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/**
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* '$RCSfile$'
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* Copyright: 2010 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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*
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* '$Author: jones $'
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* '$Date: 2010-02-03 17:58:12 -0900 (Wed, 03 Feb 2010) $'
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* '$Revision: 5211 $'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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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.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.service.types.Checksum;
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import org.dataone.service.types.ChecksumAlgorithm;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.NodeReference;
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import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.ObjectInfo;
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import org.dataone.service.types.ObjectList;
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import org.dataone.service.types.Replica;
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import org.dataone.service.types.ReplicationPolicy;
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import org.dataone.service.types.ReplicationStatus;
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import org.dataone.service.types.Subject;
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import org.dataone.service.types.SystemMetadata;
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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.properties.PropertyService;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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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 objectFormat, long size) {
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SystemMetadata sysMeta = new SystemMetadata();
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Identifier sysMetaId = new Identifier();
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sysMetaId.setValue(guid);
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sysMeta.setIdentifier(sysMetaId);
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sysMeta.setDateUploaded(dateUploaded);
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Subject rightsHolderSubject = new Subject();
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rightsHolderSubject.setValue(rightsHolder);
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sysMeta.setRightsHolder(rightsHolderSubject);
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Checksum checksumObject = new Checksum();
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checksumObject.setValue(checksum);
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checksumObject.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));
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sysMeta.setChecksum(checksumObject);
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NodeReference omn = new NodeReference();
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omn.setValue(originMemberNode);
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sysMeta.setOriginMemberNode(omn);
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NodeReference amn = new NodeReference();
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amn.setValue(authoritativeMemberNode);
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sysMeta.setAuthoritativeMemberNode(amn);
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sysMeta.setDateSysMetadataModified(dateModified);
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Subject submitterSubject = new Subject();
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submitterSubject.setValue(submitter);
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sysMeta.setSubmitter(submitterSubject);
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sysMeta.setObjectFormat(ObjectFormat.convert(objectFormat));
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sysMeta.setSize(size);
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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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*/
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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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"from systemmetadata where guid = ?";
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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.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 objectFormat = rs.getString(10);
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long size = new Long(rs.getString(11)).longValue();
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Identifier sysMetaId = new Identifier();
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sysMetaId.setValue(guid);
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sysMeta.setIdentifier(sysMetaId);
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sysMeta.setDateUploaded(dateUploaded);
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Subject rightsHolderSubject = new Subject();
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rightsHolderSubject.setValue(rightsHolder);
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sysMeta.setRightsHolder(rightsHolderSubject);
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Checksum checksumObject = new Checksum();
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checksumObject.setValue(checksum);
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checksumObject.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));
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sysMeta.setChecksum(checksumObject);
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NodeReference omn = new NodeReference();
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omn.setValue(originMemberNode);
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sysMeta.setOriginMemberNode(omn);
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NodeReference amn = new NodeReference();
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amn.setValue(authoritativeMemberNode);
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sysMeta.setAuthoritativeMemberNode(amn);
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sysMeta.setDateSysMetadataModified(dateModified);
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Subject submitterSubject = new Subject();
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submitterSubject.setValue(submitter);
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sysMeta.setSubmitter(submitterSubject);
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sysMeta.setObjectFormat(ObjectFormat.convert(objectFormat));
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sysMeta.setSize(size);
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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("Could not find " + guid);
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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 for guid " + guid + " : "
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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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// look up provenance information
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sysMeta.setObsoleteList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "obsoletes"));
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sysMeta.setObsoletedByList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "obsoletedBy"));
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sysMeta.setDescribeList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "describes"));
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sysMeta.setDescribedByList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "describedBy"));
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sysMeta.setDerivedFromList(getSystemMetadataProvenance(sysMeta.getIdentifier().getValue(), "derivedFrom"));
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// look up replication policy
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ReplicationPolicy replicationPolicy = new ReplicationPolicy();
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replicationPolicy.setBlockedMemberNodeList(getReplicationPolicy(guid, "blocked"));
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replicationPolicy.setPreferredMemberNodeList(getReplicationPolicy(guid, "preferred"));
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sysMeta.setReplicationPolicy(replicationPolicy);
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// look up replication status
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sysMeta.setReplicaList(getReplicationStatus(guid));
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return sysMeta;
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}
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private List<Identifier> getSystemMetadataProvenance(String guid, String relationship)
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throws McdbDocNotFoundException {
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List<Identifier> identifiers = new ArrayList<Identifier>();
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String sql = "select guid, relationship, target_guid " +
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"from systemMetadataProvenance where guid = ? and relationship = ?";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try {
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getSystemMetadataProvenance");
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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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stmt.setString(2, relationship);
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ResultSet rs = stmt.executeQuery();
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while (rs.next())
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{
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String targetGuid = rs.getString(3);
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Identifier id = new Identifier();
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id.setValue(targetGuid);
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identifiers.add(id);
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}
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stmt.close();
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}
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catch (SQLException e) {
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logMetacat.error("Error while getting system metadata provenance for guid " + guid, e);
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}
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finally {
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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 identifiers;
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}
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private List<NodeReference> getReplicationPolicy(String guid, String policy)
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throws McdbDocNotFoundException {
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357
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List<NodeReference> nodes = new ArrayList<NodeReference>();
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String sql = "select guid, policy, member_node " +
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"from systemMetadataReplicationPolicy where guid = ? and policy = ?";
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DBConnection dbConn = null;
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int serialNumber = -1;
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try {
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicationPolicy");
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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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stmt.setString(2, policy);
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ResultSet rs = stmt.executeQuery();
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while (rs.next())
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{
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String memberNode = rs.getString(3);
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NodeReference node = new NodeReference();
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node.setValue(memberNode);
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nodes.add(node);
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}
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stmt.close();
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382
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} catch (SQLException e) {
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384
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logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
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385
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}
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finally {
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387
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// Return database connection to the pool
|
388
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
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}
|
390
|
|
391
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return nodes;
|
392
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}
|
393
|
|
394
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private List<Replica> getReplicationStatus(String guid) throws McdbDocNotFoundException {
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395
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|
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List<Replica> replicas = new ArrayList<Replica>();
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String sql = "select guid, member_node, status, date_verified " +
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"from systemMetadataReplicationStatus where guid = ?";
|
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DBConnection dbConn = null;
|
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int serialNumber = -1;
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try {
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// Get a database connection from the pool
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dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getReplicas");
|
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serialNumber = dbConn.getCheckOutSerialNumber();
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405
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// Execute the statement
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407
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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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while (rs.next())
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411
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{
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412
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String memberNode = rs.getString(2);
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413
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String status = rs.getString(3);
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414
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java.sql.Date verified = rs.getDate(4);
|
415
|
|
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Replica replica = new Replica();
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NodeReference node = new NodeReference();
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node.setValue(memberNode);
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419
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replica.setReplicaMemberNode(node);
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replica.setReplicationStatus(ReplicationStatus.convert(status));
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replica.setReplicaVerified(new Date(verified.getTime()));
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replicas.add(replica);
|
423
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}
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424
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stmt.close();
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425
|
|
426
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} catch (SQLException e) {
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427
|
logMetacat.error("Error while getting system metadata replication policy for guid " + guid, e);
|
428
|
}
|
429
|
finally {
|
430
|
// Return database connection to the pool
|
431
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
432
|
}
|
433
|
|
434
|
return replicas;
|
435
|
}
|
436
|
|
437
|
/**
|
438
|
* return information on the document with localId. These are the fields
|
439
|
* from the xml_documents table. They can be used to contstruct metadata
|
440
|
* about the object that is stored.
|
441
|
* @param localId
|
442
|
* @return
|
443
|
* @throws McdbDocNotFoundException
|
444
|
*/
|
445
|
public Hashtable<String, Object> getDocumentInfo(String localId)
|
446
|
throws McdbDocNotFoundException
|
447
|
{
|
448
|
try
|
449
|
{
|
450
|
AccessionNumber acc = new AccessionNumber(localId, "NONE");
|
451
|
localId = acc.getDocid();
|
452
|
}
|
453
|
catch(Exception e)
|
454
|
{
|
455
|
//do nothing. just try the localId as it is
|
456
|
}
|
457
|
Hashtable<String, Object> h = new Hashtable<String, Object>();
|
458
|
String sql = "select docname, doctype, user_owner, user_updated, " +
|
459
|
"server_location, rev, date_created, date_updated from " +
|
460
|
"xml_documents where docid like '" + localId + "'";
|
461
|
DBConnection dbConn = null;
|
462
|
int serialNumber = -1;
|
463
|
try
|
464
|
{
|
465
|
// Get a database connection from the pool
|
466
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getDocumentInfo");
|
467
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
468
|
|
469
|
// Execute the insert statement
|
470
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
471
|
ResultSet rs = stmt.executeQuery();
|
472
|
if (rs.next())
|
473
|
{
|
474
|
String docname = rs.getString(1);
|
475
|
String doctype = rs.getString(2);
|
476
|
String user_owner = rs.getString(3);
|
477
|
String user_updated = rs.getString(4);
|
478
|
String server_location = rs.getString(5);
|
479
|
int rev = rs.getInt(6);
|
480
|
String date_created = rs.getString(7);
|
481
|
String date_updated = rs.getString(8);
|
482
|
h.put("docid", localId);
|
483
|
h.put("docname", docname);
|
484
|
h.put("doctype", doctype);
|
485
|
h.put("user_owner", user_owner);
|
486
|
h.put("user_updated", user_updated);
|
487
|
h.put("server_location", server_location);
|
488
|
h.put("rev", new Integer(rev).toString());
|
489
|
h.put("date_created", date_created);
|
490
|
h.put("date_updated", date_updated);
|
491
|
|
492
|
stmt.close();
|
493
|
}
|
494
|
else
|
495
|
{
|
496
|
stmt.close();
|
497
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
498
|
throw new McdbDocNotFoundException("2Could not find document " + localId);
|
499
|
}
|
500
|
|
501
|
String sql2 = "select principal_name, permission, perm_type, perm_order from xml_access " +
|
502
|
"where docid like '" + localId + "'";
|
503
|
logMetacat.debug("executing sql: " + sql2);
|
504
|
PreparedStatement stmt2 = dbConn.prepareStatement(sql2);
|
505
|
rs = stmt2.executeQuery();
|
506
|
Vector accessVector = new Vector();
|
507
|
while(rs.next())
|
508
|
{
|
509
|
Hashtable accessHash = new Hashtable();
|
510
|
String principal_name = rs.getString(1);
|
511
|
String permission = rs.getString(2);
|
512
|
String permissionType = rs.getString(3);
|
513
|
String permissionOrder = rs.getString(4);
|
514
|
accessHash.put("principal_name", principal_name);
|
515
|
accessHash.put("permission", permission);
|
516
|
accessHash.put("permission_type", permissionType);
|
517
|
accessHash.put("permission_order", permissionOrder);
|
518
|
logMetacat.debug("accessHash: " + accessHash.toString());
|
519
|
accessVector.add(accessHash);
|
520
|
}
|
521
|
h.put("access", accessVector);
|
522
|
}
|
523
|
catch (SQLException e)
|
524
|
{
|
525
|
e.printStackTrace();
|
526
|
logMetacat.error("Error while getting document info for localid " + localId + " : "
|
527
|
+ e.getMessage());
|
528
|
}
|
529
|
finally
|
530
|
{
|
531
|
// Return database connection to the pool
|
532
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
533
|
}
|
534
|
return h;
|
535
|
}
|
536
|
|
537
|
/**
|
538
|
* return the newest rev for a given localId
|
539
|
* @param localId
|
540
|
* @return
|
541
|
*/
|
542
|
public int getLatestRevForLocalId(String localId)
|
543
|
throws McdbDocNotFoundException
|
544
|
{
|
545
|
try
|
546
|
{
|
547
|
AccessionNumber acc = new AccessionNumber(localId, "NONE");
|
548
|
localId = acc.getDocid();
|
549
|
}
|
550
|
catch(Exception e)
|
551
|
{
|
552
|
//do nothing. just try the localId as it is
|
553
|
}
|
554
|
int rev = 0;
|
555
|
String sql = "select rev from xml_documents where docid like '" + localId + "'";
|
556
|
DBConnection dbConn = null;
|
557
|
int serialNumber = -1;
|
558
|
try
|
559
|
{
|
560
|
// Get a database connection from the pool
|
561
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLatestRevForLocalId");
|
562
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
563
|
|
564
|
// Execute the insert statement
|
565
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
566
|
ResultSet rs = stmt.executeQuery();
|
567
|
if (rs.next())
|
568
|
{
|
569
|
rev = rs.getInt(1);
|
570
|
stmt.close();
|
571
|
}
|
572
|
else
|
573
|
{
|
574
|
stmt.close();
|
575
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
576
|
throw new McdbDocNotFoundException("While trying to get the latest rev, could not find document " + localId);
|
577
|
}
|
578
|
}
|
579
|
catch (SQLException e)
|
580
|
{
|
581
|
logMetacat.error("Error while looking up the guid: "
|
582
|
+ e.getMessage());
|
583
|
}
|
584
|
finally
|
585
|
{
|
586
|
// Return database connection to the pool
|
587
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
588
|
}
|
589
|
return rev;
|
590
|
}
|
591
|
|
592
|
/**
|
593
|
* return all local ids in the object store that do not have associated
|
594
|
* system metadata
|
595
|
*/
|
596
|
public List<String> getLocalIdsWithNoSystemMetadata()
|
597
|
{
|
598
|
Vector<String> ids = new Vector<String>();
|
599
|
String sql = "select docid, rev from xml_documents " +
|
600
|
"where docid not in " +
|
601
|
"(select docid from identifier where guid in (select guid from systemmetadata)))";
|
602
|
DBConnection dbConn = null;
|
603
|
int serialNumber = -1;
|
604
|
try
|
605
|
{
|
606
|
// Get a database connection from the pool
|
607
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");
|
608
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
609
|
|
610
|
// Execute the insert statement
|
611
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
612
|
ResultSet rs = stmt.executeQuery();
|
613
|
while (rs.next())
|
614
|
{
|
615
|
String localid = rs.getString(1);
|
616
|
String rev = rs.getString(2);
|
617
|
localid += "." + rev;
|
618
|
logMetacat.debug("id to add SM for: " + localid);
|
619
|
ids.add(localid);
|
620
|
}
|
621
|
stmt.close();
|
622
|
}
|
623
|
catch (SQLException e)
|
624
|
{
|
625
|
logMetacat.error("Error while looking up the guid: "
|
626
|
+ e.getMessage());
|
627
|
}
|
628
|
finally
|
629
|
{
|
630
|
// Return database connection to the pool
|
631
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
632
|
}
|
633
|
|
634
|
return ids;
|
635
|
}
|
636
|
|
637
|
/**
|
638
|
* return a listing of all local ids in the object store
|
639
|
* @return a list of all local ids in metacat
|
640
|
*/
|
641
|
public List<String> getAllLocalIds()
|
642
|
throws Exception
|
643
|
{
|
644
|
Vector<String> ids = new Vector<String>();
|
645
|
String sql = "select docid from xml_documents";
|
646
|
DBConnection dbConn = null;
|
647
|
int serialNumber = -1;
|
648
|
try
|
649
|
{
|
650
|
// Get a database connection from the pool
|
651
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");
|
652
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
653
|
|
654
|
// Execute the insert statement
|
655
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
656
|
ResultSet rs = stmt.executeQuery();
|
657
|
while (rs.next())
|
658
|
{
|
659
|
String localid = rs.getString(1);
|
660
|
ids.add(localid);
|
661
|
}
|
662
|
stmt.close();
|
663
|
}
|
664
|
catch (SQLException e)
|
665
|
{
|
666
|
logMetacat.error("Error while looking up the guid: "
|
667
|
+ e.getMessage());
|
668
|
}
|
669
|
finally
|
670
|
{
|
671
|
// Return database connection to the pool
|
672
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
673
|
}
|
674
|
return ids;
|
675
|
}
|
676
|
|
677
|
|
678
|
|
679
|
/**
|
680
|
* Determine if an identifier exists already, returning true if so.
|
681
|
*
|
682
|
* @param guid the global identifier to look up
|
683
|
* @return boolean true if the identifier exists
|
684
|
*/
|
685
|
public boolean identifierExists(String guid)
|
686
|
{
|
687
|
boolean idExists = false;
|
688
|
try {
|
689
|
String id = getLocalId(guid);
|
690
|
if (id != null) {
|
691
|
idExists = true;
|
692
|
}
|
693
|
} catch (McdbDocNotFoundException e) {
|
694
|
idExists = false;
|
695
|
}
|
696
|
return idExists;
|
697
|
}
|
698
|
|
699
|
/**
|
700
|
*
|
701
|
* @param guid
|
702
|
* @param rev
|
703
|
* @return
|
704
|
*/
|
705
|
public String generateLocalId(String guid, int rev)
|
706
|
{
|
707
|
return generateLocalId(guid, rev, false);
|
708
|
}
|
709
|
|
710
|
/**
|
711
|
* Given a global identifier (guid), create a suitable local identifier that
|
712
|
* follows Metacat's docid semantics and format (scope.id.rev), and create
|
713
|
* a mapping between these two identifiers. This effectively reserves both
|
714
|
* the global and the local identifier, as they will now be present in the
|
715
|
* identifier mapping table. If the incoming guid has the syntax of a
|
716
|
* Metacat docid (scope.id.rev), then simply use it.
|
717
|
*
|
718
|
* @param guid the global string identifier
|
719
|
* @param rev the revision number to be used in the localId
|
720
|
* @return String containing the localId to be used for Metacat operations
|
721
|
*/
|
722
|
public String generateLocalId(String guid, int rev, boolean isSystemMetadata)
|
723
|
{
|
724
|
String localId = "";
|
725
|
boolean conformsToDocidFormat = false;
|
726
|
|
727
|
// Check if the guid passed in is already in docid (scope.id.rev) format
|
728
|
try {
|
729
|
AccessionNumber acc = new AccessionNumber(guid, "NONE");
|
730
|
if (new Integer(acc.getRev()).intValue() > 0) {
|
731
|
conformsToDocidFormat = true;
|
732
|
}
|
733
|
} catch (NumberFormatException e) {
|
734
|
// No action needed, simply detecting invalid AccessionNumbers
|
735
|
} catch (AccessionNumberException e) {
|
736
|
// No action needed, simply detecting invalid AccessionNumbers
|
737
|
} catch (SQLException e) {
|
738
|
// No action needed, simply detecting invalid AccessionNumbers
|
739
|
}
|
740
|
|
741
|
if (conformsToDocidFormat) {
|
742
|
// if it conforms, use it for both guid and localId
|
743
|
localId = guid;
|
744
|
} else {
|
745
|
// if not, then generate a new unique localId
|
746
|
localId = DocumentUtil.generateDocumentId(rev);
|
747
|
}
|
748
|
|
749
|
// Register this new pair in the identifier mapping table
|
750
|
logMetacat.debug("creating mapping in generateLocalId");
|
751
|
if(!isSystemMetadata)
|
752
|
{ //don't do this if we're generating for system metadata
|
753
|
createMapping(guid, localId);
|
754
|
}
|
755
|
|
756
|
return localId;
|
757
|
}
|
758
|
|
759
|
/**
|
760
|
* given a local identifer, look up the guid. Throw McdbDocNotFoundException
|
761
|
* if the docid, rev is not found in the identifiers or systemmetadata tables
|
762
|
*
|
763
|
* @param docid the docid to look up
|
764
|
* @param rev the revision of the docid to look up
|
765
|
* @return String containing the mapped guid
|
766
|
* @throws McdbDocNotFoundException if the docid, rev is not found
|
767
|
*/
|
768
|
public String getGUID(String docid, int rev)
|
769
|
throws McdbDocNotFoundException
|
770
|
{
|
771
|
logMetacat.debug("getting guid for " + docid);
|
772
|
String query = "select guid from identifier where docid = ? and rev = ?";
|
773
|
String guid = null;
|
774
|
|
775
|
DBConnection dbConn = null;
|
776
|
int serialNumber = -1;
|
777
|
try {
|
778
|
// Get a database connection from the pool
|
779
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getGUID");
|
780
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
781
|
|
782
|
// Execute the insert statement
|
783
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
784
|
stmt.setString(1, docid);
|
785
|
stmt.setInt(2, rev);
|
786
|
ResultSet rs = stmt.executeQuery();
|
787
|
if (rs.next())
|
788
|
{
|
789
|
guid = rs.getString(1);
|
790
|
}
|
791
|
else
|
792
|
{
|
793
|
throw new McdbDocNotFoundException("No guid registered for docid " + docid + "." + rev);
|
794
|
}
|
795
|
|
796
|
} catch (SQLException e) {
|
797
|
logMetacat.error("Error while looking up the guid: "
|
798
|
+ e.getMessage());
|
799
|
} finally {
|
800
|
// Return database connection to the pool
|
801
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
802
|
}
|
803
|
|
804
|
return guid;
|
805
|
}
|
806
|
|
807
|
/**
|
808
|
* creates a system metadata mapping and adds additional fields from sysmeta
|
809
|
* to the table for quick searching.
|
810
|
*
|
811
|
* @param guid the id to insert
|
812
|
* @param localId the systemMetadata object to get the local id for
|
813
|
*/
|
814
|
public void createSystemMetadata(SystemMetadata sysmeta)
|
815
|
{
|
816
|
insertSystemMetadata(sysmeta.getIdentifier().getValue());
|
817
|
updateSystemMetadata(sysmeta);
|
818
|
}
|
819
|
|
820
|
|
821
|
/**
|
822
|
* update a mapping
|
823
|
* @param guid
|
824
|
* @param localId
|
825
|
*/
|
826
|
public void updateMapping(String guid, String localId)
|
827
|
{
|
828
|
|
829
|
logMetacat.debug("$$$$$$$$$$$$$$ updating mapping table");
|
830
|
int serialNumber = -1;
|
831
|
DBConnection dbConn = null;
|
832
|
try {
|
833
|
// Parse the localId into scope and rev parts
|
834
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
835
|
String docid = acc.getDocid();
|
836
|
int rev = 1;
|
837
|
if(acc.getRev() != null)
|
838
|
{
|
839
|
rev = (new Integer(acc.getRev()).intValue());
|
840
|
}
|
841
|
|
842
|
// Get a database connection from the pool
|
843
|
dbConn =
|
844
|
DBConnectionPool.getDBConnection("IdentifierManager.updateMapping");
|
845
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
846
|
|
847
|
// Execute the update statement
|
848
|
String query = "update " + TYPE_IDENTIFIER + " set (docid, rev) = (?, ?) where guid='" + guid + "'";
|
849
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
850
|
stmt.setString(1, docid);
|
851
|
stmt.setInt(2, rev);
|
852
|
int rows = stmt.executeUpdate();
|
853
|
|
854
|
stmt.close();
|
855
|
} catch (SQLException e) {
|
856
|
e.printStackTrace();
|
857
|
logMetacat.error("SQL error while updating a mapping identifier: "
|
858
|
+ e.getMessage());
|
859
|
} catch (NumberFormatException e) {
|
860
|
e.printStackTrace();
|
861
|
logMetacat.error("NumberFormat error while updating a mapping identifier: "
|
862
|
+ e.getMessage());
|
863
|
} catch (AccessionNumberException e) {
|
864
|
e.printStackTrace();
|
865
|
logMetacat.error("AccessionNumber error while updating a mapping identifier: "
|
866
|
+ e.getMessage());
|
867
|
} finally {
|
868
|
// Return database connection to the pool
|
869
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
870
|
}
|
871
|
logMetacat.debug("done updating mapping");
|
872
|
}
|
873
|
|
874
|
private void updateSystemMetadataFields(long dateUploaded, String rightsHolder,
|
875
|
String checksum, String checksumAlgorithm, String originMemberNode,
|
876
|
String authoritativeMemberNode, long modifiedDate, String submitter,
|
877
|
String guid, String objectFormat, long size, boolean replicationAllowed,
|
878
|
int numberReplicas)
|
879
|
{
|
880
|
DBConnection dbConn = null;
|
881
|
int serialNumber = -1;
|
882
|
|
883
|
try {
|
884
|
// Get a database connection from the pool
|
885
|
dbConn =
|
886
|
DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
887
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
888
|
|
889
|
// Execute the insert statement
|
890
|
String query = "update " + TYPE_SYSTEM_METADATA +
|
891
|
" set (date_uploaded, rights_holder, checksum, checksum_algorithm, " +
|
892
|
"origin_member_node, authoritive_member_node, date_modified, " +
|
893
|
"submitter, object_format, size, replication_allowed, number_replicas) " +
|
894
|
"= (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) where guid = ?";
|
895
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
896
|
|
897
|
//data values
|
898
|
stmt.setTimestamp(1, new java.sql.Timestamp(dateUploaded));
|
899
|
stmt.setString(2, rightsHolder);
|
900
|
stmt.setString(3, checksum);
|
901
|
stmt.setString(4, checksumAlgorithm);
|
902
|
stmt.setString(5, originMemberNode);
|
903
|
stmt.setString(6, authoritativeMemberNode);
|
904
|
stmt.setTimestamp(7, new java.sql.Timestamp(modifiedDate));
|
905
|
stmt.setString(8, submitter);
|
906
|
stmt.setString(9, objectFormat);
|
907
|
stmt.setString(10, new Long(size).toString());
|
908
|
stmt.setBoolean(11, replicationAllowed);
|
909
|
stmt.setInt(12, numberReplicas);
|
910
|
//where clause
|
911
|
stmt.setString(13, guid);
|
912
|
logMetacat.debug("stmt: " + stmt.toString());
|
913
|
//execute
|
914
|
int rows = stmt.executeUpdate();
|
915
|
|
916
|
stmt.close();
|
917
|
} catch (SQLException e) {
|
918
|
e.printStackTrace();
|
919
|
logMetacat.error("insertAdditionalSystemMetadataFields: SQL error while creating a mapping to the system metadata identifier: "
|
920
|
+ e.getMessage());
|
921
|
} catch (NumberFormatException e) {
|
922
|
e.printStackTrace();
|
923
|
logMetacat.error("insertAdditionalSystemMetadataFields: NumberFormat error while creating a mapping to the system metadata identifier: "
|
924
|
+ e.getMessage());
|
925
|
} finally {
|
926
|
// Return database connection to the pool
|
927
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
928
|
}
|
929
|
}
|
930
|
|
931
|
private void insertSystemMetadataProvenance(String guid, String relationship, List<String> targetGuids)
|
932
|
{
|
933
|
DBConnection dbConn = null;
|
934
|
int serialNumber = -1;
|
935
|
|
936
|
try {
|
937
|
// Get a database connection from the pool
|
938
|
dbConn =
|
939
|
DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadataProvenance");
|
940
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
941
|
|
942
|
// remove existing values first
|
943
|
String delete = "delete from systemMetadataProvenance " +
|
944
|
"where guid = ? and relationship = ?";
|
945
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
946
|
//data values
|
947
|
stmt.setString(1, guid);
|
948
|
stmt.setString(2, relationship);
|
949
|
//execute
|
950
|
int deletedCount = stmt.executeUpdate();
|
951
|
stmt.close();
|
952
|
|
953
|
for (String targetGuid: targetGuids) {
|
954
|
// Execute the insert statement
|
955
|
String insert = "insert into systemMetadataProvenance " +
|
956
|
"(guid, relationship, target_guid) " +
|
957
|
"values (?, ?, ?)";
|
958
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
959
|
|
960
|
//data values
|
961
|
insertStatement.setString(1, guid);
|
962
|
insertStatement.setString(2, relationship);
|
963
|
insertStatement.setString(3, targetGuid);
|
964
|
//execute
|
965
|
int rows = insertStatement.executeUpdate();
|
966
|
insertStatement.close();
|
967
|
}
|
968
|
} catch (SQLException e) {
|
969
|
logMetacat.error("SQL error while adding systemMetadataProvenance for: " + guid, e);
|
970
|
} finally {
|
971
|
// Return database connection to the pool
|
972
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
973
|
}
|
974
|
}
|
975
|
|
976
|
private void insertReplicationPolicy(String guid, String policy, List<String> memberNodes)
|
977
|
{
|
978
|
DBConnection dbConn = null;
|
979
|
int serialNumber = -1;
|
980
|
|
981
|
try {
|
982
|
// Get a database connection from the pool
|
983
|
dbConn =
|
984
|
DBConnectionPool.getDBConnection("IdentifierManager.insertReplicationPolicy");
|
985
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
986
|
|
987
|
// remove existing values first
|
988
|
String delete = "delete from systemMetadataReplicationPolicy " +
|
989
|
"where guid = ? and policy = ?";
|
990
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
991
|
//data values
|
992
|
stmt.setString(1, guid);
|
993
|
stmt.setString(2, policy);
|
994
|
//execute
|
995
|
int deletedCount = stmt.executeUpdate();
|
996
|
stmt.close();
|
997
|
|
998
|
for (String memberNode: memberNodes) {
|
999
|
// Execute the insert statement
|
1000
|
String insert = "insert into systemMetadataReplicationPolicy " +
|
1001
|
"(guid, policy, member_node) " +
|
1002
|
"values (?, ?, ?)";
|
1003
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1004
|
|
1005
|
//data values
|
1006
|
insertStatement.setString(1, guid);
|
1007
|
insertStatement.setString(2, policy);
|
1008
|
insertStatement.setString(3, memberNode);
|
1009
|
//execute
|
1010
|
int rows = insertStatement.executeUpdate();
|
1011
|
insertStatement.close();
|
1012
|
}
|
1013
|
} catch (SQLException e) {
|
1014
|
logMetacat.error("SQL error while adding systemMetadataReplicationPolicy for: " + guid, e);
|
1015
|
} finally {
|
1016
|
// Return database connection to the pool
|
1017
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1018
|
}
|
1019
|
}
|
1020
|
|
1021
|
private void insertReplicationStatus(String guid, List<Replica> replicas) {
|
1022
|
DBConnection dbConn = null;
|
1023
|
int serialNumber = -1;
|
1024
|
|
1025
|
try {
|
1026
|
// Get a database connection from the pool
|
1027
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertReplicas");
|
1028
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1029
|
|
1030
|
// remove existing values first
|
1031
|
String delete = "delete from systemMetadataReplicationStatus " +
|
1032
|
"where guid = ?";
|
1033
|
PreparedStatement stmt = dbConn.prepareStatement(delete);
|
1034
|
//data values
|
1035
|
stmt.setString(1, guid);
|
1036
|
//execute
|
1037
|
int deletedCount = stmt.executeUpdate();
|
1038
|
stmt.close();
|
1039
|
|
1040
|
for (Replica replica: replicas) {
|
1041
|
// Execute the insert statement
|
1042
|
String insert = "insert into systemMetadataReplicationStatus " +
|
1043
|
"(guid, member_node, status, date_verified) " +
|
1044
|
"values (?, ?, ?, ?)";
|
1045
|
PreparedStatement insertStatement = dbConn.prepareStatement(insert);
|
1046
|
|
1047
|
//data values
|
1048
|
String memberNode = replica.getReplicaMemberNode().getValue();
|
1049
|
String status = replica.getReplicationStatus().toString();
|
1050
|
java.sql.Date sqlDate = new java.sql.Date(replica.getReplicaVerified().getTime());
|
1051
|
insertStatement.setString(1, guid);
|
1052
|
insertStatement.setString(2, memberNode);
|
1053
|
insertStatement.setString(3, status);
|
1054
|
insertStatement.setDate(4, sqlDate);
|
1055
|
|
1056
|
//execute
|
1057
|
int rows = insertStatement.executeUpdate();
|
1058
|
insertStatement.close();
|
1059
|
}
|
1060
|
} catch (SQLException e) {
|
1061
|
logMetacat.error("SQL error while adding systemMetadataReplicationStatus for: " + guid, e);
|
1062
|
} finally {
|
1063
|
// Return database connection to the pool
|
1064
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1065
|
}
|
1066
|
}
|
1067
|
|
1068
|
/**
|
1069
|
* Insert the system metadata fields into the db
|
1070
|
* @param sm
|
1071
|
*/
|
1072
|
public void updateSystemMetadata(SystemMetadata sm) {
|
1073
|
|
1074
|
Boolean replicationAllowed = false;
|
1075
|
Integer numberReplicas = -1;
|
1076
|
ReplicationPolicy replicationPolicy = sm.getReplicationPolicy();
|
1077
|
if (replicationPolicy != null) {
|
1078
|
replicationAllowed = replicationPolicy.getReplicationAllowed();
|
1079
|
numberReplicas = replicationPolicy.getNumberReplicas();
|
1080
|
replicationAllowed = replicationAllowed == null ? false: replicationAllowed;
|
1081
|
numberReplicas = numberReplicas == null ? -1: numberReplicas;
|
1082
|
}
|
1083
|
|
1084
|
// the main systemMetadata fields
|
1085
|
updateSystemMetadataFields(
|
1086
|
sm.getDateUploaded().getTime(),
|
1087
|
sm.getRightsHolder().getValue(),
|
1088
|
sm.getChecksum().getValue(),
|
1089
|
sm.getChecksum().getAlgorithm().name(),
|
1090
|
sm.getOriginMemberNode().getValue(),
|
1091
|
sm.getAuthoritativeMemberNode().getValue(),
|
1092
|
sm.getDateSysMetadataModified().getTime(),
|
1093
|
sm.getSubmitter().getValue(),
|
1094
|
sm.getIdentifier().getValue(),
|
1095
|
sm.getObjectFormat().toString(),
|
1096
|
sm.getSize(),
|
1097
|
replicationAllowed,
|
1098
|
numberReplicas);
|
1099
|
|
1100
|
// add provenance information
|
1101
|
String guid = sm.getIdentifier().getValue();
|
1102
|
List<String> targetGuids = null;
|
1103
|
String relationship = null;
|
1104
|
|
1105
|
relationship = "obsoletedBy";
|
1106
|
targetGuids = new ArrayList<String>();
|
1107
|
for (Identifier id: sm.getObsoletedByList()) {
|
1108
|
targetGuids.add(id.getValue());
|
1109
|
}
|
1110
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1111
|
|
1112
|
relationship = "obsoletes";
|
1113
|
targetGuids = new ArrayList<String>();
|
1114
|
for (Identifier id: sm.getObsoleteList()) {
|
1115
|
targetGuids.add(id.getValue());
|
1116
|
}
|
1117
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1118
|
|
1119
|
relationship = "describes";
|
1120
|
targetGuids = new ArrayList<String>();
|
1121
|
for (Identifier id: sm.getDescribeList()) {
|
1122
|
targetGuids.add(id.getValue());
|
1123
|
}
|
1124
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1125
|
|
1126
|
relationship = "describedBy";
|
1127
|
targetGuids = new ArrayList<String>();
|
1128
|
for (Identifier id: sm.getDescribedByList()) {
|
1129
|
targetGuids.add(id.getValue());
|
1130
|
}
|
1131
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1132
|
|
1133
|
relationship = "derivedFrom";
|
1134
|
targetGuids = new ArrayList<String>();
|
1135
|
for (Identifier id: sm.getDerivedFromList()) {
|
1136
|
targetGuids.add(id.getValue());
|
1137
|
}
|
1138
|
this.insertSystemMetadataProvenance(guid, relationship, targetGuids);
|
1139
|
|
1140
|
// save replication policies
|
1141
|
if (replicationPolicy != null) {
|
1142
|
List<String> nodes = null;
|
1143
|
String policy = null;
|
1144
|
|
1145
|
nodes = new ArrayList<String>();
|
1146
|
policy = "blocked";
|
1147
|
for (NodeReference node: replicationPolicy.getBlockedMemberNodeList()) {
|
1148
|
nodes.add(node.getValue());
|
1149
|
}
|
1150
|
this.insertReplicationPolicy(guid, policy, nodes);
|
1151
|
|
1152
|
nodes = new ArrayList<String>();
|
1153
|
policy = "preferred";
|
1154
|
for (NodeReference node: replicationPolicy.getPreferredMemberNodeList()) {
|
1155
|
nodes.add(node.getValue());
|
1156
|
}
|
1157
|
this.insertReplicationPolicy(guid, policy, nodes);
|
1158
|
}
|
1159
|
|
1160
|
// save replica information
|
1161
|
this.insertReplicationStatus(guid, sm.getReplicaList());
|
1162
|
|
1163
|
}
|
1164
|
|
1165
|
/**
|
1166
|
* Lookup a localId given the GUID. If
|
1167
|
* the identifier is not found, throw an exception.
|
1168
|
*
|
1169
|
* @param guid the global identifier to look up
|
1170
|
* @return String containing the corresponding LocalId
|
1171
|
* @throws McdbDocNotFoundException if the identifier is not found
|
1172
|
*/
|
1173
|
public String getLocalId(String guid) throws McdbDocNotFoundException {
|
1174
|
|
1175
|
String db_guid = "";
|
1176
|
String docid = "";
|
1177
|
int rev = 0;
|
1178
|
|
1179
|
String query = "select guid, docid, rev from " + TYPE_IDENTIFIER + " where guid = ?";
|
1180
|
|
1181
|
DBConnection dbConn = null;
|
1182
|
int serialNumber = -1;
|
1183
|
try {
|
1184
|
// Get a database connection from the pool
|
1185
|
dbConn = DBConnectionPool.getDBConnection("Identifier.getLocalId");
|
1186
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1187
|
|
1188
|
// Execute the insert statement
|
1189
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1190
|
stmt.setString(1, guid);
|
1191
|
ResultSet rs = stmt.executeQuery();
|
1192
|
if (rs.next()) {
|
1193
|
db_guid = rs.getString(1);
|
1194
|
docid = rs.getString(2);
|
1195
|
rev = rs.getInt(3);
|
1196
|
assert(db_guid.equals(guid));
|
1197
|
} else {
|
1198
|
throw new McdbDocNotFoundException("Document not found:" + guid);
|
1199
|
}
|
1200
|
stmt.close();
|
1201
|
} catch (SQLException e) {
|
1202
|
logMetacat.error("Error while looking up the local identifier: "
|
1203
|
+ e.getMessage());
|
1204
|
} finally {
|
1205
|
// Return database connection to the pool
|
1206
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1207
|
}
|
1208
|
return docid + "." + rev;
|
1209
|
}
|
1210
|
|
1211
|
/**
|
1212
|
* query the systemmetadata table based on the given parameters
|
1213
|
* @param startTime
|
1214
|
* @param endTime
|
1215
|
* @param objectFormat
|
1216
|
* @param replicaStatus
|
1217
|
* @param start
|
1218
|
* @param count
|
1219
|
* @return ObjectList
|
1220
|
*/
|
1221
|
public ObjectList querySystemMetadata(Date startTime, Date endTime,
|
1222
|
ObjectFormat objectFormat, boolean replicaStatus, int start, int count)
|
1223
|
{
|
1224
|
ObjectList ol = new ObjectList();
|
1225
|
int total = 0;
|
1226
|
DBConnection dbConn = null;
|
1227
|
int serialNumber = -1;
|
1228
|
|
1229
|
try
|
1230
|
{
|
1231
|
String sql = "select guid, date_uploaded, rights_holder, checksum, " +
|
1232
|
"checksum_algorithm, origin_member_node, authoritive_member_node, " +
|
1233
|
"date_modified, submitter, object_format, size from systemmetadata";
|
1234
|
|
1235
|
boolean f1 = false;
|
1236
|
boolean f2 = false;
|
1237
|
boolean f3 = false;
|
1238
|
|
1239
|
if(startTime != null)
|
1240
|
{
|
1241
|
sql += " where systemmetadata.date_modified > ?";
|
1242
|
f1 = true;
|
1243
|
}
|
1244
|
|
1245
|
if(endTime != null)
|
1246
|
{
|
1247
|
if(!f1)
|
1248
|
{
|
1249
|
sql += " where systemmetadata.date_modified < ?";
|
1250
|
}
|
1251
|
else
|
1252
|
{
|
1253
|
sql += " and systemmetadata.date_modified < ?";
|
1254
|
}
|
1255
|
f2 = true;
|
1256
|
}
|
1257
|
|
1258
|
if(objectFormat != null)
|
1259
|
{
|
1260
|
if(!f1 && !f2)
|
1261
|
{
|
1262
|
sql += " where object_format = ?";
|
1263
|
}
|
1264
|
else
|
1265
|
{
|
1266
|
sql += " and object_format = ?";
|
1267
|
}
|
1268
|
f3 = true;
|
1269
|
}
|
1270
|
|
1271
|
if(replicaStatus)
|
1272
|
{
|
1273
|
String currentNodeId = PropertyService.getInstance().getProperty("dataone.memberNodeId");
|
1274
|
if(!f1 && !f2 && !f3)
|
1275
|
{
|
1276
|
sql += " where authoritive_member_node != '" + currentNodeId.trim() + "'";
|
1277
|
}
|
1278
|
else
|
1279
|
{
|
1280
|
sql += " and authoritive_member_node != '" + currentNodeId.trim() + "'";
|
1281
|
}
|
1282
|
}
|
1283
|
|
1284
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.querySystemMetadata");
|
1285
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1286
|
PreparedStatement stmt = dbConn.prepareStatement(sql);
|
1287
|
|
1288
|
if(f1 && f2 && f3)
|
1289
|
{
|
1290
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1291
|
stmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1292
|
stmt.setString(3, objectFormat.toString());
|
1293
|
}
|
1294
|
else if(f1 && f2 && !f3)
|
1295
|
{
|
1296
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1297
|
stmt.setTimestamp(2, new Timestamp(endTime.getTime()));
|
1298
|
}
|
1299
|
else if(f1 && !f2 && f3)
|
1300
|
{
|
1301
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1302
|
stmt.setString(2, objectFormat.toString());
|
1303
|
}
|
1304
|
else if(f1 && !f2 && !f3)
|
1305
|
{
|
1306
|
stmt.setTimestamp(1, new Timestamp(startTime.getTime()));
|
1307
|
}
|
1308
|
else if(!f1 && f2 && f3)
|
1309
|
{
|
1310
|
stmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1311
|
stmt.setString(2, objectFormat.toString());
|
1312
|
}
|
1313
|
else if(!f1 && !f2 && f3)
|
1314
|
{
|
1315
|
stmt.setString(1, objectFormat.toString());
|
1316
|
}
|
1317
|
else if(!f1 && f2 && !f3)
|
1318
|
{
|
1319
|
stmt.setTimestamp(1, new Timestamp(endTime.getTime()));
|
1320
|
}
|
1321
|
|
1322
|
//logMetacat.debug("LISTOBJECTS QUERY: " + stmt.toString());
|
1323
|
|
1324
|
ResultSet rs = stmt.executeQuery();
|
1325
|
for(int i=0; i<start; i++)
|
1326
|
{
|
1327
|
if(rs.next())
|
1328
|
{
|
1329
|
total++;
|
1330
|
}
|
1331
|
else
|
1332
|
{
|
1333
|
break;
|
1334
|
}
|
1335
|
}
|
1336
|
|
1337
|
int countIndex = 0;
|
1338
|
|
1339
|
while(rs.next())
|
1340
|
{
|
1341
|
total++;
|
1342
|
if(countIndex >= count)
|
1343
|
{
|
1344
|
break;
|
1345
|
}
|
1346
|
String guid = rs.getString(1);
|
1347
|
//logMetacat.debug("query found doc with guid " + guid);
|
1348
|
//Timestamp dateUploaded = rs.getTimestamp(2);
|
1349
|
//String rightsHolder = rs.getString(3);
|
1350
|
String checksum = rs.getString(4);
|
1351
|
String checksumAlgorithm = rs.getString(5);
|
1352
|
//String originMemberNode = rs.getString(6);
|
1353
|
String authoritiveMemberNode = rs.getString(7);
|
1354
|
Timestamp dateModified = rs.getTimestamp(8);
|
1355
|
//String submitter = rs.getString(9);
|
1356
|
String format = rs.getString(10);
|
1357
|
String sz = rs.getString(11);
|
1358
|
long size = 0;
|
1359
|
if(sz != null && !sz.trim().equals(""))
|
1360
|
{
|
1361
|
size = new Long(rs.getString(11)).longValue();
|
1362
|
}
|
1363
|
|
1364
|
ObjectInfo oi = new ObjectInfo();
|
1365
|
|
1366
|
Identifier id = new Identifier();
|
1367
|
id.setValue(guid);
|
1368
|
oi.setIdentifier(id);
|
1369
|
|
1370
|
oi.setDateSysMetadataModified(new Date(dateModified.getTime()));
|
1371
|
|
1372
|
Checksum cs = new Checksum();
|
1373
|
cs.setValue(checksum);
|
1374
|
cs.setAlgorithm(ChecksumAlgorithm.valueOf(checksumAlgorithm));
|
1375
|
//cs.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm));
|
1376
|
oi.setChecksum(cs);
|
1377
|
|
1378
|
ObjectFormat oFormat = ObjectFormat.convert(format);
|
1379
|
if(oFormat != null)
|
1380
|
{
|
1381
|
oi.setObjectFormat(oFormat);
|
1382
|
}
|
1383
|
else
|
1384
|
{ //if there is no object format, just default to text/plain
|
1385
|
oi.setObjectFormat(ObjectFormat.OCTET_STREAM);
|
1386
|
}
|
1387
|
|
1388
|
oi.setSize(size);
|
1389
|
|
1390
|
ol.addObjectInfo(oi);
|
1391
|
countIndex++;
|
1392
|
}
|
1393
|
|
1394
|
while(rs.next())
|
1395
|
{ //expend the resultset to get the total count of possible rows
|
1396
|
total++;
|
1397
|
}
|
1398
|
}
|
1399
|
catch(Exception e)
|
1400
|
{
|
1401
|
e.printStackTrace();
|
1402
|
logMetacat.error("Error querying system metadata: " + e.getMessage());
|
1403
|
}
|
1404
|
finally
|
1405
|
{
|
1406
|
// Return database connection to the pool
|
1407
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1408
|
}
|
1409
|
|
1410
|
ol.setStart(start);
|
1411
|
ol.setCount(ol.sizeObjectInfoList());
|
1412
|
ol.setTotal(total);
|
1413
|
|
1414
|
return ol;
|
1415
|
}
|
1416
|
|
1417
|
/**
|
1418
|
* create a mapping in the identifier table
|
1419
|
* @param guid
|
1420
|
* @param localId
|
1421
|
*/
|
1422
|
public void createMapping(String guid, String localId)
|
1423
|
{
|
1424
|
|
1425
|
int serialNumber = -1;
|
1426
|
DBConnection dbConn = null;
|
1427
|
try {
|
1428
|
|
1429
|
// Parse the localId into scope and rev parts
|
1430
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
1431
|
String docid = acc.getDocid();
|
1432
|
int rev = 1;
|
1433
|
if (acc.getRev() != null) {
|
1434
|
rev = (new Integer(acc.getRev()).intValue());
|
1435
|
}
|
1436
|
|
1437
|
// Get a database connection from the pool
|
1438
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
|
1439
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1440
|
|
1441
|
// Execute the insert statement
|
1442
|
String query = "insert into " + TYPE_IDENTIFIER + " (guid, docid, rev) values (?, ?, ?)";
|
1443
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1444
|
stmt.setString(1, guid);
|
1445
|
stmt.setString(2, docid);
|
1446
|
stmt.setInt(3, rev);
|
1447
|
logMetacat.debug("mapping query: " + stmt.toString());
|
1448
|
int rows = stmt.executeUpdate();
|
1449
|
|
1450
|
stmt.close();
|
1451
|
} catch (SQLException e) {
|
1452
|
e.printStackTrace();
|
1453
|
logMetacat.error("createGenericMapping: SQL error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
1454
|
+ e.getMessage());
|
1455
|
} catch (NumberFormatException e) {
|
1456
|
e.printStackTrace();
|
1457
|
logMetacat.error("createGenericMapping: NumberFormat error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
1458
|
+ e.getMessage());
|
1459
|
} catch (AccessionNumberException e) {
|
1460
|
e.printStackTrace();
|
1461
|
logMetacat.error("createGenericMapping: AccessionNumber error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
|
1462
|
+ e.getMessage());
|
1463
|
} finally {
|
1464
|
// Return database connection to the pool
|
1465
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1466
|
}
|
1467
|
}
|
1468
|
|
1469
|
/**
|
1470
|
* create the systemmetadata record
|
1471
|
* @param guid
|
1472
|
*/
|
1473
|
public void insertSystemMetadata(String guid)
|
1474
|
{
|
1475
|
|
1476
|
int serialNumber = -1;
|
1477
|
DBConnection dbConn = null;
|
1478
|
try {
|
1479
|
|
1480
|
// Get a database connection from the pool
|
1481
|
dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadata");
|
1482
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
1483
|
|
1484
|
// Execute the insert statement
|
1485
|
String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid) values (?)";
|
1486
|
PreparedStatement stmt = dbConn.prepareStatement(query);
|
1487
|
stmt.setString(1, guid);
|
1488
|
logMetacat.debug("system metadata query: " + stmt.toString());
|
1489
|
int rows = stmt.executeUpdate();
|
1490
|
|
1491
|
stmt.close();
|
1492
|
} catch (Exception e) {
|
1493
|
e.printStackTrace();
|
1494
|
logMetacat.error("Error while creating " + TYPE_SYSTEM_METADATA + " record: "
|
1495
|
+ e.getMessage());
|
1496
|
} finally {
|
1497
|
// Return database connection to the pool
|
1498
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
1499
|
}
|
1500
|
}
|
1501
|
}
|
1502
|
|