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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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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.OutputStreamWriter;
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import java.io.UnsupportedEncodingException;
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import java.io.Writer;
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import java.math.BigInteger;
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import java.net.URISyntaxException;
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import java.security.NoSuchAlgorithmException;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.Timer;
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import java.util.UUID;
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import java.util.Vector;
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import javax.servlet.http.HttpServletRequest;
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import org.apache.commons.io.IOUtils;
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import org.apache.log4j.Logger;
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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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import org.dataone.client.auth.CertificateManager;
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import org.dataone.client.v2.formats.ObjectFormatInfo;
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import org.dataone.configuration.Settings;
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import org.dataone.ore.ResourceMapFactory;
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import org.dataone.service.exceptions.BaseException;
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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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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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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Checksum;
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import org.dataone.service.types.v1.DescribeResponse;
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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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import org.dataone.service.types.v1.MonitorInfo;
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import org.dataone.service.types.v1.MonitorList;
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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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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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import org.dataone.service.types.v2.ObjectFormat;
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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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import org.dataone.service.types.v1.ReplicationStatus;
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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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import org.dataone.service.types.v2.SystemMetadata;
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import org.dataone.service.types.v1.util.AuthUtils;
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import org.dataone.service.types.v1.util.ChecksumUtil;
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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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import org.dataone.service.types.v1_1.QueryField;
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import org.dataone.service.util.Constants;
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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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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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import edu.ucsb.nceas.ezid.EZIDException;
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import edu.ucsb.nceas.metacat.DBQuery;
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import edu.ucsb.nceas.metacat.DBTransform;
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import edu.ucsb.nceas.metacat.EventLog;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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import edu.ucsb.nceas.metacat.MetaCatServlet;
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import edu.ucsb.nceas.metacat.MetacatHandler;
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import edu.ucsb.nceas.metacat.common.query.EnabledQueryEngines;
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import edu.ucsb.nceas.metacat.common.query.stream.ContentTypeByteArrayInputStream;
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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import edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler;
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import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
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import edu.ucsb.nceas.metacat.util.DeleteOnCloseFileInputStream;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.metacat.util.SkinUtil;
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.XMLUtilities;
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import edu.ucsb.nceas.utilities.export.HtmlToPdf;
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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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/**
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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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*
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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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* MNReplication.replicate()
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*
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*/
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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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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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/**
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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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// 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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// only admin of the MN or the CN is allowed a full delete
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boolean allowed = false;
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allowed = isAdminAuthorized(session);
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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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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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| 259 |
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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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| 265 |
|
|
* @param pid - The identifier of the object to be updated
|
| 266 |
|
|
* @param object - the new object bytes
|
| 267 |
|
|
* @param sysmeta - the new system metadata describing the object
|
| 268 |
|
|
*
|
| 269 |
|
|
* @return newPid - the identifier of the new object
|
| 270 |
|
|
*
|
| 271 |
|
|
* @throws InvalidToken
|
| 272 |
|
|
* @throws ServiceFailure
|
| 273 |
|
|
* @throws NotAuthorized
|
| 274 |
|
|
* @throws NotFound
|
| 275 |
|
|
* @throws NotImplemented
|
| 276 |
|
|
* @throws IdentifierNotUnique
|
| 277 |
|
|
* @throws UnsupportedType
|
| 278 |
|
|
* @throws InsufficientResources
|
| 279 |
|
|
* @throws InvalidSystemMetadata
|
| 280 |
|
|
* @throws InvalidRequest
|
| 281 |
|
|
*/
|
| 282 |
|
|
@Override
|
| 283 |
6575
|
cjones
|
public Identifier update(Session session, Identifier pid, InputStream object,
|
| 284 |
|
|
Identifier newPid, SystemMetadata sysmeta)
|
| 285 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
| 286 |
|
|
UnsupportedType, InsufficientResources, NotFound,
|
| 287 |
|
|
InvalidSystemMetadata, NotImplemented, InvalidRequest {
|
| 288 |
6250
|
cjones
|
|
| 289 |
6475
|
jones
|
String localId = null;
|
| 290 |
|
|
boolean allowed = false;
|
| 291 |
|
|
boolean isScienceMetadata = false;
|
| 292 |
6645
|
leinfelder
|
|
| 293 |
|
|
if (session == null) {
|
| 294 |
|
|
throw new InvalidToken("1210", "No session has been provided");
|
| 295 |
|
|
}
|
| 296 |
6475
|
jones
|
Subject subject = session.getSubject();
|
| 297 |
|
|
|
| 298 |
7315
|
leinfelder
|
// verify the pid is valid format
|
| 299 |
7318
|
leinfelder
|
if (!isValidIdentifier(pid)) {
|
| 300 |
7315
|
leinfelder
|
throw new InvalidRequest("1202", "The provided identifier is invalid.");
|
| 301 |
6475
|
jones
|
}
|
| 302 |
|
|
|
| 303 |
|
|
// check for the existing identifier
|
| 304 |
|
|
try {
|
| 305 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 306 |
6575
|
cjones
|
|
| 307 |
6475
|
jones
|
} catch (McdbDocNotFoundException e) {
|
| 308 |
6575
|
cjones
|
throw new InvalidRequest("1202", "The object with the provided " +
|
| 309 |
|
|
"identifier was not found.");
|
| 310 |
|
|
|
| 311 |
6475
|
jones
|
}
|
| 312 |
6518
|
leinfelder
|
|
| 313 |
6521
|
leinfelder
|
// set the originating node
|
| 314 |
|
|
NodeReference originMemberNode = this.getCapabilities().getIdentifier();
|
| 315 |
|
|
sysmeta.setOriginMemberNode(originMemberNode);
|
| 316 |
|
|
|
| 317 |
6518
|
leinfelder
|
// set the submitter to match the certificate
|
| 318 |
|
|
sysmeta.setSubmitter(subject);
|
| 319 |
6525
|
leinfelder
|
// set the dates
|
| 320 |
|
|
Date now = Calendar.getInstance().getTime();
|
| 321 |
6575
|
cjones
|
sysmeta.setDateSysMetadataModified(now);
|
| 322 |
|
|
sysmeta.setDateUploaded(now);
|
| 323 |
7486
|
leinfelder
|
|
| 324 |
|
|
// make sure serial version is set to something
|
| 325 |
|
|
BigInteger serialVersion = sysmeta.getSerialVersion();
|
| 326 |
|
|
if (serialVersion == null) {
|
| 327 |
|
|
sysmeta.setSerialVersion(BigInteger.ZERO);
|
| 328 |
|
|
}
|
| 329 |
6475
|
jones
|
|
| 330 |
|
|
// does the subject have WRITE ( == update) priveleges on the pid?
|
| 331 |
|
|
allowed = isAuthorized(session, pid, Permission.WRITE);
|
| 332 |
|
|
|
| 333 |
|
|
if (allowed) {
|
| 334 |
6649
|
leinfelder
|
|
| 335 |
|
|
// check quality of SM
|
| 336 |
|
|
if (sysmeta.getObsoletedBy() != null) {
|
| 337 |
|
|
throw new InvalidSystemMetadata("1300", "Cannot include obsoletedBy when updating object");
|
| 338 |
|
|
}
|
| 339 |
|
|
if (sysmeta.getObsoletes() != null && !sysmeta.getObsoletes().getValue().equals(pid.getValue())) {
|
| 340 |
|
|
throw new InvalidSystemMetadata("1300", "The identifier provided in obsoletes does not match old Identifier");
|
| 341 |
|
|
}
|
| 342 |
6475
|
jones
|
|
| 343 |
|
|
// get the existing system metadata for the object
|
| 344 |
|
|
SystemMetadata existingSysMeta = getSystemMetadata(session, pid);
|
| 345 |
|
|
|
| 346 |
7400
|
leinfelder
|
// check for previous update
|
| 347 |
|
|
// see: https://redmine.dataone.org/issues/3336
|
| 348 |
|
|
Identifier existingObsoletedBy = existingSysMeta.getObsoletedBy();
|
| 349 |
|
|
if (existingObsoletedBy != null) {
|
| 350 |
|
|
throw new InvalidRequest("1202",
|
| 351 |
|
|
"The previous identifier has already been made obsolete by: " + existingObsoletedBy.getValue());
|
| 352 |
|
|
}
|
| 353 |
6475
|
jones
|
|
| 354 |
|
|
isScienceMetadata = isScienceMetadata(sysmeta);
|
| 355 |
|
|
|
| 356 |
|
|
// do we have XML metadata or a data object?
|
| 357 |
|
|
if (isScienceMetadata) {
|
| 358 |
|
|
|
| 359 |
|
|
// update the science metadata XML document
|
| 360 |
|
|
// TODO: handle non-XML metadata/data documents (like netCDF)
|
| 361 |
|
|
// TODO: don't put objects into memory using stream to string
|
| 362 |
8948
|
tao
|
//String objectAsXML = "";
|
| 363 |
6475
|
jones
|
try {
|
| 364 |
8948
|
tao
|
//objectAsXML = IOUtils.toString(object, "UTF-8");
|
| 365 |
7443
|
leinfelder
|
// give the old pid so we can calculate the new local id
|
| 366 |
8948
|
tao
|
localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update");
|
| 367 |
6475
|
jones
|
// register the newPid and the generated localId
|
| 368 |
|
|
if (newPid != null) {
|
| 369 |
|
|
IdentifierManager.getInstance().createMapping(newPid.getValue(), localId);
|
| 370 |
|
|
|
| 371 |
|
|
}
|
| 372 |
|
|
|
| 373 |
|
|
} catch (IOException e) {
|
| 374 |
|
|
String msg = "The Node is unable to create the object. " + "There was a problem converting the object to XML";
|
| 375 |
|
|
logMetacat.info(msg);
|
| 376 |
|
|
throw new ServiceFailure("1310", msg + ": " + e.getMessage());
|
| 377 |
|
|
|
| 378 |
|
|
}
|
| 379 |
|
|
|
| 380 |
|
|
} else {
|
| 381 |
|
|
|
| 382 |
|
|
// update the data object
|
| 383 |
|
|
localId = insertDataObject(object, newPid, session);
|
| 384 |
|
|
|
| 385 |
|
|
}
|
| 386 |
8267
|
leinfelder
|
|
| 387 |
|
|
// add the newPid to the obsoletedBy list for the existing sysmeta
|
| 388 |
|
|
existingSysMeta.setObsoletedBy(newPid);
|
| 389 |
6475
|
jones
|
|
| 390 |
8267
|
leinfelder
|
// then update the existing system metadata
|
| 391 |
|
|
updateSystemMetadata(existingSysMeta);
|
| 392 |
|
|
|
| 393 |
|
|
// prep the new system metadata, add pid to the affected lists
|
| 394 |
|
|
sysmeta.setObsoletes(pid);
|
| 395 |
|
|
//sysmeta.addDerivedFrom(pid);
|
| 396 |
|
|
|
| 397 |
6475
|
jones
|
// and insert the new system metadata
|
| 398 |
|
|
insertSystemMetadata(sysmeta);
|
| 399 |
|
|
|
| 400 |
|
|
// log the update event
|
| 401 |
6542
|
leinfelder
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), subject.getValue(), localId, Event.UPDATE.toString());
|
| 402 |
7507
|
leinfelder
|
|
| 403 |
|
|
// attempt to register the identifier - it checks if it is a doi
|
| 404 |
|
|
try {
|
| 405 |
7512
|
leinfelder
|
DOIService.getInstance().registerDOI(sysmeta);
|
| 406 |
8795
|
leinfelder
|
} catch (Exception e) {
|
| 407 |
7507
|
leinfelder
|
throw new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
|
| 408 |
|
|
}
|
| 409 |
6475
|
jones
|
|
| 410 |
|
|
} else {
|
| 411 |
|
|
throw new NotAuthorized("1200", "The provided identity does not have " + "permission to UPDATE the object identified by " + pid.getValue()
|
| 412 |
|
|
+ " on the Member Node.");
|
| 413 |
|
|
}
|
| 414 |
|
|
|
| 415 |
|
|
return newPid;
|
| 416 |
6250
|
cjones
|
}
|
| 417 |
6254
|
cjones
|
|
| 418 |
6475
|
jones
|
public Identifier create(Session session, Identifier pid, InputStream object, SystemMetadata sysmeta) throws InvalidToken, ServiceFailure, NotAuthorized,
|
| 419 |
|
|
IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, InvalidRequest {
|
| 420 |
6250
|
cjones
|
|
| 421 |
6916
|
cjones
|
// check for null session
|
| 422 |
6530
|
leinfelder
|
if (session == null) {
|
| 423 |
6575
|
cjones
|
throw new InvalidToken("1110", "Session is required to WRITE to the Node.");
|
| 424 |
6530
|
leinfelder
|
}
|
| 425 |
6518
|
leinfelder
|
// set the submitter to match the certificate
|
| 426 |
|
|
sysmeta.setSubmitter(session.getSubject());
|
| 427 |
6520
|
leinfelder
|
// set the originating node
|
| 428 |
|
|
NodeReference originMemberNode = this.getCapabilities().getIdentifier();
|
| 429 |
|
|
sysmeta.setOriginMemberNode(originMemberNode);
|
| 430 |
6916
|
cjones
|
sysmeta.setArchived(false);
|
| 431 |
|
|
|
| 432 |
6525
|
leinfelder
|
// set the dates
|
| 433 |
|
|
Date now = Calendar.getInstance().getTime();
|
| 434 |
6916
|
cjones
|
sysmeta.setDateSysMetadataModified(now);
|
| 435 |
|
|
sysmeta.setDateUploaded(now);
|
| 436 |
7021
|
leinfelder
|
|
| 437 |
|
|
// set the serial version
|
| 438 |
|
|
sysmeta.setSerialVersion(BigInteger.ZERO);
|
| 439 |
7083
|
cjones
|
|
| 440 |
|
|
// check that we are not attempting to subvert versioning
|
| 441 |
|
|
if (sysmeta.getObsoletes() != null && sysmeta.getObsoletes().getValue() != null) {
|
| 442 |
|
|
throw new InvalidSystemMetadata("1180",
|
| 443 |
|
|
"The supplied system metadata is invalid. " +
|
| 444 |
|
|
"The obsoletes field cannot have a value when creating entries.");
|
| 445 |
|
|
}
|
| 446 |
7021
|
leinfelder
|
|
| 447 |
7083
|
cjones
|
if (sysmeta.getObsoletedBy() != null && sysmeta.getObsoletedBy().getValue() != null) {
|
| 448 |
|
|
throw new InvalidSystemMetadata("1180",
|
| 449 |
|
|
"The supplied system metadata is invalid. " +
|
| 450 |
|
|
"The obsoletedBy field cannot have a value when creating entries.");
|
| 451 |
|
|
}
|
| 452 |
|
|
|
| 453 |
6518
|
leinfelder
|
// call the shared impl
|
| 454 |
7507
|
leinfelder
|
Identifier resultPid = super.create(session, pid, object, sysmeta);
|
| 455 |
|
|
|
| 456 |
|
|
// attempt to register the identifier - it checks if it is a doi
|
| 457 |
|
|
try {
|
| 458 |
7512
|
leinfelder
|
DOIService.getInstance().registerDOI(sysmeta);
|
| 459 |
8795
|
leinfelder
|
} catch (Exception e) {
|
| 460 |
7510
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
|
| 461 |
|
|
sf.initCause(e);
|
| 462 |
|
|
throw sf;
|
| 463 |
7507
|
leinfelder
|
}
|
| 464 |
|
|
|
| 465 |
|
|
// return
|
| 466 |
|
|
return resultPid ;
|
| 467 |
6475
|
jones
|
}
|
| 468 |
6250
|
cjones
|
|
| 469 |
6475
|
jones
|
/**
|
| 470 |
|
|
* Called by a Coordinating Node to request that the Member Node create a
|
| 471 |
|
|
* copy of the specified object by retrieving it from another Member
|
| 472 |
|
|
* Node and storing it locally so that it can be made accessible to
|
| 473 |
|
|
* the DataONE system.
|
| 474 |
|
|
*
|
| 475 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 476 |
|
|
* @param sysmeta - Copy of the CN held system metadata for the object
|
| 477 |
|
|
* @param sourceNode - A reference to node from which the content should be
|
| 478 |
|
|
* retrieved. The reference should be resolved by
|
| 479 |
|
|
* checking the CN node registry.
|
| 480 |
|
|
*
|
| 481 |
|
|
* @return true if the replication succeeds
|
| 482 |
|
|
*
|
| 483 |
|
|
* @throws ServiceFailure
|
| 484 |
|
|
* @throws NotAuthorized
|
| 485 |
|
|
* @throws NotImplemented
|
| 486 |
|
|
* @throws UnsupportedType
|
| 487 |
|
|
* @throws InsufficientResources
|
| 488 |
|
|
* @throws InvalidRequest
|
| 489 |
|
|
*/
|
| 490 |
|
|
@Override
|
| 491 |
6786
|
cjones
|
public boolean replicate(Session session, SystemMetadata sysmeta,
|
| 492 |
|
|
NodeReference sourceNode) throws NotImplemented, ServiceFailure,
|
| 493 |
|
|
NotAuthorized, InvalidRequest, InsufficientResources,
|
| 494 |
|
|
UnsupportedType {
|
| 495 |
|
|
|
| 496 |
6875
|
cjones
|
if (session != null && sysmeta != null && sourceNode != null) {
|
| 497 |
|
|
logMetacat.info("MNodeService.replicate() called with parameters: \n" +
|
| 498 |
|
|
"\tSession.Subject = " +
|
| 499 |
|
|
session.getSubject().getValue() + "\n" +
|
| 500 |
7082
|
cjones
|
"\tidentifier = " +
|
| 501 |
|
|
sysmeta.getIdentifier().getValue() +
|
| 502 |
6875
|
cjones
|
"\n" + "\tSource NodeReference =" +
|
| 503 |
|
|
sourceNode.getValue());
|
| 504 |
|
|
}
|
| 505 |
6475
|
jones
|
boolean result = false;
|
| 506 |
6786
|
cjones
|
String nodeIdStr = null;
|
| 507 |
6651
|
cjones
|
NodeReference nodeId = null;
|
| 508 |
6786
|
cjones
|
|
| 509 |
6795
|
cjones
|
// get the referenced object
|
| 510 |
|
|
Identifier pid = sysmeta.getIdentifier();
|
| 511 |
|
|
|
| 512 |
|
|
// get from the membernode
|
| 513 |
|
|
// TODO: switch credentials for the server retrieval?
|
| 514 |
|
|
this.mn = D1Client.getMN(sourceNode);
|
| 515 |
|
|
this.cn = D1Client.getCN();
|
| 516 |
|
|
InputStream object = null;
|
| 517 |
|
|
Session thisNodeSession = null;
|
| 518 |
|
|
SystemMetadata localSystemMetadata = null;
|
| 519 |
|
|
BaseException failure = null;
|
| 520 |
6818
|
cjones
|
String localId = null;
|
| 521 |
|
|
|
| 522 |
6795
|
cjones
|
// TODO: check credentials
|
| 523 |
|
|
// cannot be called by public
|
| 524 |
7063
|
leinfelder
|
if (session == null || session.getSubject() == null) {
|
| 525 |
7082
|
cjones
|
String msg = "No session was provided to replicate identifier " +
|
| 526 |
|
|
sysmeta.getIdentifier().getValue();
|
| 527 |
8414
|
tao
|
logMetacat.error(msg);
|
| 528 |
7192
|
cjones
|
throw new NotAuthorized("2152", msg);
|
| 529 |
|
|
|
| 530 |
6795
|
cjones
|
}
|
| 531 |
|
|
|
| 532 |
|
|
|
| 533 |
6651
|
cjones
|
// get the local node id
|
| 534 |
|
|
try {
|
| 535 |
7030
|
cjones
|
nodeIdStr = PropertyService.getProperty("dataone.nodeId");
|
| 536 |
6651
|
cjones
|
nodeId = new NodeReference();
|
| 537 |
|
|
nodeId.setValue(nodeIdStr);
|
| 538 |
6786
|
cjones
|
|
| 539 |
6651
|
cjones
|
} catch (PropertyNotFoundException e1) {
|
| 540 |
7030
|
cjones
|
String msg = "Couldn't get dataone.nodeId property: " + e1.getMessage();
|
| 541 |
6795
|
cjones
|
failure = new ServiceFailure("2151", msg);
|
| 542 |
8414
|
tao
|
//setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 543 |
6795
|
cjones
|
logMetacat.error(msg);
|
| 544 |
8414
|
tao
|
//return true;
|
| 545 |
|
|
throw new ServiceFailure("2151", msg);
|
| 546 |
6786
|
cjones
|
|
| 547 |
6651
|
cjones
|
}
|
| 548 |
6795
|
cjones
|
|
| 549 |
6475
|
jones
|
|
| 550 |
|
|
try {
|
| 551 |
6786
|
cjones
|
// do we already have a replica?
|
| 552 |
|
|
try {
|
| 553 |
6818
|
cjones
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 554 |
6822
|
cjones
|
// if we have a local id, get the local object
|
| 555 |
|
|
try {
|
| 556 |
|
|
object = MetacatHandler.read(localId);
|
| 557 |
|
|
} catch (Exception e) {
|
| 558 |
7127
|
leinfelder
|
// NOTE: we may already know about this ID because it could be a data file described by a metadata file
|
| 559 |
|
|
// https://redmine.dataone.org/issues/2572
|
| 560 |
|
|
// TODO: fix this so that we don't prevent ourselves from getting replicas
|
| 561 |
|
|
|
| 562 |
6822
|
cjones
|
// let the CN know that the replication failed
|
| 563 |
7127
|
leinfelder
|
logMetacat.warn("Object content not found on this node despite having localId: " + localId);
|
| 564 |
|
|
String msg = "Can't read the object bytes properly, replica is invalid.";
|
| 565 |
|
|
ServiceFailure serviceFailure = new ServiceFailure("2151", msg);
|
| 566 |
7113
|
leinfelder
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, serviceFailure);
|
| 567 |
|
|
logMetacat.warn(msg);
|
| 568 |
6822
|
cjones
|
throw serviceFailure;
|
| 569 |
|
|
|
| 570 |
|
|
}
|
| 571 |
|
|
|
| 572 |
6817
|
cjones
|
} catch (McdbDocNotFoundException e) {
|
| 573 |
6818
|
cjones
|
logMetacat.info("No replica found. Continuing.");
|
| 574 |
6817
|
cjones
|
|
| 575 |
6819
|
cjones
|
}
|
| 576 |
|
|
|
| 577 |
6786
|
cjones
|
// no local replica, get a replica
|
| 578 |
6819
|
cjones
|
if ( object == null ) {
|
| 579 |
6786
|
cjones
|
// session should be null to use the default certificate
|
| 580 |
|
|
// location set in the Certificate manager
|
| 581 |
|
|
object = mn.getReplica(thisNodeSession, pid);
|
| 582 |
7082
|
cjones
|
logMetacat.info("MNodeService.getReplica() called for identifier "
|
| 583 |
6786
|
cjones
|
+ pid.getValue());
|
| 584 |
|
|
|
| 585 |
|
|
}
|
| 586 |
|
|
|
| 587 |
6795
|
cjones
|
} catch (InvalidToken e) {
|
| 588 |
|
|
String msg = "Could not retrieve object to replicate (InvalidToken): "+ e.getMessage();
|
| 589 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 590 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 591 |
|
|
logMetacat.error(msg);
|
| 592 |
|
|
throw new ServiceFailure("2151", msg);
|
| 593 |
6786
|
cjones
|
|
| 594 |
6475
|
jones
|
} catch (NotFound e) {
|
| 595 |
6795
|
cjones
|
String msg = "Could not retrieve object to replicate (NotFound): "+ e.getMessage();
|
| 596 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 597 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 598 |
|
|
logMetacat.error(msg);
|
| 599 |
|
|
throw new ServiceFailure("2151", msg);
|
| 600 |
6786
|
cjones
|
|
| 601 |
8414
|
tao
|
} catch (NotAuthorized e) {
|
| 602 |
|
|
String msg = "Could not retrieve object to replicate (NotAuthorized): "+ e.getMessage();
|
| 603 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 604 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 605 |
|
|
logMetacat.error(msg);
|
| 606 |
|
|
throw new ServiceFailure("2151", msg);
|
| 607 |
|
|
} catch (NotImplemented e) {
|
| 608 |
|
|
String msg = "Could not retrieve object to replicate (mn.getReplica NotImplemented): "+ e.getMessage();
|
| 609 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 610 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 611 |
|
|
logMetacat.error(msg);
|
| 612 |
|
|
throw new ServiceFailure("2151", msg);
|
| 613 |
|
|
} catch (ServiceFailure e) {
|
| 614 |
|
|
String msg = "Could not retrieve object to replicate (ServiceFailure): "+ e.getMessage();
|
| 615 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 616 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 617 |
|
|
logMetacat.error(msg);
|
| 618 |
|
|
throw new ServiceFailure("2151", msg);
|
| 619 |
|
|
} catch (InsufficientResources e) {
|
| 620 |
|
|
String msg = "Could not retrieve object to replicate (InsufficientResources): "+ e.getMessage();
|
| 621 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 622 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 623 |
|
|
logMetacat.error(msg);
|
| 624 |
|
|
throw new ServiceFailure("2151", msg);
|
| 625 |
6475
|
jones
|
}
|
| 626 |
|
|
|
| 627 |
6693
|
leinfelder
|
// verify checksum on the object, if supported
|
| 628 |
|
|
if (object.markSupported()) {
|
| 629 |
6786
|
cjones
|
Checksum givenChecksum = sysmeta.getChecksum();
|
| 630 |
|
|
Checksum computedChecksum = null;
|
| 631 |
|
|
try {
|
| 632 |
7127
|
leinfelder
|
computedChecksum = ChecksumUtil.checksum(object, givenChecksum.getAlgorithm());
|
| 633 |
6786
|
cjones
|
object.reset();
|
| 634 |
6948
|
cjones
|
|
| 635 |
6786
|
cjones
|
} catch (Exception e) {
|
| 636 |
7127
|
leinfelder
|
String msg = "Error computing checksum on replica: " + e.getMessage();
|
| 637 |
7113
|
leinfelder
|
logMetacat.error(msg);
|
| 638 |
6786
|
cjones
|
ServiceFailure sf = new ServiceFailure("2151", msg);
|
| 639 |
|
|
sf.initCause(e);
|
| 640 |
8414
|
tao
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, sf);
|
| 641 |
6786
|
cjones
|
throw sf;
|
| 642 |
|
|
}
|
| 643 |
6948
|
cjones
|
if (!givenChecksum.getValue().equals(computedChecksum.getValue())) {
|
| 644 |
7113
|
leinfelder
|
logMetacat.error("Given checksum for " + pid.getValue() +
|
| 645 |
6948
|
cjones
|
"is " + givenChecksum.getValue());
|
| 646 |
7113
|
leinfelder
|
logMetacat.error("Computed checksum for " + pid.getValue() +
|
| 647 |
6948
|
cjones
|
"is " + computedChecksum.getValue());
|
| 648 |
8414
|
tao
|
String msg = "Computed checksum does not match declared checksum";
|
| 649 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 650 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 651 |
|
|
throw new ServiceFailure("2151", msg);
|
| 652 |
6786
|
cjones
|
}
|
| 653 |
6693
|
leinfelder
|
}
|
| 654 |
6786
|
cjones
|
|
| 655 |
6475
|
jones
|
// add it to local store
|
| 656 |
|
|
Identifier retPid;
|
| 657 |
|
|
try {
|
| 658 |
7127
|
leinfelder
|
// skip the MN.create -- this mutates the system metadata and we don't want it to
|
| 659 |
6818
|
cjones
|
if ( localId == null ) {
|
| 660 |
7127
|
leinfelder
|
// TODO: this will fail if we already "know" about the identifier
|
| 661 |
|
|
// FIXME: see https://redmine.dataone.org/issues/2572
|
| 662 |
6818
|
cjones
|
retPid = super.create(session, pid, object, sysmeta);
|
| 663 |
|
|
result = (retPid.getValue().equals(pid.getValue()));
|
| 664 |
|
|
}
|
| 665 |
6795
|
cjones
|
|
| 666 |
7125
|
leinfelder
|
} catch (Exception e) {
|
| 667 |
7126
|
leinfelder
|
String msg = "Could not save object to local store (" + e.getClass().getName() + "): " + e.getMessage();
|
| 668 |
7125
|
leinfelder
|
failure = new ServiceFailure("2151", msg);
|
| 669 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 670 |
|
|
logMetacat.error(msg);
|
| 671 |
|
|
throw new ServiceFailure("2151", msg);
|
| 672 |
|
|
|
| 673 |
6475
|
jones
|
}
|
| 674 |
|
|
|
| 675 |
6795
|
cjones
|
// finish by setting the replication status
|
| 676 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.COMPLETED, null);
|
| 677 |
6475
|
jones
|
return result;
|
| 678 |
|
|
|
| 679 |
6250
|
cjones
|
}
|
| 680 |
6179
|
cjones
|
|
| 681 |
6475
|
jones
|
/**
|
| 682 |
|
|
* Return the object identified by the given object identifier
|
| 683 |
|
|
*
|
| 684 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 685 |
|
|
* @param pid - the object identifier for the given object
|
| 686 |
|
|
*
|
| 687 |
|
|
* @return inputStream - the input stream of the given object
|
| 688 |
|
|
*
|
| 689 |
|
|
* @throws InvalidToken
|
| 690 |
|
|
* @throws ServiceFailure
|
| 691 |
|
|
* @throws NotAuthorized
|
| 692 |
|
|
* @throws InvalidRequest
|
| 693 |
|
|
* @throws NotImplemented
|
| 694 |
|
|
*/
|
| 695 |
|
|
@Override
|
| 696 |
6610
|
cjones
|
public InputStream get(Session session, Identifier pid)
|
| 697 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
| 698 |
6258
|
cjones
|
|
| 699 |
6475
|
jones
|
return super.get(session, pid);
|
| 700 |
6258
|
cjones
|
|
| 701 |
6259
|
cjones
|
}
|
| 702 |
6258
|
cjones
|
|
| 703 |
6475
|
jones
|
/**
|
| 704 |
|
|
* Returns a Checksum for the specified object using an accepted hashing algorithm
|
| 705 |
|
|
*
|
| 706 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 707 |
|
|
* @param pid - the object identifier for the given object
|
| 708 |
|
|
* @param algorithm - the name of an algorithm that will be used to compute
|
| 709 |
|
|
* a checksum of the bytes of the object
|
| 710 |
|
|
*
|
| 711 |
|
|
* @return checksum - the checksum of the given object
|
| 712 |
|
|
*
|
| 713 |
|
|
* @throws InvalidToken
|
| 714 |
|
|
* @throws ServiceFailure
|
| 715 |
|
|
* @throws NotAuthorized
|
| 716 |
|
|
* @throws NotFound
|
| 717 |
|
|
* @throws InvalidRequest
|
| 718 |
|
|
* @throws NotImplemented
|
| 719 |
|
|
*/
|
| 720 |
|
|
@Override
|
| 721 |
6610
|
cjones
|
public Checksum getChecksum(Session session, Identifier pid, String algorithm)
|
| 722 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 723 |
|
|
InvalidRequest, NotImplemented {
|
| 724 |
6258
|
cjones
|
|
| 725 |
6475
|
jones
|
Checksum checksum = null;
|
| 726 |
|
|
|
| 727 |
|
|
InputStream inputStream = get(session, pid);
|
| 728 |
|
|
|
| 729 |
6259
|
cjones
|
try {
|
| 730 |
6475
|
jones
|
checksum = ChecksumUtil.checksum(inputStream, algorithm);
|
| 731 |
|
|
|
| 732 |
|
|
} catch (NoSuchAlgorithmException e) {
|
| 733 |
|
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
|
| 734 |
|
|
+ e.getMessage());
|
| 735 |
6259
|
cjones
|
} catch (IOException e) {
|
| 736 |
6475
|
jones
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
|
| 737 |
|
|
+ e.getMessage());
|
| 738 |
6259
|
cjones
|
}
|
| 739 |
6382
|
cjones
|
|
| 740 |
6475
|
jones
|
if (checksum == null) {
|
| 741 |
|
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned.");
|
| 742 |
|
|
}
|
| 743 |
6258
|
cjones
|
|
| 744 |
6475
|
jones
|
return checksum;
|
| 745 |
6259
|
cjones
|
}
|
| 746 |
6179
|
cjones
|
|
| 747 |
6475
|
jones
|
/**
|
| 748 |
|
|
* Return the system metadata for a given object
|
| 749 |
|
|
*
|
| 750 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 751 |
|
|
* @param pid - the object identifier for the given object
|
| 752 |
|
|
*
|
| 753 |
|
|
* @return inputStream - the input stream of the given system metadata object
|
| 754 |
|
|
*
|
| 755 |
|
|
* @throws InvalidToken
|
| 756 |
|
|
* @throws ServiceFailure
|
| 757 |
|
|
* @throws NotAuthorized
|
| 758 |
|
|
* @throws NotFound
|
| 759 |
|
|
* @throws InvalidRequest
|
| 760 |
|
|
* @throws NotImplemented
|
| 761 |
|
|
*/
|
| 762 |
|
|
@Override
|
| 763 |
6610
|
cjones
|
public SystemMetadata getSystemMetadata(Session session, Identifier pid)
|
| 764 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 765 |
|
|
NotImplemented {
|
| 766 |
6341
|
leinfelder
|
|
| 767 |
6475
|
jones
|
return super.getSystemMetadata(session, pid);
|
| 768 |
|
|
}
|
| 769 |
6341
|
leinfelder
|
|
| 770 |
6475
|
jones
|
/**
|
| 771 |
|
|
* Retrieve the list of objects present on the MN that match the calling parameters
|
| 772 |
|
|
*
|
| 773 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 774 |
|
|
* @param startTime - Specifies the beginning of the time range from which
|
| 775 |
|
|
* to return object (>=)
|
| 776 |
|
|
* @param endTime - Specifies the beginning of the time range from which
|
| 777 |
|
|
* to return object (>=)
|
| 778 |
|
|
* @param objectFormat - Restrict results to the specified object format
|
| 779 |
|
|
* @param replicaStatus - Indicates if replicated objects should be returned in the list
|
| 780 |
|
|
* @param start - The zero-based index of the first value, relative to the
|
| 781 |
|
|
* first record of the resultset that matches the parameters.
|
| 782 |
|
|
* @param count - The maximum number of entries that should be returned in
|
| 783 |
|
|
* the response. The Member Node may return less entries
|
| 784 |
|
|
* than specified in this value.
|
| 785 |
|
|
*
|
| 786 |
|
|
* @return objectList - the list of objects matching the criteria
|
| 787 |
|
|
*
|
| 788 |
|
|
* @throws InvalidToken
|
| 789 |
|
|
* @throws ServiceFailure
|
| 790 |
|
|
* @throws NotAuthorized
|
| 791 |
|
|
* @throws InvalidRequest
|
| 792 |
|
|
* @throws NotImplemented
|
| 793 |
|
|
*/
|
| 794 |
|
|
@Override
|
| 795 |
8810
|
leinfelder
|
public ObjectList listObjects(Session session, Date startTime, Date endTime, ObjectFormatIdentifier objectFormatId, Identifier identifier, Boolean replicaStatus, Integer start,
|
| 796 |
6475
|
jones
|
Integer count) throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken {
|
| 797 |
6179
|
cjones
|
|
| 798 |
6475
|
jones
|
ObjectList objectList = null;
|
| 799 |
6332
|
leinfelder
|
|
| 800 |
6475
|
jones
|
try {
|
| 801 |
7439
|
leinfelder
|
// safeguard against large requests
|
| 802 |
|
|
if (count == null || count > MAXIMUM_DB_RECORD_COUNT) {
|
| 803 |
|
|
count = MAXIMUM_DB_RECORD_COUNT;
|
| 804 |
|
|
}
|
| 805 |
6475
|
jones
|
objectList = IdentifierManager.getInstance().querySystemMetadata(startTime, endTime, objectFormatId, replicaStatus, start, count);
|
| 806 |
|
|
} catch (Exception e) {
|
| 807 |
|
|
throw new ServiceFailure("1580", "Error querying system metadata: " + e.getMessage());
|
| 808 |
|
|
}
|
| 809 |
6332
|
leinfelder
|
|
| 810 |
6475
|
jones
|
return objectList;
|
| 811 |
6229
|
cjones
|
}
|
| 812 |
6179
|
cjones
|
|
| 813 |
6475
|
jones
|
/**
|
| 814 |
6476
|
jones
|
* Return a description of the node's capabilities and services.
|
| 815 |
6475
|
jones
|
*
|
| 816 |
|
|
* @return node - the technical capabilities of the Member Node
|
| 817 |
|
|
*
|
| 818 |
|
|
* @throws ServiceFailure
|
| 819 |
|
|
* @throws NotAuthorized
|
| 820 |
|
|
* @throws InvalidRequest
|
| 821 |
|
|
* @throws NotImplemented
|
| 822 |
|
|
*/
|
| 823 |
|
|
@Override
|
| 824 |
6610
|
cjones
|
public Node getCapabilities()
|
| 825 |
|
|
throws NotImplemented, ServiceFailure {
|
| 826 |
6179
|
cjones
|
|
| 827 |
6475
|
jones
|
String nodeName = null;
|
| 828 |
|
|
String nodeId = null;
|
| 829 |
6492
|
jones
|
String subject = null;
|
| 830 |
6938
|
cjones
|
String contactSubject = null;
|
| 831 |
6475
|
jones
|
String nodeDesc = null;
|
| 832 |
6476
|
jones
|
String nodeTypeString = null;
|
| 833 |
|
|
NodeType nodeType = null;
|
| 834 |
6475
|
jones
|
String mnCoreServiceVersion = null;
|
| 835 |
|
|
String mnReadServiceVersion = null;
|
| 836 |
|
|
String mnAuthorizationServiceVersion = null;
|
| 837 |
|
|
String mnStorageServiceVersion = null;
|
| 838 |
|
|
String mnReplicationServiceVersion = null;
|
| 839 |
6179
|
cjones
|
|
| 840 |
6475
|
jones
|
boolean nodeSynchronize = false;
|
| 841 |
|
|
boolean nodeReplicate = false;
|
| 842 |
|
|
boolean mnCoreServiceAvailable = false;
|
| 843 |
|
|
boolean mnReadServiceAvailable = false;
|
| 844 |
|
|
boolean mnAuthorizationServiceAvailable = false;
|
| 845 |
|
|
boolean mnStorageServiceAvailable = false;
|
| 846 |
|
|
boolean mnReplicationServiceAvailable = false;
|
| 847 |
6179
|
cjones
|
|
| 848 |
6475
|
jones
|
try {
|
| 849 |
|
|
// get the properties of the node based on configuration information
|
| 850 |
6492
|
jones
|
nodeName = PropertyService.getProperty("dataone.nodeName");
|
| 851 |
7030
|
cjones
|
nodeId = PropertyService.getProperty("dataone.nodeId");
|
| 852 |
6492
|
jones
|
subject = PropertyService.getProperty("dataone.subject");
|
| 853 |
6938
|
cjones
|
contactSubject = PropertyService.getProperty("dataone.contactSubject");
|
| 854 |
6475
|
jones
|
nodeDesc = PropertyService.getProperty("dataone.nodeDescription");
|
| 855 |
6476
|
jones
|
nodeTypeString = PropertyService.getProperty("dataone.nodeType");
|
| 856 |
|
|
nodeType = NodeType.convert(nodeTypeString);
|
| 857 |
6475
|
jones
|
nodeSynchronize = new Boolean(PropertyService.getProperty("dataone.nodeSynchronize")).booleanValue();
|
| 858 |
|
|
nodeReplicate = new Boolean(PropertyService.getProperty("dataone.nodeReplicate")).booleanValue();
|
| 859 |
|
|
|
| 860 |
|
|
mnCoreServiceVersion = PropertyService.getProperty("dataone.mnCore.serviceVersion");
|
| 861 |
|
|
mnReadServiceVersion = PropertyService.getProperty("dataone.mnRead.serviceVersion");
|
| 862 |
|
|
mnAuthorizationServiceVersion = PropertyService.getProperty("dataone.mnAuthorization.serviceVersion");
|
| 863 |
|
|
mnStorageServiceVersion = PropertyService.getProperty("dataone.mnStorage.serviceVersion");
|
| 864 |
|
|
mnReplicationServiceVersion = PropertyService.getProperty("dataone.mnReplication.serviceVersion");
|
| 865 |
|
|
|
| 866 |
|
|
mnCoreServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnCore.serviceAvailable")).booleanValue();
|
| 867 |
|
|
mnReadServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnRead.serviceAvailable")).booleanValue();
|
| 868 |
|
|
mnAuthorizationServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnAuthorization.serviceAvailable")).booleanValue();
|
| 869 |
|
|
mnStorageServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnStorage.serviceAvailable")).booleanValue();
|
| 870 |
|
|
mnReplicationServiceAvailable = new Boolean(PropertyService.getProperty("dataone.mnReplication.serviceAvailable")).booleanValue();
|
| 871 |
|
|
|
| 872 |
6476
|
jones
|
// Set the properties of the node based on configuration information and
|
| 873 |
|
|
// calls to current status methods
|
| 874 |
7286
|
leinfelder
|
String serviceName = SystemUtil.getSecureContextURL() + "/" + PropertyService.getProperty("dataone.serviceName");
|
| 875 |
6476
|
jones
|
Node node = new Node();
|
| 876 |
6542
|
leinfelder
|
node.setBaseURL(serviceName + "/" + nodeTypeString);
|
| 877 |
6476
|
jones
|
node.setDescription(nodeDesc);
|
| 878 |
6475
|
jones
|
|
| 879 |
6476
|
jones
|
// set the node's health information
|
| 880 |
|
|
node.setState(NodeState.UP);
|
| 881 |
|
|
|
| 882 |
|
|
// set the ping response to the current value
|
| 883 |
|
|
Ping canPing = new Ping();
|
| 884 |
|
|
canPing.setSuccess(false);
|
| 885 |
|
|
try {
|
| 886 |
6803
|
leinfelder
|
Date pingDate = ping();
|
| 887 |
|
|
canPing.setSuccess(pingDate != null);
|
| 888 |
|
|
} catch (BaseException e) {
|
| 889 |
6476
|
jones
|
e.printStackTrace();
|
| 890 |
6803
|
leinfelder
|
// guess it can't be pinged
|
| 891 |
6476
|
jones
|
}
|
| 892 |
6610
|
cjones
|
|
| 893 |
6476
|
jones
|
node.setPing(canPing);
|
| 894 |
6475
|
jones
|
|
| 895 |
6476
|
jones
|
NodeReference identifier = new NodeReference();
|
| 896 |
|
|
identifier.setValue(nodeId);
|
| 897 |
|
|
node.setIdentifier(identifier);
|
| 898 |
6492
|
jones
|
Subject s = new Subject();
|
| 899 |
|
|
s.setValue(subject);
|
| 900 |
|
|
node.addSubject(s);
|
| 901 |
6938
|
cjones
|
Subject contact = new Subject();
|
| 902 |
|
|
contact.setValue(contactSubject);
|
| 903 |
|
|
node.addContactSubject(contact);
|
| 904 |
6476
|
jones
|
node.setName(nodeName);
|
| 905 |
|
|
node.setReplicate(nodeReplicate);
|
| 906 |
|
|
node.setSynchronize(nodeSynchronize);
|
| 907 |
6475
|
jones
|
|
| 908 |
6476
|
jones
|
// services: MNAuthorization, MNCore, MNRead, MNReplication, MNStorage
|
| 909 |
|
|
Services services = new Services();
|
| 910 |
6475
|
jones
|
|
| 911 |
6476
|
jones
|
Service sMNCore = new Service();
|
| 912 |
|
|
sMNCore.setName("MNCore");
|
| 913 |
|
|
sMNCore.setVersion(mnCoreServiceVersion);
|
| 914 |
|
|
sMNCore.setAvailable(mnCoreServiceAvailable);
|
| 915 |
6475
|
jones
|
|
| 916 |
6476
|
jones
|
Service sMNRead = new Service();
|
| 917 |
|
|
sMNRead.setName("MNRead");
|
| 918 |
|
|
sMNRead.setVersion(mnReadServiceVersion);
|
| 919 |
|
|
sMNRead.setAvailable(mnReadServiceAvailable);
|
| 920 |
6475
|
jones
|
|
| 921 |
6476
|
jones
|
Service sMNAuthorization = new Service();
|
| 922 |
|
|
sMNAuthorization.setName("MNAuthorization");
|
| 923 |
|
|
sMNAuthorization.setVersion(mnAuthorizationServiceVersion);
|
| 924 |
|
|
sMNAuthorization.setAvailable(mnAuthorizationServiceAvailable);
|
| 925 |
6475
|
jones
|
|
| 926 |
6476
|
jones
|
Service sMNStorage = new Service();
|
| 927 |
|
|
sMNStorage.setName("MNStorage");
|
| 928 |
|
|
sMNStorage.setVersion(mnStorageServiceVersion);
|
| 929 |
|
|
sMNStorage.setAvailable(mnStorageServiceAvailable);
|
| 930 |
6475
|
jones
|
|
| 931 |
6476
|
jones
|
Service sMNReplication = new Service();
|
| 932 |
|
|
sMNReplication.setName("MNReplication");
|
| 933 |
|
|
sMNReplication.setVersion(mnReplicationServiceVersion);
|
| 934 |
|
|
sMNReplication.setAvailable(mnReplicationServiceAvailable);
|
| 935 |
6475
|
jones
|
|
| 936 |
6476
|
jones
|
services.addService(sMNRead);
|
| 937 |
|
|
services.addService(sMNCore);
|
| 938 |
|
|
services.addService(sMNAuthorization);
|
| 939 |
|
|
services.addService(sMNStorage);
|
| 940 |
|
|
services.addService(sMNReplication);
|
| 941 |
|
|
node.setServices(services);
|
| 942 |
6475
|
jones
|
|
| 943 |
6476
|
jones
|
// Set the schedule for synchronization
|
| 944 |
|
|
Synchronization synchronization = new Synchronization();
|
| 945 |
|
|
Schedule schedule = new Schedule();
|
| 946 |
|
|
Date now = new Date();
|
| 947 |
6689
|
leinfelder
|
schedule.setYear(PropertyService.getProperty("dataone.nodeSynchronization.schedule.year"));
|
| 948 |
|
|
schedule.setMon(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mon"));
|
| 949 |
|
|
schedule.setMday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mday"));
|
| 950 |
|
|
schedule.setWday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.wday"));
|
| 951 |
|
|
schedule.setHour(PropertyService.getProperty("dataone.nodeSynchronization.schedule.hour"));
|
| 952 |
|
|
schedule.setMin(PropertyService.getProperty("dataone.nodeSynchronization.schedule.min"));
|
| 953 |
|
|
schedule.setSec(PropertyService.getProperty("dataone.nodeSynchronization.schedule.sec"));
|
| 954 |
6476
|
jones
|
synchronization.setSchedule(schedule);
|
| 955 |
|
|
synchronization.setLastHarvested(now);
|
| 956 |
|
|
synchronization.setLastCompleteHarvest(now);
|
| 957 |
|
|
node.setSynchronization(synchronization);
|
| 958 |
6475
|
jones
|
|
| 959 |
6476
|
jones
|
node.setType(nodeType);
|
| 960 |
|
|
return node;
|
| 961 |
6475
|
jones
|
|
| 962 |
6476
|
jones
|
} catch (PropertyNotFoundException pnfe) {
|
| 963 |
|
|
String msg = "MNodeService.getCapabilities(): " + "property not found: " + pnfe.getMessage();
|
| 964 |
|
|
logMetacat.error(msg);
|
| 965 |
|
|
throw new ServiceFailure("2162", msg);
|
| 966 |
|
|
}
|
| 967 |
6228
|
cjones
|
}
|
| 968 |
6179
|
cjones
|
|
| 969 |
8810
|
leinfelder
|
|
| 970 |
6179
|
cjones
|
|
| 971 |
6475
|
jones
|
/**
|
| 972 |
|
|
* A callback method used by a CN to indicate to a MN that it cannot
|
| 973 |
|
|
* complete synchronization of the science metadata identified by pid. Log
|
| 974 |
|
|
* the event in the metacat event log.
|
| 975 |
|
|
*
|
| 976 |
|
|
* @param session
|
| 977 |
|
|
* @param syncFailed
|
| 978 |
|
|
*
|
| 979 |
|
|
* @throws ServiceFailure
|
| 980 |
|
|
* @throws NotAuthorized
|
| 981 |
|
|
* @throws NotImplemented
|
| 982 |
|
|
*/
|
| 983 |
|
|
@Override
|
| 984 |
6991
|
leinfelder
|
public boolean synchronizationFailed(Session session, SynchronizationFailed syncFailed)
|
| 985 |
6610
|
cjones
|
throws NotImplemented, ServiceFailure, NotAuthorized {
|
| 986 |
6179
|
cjones
|
|
| 987 |
6475
|
jones
|
String localId;
|
| 988 |
7075
|
cjones
|
Identifier pid;
|
| 989 |
|
|
if ( syncFailed.getPid() != null ) {
|
| 990 |
|
|
pid = new Identifier();
|
| 991 |
|
|
pid.setValue(syncFailed.getPid());
|
| 992 |
|
|
boolean allowed;
|
| 993 |
|
|
|
| 994 |
|
|
//are we allowed? only CNs
|
| 995 |
|
|
try {
|
| 996 |
7142
|
leinfelder
|
allowed = isAdminAuthorized(session);
|
| 997 |
7075
|
cjones
|
if ( !allowed ){
|
| 998 |
|
|
throw new NotAuthorized("2162",
|
| 999 |
|
|
"Not allowed to call synchronizationFailed() on this node.");
|
| 1000 |
|
|
}
|
| 1001 |
|
|
} catch (InvalidToken e) {
|
| 1002 |
|
|
throw new NotAuthorized("2162",
|
| 1003 |
|
|
"Not allowed to call synchronizationFailed() on this node.");
|
| 1004 |
6331
|
leinfelder
|
|
| 1005 |
7075
|
cjones
|
}
|
| 1006 |
|
|
|
| 1007 |
|
|
} else {
|
| 1008 |
|
|
throw new ServiceFailure("2161", "The identifier cannot be null.");
|
| 1009 |
|
|
|
| 1010 |
|
|
}
|
| 1011 |
|
|
|
| 1012 |
6475
|
jones
|
try {
|
| 1013 |
7075
|
cjones
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 1014 |
6475
|
jones
|
} catch (McdbDocNotFoundException e) {
|
| 1015 |
7075
|
cjones
|
throw new ServiceFailure("2161", "The identifier specified by " +
|
| 1016 |
|
|
syncFailed.getPid() + " was not found on this node.");
|
| 1017 |
6179
|
cjones
|
|
| 1018 |
6475
|
jones
|
}
|
| 1019 |
|
|
// TODO: update the CN URL below when the CNRead.SynchronizationFailed
|
| 1020 |
|
|
// method is changed to include the URL as a parameter
|
| 1021 |
7075
|
cjones
|
logMetacat.debug("Synchronization for the object identified by " +
|
| 1022 |
|
|
pid.getValue() + " failed from " + syncFailed.getNodeId() +
|
| 1023 |
|
|
" Logging the event to the Metacat EventLog as a 'syncFailed' event.");
|
| 1024 |
6475
|
jones
|
// TODO: use the event type enum when the SYNCHRONIZATION_FAILED event is added
|
| 1025 |
6532
|
leinfelder
|
String principal = Constants.SUBJECT_PUBLIC;
|
| 1026 |
6506
|
leinfelder
|
if (session != null && session.getSubject() != null) {
|
| 1027 |
6575
|
cjones
|
principal = session.getSubject().getValue();
|
| 1028 |
6506
|
leinfelder
|
}
|
| 1029 |
|
|
try {
|
| 1030 |
6575
|
cjones
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "synchronization_failed");
|
| 1031 |
6506
|
leinfelder
|
} catch (Exception e) {
|
| 1032 |
7075
|
cjones
|
throw new ServiceFailure("2161", "Could not log the error for: " + pid.getValue());
|
| 1033 |
6991
|
leinfelder
|
}
|
| 1034 |
6475
|
jones
|
//EventLog.getInstance().log("CN URL WILL GO HERE",
|
| 1035 |
|
|
// session.getSubject().getValue(), localId, Event.SYNCHRONIZATION_FAILED);
|
| 1036 |
6991
|
leinfelder
|
return true;
|
| 1037 |
6179
|
cjones
|
|
| 1038 |
6260
|
cjones
|
}
|
| 1039 |
|
|
|
| 1040 |
6475
|
jones
|
/**
|
| 1041 |
|
|
* Essentially a get() but with different logging behavior
|
| 1042 |
|
|
*/
|
| 1043 |
|
|
@Override
|
| 1044 |
6540
|
cjones
|
public InputStream getReplica(Session session, Identifier pid)
|
| 1045 |
6653
|
leinfelder
|
throws NotAuthorized, NotImplemented, ServiceFailure, InvalidToken {
|
| 1046 |
6179
|
cjones
|
|
| 1047 |
6540
|
cjones
|
logMetacat.info("MNodeService.getReplica() called.");
|
| 1048 |
|
|
|
| 1049 |
6653
|
leinfelder
|
// cannot be called by public
|
| 1050 |
|
|
if (session == null) {
|
| 1051 |
|
|
throw new InvalidToken("2183", "No session was provided.");
|
| 1052 |
|
|
}
|
| 1053 |
|
|
|
| 1054 |
6631
|
cjones
|
logMetacat.info("MNodeService.getReplica() called with parameters: \n" +
|
| 1055 |
|
|
"\tSession.Subject = " + session.getSubject().getValue() + "\n" +
|
| 1056 |
|
|
"\tIdentifier = " + pid.getValue());
|
| 1057 |
|
|
|
| 1058 |
6475
|
jones
|
InputStream inputStream = null; // bytes to be returned
|
| 1059 |
|
|
handler = new MetacatHandler(new Timer());
|
| 1060 |
|
|
boolean allowed = false;
|
| 1061 |
|
|
String localId; // the metacat docid for the pid
|
| 1062 |
6179
|
cjones
|
|
| 1063 |
6475
|
jones
|
// get the local docid from Metacat
|
| 1064 |
|
|
try {
|
| 1065 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 1066 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 1067 |
6610
|
cjones
|
throw new ServiceFailure("2181", "The object specified by " +
|
| 1068 |
|
|
pid.getValue() + " does not exist at this node.");
|
| 1069 |
|
|
|
| 1070 |
6475
|
jones
|
}
|
| 1071 |
6234
|
cjones
|
|
| 1072 |
6552
|
leinfelder
|
Subject targetNodeSubject = session.getSubject();
|
| 1073 |
6185
|
leinfelder
|
|
| 1074 |
6552
|
leinfelder
|
// check for authorization to replicate, null session to act as this source MN
|
| 1075 |
6610
|
cjones
|
try {
|
| 1076 |
6777
|
leinfelder
|
allowed = D1Client.getCN().isNodeAuthorized(null, targetNodeSubject, pid);
|
| 1077 |
6610
|
cjones
|
} catch (InvalidToken e1) {
|
| 1078 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
| 1079 |
|
|
+ e1.getMessage());
|
| 1080 |
|
|
|
| 1081 |
|
|
} catch (NotFound e1) {
|
| 1082 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
| 1083 |
|
|
+ e1.getMessage());
|
| 1084 |
6384
|
cjones
|
|
| 1085 |
6610
|
cjones
|
} catch (InvalidRequest e1) {
|
| 1086 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
| 1087 |
|
|
+ e1.getMessage());
|
| 1088 |
|
|
|
| 1089 |
|
|
}
|
| 1090 |
|
|
|
| 1091 |
6540
|
cjones
|
logMetacat.info("Called D1Client.isNodeAuthorized(). Allowed = " + allowed +
|
| 1092 |
|
|
" for identifier " + pid.getValue());
|
| 1093 |
|
|
|
| 1094 |
6475
|
jones
|
// if the person is authorized, perform the read
|
| 1095 |
|
|
if (allowed) {
|
| 1096 |
|
|
try {
|
| 1097 |
6986
|
jones
|
inputStream = MetacatHandler.read(localId);
|
| 1098 |
6475
|
jones
|
} catch (Exception e) {
|
| 1099 |
6610
|
cjones
|
throw new ServiceFailure("1020", "The object specified by " +
|
| 1100 |
|
|
pid.getValue() + "could not be returned due to error: " + e.getMessage());
|
| 1101 |
6475
|
jones
|
}
|
| 1102 |
|
|
}
|
| 1103 |
6384
|
cjones
|
|
| 1104 |
6475
|
jones
|
// if we fail to set the input stream
|
| 1105 |
|
|
if (inputStream == null) {
|
| 1106 |
6610
|
cjones
|
throw new ServiceFailure("2181", "The object specified by " +
|
| 1107 |
|
|
pid.getValue() + "does not exist at this node.");
|
| 1108 |
6475
|
jones
|
}
|
| 1109 |
|
|
|
| 1110 |
|
|
// log the replica event
|
| 1111 |
|
|
String principal = null;
|
| 1112 |
|
|
if (session.getSubject() != null) {
|
| 1113 |
|
|
principal = session.getSubject().getValue();
|
| 1114 |
|
|
}
|
| 1115 |
6576
|
cjones
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
| 1116 |
|
|
request.getHeader("User-Agent"), principal, localId, "replicate");
|
| 1117 |
6475
|
jones
|
|
| 1118 |
|
|
return inputStream;
|
| 1119 |
|
|
}
|
| 1120 |
|
|
|
| 1121 |
6573
|
cjones
|
/**
|
| 1122 |
6600
|
cjones
|
* A method to notify the Member Node that the authoritative copy of
|
| 1123 |
6599
|
cjones
|
* system metadata on the Coordinating Nodes has changed.
|
| 1124 |
|
|
*
|
| 1125 |
|
|
* @param session Session information that contains the identity of the
|
| 1126 |
|
|
* calling user as retrieved from the X.509 certificate
|
| 1127 |
|
|
* which must be traceable to the CILogon service.
|
| 1128 |
|
|
* @param serialVersion The serialVersion of the system metadata
|
| 1129 |
|
|
* @param dateSysMetaLastModified The time stamp for when the system metadata was changed
|
| 1130 |
|
|
* @throws NotImplemented
|
| 1131 |
|
|
* @throws ServiceFailure
|
| 1132 |
|
|
* @throws NotAuthorized
|
| 1133 |
|
|
* @throws InvalidRequest
|
| 1134 |
|
|
* @throws InvalidToken
|
| 1135 |
|
|
*/
|
| 1136 |
6991
|
leinfelder
|
public boolean systemMetadataChanged(Session session, Identifier pid,
|
| 1137 |
6599
|
cjones
|
long serialVersion, Date dateSysMetaLastModified)
|
| 1138 |
|
|
throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest,
|
| 1139 |
|
|
InvalidToken {
|
| 1140 |
|
|
|
| 1141 |
7600
|
cjones
|
// cannot be called by public
|
| 1142 |
|
|
if (session == null) {
|
| 1143 |
|
|
throw new InvalidToken("2183", "No session was provided.");
|
| 1144 |
|
|
}
|
| 1145 |
|
|
|
| 1146 |
6600
|
cjones
|
SystemMetadata currentLocalSysMeta = null;
|
| 1147 |
|
|
SystemMetadata newSysMeta = null;
|
| 1148 |
|
|
CNode cn = D1Client.getCN();
|
| 1149 |
|
|
NodeList nodeList = null;
|
| 1150 |
|
|
Subject callingSubject = null;
|
| 1151 |
|
|
boolean allowed = false;
|
| 1152 |
|
|
|
| 1153 |
|
|
// are we allowed to call this?
|
| 1154 |
|
|
callingSubject = session.getSubject();
|
| 1155 |
|
|
nodeList = cn.listNodes();
|
| 1156 |
|
|
|
| 1157 |
|
|
for(Node node : nodeList.getNodeList()) {
|
| 1158 |
|
|
// must be a CN
|
| 1159 |
|
|
if ( node.getType().equals(NodeType.CN)) {
|
| 1160 |
|
|
List<Subject> subjectList = node.getSubjectList();
|
| 1161 |
|
|
// the calling subject must be in the subject list
|
| 1162 |
|
|
if ( subjectList.contains(callingSubject)) {
|
| 1163 |
|
|
allowed = true;
|
| 1164 |
|
|
|
| 1165 |
|
|
}
|
| 1166 |
|
|
|
| 1167 |
|
|
}
|
| 1168 |
|
|
}
|
| 1169 |
|
|
|
| 1170 |
|
|
if (!allowed ) {
|
| 1171 |
|
|
String msg = "The subject identified by " + callingSubject.getValue() +
|
| 1172 |
|
|
" is not authorized to call this service.";
|
| 1173 |
|
|
throw new NotAuthorized("1331", msg);
|
| 1174 |
|
|
|
| 1175 |
|
|
}
|
| 1176 |
|
|
|
| 1177 |
|
|
// compare what we have locally to what is sent in the change notification
|
| 1178 |
|
|
try {
|
| 1179 |
6692
|
leinfelder
|
currentLocalSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
| 1180 |
|
|
|
| 1181 |
|
|
} catch (RuntimeException e) {
|
| 1182 |
6600
|
cjones
|
String msg = "SystemMetadata for pid " + pid.getValue() +
|
| 1183 |
6692
|
leinfelder
|
" couldn't be updated because it couldn't be found locally: " +
|
| 1184 |
6600
|
cjones
|
e.getMessage();
|
| 1185 |
6692
|
leinfelder
|
logMetacat.error(msg);
|
| 1186 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
| 1187 |
|
|
sf.initCause(e);
|
| 1188 |
|
|
throw sf;
|
| 1189 |
6600
|
cjones
|
}
|
| 1190 |
|
|
|
| 1191 |
|
|
if (currentLocalSysMeta.getSerialVersion().longValue() < serialVersion ) {
|
| 1192 |
|
|
try {
|
| 1193 |
|
|
newSysMeta = cn.getSystemMetadata(null, pid);
|
| 1194 |
|
|
} catch (NotFound e) {
|
| 1195 |
|
|
// huh? you just said you had it
|
| 1196 |
6692
|
leinfelder
|
String msg = "On updating the local copy of system metadata " +
|
| 1197 |
|
|
"for pid " + pid.getValue() +", the CN reports it is not found." +
|
| 1198 |
|
|
" The error message was: " + e.getMessage();
|
| 1199 |
|
|
logMetacat.error(msg);
|
| 1200 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
| 1201 |
|
|
sf.initCause(e);
|
| 1202 |
|
|
throw sf;
|
| 1203 |
6600
|
cjones
|
}
|
| 1204 |
6692
|
leinfelder
|
|
| 1205 |
6600
|
cjones
|
// update the local copy of system metadata for the pid
|
| 1206 |
|
|
try {
|
| 1207 |
6692
|
leinfelder
|
HazelcastService.getInstance().getSystemMetadataMap().put(newSysMeta.getIdentifier(), newSysMeta);
|
| 1208 |
6600
|
cjones
|
logMetacat.info("Updated local copy of system metadata for pid " +
|
| 1209 |
|
|
pid.getValue() + " after change notification from the CN.");
|
| 1210 |
|
|
|
| 1211 |
8599
|
leinfelder
|
// TODO: consider inspecting the change for archive
|
| 1212 |
|
|
// see: https://projects.ecoinformatics.org/ecoinfo/issues/6417
|
| 1213 |
|
|
// if (newSysMeta.getArchived() != null && newSysMeta.getArchived().booleanValue()) {
|
| 1214 |
|
|
// try {
|
| 1215 |
|
|
// this.archive(session, newSysMeta.getIdentifier());
|
| 1216 |
|
|
// } catch (NotFound e) {
|
| 1217 |
|
|
// // do we care? nothing to do about it now
|
| 1218 |
|
|
// logMetacat.error(e.getMessage(), e);
|
| 1219 |
|
|
// }
|
| 1220 |
|
|
// }
|
| 1221 |
|
|
|
| 1222 |
6692
|
leinfelder
|
} catch (RuntimeException e) {
|
| 1223 |
6600
|
cjones
|
String msg = "SystemMetadata for pid " + pid.getValue() +
|
| 1224 |
6692
|
leinfelder
|
" couldn't be updated: " +
|
| 1225 |
6600
|
cjones
|
e.getMessage();
|
| 1226 |
6692
|
leinfelder
|
logMetacat.error(msg);
|
| 1227 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
| 1228 |
|
|
sf.initCause(e);
|
| 1229 |
|
|
throw sf;
|
| 1230 |
6600
|
cjones
|
}
|
| 1231 |
8464
|
leinfelder
|
|
| 1232 |
|
|
// submit for indexing
|
| 1233 |
|
|
try {
|
| 1234 |
8647
|
leinfelder
|
MetacatSolrIndex.getInstance().submit(newSysMeta.getIdentifier(), newSysMeta, null, true);
|
| 1235 |
8464
|
leinfelder
|
} catch (Exception e) {
|
| 1236 |
|
|
logMetacat.error("Could not submit changed systemMetadata for indexing, pid: " + newSysMeta.getIdentifier().getValue(), e);
|
| 1237 |
|
|
}
|
| 1238 |
6600
|
cjones
|
}
|
| 1239 |
|
|
|
| 1240 |
6991
|
leinfelder
|
return true;
|
| 1241 |
|
|
|
| 1242 |
6599
|
cjones
|
}
|
| 1243 |
|
|
|
| 1244 |
6795
|
cjones
|
/*
|
| 1245 |
|
|
* Set the replication status for the object on the Coordinating Node
|
| 1246 |
|
|
*
|
| 1247 |
|
|
* @param session - the session for the this target node
|
| 1248 |
|
|
* @param pid - the identifier of the object being updated
|
| 1249 |
|
|
* @param nodeId - the identifier of this target node
|
| 1250 |
|
|
* @param status - the replication status to set
|
| 1251 |
|
|
* @param failure - the exception to include, if any
|
| 1252 |
|
|
*/
|
| 1253 |
|
|
private void setReplicationStatus(Session session, Identifier pid,
|
| 1254 |
|
|
NodeReference nodeId, ReplicationStatus status, BaseException failure)
|
| 1255 |
|
|
throws ServiceFailure, NotImplemented, NotAuthorized,
|
| 1256 |
|
|
InvalidRequest {
|
| 1257 |
|
|
|
| 1258 |
|
|
// call the CN as the MN to set the replication status
|
| 1259 |
|
|
try {
|
| 1260 |
|
|
this.cn = D1Client.getCN();
|
| 1261 |
|
|
this.cn.setReplicationStatus(session, pid, nodeId,
|
| 1262 |
|
|
status, failure);
|
| 1263 |
|
|
|
| 1264 |
|
|
} catch (InvalidToken e) {
|
| 1265 |
7091
|
leinfelder
|
String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (InvalidToken): " + e.getMessage();
|
| 1266 |
|
|
logMetacat.error(msg);
|
| 1267 |
|
|
throw new ServiceFailure("2151",
|
| 1268 |
|
|
msg);
|
| 1269 |
6795
|
cjones
|
|
| 1270 |
|
|
} catch (NotFound e) {
|
| 1271 |
7091
|
leinfelder
|
String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (NotFound): " + e.getMessage();
|
| 1272 |
|
|
logMetacat.error(msg);
|
| 1273 |
|
|
throw new ServiceFailure("2151",
|
| 1274 |
|
|
msg);
|
| 1275 |
6795
|
cjones
|
|
| 1276 |
|
|
}
|
| 1277 |
|
|
}
|
| 1278 |
8591
|
leinfelder
|
|
| 1279 |
|
|
private SystemMetadata makePublicIfNot(SystemMetadata sysmeta, Identifier pid) throws ServiceFailure, InvalidToken, NotFound, NotImplemented, InvalidRequest {
|
| 1280 |
|
|
// check if it is publicly readable
|
| 1281 |
|
|
boolean isPublic = false;
|
| 1282 |
|
|
Subject publicSubject = new Subject();
|
| 1283 |
|
|
publicSubject.setValue(Constants.SUBJECT_PUBLIC);
|
| 1284 |
|
|
Session publicSession = new Session();
|
| 1285 |
|
|
publicSession.setSubject(publicSubject);
|
| 1286 |
|
|
AccessRule publicRule = new AccessRule();
|
| 1287 |
|
|
publicRule.addPermission(Permission.READ);
|
| 1288 |
|
|
publicRule.addSubject(publicSubject);
|
| 1289 |
|
|
|
| 1290 |
|
|
// see if we need to add the rule
|
| 1291 |
|
|
try {
|
| 1292 |
|
|
isPublic = this.isAuthorized(publicSession, pid, Permission.READ);
|
| 1293 |
|
|
} catch (NotAuthorized na) {
|
| 1294 |
|
|
// well, certainly not authorized for public read!
|
| 1295 |
|
|
}
|
| 1296 |
|
|
if (!isPublic) {
|
| 1297 |
|
|
sysmeta.getAccessPolicy().addAllow(publicRule);
|
| 1298 |
|
|
}
|
| 1299 |
|
|
|
| 1300 |
|
|
return sysmeta;
|
| 1301 |
|
|
}
|
| 1302 |
7099
|
leinfelder
|
|
| 1303 |
|
|
@Override
|
| 1304 |
7441
|
leinfelder
|
public Identifier generateIdentifier(Session session, String scheme, String fragment)
|
| 1305 |
7099
|
leinfelder
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
|
| 1306 |
|
|
InvalidRequest {
|
| 1307 |
7448
|
leinfelder
|
|
| 1308 |
8210
|
leinfelder
|
// check for null session
|
| 1309 |
|
|
if (session == null) {
|
| 1310 |
|
|
throw new InvalidToken("2190", "Session is required to generate an Identifier at this Node.");
|
| 1311 |
|
|
}
|
| 1312 |
|
|
|
| 1313 |
7441
|
leinfelder
|
Identifier identifier = new Identifier();
|
| 1314 |
7448
|
leinfelder
|
|
| 1315 |
7489
|
leinfelder
|
// handle different schemes
|
| 1316 |
|
|
if (scheme.equalsIgnoreCase(UUID_SCHEME)) {
|
| 1317 |
|
|
// UUID
|
| 1318 |
|
|
UUID uuid = UUID.randomUUID();
|
| 1319 |
|
|
identifier.setValue(UUID_PREFIX + uuid.toString());
|
| 1320 |
|
|
} else if (scheme.equalsIgnoreCase(DOI_SCHEME)) {
|
| 1321 |
7512
|
leinfelder
|
// generate a DOI
|
| 1322 |
7448
|
leinfelder
|
try {
|
| 1323 |
7512
|
leinfelder
|
identifier = DOIService.getInstance().generateDOI();
|
| 1324 |
7448
|
leinfelder
|
} catch (EZIDException e) {
|
| 1325 |
7512
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("2191", "Could not generate DOI: " + e.getMessage());
|
| 1326 |
|
|
sf.initCause(e);
|
| 1327 |
|
|
throw sf;
|
| 1328 |
7448
|
leinfelder
|
}
|
| 1329 |
7489
|
leinfelder
|
} else {
|
| 1330 |
|
|
// default if we don't know the scheme
|
| 1331 |
|
|
if (fragment != null) {
|
| 1332 |
|
|
// for now, just autogen with fragment
|
| 1333 |
|
|
String autogenId = DocumentUtil.generateDocumentId(fragment, 0);
|
| 1334 |
|
|
identifier.setValue(autogenId);
|
| 1335 |
|
|
} else {
|
| 1336 |
|
|
// autogen with no fragment
|
| 1337 |
|
|
String autogenId = DocumentUtil.generateDocumentId(0);
|
| 1338 |
|
|
identifier.setValue(autogenId);
|
| 1339 |
|
|
}
|
| 1340 |
7448
|
leinfelder
|
}
|
| 1341 |
|
|
|
| 1342 |
7441
|
leinfelder
|
// TODO: reserve the identifier with the CN. We can only do this when
|
| 1343 |
|
|
// 1) the MN is part of a CN cluster
|
| 1344 |
|
|
// 2) the request is from an authenticated user
|
| 1345 |
|
|
|
| 1346 |
|
|
return identifier;
|
| 1347 |
7099
|
leinfelder
|
}
|
| 1348 |
7144
|
leinfelder
|
|
| 1349 |
8810
|
leinfelder
|
|
| 1350 |
7144
|
leinfelder
|
|
| 1351 |
|
|
@Override
|
| 1352 |
8810
|
leinfelder
|
public QueryEngineDescription getQueryEngineDescription(Session session, String engine)
|
| 1353 |
7144
|
leinfelder
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
|
| 1354 |
|
|
NotFound {
|
| 1355 |
7772
|
tao
|
if(engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1356 |
8162
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1357 |
|
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1358 |
|
|
}
|
| 1359 |
7634
|
tao
|
QueryEngineDescription qed = new QueryEngineDescription();
|
| 1360 |
7772
|
tao
|
qed.setName(EnabledQueryEngines.PATHQUERYENGINE);
|
| 1361 |
7634
|
tao
|
qed.setQueryEngineVersion("1.0");
|
| 1362 |
|
|
qed.addAdditionalInfo("This is the traditional structured query for Metacat");
|
| 1363 |
|
|
Vector<String> pathsForIndexing = null;
|
| 1364 |
|
|
try {
|
| 1365 |
|
|
pathsForIndexing = SystemUtil.getPathsForIndexing();
|
| 1366 |
|
|
} catch (MetacatUtilException e) {
|
| 1367 |
|
|
logMetacat.warn("Could not get index paths", e);
|
| 1368 |
|
|
}
|
| 1369 |
|
|
for (String fieldName: pathsForIndexing) {
|
| 1370 |
|
|
QueryField field = new QueryField();
|
| 1371 |
|
|
field.addDescription("Indexed field for path '" + fieldName + "'");
|
| 1372 |
|
|
field.setName(fieldName);
|
| 1373 |
|
|
field.setReturnable(true);
|
| 1374 |
|
|
field.setSearchable(true);
|
| 1375 |
|
|
field.setSortable(false);
|
| 1376 |
|
|
// TODO: determine type and multivaluedness
|
| 1377 |
|
|
field.setType(String.class.getName());
|
| 1378 |
|
|
//field.setMultivalued(true);
|
| 1379 |
|
|
qed.addQueryField(field);
|
| 1380 |
|
|
}
|
| 1381 |
|
|
return qed;
|
| 1382 |
7772
|
tao
|
} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
|
| 1383 |
7781
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
|
| 1384 |
7772
|
tao
|
throw new NotImplemented("0000", "MNodeService.getQueryEngineDescription - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1385 |
7781
|
tao
|
}
|
| 1386 |
7634
|
tao
|
try {
|
| 1387 |
7662
|
tao
|
QueryEngineDescription qed = MetacatSolrEngineDescriptionHandler.getInstance().getQueryEngineDescritpion();
|
| 1388 |
7634
|
tao
|
return qed;
|
| 1389 |
|
|
} catch (Exception e) {
|
| 1390 |
|
|
e.printStackTrace();
|
| 1391 |
|
|
throw new ServiceFailure("Solr server error", e.getMessage());
|
| 1392 |
|
|
}
|
| 1393 |
|
|
} else {
|
| 1394 |
|
|
throw new NotFound("404", "The Metacat member node can't find the query engine - "+engine);
|
| 1395 |
|
|
}
|
| 1396 |
|
|
|
| 1397 |
7417
|
leinfelder
|
}
|
| 1398 |
|
|
|
| 1399 |
|
|
@Override
|
| 1400 |
8810
|
leinfelder
|
public QueryEngineList listQueryEngines(Session session) throws InvalidToken,
|
| 1401 |
7417
|
leinfelder
|
ServiceFailure, NotAuthorized, NotImplemented {
|
| 1402 |
|
|
QueryEngineList qel = new QueryEngineList();
|
| 1403 |
7781
|
tao
|
//qel.addQueryEngine(EnabledQueryEngines.PATHQUERYENGINE);
|
| 1404 |
|
|
//qel.addQueryEngine(EnabledQueryEngines.SOLRENGINE);
|
| 1405 |
|
|
List<String> enables = EnabledQueryEngines.getInstance().getEnabled();
|
| 1406 |
7772
|
tao
|
for(String name : enables) {
|
| 1407 |
|
|
qel.addQueryEngine(name);
|
| 1408 |
7781
|
tao
|
}
|
| 1409 |
7417
|
leinfelder
|
return qel;
|
| 1410 |
|
|
}
|
| 1411 |
|
|
|
| 1412 |
|
|
@Override
|
| 1413 |
8810
|
leinfelder
|
public InputStream query(Session session, String engine, String query) throws InvalidToken,
|
| 1414 |
7417
|
leinfelder
|
ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented,
|
| 1415 |
|
|
NotFound {
|
| 1416 |
7648
|
tao
|
String user = Constants.SUBJECT_PUBLIC;
|
| 1417 |
|
|
String[] groups= null;
|
| 1418 |
7680
|
tao
|
Set<Subject> subjects = null;
|
| 1419 |
7648
|
tao
|
if (session != null) {
|
| 1420 |
|
|
user = session.getSubject().getValue();
|
| 1421 |
7680
|
tao
|
subjects = AuthUtils.authorizedClientSubjects(session);
|
| 1422 |
7648
|
tao
|
if (subjects != null) {
|
| 1423 |
|
|
List<String> groupList = new ArrayList<String>();
|
| 1424 |
|
|
for (Subject subject: subjects) {
|
| 1425 |
|
|
groupList.add(subject.getValue());
|
| 1426 |
|
|
}
|
| 1427 |
|
|
groups = groupList.toArray(new String[0]);
|
| 1428 |
|
|
}
|
| 1429 |
7680
|
tao
|
} else {
|
| 1430 |
|
|
//add the public user subject to the set
|
| 1431 |
|
|
Subject subject = new Subject();
|
| 1432 |
|
|
subject.setValue(Constants.SUBJECT_PUBLIC);
|
| 1433 |
7757
|
leinfelder
|
subjects = new HashSet<Subject>();
|
| 1434 |
7680
|
tao
|
subjects.add(subject);
|
| 1435 |
7648
|
tao
|
}
|
| 1436 |
7680
|
tao
|
//System.out.println("====== user is "+user);
|
| 1437 |
|
|
//System.out.println("====== groups are "+groups);
|
| 1438 |
7772
|
tao
|
if (engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1439 |
8162
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1440 |
|
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1441 |
|
|
}
|
| 1442 |
7417
|
leinfelder
|
try {
|
| 1443 |
|
|
DBQuery queryobj = new DBQuery();
|
| 1444 |
7648
|
tao
|
|
| 1445 |
7417
|
leinfelder
|
String results = queryobj.performPathquery(query, user, groups);
|
| 1446 |
7757
|
leinfelder
|
ContentTypeByteArrayInputStream ctbais = new ContentTypeByteArrayInputStream(results.getBytes(MetaCatServlet.DEFAULT_ENCODING));
|
| 1447 |
|
|
ctbais.setContentType("text/xml");
|
| 1448 |
|
|
return ctbais;
|
| 1449 |
7417
|
leinfelder
|
|
| 1450 |
|
|
} catch (Exception e) {
|
| 1451 |
7757
|
leinfelder
|
throw new ServiceFailure("Pathquery error", e.getMessage());
|
| 1452 |
7417
|
leinfelder
|
}
|
| 1453 |
|
|
|
| 1454 |
7772
|
tao
|
} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
|
| 1455 |
7781
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
|
| 1456 |
7772
|
tao
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1457 |
7781
|
tao
|
}
|
| 1458 |
7634
|
tao
|
logMetacat.info("The query is ==================================== \n"+query);
|
| 1459 |
7620
|
tao
|
try {
|
| 1460 |
7634
|
tao
|
|
| 1461 |
7680
|
tao
|
return MetacatSolrIndex.getInstance().query(query, subjects);
|
| 1462 |
7620
|
tao
|
} catch (Exception e) {
|
| 1463 |
|
|
// TODO Auto-generated catch block
|
| 1464 |
|
|
throw new ServiceFailure("Solr server error", e.getMessage());
|
| 1465 |
|
|
}
|
| 1466 |
7417
|
leinfelder
|
}
|
| 1467 |
|
|
return null;
|
| 1468 |
|
|
}
|
| 1469 |
7849
|
leinfelder
|
|
| 1470 |
|
|
/**
|
| 1471 |
|
|
* Given an existing Science Metadata PID, this method mints a DOI
|
| 1472 |
|
|
* and updates the original object "publishing" the update with the DOI.
|
| 1473 |
|
|
* This includes updating the ORE map that describes the Science Metadata+data.
|
| 1474 |
|
|
* TODO: ensure all referenced objects allow public read
|
| 1475 |
|
|
*
|
| 1476 |
|
|
* @see https://projects.ecoinformatics.org/ecoinfo/issues/6014
|
| 1477 |
|
|
*
|
| 1478 |
|
|
* @param originalIdentifier
|
| 1479 |
|
|
* @param request
|
| 1480 |
7864
|
leinfelder
|
* @throws InvalidRequest
|
| 1481 |
|
|
* @throws NotImplemented
|
| 1482 |
|
|
* @throws NotAuthorized
|
| 1483 |
|
|
* @throws ServiceFailure
|
| 1484 |
|
|
* @throws InvalidToken
|
| 1485 |
7849
|
leinfelder
|
* @throws NotFound
|
| 1486 |
7864
|
leinfelder
|
* @throws InvalidSystemMetadata
|
| 1487 |
|
|
* @throws InsufficientResources
|
| 1488 |
|
|
* @throws UnsupportedType
|
| 1489 |
|
|
* @throws IdentifierNotUnique
|
| 1490 |
7849
|
leinfelder
|
*/
|
| 1491 |
7864
|
leinfelder
|
public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata {
|
| 1492 |
7849
|
leinfelder
|
|
| 1493 |
8141
|
leinfelder
|
|
| 1494 |
|
|
// get the original SM
|
| 1495 |
|
|
SystemMetadata originalSystemMetadata = this.getSystemMetadata(session, originalIdentifier);
|
| 1496 |
|
|
|
| 1497 |
8594
|
leinfelder
|
// make copy of it using the marshaller to ensure DEEP copy
|
| 1498 |
|
|
SystemMetadata sysmeta = null;
|
| 1499 |
8141
|
leinfelder
|
try {
|
| 1500 |
8594
|
leinfelder
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 1501 |
|
|
TypeMarshaller.marshalTypeToOutputStream(originalSystemMetadata, baos);
|
| 1502 |
|
|
sysmeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
|
| 1503 |
8141
|
leinfelder
|
} catch (Exception e) {
|
| 1504 |
|
|
// report as service failure
|
| 1505 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1506 |
|
|
sf.initCause(e);
|
| 1507 |
|
|
throw sf;
|
| 1508 |
|
|
}
|
| 1509 |
|
|
|
| 1510 |
7849
|
leinfelder
|
// mint a DOI for the new revision
|
| 1511 |
|
|
Identifier newIdentifier = this.generateIdentifier(session, MNodeService.DOI_SCHEME, null);
|
| 1512 |
8141
|
leinfelder
|
|
| 1513 |
|
|
// set new metadata values
|
| 1514 |
7849
|
leinfelder
|
sysmeta.setIdentifier(newIdentifier);
|
| 1515 |
|
|
sysmeta.setObsoletes(originalIdentifier);
|
| 1516 |
|
|
sysmeta.setObsoletedBy(null);
|
| 1517 |
|
|
|
| 1518 |
8591
|
leinfelder
|
// ensure it is publicly readable
|
| 1519 |
|
|
sysmeta = makePublicIfNot(sysmeta, originalIdentifier);
|
| 1520 |
|
|
|
| 1521 |
7849
|
leinfelder
|
// get the bytes
|
| 1522 |
|
|
InputStream inputStream = this.get(session, originalIdentifier);
|
| 1523 |
|
|
|
| 1524 |
|
|
// update the object
|
| 1525 |
7864
|
leinfelder
|
this.update(session, originalIdentifier, inputStream, newIdentifier, sysmeta);
|
| 1526 |
7849
|
leinfelder
|
|
| 1527 |
7864
|
leinfelder
|
// update ORE that references the scimeta
|
| 1528 |
8190
|
leinfelder
|
// first try the naive method, then check the SOLR index
|
| 1529 |
7849
|
leinfelder
|
try {
|
| 1530 |
7864
|
leinfelder
|
String localId = IdentifierManager.getInstance().getLocalId(originalIdentifier.getValue());
|
| 1531 |
7849
|
leinfelder
|
|
| 1532 |
7864
|
leinfelder
|
Identifier potentialOreIdentifier = new Identifier();
|
| 1533 |
|
|
potentialOreIdentifier.setValue(SystemMetadataFactory.RESOURCE_MAP_PREFIX + localId);
|
| 1534 |
7849
|
leinfelder
|
|
| 1535 |
7864
|
leinfelder
|
InputStream oreInputStream = null;
|
| 1536 |
|
|
try {
|
| 1537 |
|
|
oreInputStream = this.get(session, potentialOreIdentifier);
|
| 1538 |
|
|
} catch (NotFound nf) {
|
| 1539 |
|
|
// this is probably okay for many sci meta data docs
|
| 1540 |
|
|
logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
|
| 1541 |
8190
|
leinfelder
|
// try the SOLR index
|
| 1542 |
8200
|
leinfelder
|
List<Identifier> potentialOreIdentifiers = this.lookupOreFor(originalIdentifier, false);
|
| 1543 |
8190
|
leinfelder
|
if (potentialOreIdentifiers != null) {
|
| 1544 |
|
|
potentialOreIdentifier = potentialOreIdentifiers.get(0);
|
| 1545 |
|
|
try {
|
| 1546 |
|
|
oreInputStream = this.get(session, potentialOreIdentifier);
|
| 1547 |
|
|
} catch (NotFound nf2) {
|
| 1548 |
|
|
// this is probably okay for many sci meta data docs
|
| 1549 |
|
|
logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
|
| 1550 |
|
|
}
|
| 1551 |
|
|
}
|
| 1552 |
7864
|
leinfelder
|
}
|
| 1553 |
|
|
if (oreInputStream != null) {
|
| 1554 |
|
|
Identifier newOreIdentifier = MNodeService.getInstance(request).generateIdentifier(session, MNodeService.UUID_SCHEME, null);
|
| 1555 |
|
|
|
| 1556 |
|
|
Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
|
| 1557 |
|
|
Map<Identifier, List<Identifier>> sciMetaMap = resourceMapStructure.get(potentialOreIdentifier);
|
| 1558 |
|
|
List<Identifier> dataIdentifiers = sciMetaMap.get(originalIdentifier);
|
| 1559 |
8591
|
leinfelder
|
|
| 1560 |
7864
|
leinfelder
|
// reconstruct the ORE with the new identifiers
|
| 1561 |
|
|
sciMetaMap.remove(originalIdentifier);
|
| 1562 |
|
|
sciMetaMap.put(newIdentifier, dataIdentifiers);
|
| 1563 |
|
|
|
| 1564 |
|
|
ResourceMap resourceMap = ResourceMapFactory.getInstance().createResourceMap(newOreIdentifier, sciMetaMap);
|
| 1565 |
|
|
String resourceMapString = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);
|
| 1566 |
|
|
|
| 1567 |
|
|
// get the original ORE SM and update the values
|
| 1568 |
8141
|
leinfelder
|
SystemMetadata originalOreSysMeta = this.getSystemMetadata(session, potentialOreIdentifier);
|
| 1569 |
|
|
SystemMetadata oreSysMeta = new SystemMetadata();
|
| 1570 |
|
|
try {
|
| 1571 |
8594
|
leinfelder
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 1572 |
|
|
TypeMarshaller.marshalTypeToOutputStream(originalOreSysMeta, baos);
|
| 1573 |
|
|
oreSysMeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
|
| 1574 |
8141
|
leinfelder
|
} catch (Exception e) {
|
| 1575 |
|
|
// report as service failure
|
| 1576 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1577 |
|
|
sf.initCause(e);
|
| 1578 |
|
|
throw sf;
|
| 1579 |
|
|
}
|
| 1580 |
|
|
|
| 1581 |
7864
|
leinfelder
|
oreSysMeta.setIdentifier(newOreIdentifier);
|
| 1582 |
|
|
oreSysMeta.setObsoletes(potentialOreIdentifier);
|
| 1583 |
|
|
oreSysMeta.setObsoletedBy(null);
|
| 1584 |
|
|
oreSysMeta.setSize(BigInteger.valueOf(resourceMapString.getBytes("UTF-8").length));
|
| 1585 |
|
|
oreSysMeta.setChecksum(ChecksumUtil.checksum(resourceMapString.getBytes("UTF-8"), oreSysMeta.getChecksum().getAlgorithm()));
|
| 1586 |
|
|
|
| 1587 |
8591
|
leinfelder
|
// ensure ORE is publicly readable
|
| 1588 |
8594
|
leinfelder
|
oreSysMeta = makePublicIfNot(oreSysMeta, potentialOreIdentifier);
|
| 1589 |
8591
|
leinfelder
|
|
| 1590 |
|
|
// ensure all data objects allow public read
|
| 1591 |
|
|
List<String> pidsToSync = new ArrayList<String>();
|
| 1592 |
|
|
for (Identifier dataId: dataIdentifiers) {
|
| 1593 |
|
|
SystemMetadata dataSysMeta = this.getSystemMetadata(session, dataId);
|
| 1594 |
|
|
dataSysMeta = makePublicIfNot(dataSysMeta, dataId);
|
| 1595 |
|
|
this.updateSystemMetadata(dataSysMeta);
|
| 1596 |
|
|
pidsToSync.add(dataId.getValue());
|
| 1597 |
|
|
}
|
| 1598 |
|
|
SyncAccessPolicy sap = new SyncAccessPolicy();
|
| 1599 |
|
|
try {
|
| 1600 |
|
|
sap.sync(pidsToSync);
|
| 1601 |
|
|
} catch (Exception e) {
|
| 1602 |
|
|
// ignore
|
| 1603 |
|
|
logMetacat.warn("Error attempting to sync access for data objects when publishing package");
|
| 1604 |
|
|
}
|
| 1605 |
|
|
|
| 1606 |
7864
|
leinfelder
|
// save the updated ORE
|
| 1607 |
|
|
this.update(
|
| 1608 |
|
|
session,
|
| 1609 |
|
|
potentialOreIdentifier,
|
| 1610 |
|
|
new ByteArrayInputStream(resourceMapString.getBytes("UTF-8")),
|
| 1611 |
|
|
newOreIdentifier,
|
| 1612 |
|
|
oreSysMeta);
|
| 1613 |
|
|
|
| 1614 |
8362
|
leinfelder
|
} else {
|
| 1615 |
|
|
// create a new ORE for them
|
| 1616 |
|
|
// https://projects.ecoinformatics.org/ecoinfo/issues/6194
|
| 1617 |
|
|
try {
|
| 1618 |
|
|
// find the local id for the NEW package.
|
| 1619 |
|
|
String newLocalId = IdentifierManager.getInstance().getLocalId(newIdentifier.getValue());
|
| 1620 |
|
|
|
| 1621 |
|
|
@SuppressWarnings("unused")
|
| 1622 |
|
|
SystemMetadata extraSysMeta = SystemMetadataFactory.createSystemMetadata(newLocalId, true, false);
|
| 1623 |
8591
|
leinfelder
|
// should be done generating the ORE here, and the same permissions were used from the metadata object
|
| 1624 |
8362
|
leinfelder
|
|
| 1625 |
|
|
} catch (Exception e) {
|
| 1626 |
|
|
// oops, guess there was a problem - no package for you
|
| 1627 |
|
|
logMetacat.error("Could not generate new ORE for published object: " + newIdentifier.getValue(), e);
|
| 1628 |
|
|
}
|
| 1629 |
7864
|
leinfelder
|
}
|
| 1630 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 1631 |
|
|
// report as service failure
|
| 1632 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1633 |
|
|
sf.initCause(e);
|
| 1634 |
|
|
throw sf;
|
| 1635 |
|
|
} catch (UnsupportedEncodingException e) {
|
| 1636 |
|
|
// report as service failure
|
| 1637 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1638 |
|
|
sf.initCause(e);
|
| 1639 |
|
|
throw sf;
|
| 1640 |
|
|
} catch (OREException e) {
|
| 1641 |
|
|
// report as service failure
|
| 1642 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1643 |
|
|
sf.initCause(e);
|
| 1644 |
|
|
throw sf;
|
| 1645 |
|
|
} catch (URISyntaxException e) {
|
| 1646 |
|
|
// report as service failure
|
| 1647 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1648 |
|
|
sf.initCause(e);
|
| 1649 |
|
|
throw sf;
|
| 1650 |
|
|
} catch (OREParserException e) {
|
| 1651 |
|
|
// report as service failure
|
| 1652 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1653 |
|
|
sf.initCause(e);
|
| 1654 |
|
|
throw sf;
|
| 1655 |
|
|
} catch (ORESerialiserException e) {
|
| 1656 |
|
|
// report as service failure
|
| 1657 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1658 |
|
|
sf.initCause(e);
|
| 1659 |
|
|
throw sf;
|
| 1660 |
|
|
} catch (NoSuchAlgorithmException e) {
|
| 1661 |
|
|
// report as service failure
|
| 1662 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1663 |
|
|
sf.initCause(e);
|
| 1664 |
|
|
throw sf;
|
| 1665 |
7849
|
leinfelder
|
}
|
| 1666 |
|
|
|
| 1667 |
|
|
return newIdentifier;
|
| 1668 |
|
|
}
|
| 1669 |
7850
|
leinfelder
|
|
| 1670 |
|
|
/**
|
| 1671 |
8190
|
leinfelder
|
* Determines if we already have registered an ORE map for this package
|
| 1672 |
|
|
* NOTE: uses a solr query to locate OREs for the object
|
| 1673 |
|
|
* @param guid of the EML/packaging object
|
| 1674 |
|
|
* @return list of resource map identifiers for the given pid
|
| 1675 |
|
|
*/
|
| 1676 |
8200
|
leinfelder
|
public List<Identifier> lookupOreFor(Identifier guid, boolean includeObsolete) {
|
| 1677 |
8190
|
leinfelder
|
// Search for the ORE if we can find it
|
| 1678 |
|
|
String pid = guid.getValue();
|
| 1679 |
|
|
List<Identifier> retList = null;
|
| 1680 |
|
|
try {
|
| 1681 |
8745
|
leinfelder
|
String query = "fl=id,resourceMap&wt=xml&q=-obsoletedBy:[* TO *]+resourceMap:[* TO *]+id:\"" + pid + "\"";
|
| 1682 |
8200
|
leinfelder
|
if (includeObsolete) {
|
| 1683 |
8745
|
leinfelder
|
query = "fl=id,resourceMap&wt=xml&q=resourceMap:[* TO *]+id:\"" + pid + "\"";
|
| 1684 |
8200
|
leinfelder
|
}
|
| 1685 |
|
|
|
| 1686 |
8810
|
leinfelder
|
InputStream results = this.query(null, "solr", query);
|
| 1687 |
8190
|
leinfelder
|
org.w3c.dom.Node rootNode = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new InputStreamReader(results, "UTF-8"));
|
| 1688 |
|
|
//String resultString = XMLUtilities.getDOMTreeAsString(rootNode);
|
| 1689 |
|
|
org.w3c.dom.NodeList nodeList = XMLUtilities.getNodeListWithXPath(rootNode, "//arr[@name=\"resourceMap\"]/str");
|
| 1690 |
|
|
if (nodeList != null && nodeList.getLength() > 0) {
|
| 1691 |
|
|
retList = new ArrayList<Identifier>();
|
| 1692 |
|
|
for (int i = 0; i < nodeList.getLength(); i++) {
|
| 1693 |
|
|
String found = nodeList.item(i).getFirstChild().getNodeValue();
|
| 1694 |
|
|
Identifier oreId = new Identifier();
|
| 1695 |
|
|
oreId.setValue(found);
|
| 1696 |
|
|
retList.add(oreId);
|
| 1697 |
|
|
}
|
| 1698 |
|
|
}
|
| 1699 |
|
|
} catch (Exception e) {
|
| 1700 |
|
|
logMetacat.error("Error checking for resourceMap[s] on pid " + pid + ". " + e.getMessage(), e);
|
| 1701 |
|
|
}
|
| 1702 |
|
|
|
| 1703 |
|
|
return retList;
|
| 1704 |
|
|
}
|
| 1705 |
|
|
|
| 1706 |
8810
|
leinfelder
|
|
| 1707 |
|
|
@Override
|
| 1708 |
|
|
public InputStream getPackage(Session session, ObjectFormatIdentifier formatId,
|
| 1709 |
|
|
Identifier pid) throws InvalidToken, ServiceFailure,
|
| 1710 |
|
|
NotAuthorized, InvalidRequest, NotImplemented, NotFound {
|
| 1711 |
7850
|
leinfelder
|
InputStream bagInputStream = null;
|
| 1712 |
|
|
BagFactory bagFactory = new BagFactory();
|
| 1713 |
|
|
Bag bag = bagFactory.createBag();
|
| 1714 |
|
|
|
| 1715 |
|
|
// track the temp files we use so we can delete them when finished
|
| 1716 |
|
|
List<File> tempFiles = new ArrayList<File>();
|
| 1717 |
|
|
|
| 1718 |
|
|
// the pids to include in the package
|
| 1719 |
|
|
List<Identifier> packagePids = new ArrayList<Identifier>();
|
| 1720 |
|
|
|
| 1721 |
7855
|
leinfelder
|
// catch non-D1 service errors and throw as ServiceFailures
|
| 1722 |
|
|
try {
|
| 1723 |
8437
|
walker
|
//Create a map of dataone ids and file names
|
| 1724 |
|
|
Map<Identifier, String> fileNames = new HashMap<Identifier, String>();
|
| 1725 |
7855
|
leinfelder
|
|
| 1726 |
8800
|
leinfelder
|
// track the pid-to-file mapping
|
| 1727 |
|
|
StringBuffer pidMapping = new StringBuffer();
|
| 1728 |
|
|
|
| 1729 |
7855
|
leinfelder
|
// find the package contents
|
| 1730 |
|
|
SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
|
| 1731 |
8025
|
leinfelder
|
if (ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId()).getFormatType().equals("RESOURCE")) {
|
| 1732 |
8437
|
walker
|
//Get the resource map as a map of Identifiers
|
| 1733 |
7855
|
leinfelder
|
InputStream oreInputStream = this.get(session, pid);
|
| 1734 |
|
|
Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
|
| 1735 |
|
|
packagePids.addAll(resourceMapStructure.keySet());
|
| 1736 |
8437
|
walker
|
//Loop through each object in this resource map
|
| 1737 |
7855
|
leinfelder
|
for (Map<Identifier, List<Identifier>> entries: resourceMapStructure.values()) {
|
| 1738 |
8437
|
walker
|
//Loop through each metadata object in this entry
|
| 1739 |
|
|
Set<Identifier> metadataIdentifiers = entries.keySet();
|
| 1740 |
|
|
for(Identifier metadataID: metadataIdentifiers){
|
| 1741 |
|
|
try{
|
| 1742 |
|
|
//Get the system metadata for this metadata object
|
| 1743 |
|
|
SystemMetadata metadataSysMeta = this.getSystemMetadata(session, metadataID);
|
| 1744 |
|
|
|
| 1745 |
8800
|
leinfelder
|
// include user-friendly metadata
|
| 1746 |
|
|
if (ObjectFormatCache.getInstance().getFormat(metadataSysMeta.getFormatId()).getFormatType().equals("METADATA")) {
|
| 1747 |
|
|
InputStream metadataStream = this.get(session, metadataID);
|
| 1748 |
|
|
|
| 1749 |
|
|
try {
|
| 1750 |
|
|
// transform
|
| 1751 |
|
|
String format = "default";
|
| 1752 |
|
|
|
| 1753 |
|
|
DBTransform transformer = new DBTransform();
|
| 1754 |
|
|
String documentContent = IOUtils.toString(metadataStream, "UTF-8");
|
| 1755 |
|
|
String sourceType = metadataSysMeta.getFormatId().getValue();
|
| 1756 |
|
|
String targetType = "-//W3C//HTML//EN";
|
| 1757 |
|
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 1758 |
|
|
Writer writer = new OutputStreamWriter(baos , "UTF-8");
|
| 1759 |
|
|
// TODO: include more params?
|
| 1760 |
|
|
Hashtable<String, String[]> params = new Hashtable<String, String[]>();
|
| 1761 |
|
|
String localId = null;
|
| 1762 |
|
|
try {
|
| 1763 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 1764 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 1765 |
|
|
throw new NotFound("1020", e.getMessage());
|
| 1766 |
|
|
}
|
| 1767 |
|
|
params.put("qformat", new String[] {format});
|
| 1768 |
|
|
params.put("docid", new String[] {localId});
|
| 1769 |
|
|
params.put("pid", new String[] {pid.getValue()});
|
| 1770 |
|
|
params.put("displaymodule", new String[] {"printall"});
|
| 1771 |
|
|
|
| 1772 |
|
|
transformer.transformXMLDocument(
|
| 1773 |
|
|
documentContent ,
|
| 1774 |
|
|
sourceType,
|
| 1775 |
|
|
targetType ,
|
| 1776 |
|
|
format,
|
| 1777 |
|
|
writer,
|
| 1778 |
|
|
params,
|
| 1779 |
|
|
null //sessionid
|
| 1780 |
|
|
);
|
| 1781 |
|
|
|
| 1782 |
|
|
// finally, get the HTML back
|
| 1783 |
|
|
ContentTypeByteArrayInputStream resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
|
| 1784 |
|
|
|
| 1785 |
|
|
// write to temp file with correct css path
|
| 1786 |
|
|
File tmpDir = File.createTempFile("package_", "_dir");
|
| 1787 |
|
|
tmpDir.delete();
|
| 1788 |
|
|
tmpDir.mkdir();
|
| 1789 |
|
|
File htmlFile = File.createTempFile("metadata", ".html", tmpDir);
|
| 1790 |
|
|
File cssDir = new File(tmpDir, format);
|
| 1791 |
|
|
cssDir.mkdir();
|
| 1792 |
|
|
File cssFile = new File(tmpDir, format + "/" + format + ".css");
|
| 1793 |
|
|
String pdfFileName = metadataID.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-METADATA.pdf";
|
| 1794 |
|
|
File pdfFile = new File(tmpDir, pdfFileName);
|
| 1795 |
|
|
//File pdfFile = File.createTempFile("metadata", ".pdf", tmpDir);
|
| 1796 |
|
|
|
| 1797 |
|
|
// put the CSS file in place for the html to find it
|
| 1798 |
|
|
String originalCssPath = SystemUtil.getContextDir() + "/style/skins/" + format + "/" + format + ".css";
|
| 1799 |
|
|
IOUtils.copy(new FileInputStream(originalCssPath), new FileOutputStream(cssFile));
|
| 1800 |
|
|
|
| 1801 |
|
|
// write the HTML file
|
| 1802 |
|
|
IOUtils.copy(resultInputStream, new FileOutputStream(htmlFile));
|
| 1803 |
|
|
|
| 1804 |
|
|
// convert to PDF
|
| 1805 |
|
|
HtmlToPdf.export(htmlFile.getAbsolutePath(), pdfFile.getAbsolutePath());
|
| 1806 |
|
|
|
| 1807 |
|
|
//add to the package
|
| 1808 |
|
|
bag.addFileToPayload(pdfFile);
|
| 1809 |
|
|
pidMapping.append(metadataID.getValue() + " (pdf)" + "\t" + "data/" + pdfFile.getName() + "\n");
|
| 1810 |
|
|
|
| 1811 |
|
|
// mark for clean up after we are done
|
| 1812 |
|
|
htmlFile.delete();
|
| 1813 |
|
|
cssFile.delete();
|
| 1814 |
|
|
cssDir.delete();
|
| 1815 |
|
|
tempFiles.add(tmpDir);
|
| 1816 |
|
|
tempFiles.add(pdfFile); // delete this first later on
|
| 1817 |
|
|
|
| 1818 |
|
|
} catch (Exception e) {
|
| 1819 |
|
|
logMetacat.warn("Could not transform metadata", e);
|
| 1820 |
|
|
}
|
| 1821 |
|
|
}
|
| 1822 |
|
|
|
| 1823 |
|
|
|
| 1824 |
8437
|
walker
|
//If this is in eml format, extract the filename and GUID from each entity in its package
|
| 1825 |
|
|
if (metadataSysMeta.getFormatId().getValue().startsWith("eml://")) {
|
| 1826 |
|
|
//Get the package
|
| 1827 |
|
|
DataPackageParserInterface parser = new Eml200DataPackageParser();
|
| 1828 |
|
|
InputStream emlStream = this.get(session, metadataID);
|
| 1829 |
|
|
parser.parse(emlStream);
|
| 1830 |
|
|
DataPackage dataPackage = parser.getDataPackage();
|
| 1831 |
|
|
|
| 1832 |
|
|
//Get all the entities in this package and loop through each to extract its ID and file name
|
| 1833 |
|
|
Entity[] entities = dataPackage.getEntityList();
|
| 1834 |
|
|
for(Entity entity: entities){
|
| 1835 |
|
|
try{
|
| 1836 |
|
|
//Get the file name from the metadata
|
| 1837 |
|
|
String fileNameFromMetadata = entity.getName();
|
| 1838 |
|
|
|
| 1839 |
|
|
//Get the ecogrid URL from the metadata
|
| 1840 |
|
|
String ecogridIdentifier = entity.getEntityIdentifier();
|
| 1841 |
|
|
//Parse the ecogrid URL to get the local id
|
| 1842 |
|
|
String idFromMetadata = DocumentUtil.getAccessionNumberFromEcogridIdentifier(ecogridIdentifier);
|
| 1843 |
|
|
|
| 1844 |
|
|
//Get the docid and rev pair
|
| 1845 |
|
|
String docid = DocumentUtil.getDocIdFromString(idFromMetadata);
|
| 1846 |
|
|
String rev = DocumentUtil.getRevisionStringFromString(idFromMetadata);
|
| 1847 |
|
|
|
| 1848 |
|
|
//Get the GUID
|
| 1849 |
|
|
String guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(rev));
|
| 1850 |
|
|
Identifier dataIdentifier = new Identifier();
|
| 1851 |
|
|
dataIdentifier.setValue(guid);
|
| 1852 |
|
|
|
| 1853 |
|
|
//Add the GUID to our GUID & file name map
|
| 1854 |
|
|
fileNames.put(dataIdentifier, fileNameFromMetadata);
|
| 1855 |
|
|
}
|
| 1856 |
|
|
catch(Exception e){
|
| 1857 |
|
|
//Prevent just one entity error
|
| 1858 |
|
|
e.printStackTrace();
|
| 1859 |
|
|
logMetacat.debug(e.getMessage(), e);
|
| 1860 |
|
|
}
|
| 1861 |
|
|
}
|
| 1862 |
|
|
}
|
| 1863 |
|
|
}
|
| 1864 |
|
|
catch(Exception e){
|
| 1865 |
|
|
//Catch errors that would prevent package download
|
| 1866 |
|
|
logMetacat.debug(e.toString());
|
| 1867 |
|
|
}
|
| 1868 |
|
|
}
|
| 1869 |
7855
|
leinfelder
|
packagePids.addAll(entries.keySet());
|
| 1870 |
|
|
for (List<Identifier> dataPids: entries.values()) {
|
| 1871 |
|
|
packagePids.addAll(dataPids);
|
| 1872 |
|
|
}
|
| 1873 |
7850
|
leinfelder
|
}
|
| 1874 |
7855
|
leinfelder
|
} else {
|
| 1875 |
|
|
// just the lone pid in this package
|
| 1876 |
|
|
packagePids.add(pid);
|
| 1877 |
7850
|
leinfelder
|
}
|
| 1878 |
8436
|
walker
|
|
| 1879 |
8437
|
walker
|
//Create a temp file, then delete it and make a directory with that name
|
| 1880 |
|
|
File tempDir = File.createTempFile("temp", Long.toString(System.nanoTime()));
|
| 1881 |
|
|
tempDir.delete();
|
| 1882 |
|
|
tempDir = new File(tempDir.getPath() + "_dir");
|
| 1883 |
|
|
tempDir.mkdir();
|
| 1884 |
8436
|
walker
|
tempFiles.add(tempDir);
|
| 1885 |
8800
|
leinfelder
|
File pidMappingFile = new File(tempDir, "pid-mapping.txt");
|
| 1886 |
8436
|
walker
|
|
| 1887 |
7855
|
leinfelder
|
// loop through the package contents
|
| 1888 |
|
|
for (Identifier entryPid: packagePids) {
|
| 1889 |
8436
|
walker
|
//Get the system metadata for each item
|
| 1890 |
8437
|
walker
|
SystemMetadata entrySysMeta = this.getSystemMetadata(session, entryPid);
|
| 1891 |
8436
|
walker
|
|
| 1892 |
|
|
String objectFormatType = ObjectFormatCache.getInstance().getFormat(entrySysMeta.getFormatId()).getFormatType();
|
| 1893 |
8437
|
walker
|
String fileName = null;
|
| 1894 |
8436
|
walker
|
|
| 1895 |
8437
|
walker
|
//TODO: Be more specific of what characters to replace. Make sure periods arent replaced for the filename from metadata
|
| 1896 |
|
|
//Our default file name is just the ID + format type (e.g. walker.1.1-DATA)
|
| 1897 |
|
|
fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + objectFormatType;
|
| 1898 |
|
|
|
| 1899 |
|
|
if(fileNames.containsKey(entryPid)){
|
| 1900 |
|
|
//Let's use the file name and extension from the metadata is we have it
|
| 1901 |
|
|
fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + fileNames.get(entryPid).replaceAll("[^a-zA-Z0-9\\-\\.]", "_");
|
| 1902 |
|
|
}
|
| 1903 |
|
|
else{
|
| 1904 |
|
|
//If we couldn't find a given file name, use the system metadata extension
|
| 1905 |
|
|
String extension = ObjectFormatInfo.instance().getExtension(entrySysMeta.getFormatId().getValue());
|
| 1906 |
|
|
fileName += extension;
|
| 1907 |
|
|
}
|
| 1908 |
|
|
|
| 1909 |
8436
|
walker
|
//Create a new file for this item and add to the list
|
| 1910 |
8437
|
walker
|
File tempFile = new File(tempDir, fileName);
|
| 1911 |
7855
|
leinfelder
|
tempFiles.add(tempFile);
|
| 1912 |
8436
|
walker
|
|
| 1913 |
|
|
InputStream entryInputStream = this.get(session, entryPid);
|
| 1914 |
7855
|
leinfelder
|
IOUtils.copy(entryInputStream, new FileOutputStream(tempFile));
|
| 1915 |
|
|
bag.addFileToPayload(tempFile);
|
| 1916 |
|
|
pidMapping.append(entryPid.getValue() + "\t" + "data/" + tempFile.getName() + "\n");
|
| 1917 |
|
|
}
|
| 1918 |
|
|
|
| 1919 |
|
|
//add the the pid to data file map
|
| 1920 |
|
|
IOUtils.write(pidMapping.toString(), new FileOutputStream(pidMappingFile));
|
| 1921 |
|
|
bag.addFileAsTag(pidMappingFile);
|
| 1922 |
8026
|
leinfelder
|
tempFiles.add(pidMappingFile);
|
| 1923 |
|
|
|
| 1924 |
7855
|
leinfelder
|
bag = bag.makeComplete();
|
| 1925 |
8026
|
leinfelder
|
|
| 1926 |
8436
|
walker
|
///Now create the zip file
|
| 1927 |
8437
|
walker
|
//Use the pid as the file name prefix, replacing all non-word characters
|
| 1928 |
|
|
String zipName = pid.getValue().replaceAll("\\W", "_");
|
| 1929 |
8160
|
leinfelder
|
|
| 1930 |
8436
|
walker
|
File bagFile = new File(tempDir, zipName+".zip");
|
| 1931 |
|
|
|
| 1932 |
7855
|
leinfelder
|
bag.setFile(bagFile);
|
| 1933 |
7860
|
leinfelder
|
ZipWriter zipWriter = new ZipWriter(bagFactory);
|
| 1934 |
7855
|
leinfelder
|
bag.write(zipWriter, bagFile);
|
| 1935 |
|
|
bagFile = bag.getFile();
|
| 1936 |
8026
|
leinfelder
|
// use custom FIS that will delete the file when closed
|
| 1937 |
|
|
bagInputStream = new DeleteOnCloseFileInputStream(bagFile);
|
| 1938 |
|
|
// also mark for deletion on shutdown in case the stream is never closed
|
| 1939 |
|
|
bagFile.deleteOnExit();
|
| 1940 |
8436
|
walker
|
tempFiles.add(bagFile);
|
| 1941 |
7855
|
leinfelder
|
|
| 1942 |
8026
|
leinfelder
|
// clean up other temp files
|
| 1943 |
8800
|
leinfelder
|
for (int i=tempFiles.size()-1; i>=0; i--){
|
| 1944 |
|
|
tempFiles.get(i).delete();
|
| 1945 |
7855
|
leinfelder
|
}
|
| 1946 |
8436
|
walker
|
|
| 1947 |
7855
|
leinfelder
|
} catch (IOException e) {
|
| 1948 |
|
|
// report as service failure
|
| 1949 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1950 |
|
|
sf.initCause(e);
|
| 1951 |
|
|
throw sf;
|
| 1952 |
|
|
} catch (OREException e) {
|
| 1953 |
|
|
// report as service failure
|
| 1954 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1955 |
|
|
sf.initCause(e);
|
| 1956 |
|
|
throw sf;
|
| 1957 |
|
|
} catch (URISyntaxException e) {
|
| 1958 |
|
|
// report as service failure
|
| 1959 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1960 |
|
|
sf.initCause(e);
|
| 1961 |
|
|
throw sf;
|
| 1962 |
|
|
} catch (OREParserException e) {
|
| 1963 |
|
|
// report as service failure
|
| 1964 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1965 |
|
|
sf.initCause(e);
|
| 1966 |
|
|
throw sf;
|
| 1967 |
7850
|
leinfelder
|
}
|
| 1968 |
|
|
|
| 1969 |
|
|
return bagInputStream;
|
| 1970 |
8810
|
leinfelder
|
}
|
| 1971 |
7850
|
leinfelder
|
|
| 1972 |
8810
|
leinfelder
|
@Override
|
| 1973 |
|
|
public OptionList listViews(Session arg0) throws InvalidToken,
|
| 1974 |
|
|
ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented {
|
| 1975 |
|
|
OptionList views = new OptionList();
|
| 1976 |
|
|
Vector<String> skinNames = null;
|
| 1977 |
|
|
try {
|
| 1978 |
|
|
skinNames = SkinUtil.getSkinNames();
|
| 1979 |
|
|
} catch (PropertyNotFoundException e) {
|
| 1980 |
|
|
throw new ServiceFailure("2841", e.getMessage());
|
| 1981 |
|
|
}
|
| 1982 |
|
|
for (String skinName: skinNames) {
|
| 1983 |
|
|
views.addOption(skinName);
|
| 1984 |
|
|
}
|
| 1985 |
|
|
return views;
|
| 1986 |
7850
|
leinfelder
|
}
|
| 1987 |
8810
|
leinfelder
|
|
| 1988 |
|
|
@Override
|
| 1989 |
|
|
public InputStream view(Session session, String format, Identifier pid)
|
| 1990 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,
|
| 1991 |
|
|
NotImplemented, NotFound {
|
| 1992 |
7860
|
leinfelder
|
InputStream resultInputStream = null;
|
| 1993 |
|
|
|
| 1994 |
|
|
SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
|
| 1995 |
|
|
InputStream object = this.get(session, pid);
|
| 1996 |
|
|
|
| 1997 |
|
|
try {
|
| 1998 |
|
|
// can only transform metadata, really
|
| 1999 |
8013
|
leinfelder
|
ObjectFormat objectFormat = ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId());
|
| 2000 |
7860
|
leinfelder
|
if (objectFormat.getFormatType().equals("METADATA")) {
|
| 2001 |
|
|
// transform
|
| 2002 |
|
|
DBTransform transformer = new DBTransform();
|
| 2003 |
|
|
String documentContent = IOUtils.toString(object, "UTF-8");
|
| 2004 |
|
|
String sourceType = objectFormat.getFormatId().getValue();
|
| 2005 |
|
|
String targetType = "-//W3C//HTML//EN";
|
| 2006 |
|
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 2007 |
|
|
Writer writer = new OutputStreamWriter(baos , "UTF-8");
|
| 2008 |
|
|
// TODO: include more params?
|
| 2009 |
|
|
Hashtable<String, String[]> params = new Hashtable<String, String[]>();
|
| 2010 |
8014
|
leinfelder
|
String localId = null;
|
| 2011 |
|
|
try {
|
| 2012 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 2013 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 2014 |
|
|
throw new NotFound("1020", e.getMessage());
|
| 2015 |
|
|
}
|
| 2016 |
|
|
params.put("qformat", new String[] {format});
|
| 2017 |
|
|
params.put("docid", new String[] {localId});
|
| 2018 |
|
|
params.put("pid", new String[] {pid.getValue()});
|
| 2019 |
7860
|
leinfelder
|
transformer.transformXMLDocument(
|
| 2020 |
|
|
documentContent ,
|
| 2021 |
|
|
sourceType,
|
| 2022 |
|
|
targetType ,
|
| 2023 |
|
|
format,
|
| 2024 |
|
|
writer,
|
| 2025 |
|
|
params,
|
| 2026 |
|
|
null //sessionid
|
| 2027 |
|
|
);
|
| 2028 |
|
|
|
| 2029 |
|
|
// finally, get the HTML back
|
| 2030 |
|
|
resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
|
| 2031 |
|
|
((ContentTypeByteArrayInputStream) resultInputStream).setContentType("text/html");
|
| 2032 |
|
|
|
| 2033 |
|
|
} else {
|
| 2034 |
|
|
// just return the raw bytes
|
| 2035 |
|
|
resultInputStream = object;
|
| 2036 |
|
|
}
|
| 2037 |
|
|
} catch (IOException e) {
|
| 2038 |
|
|
// report as service failure
|
| 2039 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2040 |
|
|
sf.initCause(e);
|
| 2041 |
|
|
throw sf;
|
| 2042 |
|
|
} catch (PropertyNotFoundException e) {
|
| 2043 |
|
|
// report as service failure
|
| 2044 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2045 |
|
|
sf.initCause(e);
|
| 2046 |
|
|
throw sf;
|
| 2047 |
|
|
} catch (SQLException e) {
|
| 2048 |
|
|
// report as service failure
|
| 2049 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2050 |
|
|
sf.initCause(e);
|
| 2051 |
|
|
throw sf;
|
| 2052 |
|
|
} catch (ClassNotFoundException e) {
|
| 2053 |
|
|
// report as service failure
|
| 2054 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2055 |
|
|
sf.initCause(e);
|
| 2056 |
|
|
throw sf;
|
| 2057 |
|
|
}
|
| 2058 |
|
|
|
| 2059 |
|
|
return resultInputStream;
|
| 2060 |
8026
|
leinfelder
|
}
|
| 2061 |
6795
|
cjones
|
|
| 2062 |
6179
|
cjones
|
}
|