if(sidInObsoletedBy == null|| !sidInObsoletedBy.equals(sid.getValue())) {
|
|
1054
|
// type 2 end
|
|
1055
|
logMetacat.debug(""+guidStr+" is a type 2 end for sid "+sid.getValue()+ "since it is obsoleted by the object "+sidInObsoletedBy+
|
|
1056
|
" which has a different sid or no sids");
|
|
1057
|
pid = guid;
|
|
1058
|
endsCount++;
|
|
1059
|
}
|
|
1060
|
} else {
|
|
1061
|
logMetacat.debug("The object "+obsoletedBy+" which obsoletes "+guidStr+" is missing on the host.");
|
|
1062
|
//obsoletedBySysmeta doesn't exist; it means the object is missing
|
|
1063
|
//generally, we consider it we generally consider it a type 2 end except:
|
|
1064
|
//there is another object in the chain (has the same series id) that obsoletes the missing object.
|
|
1065
|
/*String sql2 = "select guid from systemMetadata where obsoletes = ? and series_id = ?";
|
|
1066
|
PreparedStatement stmt2 = dbConn.prepareStatement(sql2);
|
|
1067
|
stmt2.setString(1, obsoletedBy.getValue());
|
|
1068
|
stmt2.setString(2, sid.getValue());
|
|
1069
|
ResultSet result = stmt2.executeQuery();
|
|
1070
|
boolean next = result.next();
|
|
1071
|
int count = 0;
|
|
1072
|
while(next) {
|
|
1073
|
count++;
|
|
1074
|
next = result.next();
|
|
1075
|
}
|
|
1076
|
if(count == 0) {
|
|
1077
|
//the exception (another object in the chain (has the same series id) that obsoletes the missing object) doesn't exist
|
|
1078
|
// it is a type 2 end
|
|
1079
|
logMetacat.debug(""+guidStr+" is a type 2 end for sid "+sid.getValue());
|
|
1080
|
pid = guid;
|
|
1081
|
endsCount++;
|
|
1082
|
} else if (count ==1) {
|
|
1083
|
// it is not end, do nothing;
|
|
1084
|
} else {
|
|
1085
|
// something is wrong - there are more than one objects obsolete the missing object!
|
|
1086
|
hasError = true;
|
|
1087
|
break;
|
|
1088
|
}*/
|
|
1089
|
if(obsoletesIdGuidMap != null && obsoletesIdGuidMap.containsKey(obsoletedByStr)) {
|
|
1090
|
//This is the exception - another object in the chain (has the same series id) that obsoletes the missing object
|
|
1091
|
//The obsoletesIdGuidMap maintains the relationship (with the same series id)
|
|
1092
|
logMetacat.debug("Though the object "+obsoletedBy+" which obsoletes "+guidStr+" is missing."+
|
|
1093
|
" However, there is another object "+obsoletesIdGuidMap.get(obsoletedByStr)+" in the chain obsoleting it. So it is not an end.");
|
|
1094
|
|
|
1095
|
} else {
|
|
1096
|
//the exception (another object in the chain (has the same series id) that obsoletes the missing object) doesn't exist
|
|
1097
|
// it is a type 2 end
|
|
1098
|
logMetacat.debug(""+guidStr+" is a type 2 end for sid "+sid.getValue());
|
|
1099
|
pid = guid;
|
|
1100
|
endsCount++;
|
|
1101
|
}
|
|
1102
|
}
|
|
1103
|
}
|
|
1104
|
hasNext = rs.next();
|
|
1105
|
}
|
|
1106
|
if(endsCount == 1) {
|
|
1107
|
//it has one end and it is an ideal chain. We already assign the guid to the pid. So do nothing.
|
|
1108
|
logMetacat.info("It is an ideal for sid "+sid.getValue());
|
|
1109
|
}
|
|
1110
|
if(hasError || endsCount >1) {
|
|
1111
|
// it is not an ideal chain, use the one with latest upload date(the first one in the result set since we have the desc order)
|
|
1112
|
logMetacat.info("It is NOT an ideal for sid "+sid.getValue());
|
|
1113
|
pid = firstOne;
|
|
1114
|
}
|
|
1115
|
} else {
|
|
1116
|
//it is not a sid or at least we don't have anything to match it.
|
|
1117
|
//do nothing, so null will be returned
|
|
1118
|
}
|
|
1119
|
|
|
1120
|
|
|
1121
|
} catch (SQLException e) {
|
|
1122
|
logMetacat.error("Error while get the head pid for the sid "+sid.getValue()+" : "
|
|
1123
|
+ e.getMessage());
|
|
1124
|
throw e;
|
|
1125
|
} finally {
|
|
1126
|
try {
|
|
1127
|
if(rs != null) {
|
|
1128
|
rs.close();
|
|
1129
|
}
|
|
1130
|
if(result != null) {
|
|
1131
|
result.close();
|
|
1132
|
}
|
|
1133
|
if(stmt != null) {
|
|
1134
|
stmt.close();
|
|
1135
|
}
|
|
1136
|
if(stmt2 != null) {
|
|
1137
|
stmt2.close();
|
|
1138
|
}
|
|
1139
|
} catch (Exception e) {
|
|
1140
|
logMetacat.warn("Couldn't close the prepared statement since "+e.getMessage());
|
|
1141
|
} finally {
|
|
1142
|
// Return database connection to the pool
|
|
1143
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1144
|
}
|
|
1145
|
}
|
|
1146
|
}
|
|
1147
|
return pid;
|
|
1148
|
}
|
|
1149
|
|
|
1150
|
/**
|
|
1151
|
* Check if the specified sid object exists on the serial id field on the system metadata table
|
|
1152
|
* @param sid
|
|
1153
|
* @return true if it exists; false otherwise.
|
|
1154
|
* @throws SQLException
|
|
1155
|
*/
|
|
1156
|
public boolean systemMetadataSIDExists(Identifier sid) throws SQLException {
|
|
1157
|
if (sid != null && sid.getValue() != null && !sid.getValue().trim().equals("")) {
|
|
1158
|
return systemMetadataSIDExists(sid.getValue());
|
|
1159
|
} else {
|
|
1160
|
return false;
|
|
1161
|
}
|
|
1162
|
}
|
|
1163
|
|
|
1164
|
/**
|
|
1165
|
* Check if the specified sid exists on the serial id field on the system metadata table
|
|
1166
|
* @param id
|
|
1167
|
* @return true if it exists; false otherwise.
|
|
1168
|
*/
|
|
1169
|
public boolean systemMetadataSIDExists(String sid) throws SQLException {
|
|
1170
|
boolean exists = false;
|
|
1171
|
logMetacat.debug("Check if the sid: " + sid +" exists on the series_id field of the system metadata table.");
|
|
1172
|
if(sid != null && !sid.trim().equals("")) {
|
|
1173
|
String sql = "select guid from systemMetadata where series_id = ?";
|
|
1174
|
DBConnection dbConn = null;
|
|
1175
|
int serialNumber = -1;
|
|
1176
|
PreparedStatement stmt = null;
|
|
1177
|
try {
|
|
1178
|
// Get a database connection from the pool
|
|
1179
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.serialIdExists");
|
|
1180
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1181
|
// Execute the insert statement
|
|
1182
|
stmt = dbConn.prepareStatement(sql);
|
|
1183
|
stmt.setString(1, sid);
|
|
1184
|
ResultSet rs = stmt.executeQuery();
|
|
1185
|
if (rs.next())
|
|
1186
|
{
|
|
1187
|
exists = true;
|
|
1188
|
}
|
|
1189
|
if(rs != null) {
|
|
1190
|
rs.close();
|
|
1191
|
}
|
|
1192
|
} catch (SQLException e) {
|
|
1193
|
logMetacat.error("Error while checking if the sid "+sid+" exists on the series_id field of the system metadata table: "
|
|
1194
|
+ e.getMessage());
|
|
1195
|
throw e;
|
|
1196
|
} finally {
|
|
1197
|
try {
|
|
1198
|
if(stmt != null) {
|
|
1199
|
stmt.close();
|
|
1200
|
}
|
|
1201
|
} catch (Exception e) {
|
|
1202
|
logMetacat.warn("Couldn't close the prepared statement since "+e.getMessage());
|
|
1203
|
} finally {
|
|
1204
|
// Return database connection to the pool
|
|
1205
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1206
|
}
|
|
1207
|
}
|
|
1208
|
}
|
|
1209
|
return exists;
|
|
1210
|
}
|
|
1211
|
|
|
1212
|
/**
|
|
1213
|
* Determine if the specified identifier object exists or not.
|
|
1214
|
* @param pid - the specified identifier
|
|
1215
|
* @return true if it is exists.
|
|
1216
|
* @throws SQLException
|
|
1217
|
* @throws NullPointerException
|
|
1218
|
*/
|
|
1219
|
public boolean systemMetadataPIDExists(Identifier pid) throws SQLException {
|
|
1220
|
if (pid != null && pid.getValue() != null && !pid.getValue().trim().equals("")) {
|
|
1221
|
return systemMetadataPIDExists(pid.getValue());
|
|
1222
|
} else {
|
|
1223
|
return false;
|
|
1224
|
}
|
|
1225
|
}
|
|
1226
|
|
|
1227
|
public boolean systemMetadataPIDExists(String guid) throws SQLException {
|
|
1228
|
logMetacat.debug("looking up system metadata for guid " + guid);
|
|
1229
|
boolean exists = false;
|
|
1230
|
String query = "select guid from systemmetadata where guid = ?";
|
|
1231
|
DBConnection dbConn = null;
|
|
1232
|
int serialNumber = -1;
|
|
1233
|
PreparedStatement stmt = null;
|
|
1234
|
if(guid != null && !guid.trim().equals("")) {
|
|
1235
|
try {
|
|
1236
|
// Get a database connection from the pool
|
|
1237
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.systemMetadataExisits");
|
|
1238
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1239
|
|
|
1240
|
// Execute the insert statement
|
|
1241
|
stmt = dbConn.prepareStatement(query);
|
|
1242
|
stmt.setString(1, guid);
|
|
1243
|
ResultSet rs = stmt.executeQuery();
|
|
1244
|
if (rs.next()) {
|
|
1245
|
exists = true;
|
|
1246
|
}
|
|
1247
|
if(rs != null) {
|
|
1248
|
rs.close();
|
|
1249
|
}
|
|
1250
|
|
|
1251
|
} catch (SQLException e) {
|
|
1252
|
logMetacat.error("Error while looking up the system metadata: "
|
|
1253
|
+ e.getMessage());
|
|
1254
|
throw e;
|
|
1255
|
} finally {
|
|
1256
|
try {
|
|
1257
|
if(stmt != null) {
|
|
1258
|
stmt.close();
|
|
1259
|
}
|
|
1260
|
} catch (Exception e) {
|
|
1261
|
logMetacat.warn("Couldn't close the prepared statement since "+e.getMessage());
|
|
1262
|
} finally {
|
|
1263
|
// Return database connection to the pool
|
|
1264
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1265
|
}
|
|
1266
|
}
|
|
1267
|
}
|
|
1268
|
return exists;
|
|
1269
|
}
|
|
1270
|
|
|
1271
|
/**
|
|
1272
|
* creates a system metadata mapping and adds additional fields from sysmeta
|
|
1273
|
* to the table for quick searching.
|
|
1274
|
*
|
|
1275
|
* @param guid the id to insert
|
|
1276
|
* @param localId the systemMetadata object to get the local id for
|
|
1277
|
* @throws McdbDocNotFoundException
|
|
1278
|
* @throws SQLException
|
|
1279
|
* @throws InvalidSystemMetadata
|
|
1280
|
*/
|
|
1281
|
public void insertOrUpdateSystemMetadata(SystemMetadata sysmeta)
|
|
1282
|
throws McdbDocNotFoundException, SQLException, InvalidSystemMetadata {
|
|
1283
|
String guid = sysmeta.getIdentifier().getValue();
|
|
1284
|
|
|
1285
|
// Get a database connection from the pool
|
|
1286
|
DBConnection dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadata");
|
|
1287
|
int serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1288
|
|
|
1289
|
try {
|
|
1290
|
// use a single transaction for it all
|
|
1291
|
dbConn.setAutoCommit(false);
|
|
1292
|
|
|
1293
|
// insert the record if needed
|
|
1294
|
if (!IdentifierManager.getInstance().systemMetadataPIDExists(guid)) {
|
|
1295
|
insertSystemMetadata(guid, dbConn);
|
|
1296
|
}
|
|
1297
|
// update with the values
|
|
1298
|
updateSystemMetadata(sysmeta, dbConn);
|
|
1299
|
|
|
1300
|
// commit if we got here with no errors
|
|
1301
|
dbConn.commit();
|
|
1302
|
} catch (Exception e) {
|
|
1303
|
e.printStackTrace();
|
|
1304
|
logMetacat.error("Error while creating " + TYPE_SYSTEM_METADATA + " record: " + guid, e );
|
|
1305
|
dbConn.rollback();
|
|
1306
|
throw new SQLException("Can't save system metadata "+e.getMessage());
|
|
1307
|
} finally {
|
|
1308
|
// Return database connection to the pool
|
|
1309
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1310
|
}
|
|
1311
|
|
|
1312
|
|
|
1313
|
}
|
|
1314
|
|
|
1315
|
|
|
1316
|
/**
|
|
1317
|
* update a mapping
|
|
1318
|
* @param guid
|
|
1319
|
* @param localId
|
|
1320
|
*/
|
|
1321
|
public void updateMapping(String guid, String localId)
|
|
1322
|
{
|
|
1323
|
|
|
1324
|
logMetacat.debug("$$$$$$$$$$$$$$ updating mapping table");
|
|
1325
|
int serialNumber = -1;
|
|
1326
|
DBConnection dbConn = null;
|
|
1327
|
try {
|
|
1328
|
// Parse the localId into scope and rev parts
|
|
1329
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
|
1330
|
String docid = acc.getDocid();
|
|
1331
|
int rev = 1;
|
|
1332
|
if(acc.getRev() != null)
|
|
1333
|
{
|
|
1334
|
rev = (new Integer(acc.getRev()).intValue());
|
|
1335
|
}
|
|
1336
|
|
|
1337
|
// Get a database connection from the pool
|
|
1338
|
dbConn =
|
|
1339
|
DBConnectionPool.getDBConnection("IdentifierManager.updateMapping");
|
|
1340
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1341
|
|
|
1342
|
// Execute the update statement
|
|
1343
|
String query = "update " + TYPE_IDENTIFIER + " set (docid, rev) = (?, ?) where guid = ?";
|
|
1344
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
|
1345
|
stmt.setString(1, docid);
|
|
1346
|
stmt.setInt(2, rev);
|
|
1347
|
stmt.setString(3, guid);
|
|
1348
|
int rows = stmt.executeUpdate();
|
|
1349
|
|
|
1350
|
stmt.close();
|
|
1351
|
} catch (SQLException e) {
|
|
1352
|
e.printStackTrace();
|
|
1353
|
logMetacat.error("SQL error while updating a mapping identifier: "
|
|
1354
|
+ e.getMessage());
|
|
1355
|
} catch (NumberFormatException e) {
|
|
1356
|
e.printStackTrace();
|
|
1357
|
logMetacat.error("NumberFormat error while updating a mapping identifier: "
|
|
1358
|
+ e.getMessage());
|
|
1359
|
} catch (AccessionNumberException e) {
|
|
1360
|
e.printStackTrace();
|
|
1361
|
logMetacat.error("AccessionNumber error while updating a mapping identifier: "
|
|
1362
|
+ e.getMessage());
|
|
1363
|
} finally {
|
|
1364
|
// Return database connection to the pool
|
|
1365
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1366
|
}
|
|
1367
|
logMetacat.debug("done updating mapping");
|
|
1368
|
}
|
|
1369
|
|
|
1370
|
private void updateSystemMetadataFields(long dateUploaded, String rightsHolder,
|
|
1371
|
String checksum, String checksumAlgorithm, String originMemberNode,
|
|
1372
|
String authoritativeMemberNode, long modifiedDate, String submitter,
|
|
1373
|
String guid, String objectFormat, BigInteger size, boolean archived,
|
|
1374
|
boolean replicationAllowed, int numberReplicas, String obsoletes,
|
|
1375
|
String obsoletedBy, BigInteger serialVersion, String seriesId,
|
|
1376
|
String fileName, MediaType mediaType, DBConnection dbConn) throws SQLException {
|
|
1377
|
PreparedStatement stmt = null;
|
|
1378
|
PreparedStatement stmt2 = null;
|
|
1379
|
try {
|
|
1380
|
dbConn.setAutoCommit(false);
|
|
1381
|
// Execute the insert statement
|
|
1382
|
String query = "update " + TYPE_SYSTEM_METADATA +
|
|
1383
|
" set (date_uploaded, rights_holder, checksum, checksum_algorithm, " +
|
|
1384
|
"origin_member_node, authoritive_member_node, date_modified, " +
|
|
1385
|
"submitter, object_format, size, archived, replication_allowed, number_replicas, " +
|
|
1386
|
"obsoletes, obsoleted_by, serial_version, series_id, file_name, media_type) " +
|
|
1387
|
"= (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,?,?) where guid = ?";
|
|
1388
|
stmt = dbConn.prepareStatement(query);
|
|
1389
|
|
|
1390
|
//data values
|
|
1391
|
stmt.setTimestamp(1, new java.sql.Timestamp(dateUploaded));
|
|
1392
|
stmt.setString(2, rightsHolder);
|
|
1393
|
stmt.setString(3, checksum);
|
|
1394
|
stmt.setString(4, checksumAlgorithm);
|
|
1395
|
stmt.setString(5, originMemberNode);
|
|
1396
|
stmt.setString(6, authoritativeMemberNode);
|
|
1397
|
stmt.setTimestamp(7, new java.sql.Timestamp(modifiedDate));
|
|
1398
|
stmt.setString(8, submitter);
|
|
1399
|
stmt.setString(9, objectFormat);
|
|
1400
|
stmt.setString(10, size.toString());
|
|
1401
|
stmt.setBoolean(11, archived);
|
|
1402
|
stmt.setBoolean(12, replicationAllowed);
|
|
1403
|
stmt.setInt(13, numberReplicas);
|
|
1404
|
stmt.setString(14, obsoletes);
|
|
1405
|
stmt.setString(15, obsoletedBy);
|
|
1406
|
if(serialVersion != null) {
|
|
1407
|
stmt.setString(16, serialVersion.toString());
|
|
1408
|
} else {
|
|
1409
|
stmt.setString(16, null);
|
|
1410
|
}
|
|
1411
|
|
|
1412
|
stmt.setString(17, seriesId);
|
|
1413
|
stmt.setString(18, fileName);
|
|
1414
|
if (mediaType == null) {
|
|
1415
|
stmt.setString(19, null);
|
|
1416
|
} else {
|
|
1417
|
stmt.setString(19, mediaType.getName());
|
|
1418
|
}
|
|
1419
|
//where clause
|
|
1420
|
stmt.setString(20, guid);
|
|
1421
|
logMetacat.debug("stmt: " + stmt.toString());
|
|
1422
|
//execute
|
|
1423
|
int rows = stmt.executeUpdate();
|
|
1424
|
|
|
1425
|
//insert media type properties into another table
|
|
1426
|
if(mediaType != null && mediaType.getPropertyList() != null) {
|
|
1427
|
String sql2 = "insert into smmediatypeproperties " +
|
|
1428
|
"(guid, name, value) " + "values (?, ?, ?)";
|
|
1429
|
stmt2 = dbConn.prepareStatement(sql2);
|
|
1430
|
for(MediaTypeProperty item : mediaType.getPropertyList()) {
|
|
1431
|
if(item != null) {
|
|
1432
|
String name = item.getName();
|
|
1433
|
String value = item.getValue();
|
|
1434
|
stmt2.setString(1, guid);
|
|
1435
|
stmt2.setString(2, name);
|
|
1436
|
stmt2.setString(3, value);
|
|
1437
|
logMetacat.debug("insert media type properties query: " + stmt2.toString());
|
|
1438
|
int row =stmt2.executeUpdate();
|
|
1439
|
}
|
|
1440
|
|
|
1441
|
}
|
|
1442
|
}
|
|
1443
|
dbConn.commit();
|
|
1444
|
dbConn.setAutoCommit(true);
|
|
1445
|
} catch (Exception e) {
|
|
1446
|
dbConn.rollback();
|
|
1447
|
dbConn.setAutoCommit(true);
|
|
1448
|
e.printStackTrace();
|
|
1449
|
throw new SQLException(e.getMessage());
|
|
1450
|
} finally {
|
|
1451
|
if(stmt != null) {
|
|
1452
|
stmt.close();
|
|
1453
|
}
|
|
1454
|
if(stmt2 != null) {
|
|
1455
|
stmt2.close();
|
|
1456
|
}
|
|
1457
|
}
|
|
1458
|
|
|
1459
|
|
|
1460
|
}
|
|
1461
|
|
|
1462
|
private void insertReplicationPolicy(String guid, String policy, List<String> memberNodes, DBConnection dbConn) throws SQLException
|
|
1463
|
{
|
|
1464
|
|
|
1465
|
// remove existing values first
|
|
1466
|
String delete = "delete from smReplicationPolicy " +
|
|
1467
|
"where guid = ? and policy = ?";
|
|
1468
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
|
1469
|
//data values
|
|
1470
|
stmt.setString(1, guid);
|
|
1471
|
stmt.setString(2, policy);
|
|
1472
|
//execute
|
|
1473
|
int deletedCount = stmt.executeUpdate();
|
|
1474
|
stmt.close();
|
|
1475
|
|
|
1476
|
for (String memberNode: memberNodes) {
|
|
1477
|
// Execute the insert statement
|
|
1478
|
String insert = "insert into smReplicationPolicy " +
|
|
1479
|
"(guid, policy, member_node) " +
|
|
1480
|
"values (?, ?, ?)";
|
|
1481
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
|
1482
|
|
|
1483
|
//data values
|
|
1484
|
insertStatement.setString(1, guid);
|
|
1485
|
insertStatement.setString(2, policy);
|
|
1486
|
insertStatement.setString(3, memberNode);
|
|
1487
|
|
|
1488
|
logMetacat.debug("smReplicationPolicy sql: " + insertStatement.toString());
|
|
1489
|
|
|
1490
|
//execute
|
|
1491
|
int rows = insertStatement.executeUpdate();
|
|
1492
|
insertStatement.close();
|
|
1493
|
}
|
|
1494
|
|
|
1495
|
}
|
|
1496
|
|
|
1497
|
private void insertReplicationStatus(String guid, List<Replica> replicas, DBConnection dbConn) throws SQLException {
|
|
1498
|
|
|
1499
|
// remove existing values first
|
|
1500
|
String delete = "delete from smReplicationStatus " +
|
|
1501
|
"where guid = ?";
|
|
1502
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
|
1503
|
//data values
|
|
1504
|
stmt.setString(1, guid);
|
|
1505
|
//execute
|
|
1506
|
int deletedCount = stmt.executeUpdate();
|
|
1507
|
stmt.close();
|
|
1508
|
|
|
1509
|
if (replicas != null) {
|
|
1510
|
for (Replica replica: replicas) {
|
|
1511
|
// Execute the insert statement
|
|
1512
|
String insert = "insert into smReplicationStatus " +
|
|
1513
|
"(guid, member_node, status, date_verified) " +
|
|
1514
|
"values (?, ?, ?, ?)";
|
|
1515
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
|
1516
|
|
|
1517
|
//data values
|
|
1518
|
String memberNode = replica.getReplicaMemberNode().getValue();
|
|
1519
|
String status = replica.getReplicationStatus().toString();
|
|
1520
|
java.sql.Timestamp sqlDate = new java.sql.Timestamp(replica.getReplicaVerified().getTime());
|
|
1521
|
insertStatement.setString(1, guid);
|
|
1522
|
insertStatement.setString(2, memberNode);
|
|
1523
|
insertStatement.setString(3, status);
|
|
1524
|
insertStatement.setTimestamp(4, sqlDate);
|
|
1525
|
|
|
1526
|
logMetacat.debug("smReplicationStatus sql: " + insertStatement.toString());
|
|
1527
|
|
|
1528
|
//execute
|
|
1529
|
int rows = insertStatement.executeUpdate();
|
|
1530
|
insertStatement.close();
|
|
1531
|
}
|
|
1532
|
}
|
|
1533
|
|
|
1534
|
}
|
|
1535
|
|
|
1536
|
/**
|
|
1537
|
* Insert the system metadata fields into the db
|
|
1538
|
* @param sm
|
|
1539
|
* @throws McdbDocNotFoundException
|
|
1540
|
* @throws SQLException
|
|
1541
|
* @throws InvalidSystemMetadata
|
|
1542
|
* @throws AccessException
|
|
1543
|
*/
|
|
1544
|
public void updateSystemMetadata(SystemMetadata sm, DBConnection dbConn)
|
|
1545
|
throws McdbDocNotFoundException, SQLException, InvalidSystemMetadata, AccessException {
|
|
1546
|
|
|
1547
|
Boolean replicationAllowed = false;
|
|
1548
|
Integer numberReplicas = -1;
|
|
1549
|
ReplicationPolicy replicationPolicy = sm.getReplicationPolicy();
|
|
1550
|
if (replicationPolicy != null) {
|
|
1551
|
replicationAllowed = replicationPolicy.getReplicationAllowed();
|
|
1552
|
numberReplicas = replicationPolicy.getNumberReplicas();
|
|
1553
|
replicationAllowed = replicationAllowed == null ? false: replicationAllowed;
|
|
1554
|
numberReplicas = numberReplicas == null ? -1: numberReplicas;
|
|
1555
|
}
|
|
1556
|
|
|
1557
|
// the main systemMetadata fields
|
|
1558
|
updateSystemMetadataFields(
|
|
1559
|
sm.getDateUploaded() == null ? null: sm.getDateUploaded().getTime(),
|
|
1560
|
sm.getRightsHolder() == null ? null: sm.getRightsHolder().getValue(),
|
|
1561
|
sm.getChecksum() == null ? null: sm.getChecksum().getValue(),
|
|
1562
|
sm.getChecksum() == null ? null: sm.getChecksum().getAlgorithm(),
|
|
1563
|
sm.getOriginMemberNode() == null ? null: sm.getOriginMemberNode().getValue(),
|
|
1564
|
sm.getAuthoritativeMemberNode() == null ? null: sm.getAuthoritativeMemberNode().getValue(),
|
|
1565
|
sm.getDateSysMetadataModified() == null ? null: sm.getDateSysMetadataModified().getTime(),
|
|
1566
|
sm.getSubmitter() == null ? null: sm.getSubmitter().getValue(),
|
|
1567
|
sm.getIdentifier().getValue(),
|
|
1568
|
sm.getFormatId() == null ? null: sm.getFormatId().getValue(),
|
|
1569
|
sm.getSize(),
|
|
1570
|
sm.getArchived() == null ? false: sm.getArchived(),
|
|
1571
|
replicationAllowed,
|
|
1572
|
numberReplicas,
|
|
1573
|
sm.getObsoletes() == null ? null:sm.getObsoletes().getValue(),
|
|
1574
|
sm.getObsoletedBy() == null ? null: sm.getObsoletedBy().getValue(),
|
|
1575
|
sm.getSerialVersion(),
|
|
1576
|
sm.getSeriesId() == null ? null: sm.getSeriesId().getValue(),
|
|
1577
|
sm.getFileName() == null ? null: sm.getFileName(),
|
|
1578
|
sm.getMediaType() == null ? null: sm.getMediaType(),
|
|
1579
|
dbConn
|
|
1580
|
);
|
|
1581
|
|
|
1582
|
String guid = sm.getIdentifier().getValue();
|
|
1583
|
|
|
1584
|
// save replication policies
|
|
1585
|
if (replicationPolicy != null) {
|
|
1586
|
List<String> nodes = null;
|
|
1587
|
String policy = null;
|
|
1588
|
|
|
1589
|
// check for null
|
|
1590
|
if (replicationPolicy.getBlockedMemberNodeList() != null) {
|
|
1591
|
nodes = new ArrayList<String>();
|
|
1592
|
policy = "blocked";
|
|
1593
|
for (NodeReference node: replicationPolicy.getBlockedMemberNodeList()) {
|
|
1594
|
nodes.add(node.getValue());
|
|
1595
|
}
|
|
1596
|
this.insertReplicationPolicy(guid, policy, nodes, dbConn);
|
|
1597
|
}
|
|
1598
|
|
|
1599
|
if (replicationPolicy.getPreferredMemberNodeList() != null) {
|
|
1600
|
nodes = new ArrayList<String>();
|
|
1601
|
policy = "preferred";
|
|
1602
|
for (NodeReference node: replicationPolicy.getPreferredMemberNodeList()) {
|
|
1603
|
nodes.add(node.getValue());
|
|
1604
|
}
|
|
1605
|
this.insertReplicationPolicy(guid, policy, nodes, dbConn);
|
|
1606
|
}
|
|
1607
|
}
|
|
1608
|
|
|
1609
|
// save replica information
|
|
1610
|
this.insertReplicationStatus(guid, sm.getReplicaList(), dbConn);
|
|
1611
|
|
|
1612
|
// save access policy
|
|
1613
|
AccessPolicy accessPolicy = sm.getAccessPolicy();
|
|
1614
|
if (accessPolicy != null) {
|
|
1615
|
this.insertAccessPolicy(guid, accessPolicy);
|
|
1616
|
}
|
|
1617
|
}
|
|
1618
|
|
|
1619
|
/**
|
|
1620
|
* Creates Metacat access rules and inserts them
|
|
1621
|
* @param accessPolicy
|
|
1622
|
* @throws McdbDocNotFoundException
|
|
1623
|
* @throws AccessException
|
|
1624
|
*/
|
|
1625
|
private void insertAccessPolicy(String guid, AccessPolicy accessPolicy) throws McdbDocNotFoundException, AccessException {
|
|
1626
|
|
|
1627
|
// check for the existing permOrder so that we remain compatible with it (DataONE does not care)
|
|
1628
|
XMLAccessAccess accessController = new XMLAccessAccess();
|
|
1629
|
String existingPermOrder = AccessControlInterface.ALLOWFIRST;
|
|
1630
|
Vector<XMLAccessDAO> existingAccess = accessController.getXMLAccessForDoc(guid);
|
|
1631
|
if (existingAccess != null && existingAccess.size() > 0) {
|
|
1632
|
existingPermOrder = existingAccess.get(0).getPermOrder();
|
|
1633
|
}
|
|
1634
|
|
|
1635
|
List<XMLAccessDAO> accessDAOs = new ArrayList<XMLAccessDAO>();
|
|
1636
|
for (AccessRule accessRule: accessPolicy.getAllowList()) {
|
|
1637
|
List<Subject> subjects = accessRule.getSubjectList();
|
|
1638
|
List<Permission> permissions = accessRule.getPermissionList();
|
|
1639
|
for (Subject subject: subjects) {
|
|
1640
|
XMLAccessDAO accessDAO = new XMLAccessDAO();
|
|
1641
|
accessDAO.setPrincipalName(subject.getValue());
|
|
1642
|
accessDAO.setGuid(guid);
|
|
1643
|
accessDAO.setPermType(AccessControlInterface.ALLOW);
|
|
1644
|
accessDAO.setPermOrder(existingPermOrder);
|
|
1645
|
if (permissions != null) {
|
|
1646
|
for (Permission permission: permissions) {
|
|
1647
|
Long metacatPermission = new Long(convertPermission(permission));
|
|
1648
|
accessDAO.addPermission(metacatPermission);
|
|
1649
|
}
|
|
1650
|
}
|
|
1651
|
accessDAOs.add(accessDAO);
|
|
1652
|
}
|
|
1653
|
}
|
|
1654
|
|
|
1655
|
|
|
1656
|
// remove all existing allow records
|
|
1657
|
accessController.deleteXMLAccessForDoc(guid, AccessControlInterface.ALLOW);
|
|
1658
|
// add the ones we can for this guid
|
|
1659
|
accessController.insertAccess(guid, accessDAOs);
|
|
1660
|
|
|
1661
|
|
|
1662
|
}
|
|
1663
|
|
|
1664
|
/**
|
|
1665
|
* Lookup access policy from Metacat
|
|
1666
|
* @param guid
|
|
1667
|
* @return
|
|
1668
|
* @throws McdbDocNotFoundException
|
|
1669
|
* @throws AccessException
|
|
1670
|
*/
|
|
1671
|
public AccessPolicy getAccessPolicy(String guid) throws McdbDocNotFoundException, AccessException {
|
|
1672
|
AccessPolicy accessPolicy = new AccessPolicy();
|
|
1673
|
|
|
1674
|
// use GUID to look up the access
|
|
1675
|
XMLAccessAccess accessController = new XMLAccessAccess();
|
|
1676
|
List<XMLAccessDAO> accessDAOs = accessController.getXMLAccessForDoc(guid);
|
|
1677
|
|
|
1678
|
for (XMLAccessDAO accessDAO: accessDAOs) {
|
|
1679
|
// only add allow rule
|
|
1680
|
if (accessDAO.getPermType().equals(AccessControlInterface.ALLOW)) {
|
|
1681
|
AccessRule accessRule = new AccessRule();
|
|
1682
|
List <Permission> permissions = convertPermission(accessDAO.getPermission().intValue());
|
|
1683
|
// cannot include if we have no permissions
|
|
1684
|
if (permissions == null || permissions.isEmpty()) {
|
|
1685
|
logMetacat.warn("skipping empty access rule permissions for " + guid);
|
|
1686
|
continue;
|
|
1687
|
}
|
|
1688
|
accessRule.setPermissionList(permissions);
|
|
1689
|
Subject subject = new Subject();
|
|
1690
|
subject.setValue(accessDAO.getPrincipalName());
|
|
1691
|
accessRule.addSubject(subject);
|
|
1692
|
accessPolicy.addAllow(accessRule);
|
|
1693
|
}
|
|
1694
|
}
|
|
1695
|
return accessPolicy;
|
|
1696
|
}
|
|
1697
|
|
|
1698
|
public int convertPermission(Permission permission) {
|
|
1699
|
if (permission.equals(Permission.READ)) {
|
|
1700
|
return AccessControlInterface.READ;
|
|
1701
|
}
|
|
1702
|
if (permission.equals(Permission.WRITE)) {
|
|
1703
|
return AccessControlInterface.WRITE;
|
|
1704
|
}
|
|
1705
|
if (permission.equals(Permission.CHANGE_PERMISSION)) {
|
|
1706
|
return AccessControlInterface.CHMOD;
|
|
1707
|
}
|
|
1708
|
return -1;
|
|
1709
|
}
|
|
1710
|
|
|
1711
|
public List<Permission> convertPermission(int permission) {
|
|
1712
|
|
|
1713
|
List<Permission> permissions = new ArrayList<Permission>();
|
|
1714
|
if (permission == AccessControlInterface.ALL) {
|
|
1715
|
permissions.add(Permission.READ);
|
|
1716
|
permissions.add(Permission.WRITE);
|
|
1717
|
permissions.add(Permission.CHANGE_PERMISSION);
|
|
1718
|
return permissions;
|
|
1719
|
}
|
|
1720
|
|
|
1721
|
if ((permission & AccessControlInterface.CHMOD) == AccessControlInterface.CHMOD) {
|
|
1722
|
permissions.add(Permission.CHANGE_PERMISSION);
|
|
1723
|
}
|
|
1724
|
if ((permission & AccessControlInterface.READ) == AccessControlInterface.READ) {
|
|
1725
|
permissions.add(Permission.READ);
|
|
1726
|
}
|
|
1727
|
if ((permission & AccessControlInterface.WRITE) == AccessControlInterface.WRITE) {
|
|
1728
|
permissions.add(Permission.WRITE);
|
|
1729
|
}
|
|
1730
|
|
|
1731
|
return permissions;
|
|
1732
|
}
|
|
1733
|
|
|
1734
|
/**
|
|
1735
|
* Lookup a localId given the GUID. If
|
|
1736
|
* the identifier is not found, throw an exception.
|
|
1737
|
*
|
|
1738
|
* @param guid the global identifier to look up
|
|
1739
|
* @return String containing the corresponding LocalId
|
|
1740
|
* @throws McdbDocNotFoundException if the identifier is not found
|
|
1741
|
*/
|
|
1742
|
public String getLocalId(String guid) throws McdbDocNotFoundException, SQLException {
|
|
1743
|
|
|
1744
|
String db_guid = "";
|
|
1745
|
String docid = "";
|
|
1746
|
int rev = 0;
|
|
1747
|
|
|
1748
|
String query = "select guid, docid, rev from " + TYPE_IDENTIFIER + " where guid = ?";
|
|
1749
|
|
|
1750
|
DBConnection dbConn = null;
|
|
1751
|
int serialNumber = -1;
|
|
1752
|
try {
|
|
1753
|
// Get a database connection from the pool
|
|
1754
|
dbConn = DBConnectionPool.getDBConnection("Identifier.getLocalId");
|
|
1755
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1756
|
|
|
1757
|
// Execute the insert statement
|
|
1758
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
|
1759
|
stmt.setString(1, guid);
|
|
1760
|
ResultSet rs = stmt.executeQuery();
|
|
1761
|
if (rs.next()) {
|
|
1762
|
db_guid = rs.getString(1);
|
|
1763
|
docid = rs.getString(2);
|
|
1764
|
rev = rs.getInt(3);
|
|
1765
|
assert(db_guid.equals(guid));
|
|
1766
|
} else {
|
|
1767
|
throw new McdbDocNotFoundException("Document not found:" + guid);
|
|
1768
|
}
|
|
1769
|
stmt.close();
|
|
1770
|
} catch (SQLException e) {
|
|
1771
|
logMetacat.error("Error while looking up the local identifier: "
|
|
1772
|
+ e.getMessage());
|
|
1773
|
throw e;
|
|
1774
|
} finally {
|
|
1775
|
// Return database connection to the pool
|
|
1776
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
1777
|
}
|
|
1778
|
return docid + "." + rev;
|
|
1779
|
}
|
|
1780
|
|
|
1781
|
/**
|
|
1782
|
* query the systemmetadata table based on the given parameters
|
|
1783
|
* @param startTime
|
|
1784
|
* @param endTime
|
|
1785
|
* @param objectFormat
|
|
1786
|
* @param nodeId
|
|
1787
|
* @param start
|
|
1788
|
* @param count
|
|
1789
|
* @return ObjectList
|
|
1790
|
* @throws SQLException
|
|
1791
|
* @throws ServiceException
|
|
1792
|
* @throws PropertyNotFoundException
|
|
1793
|
*/
|
|
1794
|
public ObjectList querySystemMetadata(Date startTime, Date endTime,
|
|
1795
|
ObjectFormatIdentifier objectFormatId, NodeReference nodeId,
|
|
1796
|
int start, int count, Identifier identifier, boolean isSID)
|
|
1797
|
throws SQLException, PropertyNotFoundException, ServiceException {
|
|
1798
|
ObjectList ol = new ObjectList();
|
|
1799
|
DBConnection dbConn = null;
|
|
1800
|
int serialNumber = -1;
|
|
1801
|
PreparedStatement countStmt=null;
|
|
1802
|
ResultSet totalResult=null;
|
|
1803
|
PreparedStatement fieldStmt = null;
|
|
1804
|
ResultSet rs= null;
|
|
1805
|
|
|
1806
|
try {
|
|
1807
|
String fieldSql = "select guid, date_uploaded, rights_holder, checksum, "
|
|
1808
|
+ "checksum_algorithm, origin_member_node, authoritive_member_node, "
|
|
1809
|
+ "date_modified, submitter, object_format, size from systemmetadata";
|
|
1810
|
|
|
1811
|
// handle special case quickly
|
|
1812
|
String countSql = "select count(guid) from systemmetadata";
|
|
1813
|
|
|
1814
|
// the clause
|
|
1815
|
String whereClauseSql = "";
|
|
1816
|
|
|
1817
|
|
|
1818
|
boolean f1 = false;
|
|
1819
|
boolean f2 = false;
|
|
1820
|
boolean f3 = false;
|
|
1821
|
boolean f4 = false;
|
|
1822
|
|
|
1823
|
|
|
1824
|
if (startTime != null) {
|
|
1825
|
whereClauseSql += " where systemmetadata.date_modified >= ?";
|
|
1826
|
f1 = true;
|
|
1827
|
}
|
|
1828
|
|
|
1829
|
if (endTime != null) {
|
|
1830
|
if (!f1) {
|
|
1831
|
whereClauseSql += " where systemmetadata.date_modified < ?";
|
|
1832
|
} else {
|
|
1833
|
whereClauseSql += " and systemmetadata.date_modified < ?";
|
|
1834
|
}
|
|
1835
|
f2 = true;
|
|
1836
|
}
|
|
1837
|
|
|
1838
|
if (objectFormatId != null) {
|
|
1839
|
if (!f1 && !f2) {
|
|
1840
|
whereClauseSql += " where object_format = ?";
|
|
1841
|
} else {
|
|
1842
|
whereClauseSql += " and object_format = ?";
|
|
1843
|
}
|
|
1844
|
f3 = true;
|
|
1845
|
}
|
|
1846
|
|
|
1847
|
if(identifier != null && identifier.getValue() != null && !identifier.getValue().equals("")) {
|
|
1848
|
if (!f1 && !f2 && !f3 ) {
|
|
1849
|
if(isSID) {
|
|
1850
|
whereClauseSql += " where series_id = ?";
|
|
1851
|
} else {
|
|
1852
|
whereClauseSql += " where guid = ?";
|
|
1853
|
}
|
|
1854
|
|
|
1855
|
} else {
|
|
1856
|
if(isSID) {
|
|
1857
|
whereClauseSql += " and series_id = ?";
|
|
1858
|
} else {
|
|
1859
|
whereClauseSql += " and guid = ?";
|
|
1860
|
}
|
|
1861
|
}
|
|
1862
|
f4 = true;
|
|
1863
|
}
|
|
1864
|
|
|
1865
|
/*if (!replicaStatus) {
|
|
1866
|
String currentNodeId = PropertyService.getInstance().getProperty("dataone.nodeId");
|
|
1867
|
if (!f1 && !f2 && !f3 && !f4) {
|
|
1868
|
whereClauseSql += " where authoritive_member_node = '" +
|
|
1869
|
currentNodeId.trim() + "'";
|
|
1870
|
} else {
|
|
1871
|
whereClauseSql += " and authoritive_member_node = '" +
|
|
1872
|
currentNodeId.trim() + "'";
|
|
1873
|
}
|
|
1874
|
}*/
|
|
1875
|
|
|
1876
|
if (nodeId != null && nodeId.getValue() != null && !nodeId.getValue().trim().equals("")) {
|
|
1877
|
if (!f1 && !f2 && !f3 && !f4) {
|
|
1878
|
whereClauseSql += " where authoritive_member_node = '" +
|
|
1879
|
nodeId.getValue().trim() + "'";
|
|
1880
|
} else {
|
|
1881
|
whereClauseSql += " and authoritive_member_node = '" +
|
|
1882
|
nodeId.getValue().trim() + "'";
|
|
1883
|
}
|
|
1884
|
}
|
|
1885
|
|
|
1886
|
|
|
1887
|
// connection
|
|
1888
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.querySystemMetadata");
|
|
1889
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
1890
|
|
|
1891
|
// the field query
|
|
1892
|
String orderBySql = " order by guid ";
|
|
1893
|
String fieldQuery = fieldSql + whereClauseSql + orderBySql;
|
|
1894
|
String finalQuery = DatabaseService.getInstance().getDBAdapter().getPagedQuery(fieldQuery, start, count);
|
|
1895
|
fieldStmt = dbConn.prepareStatement(finalQuery);
|
|
1896
|
|
|
1897
|
// construct the count query and statment
|
|
1898
|
String countQuery = countSql + whereClauseSql;
|
|
1899
|
countStmt = dbConn.prepareStatement(countQuery);
|
|
1900
|
|
|
1901
|
if (f1 && f2 && f3 && f4) {
|
|
1902
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1903
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1904
|
fieldStmt.setString(3, objectFormatId.getValue());
|
|
1905
|
fieldStmt.setString(4, identifier.getValue());
|
|
1906
|
// count
|
|
1907
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1908
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1909
|
countStmt.setString(3, objectFormatId.getValue());
|
|
1910
|
countStmt.setString(4, identifier.getValue());
|
|
1911
|
} if (f1 && f2 && f3 && !f4) {
|
|
1912
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1913
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1914
|
fieldStmt.setString(3, objectFormatId.getValue());
|
|
1915
|
// count
|
|
1916
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1917
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1918
|
countStmt.setString(3, objectFormatId.getValue());
|
|
1919
|
} else if (f1 && f2 && !f3 && f4) {
|
|
1920
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1921
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1922
|
fieldStmt.setString(3, identifier.getValue());
|
|
1923
|
// count
|
|
1924
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1925
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1926
|
countStmt.setString(3, identifier.getValue());
|
|
1927
|
} else if (f1 && f2 && !f3 && !f4) {
|
|
1928
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1929
|
fieldStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1930
|
// count
|
|
1931
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1932
|
countStmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
|
1933
|
} else if (f1 && !f2 && f3 && f4) {
|
|
1934
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1935
|
fieldStmt.setString(2, objectFormatId.getValue());
|
|
1936
|
fieldStmt.setString(3, identifier.getValue());
|
|
1937
|
// count
|
|
1938
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1939
|
countStmt.setString(2, objectFormatId.getValue());
|
|
1940
|
countStmt.setString(3, identifier.getValue());
|
|
1941
|
} else if (f1 && !f2 && f3 && !f4) {
|
|
1942
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1943
|
fieldStmt.setString(2, objectFormatId.getValue());
|
|
1944
|
// count
|
|
1945
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1946
|
countStmt.setString(2, objectFormatId.getValue());
|
|
1947
|
} else if (f1 && !f2 && !f3 && f4) {
|
|
1948
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1949
|
fieldStmt.setString(2, identifier.getValue());
|
|
1950
|
// count
|
|
1951
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1952
|
countStmt.setString(2, identifier.getValue());
|
|
1953
|
} else if (f1 && !f2 && !f3 && !f4) {
|
|
1954
|
fieldStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1955
|
// count
|
|
1956
|
countStmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
|
1957
|
} else if (!f1 && f2 && f3 && f4) {
|
|
1958
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1959
|
fieldStmt.setString(2, objectFormatId.getValue());
|
|
1960
|
fieldStmt.setString(3, identifier.getValue());
|
|
1961
|
// count
|
|
1962
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1963
|
countStmt.setString(2, objectFormatId.getValue());
|
|
1964
|
countStmt.setString(3, identifier.getValue());
|
|
1965
|
} else if (!f1 && f2 && f3 && !f4) {
|
|
1966
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1967
|
fieldStmt.setString(2, objectFormatId.getValue());
|
|
1968
|
// count
|
|
1969
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1970
|
countStmt.setString(2, objectFormatId.getValue());
|
|
1971
|
} else if (!f1 && !f2 && f3 && f4) {
|
|
1972
|
fieldStmt.setString(1, objectFormatId.getValue());
|
|
1973
|
fieldStmt.setString(2, identifier.getValue());
|
|
1974
|
// count
|
|
1975
|
countStmt.setString(1, objectFormatId.getValue());
|
|
1976
|
countStmt.setString(2, identifier.getValue());
|
|
1977
|
} else if (!f1 && !f2 && f3 && !f4) {
|
|
1978
|
fieldStmt.setString(1, objectFormatId.getValue());
|
|
1979
|
// count
|
|
1980
|
countStmt.setString(1, objectFormatId.getValue());
|
|
1981
|
} else if (!f1 && f2 && !f3 && f4) {
|
|
1982
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1983
|
fieldStmt.setString(2, identifier.getValue());
|
|
1984
|
// count
|
|
1985
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1986
|
countStmt.setString(2, identifier.getValue());
|
|
1987
|
} else if (!f1 && f2 && !f3 && !f4) {
|
|
1988
|
fieldStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1989
|
// count
|
|
1990
|
countStmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
|
1991
|
} else if (!f1 && !f2 && !f3 && f4) {
|
|
1992
|
fieldStmt.setString(1, identifier.getValue());
|
|
1993
|
// count
|
|
1994
|
countStmt.setString(1, identifier.getValue());
|
|
1995
|
} else if (!f1 && !f2 && !f3 && !f4) {
|
|
1996
|
//do nothing
|
|
1997
|
}
|
|
1998
|
|
|
1999
|
logMetacat.debug("list objects fieldStmt: " + fieldStmt.toString());
|
|
2000
|
|
|
2001
|
logMetacat.debug("list objects countStmt: " + countStmt.toString());
|
|
2002
|
|
|
2003
|
// get the total object count no matter what
|
|
2004
|
int total = 0;
|
|
2005
|
totalResult = countStmt.executeQuery();
|
|
2006
|
if (totalResult.next()) {
|
|
2007
|
total = totalResult.getInt(1);
|
|
2008
|
}
|
|
2009
|
|
|
2010
|
logMetacat.debug("list objects total: " + total);
|
|
2011
|
|
|
2012
|
// set the totals
|
|
2013
|
ol.setStart(start);
|
|
2014
|
ol.setCount(count);
|
|
2015
|
|
|
2016
|
// retrieve the actual records if requested
|
|
2017
|
if (count != 0) {
|
|
2018
|
|
|
2019
|
rs = fieldStmt.executeQuery();
|
|
2020
|
while (rs.next()) {
|
|
2021
|
|
|
2022
|
String guid = rs.getString(1);
|
|
2023
|
logMetacat.debug("query found object with guid " + guid);
|
|
2024
|
// Timestamp dateUploaded = rs.getTimestamp(2);
|
|
2025
|
// String rightsHolder = rs.getString(3);
|
|
2026
|
String checksum = rs.getString(4);
|
|
2027
|
String checksumAlgorithm = rs.getString(5);
|
|
2028
|
// String originMemberNode = rs.getString(6);
|
|
2029
|
// String authoritiveMemberNode = rs.getString(7);
|
|
2030
|
Timestamp dateModified = rs.getTimestamp(8);
|
|
2031
|
// String submitter = rs.getString(9);
|
|
2032
|
String fmtidStr = rs.getString(10);
|
|
2033
|
String sz = rs.getString(11);
|
|
2034
|
BigInteger size = new BigInteger("0");
|
|
2035
|
|
|
2036
|
if (sz != null && !sz.trim().equals("")) {
|
|
2037
|
size = new BigInteger(rs.getString(11));
|
|
2038
|
}
|
|
2039
|
|
|
2040
|
ObjectInfo oi = new ObjectInfo();
|
|
2041
|
|
|
2042
|
Identifier id = new Identifier();
|
|
2043
|
id.setValue(guid);
|
|
2044
|
oi.setIdentifier(id);
|
|
2045
|
|
|
2046
|
if (dateModified != null) {
|
|
2047
|
oi.setDateSysMetadataModified(dateModified);
|
|
2048
|
}
|
|
2049
|
|
|
2050
|
Checksum cs = new Checksum();
|
|
2051
|
cs.setValue(checksum);
|
|
2052
|
try {
|
|
2053
|
// cs.setAlgorithm(ChecksumAlgorithm.valueOf(checksumAlgorithm));
|
|
2054
|
cs.setAlgorithm(checksumAlgorithm);
|
|
2055
|
} catch (Exception e) {
|
|
2056
|
logMetacat.error("could not parse checksum algorithm", e);
|
|
2057
|
continue;
|
|
2058
|
}
|
|
2059
|
oi.setChecksum(cs);
|
|
2060
|
|
|
2061
|
// set the format type
|
|
2062
|
ObjectFormatIdentifier fmtid = new ObjectFormatIdentifier();
|
|
2063
|
fmtid.setValue(fmtidStr);
|
|
2064
|
oi.setFormatId(fmtid);
|
|
2065
|
|
|
2066
|
oi.setSize(size);
|
|
2067
|
|
|
2068
|
ol.addObjectInfo(oi);
|
|
2069
|
|
|
2070
|
}
|
|
2071
|
|
|
2072
|
logMetacat.debug("list objects count: " + ol.sizeObjectInfoList());
|
|
2073
|
// set the actual count retrieved
|
|
2074
|
ol.setCount(ol.sizeObjectInfoList());
|
|
2075
|
|
|
2076
|
|
|
2077
|
}
|
|
2078
|
ol.setTotal(total);
|
|
2079
|
} finally {
|
|
2080
|
// Return database connection to the pool
|
|
2081
|
try {
|
|
2082
|
if(totalResult !=null ){
|
|
2083
|
totalResult.close();
|
|
2084
|
}
|
|
2085
|
if(countStmt!=null ) {
|
|
2086
|
countStmt.close();
|
|
2087
|
}
|
|
2088
|
if(rs != null) {
|
|
2089
|
rs.close();
|
|
2090
|
}
|
|
2091
|
if(fieldStmt != null) {
|
|
2092
|
fieldStmt.close();
|
|
2093
|
}
|
|
2094
|
|
|
2095
|
} catch (SQLException sql) {
|
|
2096
|
|
|
2097
|
}
|
|
2098
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2099
|
|
|
2100
|
}
|
|
2101
|
if(ol != null) {
|
|
2102
|
logMetacat.debug("list objects start(before returning): " + ol.getStart());
|
|
2103
|
logMetacat.debug("list objects count: " + ol.getCount());
|
|
2104
|
logMetacat.debug("list objects total: " + ol.getTotal());
|
|
2105
|
}
|
|
2106
|
return ol;
|
|
2107
|
}
|
|
2108
|
|
|
2109
|
/**
|
|
2110
|
* create a mapping in the identifier table
|
|
2111
|
* @param guid
|
|
2112
|
* @param localId
|
|
2113
|
*/
|
|
2114
|
public void createMapping(String guid, String localId)
|
|
2115
|
{
|
|
2116
|
|
|
2117
|
int serialNumber = -1;
|
|
2118
|
DBConnection dbConn = null;
|
|
2119
|
try {
|
|
2120
|
|
|
2121
|
// Parse the localId into scope and rev parts
|
|
2122
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
|
2123
|
String docid = acc.getDocid();
|
|
2124
|
int rev = 1;
|
|
2125
|
if (acc.getRev() != null) {
|
|
2126
|
rev = (new Integer(acc.getRev()).intValue());
|
|
2127
|
}
|
|
2128
|
|
|
2129
|
// Get a database connection from the pool
|
|
2130
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
|
2131
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
2132
|
|
|
2133
|
// Execute the insert statement
|
|
2134
|
String query = "insert into " + TYPE_IDENTIFIER + " (guid, docid, rev) values (?, ?, ?)";
|
|
2135
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
|
2136
|
stmt.setString(1, guid);
|
|
2137
|
stmt.setString(2, docid);
|
|
2138
|
stmt.setInt(3, rev);
|
|
2139
|
logMetacat.debug("mapping query: " + stmt.toString());
|
|
2140
|
int rows = stmt.executeUpdate();
|
|
2141
|
|
|
2142
|
stmt.close();
|
|
2143
|
} catch (SQLException e) {
|
|
2144
|
e.printStackTrace();
|
|
2145
|
logMetacat.error("createGenericMapping: SQL error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
|
2146
|
+ e.getMessage());
|
|
2147
|
} catch (NumberFormatException e) {
|
|
2148
|
e.printStackTrace();
|
|
2149
|
logMetacat.error("createGenericMapping: NumberFormat error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
|
2150
|
+ e.getMessage());
|
|
2151
|
} catch (AccessionNumberException e) {
|
|
2152
|
e.printStackTrace();
|
|
2153
|
logMetacat.error("createGenericMapping: AccessionNumber error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
|
2154
|
+ e.getMessage());
|
|
2155
|
} finally {
|
|
2156
|
// Return database connection to the pool
|
|
2157
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2158
|
}
|
|
2159
|
}
|
|
2160
|
|
|
2161
|
/**
|
|
2162
|
* remove a mapping in the identifier table
|
|
2163
|
* @param guid
|
|
2164
|
* @param localId
|
|
2165
|
*/
|
|
2166
|
public void removeMapping(String guid, String localId)
|
|
2167
|
{
|
|
2168
|
|
|
2169
|
int serialNumber = -1;
|
|
2170
|
DBConnection dbConn = null;
|
|
2171
|
try {
|
|
2172
|
|
|
2173
|
// Parse the localId into scope and rev parts
|
|
2174
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
|
2175
|
String docid = acc.getDocid();
|
|
2176
|
int rev = 1;
|
|
2177
|
if (acc.getRev() != null) {
|
|
2178
|
rev = (new Integer(acc.getRev()).intValue());
|
|
2179
|
}
|
|
2180
|
|
|
2181
|
// Get a database connection from the pool
|
|
2182
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.removeMapping");
|
|
2183
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
2184
|
|
|
2185
|
// Execute the insert statement
|
|
2186
|
String query = "DELETE FROM " + TYPE_IDENTIFIER + " WHERE guid = ? AND docid = ? AND rev = ?";
|
|
2187
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
|
2188
|
stmt.setString(1, guid);
|
|
2189
|
stmt.setString(2, docid);
|
|
2190
|
stmt.setInt(3, rev);
|
|
2191
|
logMetacat.debug("remove mapping query: " + stmt.toString());
|
|
2192
|
int rows = stmt.executeUpdate();
|
|
2193
|
|
|
2194
|
stmt.close();
|
|
2195
|
} catch (SQLException e) {
|
|
2196
|
e.printStackTrace();
|
|
2197
|
logMetacat.error("removeMapping: SQL error while removing a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
|
2198
|
+ e.getMessage());
|
|
2199
|
} catch (NumberFormatException e) {
|
|
2200
|
e.printStackTrace();
|
|
2201
|
logMetacat.error("removeMapping: NumberFormat error while removing a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
|
2202
|
+ e.getMessage());
|
|
2203
|
} catch (AccessionNumberException e) {
|
|
2204
|
e.printStackTrace();
|
|
2205
|
logMetacat.error("removeMapping: AccessionNumber error while removing a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
|
2206
|
+ e.getMessage());
|
|
2207
|
} finally {
|
|
2208
|
// Return database connection to the pool
|
|
2209
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2210
|
}
|
|
2211
|
}
|
|
2212
|
|
|
2213
|
/**
|
|
2214
|
* create the systemmetadata record
|
|
2215
|
* @param guid
|
|
2216
|
* @param dbConn
|
|
2217
|
* @throws SQLException
|
|
2218
|
*/
|
|
2219
|
private void insertSystemMetadata(String guid, DBConnection dbConn) throws SQLException
|
|
2220
|
{
|
|
2221
|
|
|
2222
|
// Execute the insert statement
|
|
2223
|
String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid) values (?)";
|
|
2224
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
|
2225
|
stmt.setString(1, guid);
|
|
2226
|
logMetacat.debug("system metadata query: " + stmt.toString());
|
|
2227
|
int rows = stmt.executeUpdate();
|
|
2228
|
|
|
2229
|
stmt.close();
|
|
2230
|
|
|
2231
|
}
|
|
2232
|
|
|
2233
|
public boolean deleteSystemMetadata(String guid)
|
|
2234
|
{
|
|
2235
|
boolean success = false;
|
|
2236
|
int serialNumber = -1;
|
|
2237
|
DBConnection dbConn = null;
|
|
2238
|
String query = null;
|
|
2239
|
PreparedStatement stmt = null;
|
|
2240
|
int rows = 0;
|
|
2241
|
try {
|
|
2242
|
|
|
2243
|
// Get a database connection from the pool
|
|
2244
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.deleteSystemMetadata");
|
|
2245
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
2246
|
dbConn.setAutoCommit(false);
|
|
2247
|
|
|
2248
|
// remove the smReplicationPolicy
|
|
2249
|
query = "delete from smReplicationPolicy " +
|
|
2250
|
"where guid = ?";
|
|
2251
|
stmt = dbConn.prepareStatement(query);
|
|
2252
|
stmt.setString(1, guid);
|
|
2253
|
logMetacat.debug("delete smReplicationPolicy: " + stmt.toString());
|
|
2254
|
rows = stmt.executeUpdate();
|
|
2255
|
stmt.close();
|
|
2256
|
|
|
2257
|
// remove the smReplicationStatus
|
|
2258
|
query = "delete from smReplicationStatus " +
|
|
2259
|
"where guid = ?";
|
|
2260
|
stmt = dbConn.prepareStatement(query);
|
|
2261
|
stmt.setString(1, guid);
|
|
2262
|
logMetacat.debug("delete smReplicationStatus: " + stmt.toString());
|
|
2263
|
rows = stmt.executeUpdate();
|
|
2264
|
stmt.close();
|
|
2265
|
|
|
2266
|
// remove the smmediatypeproperties
|
|
2267
|
query = "delete from smmediatypeproperties " +
|
|
2268
|
"where guid = ?";
|
|
2269
|
stmt = dbConn.prepareStatement(query);
|
|
2270
|
stmt.setString(1, guid);
|
|
2271
|
logMetacat.debug("delete smmediatypeproperties: " + stmt.toString());
|
|
2272
|
rows = stmt.executeUpdate();
|
|
2273
|
stmt.close();
|
|
2274
|
|
|
2275
|
// remove main system metadata entry
|
|
2276
|
query = "delete from " + TYPE_SYSTEM_METADATA + " where guid = ? ";
|
|
2277
|
stmt = dbConn.prepareStatement(query);
|
|
2278
|
stmt.setString(1, guid);
|
|
2279
|
logMetacat.debug("delete system metadata: " + stmt.toString());
|
|
2280
|
rows = stmt.executeUpdate();
|
|
2281
|
stmt.close();
|
|
2282
|
|
|
2283
|
dbConn.commit();
|
|
2284
|
dbConn.setAutoCommit(true);
|
|
2285
|
success = true;
|
|
2286
|
// TODO: remove the access?
|
|
2287
|
// Metacat keeps "deleted" documents so we should not remove access rules.
|
|
2288
|
|
|
2289
|
} catch (Exception e) {
|
|
2290
|
e.printStackTrace();
|
|
2291
|
logMetacat.error("Error while deleting " + TYPE_SYSTEM_METADATA + " record: " + guid, e );
|
|
2292
|
try {
|
|
2293
|
dbConn.rollback();
|
|
2294
|
} catch (SQLException sqle) {
|
|
2295
|
logMetacat.error("Error while rolling back delete for record: " + guid, sqle );
|
|
2296
|
}
|
|
2297
|
} finally {
|
|
2298
|
// Return database connection to the pool
|
|
2299
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2300
|
}
|
|
2301
|
return success;
|
|
2302
|
}
|
|
2303
|
|
|
2304
|
public void updateAuthoritativeMemberNodeId(String existingMemberNodeId, String newMemberNodeId)
|
|
2305
|
{
|
|
2306
|
DBConnection dbConn = null;
|
|
2307
|
int serialNumber = -1;
|
|
2308
|
|
|
2309
|
try {
|
|
2310
|
// Get a database connection from the pool
|
|
2311
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.updateAuthoritativeMemberNodeId");
|
|
2312
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
2313
|
|
|
2314
|
// Execute the insert statement
|
|
2315
|
String query = "update " + TYPE_SYSTEM_METADATA +
|
|
2316
|
" set authoritive_member_node = ? " +
|
|
2317
|
" where authoritive_member_node = ?";
|
|
2318
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
|
2319
|
|
|
2320
|
//data values
|
|
2321
|
stmt.setString(1, newMemberNodeId);
|
|
2322
|
stmt.setString(2, existingMemberNodeId);
|
|
2323
|
|
|
2324
|
logMetacat.debug("stmt: " + stmt.toString());
|
|
2325
|
//execute
|
|
2326
|
int rows = stmt.executeUpdate();
|
|
2327
|
|
|
2328
|
stmt.close();
|
|
2329
|
} catch (SQLException e) {
|
|
2330
|
e.printStackTrace();
|
|
2331
|
logMetacat.error("updateSystemMetadataFields: SQL error while updating system metadata: "
|
|
2332
|
+ e.getMessage());
|
|
2333
|
} catch (NumberFormatException e) {
|
|
2334
|
e.printStackTrace();
|
|
2335
|
logMetacat.error("updateSystemMetadataFields: NumberFormat error while updating system metadata: "
|
|
2336
|
+ e.getMessage());
|
|
2337
|
} finally {
|
|
2338
|
// Return database connection to the pool
|
|
2339
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2340
|
}
|
|
2341
|
}
|
|
2342
|
}
|
|
2343
|
|