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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: tao $'
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* '$Date: 2017-05-17 20:37:38 -0700 (Wed, 17 May 2017) $'
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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.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileNotFoundException;
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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.OutputStream;
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import java.io.OutputStreamWriter;
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import java.io.Writer;
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import java.math.BigInteger;
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import java.security.DigestOutputStream;
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import java.security.MessageDigest;
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import java.security.NoSuchAlgorithmException;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.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.Hashtable;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.Timer;
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import java.util.Vector;
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import java.util.concurrent.locks.Lock;
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import javax.servlet.http.HttpServletRequest;
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import javax.xml.bind.DatatypeConverter;
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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.formats.ObjectFormatCache;
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import org.dataone.configuration.Settings;
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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.UnsupportedType;
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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.Group;
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import org.dataone.service.types.v1.Identifier;
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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.Person;
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import org.dataone.service.types.v1.SubjectInfo;
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import org.dataone.service.types.v2.Log;
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import org.dataone.service.types.v2.Node;
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import org.dataone.service.types.v2.OptionList;
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import org.dataone.service.types.v1.Event;
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import org.dataone.service.types.v1.NodeReference;
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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.Permission;
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import org.dataone.service.types.v1.Replica;
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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.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.util.Constants;
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import edu.ucsb.nceas.metacat.AccessionNumber;
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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import edu.ucsb.nceas.metacat.DBTransform;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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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.MetacatHandler;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.common.query.stream.ContentTypeByteArrayInputStream;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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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.replication.ForceReplicationHandler;
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import edu.ucsb.nceas.metacat.util.SkinUtil;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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public abstract class D1NodeService {
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public static final String DELETEDMESSAGE = "The object with the PID has been deleted from the node.";
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private static Logger logMetacat = Logger.getLogger(D1NodeService.class);
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/** For logging the operations */
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protected HttpServletRequest request;
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/* reference to the metacat handler */
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protected MetacatHandler handler;
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/* parameters set in the incoming request */
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//private Hashtable<String, String[]> params;
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/**
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* limit paged results sets to a configured maximum
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*/
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protected static int MAXIMUM_DB_RECORD_COUNT = 7000;
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static {
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try {
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MAXIMUM_DB_RECORD_COUNT = Integer.valueOf(PropertyService.getProperty("database.webResultsetSize"));
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} catch (Exception e) {
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logMetacat.warn("Could not set MAXIMUM_DB_RECORD_COUNT", e);
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}
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}
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/**
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* out-of-band session object to be used when not passed in as a method parameter
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*/
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protected Session session;
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/**
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* Constructor - used to set the metacatUrl from a subclass extending D1NodeService
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*
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* @param metacatUrl - the URL of the metacat service, including the ending /d1
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*/
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public D1NodeService(HttpServletRequest request) {
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this.request = request;
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}
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/**
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* retrieve the out-of-band session
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* @return
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*/
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public Session getSession() {
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return session;
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}
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/**
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* Set the out-of-band session
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* @param session
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*/
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public void setSession(Session session) {
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this.session = session;
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}
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/**
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* This method provides a lighter weight mechanism than
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* getSystemMetadata() for a client to determine basic
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* properties of the referenced 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 identifier of the object to be described
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*
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* @return describeResponse - A set of values providing a basic description
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* of the object.
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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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public DescribeResponse describe(Session session, Identifier pid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
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String serviceFailureCode = "4931";
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Identifier sid = getPIDForSID(pid, serviceFailureCode);
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if(sid != null) {
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pid = sid;
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}
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// get system metadata and construct the describe response
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SystemMetadata sysmeta = getSystemMetadata(session, pid);
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DescribeResponse describeResponse =
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new DescribeResponse(sysmeta.getFormatId(), sysmeta.getSize(),
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sysmeta.getDateSysMetadataModified(),
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sysmeta.getChecksum(), sysmeta.getSerialVersion());
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return describeResponse;
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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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public Identifier delete(Session session, Identifier pid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
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String localId = null;
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if (session == null) {
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throw new InvalidToken("1330", "No session has been provided");
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}
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// just for logging purposes
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String username = session.getSubject().getValue();
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// do we have a valid pid?
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if (pid == null || pid.getValue().trim().equals("")) {
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throw new ServiceFailure("1350", "The provided identifier was invalid.");
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}
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// check for the existing identifier
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try {
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localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
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} catch (McdbDocNotFoundException e) {
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throw new NotFound("1340", "The object with the provided " + "identifier was not found.");
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} catch (SQLException e) {
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throw new ServiceFailure("1350", "The object with the provided " + "identifier "+pid.getValue()+" couldn't be identified since "+e.getMessage());
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}
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try {
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// delete the document, as admin
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DocumentImpl.delete(localId, null, null, null, true);
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EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, Event.DELETE.xmlValue());
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// archive it
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// DocumentImpl.delete() now sets this
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// see https://redmine.dataone.org/issues/3406
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// SystemMetadata sysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
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// sysMeta.setArchived(true);
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// sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
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// HazelcastService.getInstance().getSystemMetadataMap().put(pid, sysMeta);
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265
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} catch (McdbDocNotFoundException e) {
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throw new NotFound("1340", "The provided identifier was invalid.");
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268
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} catch (SQLException e) {
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throw new ServiceFailure("1350", "There was a problem deleting the object." + "The error message was: " + e.getMessage());
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} catch (InsufficientKarmaException e) {
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273
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if ( logMetacat.isDebugEnabled() ) {
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e.printStackTrace();
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275
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}
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throw new NotAuthorized("1320", "The provided identity does not have " + "permission to DELETE objects on the Member Node.");
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277
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} catch (Exception e) { // for some reason DocumentImpl throws a general Exception
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throw new ServiceFailure("1350", "There was a problem deleting the object." + "The error message was: " + e.getMessage());
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}
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return pid;
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283
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}
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284
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285
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/**
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286
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* Low level, "are you alive" operation. A valid ping response is
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287
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* indicated by a HTTP status of 200.
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288
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*
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289
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* @return true if the service is alive
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290
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*
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291
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* @throws NotImplemented
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292
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* @throws ServiceFailure
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293
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* @throws InsufficientResources
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294
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*/
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295
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public Date ping()
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296
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throws NotImplemented, ServiceFailure, InsufficientResources {
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297
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298
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// test if we can get a database connection
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299
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int serialNumber = -1;
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300
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DBConnection dbConn = null;
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301
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try {
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302
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dbConn = DBConnectionPool.getDBConnection("MNodeService.ping");
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303
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serialNumber = dbConn.getCheckOutSerialNumber();
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304
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} catch (SQLException e) {
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305
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ServiceFailure sf = new ServiceFailure("", e.getMessage());
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306
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sf.initCause(e);
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throw sf;
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308
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} finally {
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309
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// Return the database connection
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310
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DBConnectionPool.returnDBConnection(dbConn, serialNumber);
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311
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}
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312
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313
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return Calendar.getInstance().getTime();
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314
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}
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315
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|
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316
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/**
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317
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* Adds a new object to the Node, where the object is either a data
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318
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* object or a science metadata object. This method is called by clients
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319
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* to create new data objects on Member Nodes or internally for Coordinating
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320
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* Nodes
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321
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*
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322
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* @param session - the Session object containing the credentials for the Subject
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323
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* @param pid - The object identifier to be created
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324
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* @param object - the object bytes
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325
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* @param sysmeta - the system metadata that describes the object
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326
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*
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327
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* @return pid - the object identifier created
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328
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*
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329
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* @throws InvalidToken
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330
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* @throws ServiceFailure
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331
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* @throws NotAuthorized
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332
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* @throws IdentifierNotUnique
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333
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* @throws UnsupportedType
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334
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* @throws InsufficientResources
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335
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* @throws InvalidSystemMetadata
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336
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* @throws NotImplemented
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337
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* @throws InvalidRequest
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338
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*/
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339
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public Identifier create(Session session, Identifier pid, InputStream object,
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|
340
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SystemMetadata sysmeta)
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341
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throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
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342
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UnsupportedType, InsufficientResources, InvalidSystemMetadata,
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343
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NotImplemented, InvalidRequest {
|
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344
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|
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345
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Identifier resultPid = null;
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346
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String localId = null;
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347
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boolean allowed = false;
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|
348
|
|
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349
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// check for null session
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|
350
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if (session == null) {
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351
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throw new InvalidToken("4894", "Session is required to WRITE to the Node.");
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|
352
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}
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|
353
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Subject subject = session.getSubject();
|
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354
|
|
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355
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Subject publicSubject = new Subject();
|
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356
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publicSubject.setValue(Constants.SUBJECT_PUBLIC);
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357
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// be sure the user is authenticated for create()
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358
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if (subject == null || subject.getValue() == null ||
|
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359
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subject.equals(publicSubject) ) {
|
|
360
|
throw new NotAuthorized("1100", "The provided identity does not have " +
|
|
361
|
"permission to WRITE to the Node.");
|
|
362
|
|
|
363
|
}
|
|
364
|
|
|
365
|
// verify that pid == SystemMetadata.getIdentifier()
|
|
366
|
logMetacat.debug("Comparing pid|sysmeta_pid: " +
|
|
367
|
pid.getValue() + "|" + sysmeta.getIdentifier().getValue());
|
|
368
|
if (!pid.getValue().equals(sysmeta.getIdentifier().getValue())) {
|
|
369
|
throw new InvalidSystemMetadata("1180",
|
|
370
|
"The supplied system metadata is invalid. " +
|
|
371
|
"The identifier " + pid.getValue() + " does not match identifier" +
|
|
372
|
"in the system metadata identified by " +
|
|
373
|
sysmeta.getIdentifier().getValue() + ".");
|
|
374
|
|
|
375
|
}
|
|
376
|
|
|
377
|
if(sysmeta.getChecksum() == null) {
|
|
378
|
logMetacat.error("D1NodeService.create - the checksum object from the system metadata shouldn't be null for the object "+pid.getValue());
|
|
379
|
throw new InvalidSystemMetadata("1180", "The checksum object from the system metadata shouldn't be null.");
|
|
380
|
}
|
|
381
|
|
|
382
|
|
|
383
|
logMetacat.debug("Checking if identifier exists: " + pid.getValue());
|
|
384
|
// Check that the identifier does not already exist
|
|
385
|
boolean idExists = false;
|
|
386
|
try {
|
|
387
|
idExists = IdentifierManager.getInstance().identifierExists(pid.getValue());
|
|
388
|
} catch (SQLException e) {
|
|
389
|
throw new ServiceFailure("1190",
|
|
390
|
"The requested identifier " + pid.getValue() +
|
|
391
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
|
392
|
}
|
|
393
|
if (idExists) {
|
|
394
|
throw new IdentifierNotUnique("1120",
|
|
395
|
"The requested identifier " + pid.getValue() +
|
|
396
|
" is already used by another object and" +
|
|
397
|
"therefore can not be used for this object. Clients should choose" +
|
|
398
|
"a new identifier that is unique and retry the operation or " +
|
|
399
|
"use CN.reserveIdentifier() to reserve one.");
|
|
400
|
|
|
401
|
}
|
|
402
|
|
|
403
|
|
|
404
|
// TODO: this probably needs to be refined more
|
|
405
|
try {
|
|
406
|
allowed = isAuthorized(session, pid, Permission.WRITE);
|
|
407
|
|
|
408
|
} catch (NotFound e) {
|
|
409
|
// The identifier doesn't exist, writing should be fine.
|
|
410
|
allowed = true;
|
|
411
|
}
|
|
412
|
|
|
413
|
if(!allowed) {
|
|
414
|
throw new NotAuthorized("1100", "Provited Identity doesn't have the WRITE permission on the pid "+pid.getValue());
|
|
415
|
}
|
|
416
|
|
|
417
|
|
|
418
|
// we have the go ahead
|
|
419
|
//if ( allowed ) {
|
|
420
|
|
|
421
|
|
|
422
|
logMetacat.debug("Allowed to insert: " + pid.getValue());
|
|
423
|
|
|
424
|
// save the sysmeta
|
|
425
|
try {
|
|
426
|
// lock and unlock of the pid happens in the subclass
|
|
427
|
HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);
|
|
428
|
|
|
429
|
} catch (Exception e) {
|
|
430
|
logMetacat.error("D1Node.create - There was problem to save the system metadata: " + pid.getValue(), e);
|
|
431
|
throw new ServiceFailure("1190", "There was problem to save the system metadata: " + pid.getValue()+" since "+e.getMessage());
|
|
432
|
}
|
|
433
|
boolean isScienceMetadata = false;
|
|
434
|
// Science metadata (XML) or science data object?
|
|
435
|
// TODO: there are cases where certain object formats are science metadata
|
|
436
|
// but are not XML (netCDF ...). Handle this.
|
|
437
|
if ( isScienceMetadata(sysmeta) ) {
|
|
438
|
isScienceMetadata = true;
|
|
439
|
// CASE METADATA:
|
|
440
|
//String objectAsXML = "";
|
|
441
|
try {
|
|
442
|
//objectAsXML = IOUtils.toString(object, "UTF-8");
|
|
443
|
String formatId = null;
|
|
444
|
if(sysmeta.getFormatId() != null) {
|
|
445
|
formatId = sysmeta.getFormatId().getValue();
|
|
446
|
}
|
|
447
|
localId = insertOrUpdateDocument(object,"UTF-8", pid, session, "insert", formatId, sysmeta.getChecksum());
|
|
448
|
//localId = im.getLocalId(pid.getValue());
|
|
449
|
|
|
450
|
} catch (IOException e) {
|
|
451
|
removeSystemMetaAndIdentifier(pid);
|
|
452
|
String msg = "The Node is unable to create the object "+pid.getValue() +
|
|
453
|
" There was a problem converting the object to XML";
|
|
454
|
logMetacat.error(msg, e);
|
|
455
|
throw new ServiceFailure("1190", msg + ": " + e.getMessage());
|
|
456
|
|
|
457
|
} catch (ServiceFailure e) {
|
|
458
|
removeSystemMetaAndIdentifier(pid);
|
|
459
|
logMetacat.error("D1NodeService.create - the node couldn't create the object "+pid.getValue()+" since "+e.getMessage(), e);
|
|
460
|
throw e;
|
|
461
|
} catch (Exception e) {
|
|
462
|
removeSystemMetaAndIdentifier(pid);
|
|
463
|
logMetacat.error("The node is unable to create the object: "+pid.getValue()+ " since " + e.getMessage(), e);
|
|
464
|
throw new ServiceFailure("1190", "The node is unable to create the object: " +pid.getValue()+" since "+ e.getMessage());
|
|
465
|
}
|
|
466
|
|
|
467
|
} else {
|
|
468
|
|
|
469
|
// DEFAULT CASE: DATA (needs to be checked and completed)
|
|
470
|
try {
|
|
471
|
localId = insertDataObject(object, pid, session, sysmeta.getChecksum());
|
|
472
|
} catch (ServiceFailure e) {
|
|
473
|
removeSystemMetaAndIdentifier(pid);
|
|
474
|
throw e;
|
|
475
|
} catch (InvalidSystemMetadata e) {
|
|
476
|
removeSystemMetaAndIdentifier(pid);
|
|
477
|
throw e;
|
|
478
|
} catch (Exception e) {
|
|
479
|
removeSystemMetaAndIdentifier(pid);
|
|
480
|
throw new ServiceFailure("1190", "The node is unable to create the object "+pid.getValue()+" since " + e.getMessage());
|
|
481
|
}
|
|
482
|
|
|
483
|
}
|
|
484
|
|
|
485
|
//}
|
|
486
|
|
|
487
|
logMetacat.debug("Done inserting new object: " + pid.getValue());
|
|
488
|
|
|
489
|
// setting the resulting identifier failed. We will check if the object does exist.
|
|
490
|
try {
|
|
491
|
if (localId == null || !IdentifierManager.getInstance().objectFileExists(localId, isScienceMetadata) ) {
|
|
492
|
removeSystemMetaAndIdentifier(pid);
|
|
493
|
throw new ServiceFailure("1190", "The Node is unable to create the object. "+pid.getValue());
|
|
494
|
}
|
|
495
|
} catch (PropertyNotFoundException e) {
|
|
496
|
removeSystemMetaAndIdentifier(pid);
|
|
497
|
throw new ServiceFailure("1190", "The Node is unable to create the object. "+pid.getValue() + " since "+e.getMessage());
|
|
498
|
}
|
|
499
|
|
|
500
|
|
|
501
|
|
|
502
|
|
|
503
|
|
|
504
|
try {
|
|
505
|
// submit for indexing
|
|
506
|
MetacatSolrIndex.getInstance().submit(sysmeta.getIdentifier(), sysmeta, null, true);
|
|
507
|
} catch (Exception e) {
|
|
508
|
logMetacat.warn("Couldn't create solr index for object "+pid.getValue());
|
|
509
|
}
|
|
510
|
|
|
511
|
resultPid = pid;
|
|
512
|
|
|
513
|
logMetacat.info("create() complete for object: " + pid.getValue());
|
|
514
|
|
|
515
|
return resultPid;
|
|
516
|
}
|
|
517
|
|
|
518
|
/*
|
|
519
|
* Roll-back method when inserting data object fails.
|
|
520
|
*/
|
|
521
|
protected void removeSystemMetaAndIdentifier(Identifier id){
|
|
522
|
if(id != null) {
|
|
523
|
logMetacat.debug("D1NodeService.removeSystemMeta - the system metadata of object "+id.getValue()+" will removed from both hazelcast and db tables since the object creation failed");
|
|
524
|
HazelcastService.getInstance().getSystemMetadataMap().remove(id);
|
|
525
|
logMetacat.info("D1NodeService.removeSystemMeta - the system metadata of object "+id.getValue()+" has been removed from both hazelcast and db tables since the object creation failed");
|
|
526
|
try {
|
|
527
|
if(IdentifierManager.getInstance().mappingExists(id.getValue())) {
|
|
528
|
String localId = IdentifierManager.getInstance().getLocalId(id.getValue());
|
|
529
|
IdentifierManager.getInstance().removeMapping(id.getValue(), localId);
|
|
530
|
logMetacat.info("D1NodeService.removeSystemMeta - the identifier "+id.getValue()+" and local id "+localId+" have been removed from the identifier table since the object creation failed");
|
|
531
|
}
|
|
532
|
} catch (Exception e) {
|
|
533
|
logMetacat.warn("D1NodeService.removeSysteMeta - can't decide if the mapping of the pid "+id.getValue()+" exists on the identifier table.");
|
|
534
|
}
|
|
535
|
}
|
|
536
|
}
|
|
537
|
|
|
538
|
/*
|
|
539
|
* Roll-back method when inserting data object fails.
|
|
540
|
*/
|
|
541
|
protected void removeSolrIndex(SystemMetadata sysMeta) {
|
|
542
|
sysMeta.setSerialVersion(sysMeta.getSerialVersion().add(BigInteger.ONE));
|
|
543
|
sysMeta.setArchived(true);
|
|
544
|
sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
|
545
|
try {
|
|
546
|
MetacatSolrIndex.getInstance().submit(sysMeta.getIdentifier(), sysMeta, null, false);
|
|
547
|
} catch (Exception e) {
|
|
548
|
logMetacat.warn("Can't remove the solr index for pid "+sysMeta.getIdentifier().getValue());
|
|
549
|
}
|
|
550
|
|
|
551
|
}
|
|
552
|
|
|
553
|
/**
|
|
554
|
* Return the log records associated with a given event between the start and
|
|
555
|
* end dates listed given a particular Subject listed in the Session
|
|
556
|
*
|
|
557
|
* @param session - the Session object containing the credentials for the Subject
|
|
558
|
* @param fromDate - the start date of the desired log records
|
|
559
|
* @param toDate - the end date of the desired log records
|
|
560
|
* @param event - restrict log records of a specific event type
|
|
561
|
* @param start - zero based offset from the first record in the
|
|
562
|
* set of matching log records. Used to assist with
|
|
563
|
* paging the response.
|
|
564
|
* @param count - maximum number of log records to return in the response.
|
|
565
|
* Used to assist with paging the response.
|
|
566
|
*
|
|
567
|
* @return the desired log records
|
|
568
|
*
|
|
569
|
* @throws InvalidToken
|
|
570
|
* @throws ServiceFailure
|
|
571
|
* @throws NotAuthorized
|
|
572
|
* @throws InvalidRequest
|
|
573
|
* @throws NotImplemented
|
|
574
|
*/
|
|
575
|
public Log getLogRecords(Session session, Date fromDate, Date toDate,
|
|
576
|
String event, String pidFilter, Integer start, Integer count) throws InvalidToken, ServiceFailure,
|
|
577
|
NotAuthorized, InvalidRequest, NotImplemented {
|
|
578
|
|
|
579
|
// only admin access to this method
|
|
580
|
// see https://redmine.dataone.org/issues/2855
|
|
581
|
if (!isAdminAuthorized(session)) {
|
|
582
|
throw new NotAuthorized("1460", "Only the CN or admin is allowed to harvest logs from this node");
|
|
583
|
}
|
|
584
|
Log log = new Log();
|
|
585
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
586
|
EventLog el = EventLog.getInstance();
|
|
587
|
if ( fromDate == null ) {
|
|
588
|
logMetacat.debug("setting fromdate from null");
|
|
589
|
fromDate = new Date(1);
|
|
590
|
}
|
|
591
|
if ( toDate == null ) {
|
|
592
|
logMetacat.debug("setting todate from null");
|
|
593
|
toDate = new Date();
|
|
594
|
}
|
|
595
|
|
|
596
|
if ( start == null ) {
|
|
597
|
start = 0;
|
|
598
|
}
|
|
599
|
|
|
600
|
if ( count == null ) {
|
|
601
|
count = 1000;
|
|
602
|
}
|
|
603
|
|
|
604
|
// safeguard against large requests
|
|
605
|
if (count > MAXIMUM_DB_RECORD_COUNT) {
|
|
606
|
count = MAXIMUM_DB_RECORD_COUNT;
|
|
607
|
}
|
|
608
|
|
|
609
|
String[] filterDocid = null;
|
|
610
|
if (pidFilter != null && !pidFilter.trim().equals("")) {
|
|
611
|
//check if the given identifier is a sid. If it is sid, choose the current pid of the sid.
|
|
612
|
Identifier pid = new Identifier();
|
|
613
|
pid.setValue(pidFilter);
|
|
614
|
String serviceFailureCode = "1490";
|
|
615
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
|
616
|
if(sid != null) {
|
|
617
|
pid = sid;
|
|
618
|
}
|
|
619
|
pidFilter = pid.getValue();
|
|
620
|
try {
|
|
621
|
String localId = im.getLocalId(pidFilter);
|
|
622
|
filterDocid = new String[] {localId};
|
|
623
|
} catch (Exception ex) {
|
|
624
|
String msg = "Could not find localId for given pidFilter '" + pidFilter + "'";
|
|
625
|
logMetacat.warn(msg, ex);
|
|
626
|
//throw new InvalidRequest("1480", msg);
|
|
627
|
return log; //return 0 record
|
|
628
|
}
|
|
629
|
}
|
|
630
|
|
|
631
|
logMetacat.debug("fromDate: " + fromDate);
|
|
632
|
logMetacat.debug("toDate: " + toDate);
|
|
633
|
|
|
634
|
log = el.getD1Report(null, null, filterDocid, event,
|
|
635
|
new java.sql.Timestamp(fromDate.getTime()),
|
|
636
|
new java.sql.Timestamp(toDate.getTime()), false, start, count);
|
|
637
|
|
|
638
|
logMetacat.info("getLogRecords");
|
|
639
|
return log;
|
|
640
|
}
|
|
641
|
|
|
642
|
/**
|
|
643
|
* Return the object identified by the given object identifier
|
|
644
|
*
|
|
645
|
* @param session - the Session object containing the credentials for the Subject
|
|
646
|
* @param pid - the object identifier for the given object
|
|
647
|
*
|
|
648
|
* TODO: The D1 Authorization API doesn't provide information on which
|
|
649
|
* authentication system the Subject belongs to, and so it's not possible to
|
|
650
|
* discern which Person or Group is a valid KNB LDAP DN. Fix this.
|
|
651
|
*
|
|
652
|
* @return inputStream - the input stream of the given object
|
|
653
|
*
|
|
654
|
* @throws InvalidToken
|
|
655
|
* @throws ServiceFailure
|
|
656
|
* @throws NotAuthorized
|
|
657
|
* @throws InvalidRequest
|
|
658
|
* @throws NotImplemented
|
|
659
|
*/
|
|
660
|
public InputStream get(Session session, Identifier pid)
|
|
661
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
|
662
|
NotImplemented {
|
|
663
|
|
|
664
|
String serviceFailureCode = "1030";
|
|
665
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
|
666
|
if(sid != null) {
|
|
667
|
pid = sid;
|
|
668
|
}
|
|
669
|
|
|
670
|
InputStream inputStream = null; // bytes to be returned
|
|
671
|
handler = new MetacatHandler(new Timer());
|
|
672
|
boolean allowed = false;
|
|
673
|
String localId; // the metacat docid for the pid
|
|
674
|
|
|
675
|
// get the local docid from Metacat
|
|
676
|
try {
|
|
677
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
678
|
|
|
679
|
} catch (McdbDocNotFoundException e) {
|
|
680
|
throw new NotFound("1020", "The object specified by " +
|
|
681
|
pid.getValue() +
|
|
682
|
" does not exist at this node.");
|
|
683
|
} catch (SQLException e) {
|
|
684
|
throw new ServiceFailure("1030", "The object specified by "+ pid.getValue()+
|
|
685
|
" couldn't be identified at this node since "+e.getMessage());
|
|
686
|
}
|
|
687
|
|
|
688
|
// check for authorization
|
|
689
|
try {
|
|
690
|
allowed = isAuthorized(session, pid, Permission.READ);
|
|
691
|
} catch (InvalidRequest e) {
|
|
692
|
throw new ServiceFailure("1030", e.getDescription());
|
|
693
|
}
|
|
694
|
|
|
695
|
// if the person is authorized, perform the read
|
|
696
|
if (allowed) {
|
|
697
|
try {
|
|
698
|
inputStream = handler.read(localId);
|
|
699
|
} catch (McdbDocNotFoundException de) {
|
|
700
|
String error ="";
|
|
701
|
if(EventLog.getInstance().isDeleted(localId)) {
|
|
702
|
error=DELETEDMESSAGE;
|
|
703
|
}
|
|
704
|
throw new NotFound("1020", "The object specified by " +
|
|
705
|
pid.getValue() +
|
|
706
|
" does not exist at this node. "+error);
|
|
707
|
} catch (Exception e) {
|
|
708
|
throw new ServiceFailure("1030", "The object specified by " +
|
|
709
|
pid.getValue() +
|
|
710
|
" could not be returned due to error: " +
|
|
711
|
e.getMessage()+". ");
|
|
712
|
}
|
|
713
|
}
|
|
714
|
|
|
715
|
// if we fail to set the input stream
|
|
716
|
if ( inputStream == null ) {
|
|
717
|
String error ="";
|
|
718
|
if(EventLog.getInstance().isDeleted(localId)) {
|
|
719
|
error=DELETEDMESSAGE;
|
|
720
|
}
|
|
721
|
throw new NotFound("1020", "The object specified by " +
|
|
722
|
pid.getValue() +
|
|
723
|
" does not exist at this node. "+error);
|
|
724
|
}
|
|
725
|
|
|
726
|
// log the read event
|
|
727
|
String principal = Constants.SUBJECT_PUBLIC;
|
|
728
|
if (session != null && session.getSubject() != null) {
|
|
729
|
principal = session.getSubject().getValue();
|
|
730
|
}
|
|
731
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "read");
|
|
732
|
|
|
733
|
return inputStream;
|
|
734
|
}
|
|
735
|
|
|
736
|
/**
|
|
737
|
* Return the system metadata for a given object
|
|
738
|
*
|
|
739
|
* @param session - the Session object containing the credentials for the Subject
|
|
740
|
* @param pid - the object identifier for the given object
|
|
741
|
*
|
|
742
|
* @return inputStream - the input stream of the given system metadata object
|
|
743
|
*
|
|
744
|
* @throws InvalidToken
|
|
745
|
* @throws ServiceFailure
|
|
746
|
* @throws NotAuthorized
|
|
747
|
* @throws NotFound
|
|
748
|
* @throws InvalidRequest
|
|
749
|
* @throws NotImplemented
|
|
750
|
*/
|
|
751
|
public SystemMetadata getSystemMetadata(Session session, Identifier pid)
|
|
752
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
|
753
|
NotImplemented {
|
|
754
|
|
|
755
|
String serviceFailureCode = "1090";
|
|
756
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
|
757
|
if(sid != null) {
|
|
758
|
pid = sid;
|
|
759
|
}
|
|
760
|
boolean isAuthorized = false;
|
|
761
|
SystemMetadata systemMetadata = null;
|
|
762
|
List<Replica> replicaList = null;
|
|
763
|
NodeReference replicaNodeRef = null;
|
|
764
|
List<Node> nodeListBySubject = null;
|
|
765
|
Subject subject = null;
|
|
766
|
|
|
767
|
if (session != null ) {
|
|
768
|
subject = session.getSubject();
|
|
769
|
}
|
|
770
|
|
|
771
|
// check normal authorization
|
|
772
|
BaseException originalAuthorizationException = null;
|
|
773
|
if (!isAuthorized) {
|
|
774
|
try {
|
|
775
|
isAuthorized = isAuthorized(session, pid, Permission.READ);
|
|
776
|
|
|
777
|
} catch (InvalidRequest e) {
|
|
778
|
throw new ServiceFailure("1090", e.getDescription());
|
|
779
|
} catch (NotAuthorized nae) {
|
|
780
|
// catch this for later
|
|
781
|
originalAuthorizationException = nae;
|
|
782
|
}
|
|
783
|
}
|
|
784
|
|
|
785
|
// get the system metadata first because we need the replica list for auth
|
|
786
|
systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
|
787
|
|
|
788
|
// check the replica information to expand access to MNs that might need it
|
|
789
|
if (!isAuthorized) {
|
|
790
|
|
|
791
|
try {
|
|
792
|
|
|
793
|
// if MNs are listed as replicas, allow access
|
|
794
|
if ( systemMetadata != null ) {
|
|
795
|
replicaList = systemMetadata.getReplicaList();
|
|
796
|
// only check if there are in fact replicas listed
|
|
797
|
if ( replicaList != null ) {
|
|
798
|
|
|
799
|
if ( subject != null ) {
|
|
800
|
// get the list of nodes with a matching node subject
|
|
801
|
try {
|
|
802
|
nodeListBySubject = listNodesBySubject(session.getSubject());
|
|
803
|
|
|
804
|
} catch (BaseException e) {
|
|
805
|
// Unexpected error contacting the CN via D1Client
|
|
806
|
String msg = "Caught an unexpected error while trying "
|
|
807
|
+ "to potentially authorize system metadata access "
|
|
808
|
+ "based on the session subject. The error was "
|
|
809
|
+ e.getMessage();
|
|
810
|
logMetacat.error(msg);
|
|
811
|
if (logMetacat.isDebugEnabled()) {
|
|
812
|
e.printStackTrace();
|
|
813
|
|
|
814
|
}
|
|
815
|
// isAuthorized is still false
|
|
816
|
}
|
|
817
|
|
|
818
|
}
|
|
819
|
if (nodeListBySubject != null) {
|
|
820
|
// compare node ids to replica node ids
|
|
821
|
outer: for (Replica replica : replicaList) {
|
|
822
|
replicaNodeRef = replica.getReplicaMemberNode();
|
|
823
|
|
|
824
|
for (Node node : nodeListBySubject) {
|
|
825
|
if (node.getIdentifier().equals(replicaNodeRef)) {
|
|
826
|
// node id via session subject matches a replica node
|
|
827
|
isAuthorized = true;
|
|
828
|
break outer;
|
|
829
|
}
|
|
830
|
}
|
|
831
|
}
|
|
832
|
}
|
|
833
|
}
|
|
834
|
}
|
|
835
|
|
|
836
|
// if we still aren't authorized, then we are done
|
|
837
|
if (!isAuthorized) {
|
|
838
|
throw new NotAuthorized("1400", Permission.READ
|
|
839
|
+ " not allowed on " + pid.getValue());
|
|
840
|
}
|
|
841
|
|
|
842
|
} catch (RuntimeException e) {
|
|
843
|
e.printStackTrace();
|
|
844
|
// convert hazelcast RuntimeException to ServiceFailure
|
|
845
|
throw new ServiceFailure("1090", "Unexpected error getting system metadata for: " +
|
|
846
|
pid.getValue());
|
|
847
|
}
|
|
848
|
|
|
849
|
}
|
|
850
|
|
|
851
|
// It wasn't in the map
|
|
852
|
if ( systemMetadata == null ) {
|
|
853
|
String error ="";
|
|
854
|
String localId = null;
|
|
855
|
try {
|
|
856
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
857
|
|
|
858
|
} catch (Exception e) {
|
|
859
|
logMetacat.warn("Couldn't find the local id for the pid "+pid.getValue());
|
|
860
|
}
|
|
861
|
|
|
862
|
if(localId != null && EventLog.getInstance().isDeleted(localId)) {
|
|
863
|
error = DELETEDMESSAGE;
|
|
864
|
} else if (localId == null && EventLog.getInstance().isDeleted(pid.getValue())) {
|
|
865
|
error = DELETEDMESSAGE;
|
|
866
|
}
|
|
867
|
throw new NotFound("1420", "No record found for: " + pid.getValue()+". "+error);
|
|
868
|
}
|
|
869
|
|
|
870
|
return systemMetadata;
|
|
871
|
}
|
|
872
|
|
|
873
|
|
|
874
|
/**
|
|
875
|
* Test if the specified session represents the authoritative member node for the
|
|
876
|
* given object specified by the identifier. According the the DataONE documentation,
|
|
877
|
* the authoritative member node has all the rights of the *rightsHolder*.
|
|
878
|
* @param session - the Session object containing the credentials for the Subject
|
|
879
|
* @param pid - the Identifier of the data object
|
|
880
|
* @return true if the session represents the authoritative mn.
|
|
881
|
* @throws ServiceFailure
|
|
882
|
* @throws NotImplemented
|
|
883
|
*/
|
|
884
|
public boolean isAuthoritativeMNodeAdmin(Session session, Identifier pid) {
|
|
885
|
boolean allowed = false;
|
|
886
|
//check the parameters
|
|
887
|
if(session == null) {
|
|
888
|
logMetacat.debug("D1NodeService.isAuthoritativeMNodeAdmin - the session object is null and return false.");
|
|
889
|
return allowed;
|
|
890
|
} else if (pid == null || pid.getValue() == null || pid.getValue().trim().equals("")) {
|
|
891
|
logMetacat.debug("D1NodeService.isAuthoritativeMNodeAdmin - the Identifier object is null (not being specified) and return false.");
|
|
892
|
return allowed;
|
|
893
|
}
|
|
894
|
|
|
895
|
//Get the subject from the session
|
|
896
|
Subject subject = session.getSubject();
|
|
897
|
if(subject != null) {
|
|
898
|
//Get the authoritative member node info from the system metadata
|
|
899
|
SystemMetadata sysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
|
900
|
if(sysMeta != null) {
|
|
901
|
NodeReference authoritativeMNode = sysMeta.getAuthoritativeMemberNode();
|
|
902
|
if(authoritativeMNode != null) {
|
|
903
|
CNode cn = null;
|
|
904
|
try {
|
|
905
|
cn = D1Client.getCN();
|
|
906
|
} catch (BaseException e) {
|
|
907
|
logMetacat.error("D1NodeService.isAuthoritativeMNodeAdmin - couldn't connect to the CN since "+
|
|
908
|
e.getDescription()+ ". The false value will be returned for the AuthoritativeMNodeAdmin.");
|
|
909
|
return allowed;
|
|
910
|
}
|
|
911
|
|
|
912
|
if(cn != null) {
|
|
913
|
List<Node> nodes = null;
|
|
914
|
try {
|
|
915
|
nodes = cn.listNodes().getNodeList();
|
|
916
|
} catch (NotImplemented e) {
|
|
917
|
logMetacat.error("D1NodeService.isAuthoritativeMNodeAdmin - couldn't get the member nodes list from the CN since "+e.getDescription()+
|
|
918
|
". The false value will be returned for the AuthoritativeMNodeAdmin.");
|
|
919
|
return allowed;
|
|
920
|
} catch (ServiceFailure ee) {
|
|
921
|
logMetacat.error("D1NodeService.isAuthoritativeMNodeAdmin - couldn't get the member nodes list from the CN since "+ee.getDescription()+
|
|
922
|
". The false value will be returned for the AuthoritativeMNodeAdmin.");
|
|
923
|
return allowed;
|
|
924
|
}
|
|
925
|
if(nodes != null) {
|
|
926
|
for(Node node : nodes) {
|
|
927
|
//find the authoritative node and get its subjects
|
|
928
|
if (node.getType() == NodeType.MN && node.getIdentifier() != null && node.getIdentifier().equals(authoritativeMNode)) {
|
|
929
|
List<Subject> nodeSubjects = node.getSubjectList();
|
|
930
|
if(nodeSubjects != null) {
|
|
931
|
// check if the session subject is in the node subject list
|
|
932
|
for (Subject nodeSubject : nodeSubjects) {
|
|
933
|
logMetacat.debug("D1NodeService.isAuthoritativeMNodeAdmin(), comparing subjects: " +
|
|
934
|
nodeSubject.getValue() + " and " + subject.getValue());
|
|
935
|
if ( nodeSubject != null && nodeSubject.equals(subject) ) {
|
|
936
|
allowed = true; // subject of session == target node subject
|
|
937
|
break;
|
|
938
|
}
|
|
939
|
}
|
|
940
|
}
|
|
941
|
|
|
942
|
}
|
|
943
|
}
|
|
944
|
}
|
|
945
|
}
|
|
946
|
}
|
|
947
|
}
|
|
948
|
}
|
|
949
|
return allowed;
|
|
950
|
}
|
|
951
|
|
|
952
|
|
|
953
|
/**
|
|
954
|
* Test if the user identified by the provided token has administrative authorization
|
|
955
|
*
|
|
956
|
* @param session - the Session object containing the credentials for the Subject
|
|
957
|
*
|
|
958
|
* @return true if the user is admin (mn itself or a cn )
|
|
959
|
*
|
|
960
|
* @throws ServiceFailure
|
|
961
|
* @throws InvalidToken
|
|
962
|
* @throws NotFound
|
|
963
|
* @throws NotAuthorized
|
|
964
|
* @throws NotImplemented
|
|
965
|
*/
|
|
966
|
public boolean isAdminAuthorized(Session session)
|
|
967
|
throws ServiceFailure, InvalidToken, NotAuthorized,
|
|
968
|
NotImplemented {
|
|
969
|
|
|
970
|
boolean allowed = false;
|
|
971
|
|
|
972
|
// must have a session in order to check admin
|
|
973
|
if (session == null) {
|
|
974
|
logMetacat.debug("In isAdminAuthorized(), session is null ");
|
|
975
|
return false;
|
|
976
|
}
|
|
977
|
|
|
978
|
logMetacat.debug("In isAdminAuthorized(), checking CN or MN authorization for " +
|
|
979
|
session.getSubject().getValue());
|
|
980
|
|
|
981
|
// check if this is the node calling itself (MN)
|
|
982
|
try {
|
|
983
|
allowed = isNodeAdmin(session);
|
|
984
|
} catch (Exception e) {
|
|
985
|
logMetacat.warn("We can't determine if the session is a node subject. But we will contiune to check if it is a cn subject.");
|
|
986
|
}
|
|
987
|
|
|
988
|
|
|
989
|
// check the CN list
|
|
990
|
if (!allowed) {
|
|
991
|
allowed = isCNAdmin(session);
|
|
992
|
}
|
|
993
|
|
|
994
|
return allowed;
|
|
995
|
}
|
|
996
|
|
|
997
|
/*
|
|
998
|
* Determine if the specified session is a CN or not. Return true if it is; otherwise false.
|
|
999
|
*/
|
|
1000
|
protected boolean isCNAdmin (Session session) {
|
|
1001
|
boolean allowed = false;
|
|
1002
|
List<Node> nodes = null;
|
|
1003
|
logMetacat.debug("D1NodeService.isCNAdmin - the beginning");
|
|
1004
|
try {
|
|
1005
|
// are we allowed to do this? only CNs are allowed
|
|
1006
|
CNode cn = D1Client.getCN();
|
|
1007
|
logMetacat.debug("D1NodeService.isCNAdmin - after getting the cn.");
|
|
1008
|
nodes = cn.listNodes().getNodeList();
|
|
1009
|
logMetacat.debug("D1NodeService.isCNAdmin - after getting the node list.");
|
|
1010
|
}
|
|
1011
|
catch (Throwable e) {
|
|
1012
|
logMetacat.warn("Couldn't get the node list from the cn since "+e.getMessage()+". So we can't determine if the subject is a CN.");
|
|
1013
|
return false;
|
|
1014
|
}
|
|
1015
|
|
|
1016
|
if ( nodes == null ) {
|
|
1017
|
return false;
|
|
1018
|
//throw new ServiceFailure("4852", "Couldn't get node list.");
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
// find the node in the node list
|
|
1022
|
for ( Node node : nodes ) {
|
|
1023
|
|
|
1024
|
NodeReference nodeReference = node.getIdentifier();
|
|
1025
|
logMetacat.debug("In isCNAdmin(), a Node reference from the CN node list is: " + nodeReference.getValue());
|
|
1026
|
|
|
1027
|
Subject subject = session.getSubject();
|
|
1028
|
|
|
1029
|
if (node.getType() == NodeType.CN) {
|
|
1030
|
List<Subject> nodeSubjects = node.getSubjectList();
|
|
1031
|
|
|
1032
|
// check if the session subject is in the node subject list
|
|
1033
|
for (Subject nodeSubject : nodeSubjects) {
|
|
1034
|
logMetacat.debug("In isCNAdmin(), comparing subjects: " +
|
|
1035
|
nodeSubject.getValue() + " and the user " + subject.getValue());
|
|
1036
|
if ( nodeSubject.equals(subject) ) {
|
|
1037
|
allowed = true; // subject of session == target node subject
|
|
1038
|
break;
|
|
1039
|
|
|
1040
|
}
|
|
1041
|
}
|
|
1042
|
}
|
|
1043
|
}
|
|
1044
|
logMetacat.debug("D1NodeService.isCNAdmin. Is it a cn admin? "+allowed);
|
|
1045
|
return allowed;
|
|
1046
|
}
|
|
1047
|
|
|
1048
|
/**
|
|
1049
|
* Test if the user identified by the provided token has administrative authorization
|
|
1050
|
* on this node because they are calling themselves
|
|
1051
|
*
|
|
1052
|
* @param session - the Session object containing the credentials for the Subject
|
|
1053
|
*
|
|
1054
|
* @return true if the user is this node
|
|
1055
|
* @throws ServiceFailure
|
|
1056
|
* @throws NotImplemented
|
|
1057
|
*/
|
|
1058
|
public boolean isNodeAdmin(Session session) throws NotImplemented, ServiceFailure {
|
|
1059
|
|
|
1060
|
boolean allowed = false;
|
|
1061
|
|
|
1062
|
// must have a session in order to check admin
|
|
1063
|
if (session == null) {
|
|
1064
|
logMetacat.debug("In isNodeAdmin(), session is null ");
|
|
1065
|
return false;
|
|
1066
|
}
|
|
1067
|
|
|
1068
|
logMetacat.debug("In isNodeAdmin(), MN authorization for the user " +
|
|
1069
|
session.getSubject().getValue());
|
|
1070
|
|
|
1071
|
Node node = MNodeService.getInstance(request).getCapabilities();
|
|
1072
|
NodeReference nodeReference = node.getIdentifier();
|
|
1073
|
logMetacat.debug("In isNodeAdmin(), Node reference is: " + nodeReference.getValue());
|
|
1074
|
|
|
1075
|
Subject subject = session.getSubject();
|
|
1076
|
|
|
1077
|
if (node.getType() == NodeType.MN) {
|
|
1078
|
List<Subject> nodeSubjects = node.getSubjectList();
|
|
1079
|
|
|
1080
|
// check if the session subject is in the node subject list
|
|
1081
|
for (Subject nodeSubject : nodeSubjects) {
|
|
1082
|
logMetacat.debug("In isNodeAdmin(), comparing subjects: " +
|
|
1083
|
nodeSubject.getValue() + " and the user" + subject.getValue());
|
|
1084
|
if ( nodeSubject.equals(subject) ) {
|
|
1085
|
allowed = true; // subject of session == this node's subect
|
|
1086
|
break;
|
|
1087
|
}
|
|
1088
|
}
|
|
1089
|
}
|
|
1090
|
logMetacat.debug("In is NodeAdmin method. Is this a node admin? "+allowed);
|
|
1091
|
return allowed;
|
|
1092
|
}
|
|
1093
|
|
|
1094
|
/**
|
|
1095
|
* Test if the user identified by the provided token has authorization
|
|
1096
|
* for the operation on the specified object.
|
|
1097
|
* Allowed subjects include:
|
|
1098
|
* 1. CNs
|
|
1099
|
* 2. Authoritative node
|
|
1100
|
* 3. Owner of the object
|
|
1101
|
* 4. Users with the specified permission in the access rules.
|
|
1102
|
*
|
|
1103
|
* @param session - the Session object containing the credentials for the Subject
|
|
1104
|
* @param pid - The identifer of the resource for which access is being checked
|
|
1105
|
* @param operation - The type of operation which is being requested for the given pid
|
|
1106
|
*
|
|
1107
|
* @return true if the operation is allowed
|
|
1108
|
*
|
|
1109
|
* @throws ServiceFailure
|
|
1110
|
* @throws InvalidToken
|
|
1111
|
* @throws NotFound
|
|
1112
|
* @throws NotAuthorized
|
|
1113
|
* @throws NotImplemented
|
|
1114
|
* @throws InvalidRequest
|
|
1115
|
*/
|
|
1116
|
public boolean isAuthorized(Session session, Identifier pid, Permission permission)
|
|
1117
|
throws ServiceFailure, InvalidToken, NotFound, NotAuthorized,
|
|
1118
|
NotImplemented, InvalidRequest {
|
|
1119
|
|
|
1120
|
boolean allowed = false;
|
|
1121
|
|
|
1122
|
if (permission == null) {
|
|
1123
|
throw new InvalidRequest("1761", "Permission was not provided or is invalid");
|
|
1124
|
}
|
|
1125
|
|
|
1126
|
// always allow CN access
|
|
1127
|
if ( isAdminAuthorized(session) ) {
|
|
1128
|
allowed = true;
|
|
1129
|
return allowed;
|
|
1130
|
|
|
1131
|
}
|
|
1132
|
|
|
1133
|
String serviceFailureCode = "1760";
|
|
1134
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
|
1135
|
if(sid != null) {
|
|
1136
|
pid = sid;
|
|
1137
|
}
|
|
1138
|
|
|
1139
|
// the authoritative member node of the pid always has the access as well.
|
|
1140
|
if (isAuthoritativeMNodeAdmin(session, pid)) {
|
|
1141
|
allowed = true;
|
|
1142
|
return allowed;
|
|
1143
|
}
|
|
1144
|
|
|
1145
|
//is it the owner of the object or the access rules allow the user?
|
|
1146
|
allowed = userHasPermission(session, pid, permission );
|
|
1147
|
|
|
1148
|
// throw or return?
|
|
1149
|
if (!allowed) {
|
|
1150
|
// track the identities we have checked against
|
|
1151
|
StringBuffer includedSubjects = new StringBuffer();
|
|
1152
|
Set<Subject> subjects = AuthUtils.authorizedClientSubjects(session);
|
|
1153
|
for (Subject s: subjects) {
|
|
1154
|
includedSubjects.append(s.getValue() + "; ");
|
|
1155
|
}
|
|
1156
|
throw new NotAuthorized("1820", permission + " not allowed on " + pid.getValue() + " for subject[s]: " + includedSubjects.toString() );
|
|
1157
|
}
|
|
1158
|
|
|
1159
|
return allowed;
|
|
1160
|
|
|
1161
|
}
|
|
1162
|
|
|
1163
|
|
|
1164
|
/*
|
|
1165
|
* Determine if a user has the permission to perform the specified permission.
|
|
1166
|
* 1. Owner can have any permission.
|
|
1167
|
* 2. Access table allow the user has the permission
|
|
1168
|
*/
|
|
1169
|
public static boolean userHasPermission(Session userSession, Identifier pid, Permission permission ) throws NotFound, ServiceFailure, NotImplemented, InvalidRequest, InvalidToken, NotAuthorized {
|
|
1170
|
boolean allowed = false;
|
|
1171
|
// permissions are hierarchical
|
|
1172
|
List<Permission> expandedPermissions = null;
|
|
1173
|
// get the subject[s] from the session
|
|
1174
|
//defer to the shared util for recursively compiling the subjects
|
|
1175
|
Set<Subject> subjects = AuthUtils.authorizedClientSubjects(userSession);
|
|
1176
|
|
|
1177
|
// get the system metadata
|
|
1178
|
String pidStr = pid.getValue();
|
|
1179
|
SystemMetadata systemMetadata = null;
|
|
1180
|
try {
|
|
1181
|
systemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
|
1182
|
|
|
1183
|
} catch (Exception e) {
|
|
1184
|
// convert Hazelcast RuntimeException to NotFound
|
|
1185
|
logMetacat.error("An error occurred while getting system metadata for identifier " +
|
|
1186
|
pid.getValue() + ". The error message was: " + e.getMessage(), e);
|
|
1187
|
throw new ServiceFailure("1090", "Can't get the system metadata for " + pidStr+ " since "+e.getMessage());
|
|
1188
|
|
|
1189
|
}
|
|
1190
|
|
|
1191
|
// throw not found if it was not found
|
|
1192
|
if (systemMetadata == null) {
|
|
1193
|
String localId = null;
|
|
1194
|
String error = "No system metadata could be found for given PID: " + pidStr;
|
|
1195
|
try {
|
|
1196
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
1197
|
|
|
1198
|
} catch (Exception e) {
|
|
1199
|
logMetacat.warn("Couldn't find the local id for the pid "+pidStr);
|
|
1200
|
}
|
|
1201
|
|
|
1202
|
if(localId != null && EventLog.getInstance().isDeleted(localId)) {
|
|
1203
|
error = error + ". "+DELETEDMESSAGE;
|
|
1204
|
} else if (localId == null && EventLog.getInstance().isDeleted(pid.getValue())) {
|
|
1205
|
error = error + ". "+DELETEDMESSAGE;
|
|
1206
|
}
|
|
1207
|
throw new NotFound("1800", error);
|
|
1208
|
}
|
|
1209
|
|
|
1210
|
// do we own it?
|
|
1211
|
for (Subject s: subjects) {
|
|
1212
|
logMetacat.debug("Comparing \t" +
|
|
1213
|
systemMetadata.getRightsHolder().getValue() +
|
|
1214
|
" \tagainst \t" + s.getValue());
|
|
1215
|
//includedSubjects.append(s.getValue() + "; ");
|
|
1216
|
allowed = systemMetadata.getRightsHolder().equals(s);
|
|
1217
|
if (allowed) {
|
|
1218
|
return allowed;
|
|
1219
|
} else {
|
|
1220
|
//check if the rightHolder is a group name. If it is, any member of the group can be considered a the right holder.
|
|
1221
|
allowed = expandRightsHolder(systemMetadata.getRightsHolder(), s);
|
|
1222
|
if(allowed) {
|
|
1223
|
return allowed;
|
|
1224
|
}
|
|
1225
|
}
|
|
1226
|
}
|
|
1227
|
|
|
1228
|
// otherwise check the access rules
|
|
1229
|
try {
|
|
1230
|
List<AccessRule> allows = systemMetadata.getAccessPolicy().getAllowList();
|
|
1231
|
search: // label break
|
|
1232
|
for (AccessRule accessRule: allows) {
|
|
1233
|
for (Subject s: subjects) {
|
|
1234
|
logMetacat.debug("Checking allow access rule for subject: " + s.getValue());
|
|
1235
|
if (accessRule.getSubjectList().contains(s)) {
|
|
1236
|
logMetacat.debug("Access rule contains subject: " + s.getValue());
|
|
1237
|
for (Permission p: accessRule.getPermissionList()) {
|
|
1238
|
logMetacat.debug("Checking permission: " + p.xmlValue());
|
|
1239
|
expandedPermissions = expandPermissions(p);
|
|
1240
|
allowed = expandedPermissions.contains(permission);
|
|
1241
|
if (allowed) {
|
|
1242
|
logMetacat.info("Permission granted: " + p.xmlValue() + " to " + s.getValue());
|
|
1243
|
break search; //label break
|
|
1244
|
}
|
|
1245
|
}
|
|
1246
|
|
|
1247
|
}
|
|
1248
|
}
|
|
1249
|
}
|
|
1250
|
} catch (Exception e) {
|
|
1251
|
// catch all for errors - safe side should be to deny the access
|
|
1252
|
logMetacat.error("Problem checking authorization - defaulting to deny", e);
|
|
1253
|
allowed = false;
|
|
1254
|
|
|
1255
|
}
|
|
1256
|
return allowed;
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
|
|
1260
|
/**
|
|
1261
|
* Check if the given userSession is the member of the right holder group (if the right holder is a group subject).
|
|
1262
|
* If the right holder is not a group, it will be false of course.
|
|
1263
|
* @param rightHolder the subject of the right holder.
|
|
1264
|
* @param userSession the subject will be compared
|
|
1265
|
* @return true if the user session is a member of the right holder group; false otherwise.
|
|
1266
|
* @throws NotImplemented
|
|
1267
|
* @throws ServiceFailure
|
|
1268
|
* @throws NotAuthorized
|
|
1269
|
* @throws InvalidToken
|
|
1270
|
* @throws InvalidRequest
|
|
1271
|
*/
|
|
1272
|
public static boolean expandRightsHolder(Subject rightHolder, Subject userSession) throws ServiceFailure, NotImplemented, InvalidRequest, InvalidToken, NotAuthorized {
|
|
1273
|
boolean is = false;
|
|
1274
|
if(rightHolder != null && userSession != null && rightHolder.getValue() != null && !rightHolder.getValue().trim().equals("") && userSession.getValue() != null && !userSession.getValue().trim().equals("")) {
|
|
1275
|
CNode cn = D1Client.getCN();
|
|
1276
|
logMetacat.debug("D1NodeService.expandRightHolder - at the start of method: after getting the cn node and cn node is "+cn.getNodeBaseServiceUrl());
|
|
1277
|
String query= rightHolder.getValue();
|
|
1278
|
int start =0;
|
|
1279
|
int count= 200;
|
|
1280
|
String status = null;
|
|
1281
|
Session session = null;
|
|
1282
|
SubjectInfo subjects = cn.listSubjects(session, query, status, start, count);
|
|
1283
|
|
|
1284
|
while(subjects != null) {
|
|
1285
|
logMetacat.debug("D1NodeService.expandRightHolder - search the subject "+query+" in the cn and the returned result is not null");
|
|
1286
|
List<Group> groups = subjects.getGroupList();
|
|
1287
|
is = isInGroups(userSession, rightHolder, groups);
|
|
1288
|
if(is) {
|
|
1289
|
//since we find it, return it.
|
|
1290
|
return is;
|
|
1291
|
} else {
|
|
1292
|
//decide if we need to try the page query for another trying.
|
|
1293
|
int sizeOfGroups = 0;
|
|
1294
|
if(groups != null) {
|
|
1295
|
sizeOfGroups = groups.size();
|
|
1296
|
}
|
|
1297
|
List<Person> persons = subjects.getPersonList();
|
|
1298
|
int sizeOfPersons = 0;
|
|
1299
|
if(persons != null) {
|
|
1300
|
sizeOfPersons = persons.size();
|
|
1301
|
}
|
|
1302
|
int totalSize = sizeOfGroups+sizeOfPersons;
|
|
1303
|
//logMetacat.debug("D1NodeService.expandRightHolder - search the subject "+query+" in the cn and the size of return result is "+totalSize);
|
|
1304
|
//we can't find the target on the first query, maybe query again.
|
|
1305
|
if(totalSize == count) {
|
|
1306
|
start = start+count;
|
|
1307
|
logMetacat.debug("D1NodeService.expandRightHolder - search the subject "+query+" in the cn and the size of return result equals the count "+totalSize+" .And we didn't find the target in the this query. So we have to use the page query with the start number "+start);
|
|
1308
|
subjects = cn.listSubjects(session, query, status, start, count);
|
|
1309
|
} else if (totalSize < count){
|
|
1310
|
logMetacat.debug("D1NodeService.expandRightHolder - we are already at the end of the returned restult since the size of returned results "+totalSize+
|
|
1311
|
" is less than the count "+count+". So we have to break the loop and finish the try.");
|
|
1312
|
break;
|
|
1313
|
} else if (totalSize >count) {
|
|
1314
|
logMetacat.warn("D1NodeService.expandRightHolder - Something is wrong on the implementation of the method listSubject since the size of returned results "+totalSize+
|
|
1315
|
" is greater than the count "+count+". So we have to break the loop and finish the try.");
|
|
1316
|
break;
|
|
1317
|
}
|
|
1318
|
}
|
|
1319
|
|
|
1320
|
}
|
|
1321
|
//logMetacat.debug("D1NodeService.expandRightHolder - search the subject "+query+" in the cn and the returned result is null");
|
|
1322
|
if(!is) {
|
|
1323
|
logMetacat.debug("D1NodeService.expandRightHolder - We can NOT find any member in the group "+query+" (if it is a group) matches the user "+userSession.getValue());
|
|
1324
|
}
|
|
1325
|
} else {
|
|
1326
|
logMetacat.debug("D1NodeService.expandRightHolder - We can't determine if the use subject is a member of the right holder group since one of them is null or blank");
|
|
1327
|
}
|
|
1328
|
|
|
1329
|
return is;
|
|
1330
|
}
|
|
1331
|
|
|
1332
|
/*
|
|
1333
|
* If the given useSession is a member of a group which is in the given list of groups and has the name of righHolder.
|
|
1334
|
*/
|
|
1335
|
private static boolean isInGroups(Subject userSession, Subject rightHolder, List<Group> groups) {
|
|
1336
|
boolean is = false;
|
|
1337
|
if(groups != null) {
|
|
1338
|
logMetacat.debug("D1NodeService.isInGroups - the given groups' (the returned result including groups) size is "+groups.size());
|
|
1339
|
for(Group group : groups) {
|
|
1340
|
//logMetacat.debug("D1NodeService.expandRightHolder - group has the subject "+group.getSubject().getValue());
|
|
1341
|
if(group != null && group.getSubject() != null && group.getSubject().equals(rightHolder)) {
|
|
1342
|
logMetacat.debug("D1NodeService.isInGroups - there is a group in the list having the subjecct "+group.getSubject().getValue()+" which matches the right holder's subject "+rightHolder.getValue());
|
|
1343
|
List<Subject> members = group.getHasMemberList();
|
|
1344
|
if(members != null ){
|
|
1345
|
logMetacat.debug("D1NodeService.isInGroups - the group "+group.getSubject().getValue()+" in the cn has members");
|
|
1346
|
for(Subject member : members) {
|
|
1347
|
logMetacat.debug("D1NodeService.isInGroups - compare the member "+member.getValue()+" with the user "+userSession.getValue());
|
|
1348
|
if(member.getValue() != null && !member.getValue().trim().equals("") && userSession.getValue() != null && member.getValue().equals(userSession.getValue())) {
|
|
1349
|
logMetacat.debug("D1NodeService.isInGroups - Find it! The member "+member.getValue()+" in the group "+group.getSubject().getValue()+" matches the user "+userSession.getValue());
|
|
1350
|
is = true;
|
|
1351
|
return is;
|
|
1352
|
}
|
|
1353
|
}
|
|
1354
|
}
|
|
1355
|
break;//we found the group but can't find the member matches the user. so break it.
|
|
1356
|
}
|
|
1357
|
}
|
|
1358
|
} else {
|
|
1359
|
logMetacat.debug("D1NodeService.isInGroups - the given group is null (the returned result does NOT have a group");
|
|
1360
|
}
|
|
1361
|
return is;
|
|
1362
|
}
|
|
1363
|
/*
|
|
1364
|
* parse a logEntry and get the relevant field from it
|
|
1365
|
*
|
|
1366
|
* @param fieldname
|
|
1367
|
* @param entry
|
|
1368
|
* @return
|
|
1369
|
*/
|
|
1370
|
private String getLogEntryField(String fieldname, String entry) {
|
|
1371
|
String begin = "<" + fieldname + ">";
|
|
1372
|
String end = "</" + fieldname + ">";
|
|
1373
|
// logMetacat.debug("looking for " + begin + " and " + end +
|
|
1374
|
// " in entry " + entry);
|
|
1375
|
String s = entry.substring(entry.indexOf(begin) + begin.length(), entry
|
|
1376
|
.indexOf(end));
|
|
1377
|
logMetacat.debug("entry " + fieldname + " : " + s);
|
|
1378
|
return s;
|
|
1379
|
}
|
|
1380
|
|
|
1381
|
/**
|
|
1382
|
* Determine if a given object should be treated as an XML science metadata
|
|
1383
|
* object.
|
|
1384
|
*
|
|
1385
|
* @param sysmeta - the SystemMetadata describing the object
|
|
1386
|
* @return true if the object should be treated as science metadata
|
|
1387
|
*/
|
|
1388
|
public static boolean isScienceMetadata(SystemMetadata sysmeta) {
|
|
1389
|
|
|
1390
|
ObjectFormat objectFormat = null;
|
|
1391
|
boolean isScienceMetadata = false;
|
|
1392
|
|
|
1393
|
try {
|
|
1394
|
objectFormat = ObjectFormatCache.getInstance().getFormat(sysmeta.getFormatId());
|
|
1395
|
if ( objectFormat.getFormatType().equals("METADATA") ) {
|
|
1396
|
isScienceMetadata = true;
|
|
1397
|
|
|
1398
|
}
|
|
1399
|
|
|
1400
|
|
|
1401
|
/*} catch (ServiceFailure e) {
|
|
1402
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
|
1403
|
sysmeta.getIdentifier().getValue() +
|
|
1404
|
" is science metadata: " + e.getMessage());*/
|
|
1405
|
|
|
1406
|
} catch (NotFound e) {
|
|
1407
|
logMetacat.debug("There was a problem determining if the object identified by" +
|
|
1408
|
sysmeta.getIdentifier().getValue() +
|
|
1409
|
" is science metadata: " + e.getMessage());
|
|
1410
|
|
|
1411
|
}
|
|
1412
|
|
|
1413
|
return isScienceMetadata;
|
|
1414
|
|
|
1415
|
}
|
|
1416
|
|
|
1417
|
/**
|
|
1418
|
* Check fro whitespace in the given pid.
|
|
1419
|
* null pids are also invalid by default
|
|
1420
|
* @param pid
|
|
1421
|
* @return
|
|
1422
|
*/
|
|
1423
|
public static boolean isValidIdentifier(Identifier pid) {
|
|
1424
|
if (pid != null && pid.getValue() != null && pid.getValue().length() > 0) {
|
|
1425
|
return !pid.getValue().matches(".*\\s+.*");
|
|
1426
|
}
|
|
1427
|
return false;
|
|
1428
|
}
|
|
1429
|
|
|
1430
|
|
|
1431
|
/**
|
|
1432
|
* Insert or update an XML document into Metacat
|
|
1433
|
*
|
|
1434
|
* @param xml - the XML document to insert or update
|
|
1435
|
* @param pid - the identifier to be used for the resulting object
|
|
1436
|
*
|
|
1437
|
* @return localId - the resulting docid of the document created or updated
|
|
1438
|
*
|
|
1439
|
*/
|
|
1440
|
public String insertOrUpdateDocument(InputStream xmlStream, String encoding, Identifier pid,
|
|
1441
|
Session session, String insertOrUpdate, String formatId, Checksum checksum)
|
|
1442
|
throws ServiceFailure, IOException, PropertyNotFoundException{
|
|
1443
|
|
|
1444
|
logMetacat.debug("Starting to insert xml document...");
|
|
1445
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
1446
|
|
|
1447
|
// generate pid/localId pair for sysmeta
|
|
1448
|
String localId = null;
|
|
1449
|
byte[] xmlBytes = IOUtils.toByteArray(xmlStream);
|
|
1450
|
IOUtils.closeQuietly(xmlStream);
|
|
1451
|
String xmlStr = new String(xmlBytes, encoding);
|
|
1452
|
if(insertOrUpdate.equals("insert")) {
|
|
1453
|
localId = im.generateLocalId(pid.getValue(), 1);
|
|
1454
|
|
|
1455
|
} else {
|
|
1456
|
//localid should already exist in the identifier table, so just find it
|
|
1457
|
try {
|
|
1458
|
logMetacat.debug("Updating pid " + pid.getValue());
|
|
1459
|
logMetacat.debug("looking in identifier table for pid " + pid.getValue());
|
|
1460
|
|
|
1461
|
localId = im.getLocalId(pid.getValue());
|
|
1462
|
|
|
1463
|
logMetacat.debug("localId: " + localId);
|
|
1464
|
//increment the revision
|
|
1465
|
String docid = localId.substring(0, localId.lastIndexOf("."));
|
|
1466
|
String revS = localId.substring(localId.lastIndexOf(".") + 1, localId.length());
|
|
1467
|
int rev = new Integer(revS).intValue();
|
|
1468
|
rev++;
|
|
1469
|
docid = docid + "." + rev;
|
|
1470
|
localId = docid;
|
|
1471
|
logMetacat.debug("incremented localId: " + localId);
|
|
1472
|
|
|
1473
|
} catch(McdbDocNotFoundException e) {
|
|
1474
|
throw new ServiceFailure("1030", "D1NodeService.insertOrUpdateDocument(): " +
|
|
1475
|
"pid " + pid.getValue() +
|
|
1476
|
" should have been in the identifier table, but it wasn't: " +
|
|
1477
|
e.getMessage());
|
|
1478
|
|
|
1479
|
} catch (SQLException e) {
|
|
1480
|
throw new ServiceFailure("1030", "D1NodeService.insertOrUpdateDocument() -"+
|
|
1481
|
" couldn't identify if the pid "+pid.getValue()+" is in the identifier table since "+e.getMessage());
|
|
1482
|
}
|
|
1483
|
|
|
1484
|
}
|
|
1485
|
|
|
1486
|
Hashtable<String, String[]> params = new Hashtable<String, String[]>();
|
|
1487
|
String[] action = new String[1];
|
|
1488
|
action[0] = insertOrUpdate;
|
|
1489
|
params.put("action", action);
|
|
1490
|
String[] docid = new String[1];
|
|
1491
|
docid[0] = localId;
|
|
1492
|
params.put("docid", docid);
|
|
1493
|
String[] doctext = new String[1];
|
|
1494
|
doctext[0] = xmlStr;
|
|
1495
|
params.put("doctext", doctext);
|
|
1496
|
|
|
1497
|
String username = Constants.SUBJECT_PUBLIC;
|
|
1498
|
String[] groupnames = null;
|
|
1499
|
if (session != null ) {
|
|
1500
|
username = session.getSubject().getValue();
|
|
1501
|
Set<Subject> otherSubjects = AuthUtils.authorizedClientSubjects(session);
|
|
1502
|
if (otherSubjects != null) {
|
|
1503
|
groupnames = new String[otherSubjects.size()];
|
|
1504
|
int i = 0;
|
|
1505
|
Iterator<Subject> iter = otherSubjects.iterator();
|
|
1506
|
while (iter.hasNext()) {
|
|
1507
|
groupnames[i] = iter.next().getValue();
|
|
1508
|
i++;
|
|
1509
|
}
|
|
1510
|
}
|
|
1511
|
}
|
|
1512
|
|
|
1513
|
// do the insert or update action
|
|
1514
|
handler = new MetacatHandler(new Timer());
|
|
1515
|
String result = handler.handleInsertOrUpdateAction(request.getRemoteAddr(), request.getHeader("User-Agent"), null,
|
|
1516
|
null, params, username, groupnames, false, false, xmlBytes, formatId, checksum);
|
|
1517
|
boolean isScienceMetadata = true;
|
|
1518
|
if(result.indexOf("<error>") != -1 || !IdentifierManager.getInstance().objectFileExists(localId, isScienceMetadata)) {
|
|
1519
|
String detailCode = "";
|
|
1520
|
if ( insertOrUpdate.equals("insert") ) {
|
|
1521
|
// make sure to remove the mapping so that subsequent attempts do not fail with IdentifierNotUnique
|
|
1522
|
im.removeMapping(pid.getValue(), localId);
|
|
1523
|
detailCode = "1190";
|
|
1524
|
|
|
1525
|
} else if ( insertOrUpdate.equals("update") ) {
|
|
1526
|
detailCode = "1310";
|
|
1527
|
|
|
1528
|
}
|
|
1529
|
logMetacat.error("D1NodeService.insertOrUpdateDocument - Error inserting or updating document: "+pid.getValue()+" since "+result);
|
|
1530
|
throw new ServiceFailure(detailCode,
|
|
1531
|
"Error inserting or updating document: " +pid.getValue()+" since "+ result);
|
|
1532
|
}
|
|
1533
|
logMetacat.info("D1NodeService.insertOrUpdateDocument - Finsished inserting xml document with local id " + localId +" and its pid is "+pid.getValue());
|
|
1534
|
|
|
1535
|
return localId;
|
|
1536
|
}
|
|
1537
|
|
|
1538
|
/**
|
|
1539
|
* Insert a data document
|
|
1540
|
*
|
|
1541
|
* @param object
|
|
1542
|
* @param pid
|
|
1543
|
* @param sessionData
|
|
1544
|
* @throws ServiceFailure
|
|
1545
|
* @returns localId of the data object inserted
|
|
1546
|
*/
|
|
1547
|
public String insertDataObject(InputStream object, Identifier pid,
|
|
1548
|
Session session, Checksum checksum) throws ServiceFailure, InvalidSystemMetadata {
|
|
1549
|
|
|
1550
|
String username = Constants.SUBJECT_PUBLIC;
|
|
1551
|
String[] groupnames = null;
|
|
1552
|
if (session != null ) {
|
|
1553
|
username = session.getSubject().getValue();
|
|
1554
|
Set<Subject> otherSubjects = AuthUtils.authorizedClientSubjects(session);
|
|
1555
|
if (otherSubjects != null) {
|
|
1556
|
groupnames = new String[otherSubjects.size()];
|
|
1557
|
int i = 0;
|
|
1558
|
Iterator<Subject> iter = otherSubjects.iterator();
|
|
1559
|
while (iter.hasNext()) {
|
|
1560
|
groupnames[i] = iter.next().getValue();
|
|
1561
|
i++;
|
|
1562
|
}
|
|
1563
|
}
|
|
1564
|
}
|
|
1565
|
|
|
1566
|
// generate pid/localId pair for object
|
|
1567
|
logMetacat.debug("Generating a pid/localId mapping");
|
|
1568
|
IdentifierManager im = IdentifierManager.getInstance();
|
|
1569
|
String localId = im.generateLocalId(pid.getValue(), 1);
|
|
1570
|
|
|
1571
|
// Save the data file to disk using "localId" as the name
|
|
1572
|
String datafilepath = null;
|
|
1573
|
try {
|
|
1574
|
datafilepath = PropertyService.getProperty("application.datafilepath");
|
|
1575
|
} catch (PropertyNotFoundException e) {
|
|
1576
|
ServiceFailure sf = new ServiceFailure("1190", "Lookup data file path" + e.getMessage());
|
|
1577
|
sf.initCause(e);
|
|
1578
|
throw sf;
|
|
1579
|
}
|
|
1580
|
boolean locked = false;
|
|
1581
|
try {
|
|
1582
|
locked = DocumentImpl.getDataFileLockGrant(localId);
|
|
1583
|
} catch (Exception e) {
|
|
1584
|
ServiceFailure sf = new ServiceFailure("1190", "Could not lock file for writing:" + e.getMessage());
|
|
1585
|
sf.initCause(e);
|
|
1586
|
throw sf;
|
|
1587
|
}
|
|
1588
|
|
|
1589
|
logMetacat.debug("Case DATA: starting to write to disk.");
|
|
1590
|
if (locked) {
|
|
1591
|
|
|
1592
|
File dataDirectory = new File(datafilepath);
|
|
1593
|
dataDirectory.mkdirs();
|
|
1594
|
|
|
1595
|
File newFile = writeStreamToFile(dataDirectory, localId, object, checksum, pid);
|
|
1596
|
|
|
1597
|
// TODO: Check that the file size matches SystemMetadata
|
|
1598
|
// long size = newFile.length();
|
|
1599
|
// if (size == 0) {
|
|
1600
|
// throw new IOException("Uploaded file is 0 bytes!");
|
|
1601
|
// }
|
|
1602
|
|
|
1603
|
// Register the file in the database (which generates an exception
|
|
1604
|
// if the localId is not acceptable or other untoward things happen
|
|
1605
|
try {
|
|
1606
|
logMetacat.debug("Registering document...");
|
|
1607
|
DocumentImpl.registerDocument(localId, "BIN", localId,
|
|
1608
|
username, groupnames);
|
|
1609
|
logMetacat.debug("Registration step completed.");
|
|
1610
|
|
|
1611
|
} catch (SQLException e) {
|
|
1612
|
//newFile.delete();
|
|
1613
|
logMetacat.debug("SQLE: " + e.getMessage());
|
|
1614
|
e.printStackTrace(System.out);
|
|
1615
|
throw new ServiceFailure("1190", "Registration failed: " +
|
|
1616
|
e.getMessage());
|
|
1617
|
|
|
1618
|
} catch (AccessionNumberException e) {
|
|
1619
|
//newFile.delete();
|
|
1620
|
logMetacat.debug("ANE: " + e.getMessage());
|
|
1621
|
e.printStackTrace(System.out);
|
|
1622
|
throw new ServiceFailure("1190", "Registration failed: " +
|
|
1623
|
e.getMessage());
|
|
1624
|
|
|
1625
|
} catch (Exception e) {
|
|
1626
|
//newFile.delete();
|
|
1627
|
logMetacat.debug("Exception: " + e.getMessage());
|
|
1628
|
e.printStackTrace(System.out);
|
|
1629
|
throw new ServiceFailure("1190", "Registration failed: " +
|
|
1630
|
e.getMessage());
|
|
1631
|
}
|
|
1632
|
|
|
1633
|
logMetacat.debug("Logging the creation event.");
|
|
1634
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, "create");
|
|
1635
|
|
|
1636
|
// Schedule replication for this data file, the "insert" action is important here!
|
|
1637
|
logMetacat.debug("Scheduling replication.");
|
|
1638
|
ForceReplicationHandler frh = new ForceReplicationHandler(localId, "insert", false, null);
|
|
1639
|
}
|
|
1640
|
|
|
1641
|
return localId;
|
|
1642
|
|
|
1643
|
}
|
|
1644
|
|
|
1645
|
/**
|
|
1646
|
* Insert a systemMetadata document and return its localId
|
|
1647
|
*/
|
|
1648
|
public void insertSystemMetadata(SystemMetadata sysmeta)
|
|
1649
|
throws ServiceFailure {
|
|
1650
|
|
|
1651
|
logMetacat.debug("Starting to insert SystemMetadata...");
|
|
1652
|
sysmeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
|
1653
|
logMetacat.debug("Inserting new system metadata with modified date " +
|
|
1654
|
sysmeta.getDateSysMetadataModified());
|
|
1655
|
|
|
1656
|
//insert the system metadata
|
|
1657
|
try {
|
|
1658
|
// note: the calling subclass handles the map hazelcast lock/unlock
|
|
1659
|
HazelcastService.getInstance().getSystemMetadataMap().put(sysmeta.getIdentifier(), sysmeta);
|
|
1660
|
// submit for indexing
|
|
1661
|
MetacatSolrIndex.getInstance().submit(sysmeta.getIdentifier(), sysmeta, null, true);
|
|
1662
|
} catch (Exception e) {
|
|
1663
|
throw new ServiceFailure("1190", e.getMessage());
|
|
1664
|
|
|
1665
|
}
|
|
1666
|
}
|
|
1667
|
|
|
1668
|
/**
|
|
1669
|
* Retrieve the list of objects present on the MN that match the calling parameters
|
|
1670
|
*
|
|
1671
|
* @param session - the Session object containing the credentials for the Subject
|
|
1672
|
* @param startTime - Specifies the beginning of the time range from which
|
|
1673
|
* to return object (>=)
|
|
1674
|
* @param endTime - Specifies the beginning of the time range from which
|
|
1675
|
* to return object (>=)
|
|
1676
|
* @param objectFormat - Restrict results to the specified object format
|
|
1677
|
* @param replicaStatus - Indicates if replicated objects should be returned in the list
|
|
1678
|
* @param start - The zero-based index of the first value, relative to the
|
|
1679
|
* first record of the resultset that matches the parameters.
|
|
1680
|
* @param count - The maximum number of entries that should be returned in
|
|
1681
|
* the response. The Member Node may return less entries
|
|
1682
|
* than specified in this value.
|
|
1683
|
*
|
|
1684
|
* @return objectList - the list of objects matching the criteria
|
|
1685
|
*
|
|
1686
|
* @throws InvalidToken
|
|
1687
|
* @throws ServiceFailure
|
|
1688
|
* @throws NotAuthorized
|
|
1689
|
* @throws InvalidRequest
|
|
1690
|
* @throws NotImplemented
|
|
1691
|
*/
|
|
1692
|
public ObjectList listObjects(Session session, Date startTime, Date endTime, ObjectFormatIdentifier objectFormatId, Identifier identifier, NodeReference nodeId, Integer start,
|
|
1693
|
Integer count) throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken {
|
|
1694
|
|
|
1695
|
ObjectList objectList = null;
|
|
1696
|
|
|
1697
|
try {
|
|
1698
|
// safeguard against large requests
|
|
1699
|
if (count == null || count > MAXIMUM_DB_RECORD_COUNT) {
|
|
1700
|
count = MAXIMUM_DB_RECORD_COUNT;
|
|
1701
|
}
|
|
1702
|
boolean isSid = false;
|
|
1703
|
if(identifier != null) {
|
|
1704
|
isSid = IdentifierManager.getInstance().systemMetadataSIDExists(identifier);
|
|
1705
|
}
|
|
1706
|
objectList = IdentifierManager.getInstance().querySystemMetadata(startTime, endTime, objectFormatId, nodeId, start, count, identifier, isSid);
|
|
1707
|
} catch (Exception e) {
|
|
1708
|
throw new ServiceFailure("1580", "Error querying system metadata: " + e.getMessage());
|
|
1709
|
}
|
|
1710
|
|
|
1711
|
return objectList;
|
|
1712
|
}
|
|
1713
|
|
|
1714
|
|
|
1715
|
/**
|
|
1716
|
* Update a systemMetadata document
|
|
1717
|
*
|
|
1718
|
* @param sysMeta - the system metadata object in the system to update
|
|
1719
|
*/
|
|
1720
|
protected void updateSystemMetadata(SystemMetadata sysMeta)
|
|
1721
|
throws ServiceFailure {
|
|
1722
|
logMetacat.debug("D1NodeService.updateSystemMetadata() called.");
|
|
1723
|
try {
|
|
1724
|
HazelcastService.getInstance().getSystemMetadataMap().lock(sysMeta.getIdentifier());
|
|
1725
|
boolean needUpdateModificationDate = true;
|
|
1726
|
updateSystemMetadataWithoutLock(sysMeta, needUpdateModificationDate);
|
|
1727
|
} catch (Exception e) {
|
|
1728
|
throw new ServiceFailure("4862", e.getMessage());
|
|
1729
|
} finally {
|
|
1730
|
HazelcastService.getInstance().getSystemMetadataMap().unlock(sysMeta.getIdentifier());
|
|
1731
|
|
|
1732
|
}
|
|
1733
|
|
|
1734
|
}
|
|
1735
|
|
|
1736
|
/**
|
|
1737
|
* Update system metadata without locking the system metadata in hazelcast server. So the caller should lock it first.
|
|
1738
|
* @param sysMeta
|
|
1739
|
* @param needUpdateModificationDate
|
|
1740
|
* @throws ServiceFailure
|
|
1741
|
*/
|
|
1742
|
private void updateSystemMetadataWithoutLock(SystemMetadata sysMeta, boolean needUpdateModificationDate) throws ServiceFailure {
|
|
1743
|
logMetacat.debug("D1NodeService.updateSystemMetadataWithoutLock() called.");
|
|
1744
|
if(needUpdateModificationDate) {
|
|
1745
|
logMetacat.debug("D1NodeService.updateSystemMetadataWithoutLock() - update the modification date.");
|
|
1746
|
sysMeta.setDateSysMetadataModified(new Date());
|
|
1747
|
}
|
|
1748
|
|
|
1749
|
// submit for indexing
|
|
1750
|
try {
|
|
1751
|
HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
|
|
1752
|
MetacatSolrIndex.getInstance().submit(sysMeta.getIdentifier(), sysMeta, null, true);
|
|
1753
|
} catch (Exception e) {
|
|
1754
|
throw new ServiceFailure("4862", e.getMessage());
|
|
1755
|
//logMetacat.warn("D1NodeService.updateSystemMetadataWithoutLock - we can't submit the change of the system metadata to the solr index since "+e.getMessage());
|
|
1756
|
}
|
|
1757
|
}
|
|
1758
|
|
|
1759
|
/**
|
|
1760
|
* Update the system metadata of the specified pid. The caller of this method should lock the system metadata in hazelcast server.
|
|
1761
|
* @param session - the identity of the client which calls the method
|
|
1762
|
* @param pid - the identifier of the object which will be updated
|
|
1763
|
* @param sysmeta - the new system metadata
|
|
1764
|
* @return
|
|
1765
|
* @throws NotImplemented
|
|
1766
|
* @throws NotAuthorized
|
|
1767
|
* @throws ServiceFailure
|
|
1768
|
* @throws InvalidRequest
|
|
1769
|
* @throws InvalidSystemMetadata
|
|
1770
|
* @throws InvalidToken
|
|
1771
|
*/
|
|
1772
|
protected boolean updateSystemMetadata(Session session, Identifier pid,
|
|
1773
|
SystemMetadata sysmeta, boolean needUpdateModificationDate, SystemMetadata currentSysmeta, boolean fromCN) throws NotImplemented, NotAuthorized,
|
|
1774
|
ServiceFailure, InvalidRequest, InvalidSystemMetadata, InvalidToken {
|
|
1775
|
|
|
1776
|
// The lock to be used for this identifier
|
|
1777
|
Lock lock = null;
|
|
1778
|
|
|
1779
|
// verify that guid == SystemMetadata.getIdentifier()
|
|
1780
|
logMetacat.debug("Comparing guid|sysmeta_guid: " + pid.getValue() +
|
|
1781
|
"|" + sysmeta.getIdentifier().getValue());
|
|
1782
|
|
|
1783
|
if (!pid.getValue().equals(sysmeta.getIdentifier().getValue())) {
|
|
1784
|
throw new InvalidRequest("4863",
|
|
1785
|
"The identifier in method call (" + pid.getValue() +
|
|
1786
|
") does not match identifier in system metadata (" +
|
|
1787
|
sysmeta.getIdentifier().getValue() + ").");
|
|
1788
|
}
|
|
1789
|
//compare serial version.
|
|
1790
|
|
|
1791
|
//check the sid
|
|
1792
|
//SystemMetadata currentSysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
|
1793
|
logMetacat.debug("The current dateUploaded is ============"+currentSysmeta.getDateUploaded());
|
|
1794
|
logMetacat.debug("the dateUploaded in the new system metadata is "+sysmeta.getDateUploaded());
|
|
1795
|
logMetacat.debug("The current dateUploaded is (by time) ============"+currentSysmeta.getDateUploaded().getTime());
|
|
1796
|
logMetacat.debug("the dateUploaded in the new system metadata is (by time) "+sysmeta.getDateUploaded().getTime());
|
|
1797
|
if(currentSysmeta == null ) {
|
|
1798
|
//do we need throw an exception?
|
|
1799
|
logMetacat.warn("D1NodeService.updateSystemMetadata: Currently there is no system metadata in this node associated with the pid "+pid.getValue());
|
|
1800
|
} else {
|
|
1801
|
|
|
1802
|
/*BigInteger newVersion = sysmeta.getSerialVersion();
|
|
1803
|
if(newVersion == null) {
|
|
1804
|
throw new InvalidRequest("4869", "The serial version can't be null in the new system metadata");
|
|
1805
|
}
|
|
1806
|
BigInteger currentVersion = currentSysmeta.getSerialVersion();
|
|
1807
|
if(currentVersion != null && newVersion.compareTo(currentVersion) <= 0) {
|
|
1808
|
throw new InvalidRequest("4869", "The serial version in the new system metadata is "+newVersion.toString()+
|
|
1809
|
" which is less than or equals the previous version "+currentVersion.toString()+". This is illegal in the updateSystemMetadata method.");
|
|
1810
|
}*/
|
|
1811
|
Identifier currentSid = currentSysmeta.getSeriesId();
|
|
1812
|
if(currentSid != null) {
|
|
1813
|
logMetacat.debug("In the branch that the sid is not null in the current system metadata and the current sid is "+currentSid.getValue());
|
|
1814
|
//new sid must match the current sid
|
|
1815
|
Identifier newSid = sysmeta.getSeriesId();
|
|
1816
|
if (!isValidIdentifier(newSid)) {
|
|
1817
|
throw new InvalidRequest("4869", "The series id in the system metadata is invalid in the request.");
|
|
1818
|
} else {
|
|
1819
|
if(!newSid.getValue().equals(currentSid.getValue())) {
|
|
1820
|
throw new InvalidRequest("4869", "The series id "+newSid.getValue() +" in the system metadata doesn't match the current sid "+currentSid.getValue());
|
|
1821
|
}
|
|
1822
|
}
|
|
1823
|
} else {
|
|
1824
|
//current system metadata doesn't have a sid. So we can have those scenarios
|
|
1825
|
//1. The new sid may be null as well
|
|
1826
|
//2. If the new sid does exist, it may be an identifier which hasn't bee used.
|
|
1827
|
//3. If the new sid does exist, it may be an sid which equals the SID it obsoletes
|
|
1828
|
//4. If the new sid does exist, it may be an sid which equauls the SID it was obsoleted by
|
|
1829
|
Identifier newSid = sysmeta.getSeriesId();
|
|
1830
|
if(newSid != null) {
|
|
1831
|
//It matches the rules of the checkSidInModifyingSystemMetadata
|
|
1832
|
checkSidInModifyingSystemMetadata(sysmeta, "4956", "4868");
|
|
1833
|
}
|
|
1834
|
}
|
|
1835
|
checkModifiedImmutableFields(currentSysmeta, sysmeta);
|
|
1836
|
checkOneTimeSettableSysmMetaFields(currentSysmeta, sysmeta);
|
|
1837
|
if(currentSysmeta.getObsoletes() == null && sysmeta.getObsoletes() != null) {
|
|
1838
|
//we are setting a value to the obsoletes field, so we should make sure if there is not object obsoletes the value
|
|
1839
|
String obsoletes = existsInObsoletes(sysmeta.getObsoletes());
|
|
1840
|
if( obsoletes != null) {
|
|
1841
|
throw new InvalidSystemMetadata("4956", "There is an object with id "+obsoletes +
|
|
1842
|
" already obsoletes the pid "+sysmeta.getObsoletes().getValue() +". You can't set the object "+pid.getValue()+" to obsolete the pid "+sysmeta.getObsoletes().getValue()+" again.");
|
|
1843
|
}
|
|
1844
|
}
|
|
1845
|
checkCircularObsoletesChain(sysmeta);
|
|
1846
|
if(currentSysmeta.getObsoletedBy() == null && sysmeta.getObsoletedBy() != null) {
|
|
1847
|
//we are setting a value to the obsoletedBy field, so we should make sure that the no another object obsoletes the pid we are updating.
|
|
1848
|
String obsoletedBy = existsInObsoletedBy(sysmeta.getObsoletedBy());
|
|
1849
|
if( obsoletedBy != null) {
|
|
1850
|
throw new InvalidSystemMetadata("4956", "There is an object with id "+obsoletedBy +
|
|
1851
|
" already is obsoleted by the pid "+sysmeta.getObsoletedBy().getValue() +". You can't set the pid "+pid.getValue()+" to be obsoleted by the pid "+sysmeta.getObsoletedBy().getValue()+" again.");
|
|
1852
|
}
|
|
1853
|
}
|
|
1854
|
checkCircularObsoletedByChain(sysmeta);
|
|
1855
|
}
|
|
1856
|
|
|
1857
|
// do the actual update
|
|
1858
|
if(sysmeta.getArchived() != null && sysmeta.getArchived() == true &&
|
|
1859
|
((currentSysmeta.getArchived() != null && currentSysmeta.getArchived() == false ) || currentSysmeta.getArchived() == null)) {
|
|
1860
|
boolean logArchive = false;//we log it as the update system metadata event. So don't log it again.
|
|
1861
|
if(fromCN) {
|
|
1862
|
logMetacat.debug("D1Node.update - this is to archive a cn object "+pid.getValue());
|
|
1863
|
try {
|
|
1864
|
archiveCNObject(logArchive, session, pid, sysmeta, needUpdateModificationDate);
|
|
1865
|
} catch (NotFound e) {
|
|
1866
|
throw new InvalidRequest("4869", "Can't find the pid "+pid.getValue()+" for archive.");
|
|
1867
|
}
|
|
1868
|
} else {
|
|
1869
|
logMetacat.debug("D1Node.update - this is to archive a MN object "+pid.getValue());
|
|
1870
|
try {
|
|
1871
|
archiveObject(logArchive, session, pid, sysmeta, needUpdateModificationDate);
|
|
1872
|
} catch (NotFound e) {
|
|
1873
|
throw new InvalidRequest("4869", "Can't find the pid "+pid.getValue()+" for archive.");
|
|
1874
|
}
|
|
1875
|
}
|
|
1876
|
} else {
|
|
1877
|
logMetacat.debug("D1Node.update - regularly update the system metadata of the pid "+pid.getValue());
|
|
1878
|
updateSystemMetadataWithoutLock(sysmeta, needUpdateModificationDate);
|
|
1879
|
}
|
|
1880
|
|
|
1881
|
try {
|
|
1882
|
String localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
1883
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
|
1884
|
request.getHeader("User-Agent"), session.getSubject().getValue(),
|
|
1885
|
localId, "updateSystemMetadata");
|
|
1886
|
} catch (McdbDocNotFoundException e) {
|
|
1887
|
// do nothing, no localId to log with
|
|
1888
|
logMetacat.warn("Could not log 'updateSystemMetadata' event because no localId was found for pid: " + pid.getValue());
|
|
1889
|
} catch (SQLException e) {
|
|
1890
|
logMetacat.warn("Could not log 'updateSystemMetadata' event because the localId couldn't be identified for the pid: " + pid.getValue());
|
|
1891
|
}
|
|
1892
|
return true;
|
|
1893
|
}
|
|
1894
|
|
|
1895
|
|
|
1896
|
/*
|
|
1897
|
* Check if the newMeta modifies an immutable field.
|
|
1898
|
*/
|
|
1899
|
private void checkModifiedImmutableFields(SystemMetadata orgMeta, SystemMetadata newMeta) throws InvalidRequest{
|
|
1900
|
logMetacat.debug("in the start of the checkModifiedImmutableFields method");
|
|
1901
|
if(orgMeta != null && newMeta != null) {
|
|
1902
|
logMetacat.debug("in the checkModifiedImmutableFields method when the org and new system metadata is not null");
|
|
1903
|
if(newMeta.getIdentifier() == null) {
|
|
1904
|
throw new InvalidRequest("4869", "The new version of the system metadata is invalid since the identifier is null");
|
|
1905
|
}
|
|
1906
|
if(!orgMeta.getIdentifier().equals(newMeta.getIdentifier())) {
|
|
1907
|
throw new InvalidRequest("4869","The request is trying to modify an immutable field in the SystemMeta: the new system meta's identifier "+newMeta.getIdentifier().getValue()+" is "+
|
|
1908
|
"different to the orginal one "+orgMeta.getIdentifier().getValue());
|
|
1909
|
}
|
|
1910
|
if(newMeta.getSize() == null) {
|
|
1911
|
throw new InvalidRequest("4869", "The new version of the system metadata is invalid since the size is null");
|
|
1912
|
}
|
|
1913
|
if(!orgMeta.getSize().equals(newMeta.getSize())) {
|
|
1914
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's size "+newMeta.getSize().longValue()+" is "+
|
|
1915
|
"different to the orginal one "+orgMeta.getSize().longValue());
|
|
1916
|
}
|
|
1917
|
if(newMeta.getChecksum()!= null && orgMeta.getChecksum() != null && !orgMeta.getChecksum().getValue().equals(newMeta.getChecksum().getValue())) {
|
|
1918
|
logMetacat.error("The request is trying to modify an immutable field in the SystemMeta: the new system meta's checksum "+newMeta.getChecksum().getValue()+" is "+
|
|
1919
|
"different to the orginal one "+orgMeta.getChecksum().getValue());
|
|
1920
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's checksum "+newMeta.getChecksum().getValue()+" is "+
|
|
1921
|
"different to the orginal one "+orgMeta.getChecksum().getValue());
|
|
1922
|
}
|
|
1923
|
if(orgMeta.getSubmitter() != null) {
|
|
1924
|
logMetacat.debug("in the checkModifiedImmutableFields method and orgMeta.getSubmitter is not null and the orginal submiter is "+orgMeta.getSubmitter().getValue());
|
|
1925
|
}
|
|
1926
|
|
|
1927
|
if(newMeta.getSubmitter() != null) {
|
|
1928
|
logMetacat.debug("in the checkModifiedImmutableFields method and newMeta.getSubmitter is not null and the submiter in the new system metadata is "+newMeta.getSubmitter().getValue());
|
|
1929
|
}
|
|
1930
|
if(orgMeta.getSubmitter() != null && newMeta.getSubmitter() != null && !orgMeta.getSubmitter().equals(newMeta.getSubmitter())) {
|
|
1931
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's submitter "+newMeta.getSubmitter().getValue()+" is "+
|
|
1932
|
"different to the orginal one "+orgMeta.getSubmitter().getValue());
|
|
1933
|
}
|
|
1934
|
|
|
1935
|
if(orgMeta.getDateUploaded() != null && newMeta.getDateUploaded() != null && orgMeta.getDateUploaded().getTime() != newMeta.getDateUploaded().getTime()) {
|
|
1936
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's date of uploaded "+newMeta.getDateUploaded()+" is "+
|
|
1937
|
"different to the orginal one "+orgMeta.getDateUploaded());
|
|
1938
|
}
|
|
1939
|
|
|
1940
|
if(orgMeta.getOriginMemberNode() != null && newMeta.getOriginMemberNode() != null && !orgMeta.getOriginMemberNode().equals(newMeta.getOriginMemberNode())) {
|
|
1941
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's orginal member node "+newMeta.getOriginMemberNode().getValue()+" is "+
|
|
1942
|
"different to the orginal one "+orgMeta.getOriginMemberNode().getValue());
|
|
1943
|
}
|
|
1944
|
|
|
1945
|
if (orgMeta.getOriginMemberNode() != null && newMeta.getOriginMemberNode() == null ) {
|
|
1946
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's orginal member node is null and it "+" is "+
|
|
1947
|
"different to the orginal one "+orgMeta.getOriginMemberNode().getValue());
|
|
1948
|
}
|
|
1949
|
|
|
1950
|
if(orgMeta.getSeriesId() != null && newMeta.getSeriesId() != null && !orgMeta.getSeriesId().equals(newMeta.getSeriesId())) {
|
|
1951
|
throw new InvalidRequest("4869", "The request is trying to modify an immutable field in the SystemMeta: the new system meta's series id "+newMeta.getSeriesId().getValue()+" is "+
|
|
1952
|
"different to the orginal one "+orgMeta.getSeriesId().getValue());
|
|
1953
|
}
|
|
1954
|
|
|
1955
|
}
|
|
1956
|
}
|
|
1957
|
|
|
1958
|
/*
|
|
1959
|
* Some fields in the system metadata, such as obsoletes or obsoletedBy can be set only once.
|
|
1960
|
* After set, they are not allowed to be changed.
|
|
1961
|
*/
|
|
1962
|
private void checkOneTimeSettableSysmMetaFields(SystemMetadata orgMeta, SystemMetadata newMeta) throws InvalidRequest {
|
|
1963
|
if(orgMeta.getObsoletedBy() != null ) {
|
|
1964
|
if(newMeta.getObsoletedBy() == null || !orgMeta.getObsoletedBy().equals(newMeta.getObsoletedBy())) {
|
|
1965
|
throw new InvalidRequest("4869", "The request is trying to reset the obsoletedBy field in the system metadata of the object "
|
|
1966
|
+ orgMeta.getIdentifier().getValue() +". This is illegal since the obsoletedBy filed is set, you can't change it again.");
|
|
1967
|
}
|
|
1968
|
}
|
|
1969
|
if(orgMeta.getObsoletes() != null) {
|
|
1970
|
if(newMeta.getObsoletes() == null || !orgMeta.getObsoletes().equals(newMeta.getObsoletes())) {
|
|
1971
|
throw new InvalidRequest("4869", "The request is trying to reset the obsoletes field in the system metadata of the object"+
|
|
1972
|
orgMeta.getIdentifier().getValue()+". This is illegal since the obsoletes filed is set, you can't change it again.");
|
|
1973
|
}
|
|
1974
|
}
|
|
1975
|
}
|
|
1976
|
|
|
1977
|
|
|
1978
|
/**
|
|
1979
|
* Try to check the scenario of a circular obsoletes chain:
|
|
1980
|
* A obsoletes B
|
|
1981
|
* B obsoletes C
|
|
1982
|
* C obsoletes A
|
|
1983
|
* @param sys
|
|
1984
|
* @throws InvalidRequest
|
|
1985
|
*/
|
|
1986
|
private void checkCircularObsoletesChain(SystemMetadata sys) throws InvalidRequest {
|
|
1987
|
if(sys != null && sys.getObsoletes() != null && sys.getObsoletes().getValue() != null && !sys.getObsoletes().getValue().trim().equals("")) {
|
|
1988
|
logMetacat.debug("D1NodeService.checkCircularObsoletesChain - the object "+sys.getIdentifier().getValue() +" obsoletes "+sys.getObsoletes().getValue());
|
|
1989
|
if(sys.getObsoletes().getValue().equals(sys.getIdentifier().getValue())) {
|
|
1990
|
// the obsoletes field points to itself and creates a circular chain
|
|
1991
|
throw new InvalidRequest("4869", "The obsoletes field and identifier of the system metadata has the same value "+sys.getObsoletes().getValue()+
|
|
1992
|
". This creates a circular chain and it is illegal.");
|
|
1993
|
} else {
|
|
1994
|
Vector <Identifier> pidList = new Vector<Identifier>();
|
|
1995
|
pidList.add(sys.getIdentifier());
|
|
1996
|
SystemMetadata obsoletesSym = HazelcastService.getInstance().getSystemMetadataMap().get(sys.getObsoletes());
|
|
1997
|
while (obsoletesSym != null && obsoletesSym.getObsoletes() != null && obsoletesSym.getObsoletes().getValue() != null && !obsoletesSym.getObsoletes().getValue().trim().equals("")) {
|
|
1998
|
pidList.add(obsoletesSym.getIdentifier());
|
|
1999
|
logMetacat.debug("D1NodeService.checkCircularObsoletesChain - the object "+obsoletesSym.getIdentifier().getValue() +" obsoletes "+obsoletesSym.getObsoletes().getValue());
|
|
2000
|
/*for(Identifier id: pidList) {
|
|
2001
|
logMetacat.debug("D1NodeService.checkCircularObsoletesChain - the pid in the chanin"+id.getValue());
|
|
2002
|
}*/
|
|
2003
|
if(pidList.contains(obsoletesSym.getObsoletes())) {
|
|
2004
|
logMetacat.error("D1NodeService.checkCircularObsoletesChain - when Metacat updated the system metadata of object "+sys.getIdentifier().getValue()+", it found the obsoletes field value "+sys.getObsoletes().getValue()+
|
|
2005
|
" in its new system metadata creating a circular chain at the object "+obsoletesSym.getObsoletes().getValue()+". This is illegal");
|
|
2006
|
throw new InvalidRequest("4869", "When Metacat updated the system metadata of object "+sys.getIdentifier().getValue()+", it found the obsoletes field value "+sys.getObsoletes().getValue()+
|
|
2007
|
" in its new system metadata creating a circular chain at the object "+obsoletesSym.getObsoletes().getValue()+". This is illegal");
|
|
2008
|
} else {
|
|
2009
|
obsoletesSym = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletesSym.getObsoletes());
|
|
2010
|
}
|
|
2011
|
}
|
|
2012
|
}
|
|
2013
|
}
|
|
2014
|
}
|
|
2015
|
|
|
2016
|
|
|
2017
|
/**
|
|
2018
|
* Try to check the scenario of a circular obsoletedBy chain:
|
|
2019
|
* A obsoletedBy B
|
|
2020
|
* B obsoletedBy C
|
|
2021
|
* C obsoletedBy A
|
|
2022
|
* @param sys
|
|
2023
|
* @throws InvalidRequest
|
|
2024
|
*/
|
|
2025
|
private void checkCircularObsoletedByChain(SystemMetadata sys) throws InvalidRequest {
|
|
2026
|
if(sys != null && sys.getObsoletedBy() != null && sys.getObsoletedBy().getValue() != null && !sys.getObsoletedBy().getValue().trim().equals("")) {
|
|
2027
|
logMetacat.debug("D1NodeService.checkCircularObsoletedByChain - the object "+sys.getIdentifier().getValue() +" is obsoletedBy "+sys.getObsoletedBy().getValue());
|
|
2028
|
if(sys.getObsoletedBy().getValue().equals(sys.getIdentifier().getValue())) {
|
|
2029
|
// the obsoletedBy field points to itself and creates a circular chain
|
|
2030
|
throw new InvalidRequest("4869", "The obsoletedBy field and identifier of the system metadata has the same value "+sys.getObsoletedBy().getValue()+
|
|
2031
|
". This creates a circular chain and it is illegal.");
|
|
2032
|
} else {
|
|
2033
|
Vector <Identifier> pidList = new Vector<Identifier>();
|
|
2034
|
pidList.add(sys.getIdentifier());
|
|
2035
|
SystemMetadata obsoletedBySym = HazelcastService.getInstance().getSystemMetadataMap().get(sys.getObsoletedBy());
|
|
2036
|
while (obsoletedBySym != null && obsoletedBySym.getObsoletedBy() != null && obsoletedBySym.getObsoletedBy().getValue() != null && !obsoletedBySym.getObsoletedBy().getValue().trim().equals("")) {
|
|
2037
|
pidList.add(obsoletedBySym.getIdentifier());
|
|
2038
|
logMetacat.debug("D1NodeService.checkCircularObsoletedByChain - the object "+obsoletedBySym.getIdentifier().getValue() +" is obsoletedBy "+obsoletedBySym.getObsoletedBy().getValue());
|
|
2039
|
/*for(Identifier id: pidList) {
|
|
2040
|
logMetacat.debug("D1NodeService.checkCircularObsoletedByChain - the pid in the chanin"+id.getValue());
|
|
2041
|
}*/
|
|
2042
|
if(pidList.contains(obsoletedBySym.getObsoletedBy())) {
|
|
2043
|
logMetacat.error("D1NodeService.checkCircularObsoletedByChain - When Metacat updated the system metadata of object "+sys.getIdentifier().getValue()+", it found the obsoletedBy field value "+sys.getObsoletedBy().getValue()+
|
|
2044
|
" in its new system metadata creating a circular chain at the object "+obsoletedBySym.getObsoletedBy().getValue()+". This is illegal");
|
|
2045
|
throw new InvalidRequest("4869", "When Metacat updated the system metadata of object "+sys.getIdentifier().getValue()+", it found the obsoletedBy field value "+sys.getObsoletedBy().getValue()+
|
|
2046
|
" in its new system metadata creating a circular chain at the object "+obsoletedBySym.getObsoletedBy().getValue()+". This is illegal");
|
|
2047
|
} else {
|
|
2048
|
obsoletedBySym = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletedBySym.getObsoletedBy());
|
|
2049
|
}
|
|
2050
|
}
|
|
2051
|
}
|
|
2052
|
}
|
|
2053
|
}
|
|
2054
|
|
|
2055
|
/**
|
|
2056
|
* Given a Permission, returns a list of all permissions that it encompasses
|
|
2057
|
* Permissions are hierarchical so that WRITE also allows READ.
|
|
2058
|
* @param permission
|
|
2059
|
* @return list of included Permissions for the given permission
|
|
2060
|
*/
|
|
2061
|
protected static List<Permission> expandPermissions(Permission permission) {
|
|
2062
|
List<Permission> expandedPermissions = new ArrayList<Permission>();
|
|
2063
|
if (permission.equals(Permission.READ)) {
|
|
2064
|
expandedPermissions.add(Permission.READ);
|
|
2065
|
}
|
|
2066
|
if (permission.equals(Permission.WRITE)) {
|
|
2067
|
expandedPermissions.add(Permission.READ);
|
|
2068
|
expandedPermissions.add(Permission.WRITE);
|
|
2069
|
}
|
|
2070
|
if (permission.equals(Permission.CHANGE_PERMISSION)) {
|
|
2071
|
expandedPermissions.add(Permission.READ);
|
|
2072
|
expandedPermissions.add(Permission.WRITE);
|
|
2073
|
expandedPermissions.add(Permission.CHANGE_PERMISSION);
|
|
2074
|
}
|
|
2075
|
return expandedPermissions;
|
|
2076
|
}
|
|
2077
|
|
|
2078
|
/*
|
|
2079
|
* Write a stream to a file
|
|
2080
|
*
|
|
2081
|
* @param dir - the directory to write to
|
|
2082
|
* @param fileName - the file name to write to
|
|
2083
|
* @param data - the object bytes as an input stream
|
|
2084
|
*
|
|
2085
|
* @return newFile - the new file created
|
|
2086
|
*
|
|
2087
|
* @throws ServiceFailure
|
|
2088
|
*/
|
|
2089
|
private File writeStreamToFile(File dir, String fileName, InputStream dataStream, Checksum checksum, Identifier pid)
|
|
2090
|
throws ServiceFailure, InvalidSystemMetadata {
|
|
2091
|
|
|
2092
|
File newFile = new File(dir, fileName);
|
|
2093
|
logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath()+" for the data object pid "+pid.getValue());
|
|
2094
|
|
|
2095
|
try {
|
|
2096
|
if (newFile.createNewFile()) {
|
|
2097
|
String checksumValue = checksum.getValue();
|
|
2098
|
logMetacat.info("D1NodeService.writeStreamToFile - the checksum value from the system metadata is "+checksumValue+" for the data object "+pid.getValue());
|
|
2099
|
if(checksumValue == null || checksumValue.trim().equals("")) {
|
|
2100
|
logMetacat.error("D1NodeService.writeStreamToFile - the checksum value from the system metadata shouldn't be null or blank for the data object "+pid.getValue());
|
|
2101
|
throw new InvalidSystemMetadata("1180", "The checksum value from the system metadata shouldn't be null or blank.");
|
|
2102
|
}
|
|
2103
|
String algorithm = checksum.getAlgorithm();
|
|
2104
|
logMetacat.info("D1NodeService.writeStreamToFile - the algorithm to calculate the checksum from the system metadata is "+algorithm+" for the data object "+pid.getValue());
|
|
2105
|
if(algorithm == null || algorithm.trim().equals("")) {
|
|
2106
|
logMetacat.error("D1NodeService.writeStreamToFile - the algorithm to calculate the checksum from the system metadata shouldn't be null or blank for the data object "+pid.getValue());
|
|
2107
|
throw new InvalidSystemMetadata("1180", "The algorithm to calculate the checksum from the system metadata shouldn't be null or blank.");
|
|
2108
|
}
|
|
2109
|
MessageDigest md = MessageDigest.getInstance(algorithm);
|
|
2110
|
// write data stream to desired file
|
|
2111
|
DigestOutputStream os = new DigestOutputStream( new FileOutputStream(newFile), md);
|
|
2112
|
long length = IOUtils.copyLarge(dataStream, os);
|
|
2113
|
os.flush();
|
|
2114
|
os.close();
|
|
2115
|
String localChecksum = DatatypeConverter.printHexBinary(md.digest());
|
|
2116
|
logMetacat.info("D1NodeService.writeStreamToFile - the check sum calculated from the saved local file is "+localChecksum);
|
|
2117
|
if(localChecksum == null || localChecksum.trim().equals("") || !localChecksum.equalsIgnoreCase(checksumValue)) {
|
|
2118
|
logMetacat.error("D1NodeService.writeStreamToFile - the check sum calculated from the saved local file is "+localChecksum+ ". But it doesn't match the value from the system metadata "+checksumValue+" for the object "+pid.getValue());
|
|
2119
|
boolean success = newFile.delete();
|
|
2120
|
logMetacat.info("delete the file "+newFile.getAbsolutePath()+" for the object "+pid.getValue()+" sucessfully?"+success);
|
|
2121
|
throw new InvalidSystemMetadata("1180", "The checksum calculated from the saved local file is "+localChecksum+ ". But it doesn't match the value from the system metadata "+checksumValue+".");
|
|
2122
|
}
|
|
2123
|
|
|
2124
|
} else {
|
|
2125
|
logMetacat.debug("File creation failed, or file already exists.");
|
|
2126
|
throw new ServiceFailure("1190", "File already exists: " + fileName);
|
|
2127
|
}
|
|
2128
|
} catch (FileNotFoundException e) {
|
|
2129
|
logMetacat.error("FNF: " + e.getMessage()+" for the data object "+pid.getValue(), e);
|
|
2130
|
throw new ServiceFailure("1190", "File not found: " + fileName + " "
|
|
2131
|
+ e.getMessage());
|
|
2132
|
} catch (IOException e) {
|
|
2133
|
logMetacat.error("IOE: " + e.getMessage()+" for the data object "+pid.getValue(), e);
|
|
2134
|
throw new ServiceFailure("1190", "File was not written: " + fileName
|
|
2135
|
+ " " + e.getMessage());
|
|
2136
|
} catch (NoSuchAlgorithmException e) {
|
|
2137
|
logMetacat.error("D1NodeService.writeStreamToFile - no such checksum algorithm exception " + e.getMessage()+" for the data object "+pid.getValue(), e);
|
|
2138
|
throw new ServiceFailure("1190", "No such checksum algorithm: "
|
|
2139
|
+ " " + e.getMessage());
|
|
2140
|
} finally {
|
|
2141
|
IOUtils.closeQuietly(dataStream);
|
|
2142
|
}
|
|
2143
|
|
|
2144
|
return newFile;
|
|
2145
|
}
|
|
2146
|
|
|
2147
|
/*
|
|
2148
|
* Returns a list of nodes that have been registered with the DataONE infrastructure
|
|
2149
|
* that match the given session subject
|
|
2150
|
* @return nodes - List of nodes from the registry with a matching session subject
|
|
2151
|
*
|
|
2152
|
* @throws ServiceFailure
|
|
2153
|
* @throws NotImplemented
|
|
2154
|
*/
|
|
2155
|
protected List<Node> listNodesBySubject(Subject subject)
|
|
2156
|
throws ServiceFailure, NotImplemented {
|
|
2157
|
List<Node> nodeList = new ArrayList<Node>();
|
|
2158
|
|
|
2159
|
CNode cn = D1Client.getCN();
|
|
2160
|
List<Node> nodes = cn.listNodes().getNodeList();
|
|
2161
|
|
|
2162
|
// find the node in the node list
|
|
2163
|
for ( Node node : nodes ) {
|
|
2164
|
|
|
2165
|
List<Subject> nodeSubjects = node.getSubjectList();
|
|
2166
|
if (nodeSubjects != null) {
|
|
2167
|
// check if the session subject is in the node subject list
|
|
2168
|
for (Subject nodeSubject : nodeSubjects) {
|
|
2169
|
if ( nodeSubject.equals(subject) ) { // subject of session == node subject
|
|
2170
|
nodeList.add(node);
|
|
2171
|
}
|
|
2172
|
}
|
|
2173
|
}
|
|
2174
|
}
|
|
2175
|
|
|
2176
|
return nodeList;
|
|
2177
|
|
|
2178
|
}
|
|
2179
|
|
|
2180
|
/**
|
|
2181
|
* Archives an object, where the object is either a
|
|
2182
|
* data object or a science metadata object.
|
|
2183
|
* Note: it doesn't check the authorization; it doesn't lock the system metadata;it only accept pid.
|
|
2184
|
* @param session - the Session object containing the credentials for the Subject
|
|
2185
|
* @param pid - The object identifier to be archived
|
|
2186
|
*
|
|
2187
|
* @return pid - the identifier of the object used for the archiving
|
|
2188
|
*
|
|
2189
|
* @throws InvalidToken
|
|
2190
|
* @throws ServiceFailure
|
|
2191
|
* @throws NotAuthorized
|
|
2192
|
* @throws NotFound
|
|
2193
|
* @throws NotImplemented
|
|
2194
|
* @throws InvalidRequest
|
|
2195
|
*/
|
|
2196
|
protected Identifier archiveObject(boolean log, Session session, Identifier pid, SystemMetadata sysMeta, boolean needModifyDate)
|
|
2197
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
|
2198
|
|
|
2199
|
String localId = null;
|
|
2200
|
boolean allowed = false;
|
|
2201
|
String username = Constants.SUBJECT_PUBLIC;
|
|
2202
|
if (session == null) {
|
|
2203
|
throw new InvalidToken("1330", "No session has been provided");
|
|
2204
|
} else {
|
|
2205
|
username = session.getSubject().getValue();
|
|
2206
|
}
|
|
2207
|
// do we have a valid pid?
|
|
2208
|
if (pid == null || pid.getValue().trim().equals("")) {
|
|
2209
|
throw new ServiceFailure("1350", "The provided identifier was invalid.");
|
|
2210
|
}
|
|
2211
|
|
|
2212
|
if(sysMeta == null) {
|
|
2213
|
throw new NotFound("2911", "There is no system metadata associated with "+pid.getValue());
|
|
2214
|
}
|
|
2215
|
|
|
2216
|
// check for the existing identifier
|
|
2217
|
try {
|
|
2218
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
2219
|
} catch (McdbDocNotFoundException e) {
|
|
2220
|
throw new NotFound("1340", "The object with the provided " + "identifier was not found.");
|
|
2221
|
} catch (SQLException e) {
|
|
2222
|
throw new ServiceFailure("1350", "The object with the provided identifier "+pid.getValue()+" couldn't be identified since "+e.getMessage());
|
|
2223
|
}
|
|
2224
|
|
|
2225
|
|
|
2226
|
try {
|
|
2227
|
// archive the document
|
|
2228
|
DocumentImpl.delete(localId, null, null, null, false);
|
|
2229
|
if(log) {
|
|
2230
|
try {
|
|
2231
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), username, localId, Event.DELETE.xmlValue());
|
|
2232
|
} catch (Exception e) {
|
|
2233
|
logMetacat.warn("D1NodeService.archiveObject - can't log the delete event since "+e.getMessage());
|
|
2234
|
}
|
|
2235
|
}
|
|
2236
|
|
|
2237
|
|
|
2238
|
// archive it
|
|
2239
|
sysMeta.setArchived(true);
|
|
2240
|
if(needModifyDate) {
|
|
2241
|
sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
|
2242
|
sysMeta.setSerialVersion(sysMeta.getSerialVersion().add(BigInteger.ONE));
|
|
2243
|
}
|
|
2244
|
HazelcastService.getInstance().getSystemMetadataMap().put(pid, sysMeta);
|
|
2245
|
|
|
2246
|
// submit for indexing
|
|
2247
|
// DocumentImpl call above should do this.
|
|
2248
|
// see: https://projects.ecoinformatics.org/ecoinfo/issues/6030
|
|
2249
|
//HazelcastService.getInstance().getIndexQueue().add(sysMeta);
|
|
2250
|
|
|
2251
|
} catch (McdbDocNotFoundException e) {
|
|
2252
|
try {
|
|
2253
|
AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
|
|
2254
|
String docid = acc.getDocid();
|
|
2255
|
int rev = 1;
|
|
2256
|
if (acc.getRev() != null) {
|
|
2257
|
rev = (new Integer(acc.getRev()).intValue());
|
|
2258
|
}
|
|
2259
|
if(IdentifierManager.getInstance().existsInXmlLRevisionTable(docid, rev)) {
|
|
2260
|
//somehow the document is in the xml_revision table.
|
|
2261
|
// archive it
|
|
2262
|
sysMeta.setArchived(true);
|
|
2263
|
if(needModifyDate) {
|
|
2264
|
sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
|
2265
|
sysMeta.setSerialVersion(sysMeta.getSerialVersion().add(BigInteger.ONE));
|
|
2266
|
}
|
|
2267
|
HazelcastService.getInstance().getSystemMetadataMap().put(pid, sysMeta);
|
|
2268
|
} else {
|
|
2269
|
throw new NotFound("1340", "The provided identifier "+ pid.getValue()+" is invalid");
|
|
2270
|
}
|
|
2271
|
} catch (SQLException ee) {
|
|
2272
|
ee.printStackTrace();
|
|
2273
|
throw new NotFound("1340", "The provided identifier "+ pid.getValue()+" is invalid");
|
|
2274
|
} catch (AccessionNumberException ee) {
|
|
2275
|
ee.printStackTrace();
|
|
2276
|
throw new NotFound("1340", "The provided identifier "+ pid.getValue()+" is invalid");
|
|
2277
|
}
|
|
2278
|
} catch (SQLException e) {
|
|
2279
|
throw new ServiceFailure("1350", "There was a problem archiving the object." + "The error message was: " + e.getMessage());
|
|
2280
|
|
|
2281
|
} catch (InsufficientKarmaException e) {
|
|
2282
|
throw new NotAuthorized("1320", "The provided identity does not have " + "permission to archive this object.");
|
|
2283
|
|
|
2284
|
} catch (Exception e) { // for some reason DocumentImpl throws a general Exception
|
|
2285
|
throw new ServiceFailure("1350", "There was a problem archiving the object." + "The error message was: " + e.getMessage());
|
|
2286
|
}
|
|
2287
|
|
|
2288
|
|
|
2289
|
return pid;
|
|
2290
|
}
|
|
2291
|
|
|
2292
|
/**
|
|
2293
|
* Archive a object on cn and notify the replica. This method doesn't lock the system metadata map. The caller should lock it.
|
|
2294
|
* This method doesn't check the authorization; this method only accept a pid.
|
|
2295
|
* It wouldn't notify the replca that the system metadata has been changed.
|
|
2296
|
* @param session
|
|
2297
|
* @param pid
|
|
2298
|
* @param sysMeta
|
|
2299
|
* @param notifyReplica
|
|
2300
|
* @return
|
|
2301
|
* @throws InvalidToken
|
|
2302
|
* @throws ServiceFailure
|
|
2303
|
* @throws NotAuthorized
|
|
2304
|
* @throws NotFound
|
|
2305
|
* @throws NotImplemented
|
|
2306
|
*/
|
|
2307
|
protected void archiveCNObject(boolean log, Session session, Identifier pid, SystemMetadata sysMeta, boolean needModifyDate)
|
|
2308
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
|
2309
|
|
|
2310
|
String localId = null; // The corresponding docid for this pid
|
|
2311
|
|
|
2312
|
// Check for the existing identifier
|
|
2313
|
try {
|
|
2314
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
2315
|
archiveObject(log, session, pid, sysMeta, needModifyDate);
|
|
2316
|
|
|
2317
|
} catch (McdbDocNotFoundException e) {
|
|
2318
|
// This object is not registered in the identifier table. Assume it is of formatType DATA,
|
|
2319
|
// and set the archive flag. (i.e. the *object* doesn't exist on the CN)
|
|
2320
|
|
|
2321
|
try {
|
|
2322
|
if ( sysMeta != null ) {
|
|
2323
|
sysMeta.setArchived(true);
|
|
2324
|
if (needModifyDate) {
|
|
2325
|
sysMeta.setSerialVersion(sysMeta.getSerialVersion().add(BigInteger.ONE));
|
|
2326
|
sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
|
2327
|
}
|
|
2328
|
HazelcastService.getInstance().getSystemMetadataMap().put(pid, sysMeta);
|
|
2329
|
|
|
2330
|
} else {
|
|
2331
|
throw new ServiceFailure("4972", "Couldn't archive the object " + pid.getValue() +
|
|
2332
|
". Couldn't obtain the system metadata record.");
|
|
2333
|
|
|
2334
|
}
|
|
2335
|
|
|
2336
|
} catch (RuntimeException re) {
|
|
2337
|
throw new ServiceFailure("4972", "Couldn't archive " + pid.getValue() +
|
|
2338
|
". The error message was: " + re.getMessage());
|
|
2339
|
|
|
2340
|
}
|
|
2341
|
|
|
2342
|
} catch (SQLException e) {
|
|
2343
|
throw new ServiceFailure("4972", "Couldn't archive the object " + pid.getValue() +
|
|
2344
|
". The local id of the object with the identifier can't be identified since "+e.getMessage());
|
|
2345
|
}
|
|
2346
|
|
|
2347
|
}
|
|
2348
|
|
|
2349
|
|
|
2350
|
/**
|
|
2351
|
* A utility method for v1 api to check the specified identifier exists as a pid
|
|
2352
|
* @param identifier the specified identifier
|
|
2353
|
* @param serviceFailureCode the detail error code for the service failure exception
|
|
2354
|
* @param noFoundCode the detail error code for the not found exception
|
|
2355
|
* @throws ServiceFailure
|
|
2356
|
* @throws NotFound
|
|
2357
|
*/
|
|
2358
|
public void checkV1SystemMetaPidExist(Identifier identifier, String serviceFailureCode, String serviceFailureMessage,
|
|
2359
|
String noFoundCode, String notFoundMessage) throws ServiceFailure, NotFound {
|
|
2360
|
boolean exists = false;
|
|
2361
|
try {
|
|
2362
|
exists = IdentifierManager.getInstance().systemMetadataPIDExists(identifier);
|
|
2363
|
} catch (SQLException e) {
|
|
2364
|
throw new ServiceFailure(serviceFailureCode, serviceFailureMessage+" since "+e.getMessage());
|
|
2365
|
}
|
|
2366
|
if(!exists) {
|
|
2367
|
//the v1 method only handles a pid. so it should throw a not-found exception.
|
|
2368
|
// check if the pid was deleted.
|
|
2369
|
try {
|
|
2370
|
String localId = IdentifierManager.getInstance().getLocalId(identifier.getValue());
|
|
2371
|
if(EventLog.getInstance().isDeleted(localId)) {
|
|
2372
|
notFoundMessage=notFoundMessage+" "+DELETEDMESSAGE;
|
|
2373
|
}
|
|
2374
|
} catch (Exception e) {
|
|
2375
|
logMetacat.info("Couldn't determine if the not-found identifier "+identifier.getValue()+" was deleted since "+e.getMessage());
|
|
2376
|
}
|
|
2377
|
throw new NotFound(noFoundCode, notFoundMessage);
|
|
2378
|
}
|
|
2379
|
}
|
|
2380
|
|
|
2381
|
/**
|
|
2382
|
* Utility method to get the PID for an SID. If the specified identifier is not an SID
|
|
2383
|
* , null will be returned.
|
|
2384
|
* @param sid the specified sid
|
|
2385
|
* @param serviceFailureCode the detail error code for the service failure exception
|
|
2386
|
* @return the pid for the sid. If the specified identifier is not an SID, null will be returned.
|
|
2387
|
* @throws ServiceFailure
|
|
2388
|
*/
|
|
2389
|
protected Identifier getPIDForSID(Identifier sid, String serviceFailureCode) throws ServiceFailure {
|
|
2390
|
Identifier id = null;
|
|
2391
|
String serviceFailureMessage = "The PID "+" couldn't be identified for the sid " + sid.getValue();
|
|
2392
|
try {
|
|
2393
|
//determine if the given pid is a sid or not.
|
|
2394
|
if(IdentifierManager.getInstance().systemMetadataSIDExists(sid)) {
|
|
2395
|
try {
|
|
2396
|
//set the header pid for the sid if the identifier is a sid.
|
|
2397
|
id = IdentifierManager.getInstance().getHeadPID(sid);
|
|
2398
|
} catch (SQLException sqle) {
|
|
2399
|
throw new ServiceFailure(serviceFailureCode, serviceFailureMessage+" since "+sqle.getMessage());
|
|
2400
|
}
|
|
2401
|
|
|
2402
|
}
|
|
2403
|
} catch (SQLException e) {
|
|
2404
|
throw new ServiceFailure(serviceFailureCode, serviceFailureMessage + " since "+e.getMessage());
|
|
2405
|
}
|
|
2406
|
return id;
|
|
2407
|
}
|
|
2408
|
|
|
2409
|
/*
|
|
2410
|
* Determine if the sid is legitimate in CN.create and CN.registerSystemMetadata methods. It also is used as a part of rules of the updateSystemMetadata method. Here are the rules:
|
|
2411
|
* A. If the sysmeta doesn't have an SID, nothing needs to be checked for the SID.
|
|
2412
|
* B. If the sysmeta does have an SID, it may be an identifier which doesn't exist in the system.
|
|
2413
|
* C. If the sysmeta does have an SID and it exists as an SID in the system, those scenarios are acceptable:
|
|
2414
|
* i. The sysmeta has an obsoletes field, the SID has the same value as the SID of the system metadata of the obsoleting pid.
|
|
2415
|
* ii. The sysmeta has an obsoletedBy field, the SID has the same value as the SID of the system metadata of the obsoletedBy pid.
|
|
2416
|
*/
|
|
2417
|
protected boolean checkSidInModifyingSystemMetadata(SystemMetadata sysmeta, String invalidSystemMetadataCode, String serviceFailureCode) throws InvalidSystemMetadata, ServiceFailure{
|
|
2418
|
boolean pass = false;
|
|
2419
|
if(sysmeta == null) {
|
|
2420
|
throw new InvalidSystemMetadata(invalidSystemMetadataCode, "The system metadata is null in the request.");
|
|
2421
|
}
|
|
2422
|
Identifier sid = sysmeta.getSeriesId();
|
|
2423
|
if(sid != null) {
|
|
2424
|
// the series id exists
|
|
2425
|
if (!isValidIdentifier(sid)) {
|
|
2426
|
throw new InvalidSystemMetadata(invalidSystemMetadataCode, "The series id in the system metadata is invalid in the request.");
|
|
2427
|
}
|
|
2428
|
Identifier pid = sysmeta.getIdentifier();
|
|
2429
|
if (!isValidIdentifier(pid)) {
|
|
2430
|
throw new InvalidSystemMetadata(invalidSystemMetadataCode, "The pid in the system metadata is invalid in the request.");
|
|
2431
|
}
|
|
2432
|
//the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario )
|
|
2433
|
if(sid.getValue().equals(pid.getValue())) {
|
|
2434
|
throw new InvalidSystemMetadata(invalidSystemMetadataCode, "The series id "+sid.getValue()+" in the system metadata shouldn't have the same value of the pid.");
|
|
2435
|
}
|
|
2436
|
try {
|
|
2437
|
if (IdentifierManager.getInstance().identifierExists(sid.getValue())) {
|
|
2438
|
//the sid exists in system
|
|
2439
|
if(sysmeta.getObsoletes() != null) {
|
|
2440
|
SystemMetadata obsoletesSysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(sysmeta.getObsoletes());
|
|
2441
|
if(obsoletesSysmeta != null) {
|
|
2442
|
Identifier obsoletesSid = obsoletesSysmeta.getSeriesId();
|
|
2443
|
if(obsoletesSid != null && obsoletesSid.getValue() != null && !obsoletesSid.getValue().trim().equals("")) {
|
|
2444
|
if(sid.getValue().equals(obsoletesSid.getValue())) {
|
|
2445
|
pass = true;// the i of rule C
|
|
2446
|
}
|
|
2447
|
}
|
|
2448
|
} else {
|
|
2449
|
logMetacat.warn("D1NodeService.checkSidInModifyingSystemMetacat - Can't find the system metadata for the pid "+sysmeta.getObsoletes().getValue()+
|
|
2450
|
" which is the value of the obsoletes. So we can't check if the sid " +sid.getValue()+" is legitimate ");
|
|
2451
|
}
|
|
2452
|
}
|
|
2453
|
if(!pass) {
|
|
2454
|
// the sid doesn't match the sid of the obsoleting identifier. So we check the obsoletedBy
|
|
2455
|
if(sysmeta.getObsoletedBy() != null) {
|
|
2456
|
SystemMetadata obsoletedBySysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(sysmeta.getObsoletedBy());
|
|
2457
|
if(obsoletedBySysmeta != null) {
|
|
2458
|
Identifier obsoletedBySid = obsoletedBySysmeta.getSeriesId();
|
|
2459
|
if(obsoletedBySid != null && obsoletedBySid.getValue() != null && !obsoletedBySid.getValue().trim().equals("")) {
|
|
2460
|
if(sid.getValue().equals(obsoletedBySid.getValue())) {
|
|
2461
|
pass = true;// the ii of the rule C
|
|
2462
|
}
|
|
2463
|
}
|
|
2464
|
} else {
|
|
2465
|
logMetacat.warn("D1NodeService.checkSidInModifyingSystemMetacat - Can't find the system metadata for the pid "+sysmeta.getObsoletes().getValue()
|
|
2466
|
+" which is the value of the obsoletedBy. So we can't check if the sid "+sid.getValue()+" is legitimate.");
|
|
2467
|
}
|
|
2468
|
}
|
|
2469
|
}
|
|
2470
|
if(!pass) {
|
|
2471
|
throw new InvalidSystemMetadata(invalidSystemMetadataCode, "The series id "+sid.getValue()+
|
|
2472
|
" in the system metadata exists in the system. And it doesn't match either previous object's sid or the next object's sid.");
|
|
2473
|
}
|
|
2474
|
} else {
|
|
2475
|
pass = true; //Rule B
|
|
2476
|
}
|
|
2477
|
} catch (SQLException e) {
|
|
2478
|
throw new ServiceFailure(serviceFailureCode, "Can't determine if the sid in the system metadata is unique or not since "+e.getMessage());
|
|
2479
|
}
|
|
2480
|
|
|
2481
|
} else {
|
|
2482
|
//no sid. Rule A.
|
|
2483
|
pass = true;
|
|
2484
|
}
|
|
2485
|
return pass;
|
|
2486
|
|
|
2487
|
}
|
|
2488
|
|
|
2489
|
//@Override
|
|
2490
|
public OptionList listViews(Session arg0) throws InvalidToken,
|
|
2491
|
ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented {
|
|
2492
|
OptionList views = new OptionList();
|
|
2493
|
views.setKey("views");
|
|
2494
|
views.setDescription("List of views for objects on the node");
|
|
2495
|
Vector<String> skinNames = null;
|
|
2496
|
try {
|
|
2497
|
skinNames = SkinUtil.getSkinNames();
|
|
2498
|
} catch (PropertyNotFoundException e) {
|
|
2499
|
throw new ServiceFailure("2841", e.getMessage());
|
|
2500
|
}
|
|
2501
|
for (String skinName: skinNames) {
|
|
2502
|
views.addOption(skinName);
|
|
2503
|
}
|
|
2504
|
return views;
|
|
2505
|
}
|
|
2506
|
|
|
2507
|
public OptionList listViews() throws InvalidToken,
|
|
2508
|
ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented {
|
|
2509
|
return listViews(null);
|
|
2510
|
}
|
|
2511
|
|
|
2512
|
//@Override
|
|
2513
|
public InputStream view(Session session, String format, Identifier pid)
|
|
2514
|
throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,
|
|
2515
|
NotImplemented, NotFound {
|
|
2516
|
InputStream resultInputStream = null;
|
|
2517
|
|
|
2518
|
String serviceFailureCode = "2831";
|
|
2519
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
|
2520
|
if(sid != null) {
|
|
2521
|
pid = sid;
|
|
2522
|
}
|
|
2523
|
|
|
2524
|
SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
|
|
2525
|
InputStream object = this.get(session, pid);
|
|
2526
|
|
|
2527
|
try {
|
|
2528
|
// can only transform metadata, really
|
|
2529
|
ObjectFormat objectFormat = ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId());
|
|
2530
|
if (objectFormat.getFormatType().equals("METADATA")) {
|
|
2531
|
// transform
|
|
2532
|
DBTransform transformer = new DBTransform();
|
|
2533
|
String documentContent = IOUtils.toString(object, "UTF-8");
|
|
2534
|
String sourceType = objectFormat.getFormatId().getValue();
|
|
2535
|
String targetType = "-//W3C//HTML//EN";
|
|
2536
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
|
2537
|
Writer writer = new OutputStreamWriter(baos , "UTF-8");
|
|
2538
|
// TODO: include more params?
|
|
2539
|
Hashtable<String, String[]> params = new Hashtable<String, String[]>();
|
|
2540
|
String localId = null;
|
|
2541
|
try {
|
|
2542
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
|
2543
|
} catch (McdbDocNotFoundException e) {
|
|
2544
|
throw new NotFound("1020", e.getMessage());
|
|
2545
|
}
|
|
2546
|
params.put("qformat", new String[] {format});
|
|
2547
|
params.put("docid", new String[] {localId});
|
|
2548
|
params.put("pid", new String[] {pid.getValue()});
|
|
2549
|
transformer.transformXMLDocument(
|
|
2550
|
documentContent ,
|
|
2551
|
sourceType,
|
|
2552
|
targetType ,
|
|
2553
|
format,
|
|
2554
|
writer,
|
|
2555
|
params,
|
|
2556
|
null //sessionid
|
|
2557
|
);
|
|
2558
|
|
|
2559
|
// finally, get the HTML back
|
|
2560
|
resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
|
|
2561
|
((ContentTypeByteArrayInputStream) resultInputStream).setContentType("text/html");
|
|
2562
|
|
|
2563
|
} else {
|
|
2564
|
// just return the raw bytes
|
|
2565
|
resultInputStream = object;
|
|
2566
|
}
|
|
2567
|
} catch (IOException e) {
|
|
2568
|
// report as service failure
|
|
2569
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
|
2570
|
sf.initCause(e);
|
|
2571
|
throw sf;
|
|
2572
|
} catch (PropertyNotFoundException e) {
|
|
2573
|
// report as service failure
|
|
2574
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
|
2575
|
sf.initCause(e);
|
|
2576
|
throw sf;
|
|
2577
|
} catch (SQLException e) {
|
|
2578
|
// report as service failure
|
|
2579
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
|
2580
|
sf.initCause(e);
|
|
2581
|
throw sf;
|
|
2582
|
} catch (ClassNotFoundException e) {
|
|
2583
|
// report as service failure
|
|
2584
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
|
2585
|
sf.initCause(e);
|
|
2586
|
throw sf;
|
|
2587
|
}
|
|
2588
|
|
|
2589
|
return resultInputStream;
|
|
2590
|
}
|
|
2591
|
|
|
2592
|
/*
|
|
2593
|
* Determine if the given identifier exists in the obsoletes field in the system metadata table.
|
|
2594
|
* If the return value is not null, the given identifier exists in the given cloumn. The return value is
|
|
2595
|
* the guid of the first row.
|
|
2596
|
*/
|
|
2597
|
protected String existsInObsoletes(Identifier id) throws InvalidRequest, ServiceFailure{
|
|
2598
|
String guid = existsInFields("obsoletes", id);
|
|
2599
|
return guid;
|
|
2600
|
}
|
|
2601
|
|
|
2602
|
/*
|
|
2603
|
* Determine if the given identifier exists in the obsoletes field in the system metadata table.
|
|
2604
|
* If the return value is not null, the given identifier exists in the given cloumn. The return value is
|
|
2605
|
* the guid of the first row.
|
|
2606
|
*/
|
|
2607
|
protected String existsInObsoletedBy(Identifier id) throws InvalidRequest, ServiceFailure{
|
|
2608
|
String guid = existsInFields("obsoleted_by", id);
|
|
2609
|
return guid;
|
|
2610
|
}
|
|
2611
|
|
|
2612
|
/*
|
|
2613
|
* Determine if the given identifier exists in the given column in the system metadata table.
|
|
2614
|
* If the return value is not null, the given identifier exists in the given cloumn. The return value is
|
|
2615
|
* the guid of the first row.
|
|
2616
|
*/
|
|
2617
|
private String existsInFields(String column, Identifier id) throws InvalidRequest, ServiceFailure {
|
|
2618
|
String guid = null;
|
|
2619
|
if(id == null ) {
|
|
2620
|
throw new InvalidRequest("4863", "The given identifier is null and we can't determine if the guid exists in the field "+column+" in the systemmetadata table");
|
|
2621
|
}
|
|
2622
|
String sql = "SELECT guid FROM systemmetadata WHERE "+column+" = ?";
|
|
2623
|
int serialNumber = -1;
|
|
2624
|
DBConnection dbConn = null;
|
|
2625
|
PreparedStatement stmt = null;
|
|
2626
|
ResultSet result = null;
|
|
2627
|
try {
|
|
2628
|
dbConn =
|
|
2629
|
DBConnectionPool.getDBConnection("D1NodeService.existsInFields");
|
|
2630
|
serialNumber = dbConn.getCheckOutSerialNumber();
|
|
2631
|
stmt = dbConn.prepareStatement(sql);
|
|
2632
|
stmt.setString(1, id.getValue());
|
|
2633
|
result = stmt.executeQuery();
|
|
2634
|
if(result.next()) {
|
|
2635
|
guid = result.getString(1);
|
|
2636
|
}
|
|
2637
|
stmt.close();
|
|
2638
|
} catch (SQLException e) {
|
|
2639
|
e.printStackTrace();
|
|
2640
|
throw new ServiceFailure("4862","We can't determine if the id "+id.getValue()+" exists in field "+column+" in the systemmetadata table since "+e.getMessage());
|
|
2641
|
} finally {
|
|
2642
|
// Return database connection to the pool
|
|
2643
|
DBConnectionPool.returnDBConnection(dbConn, serialNumber);
|
|
2644
|
if(stmt != null) {
|
|
2645
|
try {
|
|
2646
|
stmt.close();
|
|
2647
|
} catch (SQLException e) {
|
|
2648
|
logMetacat.warn("We can close the PreparedStatment in D1NodeService.existsInFields since "+e.getMessage());
|
|
2649
|
}
|
|
2650
|
}
|
|
2651
|
|
|
2652
|
}
|
|
2653
|
return guid;
|
|
2654
|
|
|
2655
|
}
|
|
2656
|
}
|