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/**
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* '$RCSfile$'
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* Copyright: 2000-2011 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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*
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* '$Author: $'
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* '$Date: $'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat.dataone;
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7417
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leinfelder
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import java.io.ByteArrayInputStream;
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7860
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leinfelder
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import java.io.ByteArrayOutputStream;
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7850
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leinfelder
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import java.io.File;
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8800
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leinfelder
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import java.io.FileInputStream;
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7850
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leinfelder
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import java.io.FileOutputStream;
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6228
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cjones
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import java.io.IOException;
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6179
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cjones
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import java.io.InputStream;
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8190
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leinfelder
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import java.io.InputStreamReader;
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7860
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leinfelder
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import java.io.OutputStreamWriter;
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7849
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leinfelder
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import java.io.UnsupportedEncodingException;
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7860
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leinfelder
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import java.io.Writer;
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7021
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leinfelder
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import java.math.BigInteger;
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7849
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leinfelder
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import java.net.URISyntaxException;
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6228
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cjones
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import java.security.NoSuchAlgorithmException;
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7860
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leinfelder
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import java.sql.SQLException;
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7417
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leinfelder
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import java.util.ArrayList;
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6525
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leinfelder
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import java.util.Calendar;
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6179
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cjones
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import java.util.Date;
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8437
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walker
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import java.util.HashMap;
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7680
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tao
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import java.util.HashSet;
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7860
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leinfelder
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import java.util.Hashtable;
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6250
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cjones
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import java.util.List;
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7849
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leinfelder
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import java.util.Map;
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7417
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leinfelder
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import java.util.Set;
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6389
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leinfelder
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import java.util.Timer;
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7489
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leinfelder
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import java.util.UUID;
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7418
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leinfelder
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import java.util.Vector;
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6179
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cjones
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6542
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leinfelder
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import javax.servlet.http.HttpServletRequest;
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6258
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cjones
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import org.apache.commons.io.IOUtils;
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6179
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cjones
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import org.apache.log4j.Logger;
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8810
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leinfelder
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import org.dataone.client.v2.CNode;
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import org.dataone.client.v2.itk.D1Client;
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import org.dataone.client.v2.MNode;
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import org.dataone.client.v2.formats.ObjectFormatCache;
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6552
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import org.dataone.client.auth.CertificateManager;
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8810
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leinfelder
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import org.dataone.client.v2.formats.ObjectFormatInfo;
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6552
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leinfelder
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import org.dataone.configuration.Settings;
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7849
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leinfelder
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import org.dataone.ore.ResourceMapFactory;
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6795
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cjones
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import org.dataone.service.exceptions.BaseException;
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6179
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cjones
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import org.dataone.service.exceptions.IdentifierNotUnique;
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import org.dataone.service.exceptions.InsufficientResources;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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6185
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import org.dataone.service.exceptions.SynchronizationFailed;
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import org.dataone.service.exceptions.UnsupportedType;
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import org.dataone.service.mn.tier1.v2.MNCore;
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import org.dataone.service.mn.tier1.v2.MNRead;
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import org.dataone.service.mn.tier2.v2.MNAuthorization;
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import org.dataone.service.mn.tier3.v2.MNStorage;
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import org.dataone.service.mn.tier4.v2.MNReplication;
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import org.dataone.service.mn.v2.MNPackage;
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import org.dataone.service.mn.v2.MNQuery;
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import org.dataone.service.mn.v2.MNView;
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8591
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leinfelder
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import org.dataone.service.types.v1.AccessRule;
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6366
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leinfelder
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import org.dataone.service.types.v1.Checksum;
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7144
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leinfelder
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import org.dataone.service.types.v1.DescribeResponse;
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6366
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import org.dataone.service.types.v1.Event;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v2.Log;
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import org.dataone.service.types.v2.LogEntry;
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import org.dataone.service.types.v2.OptionList;
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6366
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leinfelder
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import org.dataone.service.types.v1.MonitorInfo;
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import org.dataone.service.types.v1.MonitorList;
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leinfelder
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import org.dataone.service.types.v2.Node;
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import org.dataone.service.types.v2.NodeList;
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6366
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leinfelder
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.NodeState;
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import org.dataone.service.types.v1.NodeType;
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8810
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leinfelder
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import org.dataone.service.types.v2.ObjectFormat;
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6366
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leinfelder
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import org.dataone.service.types.v1.ObjectFormatIdentifier;
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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.Ping;
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6528
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cjones
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import org.dataone.service.types.v1.ReplicationStatus;
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6366
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leinfelder
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import org.dataone.service.types.v1.Schedule;
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import org.dataone.service.types.v1.Service;
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import org.dataone.service.types.v1.Services;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import org.dataone.service.types.v1.Synchronization;
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8810
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leinfelder
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import org.dataone.service.types.v2.SystemMetadata;
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7417
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leinfelder
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import org.dataone.service.types.v1.util.AuthUtils;
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6366
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import org.dataone.service.types.v1.util.ChecksumUtil;
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7417
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leinfelder
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import org.dataone.service.types.v1_1.QueryEngineDescription;
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import org.dataone.service.types.v1_1.QueryEngineList;
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leinfelder
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import org.dataone.service.types.v1_1.QueryField;
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6476
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jones
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import org.dataone.service.util.Constants;
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8594
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leinfelder
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import org.dataone.service.util.TypeMarshaller;
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import org.dspace.foresite.OREException;
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import org.dspace.foresite.OREParserException;
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import org.dspace.foresite.ORESerialiserException;
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import org.dspace.foresite.ResourceMap;
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8437
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walker
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import org.ecoinformatics.datamanager.parser.DataPackage;
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import org.ecoinformatics.datamanager.parser.Entity;
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import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
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import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;
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6179
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cjones
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7448
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leinfelder
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import edu.ucsb.nceas.ezid.EZIDException;
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7417
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leinfelder
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import edu.ucsb.nceas.metacat.DBQuery;
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import edu.ucsb.nceas.metacat.DBTransform;
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6234
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cjones
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import edu.ucsb.nceas.metacat.EventLog;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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6234
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cjones
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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7417
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leinfelder
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import edu.ucsb.nceas.metacat.MetaCatServlet;
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6389
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import edu.ucsb.nceas.metacat.MetacatHandler;
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7772
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tao
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import edu.ucsb.nceas.metacat.common.query.EnabledQueryEngines;
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7757
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leinfelder
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import edu.ucsb.nceas.metacat.common.query.stream.ContentTypeByteArrayInputStream;
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6648
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leinfelder
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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7662
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tao
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import edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler;
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7620
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tao
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import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
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6340
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cjones
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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leinfelder
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
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8026
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leinfelder
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import edu.ucsb.nceas.metacat.util.DeleteOnCloseFileInputStream;
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7441
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leinfelder
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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leinfelder
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import edu.ucsb.nceas.metacat.util.SkinUtil;
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leinfelder
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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cjones
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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8190
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leinfelder
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import edu.ucsb.nceas.utilities.XMLUtilities;
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8800
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leinfelder
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import edu.ucsb.nceas.utilities.export.HtmlToPdf;
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leinfelder
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import gov.loc.repository.bagit.Bag;
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import gov.loc.repository.bagit.BagFactory;
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import gov.loc.repository.bagit.writer.impl.ZipWriter;
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cjones
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6179
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cjones
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/**
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* Represents Metacat's implementation of the DataONE Member Node
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* service API. Methods implement the various MN* interfaces, and methods common
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* to both Member Node and Coordinating Node interfaces are found in the
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* D1NodeService base class.
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cjones
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*
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* Implements:
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* MNCore.ping()
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* MNCore.getLogRecords()
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* MNCore.getObjectStatistics()
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* MNCore.getOperationStatistics()
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* MNCore.getStatus()
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* MNCore.getCapabilities()
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* MNRead.get()
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* MNRead.getSystemMetadata()
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* MNRead.describe()
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* MNRead.getChecksum()
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* MNRead.listObjects()
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* MNRead.synchronizationFailed()
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* MNAuthorization.isAuthorized()
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* MNAuthorization.setAccessPolicy()
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* MNStorage.create()
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* MNStorage.update()
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* MNStorage.delete()
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* MNStorage.updateSystemMetadata()
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* MNReplication.replicate()
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*
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*/
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6599
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cjones
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public class MNodeService extends D1NodeService
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implements MNAuthorization, MNCore, MNRead, MNReplication, MNStorage, MNQuery, MNView, MNPackage {
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//private static final String PATHQUERY = "pathquery";
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public static final String UUID_SCHEME = "UUID";
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public static final String DOI_SCHEME = "DOI";
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7489
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private static final String UUID_PREFIX = "urn:uuid:";
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/* the logger instance */
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private Logger logMetacat = null;
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/* A reference to a remote Memeber Node */
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private MNode mn;
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/* A reference to a Coordinating Node */
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private CNode cn;
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6475
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/**
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* Singleton accessor to get an instance of MNodeService.
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*
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* @return instance - the instance of MNodeService
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*/
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public static MNodeService getInstance(HttpServletRequest request) {
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return new MNodeService(request);
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}
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/**
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* Constructor, private for singleton access
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*/
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private MNodeService(HttpServletRequest request) {
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super(request);
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logMetacat = Logger.getLogger(MNodeService.class);
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leinfelder
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// set the Member Node certificate file location
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CertificateManager.getInstance().setCertificateLocation(Settings.getConfiguration().getString("D1Client.certificate.file"));
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}
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/**
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* Deletes an object from the Member Node, where the object is either a
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* data object or a science metadata object.
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - The object identifier to be deleted
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*
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* @return pid - the identifier of the object used for the deletion
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*
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* @throws InvalidToken
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* @throws ServiceFailure
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* @throws NotAuthorized
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* @throws NotFound
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* @throws NotImplemented
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* @throws InvalidRequest
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*/
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@Override
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public Identifier delete(Session session, Identifier pid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
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7162
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leinfelder
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// only admin of the MN or the CN is allowed a full delete
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boolean allowed = false;
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7330
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leinfelder
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allowed = isAdminAuthorized(session);
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tao
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9050
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tao
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String serviceFailureCode = "2902";
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Identifier sid = getPIDForSID(pid, serviceFailureCode);
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if(sid != null) {
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pid = sid;
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}
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8360
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tao
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//check if it is the authoritative member node
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if(!allowed) {
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allowed = isAuthoritativeMNodeAdmin(session, pid);
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}
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257 |
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leinfelder
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if (!allowed) {
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throw new NotAuthorized("1320", "The provided identity does not have " + "permission to delete objects on the Node.");
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}
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// defer to superclass implementation
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return super.delete(session, pid);
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}
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/**
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266 |
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* Updates an existing object by creating a new object identified by
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* newPid on the Member Node which explicitly obsoletes the object
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* identified by pid through appropriate changes to the SystemMetadata
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* of pid and newPid
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - The identifier of the object to be updated
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* @param object - the new object bytes
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* @param sysmeta - the new system metadata describing the object
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*
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276 |
|
|
* @return newPid - the identifier of the new object
|
277 |
|
|
*
|
278 |
|
|
* @throws InvalidToken
|
279 |
|
|
* @throws ServiceFailure
|
280 |
|
|
* @throws NotAuthorized
|
281 |
|
|
* @throws NotFound
|
282 |
|
|
* @throws NotImplemented
|
283 |
|
|
* @throws IdentifierNotUnique
|
284 |
|
|
* @throws UnsupportedType
|
285 |
|
|
* @throws InsufficientResources
|
286 |
|
|
* @throws InvalidSystemMetadata
|
287 |
|
|
* @throws InvalidRequest
|
288 |
|
|
*/
|
289 |
|
|
@Override
|
290 |
6575
|
cjones
|
public Identifier update(Session session, Identifier pid, InputStream object,
|
291 |
|
|
Identifier newPid, SystemMetadata sysmeta)
|
292 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
293 |
|
|
UnsupportedType, InsufficientResources, NotFound,
|
294 |
|
|
InvalidSystemMetadata, NotImplemented, InvalidRequest {
|
295 |
6250
|
cjones
|
|
296 |
9044
|
tao
|
//transform a sid to a pid if it is applicable
|
297 |
|
|
String serviceFailureCode = "1310";
|
298 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
299 |
|
|
if(sid != null) {
|
300 |
|
|
pid = sid;
|
301 |
|
|
}
|
302 |
|
|
|
303 |
6475
|
jones
|
String localId = null;
|
304 |
|
|
boolean allowed = false;
|
305 |
|
|
boolean isScienceMetadata = false;
|
306 |
6645
|
leinfelder
|
|
307 |
|
|
if (session == null) {
|
308 |
|
|
throw new InvalidToken("1210", "No session has been provided");
|
309 |
|
|
}
|
310 |
6475
|
jones
|
Subject subject = session.getSubject();
|
311 |
|
|
|
312 |
7315
|
leinfelder
|
// verify the pid is valid format
|
313 |
7318
|
leinfelder
|
if (!isValidIdentifier(pid)) {
|
314 |
7315
|
leinfelder
|
throw new InvalidRequest("1202", "The provided identifier is invalid.");
|
315 |
6475
|
jones
|
}
|
316 |
9044
|
tao
|
|
317 |
|
|
// verify the new pid is valid format
|
318 |
|
|
if (!isValidIdentifier(newPid)) {
|
319 |
|
|
throw new InvalidRequest("1202", "The provided identifier is invalid.");
|
320 |
|
|
}
|
321 |
|
|
|
322 |
|
|
// make sure that the newPid doesn't exists
|
323 |
|
|
boolean idExists = true;
|
324 |
|
|
try {
|
325 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(newPid.getValue());
|
326 |
|
|
} catch (SQLException e) {
|
327 |
|
|
throw new ServiceFailure("1310",
|
328 |
|
|
"The requested identifier " + newPid.getValue() +
|
329 |
|
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
330 |
|
|
}
|
331 |
|
|
if (idExists) {
|
332 |
|
|
throw new IdentifierNotUnique("1220",
|
333 |
|
|
"The requested identifier " + newPid.getValue() +
|
334 |
|
|
" is already used by another object and" +
|
335 |
|
|
"therefore can not be used for this object. Clients should choose" +
|
336 |
|
|
"a new identifier that is unique and retry the operation or " +
|
337 |
|
|
"use CN.reserveIdentifier() to reserve one.");
|
338 |
|
|
|
339 |
|
|
}
|
340 |
|
|
|
341 |
|
|
|
342 |
6475
|
jones
|
|
343 |
|
|
// check for the existing identifier
|
344 |
|
|
try {
|
345 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
346 |
6575
|
cjones
|
|
347 |
6475
|
jones
|
} catch (McdbDocNotFoundException e) {
|
348 |
6575
|
cjones
|
throw new InvalidRequest("1202", "The object with the provided " +
|
349 |
|
|
"identifier was not found.");
|
350 |
|
|
|
351 |
9024
|
tao
|
} catch (SQLException ee) {
|
352 |
|
|
throw new ServiceFailure("1310", "The object with the provided " +
|
353 |
|
|
"identifier "+pid.getValue()+" can't be identified since - "+ee.getMessage());
|
354 |
6475
|
jones
|
}
|
355 |
6518
|
leinfelder
|
|
356 |
6521
|
leinfelder
|
// set the originating node
|
357 |
|
|
NodeReference originMemberNode = this.getCapabilities().getIdentifier();
|
358 |
|
|
sysmeta.setOriginMemberNode(originMemberNode);
|
359 |
|
|
|
360 |
6518
|
leinfelder
|
// set the submitter to match the certificate
|
361 |
|
|
sysmeta.setSubmitter(subject);
|
362 |
6525
|
leinfelder
|
// set the dates
|
363 |
|
|
Date now = Calendar.getInstance().getTime();
|
364 |
6575
|
cjones
|
sysmeta.setDateSysMetadataModified(now);
|
365 |
|
|
sysmeta.setDateUploaded(now);
|
366 |
7486
|
leinfelder
|
|
367 |
|
|
// make sure serial version is set to something
|
368 |
|
|
BigInteger serialVersion = sysmeta.getSerialVersion();
|
369 |
|
|
if (serialVersion == null) {
|
370 |
|
|
sysmeta.setSerialVersion(BigInteger.ZERO);
|
371 |
|
|
}
|
372 |
6475
|
jones
|
|
373 |
|
|
// does the subject have WRITE ( == update) priveleges on the pid?
|
374 |
|
|
allowed = isAuthorized(session, pid, Permission.WRITE);
|
375 |
|
|
|
376 |
|
|
if (allowed) {
|
377 |
6649
|
leinfelder
|
|
378 |
|
|
// check quality of SM
|
379 |
|
|
if (sysmeta.getObsoletedBy() != null) {
|
380 |
|
|
throw new InvalidSystemMetadata("1300", "Cannot include obsoletedBy when updating object");
|
381 |
|
|
}
|
382 |
|
|
if (sysmeta.getObsoletes() != null && !sysmeta.getObsoletes().getValue().equals(pid.getValue())) {
|
383 |
|
|
throw new InvalidSystemMetadata("1300", "The identifier provided in obsoletes does not match old Identifier");
|
384 |
|
|
}
|
385 |
6475
|
jones
|
|
386 |
|
|
// get the existing system metadata for the object
|
387 |
|
|
SystemMetadata existingSysMeta = getSystemMetadata(session, pid);
|
388 |
9200
|
tao
|
//System.out.println("the archive is "+existingSysMeta.getArchived());
|
389 |
|
|
//Base on documentation, we can't update an archived object:
|
390 |
|
|
//The update operation MUST fail with Exceptions.InvalidRequest on objects that have the Types.SystemMetadata.archived property set to true.
|
391 |
|
|
if(existingSysMeta.getArchived() != null && existingSysMeta.getArchived()) {
|
392 |
|
|
throw new InvalidRequest("1202","An archived object"+pid.getValue()+" can't be updated");
|
393 |
|
|
}
|
394 |
6475
|
jones
|
|
395 |
7400
|
leinfelder
|
// check for previous update
|
396 |
|
|
// see: https://redmine.dataone.org/issues/3336
|
397 |
|
|
Identifier existingObsoletedBy = existingSysMeta.getObsoletedBy();
|
398 |
|
|
if (existingObsoletedBy != null) {
|
399 |
|
|
throw new InvalidRequest("1202",
|
400 |
|
|
"The previous identifier has already been made obsolete by: " + existingObsoletedBy.getValue());
|
401 |
|
|
}
|
402 |
9044
|
tao
|
//check the sid in the system metadata. If it exists, it should be non-exist or match the old sid in the previous system metadata.
|
403 |
|
|
Identifier sidInSys = sysmeta.getSeriesId();
|
404 |
|
|
if(sidInSys != null) {
|
405 |
9046
|
tao
|
if (!isValidIdentifier(sidInSys)) {
|
406 |
|
|
throw new InvalidSystemMetadata("1300", "The provided series id in the system metadata is invalid.");
|
407 |
|
|
}
|
408 |
9044
|
tao
|
Identifier previousSid = existingSysMeta.getSeriesId();
|
409 |
|
|
if(previousSid != null) {
|
410 |
|
|
// there is a previous sid, if the new sid doesn't match it, the new sid should be non-existing.
|
411 |
9048
|
tao
|
if(!sidInSys.getValue().equals(previousSid.getValue())) {
|
412 |
9044
|
tao
|
try {
|
413 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(sidInSys.getValue());
|
414 |
|
|
} catch (SQLException e) {
|
415 |
|
|
throw new ServiceFailure("1310",
|
416 |
|
|
"The requested identifier " + sidInSys.getValue() +
|
417 |
|
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
418 |
|
|
}
|
419 |
|
|
if(idExists) {
|
420 |
|
|
throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata doesn't match the previous series id "
|
421 |
|
|
+previousSid.getValue()+", so it should NOT exist. However, it was used by another object.");
|
422 |
|
|
}
|
423 |
|
|
}
|
424 |
|
|
} else {
|
425 |
|
|
// there is no previous sid, the new sid should be non-existing.
|
426 |
|
|
try {
|
427 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(sidInSys.getValue());
|
428 |
|
|
} catch (SQLException e) {
|
429 |
|
|
throw new ServiceFailure("1310",
|
430 |
|
|
"The requested identifier " + sidInSys.getValue() +
|
431 |
|
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
432 |
|
|
}
|
433 |
|
|
if(idExists) {
|
434 |
|
|
throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata should NOT exist since the previous series id is null."
|
435 |
|
|
+"However, it was used by another object.");
|
436 |
|
|
}
|
437 |
|
|
}
|
438 |
9047
|
tao
|
//the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario)
|
439 |
|
|
if(sidInSys.getValue().equals(newPid.getValue())) {
|
440 |
|
|
throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata shouldn't have the same value of the pid.");
|
441 |
|
|
}
|
442 |
9044
|
tao
|
}
|
443 |
6475
|
jones
|
|
444 |
|
|
isScienceMetadata = isScienceMetadata(sysmeta);
|
445 |
|
|
|
446 |
|
|
// do we have XML metadata or a data object?
|
447 |
|
|
if (isScienceMetadata) {
|
448 |
|
|
|
449 |
|
|
// update the science metadata XML document
|
450 |
|
|
// TODO: handle non-XML metadata/data documents (like netCDF)
|
451 |
|
|
// TODO: don't put objects into memory using stream to string
|
452 |
8948
|
tao
|
//String objectAsXML = "";
|
453 |
6475
|
jones
|
try {
|
454 |
8948
|
tao
|
//objectAsXML = IOUtils.toString(object, "UTF-8");
|
455 |
7443
|
leinfelder
|
// give the old pid so we can calculate the new local id
|
456 |
8948
|
tao
|
localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update");
|
457 |
6475
|
jones
|
// register the newPid and the generated localId
|
458 |
|
|
if (newPid != null) {
|
459 |
|
|
IdentifierManager.getInstance().createMapping(newPid.getValue(), localId);
|
460 |
|
|
|
461 |
|
|
}
|
462 |
|
|
|
463 |
|
|
} catch (IOException e) {
|
464 |
|
|
String msg = "The Node is unable to create the object. " + "There was a problem converting the object to XML";
|
465 |
|
|
logMetacat.info(msg);
|
466 |
|
|
throw new ServiceFailure("1310", msg + ": " + e.getMessage());
|
467 |
|
|
|
468 |
|
|
}
|
469 |
|
|
|
470 |
|
|
} else {
|
471 |
|
|
|
472 |
|
|
// update the data object
|
473 |
|
|
localId = insertDataObject(object, newPid, session);
|
474 |
|
|
|
475 |
|
|
}
|
476 |
8267
|
leinfelder
|
|
477 |
|
|
// add the newPid to the obsoletedBy list for the existing sysmeta
|
478 |
|
|
existingSysMeta.setObsoletedBy(newPid);
|
479 |
6475
|
jones
|
|
480 |
8267
|
leinfelder
|
// then update the existing system metadata
|
481 |
|
|
updateSystemMetadata(existingSysMeta);
|
482 |
|
|
|
483 |
|
|
// prep the new system metadata, add pid to the affected lists
|
484 |
|
|
sysmeta.setObsoletes(pid);
|
485 |
|
|
//sysmeta.addDerivedFrom(pid);
|
486 |
|
|
|
487 |
6475
|
jones
|
// and insert the new system metadata
|
488 |
|
|
insertSystemMetadata(sysmeta);
|
489 |
|
|
|
490 |
|
|
// log the update event
|
491 |
6542
|
leinfelder
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), subject.getValue(), localId, Event.UPDATE.toString());
|
492 |
7507
|
leinfelder
|
|
493 |
|
|
// attempt to register the identifier - it checks if it is a doi
|
494 |
|
|
try {
|
495 |
7512
|
leinfelder
|
DOIService.getInstance().registerDOI(sysmeta);
|
496 |
8795
|
leinfelder
|
} catch (Exception e) {
|
497 |
7507
|
leinfelder
|
throw new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
|
498 |
|
|
}
|
499 |
6475
|
jones
|
|
500 |
|
|
} else {
|
501 |
|
|
throw new NotAuthorized("1200", "The provided identity does not have " + "permission to UPDATE the object identified by " + pid.getValue()
|
502 |
|
|
+ " on the Member Node.");
|
503 |
|
|
}
|
504 |
|
|
|
505 |
|
|
return newPid;
|
506 |
6250
|
cjones
|
}
|
507 |
6254
|
cjones
|
|
508 |
6475
|
jones
|
public Identifier create(Session session, Identifier pid, InputStream object, SystemMetadata sysmeta) throws InvalidToken, ServiceFailure, NotAuthorized,
|
509 |
|
|
IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, InvalidRequest {
|
510 |
6250
|
cjones
|
|
511 |
6916
|
cjones
|
// check for null session
|
512 |
6530
|
leinfelder
|
if (session == null) {
|
513 |
6575
|
cjones
|
throw new InvalidToken("1110", "Session is required to WRITE to the Node.");
|
514 |
6530
|
leinfelder
|
}
|
515 |
9068
|
tao
|
// verify the pid is valid format
|
516 |
|
|
if (!isValidIdentifier(pid)) {
|
517 |
|
|
throw new InvalidRequest("1102", "The provided identifier is invalid.");
|
518 |
|
|
}
|
519 |
6518
|
leinfelder
|
// set the submitter to match the certificate
|
520 |
|
|
sysmeta.setSubmitter(session.getSubject());
|
521 |
6520
|
leinfelder
|
// set the originating node
|
522 |
|
|
NodeReference originMemberNode = this.getCapabilities().getIdentifier();
|
523 |
|
|
sysmeta.setOriginMemberNode(originMemberNode);
|
524 |
6916
|
cjones
|
sysmeta.setArchived(false);
|
525 |
|
|
|
526 |
6525
|
leinfelder
|
// set the dates
|
527 |
|
|
Date now = Calendar.getInstance().getTime();
|
528 |
6916
|
cjones
|
sysmeta.setDateSysMetadataModified(now);
|
529 |
|
|
sysmeta.setDateUploaded(now);
|
530 |
7021
|
leinfelder
|
|
531 |
|
|
// set the serial version
|
532 |
|
|
sysmeta.setSerialVersion(BigInteger.ZERO);
|
533 |
7083
|
cjones
|
|
534 |
|
|
// check that we are not attempting to subvert versioning
|
535 |
|
|
if (sysmeta.getObsoletes() != null && sysmeta.getObsoletes().getValue() != null) {
|
536 |
|
|
throw new InvalidSystemMetadata("1180",
|
537 |
|
|
"The supplied system metadata is invalid. " +
|
538 |
|
|
"The obsoletes field cannot have a value when creating entries.");
|
539 |
|
|
}
|
540 |
7021
|
leinfelder
|
|
541 |
7083
|
cjones
|
if (sysmeta.getObsoletedBy() != null && sysmeta.getObsoletedBy().getValue() != null) {
|
542 |
|
|
throw new InvalidSystemMetadata("1180",
|
543 |
|
|
"The supplied system metadata is invalid. " +
|
544 |
|
|
"The obsoletedBy field cannot have a value when creating entries.");
|
545 |
|
|
}
|
546 |
9068
|
tao
|
|
547 |
|
|
// verify the sid in the system metadata
|
548 |
|
|
Identifier sid = sysmeta.getSeriesId();
|
549 |
|
|
boolean idExists = false;
|
550 |
|
|
if(sid != null) {
|
551 |
|
|
if (!isValidIdentifier(sid)) {
|
552 |
|
|
throw new InvalidSystemMetadata("1180", "The provided series id is invalid.");
|
553 |
|
|
}
|
554 |
|
|
try {
|
555 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(sid.getValue());
|
556 |
|
|
} catch (SQLException e) {
|
557 |
|
|
throw new ServiceFailure("1190",
|
558 |
|
|
"The series identifier " + sid.getValue() +
|
559 |
|
|
" in the system metadata couldn't be determined if it is unique since : "+e.getMessage());
|
560 |
|
|
}
|
561 |
|
|
if (idExists) {
|
562 |
|
|
throw new InvalidSystemMetadata("1180",
|
563 |
|
|
"The series identifier " + sid.getValue() +
|
564 |
|
|
" is already used by another object and" +
|
565 |
|
|
"therefore can not be used for this object. Clients should choose" +
|
566 |
|
|
"a new identifier that is unique and retry the operation or " +
|
567 |
|
|
"use CN.reserveIdentifier() to reserve one.");
|
568 |
|
|
|
569 |
|
|
}
|
570 |
|
|
//the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario )
|
571 |
|
|
if(sid.getValue().equals(pid.getValue())) {
|
572 |
|
|
throw new InvalidSystemMetadata("1180", "The series id "+sid.getValue()+" in the system metadata shouldn't have the same value of the pid.");
|
573 |
|
|
}
|
574 |
|
|
}
|
575 |
7083
|
cjones
|
|
576 |
6518
|
leinfelder
|
// call the shared impl
|
577 |
7507
|
leinfelder
|
Identifier resultPid = super.create(session, pid, object, sysmeta);
|
578 |
|
|
|
579 |
|
|
// attempt to register the identifier - it checks if it is a doi
|
580 |
|
|
try {
|
581 |
7512
|
leinfelder
|
DOIService.getInstance().registerDOI(sysmeta);
|
582 |
8795
|
leinfelder
|
} catch (Exception e) {
|
583 |
7510
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
|
584 |
|
|
sf.initCause(e);
|
585 |
|
|
throw sf;
|
586 |
7507
|
leinfelder
|
}
|
587 |
|
|
|
588 |
|
|
// return
|
589 |
|
|
return resultPid ;
|
590 |
6475
|
jones
|
}
|
591 |
6250
|
cjones
|
|
592 |
6475
|
jones
|
/**
|
593 |
|
|
* Called by a Coordinating Node to request that the Member Node create a
|
594 |
|
|
* copy of the specified object by retrieving it from another Member
|
595 |
|
|
* Node and storing it locally so that it can be made accessible to
|
596 |
|
|
* the DataONE system.
|
597 |
|
|
*
|
598 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
599 |
|
|
* @param sysmeta - Copy of the CN held system metadata for the object
|
600 |
|
|
* @param sourceNode - A reference to node from which the content should be
|
601 |
|
|
* retrieved. The reference should be resolved by
|
602 |
|
|
* checking the CN node registry.
|
603 |
|
|
*
|
604 |
|
|
* @return true if the replication succeeds
|
605 |
|
|
*
|
606 |
|
|
* @throws ServiceFailure
|
607 |
|
|
* @throws NotAuthorized
|
608 |
|
|
* @throws NotImplemented
|
609 |
|
|
* @throws UnsupportedType
|
610 |
|
|
* @throws InsufficientResources
|
611 |
|
|
* @throws InvalidRequest
|
612 |
|
|
*/
|
613 |
|
|
@Override
|
614 |
6786
|
cjones
|
public boolean replicate(Session session, SystemMetadata sysmeta,
|
615 |
|
|
NodeReference sourceNode) throws NotImplemented, ServiceFailure,
|
616 |
|
|
NotAuthorized, InvalidRequest, InsufficientResources,
|
617 |
|
|
UnsupportedType {
|
618 |
|
|
|
619 |
6875
|
cjones
|
if (session != null && sysmeta != null && sourceNode != null) {
|
620 |
|
|
logMetacat.info("MNodeService.replicate() called with parameters: \n" +
|
621 |
|
|
"\tSession.Subject = " +
|
622 |
|
|
session.getSubject().getValue() + "\n" +
|
623 |
7082
|
cjones
|
"\tidentifier = " +
|
624 |
|
|
sysmeta.getIdentifier().getValue() +
|
625 |
6875
|
cjones
|
"\n" + "\tSource NodeReference =" +
|
626 |
|
|
sourceNode.getValue());
|
627 |
|
|
}
|
628 |
6475
|
jones
|
boolean result = false;
|
629 |
6786
|
cjones
|
String nodeIdStr = null;
|
630 |
6651
|
cjones
|
NodeReference nodeId = null;
|
631 |
6786
|
cjones
|
|
632 |
6795
|
cjones
|
// get the referenced object
|
633 |
|
|
Identifier pid = sysmeta.getIdentifier();
|
634 |
9068
|
tao
|
// verify the pid is valid format
|
635 |
|
|
if (!isValidIdentifier(pid)) {
|
636 |
|
|
throw new InvalidRequest("2153", "The provided identifier in the system metadata is invalid.");
|
637 |
|
|
}
|
638 |
6795
|
cjones
|
|
639 |
|
|
// get from the membernode
|
640 |
|
|
// TODO: switch credentials for the server retrieval?
|
641 |
|
|
this.mn = D1Client.getMN(sourceNode);
|
642 |
|
|
this.cn = D1Client.getCN();
|
643 |
|
|
InputStream object = null;
|
644 |
|
|
Session thisNodeSession = null;
|
645 |
|
|
SystemMetadata localSystemMetadata = null;
|
646 |
|
|
BaseException failure = null;
|
647 |
6818
|
cjones
|
String localId = null;
|
648 |
|
|
|
649 |
6795
|
cjones
|
// TODO: check credentials
|
650 |
|
|
// cannot be called by public
|
651 |
7063
|
leinfelder
|
if (session == null || session.getSubject() == null) {
|
652 |
7082
|
cjones
|
String msg = "No session was provided to replicate identifier " +
|
653 |
|
|
sysmeta.getIdentifier().getValue();
|
654 |
8414
|
tao
|
logMetacat.error(msg);
|
655 |
7192
|
cjones
|
throw new NotAuthorized("2152", msg);
|
656 |
|
|
|
657 |
6795
|
cjones
|
}
|
658 |
|
|
|
659 |
|
|
|
660 |
6651
|
cjones
|
// get the local node id
|
661 |
|
|
try {
|
662 |
7030
|
cjones
|
nodeIdStr = PropertyService.getProperty("dataone.nodeId");
|
663 |
6651
|
cjones
|
nodeId = new NodeReference();
|
664 |
|
|
nodeId.setValue(nodeIdStr);
|
665 |
6786
|
cjones
|
|
666 |
6651
|
cjones
|
} catch (PropertyNotFoundException e1) {
|
667 |
7030
|
cjones
|
String msg = "Couldn't get dataone.nodeId property: " + e1.getMessage();
|
668 |
6795
|
cjones
|
failure = new ServiceFailure("2151", msg);
|
669 |
8414
|
tao
|
//setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
670 |
6795
|
cjones
|
logMetacat.error(msg);
|
671 |
8414
|
tao
|
//return true;
|
672 |
|
|
throw new ServiceFailure("2151", msg);
|
673 |
6786
|
cjones
|
|
674 |
6651
|
cjones
|
}
|
675 |
6795
|
cjones
|
|
676 |
6475
|
jones
|
|
677 |
|
|
try {
|
678 |
6786
|
cjones
|
// do we already have a replica?
|
679 |
|
|
try {
|
680 |
6818
|
cjones
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
681 |
6822
|
cjones
|
// if we have a local id, get the local object
|
682 |
|
|
try {
|
683 |
|
|
object = MetacatHandler.read(localId);
|
684 |
|
|
} catch (Exception e) {
|
685 |
7127
|
leinfelder
|
// NOTE: we may already know about this ID because it could be a data file described by a metadata file
|
686 |
|
|
// https://redmine.dataone.org/issues/2572
|
687 |
|
|
// TODO: fix this so that we don't prevent ourselves from getting replicas
|
688 |
|
|
|
689 |
6822
|
cjones
|
// let the CN know that the replication failed
|
690 |
7127
|
leinfelder
|
logMetacat.warn("Object content not found on this node despite having localId: " + localId);
|
691 |
|
|
String msg = "Can't read the object bytes properly, replica is invalid.";
|
692 |
|
|
ServiceFailure serviceFailure = new ServiceFailure("2151", msg);
|
693 |
7113
|
leinfelder
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, serviceFailure);
|
694 |
|
|
logMetacat.warn(msg);
|
695 |
6822
|
cjones
|
throw serviceFailure;
|
696 |
|
|
|
697 |
|
|
}
|
698 |
|
|
|
699 |
6817
|
cjones
|
} catch (McdbDocNotFoundException e) {
|
700 |
6818
|
cjones
|
logMetacat.info("No replica found. Continuing.");
|
701 |
6817
|
cjones
|
|
702 |
9024
|
tao
|
} catch (SQLException ee) {
|
703 |
|
|
throw new ServiceFailure("2151", "Couldn't identify the local id of the object with the specified identifier "
|
704 |
|
|
+pid.getValue()+" since - "+ee.getMessage());
|
705 |
6819
|
cjones
|
}
|
706 |
|
|
|
707 |
6786
|
cjones
|
// no local replica, get a replica
|
708 |
6819
|
cjones
|
if ( object == null ) {
|
709 |
6786
|
cjones
|
// session should be null to use the default certificate
|
710 |
|
|
// location set in the Certificate manager
|
711 |
|
|
object = mn.getReplica(thisNodeSession, pid);
|
712 |
7082
|
cjones
|
logMetacat.info("MNodeService.getReplica() called for identifier "
|
713 |
6786
|
cjones
|
+ pid.getValue());
|
714 |
|
|
|
715 |
|
|
}
|
716 |
|
|
|
717 |
6795
|
cjones
|
} catch (InvalidToken e) {
|
718 |
|
|
String msg = "Could not retrieve object to replicate (InvalidToken): "+ e.getMessage();
|
719 |
|
|
failure = new ServiceFailure("2151", msg);
|
720 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
721 |
|
|
logMetacat.error(msg);
|
722 |
|
|
throw new ServiceFailure("2151", msg);
|
723 |
6786
|
cjones
|
|
724 |
6475
|
jones
|
} catch (NotFound e) {
|
725 |
6795
|
cjones
|
String msg = "Could not retrieve object to replicate (NotFound): "+ e.getMessage();
|
726 |
|
|
failure = new ServiceFailure("2151", msg);
|
727 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
728 |
|
|
logMetacat.error(msg);
|
729 |
|
|
throw new ServiceFailure("2151", msg);
|
730 |
6786
|
cjones
|
|
731 |
8414
|
tao
|
} catch (NotAuthorized e) {
|
732 |
|
|
String msg = "Could not retrieve object to replicate (NotAuthorized): "+ e.getMessage();
|
733 |
|
|
failure = new ServiceFailure("2151", msg);
|
734 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
735 |
|
|
logMetacat.error(msg);
|
736 |
|
|
throw new ServiceFailure("2151", msg);
|
737 |
|
|
} catch (NotImplemented e) {
|
738 |
|
|
String msg = "Could not retrieve object to replicate (mn.getReplica NotImplemented): "+ e.getMessage();
|
739 |
|
|
failure = new ServiceFailure("2151", msg);
|
740 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
741 |
|
|
logMetacat.error(msg);
|
742 |
|
|
throw new ServiceFailure("2151", msg);
|
743 |
|
|
} catch (ServiceFailure e) {
|
744 |
|
|
String msg = "Could not retrieve object to replicate (ServiceFailure): "+ e.getMessage();
|
745 |
|
|
failure = new ServiceFailure("2151", msg);
|
746 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
747 |
|
|
logMetacat.error(msg);
|
748 |
|
|
throw new ServiceFailure("2151", msg);
|
749 |
|
|
} catch (InsufficientResources e) {
|
750 |
|
|
String msg = "Could not retrieve object to replicate (InsufficientResources): "+ e.getMessage();
|
751 |
|
|
failure = new ServiceFailure("2151", msg);
|
752 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
753 |
|
|
logMetacat.error(msg);
|
754 |
|
|
throw new ServiceFailure("2151", msg);
|
755 |
6475
|
jones
|
}
|
756 |
|
|
|
757 |
6693
|
leinfelder
|
// verify checksum on the object, if supported
|
758 |
|
|
if (object.markSupported()) {
|
759 |
6786
|
cjones
|
Checksum givenChecksum = sysmeta.getChecksum();
|
760 |
|
|
Checksum computedChecksum = null;
|
761 |
|
|
try {
|
762 |
7127
|
leinfelder
|
computedChecksum = ChecksumUtil.checksum(object, givenChecksum.getAlgorithm());
|
763 |
6786
|
cjones
|
object.reset();
|
764 |
6948
|
cjones
|
|
765 |
6786
|
cjones
|
} catch (Exception e) {
|
766 |
7127
|
leinfelder
|
String msg = "Error computing checksum on replica: " + e.getMessage();
|
767 |
7113
|
leinfelder
|
logMetacat.error(msg);
|
768 |
6786
|
cjones
|
ServiceFailure sf = new ServiceFailure("2151", msg);
|
769 |
|
|
sf.initCause(e);
|
770 |
8414
|
tao
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, sf);
|
771 |
6786
|
cjones
|
throw sf;
|
772 |
|
|
}
|
773 |
6948
|
cjones
|
if (!givenChecksum.getValue().equals(computedChecksum.getValue())) {
|
774 |
7113
|
leinfelder
|
logMetacat.error("Given checksum for " + pid.getValue() +
|
775 |
6948
|
cjones
|
"is " + givenChecksum.getValue());
|
776 |
7113
|
leinfelder
|
logMetacat.error("Computed checksum for " + pid.getValue() +
|
777 |
6948
|
cjones
|
"is " + computedChecksum.getValue());
|
778 |
8414
|
tao
|
String msg = "Computed checksum does not match declared checksum";
|
779 |
|
|
failure = new ServiceFailure("2151", msg);
|
780 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
781 |
|
|
throw new ServiceFailure("2151", msg);
|
782 |
6786
|
cjones
|
}
|
783 |
6693
|
leinfelder
|
}
|
784 |
6786
|
cjones
|
|
785 |
6475
|
jones
|
// add it to local store
|
786 |
|
|
Identifier retPid;
|
787 |
|
|
try {
|
788 |
7127
|
leinfelder
|
// skip the MN.create -- this mutates the system metadata and we don't want it to
|
789 |
6818
|
cjones
|
if ( localId == null ) {
|
790 |
7127
|
leinfelder
|
// TODO: this will fail if we already "know" about the identifier
|
791 |
|
|
// FIXME: see https://redmine.dataone.org/issues/2572
|
792 |
6818
|
cjones
|
retPid = super.create(session, pid, object, sysmeta);
|
793 |
|
|
result = (retPid.getValue().equals(pid.getValue()));
|
794 |
|
|
}
|
795 |
6795
|
cjones
|
|
796 |
7125
|
leinfelder
|
} catch (Exception e) {
|
797 |
7126
|
leinfelder
|
String msg = "Could not save object to local store (" + e.getClass().getName() + "): " + e.getMessage();
|
798 |
7125
|
leinfelder
|
failure = new ServiceFailure("2151", msg);
|
799 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
800 |
|
|
logMetacat.error(msg);
|
801 |
|
|
throw new ServiceFailure("2151", msg);
|
802 |
|
|
|
803 |
6475
|
jones
|
}
|
804 |
|
|
|
805 |
6795
|
cjones
|
// finish by setting the replication status
|
806 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.COMPLETED, null);
|
807 |
6475
|
jones
|
return result;
|
808 |
|
|
|
809 |
6250
|
cjones
|
}
|
810 |
6179
|
cjones
|
|
811 |
6475
|
jones
|
/**
|
812 |
|
|
* Return the object identified by the given object identifier
|
813 |
|
|
*
|
814 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
815 |
|
|
* @param pid - the object identifier for the given object
|
816 |
|
|
*
|
817 |
|
|
* @return inputStream - the input stream of the given object
|
818 |
|
|
*
|
819 |
|
|
* @throws InvalidToken
|
820 |
|
|
* @throws ServiceFailure
|
821 |
|
|
* @throws NotAuthorized
|
822 |
|
|
* @throws InvalidRequest
|
823 |
|
|
* @throws NotImplemented
|
824 |
|
|
*/
|
825 |
|
|
@Override
|
826 |
6610
|
cjones
|
public InputStream get(Session session, Identifier pid)
|
827 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
828 |
6258
|
cjones
|
|
829 |
6475
|
jones
|
return super.get(session, pid);
|
830 |
6258
|
cjones
|
|
831 |
6259
|
cjones
|
}
|
832 |
6258
|
cjones
|
|
833 |
6475
|
jones
|
/**
|
834 |
|
|
* Returns a Checksum for the specified object using an accepted hashing algorithm
|
835 |
|
|
*
|
836 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
837 |
|
|
* @param pid - the object identifier for the given object
|
838 |
|
|
* @param algorithm - the name of an algorithm that will be used to compute
|
839 |
|
|
* a checksum of the bytes of the object
|
840 |
|
|
*
|
841 |
|
|
* @return checksum - the checksum of the given object
|
842 |
|
|
*
|
843 |
|
|
* @throws InvalidToken
|
844 |
|
|
* @throws ServiceFailure
|
845 |
|
|
* @throws NotAuthorized
|
846 |
|
|
* @throws NotFound
|
847 |
|
|
* @throws InvalidRequest
|
848 |
|
|
* @throws NotImplemented
|
849 |
|
|
*/
|
850 |
|
|
@Override
|
851 |
6610
|
cjones
|
public Checksum getChecksum(Session session, Identifier pid, String algorithm)
|
852 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
853 |
|
|
InvalidRequest, NotImplemented {
|
854 |
6258
|
cjones
|
|
855 |
6475
|
jones
|
Checksum checksum = null;
|
856 |
9040
|
tao
|
String serviceFailure = "1410";
|
857 |
|
|
String notFound = "1420";
|
858 |
|
|
//Checkum only handles the pid, not sid
|
859 |
|
|
checkV1SystemMetaPidExist(pid, serviceFailure, "The checksum for the object specified by "+pid.getValue()+" couldn't be returned ", notFound,
|
860 |
|
|
"The object specified by "+pid.getValue()+" does not exist at this node.");
|
861 |
6475
|
jones
|
InputStream inputStream = get(session, pid);
|
862 |
|
|
|
863 |
6259
|
cjones
|
try {
|
864 |
6475
|
jones
|
checksum = ChecksumUtil.checksum(inputStream, algorithm);
|
865 |
|
|
|
866 |
|
|
} catch (NoSuchAlgorithmException e) {
|
867 |
|
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
|
868 |
|
|
+ e.getMessage());
|
869 |
6259
|
cjones
|
} catch (IOException e) {
|
870 |
6475
|
jones
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
|
871 |
|
|
+ e.getMessage());
|
872 |
6259
|
cjones
|
}
|
873 |
6382
|
cjones
|
|
874 |
6475
|
jones
|
if (checksum == null) {
|
875 |
|
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned.");
|
876 |
|
|
}
|
877 |
6258
|
cjones
|
|
878 |
6475
|
jones
|
return checksum;
|
879 |
6259
|
cjones
|
}
|
880 |
6179
|
cjones
|
|
881 |
6475
|
jones
|
/**
|
882 |
|
|
* Return the system metadata for a given object
|
883 |
|
|
*
|
884 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
885 |
|
|
* @param pid - the object identifier for the given object
|
886 |
|
|
*
|
887 |
|
|
* @return inputStream - the input stream of the given system metadata object
|
888 |
|
|
*
|
889 |
|
|
* @throws InvalidToken
|
890 |
|
|
* @throws ServiceFailure
|
891 |
|
|
* @throws NotAuthorized
|
892 |
|
|
* @throws NotFound
|
893 |
|
|
* @throws InvalidRequest
|
894 |
|
|
* @throws NotImplemented
|
895 |
|
|
*/
|
896 |
|
|
@Override
|
897 |
6610
|
cjones
|
public SystemMetadata getSystemMetadata(Session session, Identifier pid)
|
898 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
899 |
|
|
NotImplemented {
|
900 |
6341
|
leinfelder
|
|
901 |
6475
|
jones
|
return super.getSystemMetadata(session, pid);
|
902 |
|
|
}
|
903 |
6341
|
leinfelder
|
|
904 |
6475
|
jones
|
/**
|
905 |
|
|
* Retrieve the list of objects present on the MN that match the calling parameters
|
906 |
|
|
*
|
907 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
908 |
|
|
* @param startTime - Specifies the beginning of the time range from which
|
909 |
|
|
* to return object (>=)
|
910 |
|
|
* @param endTime - Specifies the beginning of the time range from which
|
911 |
|
|
* to return object (>=)
|
912 |
|
|
* @param objectFormat - Restrict results to the specified object format
|
913 |
|
|
* @param replicaStatus - Indicates if replicated objects should be returned in the list
|
914 |
|
|
* @param start - The zero-based index of the first value, relative to the
|
915 |
|
|
* first record of the resultset that matches the parameters.
|
916 |
|
|
* @param count - The maximum number of entries that should be returned in
|
917 |
|
|
* the response. The Member Node may return less entries
|
918 |
|
|
* than specified in this value.
|
919 |
|
|
*
|
920 |
|
|
* @return objectList - the list of objects matching the criteria
|
921 |
|
|
*
|
922 |
|
|
* @throws InvalidToken
|
923 |
|
|
* @throws ServiceFailure
|
924 |
|
|
* @throws NotAuthorized
|
925 |
|
|
* @throws InvalidRequest
|
926 |
|
|
* @throws NotImplemented
|
927 |
|
|
*/
|
928 |
|
|
@Override
|
929 |
8810
|
leinfelder
|
public ObjectList listObjects(Session session, Date startTime, Date endTime, ObjectFormatIdentifier objectFormatId, Identifier identifier, Boolean replicaStatus, Integer start,
|
930 |
6475
|
jones
|
Integer count) throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken {
|
931 |
6179
|
cjones
|
|
932 |
9071
|
tao
|
return super.listObjects(session, startTime, endTime, objectFormatId, identifier, replicaStatus, start, count);
|
933 |
6229
|
cjones
|
}
|
934 |
6179
|
cjones
|
|
935 |
6475
|
jones
|
/**
|
936 |
6476
|
jones
|
* Return a description of the node's capabilities and services.
|
937 |
6475
|
jones
|
*
|
938 |
|
|
* @return node - the technical capabilities of the Member Node
|
939 |
|
|
*
|
940 |
|
|
* @throws ServiceFailure
|
941 |
|
|
* @throws NotAuthorized
|
942 |
|
|
* @throws InvalidRequest
|
943 |
|
|
* @throws NotImplemented
|
944 |
|
|
*/
|
945 |
|
|
@Override
|
946 |
6610
|
cjones
|
public Node getCapabilities()
|
947 |
|
|
throws NotImplemented, ServiceFailure {
|
948 |
6179
|
cjones
|
|
949 |
6475
|
jones
|
String nodeName = null;
|
950 |
|
|
String nodeId = null;
|
951 |
6492
|
jones
|
String subject = null;
|
952 |
6938
|
cjones
|
String contactSubject = null;
|
953 |
6475
|
jones
|
String nodeDesc = null;
|
954 |
6476
|
jones
|
String nodeTypeString = null;
|
955 |
|
|
NodeType nodeType = null;
|
956 |
6475
|
jones
|
String mnCoreServiceVersion = null;
|
957 |
|
|
String mnReadServiceVersion = null;
|
958 |
|
|
String mnAuthorizationServiceVersion = null;
|
959 |
|
|
String mnStorageServiceVersion = null;
|
960 |
|
|
String mnReplicationServiceVersion = null;
|
961 |
6179
|
cjones
|
|
962 |
6475
|
jones
|
boolean nodeSynchronize = false;
|
963 |
|
|
boolean nodeReplicate = false;
|
964 |
|
|
boolean mnCoreServiceAvailable = false;
|
965 |
|
|
boolean mnReadServiceAvailable = false;
|
966 |
|
|
boolean mnAuthorizationServiceAvailable = false;
|
967 |
|
|
boolean mnStorageServiceAvailable = false;
|
968 |
|
|
boolean mnReplicationServiceAvailable = false;
|
969 |
6179
|
cjones
|
|
970 |
6475
|
jones
|
try {
|
971 |
|
|
// get the properties of the node based on configuration information
|
972 |
6492
|
jones
|
nodeName = PropertyService.getProperty("dataone.nodeName");
|
973 |
7030
|
cjones
|
nodeId = PropertyService.getProperty("dataone.nodeId");
|
974 |
6492
|
jones
|
subject = PropertyService.getProperty("dataone.subject");
|
975 |
6938
|
cjones
|
contactSubject = PropertyService.getProperty("dataone.contactSubject");
|
976 |
6475
|
jones
|
nodeDesc = PropertyService.getProperty("dataone.nodeDescription");
|
977 |
6476
|
jones
|
nodeTypeString = PropertyService.getProperty("dataone.nodeType");
|
978 |
|
|
nodeType = NodeType.convert(nodeTypeString);
|
979 |
6475
|
jones
|
nodeSynchronize = new Boolean(PropertyService.getProperty("dataone.nodeSynchronize")).booleanValue();
|
980 |
|
|
nodeReplicate = new Boolean(PropertyService.getProperty("dataone.nodeReplicate")).booleanValue();
|
981 |
|
|
|
982 |
|
|
mnCoreServiceVersion = PropertyService.getProperty("dataone.mnCore.serviceVersion");
|
983 |
|
|
mnReadServiceVersion = PropertyService.getProperty("dataone.mnRead.serviceVersion");
|
984 |
|
|
mnAuthorizationServiceVersion = PropertyService.getProperty("dataone.mnAuthorization.serviceVersion");
|
985 |
|
|
mnStorageServiceVersion = PropertyService.getProperty("dataone.mnStorage.serviceVersion");
|
986 |
|
|
mnReplicationServiceVersion = PropertyService.getProperty("dataone.mnReplication.serviceVersion");
|
987 |
|
|
|
988 |
|
|
mnCoreServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnCore.serviceAvailable")).booleanValue();
|
989 |
|
|
mnReadServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnRead.serviceAvailable")).booleanValue();
|
990 |
|
|
mnAuthorizationServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnAuthorization.serviceAvailable")).booleanValue();
|
991 |
|
|
mnStorageServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnStorage.serviceAvailable")).booleanValue();
|
992 |
|
|
mnReplicationServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnReplication.serviceAvailable")).booleanValue();
|
993 |
|
|
|
994 |
6476
|
jones
|
// Set the properties of the node based on configuration information and
|
995 |
|
|
// calls to current status methods
|
996 |
7286
|
leinfelder
|
String serviceName = SystemUtil.getSecureContextURL() + "/" + PropertyService.getProperty("dataone.serviceName");
|
997 |
6476
|
jones
|
Node node = new Node();
|
998 |
6542
|
leinfelder
|
node.setBaseURL(serviceName + "/" + nodeTypeString);
|
999 |
6476
|
jones
|
node.setDescription(nodeDesc);
|
1000 |
6475
|
jones
|
|
1001 |
6476
|
jones
|
// set the node's health information
|
1002 |
|
|
node.setState(NodeState.UP);
|
1003 |
|
|
|
1004 |
|
|
// set the ping response to the current value
|
1005 |
|
|
Ping canPing = new Ping();
|
1006 |
|
|
canPing.setSuccess(false);
|
1007 |
|
|
try {
|
1008 |
6803
|
leinfelder
|
Date pingDate = ping();
|
1009 |
|
|
canPing.setSuccess(pingDate != null);
|
1010 |
|
|
} catch (BaseException e) {
|
1011 |
6476
|
jones
|
e.printStackTrace();
|
1012 |
6803
|
leinfelder
|
// guess it can't be pinged
|
1013 |
6476
|
jones
|
}
|
1014 |
6610
|
cjones
|
|
1015 |
6476
|
jones
|
node.setPing(canPing);
|
1016 |
6475
|
jones
|
|
1017 |
6476
|
jones
|
NodeReference identifier = new NodeReference();
|
1018 |
|
|
identifier.setValue(nodeId);
|
1019 |
|
|
node.setIdentifier(identifier);
|
1020 |
6492
|
jones
|
Subject s = new Subject();
|
1021 |
|
|
s.setValue(subject);
|
1022 |
|
|
node.addSubject(s);
|
1023 |
6938
|
cjones
|
Subject contact = new Subject();
|
1024 |
|
|
contact.setValue(contactSubject);
|
1025 |
|
|
node.addContactSubject(contact);
|
1026 |
6476
|
jones
|
node.setName(nodeName);
|
1027 |
|
|
node.setReplicate(nodeReplicate);
|
1028 |
|
|
node.setSynchronize(nodeSynchronize);
|
1029 |
6475
|
jones
|
|
1030 |
6476
|
jones
|
// services: MNAuthorization, MNCore, MNRead, MNReplication, MNStorage
|
1031 |
|
|
Services services = new Services();
|
1032 |
6475
|
jones
|
|
1033 |
6476
|
jones
|
Service sMNCore = new Service();
|
1034 |
|
|
sMNCore.setName("MNCore");
|
1035 |
|
|
sMNCore.setVersion(mnCoreServiceVersion);
|
1036 |
|
|
sMNCore.setAvailable(mnCoreServiceAvailable);
|
1037 |
6475
|
jones
|
|
1038 |
6476
|
jones
|
Service sMNRead = new Service();
|
1039 |
|
|
sMNRead.setName("MNRead");
|
1040 |
|
|
sMNRead.setVersion(mnReadServiceVersion);
|
1041 |
|
|
sMNRead.setAvailable(mnReadServiceAvailable);
|
1042 |
6475
|
jones
|
|
1043 |
6476
|
jones
|
Service sMNAuthorization = new Service();
|
1044 |
|
|
sMNAuthorization.setName("MNAuthorization");
|
1045 |
|
|
sMNAuthorization.setVersion(mnAuthorizationServiceVersion);
|
1046 |
|
|
sMNAuthorization.setAvailable(mnAuthorizationServiceAvailable);
|
1047 |
6475
|
jones
|
|
1048 |
6476
|
jones
|
Service sMNStorage = new Service();
|
1049 |
|
|
sMNStorage.setName("MNStorage");
|
1050 |
|
|
sMNStorage.setVersion(mnStorageServiceVersion);
|
1051 |
|
|
sMNStorage.setAvailable(mnStorageServiceAvailable);
|
1052 |
6475
|
jones
|
|
1053 |
6476
|
jones
|
Service sMNReplication = new Service();
|
1054 |
|
|
sMNReplication.setName("MNReplication");
|
1055 |
|
|
sMNReplication.setVersion(mnReplicationServiceVersion);
|
1056 |
|
|
sMNReplication.setAvailable(mnReplicationServiceAvailable);
|
1057 |
6475
|
jones
|
|
1058 |
6476
|
jones
|
services.addService(sMNRead);
|
1059 |
|
|
services.addService(sMNCore);
|
1060 |
|
|
services.addService(sMNAuthorization);
|
1061 |
|
|
services.addService(sMNStorage);
|
1062 |
|
|
services.addService(sMNReplication);
|
1063 |
|
|
node.setServices(services);
|
1064 |
6475
|
jones
|
|
1065 |
6476
|
jones
|
// Set the schedule for synchronization
|
1066 |
|
|
Synchronization synchronization = new Synchronization();
|
1067 |
|
|
Schedule schedule = new Schedule();
|
1068 |
|
|
Date now = new Date();
|
1069 |
6689
|
leinfelder
|
schedule.setYear(PropertyService.getProperty("dataone.nodeSynchronization.schedule.year"));
|
1070 |
|
|
schedule.setMon(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mon"));
|
1071 |
|
|
schedule.setMday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mday"));
|
1072 |
|
|
schedule.setWday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.wday"));
|
1073 |
|
|
schedule.setHour(PropertyService.getProperty("dataone.nodeSynchronization.schedule.hour"));
|
1074 |
|
|
schedule.setMin(PropertyService.getProperty("dataone.nodeSynchronization.schedule.min"));
|
1075 |
|
|
schedule.setSec(PropertyService.getProperty("dataone.nodeSynchronization.schedule.sec"));
|
1076 |
6476
|
jones
|
synchronization.setSchedule(schedule);
|
1077 |
|
|
synchronization.setLastHarvested(now);
|
1078 |
|
|
synchronization.setLastCompleteHarvest(now);
|
1079 |
|
|
node.setSynchronization(synchronization);
|
1080 |
6475
|
jones
|
|
1081 |
6476
|
jones
|
node.setType(nodeType);
|
1082 |
|
|
return node;
|
1083 |
6475
|
jones
|
|
1084 |
6476
|
jones
|
} catch (PropertyNotFoundException pnfe) {
|
1085 |
|
|
String msg = "MNodeService.getCapabilities(): " + "property not found: " + pnfe.getMessage();
|
1086 |
|
|
logMetacat.error(msg);
|
1087 |
|
|
throw new ServiceFailure("2162", msg);
|
1088 |
|
|
}
|
1089 |
6228
|
cjones
|
}
|
1090 |
6179
|
cjones
|
|
1091 |
8810
|
leinfelder
|
|
1092 |
6179
|
cjones
|
|
1093 |
6475
|
jones
|
/**
|
1094 |
|
|
* A callback method used by a CN to indicate to a MN that it cannot
|
1095 |
|
|
* complete synchronization of the science metadata identified by pid. Log
|
1096 |
|
|
* the event in the metacat event log.
|
1097 |
|
|
*
|
1098 |
|
|
* @param session
|
1099 |
|
|
* @param syncFailed
|
1100 |
|
|
*
|
1101 |
|
|
* @throws ServiceFailure
|
1102 |
|
|
* @throws NotAuthorized
|
1103 |
|
|
* @throws NotImplemented
|
1104 |
|
|
*/
|
1105 |
|
|
@Override
|
1106 |
6991
|
leinfelder
|
public boolean synchronizationFailed(Session session, SynchronizationFailed syncFailed)
|
1107 |
6610
|
cjones
|
throws NotImplemented, ServiceFailure, NotAuthorized {
|
1108 |
6179
|
cjones
|
|
1109 |
6475
|
jones
|
String localId;
|
1110 |
7075
|
cjones
|
Identifier pid;
|
1111 |
|
|
if ( syncFailed.getPid() != null ) {
|
1112 |
|
|
pid = new Identifier();
|
1113 |
|
|
pid.setValue(syncFailed.getPid());
|
1114 |
|
|
boolean allowed;
|
1115 |
|
|
|
1116 |
|
|
//are we allowed? only CNs
|
1117 |
|
|
try {
|
1118 |
7142
|
leinfelder
|
allowed = isAdminAuthorized(session);
|
1119 |
7075
|
cjones
|
if ( !allowed ){
|
1120 |
|
|
throw new NotAuthorized("2162",
|
1121 |
|
|
"Not allowed to call synchronizationFailed() on this node.");
|
1122 |
|
|
}
|
1123 |
|
|
} catch (InvalidToken e) {
|
1124 |
|
|
throw new NotAuthorized("2162",
|
1125 |
|
|
"Not allowed to call synchronizationFailed() on this node.");
|
1126 |
6331
|
leinfelder
|
|
1127 |
7075
|
cjones
|
}
|
1128 |
|
|
|
1129 |
|
|
} else {
|
1130 |
|
|
throw new ServiceFailure("2161", "The identifier cannot be null.");
|
1131 |
|
|
|
1132 |
|
|
}
|
1133 |
|
|
|
1134 |
6475
|
jones
|
try {
|
1135 |
7075
|
cjones
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
1136 |
6475
|
jones
|
} catch (McdbDocNotFoundException e) {
|
1137 |
7075
|
cjones
|
throw new ServiceFailure("2161", "The identifier specified by " +
|
1138 |
|
|
syncFailed.getPid() + " was not found on this node.");
|
1139 |
6179
|
cjones
|
|
1140 |
9024
|
tao
|
} catch (SQLException e) {
|
1141 |
|
|
throw new ServiceFailure("2161", "Couldn't identify the local id of the identifier specified by " +
|
1142 |
|
|
syncFailed.getPid() + " since "+e.getMessage());
|
1143 |
6475
|
jones
|
}
|
1144 |
|
|
// TODO: update the CN URL below when the CNRead.SynchronizationFailed
|
1145 |
|
|
// method is changed to include the URL as a parameter
|
1146 |
7075
|
cjones
|
logMetacat.debug("Synchronization for the object identified by " +
|
1147 |
|
|
pid.getValue() + " failed from " + syncFailed.getNodeId() +
|
1148 |
|
|
" Logging the event to the Metacat EventLog as a 'syncFailed' event.");
|
1149 |
6475
|
jones
|
// TODO: use the event type enum when the SYNCHRONIZATION_FAILED event is added
|
1150 |
6532
|
leinfelder
|
String principal = Constants.SUBJECT_PUBLIC;
|
1151 |
6506
|
leinfelder
|
if (session != null && session.getSubject() != null) {
|
1152 |
6575
|
cjones
|
principal = session.getSubject().getValue();
|
1153 |
6506
|
leinfelder
|
}
|
1154 |
|
|
try {
|
1155 |
6575
|
cjones
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "synchronization_failed");
|
1156 |
6506
|
leinfelder
|
} catch (Exception e) {
|
1157 |
7075
|
cjones
|
throw new ServiceFailure("2161", "Could not log the error for: " + pid.getValue());
|
1158 |
6991
|
leinfelder
|
}
|
1159 |
6475
|
jones
|
//EventLog.getInstance().log("CN URL WILL GO HERE",
|
1160 |
|
|
// session.getSubject().getValue(), localId, Event.SYNCHRONIZATION_FAILED);
|
1161 |
6991
|
leinfelder
|
return true;
|
1162 |
6179
|
cjones
|
|
1163 |
6260
|
cjones
|
}
|
1164 |
|
|
|
1165 |
6475
|
jones
|
/**
|
1166 |
|
|
* Essentially a get() but with different logging behavior
|
1167 |
|
|
*/
|
1168 |
|
|
@Override
|
1169 |
6540
|
cjones
|
public InputStream getReplica(Session session, Identifier pid)
|
1170 |
6653
|
leinfelder
|
throws NotAuthorized, NotImplemented, ServiceFailure, InvalidToken {
|
1171 |
6179
|
cjones
|
|
1172 |
6540
|
cjones
|
logMetacat.info("MNodeService.getReplica() called.");
|
1173 |
|
|
|
1174 |
6653
|
leinfelder
|
// cannot be called by public
|
1175 |
|
|
if (session == null) {
|
1176 |
|
|
throw new InvalidToken("2183", "No session was provided.");
|
1177 |
|
|
}
|
1178 |
|
|
|
1179 |
6631
|
cjones
|
logMetacat.info("MNodeService.getReplica() called with parameters: \n" +
|
1180 |
|
|
"\tSession.Subject = " + session.getSubject().getValue() + "\n" +
|
1181 |
|
|
"\tIdentifier = " + pid.getValue());
|
1182 |
|
|
|
1183 |
6475
|
jones
|
InputStream inputStream = null; // bytes to be returned
|
1184 |
|
|
handler = new MetacatHandler(new Timer());
|
1185 |
|
|
boolean allowed = false;
|
1186 |
|
|
String localId; // the metacat docid for the pid
|
1187 |
6179
|
cjones
|
|
1188 |
6475
|
jones
|
// get the local docid from Metacat
|
1189 |
|
|
try {
|
1190 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
1191 |
|
|
} catch (McdbDocNotFoundException e) {
|
1192 |
6610
|
cjones
|
throw new ServiceFailure("2181", "The object specified by " +
|
1193 |
|
|
pid.getValue() + " does not exist at this node.");
|
1194 |
|
|
|
1195 |
9024
|
tao
|
} catch (SQLException e) {
|
1196 |
|
|
throw new ServiceFailure("2181", "The local id of the object specified by " +
|
1197 |
|
|
pid.getValue() + " couldn't be identified since "+e.getMessage());
|
1198 |
6475
|
jones
|
}
|
1199 |
6234
|
cjones
|
|
1200 |
6552
|
leinfelder
|
Subject targetNodeSubject = session.getSubject();
|
1201 |
6185
|
leinfelder
|
|
1202 |
6552
|
leinfelder
|
// check for authorization to replicate, null session to act as this source MN
|
1203 |
6610
|
cjones
|
try {
|
1204 |
6777
|
leinfelder
|
allowed = D1Client.getCN().isNodeAuthorized(null, targetNodeSubject, pid);
|
1205 |
6610
|
cjones
|
} catch (InvalidToken e1) {
|
1206 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
1207 |
|
|
+ e1.getMessage());
|
1208 |
|
|
|
1209 |
|
|
} catch (NotFound e1) {
|
1210 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
1211 |
|
|
+ e1.getMessage());
|
1212 |
6384
|
cjones
|
|
1213 |
6610
|
cjones
|
} catch (InvalidRequest e1) {
|
1214 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
1215 |
|
|
+ e1.getMessage());
|
1216 |
|
|
|
1217 |
|
|
}
|
1218 |
|
|
|
1219 |
6540
|
cjones
|
logMetacat.info("Called D1Client.isNodeAuthorized(). Allowed = " + allowed +
|
1220 |
|
|
" for identifier " + pid.getValue());
|
1221 |
|
|
|
1222 |
6475
|
jones
|
// if the person is authorized, perform the read
|
1223 |
|
|
if (allowed) {
|
1224 |
|
|
try {
|
1225 |
6986
|
jones
|
inputStream = MetacatHandler.read(localId);
|
1226 |
6475
|
jones
|
} catch (Exception e) {
|
1227 |
6610
|
cjones
|
throw new ServiceFailure("1020", "The object specified by " +
|
1228 |
|
|
pid.getValue() + "could not be returned due to error: " + e.getMessage());
|
1229 |
6475
|
jones
|
}
|
1230 |
|
|
}
|
1231 |
6384
|
cjones
|
|
1232 |
6475
|
jones
|
// if we fail to set the input stream
|
1233 |
|
|
if (inputStream == null) {
|
1234 |
6610
|
cjones
|
throw new ServiceFailure("2181", "The object specified by " +
|
1235 |
|
|
pid.getValue() + "does not exist at this node.");
|
1236 |
6475
|
jones
|
}
|
1237 |
|
|
|
1238 |
|
|
// log the replica event
|
1239 |
|
|
String principal = null;
|
1240 |
|
|
if (session.getSubject() != null) {
|
1241 |
|
|
principal = session.getSubject().getValue();
|
1242 |
|
|
}
|
1243 |
6576
|
cjones
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
1244 |
|
|
request.getHeader("User-Agent"), principal, localId, "replicate");
|
1245 |
6475
|
jones
|
|
1246 |
|
|
return inputStream;
|
1247 |
|
|
}
|
1248 |
|
|
|
1249 |
6573
|
cjones
|
/**
|
1250 |
6600
|
cjones
|
* A method to notify the Member Node that the authoritative copy of
|
1251 |
6599
|
cjones
|
* system metadata on the Coordinating Nodes has changed.
|
1252 |
|
|
*
|
1253 |
|
|
* @param session Session information that contains the identity of the
|
1254 |
|
|
* calling user as retrieved from the X.509 certificate
|
1255 |
|
|
* which must be traceable to the CILogon service.
|
1256 |
|
|
* @param serialVersion The serialVersion of the system metadata
|
1257 |
|
|
* @param dateSysMetaLastModified The time stamp for when the system metadata was changed
|
1258 |
|
|
* @throws NotImplemented
|
1259 |
|
|
* @throws ServiceFailure
|
1260 |
|
|
* @throws NotAuthorized
|
1261 |
|
|
* @throws InvalidRequest
|
1262 |
|
|
* @throws InvalidToken
|
1263 |
|
|
*/
|
1264 |
6991
|
leinfelder
|
public boolean systemMetadataChanged(Session session, Identifier pid,
|
1265 |
6599
|
cjones
|
long serialVersion, Date dateSysMetaLastModified)
|
1266 |
|
|
throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest,
|
1267 |
|
|
InvalidToken {
|
1268 |
|
|
|
1269 |
7600
|
cjones
|
// cannot be called by public
|
1270 |
|
|
if (session == null) {
|
1271 |
9051
|
tao
|
throw new InvalidToken("1332", "No session was provided.");
|
1272 |
7600
|
cjones
|
}
|
1273 |
|
|
|
1274 |
9051
|
tao
|
String serviceFailureCode = "1333";
|
1275 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
1276 |
|
|
if(sid != null) {
|
1277 |
|
|
pid = sid;
|
1278 |
|
|
}
|
1279 |
|
|
|
1280 |
6600
|
cjones
|
SystemMetadata currentLocalSysMeta = null;
|
1281 |
|
|
SystemMetadata newSysMeta = null;
|
1282 |
|
|
CNode cn = D1Client.getCN();
|
1283 |
|
|
NodeList nodeList = null;
|
1284 |
|
|
Subject callingSubject = null;
|
1285 |
|
|
boolean allowed = false;
|
1286 |
|
|
|
1287 |
|
|
// are we allowed to call this?
|
1288 |
|
|
callingSubject = session.getSubject();
|
1289 |
|
|
nodeList = cn.listNodes();
|
1290 |
|
|
|
1291 |
|
|
for(Node node : nodeList.getNodeList()) {
|
1292 |
|
|
// must be a CN
|
1293 |
|
|
if ( node.getType().equals(NodeType.CN)) {
|
1294 |
|
|
List<Subject> subjectList = node.getSubjectList();
|
1295 |
|
|
// the calling subject must be in the subject list
|
1296 |
|
|
if ( subjectList.contains(callingSubject)) {
|
1297 |
|
|
allowed = true;
|
1298 |
|
|
|
1299 |
|
|
}
|
1300 |
|
|
|
1301 |
|
|
}
|
1302 |
|
|
}
|
1303 |
|
|
|
1304 |
|
|
if (!allowed ) {
|
1305 |
|
|
String msg = "The subject identified by " + callingSubject.getValue() +
|
1306 |
|
|
" is not authorized to call this service.";
|
1307 |
|
|
throw new NotAuthorized("1331", msg);
|
1308 |
|
|
|
1309 |
|
|
}
|
1310 |
|
|
|
1311 |
|
|
// compare what we have locally to what is sent in the change notification
|
1312 |
|
|
try {
|
1313 |
6692
|
leinfelder
|
currentLocalSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
1314 |
|
|
|
1315 |
|
|
} catch (RuntimeException e) {
|
1316 |
6600
|
cjones
|
String msg = "SystemMetadata for pid " + pid.getValue() +
|
1317 |
6692
|
leinfelder
|
" couldn't be updated because it couldn't be found locally: " +
|
1318 |
6600
|
cjones
|
e.getMessage();
|
1319 |
6692
|
leinfelder
|
logMetacat.error(msg);
|
1320 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
1321 |
|
|
sf.initCause(e);
|
1322 |
|
|
throw sf;
|
1323 |
6600
|
cjones
|
}
|
1324 |
|
|
|
1325 |
|
|
if (currentLocalSysMeta.getSerialVersion().longValue() < serialVersion ) {
|
1326 |
|
|
try {
|
1327 |
|
|
newSysMeta = cn.getSystemMetadata(null, pid);
|
1328 |
|
|
} catch (NotFound e) {
|
1329 |
|
|
// huh? you just said you had it
|
1330 |
6692
|
leinfelder
|
String msg = "On updating the local copy of system metadata " +
|
1331 |
|
|
"for pid " + pid.getValue() +", the CN reports it is not found." +
|
1332 |
|
|
" The error message was: " + e.getMessage();
|
1333 |
|
|
logMetacat.error(msg);
|
1334 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
1335 |
|
|
sf.initCause(e);
|
1336 |
|
|
throw sf;
|
1337 |
6600
|
cjones
|
}
|
1338 |
6692
|
leinfelder
|
|
1339 |
9056
|
tao
|
//check about the sid in the system metadata
|
1340 |
|
|
Identifier newSID = newSysMeta.getSeriesId();
|
1341 |
|
|
if(newSID != null) {
|
1342 |
|
|
if (!isValidIdentifier(newSID)) {
|
1343 |
|
|
throw new InvalidRequest("1334", "The series identifier in the new system metadata is invalid.");
|
1344 |
|
|
}
|
1345 |
|
|
Identifier currentSID = currentLocalSysMeta.getSeriesId();
|
1346 |
|
|
if( currentSID != null && currentSID.getValue() != null) {
|
1347 |
|
|
if(!newSID.getValue().equals(currentSID.getValue())) {
|
1348 |
|
|
//newSID doesn't match the currentSID. The newSID shouldn't be used.
|
1349 |
|
|
try {
|
1350 |
|
|
if(IdentifierManager.getInstance().identifierExists(newSID.getValue())) {
|
1351 |
|
|
throw new InvalidRequest("1334", "The series identifier "+newSID.getValue()+" in the new system metadata has been used by another object.");
|
1352 |
|
|
}
|
1353 |
|
|
} catch (SQLException sql) {
|
1354 |
|
|
throw new ServiceFailure("1333", "Couldn't determine if the SID "+newSID.getValue()+" in the system metadata exists in the node since "+sql.getMessage());
|
1355 |
|
|
}
|
1356 |
|
|
|
1357 |
|
|
}
|
1358 |
|
|
} else {
|
1359 |
|
|
//newSID shouldn't be used
|
1360 |
|
|
try {
|
1361 |
|
|
if(IdentifierManager.getInstance().identifierExists(newSID.getValue())) {
|
1362 |
|
|
throw new InvalidRequest("1334", "The series identifier "+newSID.getValue()+" in the new system metadata has been used by another object.");
|
1363 |
|
|
}
|
1364 |
|
|
} catch (SQLException sql) {
|
1365 |
|
|
throw new ServiceFailure("1333", "Couldn't determine if the SID "+newSID.getValue()+" in the system metadata exists in the node since "+sql.getMessage());
|
1366 |
|
|
}
|
1367 |
|
|
}
|
1368 |
|
|
}
|
1369 |
6600
|
cjones
|
// update the local copy of system metadata for the pid
|
1370 |
|
|
try {
|
1371 |
6692
|
leinfelder
|
HazelcastService.getInstance().getSystemMetadataMap().put(newSysMeta.getIdentifier(), newSysMeta);
|
1372 |
6600
|
cjones
|
logMetacat.info("Updated local copy of system metadata for pid " +
|
1373 |
|
|
pid.getValue() + " after change notification from the CN.");
|
1374 |
|
|
|
1375 |
8599
|
leinfelder
|
// TODO: consider inspecting the change for archive
|
1376 |
|
|
// see: https://projects.ecoinformatics.org/ecoinfo/issues/6417
|
1377 |
|
|
// if (newSysMeta.getArchived() != null && newSysMeta.getArchived().booleanValue()) {
|
1378 |
|
|
// try {
|
1379 |
|
|
// this.archive(session, newSysMeta.getIdentifier());
|
1380 |
|
|
// } catch (NotFound e) {
|
1381 |
|
|
// // do we care? nothing to do about it now
|
1382 |
|
|
// logMetacat.error(e.getMessage(), e);
|
1383 |
|
|
// }
|
1384 |
|
|
// }
|
1385 |
|
|
|
1386 |
6692
|
leinfelder
|
} catch (RuntimeException e) {
|
1387 |
6600
|
cjones
|
String msg = "SystemMetadata for pid " + pid.getValue() +
|
1388 |
6692
|
leinfelder
|
" couldn't be updated: " +
|
1389 |
6600
|
cjones
|
e.getMessage();
|
1390 |
6692
|
leinfelder
|
logMetacat.error(msg);
|
1391 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
1392 |
|
|
sf.initCause(e);
|
1393 |
|
|
throw sf;
|
1394 |
6600
|
cjones
|
}
|
1395 |
8464
|
leinfelder
|
|
1396 |
|
|
// submit for indexing
|
1397 |
|
|
try {
|
1398 |
8647
|
leinfelder
|
MetacatSolrIndex.getInstance().submit(newSysMeta.getIdentifier(), newSysMeta, null, true);
|
1399 |
8464
|
leinfelder
|
} catch (Exception e) {
|
1400 |
|
|
logMetacat.error("Could not submit changed systemMetadata for indexing, pid: " + newSysMeta.getIdentifier().getValue(), e);
|
1401 |
|
|
}
|
1402 |
6600
|
cjones
|
}
|
1403 |
|
|
|
1404 |
6991
|
leinfelder
|
return true;
|
1405 |
|
|
|
1406 |
6599
|
cjones
|
}
|
1407 |
|
|
|
1408 |
6795
|
cjones
|
/*
|
1409 |
|
|
* Set the replication status for the object on the Coordinating Node
|
1410 |
|
|
*
|
1411 |
|
|
* @param session - the session for the this target node
|
1412 |
|
|
* @param pid - the identifier of the object being updated
|
1413 |
|
|
* @param nodeId - the identifier of this target node
|
1414 |
|
|
* @param status - the replication status to set
|
1415 |
|
|
* @param failure - the exception to include, if any
|
1416 |
|
|
*/
|
1417 |
|
|
private void setReplicationStatus(Session session, Identifier pid,
|
1418 |
|
|
NodeReference nodeId, ReplicationStatus status, BaseException failure)
|
1419 |
|
|
throws ServiceFailure, NotImplemented, NotAuthorized,
|
1420 |
|
|
InvalidRequest {
|
1421 |
|
|
|
1422 |
|
|
// call the CN as the MN to set the replication status
|
1423 |
|
|
try {
|
1424 |
|
|
this.cn = D1Client.getCN();
|
1425 |
|
|
this.cn.setReplicationStatus(session, pid, nodeId,
|
1426 |
|
|
status, failure);
|
1427 |
|
|
|
1428 |
|
|
} catch (InvalidToken e) {
|
1429 |
7091
|
leinfelder
|
String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (InvalidToken): " + e.getMessage();
|
1430 |
|
|
logMetacat.error(msg);
|
1431 |
|
|
throw new ServiceFailure("2151",
|
1432 |
|
|
msg);
|
1433 |
6795
|
cjones
|
|
1434 |
|
|
} catch (NotFound e) {
|
1435 |
7091
|
leinfelder
|
String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (NotFound): " + e.getMessage();
|
1436 |
|
|
logMetacat.error(msg);
|
1437 |
|
|
throw new ServiceFailure("2151",
|
1438 |
|
|
msg);
|
1439 |
6795
|
cjones
|
|
1440 |
|
|
}
|
1441 |
|
|
}
|
1442 |
8591
|
leinfelder
|
|
1443 |
|
|
private SystemMetadata makePublicIfNot(SystemMetadata sysmeta, Identifier pid) throws ServiceFailure, InvalidToken, NotFound, NotImplemented, InvalidRequest {
|
1444 |
|
|
// check if it is publicly readable
|
1445 |
|
|
boolean isPublic = false;
|
1446 |
|
|
Subject publicSubject = new Subject();
|
1447 |
|
|
publicSubject.setValue(Constants.SUBJECT_PUBLIC);
|
1448 |
|
|
Session publicSession = new Session();
|
1449 |
|
|
publicSession.setSubject(publicSubject);
|
1450 |
|
|
AccessRule publicRule = new AccessRule();
|
1451 |
|
|
publicRule.addPermission(Permission.READ);
|
1452 |
|
|
publicRule.addSubject(publicSubject);
|
1453 |
|
|
|
1454 |
|
|
// see if we need to add the rule
|
1455 |
|
|
try {
|
1456 |
|
|
isPublic = this.isAuthorized(publicSession, pid, Permission.READ);
|
1457 |
|
|
} catch (NotAuthorized na) {
|
1458 |
|
|
// well, certainly not authorized for public read!
|
1459 |
|
|
}
|
1460 |
|
|
if (!isPublic) {
|
1461 |
|
|
sysmeta.getAccessPolicy().addAllow(publicRule);
|
1462 |
|
|
}
|
1463 |
|
|
|
1464 |
|
|
return sysmeta;
|
1465 |
|
|
}
|
1466 |
7099
|
leinfelder
|
|
1467 |
|
|
@Override
|
1468 |
7441
|
leinfelder
|
public Identifier generateIdentifier(Session session, String scheme, String fragment)
|
1469 |
7099
|
leinfelder
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
|
1470 |
|
|
InvalidRequest {
|
1471 |
7448
|
leinfelder
|
|
1472 |
8210
|
leinfelder
|
// check for null session
|
1473 |
|
|
if (session == null) {
|
1474 |
|
|
throw new InvalidToken("2190", "Session is required to generate an Identifier at this Node.");
|
1475 |
|
|
}
|
1476 |
|
|
|
1477 |
7441
|
leinfelder
|
Identifier identifier = new Identifier();
|
1478 |
7448
|
leinfelder
|
|
1479 |
7489
|
leinfelder
|
// handle different schemes
|
1480 |
|
|
if (scheme.equalsIgnoreCase(UUID_SCHEME)) {
|
1481 |
|
|
// UUID
|
1482 |
|
|
UUID uuid = UUID.randomUUID();
|
1483 |
|
|
identifier.setValue(UUID_PREFIX + uuid.toString());
|
1484 |
|
|
} else if (scheme.equalsIgnoreCase(DOI_SCHEME)) {
|
1485 |
7512
|
leinfelder
|
// generate a DOI
|
1486 |
7448
|
leinfelder
|
try {
|
1487 |
7512
|
leinfelder
|
identifier = DOIService.getInstance().generateDOI();
|
1488 |
7448
|
leinfelder
|
} catch (EZIDException e) {
|
1489 |
7512
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("2191", "Could not generate DOI: " + e.getMessage());
|
1490 |
|
|
sf.initCause(e);
|
1491 |
|
|
throw sf;
|
1492 |
7448
|
leinfelder
|
}
|
1493 |
7489
|
leinfelder
|
} else {
|
1494 |
|
|
// default if we don't know the scheme
|
1495 |
|
|
if (fragment != null) {
|
1496 |
|
|
// for now, just autogen with fragment
|
1497 |
|
|
String autogenId = DocumentUtil.generateDocumentId(fragment, 0);
|
1498 |
|
|
identifier.setValue(autogenId);
|
1499 |
|
|
} else {
|
1500 |
|
|
// autogen with no fragment
|
1501 |
|
|
String autogenId = DocumentUtil.generateDocumentId(0);
|
1502 |
|
|
identifier.setValue(autogenId);
|
1503 |
|
|
}
|
1504 |
7448
|
leinfelder
|
}
|
1505 |
|
|
|
1506 |
7441
|
leinfelder
|
// TODO: reserve the identifier with the CN. We can only do this when
|
1507 |
|
|
// 1) the MN is part of a CN cluster
|
1508 |
|
|
// 2) the request is from an authenticated user
|
1509 |
|
|
|
1510 |
|
|
return identifier;
|
1511 |
7099
|
leinfelder
|
}
|
1512 |
7144
|
leinfelder
|
|
1513 |
8810
|
leinfelder
|
|
1514 |
7144
|
leinfelder
|
|
1515 |
|
|
@Override
|
1516 |
8810
|
leinfelder
|
public QueryEngineDescription getQueryEngineDescription(Session session, String engine)
|
1517 |
7144
|
leinfelder
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
|
1518 |
|
|
NotFound {
|
1519 |
7772
|
tao
|
if(engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
|
1520 |
8162
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
|
1521 |
|
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
1522 |
|
|
}
|
1523 |
7634
|
tao
|
QueryEngineDescription qed = new QueryEngineDescription();
|
1524 |
7772
|
tao
|
qed.setName(EnabledQueryEngines.PATHQUERYENGINE);
|
1525 |
7634
|
tao
|
qed.setQueryEngineVersion("1.0");
|
1526 |
|
|
qed.addAdditionalInfo("This is the traditional structured query for Metacat");
|
1527 |
|
|
Vector<String> pathsForIndexing = null;
|
1528 |
|
|
try {
|
1529 |
|
|
pathsForIndexing = SystemUtil.getPathsForIndexing();
|
1530 |
|
|
} catch (MetacatUtilException e) {
|
1531 |
|
|
logMetacat.warn("Could not get index paths", e);
|
1532 |
|
|
}
|
1533 |
|
|
for (String fieldName: pathsForIndexing) {
|
1534 |
|
|
QueryField field = new QueryField();
|
1535 |
|
|
field.addDescription("Indexed field for path '" + fieldName + "'");
|
1536 |
|
|
field.setName(fieldName);
|
1537 |
|
|
field.setReturnable(true);
|
1538 |
|
|
field.setSearchable(true);
|
1539 |
|
|
field.setSortable(false);
|
1540 |
|
|
// TODO: determine type and multivaluedness
|
1541 |
|
|
field.setType(String.class.getName());
|
1542 |
|
|
//field.setMultivalued(true);
|
1543 |
|
|
qed.addQueryField(field);
|
1544 |
|
|
}
|
1545 |
|
|
return qed;
|
1546 |
7772
|
tao
|
} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
|
1547 |
7781
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
|
1548 |
7772
|
tao
|
throw new NotImplemented("0000", "MNodeService.getQueryEngineDescription - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
1549 |
7781
|
tao
|
}
|
1550 |
7634
|
tao
|
try {
|
1551 |
7662
|
tao
|
QueryEngineDescription qed = MetacatSolrEngineDescriptionHandler.getInstance().getQueryEngineDescritpion();
|
1552 |
7634
|
tao
|
return qed;
|
1553 |
|
|
} catch (Exception e) {
|
1554 |
|
|
e.printStackTrace();
|
1555 |
|
|
throw new ServiceFailure("Solr server error", e.getMessage());
|
1556 |
|
|
}
|
1557 |
|
|
} else {
|
1558 |
|
|
throw new NotFound("404", "The Metacat member node can't find the query engine - "+engine);
|
1559 |
|
|
}
|
1560 |
|
|
|
1561 |
7417
|
leinfelder
|
}
|
1562 |
|
|
|
1563 |
|
|
@Override
|
1564 |
8810
|
leinfelder
|
public QueryEngineList listQueryEngines(Session session) throws InvalidToken,
|
1565 |
7417
|
leinfelder
|
ServiceFailure, NotAuthorized, NotImplemented {
|
1566 |
|
|
QueryEngineList qel = new QueryEngineList();
|
1567 |
7781
|
tao
|
//qel.addQueryEngine(EnabledQueryEngines.PATHQUERYENGINE);
|
1568 |
|
|
//qel.addQueryEngine(EnabledQueryEngines.SOLRENGINE);
|
1569 |
|
|
List<String> enables = EnabledQueryEngines.getInstance().getEnabled();
|
1570 |
7772
|
tao
|
for(String name : enables) {
|
1571 |
|
|
qel.addQueryEngine(name);
|
1572 |
7781
|
tao
|
}
|
1573 |
7417
|
leinfelder
|
return qel;
|
1574 |
|
|
}
|
1575 |
|
|
|
1576 |
|
|
@Override
|
1577 |
8810
|
leinfelder
|
public InputStream query(Session session, String engine, String query) throws InvalidToken,
|
1578 |
7417
|
leinfelder
|
ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented,
|
1579 |
|
|
NotFound {
|
1580 |
7648
|
tao
|
String user = Constants.SUBJECT_PUBLIC;
|
1581 |
|
|
String[] groups= null;
|
1582 |
7680
|
tao
|
Set<Subject> subjects = null;
|
1583 |
7648
|
tao
|
if (session != null) {
|
1584 |
|
|
user = session.getSubject().getValue();
|
1585 |
7680
|
tao
|
subjects = AuthUtils.authorizedClientSubjects(session);
|
1586 |
7648
|
tao
|
if (subjects != null) {
|
1587 |
|
|
List<String> groupList = new ArrayList<String>();
|
1588 |
|
|
for (Subject subject: subjects) {
|
1589 |
|
|
groupList.add(subject.getValue());
|
1590 |
|
|
}
|
1591 |
|
|
groups = groupList.toArray(new String[0]);
|
1592 |
|
|
}
|
1593 |
7680
|
tao
|
} else {
|
1594 |
|
|
//add the public user subject to the set
|
1595 |
|
|
Subject subject = new Subject();
|
1596 |
|
|
subject.setValue(Constants.SUBJECT_PUBLIC);
|
1597 |
7757
|
leinfelder
|
subjects = new HashSet<Subject>();
|
1598 |
7680
|
tao
|
subjects.add(subject);
|
1599 |
7648
|
tao
|
}
|
1600 |
7680
|
tao
|
//System.out.println("====== user is "+user);
|
1601 |
|
|
//System.out.println("====== groups are "+groups);
|
1602 |
7772
|
tao
|
if (engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
|
1603 |
8162
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
|
1604 |
|
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
1605 |
|
|
}
|
1606 |
7417
|
leinfelder
|
try {
|
1607 |
|
|
DBQuery queryobj = new DBQuery();
|
1608 |
7648
|
tao
|
|
1609 |
7417
|
leinfelder
|
String results = queryobj.performPathquery(query, user, groups);
|
1610 |
7757
|
leinfelder
|
ContentTypeByteArrayInputStream ctbais = new ContentTypeByteArrayInputStream(results.getBytes(MetaCatServlet.DEFAULT_ENCODING));
|
1611 |
|
|
ctbais.setContentType("text/xml");
|
1612 |
|
|
return ctbais;
|
1613 |
7417
|
leinfelder
|
|
1614 |
|
|
} catch (Exception e) {
|
1615 |
7757
|
leinfelder
|
throw new ServiceFailure("Pathquery error", e.getMessage());
|
1616 |
7417
|
leinfelder
|
}
|
1617 |
|
|
|
1618 |
7772
|
tao
|
} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
|
1619 |
7781
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
|
1620 |
7772
|
tao
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
1621 |
7781
|
tao
|
}
|
1622 |
7634
|
tao
|
logMetacat.info("The query is ==================================== \n"+query);
|
1623 |
7620
|
tao
|
try {
|
1624 |
7634
|
tao
|
|
1625 |
7680
|
tao
|
return MetacatSolrIndex.getInstance().query(query, subjects);
|
1626 |
7620
|
tao
|
} catch (Exception e) {
|
1627 |
|
|
// TODO Auto-generated catch block
|
1628 |
|
|
throw new ServiceFailure("Solr server error", e.getMessage());
|
1629 |
|
|
}
|
1630 |
7417
|
leinfelder
|
}
|
1631 |
|
|
return null;
|
1632 |
|
|
}
|
1633 |
7849
|
leinfelder
|
|
1634 |
|
|
/**
|
1635 |
|
|
* Given an existing Science Metadata PID, this method mints a DOI
|
1636 |
|
|
* and updates the original object "publishing" the update with the DOI.
|
1637 |
|
|
* This includes updating the ORE map that describes the Science Metadata+data.
|
1638 |
|
|
* TODO: ensure all referenced objects allow public read
|
1639 |
|
|
*
|
1640 |
|
|
* @see https://projects.ecoinformatics.org/ecoinfo/issues/6014
|
1641 |
|
|
*
|
1642 |
|
|
* @param originalIdentifier
|
1643 |
|
|
* @param request
|
1644 |
7864
|
leinfelder
|
* @throws InvalidRequest
|
1645 |
|
|
* @throws NotImplemented
|
1646 |
|
|
* @throws NotAuthorized
|
1647 |
|
|
* @throws ServiceFailure
|
1648 |
|
|
* @throws InvalidToken
|
1649 |
7849
|
leinfelder
|
* @throws NotFound
|
1650 |
7864
|
leinfelder
|
* @throws InvalidSystemMetadata
|
1651 |
|
|
* @throws InsufficientResources
|
1652 |
|
|
* @throws UnsupportedType
|
1653 |
|
|
* @throws IdentifierNotUnique
|
1654 |
7849
|
leinfelder
|
*/
|
1655 |
7864
|
leinfelder
|
public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata {
|
1656 |
7849
|
leinfelder
|
|
1657 |
9092
|
tao
|
String serviceFailureCode = "1030";
|
1658 |
|
|
Identifier sid = getPIDForSID(originalIdentifier, serviceFailureCode);
|
1659 |
|
|
if(sid != null) {
|
1660 |
|
|
originalIdentifier = sid;
|
1661 |
|
|
}
|
1662 |
8141
|
leinfelder
|
// get the original SM
|
1663 |
|
|
SystemMetadata originalSystemMetadata = this.getSystemMetadata(session, originalIdentifier);
|
1664 |
|
|
|
1665 |
8594
|
leinfelder
|
// make copy of it using the marshaller to ensure DEEP copy
|
1666 |
|
|
SystemMetadata sysmeta = null;
|
1667 |
8141
|
leinfelder
|
try {
|
1668 |
8594
|
leinfelder
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
1669 |
|
|
TypeMarshaller.marshalTypeToOutputStream(originalSystemMetadata, baos);
|
1670 |
|
|
sysmeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
|
1671 |
8141
|
leinfelder
|
} catch (Exception e) {
|
1672 |
|
|
// report as service failure
|
1673 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1674 |
|
|
sf.initCause(e);
|
1675 |
|
|
throw sf;
|
1676 |
|
|
}
|
1677 |
|
|
|
1678 |
7849
|
leinfelder
|
// mint a DOI for the new revision
|
1679 |
|
|
Identifier newIdentifier = this.generateIdentifier(session, MNodeService.DOI_SCHEME, null);
|
1680 |
8141
|
leinfelder
|
|
1681 |
|
|
// set new metadata values
|
1682 |
7849
|
leinfelder
|
sysmeta.setIdentifier(newIdentifier);
|
1683 |
|
|
sysmeta.setObsoletes(originalIdentifier);
|
1684 |
|
|
sysmeta.setObsoletedBy(null);
|
1685 |
|
|
|
1686 |
8591
|
leinfelder
|
// ensure it is publicly readable
|
1687 |
|
|
sysmeta = makePublicIfNot(sysmeta, originalIdentifier);
|
1688 |
|
|
|
1689 |
7849
|
leinfelder
|
// get the bytes
|
1690 |
|
|
InputStream inputStream = this.get(session, originalIdentifier);
|
1691 |
|
|
|
1692 |
|
|
// update the object
|
1693 |
7864
|
leinfelder
|
this.update(session, originalIdentifier, inputStream, newIdentifier, sysmeta);
|
1694 |
7849
|
leinfelder
|
|
1695 |
7864
|
leinfelder
|
// update ORE that references the scimeta
|
1696 |
8190
|
leinfelder
|
// first try the naive method, then check the SOLR index
|
1697 |
7849
|
leinfelder
|
try {
|
1698 |
7864
|
leinfelder
|
String localId = IdentifierManager.getInstance().getLocalId(originalIdentifier.getValue());
|
1699 |
7849
|
leinfelder
|
|
1700 |
7864
|
leinfelder
|
Identifier potentialOreIdentifier = new Identifier();
|
1701 |
|
|
potentialOreIdentifier.setValue(SystemMetadataFactory.RESOURCE_MAP_PREFIX + localId);
|
1702 |
7849
|
leinfelder
|
|
1703 |
7864
|
leinfelder
|
InputStream oreInputStream = null;
|
1704 |
|
|
try {
|
1705 |
|
|
oreInputStream = this.get(session, potentialOreIdentifier);
|
1706 |
|
|
} catch (NotFound nf) {
|
1707 |
|
|
// this is probably okay for many sci meta data docs
|
1708 |
|
|
logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
|
1709 |
8190
|
leinfelder
|
// try the SOLR index
|
1710 |
8200
|
leinfelder
|
List<Identifier> potentialOreIdentifiers = this.lookupOreFor(originalIdentifier, false);
|
1711 |
8190
|
leinfelder
|
if (potentialOreIdentifiers != null) {
|
1712 |
|
|
potentialOreIdentifier = potentialOreIdentifiers.get(0);
|
1713 |
|
|
try {
|
1714 |
|
|
oreInputStream = this.get(session, potentialOreIdentifier);
|
1715 |
|
|
} catch (NotFound nf2) {
|
1716 |
|
|
// this is probably okay for many sci meta data docs
|
1717 |
|
|
logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
|
1718 |
|
|
}
|
1719 |
|
|
}
|
1720 |
7864
|
leinfelder
|
}
|
1721 |
|
|
if (oreInputStream != null) {
|
1722 |
|
|
Identifier newOreIdentifier = MNodeService.getInstance(request).generateIdentifier(session, MNodeService.UUID_SCHEME, null);
|
1723 |
|
|
|
1724 |
|
|
Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
|
1725 |
|
|
Map<Identifier, List<Identifier>> sciMetaMap = resourceMapStructure.get(potentialOreIdentifier);
|
1726 |
|
|
List<Identifier> dataIdentifiers = sciMetaMap.get(originalIdentifier);
|
1727 |
8591
|
leinfelder
|
|
1728 |
7864
|
leinfelder
|
// reconstruct the ORE with the new identifiers
|
1729 |
|
|
sciMetaMap.remove(originalIdentifier);
|
1730 |
|
|
sciMetaMap.put(newIdentifier, dataIdentifiers);
|
1731 |
|
|
|
1732 |
|
|
ResourceMap resourceMap = ResourceMapFactory.getInstance().createResourceMap(newOreIdentifier, sciMetaMap);
|
1733 |
|
|
String resourceMapString = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);
|
1734 |
|
|
|
1735 |
|
|
// get the original ORE SM and update the values
|
1736 |
8141
|
leinfelder
|
SystemMetadata originalOreSysMeta = this.getSystemMetadata(session, potentialOreIdentifier);
|
1737 |
|
|
SystemMetadata oreSysMeta = new SystemMetadata();
|
1738 |
|
|
try {
|
1739 |
8594
|
leinfelder
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
1740 |
|
|
TypeMarshaller.marshalTypeToOutputStream(originalOreSysMeta, baos);
|
1741 |
|
|
oreSysMeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
|
1742 |
8141
|
leinfelder
|
} catch (Exception e) {
|
1743 |
|
|
// report as service failure
|
1744 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1745 |
|
|
sf.initCause(e);
|
1746 |
|
|
throw sf;
|
1747 |
|
|
}
|
1748 |
|
|
|
1749 |
7864
|
leinfelder
|
oreSysMeta.setIdentifier(newOreIdentifier);
|
1750 |
|
|
oreSysMeta.setObsoletes(potentialOreIdentifier);
|
1751 |
|
|
oreSysMeta.setObsoletedBy(null);
|
1752 |
|
|
oreSysMeta.setSize(BigInteger.valueOf(resourceMapString.getBytes("UTF-8").length));
|
1753 |
|
|
oreSysMeta.setChecksum(ChecksumUtil.checksum(resourceMapString.getBytes("UTF-8"), oreSysMeta.getChecksum().getAlgorithm()));
|
1754 |
|
|
|
1755 |
8591
|
leinfelder
|
// ensure ORE is publicly readable
|
1756 |
8594
|
leinfelder
|
oreSysMeta = makePublicIfNot(oreSysMeta, potentialOreIdentifier);
|
1757 |
8591
|
leinfelder
|
|
1758 |
|
|
// ensure all data objects allow public read
|
1759 |
|
|
List<String> pidsToSync = new ArrayList<String>();
|
1760 |
|
|
for (Identifier dataId: dataIdentifiers) {
|
1761 |
|
|
SystemMetadata dataSysMeta = this.getSystemMetadata(session, dataId);
|
1762 |
|
|
dataSysMeta = makePublicIfNot(dataSysMeta, dataId);
|
1763 |
|
|
this.updateSystemMetadata(dataSysMeta);
|
1764 |
|
|
pidsToSync.add(dataId.getValue());
|
1765 |
|
|
}
|
1766 |
|
|
SyncAccessPolicy sap = new SyncAccessPolicy();
|
1767 |
|
|
try {
|
1768 |
|
|
sap.sync(pidsToSync);
|
1769 |
|
|
} catch (Exception e) {
|
1770 |
|
|
// ignore
|
1771 |
|
|
logMetacat.warn("Error attempting to sync access for data objects when publishing package");
|
1772 |
|
|
}
|
1773 |
|
|
|
1774 |
7864
|
leinfelder
|
// save the updated ORE
|
1775 |
|
|
this.update(
|
1776 |
|
|
session,
|
1777 |
|
|
potentialOreIdentifier,
|
1778 |
|
|
new ByteArrayInputStream(resourceMapString.getBytes("UTF-8")),
|
1779 |
|
|
newOreIdentifier,
|
1780 |
|
|
oreSysMeta);
|
1781 |
|
|
|
1782 |
8362
|
leinfelder
|
} else {
|
1783 |
|
|
// create a new ORE for them
|
1784 |
|
|
// https://projects.ecoinformatics.org/ecoinfo/issues/6194
|
1785 |
|
|
try {
|
1786 |
|
|
// find the local id for the NEW package.
|
1787 |
|
|
String newLocalId = IdentifierManager.getInstance().getLocalId(newIdentifier.getValue());
|
1788 |
|
|
|
1789 |
|
|
@SuppressWarnings("unused")
|
1790 |
|
|
SystemMetadata extraSysMeta = SystemMetadataFactory.createSystemMetadata(newLocalId, true, false);
|
1791 |
8591
|
leinfelder
|
// should be done generating the ORE here, and the same permissions were used from the metadata object
|
1792 |
8362
|
leinfelder
|
|
1793 |
|
|
} catch (Exception e) {
|
1794 |
|
|
// oops, guess there was a problem - no package for you
|
1795 |
|
|
logMetacat.error("Could not generate new ORE for published object: " + newIdentifier.getValue(), e);
|
1796 |
|
|
}
|
1797 |
7864
|
leinfelder
|
}
|
1798 |
|
|
} catch (McdbDocNotFoundException e) {
|
1799 |
|
|
// report as service failure
|
1800 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1801 |
|
|
sf.initCause(e);
|
1802 |
|
|
throw sf;
|
1803 |
|
|
} catch (UnsupportedEncodingException e) {
|
1804 |
|
|
// report as service failure
|
1805 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1806 |
|
|
sf.initCause(e);
|
1807 |
|
|
throw sf;
|
1808 |
|
|
} catch (OREException e) {
|
1809 |
|
|
// report as service failure
|
1810 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1811 |
|
|
sf.initCause(e);
|
1812 |
|
|
throw sf;
|
1813 |
|
|
} catch (URISyntaxException e) {
|
1814 |
|
|
// report as service failure
|
1815 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1816 |
|
|
sf.initCause(e);
|
1817 |
|
|
throw sf;
|
1818 |
|
|
} catch (OREParserException e) {
|
1819 |
|
|
// report as service failure
|
1820 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1821 |
|
|
sf.initCause(e);
|
1822 |
|
|
throw sf;
|
1823 |
|
|
} catch (ORESerialiserException e) {
|
1824 |
|
|
// report as service failure
|
1825 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1826 |
|
|
sf.initCause(e);
|
1827 |
|
|
throw sf;
|
1828 |
|
|
} catch (NoSuchAlgorithmException e) {
|
1829 |
|
|
// report as service failure
|
1830 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1831 |
|
|
sf.initCause(e);
|
1832 |
|
|
throw sf;
|
1833 |
9024
|
tao
|
} catch (SQLException e) {
|
1834 |
|
|
// report as service failure
|
1835 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
1836 |
|
|
sf.initCause(e);
|
1837 |
|
|
throw sf;
|
1838 |
|
|
}
|
1839 |
7849
|
leinfelder
|
|
1840 |
|
|
return newIdentifier;
|
1841 |
|
|
}
|
1842 |
7850
|
leinfelder
|
|
1843 |
|
|
/**
|
1844 |
8190
|
leinfelder
|
* Determines if we already have registered an ORE map for this package
|
1845 |
|
|
* NOTE: uses a solr query to locate OREs for the object
|
1846 |
|
|
* @param guid of the EML/packaging object
|
1847 |
|
|
* @return list of resource map identifiers for the given pid
|
1848 |
|
|
*/
|
1849 |
8200
|
leinfelder
|
public List<Identifier> lookupOreFor(Identifier guid, boolean includeObsolete) {
|
1850 |
8190
|
leinfelder
|
// Search for the ORE if we can find it
|
1851 |
|
|
String pid = guid.getValue();
|
1852 |
|
|
List<Identifier> retList = null;
|
1853 |
|
|
try {
|
1854 |
8745
|
leinfelder
|
String query = "fl=id,resourceMap&wt=xml&q=-obsoletedBy:[* TO *]+resourceMap:[* TO *]+id:\"" + pid + "\"";
|
1855 |
8200
|
leinfelder
|
if (includeObsolete) {
|
1856 |
8745
|
leinfelder
|
query = "fl=id,resourceMap&wt=xml&q=resourceMap:[* TO *]+id:\"" + pid + "\"";
|
1857 |
8200
|
leinfelder
|
}
|
1858 |
|
|
|
1859 |
8810
|
leinfelder
|
InputStream results = this.query(null, "solr", query);
|
1860 |
8190
|
leinfelder
|
org.w3c.dom.Node rootNode = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new InputStreamReader(results, "UTF-8"));
|
1861 |
|
|
//String resultString = XMLUtilities.getDOMTreeAsString(rootNode);
|
1862 |
|
|
org.w3c.dom.NodeList nodeList = XMLUtilities.getNodeListWithXPath(rootNode, "//arr[@name=\"resourceMap\"]/str");
|
1863 |
|
|
if (nodeList != null && nodeList.getLength() > 0) {
|
1864 |
|
|
retList = new ArrayList<Identifier>();
|
1865 |
|
|
for (int i = 0; i < nodeList.getLength(); i++) {
|
1866 |
|
|
String found = nodeList.item(i).getFirstChild().getNodeValue();
|
1867 |
|
|
Identifier oreId = new Identifier();
|
1868 |
|
|
oreId.setValue(found);
|
1869 |
|
|
retList.add(oreId);
|
1870 |
|
|
}
|
1871 |
|
|
}
|
1872 |
|
|
} catch (Exception e) {
|
1873 |
|
|
logMetacat.error("Error checking for resourceMap[s] on pid " + pid + ". " + e.getMessage(), e);
|
1874 |
|
|
}
|
1875 |
|
|
|
1876 |
|
|
return retList;
|
1877 |
|
|
}
|
1878 |
|
|
|
1879 |
8810
|
leinfelder
|
|
1880 |
|
|
@Override
|
1881 |
|
|
public InputStream getPackage(Session session, ObjectFormatIdentifier formatId,
|
1882 |
|
|
Identifier pid) throws InvalidToken, ServiceFailure,
|
1883 |
|
|
NotAuthorized, InvalidRequest, NotImplemented, NotFound {
|
1884 |
9092
|
tao
|
|
1885 |
|
|
String serviceFailureCode = "2871";
|
1886 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
1887 |
|
|
if(sid != null) {
|
1888 |
|
|
pid = sid;
|
1889 |
|
|
}
|
1890 |
7850
|
leinfelder
|
InputStream bagInputStream = null;
|
1891 |
|
|
BagFactory bagFactory = new BagFactory();
|
1892 |
|
|
Bag bag = bagFactory.createBag();
|
1893 |
|
|
|
1894 |
|
|
// track the temp files we use so we can delete them when finished
|
1895 |
|
|
List<File> tempFiles = new ArrayList<File>();
|
1896 |
|
|
|
1897 |
|
|
// the pids to include in the package
|
1898 |
|
|
List<Identifier> packagePids = new ArrayList<Identifier>();
|
1899 |
|
|
|
1900 |
7855
|
leinfelder
|
// catch non-D1 service errors and throw as ServiceFailures
|
1901 |
|
|
try {
|
1902 |
8437
|
walker
|
//Create a map of dataone ids and file names
|
1903 |
|
|
Map<Identifier, String> fileNames = new HashMap<Identifier, String>();
|
1904 |
7855
|
leinfelder
|
|
1905 |
8800
|
leinfelder
|
// track the pid-to-file mapping
|
1906 |
|
|
StringBuffer pidMapping = new StringBuffer();
|
1907 |
|
|
|
1908 |
7855
|
leinfelder
|
// find the package contents
|
1909 |
|
|
SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
|
1910 |
8025
|
leinfelder
|
if (ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId()).getFormatType().equals("RESOURCE")) {
|
1911 |
8437
|
walker
|
//Get the resource map as a map of Identifiers
|
1912 |
7855
|
leinfelder
|
InputStream oreInputStream = this.get(session, pid);
|
1913 |
|
|
Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
|
1914 |
|
|
packagePids.addAll(resourceMapStructure.keySet());
|
1915 |
8437
|
walker
|
//Loop through each object in this resource map
|
1916 |
7855
|
leinfelder
|
for (Map<Identifier, List<Identifier>> entries: resourceMapStructure.values()) {
|
1917 |
8437
|
walker
|
//Loop through each metadata object in this entry
|
1918 |
|
|
Set<Identifier> metadataIdentifiers = entries.keySet();
|
1919 |
|
|
for(Identifier metadataID: metadataIdentifiers){
|
1920 |
|
|
try{
|
1921 |
|
|
//Get the system metadata for this metadata object
|
1922 |
|
|
SystemMetadata metadataSysMeta = this.getSystemMetadata(session, metadataID);
|
1923 |
|
|
|
1924 |
8800
|
leinfelder
|
// include user-friendly metadata
|
1925 |
|
|
if (ObjectFormatCache.getInstance().getFormat(metadataSysMeta.getFormatId()).getFormatType().equals("METADATA")) {
|
1926 |
|
|
InputStream metadataStream = this.get(session, metadataID);
|
1927 |
|
|
|
1928 |
|
|
try {
|
1929 |
|
|
// transform
|
1930 |
|
|
String format = "default";
|
1931 |
|
|
|
1932 |
|
|
DBTransform transformer = new DBTransform();
|
1933 |
|
|
String documentContent = IOUtils.toString(metadataStream, "UTF-8");
|
1934 |
|
|
String sourceType = metadataSysMeta.getFormatId().getValue();
|
1935 |
|
|
String targetType = "-//W3C//HTML//EN";
|
1936 |
|
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
1937 |
|
|
Writer writer = new OutputStreamWriter(baos , "UTF-8");
|
1938 |
|
|
// TODO: include more params?
|
1939 |
|
|
Hashtable<String, String[]> params = new Hashtable<String, String[]>();
|
1940 |
|
|
String localId = null;
|
1941 |
|
|
try {
|
1942 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
1943 |
|
|
} catch (McdbDocNotFoundException e) {
|
1944 |
|
|
throw new NotFound("1020", e.getMessage());
|
1945 |
|
|
}
|
1946 |
|
|
params.put("qformat", new String[] {format});
|
1947 |
|
|
params.put("docid", new String[] {localId});
|
1948 |
|
|
params.put("pid", new String[] {pid.getValue()});
|
1949 |
|
|
params.put("displaymodule", new String[] {"printall"});
|
1950 |
|
|
|
1951 |
|
|
transformer.transformXMLDocument(
|
1952 |
|
|
documentContent ,
|
1953 |
|
|
sourceType,
|
1954 |
|
|
targetType ,
|
1955 |
|
|
format,
|
1956 |
|
|
writer,
|
1957 |
|
|
params,
|
1958 |
|
|
null //sessionid
|
1959 |
|
|
);
|
1960 |
|
|
|
1961 |
|
|
// finally, get the HTML back
|
1962 |
|
|
ContentTypeByteArrayInputStream resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
|
1963 |
|
|
|
1964 |
|
|
// write to temp file with correct css path
|
1965 |
|
|
File tmpDir = File.createTempFile("package_", "_dir");
|
1966 |
|
|
tmpDir.delete();
|
1967 |
|
|
tmpDir.mkdir();
|
1968 |
|
|
File htmlFile = File.createTempFile("metadata", ".html", tmpDir);
|
1969 |
|
|
File cssDir = new File(tmpDir, format);
|
1970 |
|
|
cssDir.mkdir();
|
1971 |
|
|
File cssFile = new File(tmpDir, format + "/" + format + ".css");
|
1972 |
|
|
String pdfFileName = metadataID.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-METADATA.pdf";
|
1973 |
|
|
File pdfFile = new File(tmpDir, pdfFileName);
|
1974 |
|
|
//File pdfFile = File.createTempFile("metadata", ".pdf", tmpDir);
|
1975 |
|
|
|
1976 |
|
|
// put the CSS file in place for the html to find it
|
1977 |
|
|
String originalCssPath = SystemUtil.getContextDir() + "/style/skins/" + format + "/" + format + ".css";
|
1978 |
|
|
IOUtils.copy(new FileInputStream(originalCssPath), new FileOutputStream(cssFile));
|
1979 |
|
|
|
1980 |
|
|
// write the HTML file
|
1981 |
|
|
IOUtils.copy(resultInputStream, new FileOutputStream(htmlFile));
|
1982 |
|
|
|
1983 |
|
|
// convert to PDF
|
1984 |
|
|
HtmlToPdf.export(htmlFile.getAbsolutePath(), pdfFile.getAbsolutePath());
|
1985 |
|
|
|
1986 |
|
|
//add to the package
|
1987 |
|
|
bag.addFileToPayload(pdfFile);
|
1988 |
|
|
pidMapping.append(metadataID.getValue() + " (pdf)" + "\t" + "data/" + pdfFile.getName() + "\n");
|
1989 |
|
|
|
1990 |
|
|
// mark for clean up after we are done
|
1991 |
|
|
htmlFile.delete();
|
1992 |
|
|
cssFile.delete();
|
1993 |
|
|
cssDir.delete();
|
1994 |
|
|
tempFiles.add(tmpDir);
|
1995 |
|
|
tempFiles.add(pdfFile); // delete this first later on
|
1996 |
|
|
|
1997 |
|
|
} catch (Exception e) {
|
1998 |
|
|
logMetacat.warn("Could not transform metadata", e);
|
1999 |
|
|
}
|
2000 |
|
|
}
|
2001 |
|
|
|
2002 |
|
|
|
2003 |
8437
|
walker
|
//If this is in eml format, extract the filename and GUID from each entity in its package
|
2004 |
|
|
if (metadataSysMeta.getFormatId().getValue().startsWith("eml://")) {
|
2005 |
|
|
//Get the package
|
2006 |
|
|
DataPackageParserInterface parser = new Eml200DataPackageParser();
|
2007 |
|
|
InputStream emlStream = this.get(session, metadataID);
|
2008 |
|
|
parser.parse(emlStream);
|
2009 |
|
|
DataPackage dataPackage = parser.getDataPackage();
|
2010 |
|
|
|
2011 |
|
|
//Get all the entities in this package and loop through each to extract its ID and file name
|
2012 |
|
|
Entity[] entities = dataPackage.getEntityList();
|
2013 |
|
|
for(Entity entity: entities){
|
2014 |
|
|
try{
|
2015 |
|
|
//Get the file name from the metadata
|
2016 |
|
|
String fileNameFromMetadata = entity.getName();
|
2017 |
|
|
|
2018 |
|
|
//Get the ecogrid URL from the metadata
|
2019 |
|
|
String ecogridIdentifier = entity.getEntityIdentifier();
|
2020 |
|
|
//Parse the ecogrid URL to get the local id
|
2021 |
|
|
String idFromMetadata = DocumentUtil.getAccessionNumberFromEcogridIdentifier(ecogridIdentifier);
|
2022 |
|
|
|
2023 |
|
|
//Get the docid and rev pair
|
2024 |
|
|
String docid = DocumentUtil.getDocIdFromString(idFromMetadata);
|
2025 |
|
|
String rev = DocumentUtil.getRevisionStringFromString(idFromMetadata);
|
2026 |
|
|
|
2027 |
|
|
//Get the GUID
|
2028 |
|
|
String guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(rev));
|
2029 |
|
|
Identifier dataIdentifier = new Identifier();
|
2030 |
|
|
dataIdentifier.setValue(guid);
|
2031 |
|
|
|
2032 |
|
|
//Add the GUID to our GUID & file name map
|
2033 |
|
|
fileNames.put(dataIdentifier, fileNameFromMetadata);
|
2034 |
|
|
}
|
2035 |
|
|
catch(Exception e){
|
2036 |
|
|
//Prevent just one entity error
|
2037 |
|
|
e.printStackTrace();
|
2038 |
|
|
logMetacat.debug(e.getMessage(), e);
|
2039 |
|
|
}
|
2040 |
|
|
}
|
2041 |
|
|
}
|
2042 |
|
|
}
|
2043 |
|
|
catch(Exception e){
|
2044 |
|
|
//Catch errors that would prevent package download
|
2045 |
|
|
logMetacat.debug(e.toString());
|
2046 |
|
|
}
|
2047 |
|
|
}
|
2048 |
7855
|
leinfelder
|
packagePids.addAll(entries.keySet());
|
2049 |
|
|
for (List<Identifier> dataPids: entries.values()) {
|
2050 |
|
|
packagePids.addAll(dataPids);
|
2051 |
|
|
}
|
2052 |
7850
|
leinfelder
|
}
|
2053 |
7855
|
leinfelder
|
} else {
|
2054 |
|
|
// just the lone pid in this package
|
2055 |
|
|
packagePids.add(pid);
|
2056 |
7850
|
leinfelder
|
}
|
2057 |
8436
|
walker
|
|
2058 |
8437
|
walker
|
//Create a temp file, then delete it and make a directory with that name
|
2059 |
|
|
File tempDir = File.createTempFile("temp", Long.toString(System.nanoTime()));
|
2060 |
|
|
tempDir.delete();
|
2061 |
|
|
tempDir = new File(tempDir.getPath() + "_dir");
|
2062 |
|
|
tempDir.mkdir();
|
2063 |
8436
|
walker
|
tempFiles.add(tempDir);
|
2064 |
8800
|
leinfelder
|
File pidMappingFile = new File(tempDir, "pid-mapping.txt");
|
2065 |
8436
|
walker
|
|
2066 |
7855
|
leinfelder
|
// loop through the package contents
|
2067 |
|
|
for (Identifier entryPid: packagePids) {
|
2068 |
8436
|
walker
|
//Get the system metadata for each item
|
2069 |
8437
|
walker
|
SystemMetadata entrySysMeta = this.getSystemMetadata(session, entryPid);
|
2070 |
8436
|
walker
|
|
2071 |
|
|
String objectFormatType = ObjectFormatCache.getInstance().getFormat(entrySysMeta.getFormatId()).getFormatType();
|
2072 |
8437
|
walker
|
String fileName = null;
|
2073 |
8436
|
walker
|
|
2074 |
8437
|
walker
|
//TODO: Be more specific of what characters to replace. Make sure periods arent replaced for the filename from metadata
|
2075 |
|
|
//Our default file name is just the ID + format type (e.g. walker.1.1-DATA)
|
2076 |
|
|
fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + objectFormatType;
|
2077 |
|
|
|
2078 |
|
|
if(fileNames.containsKey(entryPid)){
|
2079 |
|
|
//Let's use the file name and extension from the metadata is we have it
|
2080 |
|
|
fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + fileNames.get(entryPid).replaceAll("[^a-zA-Z0-9\\-\\.]", "_");
|
2081 |
|
|
}
|
2082 |
|
|
else{
|
2083 |
|
|
//If we couldn't find a given file name, use the system metadata extension
|
2084 |
|
|
String extension = ObjectFormatInfo.instance().getExtension(entrySysMeta.getFormatId().getValue());
|
2085 |
|
|
fileName += extension;
|
2086 |
|
|
}
|
2087 |
|
|
|
2088 |
8436
|
walker
|
//Create a new file for this item and add to the list
|
2089 |
8437
|
walker
|
File tempFile = new File(tempDir, fileName);
|
2090 |
7855
|
leinfelder
|
tempFiles.add(tempFile);
|
2091 |
8436
|
walker
|
|
2092 |
|
|
InputStream entryInputStream = this.get(session, entryPid);
|
2093 |
7855
|
leinfelder
|
IOUtils.copy(entryInputStream, new FileOutputStream(tempFile));
|
2094 |
|
|
bag.addFileToPayload(tempFile);
|
2095 |
|
|
pidMapping.append(entryPid.getValue() + "\t" + "data/" + tempFile.getName() + "\n");
|
2096 |
|
|
}
|
2097 |
|
|
|
2098 |
|
|
//add the the pid to data file map
|
2099 |
|
|
IOUtils.write(pidMapping.toString(), new FileOutputStream(pidMappingFile));
|
2100 |
|
|
bag.addFileAsTag(pidMappingFile);
|
2101 |
8026
|
leinfelder
|
tempFiles.add(pidMappingFile);
|
2102 |
|
|
|
2103 |
7855
|
leinfelder
|
bag = bag.makeComplete();
|
2104 |
8026
|
leinfelder
|
|
2105 |
8436
|
walker
|
///Now create the zip file
|
2106 |
8437
|
walker
|
//Use the pid as the file name prefix, replacing all non-word characters
|
2107 |
|
|
String zipName = pid.getValue().replaceAll("\\W", "_");
|
2108 |
8160
|
leinfelder
|
|
2109 |
8436
|
walker
|
File bagFile = new File(tempDir, zipName+".zip");
|
2110 |
|
|
|
2111 |
7855
|
leinfelder
|
bag.setFile(bagFile);
|
2112 |
7860
|
leinfelder
|
ZipWriter zipWriter = new ZipWriter(bagFactory);
|
2113 |
7855
|
leinfelder
|
bag.write(zipWriter, bagFile);
|
2114 |
|
|
bagFile = bag.getFile();
|
2115 |
8026
|
leinfelder
|
// use custom FIS that will delete the file when closed
|
2116 |
|
|
bagInputStream = new DeleteOnCloseFileInputStream(bagFile);
|
2117 |
|
|
// also mark for deletion on shutdown in case the stream is never closed
|
2118 |
|
|
bagFile.deleteOnExit();
|
2119 |
8436
|
walker
|
tempFiles.add(bagFile);
|
2120 |
7855
|
leinfelder
|
|
2121 |
8026
|
leinfelder
|
// clean up other temp files
|
2122 |
8800
|
leinfelder
|
for (int i=tempFiles.size()-1; i>=0; i--){
|
2123 |
|
|
tempFiles.get(i).delete();
|
2124 |
7855
|
leinfelder
|
}
|
2125 |
8436
|
walker
|
|
2126 |
7855
|
leinfelder
|
} catch (IOException e) {
|
2127 |
|
|
// report as service failure
|
2128 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
2129 |
|
|
sf.initCause(e);
|
2130 |
|
|
throw sf;
|
2131 |
|
|
} catch (OREException e) {
|
2132 |
|
|
// report as service failure
|
2133 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
2134 |
|
|
sf.initCause(e);
|
2135 |
|
|
throw sf;
|
2136 |
|
|
} catch (URISyntaxException e) {
|
2137 |
|
|
// report as service failure
|
2138 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
2139 |
|
|
sf.initCause(e);
|
2140 |
|
|
throw sf;
|
2141 |
|
|
} catch (OREParserException e) {
|
2142 |
|
|
// report as service failure
|
2143 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
2144 |
|
|
sf.initCause(e);
|
2145 |
|
|
throw sf;
|
2146 |
7850
|
leinfelder
|
}
|
2147 |
|
|
|
2148 |
|
|
return bagInputStream;
|
2149 |
8810
|
leinfelder
|
}
|
2150 |
9190
|
tao
|
|
2151 |
|
|
/**
|
2152 |
|
|
* Update the system metadata of the specified pid.
|
2153 |
|
|
*/
|
2154 |
9177
|
tao
|
@Override
|
2155 |
|
|
public boolean updateSystemMetadata(Session session, Identifier pid,
|
2156 |
|
|
SystemMetadata sysmeta) throws NotImplemented, NotAuthorized,
|
2157 |
|
|
ServiceFailure, InvalidRequest, InvalidSystemMetadata, InvalidToken {
|
2158 |
|
|
if(sysmeta == null) {
|
2159 |
|
|
throw new InvalidRequest("4863", "The system metadata object should NOT be null in the updateSystemMetadata request.");
|
2160 |
|
|
}
|
2161 |
9190
|
tao
|
if(pid == null || pid.getValue() == null) {
|
2162 |
|
|
throw new InvalidRequest("4863", "Please specify the id in the updateSystemMetadata request ") ;
|
2163 |
|
|
}
|
2164 |
|
|
|
2165 |
9177
|
tao
|
if(!isAuthoritativeNode(pid)) {
|
2166 |
|
|
throw new InvalidRequest("4863", "Client can only call updateSystemMetadata request on the authoritative memember node.");
|
2167 |
|
|
}
|
2168 |
9190
|
tao
|
|
2169 |
|
|
if (session == null) {
|
2170 |
|
|
//TODO: many of the thrown exceptions do not use the correct error codes
|
2171 |
|
|
//check these against the docs and correct them
|
2172 |
|
|
throw new NotAuthorized("4861", "No Session - could not authorize for updating system metadata." +
|
2173 |
|
|
" If you are not logged in, please do so and retry the request.");
|
2174 |
|
|
} else {
|
2175 |
|
|
try {
|
2176 |
|
|
//Following session can do the change:
|
2177 |
|
|
//- Authoritative Member Node (we can use isNodeAdmin since we checked isAuthoritativeNode in line 2159)
|
2178 |
|
|
//- Owner of object (coved by the userHasPermission method)
|
2179 |
|
|
//- user subjects with the change permission
|
2180 |
|
|
//Note: Coordinating Node can not because MN is authoritative
|
2181 |
|
|
if(!isNodeAdmin(session) && !userHasPermission(session, pid, Permission.CHANGE_PERMISSION)) {
|
2182 |
|
|
throw new NotAuthorized("4861", "The client -"+ session.getSubject().getValue()+ "is not authorized for updating the system metadata of the object "+pid.getValue());
|
2183 |
|
|
}
|
2184 |
|
|
} catch (NotFound e) {
|
2185 |
|
|
throw new InvalidRequest("4863", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
2186 |
|
|
}
|
2187 |
|
|
|
2188 |
|
|
}
|
2189 |
9177
|
tao
|
//update the system metadata locally
|
2190 |
|
|
boolean success = super.updateSystemMetadata(session, pid, sysmeta);
|
2191 |
|
|
|
2192 |
|
|
if(success) {
|
2193 |
9190
|
tao
|
//TODO
|
2194 |
9177
|
tao
|
//notify the cns the synchornize the new system metadata.
|
2195 |
9246
|
tao
|
this.cn = D1Client.getCN();
|
2196 |
|
|
try {
|
2197 |
|
|
this.cn.synchronize(null, pid);
|
2198 |
|
|
} catch (Exception e) {
|
2199 |
|
|
logMetacat.error("Can't update the systemmetadata of pid "+pid.getValue()+" in CNs since "+e.getMessage());
|
2200 |
|
|
}
|
2201 |
9177
|
tao
|
}
|
2202 |
|
|
return success;
|
2203 |
|
|
}
|
2204 |
9190
|
tao
|
|
2205 |
|
|
/*
|
2206 |
|
|
* Determine if the current node is the authoritative node for the given pid.
|
2207 |
|
|
*/
|
2208 |
|
|
protected boolean isAuthoritativeNode(Identifier pid) {
|
2209 |
|
|
boolean isAuthoritativeNode = false;
|
2210 |
|
|
if(pid != null && pid.getValue() != null) {
|
2211 |
|
|
SystemMetadata sys = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
2212 |
|
|
if(sys != null) {
|
2213 |
|
|
NodeReference node = sys.getAuthoritativeMemberNode();
|
2214 |
|
|
if(node != null) {
|
2215 |
|
|
String nodeValue = node.getValue();
|
2216 |
|
|
logMetacat.debug("The authoritative node for id "+pid.getValue()+" is "+nodeValue);
|
2217 |
|
|
//System.out.println("The authoritative node for id "+pid.getValue()+" is "+nodeValue);
|
2218 |
|
|
String currentNodeId = Settings.getConfiguration().getString("dataone.nodeId");
|
2219 |
|
|
logMetacat.debug("The node id in metacat.properties is "+currentNodeId);
|
2220 |
|
|
//System.out.println("The node id in metacat.properties is "+currentNodeId);
|
2221 |
|
|
if(currentNodeId != null && !currentNodeId.trim().equals("") && currentNodeId.equals(nodeValue)) {
|
2222 |
|
|
logMetacat.debug("They are matching");
|
2223 |
|
|
//System.out.println("They are matching");
|
2224 |
|
|
isAuthoritativeNode = true;
|
2225 |
|
|
}
|
2226 |
|
|
}
|
2227 |
|
|
}
|
2228 |
|
|
}
|
2229 |
|
|
return isAuthoritativeNode;
|
2230 |
|
|
}
|
2231 |
6795
|
cjones
|
|
2232 |
6179
|
cjones
|
}
|