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/**
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* '$RCSfile$'
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* Purpose: A Class for upgrading the database to version 1.5
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* Copyright: 2000 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Authors: Saurabh Garg
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*
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* '$Author$'
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* '$Date$'
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* '$Revision$'
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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.File;
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import java.io.IOException;
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import java.io.InputStream;
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import java.math.BigInteger;
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6852
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import java.net.URL;
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6873
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import java.net.URLConnection;
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import java.security.NoSuchAlgorithmException;
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import java.sql.SQLException;
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6712
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import java.util.ArrayList;
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6727
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leinfelder
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import java.util.Collections;
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6705
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import java.util.Date;
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6712
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leinfelder
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import java.util.HashMap;
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import java.util.Hashtable;
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6712
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import java.util.List;
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import java.util.Map;
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6709
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import java.util.Vector;
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6705
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.xpath.XPathExpressionException;
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6712
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leinfelder
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import org.apache.commons.beanutils.BeanUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.log4j.Logger;
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7622
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import org.apache.wicket.protocol.http.mock.MockHttpServletRequest;
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8810
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leinfelder
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import org.dataone.client.v2.formats.ObjectFormatCache;
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6960
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leinfelder
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import org.dataone.eml.DataoneEMLParser;
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import org.dataone.eml.EMLDocument;
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import org.dataone.eml.EMLDocument.DistributionMetadata;
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6712
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import org.dataone.ore.ResourceMapFactory;
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import org.dataone.service.exceptions.BaseException;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.types.v1.AccessPolicy;
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Checksum;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.ObjectFormatIdentifier;
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6988
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jones
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import org.dataone.service.types.v1.ReplicationPolicy;
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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.ChecksumUtil;
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import org.dataone.service.util.DateTimeMarshaller;
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import org.dspace.foresite.ResourceMap;
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import org.jibx.runtime.JiBXException;
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import org.xml.sax.SAXException;
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cjones
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import java.util.Calendar;
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7084
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6705
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import edu.ucsb.nceas.metacat.AccessionNumber;
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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6709
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import edu.ucsb.nceas.metacat.DBUtil;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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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.McdbException;
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import edu.ucsb.nceas.metacat.MetaCatServlet;
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import edu.ucsb.nceas.metacat.MetacatHandler;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
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8986
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tao
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import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
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6705
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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6708
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import edu.ucsb.nceas.metacat.replication.ReplicationService;
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6721
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import edu.ucsb.nceas.metacat.shared.AccessException;
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6708
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import edu.ucsb.nceas.metacat.shared.HandlerException;
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6705
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.utilities.ParseLSIDException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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public class SystemMetadataFactory {
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public static final String RESOURCE_MAP_PREFIX = "resourceMap_";
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private static Logger logMetacat = Logger.getLogger(SystemMetadataFactory.class);
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6961
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/**
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* use this flag if you want to update any existing system metadata values with generated content
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*/
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private static boolean updateExisting = true;
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6712
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8986
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tao
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6705
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/**
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8986
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tao
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* Create a system metadata object for insertion into metacat
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* @param localId
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* @param includeORE
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* @param downloadData
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* @return
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* @throws McdbException
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* @throws McdbDocNotFoundException
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* @throws SQLException
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* @throws IOException
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* @throws AccessionNumberException
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* @throws ClassNotFoundException
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* @throws InsufficientKarmaException
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* @throws ParseLSIDException
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* @throws PropertyNotFoundException
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* @throws BaseException
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* @throws NoSuchAlgorithmException
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* @throws JiBXException
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* @throws AccessControlException
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* @throws HandlerException
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* @throws SAXException
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* @throws AccessException
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*/
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public static SystemMetadata createSystemMetadata(String localId, boolean includeORE, boolean downloadData)
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throws McdbException, McdbDocNotFoundException, SQLException,
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IOException, AccessionNumberException, ClassNotFoundException,
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InsufficientKarmaException, ParseLSIDException,
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PropertyNotFoundException, BaseException, NoSuchAlgorithmException,
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JiBXException, AccessControlException, HandlerException, SAXException, AccessException {
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boolean indexDataFile = false;
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return createSystemMetadata(indexDataFile, localId, includeORE, downloadData);
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}
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/**
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6706
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* Creates a system metadata object for insertion into metacat
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8986
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tao
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* @param indexDataFile
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* Indicate if we need to index data file.
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6706
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*
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* @param localId
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* The local document identifier
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* @param user
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* The user submitting the system metadata document
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* @param groups
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* The groups the user belongs to
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*
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* @return sysMeta The system metadata object created
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6708
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leinfelder
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* @throws SAXException
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* @throws HandlerException
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* @throws AccessControlException
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6721
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leinfelder
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* @throws AccessException
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6706
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leinfelder
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*/
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8986
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tao
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public static SystemMetadata createSystemMetadata(boolean indexDataFile, String localId, boolean includeORE, boolean downloadData)
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6706
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leinfelder
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throws McdbException, McdbDocNotFoundException, SQLException,
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IOException, AccessionNumberException, ClassNotFoundException,
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InsufficientKarmaException, ParseLSIDException,
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PropertyNotFoundException, BaseException, NoSuchAlgorithmException,
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6721
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leinfelder
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JiBXException, AccessControlException, HandlerException, SAXException, AccessException {
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165 |
6707
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6964
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logMetacat.debug("createSystemMetadata() called for localId " + localId);
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6705
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leinfelder
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6961
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leinfelder
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// check for system metadata
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SystemMetadata sysMeta = null;
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6706
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leinfelder
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AccessionNumber accNum = new AccessionNumber(localId, "NONE");
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172 |
6808
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leinfelder
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int rev = Integer.valueOf(accNum.getRev());
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173 |
6961
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leinfelder
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174 |
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// get/make the guid
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175 |
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String guid = null;
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try {
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177 |
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// get the guid if it exists
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178 |
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guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);
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} catch (McdbDocNotFoundException dnfe) {
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180 |
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// otherwise create the mapping
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6964
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leinfelder
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logMetacat.debug("No guid found in the identifier table. Creating mapping for " + localId);
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182 |
6961
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IdentifierManager.getInstance().createMapping(localId, localId);
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6964
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guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);
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184 |
6961
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}
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185 |
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186 |
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// look up existing system metadata if it exists
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Identifier identifier = new Identifier();
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identifier.setValue(guid);
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189 |
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try {
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6964
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leinfelder
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logMetacat.debug("Using hazelcast to get system metadata");
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191 |
6961
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leinfelder
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sysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(identifier);
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// TODO: if this is the case, we could return here -- what else do we gain?
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if (!updateExisting ) {
|
194 |
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return sysMeta;
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}
|
196 |
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} catch (Exception e) {
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197 |
6964
|
leinfelder
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logMetacat.debug("No system metadata found in hz: " + e.getMessage());
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198 |
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199 |
6970
|
leinfelder
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}
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200 |
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|
201 |
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if (sysMeta == null) {
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202 |
6961
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leinfelder
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// create system metadata
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203 |
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sysMeta = new SystemMetadata();
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204 |
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sysMeta.setIdentifier(identifier);
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sysMeta.setSerialVersion(BigInteger.valueOf(1));
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206 |
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sysMeta.setArchived(false);
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207 |
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}
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208 |
6962
|
leinfelder
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209 |
6706
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leinfelder
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// get additional docinfo
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210 |
6708
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leinfelder
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Hashtable<String, String> docInfo = ReplicationService.getDocumentInfoMap(localId);
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211 |
6706
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leinfelder
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// set the default object format
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212 |
6708
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leinfelder
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String doctype = docInfo.get("doctype");
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213 |
6706
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leinfelder
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ObjectFormatIdentifier fmtid = null;
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214 |
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215 |
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// set the object format, fall back to defaults
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216 |
6982
|
leinfelder
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if (doctype.trim().equals("BIN")) {
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217 |
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// we don't know much about this file (yet)
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218 |
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fmtid = ObjectFormatCache.getInstance().getFormat("application/octet-stream").getFormatId();
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219 |
8028
|
leinfelder
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} else if (doctype.trim().equals("metadata")) {
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220 |
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// special ESRI FGDC format
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fmtid = ObjectFormatCache.getInstance().getFormat("FGDC-STD-001-1998").getFormatId();
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222 |
6982
|
leinfelder
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} else {
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223 |
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try {
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224 |
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// do we know the given format?
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225 |
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fmtid = ObjectFormatCache.getInstance().getFormat(doctype).getFormatId();
|
226 |
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} catch (NotFound nfe) {
|
227 |
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// format is not registered, use default
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228 |
6964
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leinfelder
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fmtid = ObjectFormatCache.getInstance().getFormat("text/plain").getFormatId();
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229 |
6706
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leinfelder
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}
|
230 |
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}
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231 |
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232 |
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sysMeta.setFormatId(fmtid);
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233 |
6707
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leinfelder
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logMetacat.debug("The ObjectFormat for " + localId + " is " + fmtid.getValue());
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234 |
6706
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leinfelder
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235 |
6962
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leinfelder
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// for retrieving the actual object
|
236 |
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InputStream inputStream = null;
|
237 |
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inputStream = MetacatHandler.read(localId);
|
238 |
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239 |
6721
|
leinfelder
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// create the checksum
|
240 |
7222
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leinfelder
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String algorithm = PropertyService.getProperty("dataone.checksumAlgorithm.default");
|
241 |
6721
|
leinfelder
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Checksum checksum = ChecksumUtil.checksum(inputStream, algorithm);
|
242 |
7084
|
leinfelder
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logMetacat.debug("The checksum for " + localId + " is " + checksum.getValue());
|
243 |
6721
|
leinfelder
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sysMeta.setChecksum(checksum);
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244 |
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|
245 |
6962
|
leinfelder
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// set the size from file on disk, don't read bytes again
|
246 |
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File fileOnDisk = getFileOnDisk(localId);
|
247 |
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long fileSize = 0;
|
248 |
|
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if (fileOnDisk.exists()) {
|
249 |
|
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fileSize = fileOnDisk.length();
|
250 |
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}
|
251 |
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sysMeta.setSize(BigInteger.valueOf(fileSize));
|
252 |
6721
|
leinfelder
|
|
253 |
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// submitter
|
254 |
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Subject submitter = new Subject();
|
255 |
|
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submitter.setValue(docInfo.get("user_updated"));
|
256 |
|
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sysMeta.setSubmitter(submitter);
|
257 |
|
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|
258 |
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// rights holder
|
259 |
|
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Subject owner = new Subject();
|
260 |
|
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owner.setValue(docInfo.get("user_owner"));
|
261 |
|
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sysMeta.setRightsHolder(owner);
|
262 |
|
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|
263 |
|
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// dates
|
264 |
|
|
String createdDateString = docInfo.get("date_created");
|
265 |
|
|
String updatedDateString = docInfo.get("date_updated");
|
266 |
|
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Date createdDate = DateTimeMarshaller.deserializeDateToUTC(createdDateString);
|
267 |
|
|
Date updatedDate = DateTimeMarshaller.deserializeDateToUTC(updatedDateString);
|
268 |
|
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sysMeta.setDateUploaded(createdDate);
|
269 |
7084
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leinfelder
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//sysMeta.setDateSysMetadataModified(updatedDate);
|
270 |
|
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// use current datetime
|
271 |
|
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sysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
272 |
6721
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leinfelder
|
|
273 |
|
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// set the revision history
|
274 |
|
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String docidWithoutRev = accNum.getDocid();
|
275 |
|
|
Identifier obsoletedBy = null;
|
276 |
|
|
Identifier obsoletes = null;
|
277 |
|
|
Vector<Integer> revisions = DBUtil.getRevListFromRevisionTable(docidWithoutRev);
|
278 |
6727
|
leinfelder
|
// ensure this ordering since processing depends on it
|
279 |
|
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Collections.sort(revisions);
|
280 |
6721
|
leinfelder
|
for (int existingRev: revisions) {
|
281 |
|
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// use the docid+rev as the guid
|
282 |
|
|
String existingPid = docidWithoutRev + "." + existingRev;
|
283 |
7001
|
leinfelder
|
try {
|
284 |
|
|
existingPid = IdentifierManager.getInstance().getGUID(docidWithoutRev, existingRev);
|
285 |
|
|
} catch (McdbDocNotFoundException mdfe) {
|
286 |
|
|
// we'll be defaulting to the local id
|
287 |
|
|
logMetacat.warn("could not locate guid when processing revision history for localId: " + localId);
|
288 |
|
|
}
|
289 |
6721
|
leinfelder
|
if (existingRev < rev) {
|
290 |
|
|
// it's the old docid, until it's not
|
291 |
|
|
obsoletes = new Identifier();
|
292 |
|
|
obsoletes.setValue(existingPid);
|
293 |
|
|
}
|
294 |
|
|
if (existingRev > rev) {
|
295 |
|
|
// it's the newer docid
|
296 |
|
|
obsoletedBy = new Identifier();
|
297 |
|
|
obsoletedBy.setValue(existingPid);
|
298 |
|
|
// only want the version just after it
|
299 |
|
|
break;
|
300 |
|
|
}
|
301 |
|
|
}
|
302 |
6725
|
leinfelder
|
// set them on our object
|
303 |
6721
|
leinfelder
|
sysMeta.setObsoletedBy(obsoletedBy);
|
304 |
|
|
sysMeta.setObsoletes(obsoletes);
|
305 |
|
|
|
306 |
6725
|
leinfelder
|
// update the system metadata for the object[s] we are revising
|
307 |
|
|
if (obsoletedBy != null) {
|
308 |
6971
|
leinfelder
|
SystemMetadata obsoletedBySysMeta = null;
|
309 |
|
|
try {
|
310 |
|
|
//obsoletedBySysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletedBy);
|
311 |
|
|
obsoletedBySysMeta = IdentifierManager.getInstance().getSystemMetadata(obsoletedBy.getValue());
|
312 |
|
|
} catch (McdbDocNotFoundException e) {
|
313 |
|
|
// ignore
|
314 |
|
|
}
|
315 |
6725
|
leinfelder
|
if (obsoletedBySysMeta != null) {
|
316 |
|
|
obsoletedBySysMeta.setObsoletes(identifier);
|
317 |
7297
|
leinfelder
|
obsoletedBySysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
318 |
6725
|
leinfelder
|
HazelcastService.getInstance().getSystemMetadataMap().put(obsoletedBy, obsoletedBySysMeta);
|
319 |
|
|
}
|
320 |
|
|
}
|
321 |
|
|
if (obsoletes != null) {
|
322 |
6971
|
leinfelder
|
SystemMetadata obsoletesSysMeta = null;
|
323 |
|
|
try {
|
324 |
|
|
//obsoletesSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletes);
|
325 |
|
|
obsoletesSysMeta = IdentifierManager.getInstance().getSystemMetadata(obsoletes.getValue());
|
326 |
|
|
} catch (McdbDocNotFoundException e) {
|
327 |
|
|
// ignore
|
328 |
|
|
}
|
329 |
6725
|
leinfelder
|
if (obsoletesSysMeta != null) {
|
330 |
|
|
obsoletesSysMeta.setObsoletedBy(identifier);
|
331 |
8566
|
leinfelder
|
// DO NOT set archived to true -- it will have unintended consequences if the CN sees this.
|
332 |
|
|
//obsoletesSysMeta.setArchived(true);
|
333 |
7297
|
leinfelder
|
obsoletesSysMeta.setDateSysMetadataModified(Calendar.getInstance().getTime());
|
334 |
6911
|
leinfelder
|
HazelcastService.getInstance().getSystemMetadataMap().put(obsoletes, obsoletesSysMeta);
|
335 |
6725
|
leinfelder
|
}
|
336 |
|
|
}
|
337 |
|
|
|
338 |
6744
|
leinfelder
|
// look up the access control policy we have in metacat
|
339 |
|
|
AccessPolicy accessPolicy = IdentifierManager.getInstance().getAccessPolicy(guid);
|
340 |
7214
|
cjones
|
try {
|
341 |
|
|
List<AccessRule> allowList = accessPolicy.getAllowList();
|
342 |
7215
|
cjones
|
int listSize = allowList.size();
|
343 |
7214
|
cjones
|
sysMeta.setAccessPolicy(accessPolicy);
|
344 |
|
|
|
345 |
|
|
} catch (NullPointerException npe) {
|
346 |
|
|
logMetacat.info("The allow list is empty, can't include an empty " +
|
347 |
|
|
"access policy in the system metadata for " + guid);
|
348 |
|
|
|
349 |
|
|
}
|
350 |
6721
|
leinfelder
|
|
351 |
|
|
// authoritative node
|
352 |
|
|
NodeReference nr = new NodeReference();
|
353 |
7030
|
cjones
|
nr.setValue(PropertyService.getProperty("dataone.nodeId"));
|
354 |
6721
|
leinfelder
|
sysMeta.setOriginMemberNode(nr);
|
355 |
|
|
sysMeta.setAuthoritativeMemberNode(nr);
|
356 |
|
|
|
357 |
6988
|
jones
|
// Set a default replication policy
|
358 |
|
|
ReplicationPolicy rp = getDefaultReplicationPolicy();
|
359 |
|
|
if (rp != null) {
|
360 |
|
|
sysMeta.setReplicationPolicy(rp);
|
361 |
|
|
}
|
362 |
|
|
|
363 |
6706
|
leinfelder
|
// further parse EML documents to get data object format,
|
364 |
|
|
// describes and describedBy information
|
365 |
|
|
if (fmtid == ObjectFormatCache.getInstance().getFormat(
|
366 |
|
|
"eml://ecoinformatics.org/eml-2.0.0").getFormatId()
|
367 |
|
|
|| fmtid == ObjectFormatCache.getInstance().getFormat(
|
368 |
|
|
"eml://ecoinformatics.org/eml-2.0.1").getFormatId()
|
369 |
|
|
|| fmtid == ObjectFormatCache.getInstance().getFormat(
|
370 |
|
|
"eml://ecoinformatics.org/eml-2.1.0").getFormatId()
|
371 |
|
|
|| fmtid == ObjectFormatCache.getInstance().getFormat(
|
372 |
|
|
"eml://ecoinformatics.org/eml-2.1.1").getFormatId()) {
|
373 |
|
|
|
374 |
|
|
try {
|
375 |
6962
|
leinfelder
|
|
376 |
|
|
// get it again to parse the document
|
377 |
|
|
logMetacat.debug("Re-reading document inputStream");
|
378 |
6721
|
leinfelder
|
inputStream = MetacatHandler.read(localId);
|
379 |
6960
|
leinfelder
|
|
380 |
|
|
DataoneEMLParser emlParser = DataoneEMLParser.getInstance();
|
381 |
|
|
EMLDocument emlDocument = emlParser.parseDocument(inputStream);
|
382 |
|
|
|
383 |
6721
|
leinfelder
|
// iterate through the data objects in the EML doc and add sysmeta
|
384 |
6707
|
leinfelder
|
logMetacat.debug("In createSystemMetadata() the number of data "
|
385 |
6706
|
leinfelder
|
+ "entities is: "
|
386 |
6960
|
leinfelder
|
+ emlDocument.distributionMetadata);
|
387 |
6706
|
leinfelder
|
|
388 |
6712
|
leinfelder
|
// for generating the ORE map
|
389 |
|
|
Map<Identifier, List<Identifier>> idMap = new HashMap<Identifier, List<Identifier>>();
|
390 |
|
|
List<Identifier> dataIds = new ArrayList<Identifier>();
|
391 |
|
|
|
392 |
6706
|
leinfelder
|
// iterate through data objects described by the EML
|
393 |
6960
|
leinfelder
|
if (emlDocument.distributionMetadata != null) {
|
394 |
|
|
for (int j = 0; j < emlDocument.distributionMetadata.size(); j++) {
|
395 |
6744
|
leinfelder
|
|
396 |
6960
|
leinfelder
|
DistributionMetadata distMetadata = emlDocument.distributionMetadata.elementAt(j);
|
397 |
|
|
String dataDocUrl = distMetadata.url;
|
398 |
|
|
String dataDocMimeType = distMetadata.mimeType;
|
399 |
6744
|
leinfelder
|
// default to binary
|
400 |
|
|
if (dataDocMimeType == null) {
|
401 |
6982
|
leinfelder
|
dataDocMimeType = "application/octet-stream";
|
402 |
6721
|
leinfelder
|
}
|
403 |
6852
|
leinfelder
|
|
404 |
|
|
// process the data
|
405 |
6855
|
leinfelder
|
boolean remoteData = false;
|
406 |
6852
|
leinfelder
|
String dataDocLocalId = null;
|
407 |
|
|
Identifier dataGuid = new Identifier();
|
408 |
|
|
|
409 |
|
|
// handle ecogrid, or downloadable data
|
410 |
|
|
String ecogridPrefix = "ecogrid://knb/";
|
411 |
|
|
if (dataDocUrl.trim().startsWith(ecogridPrefix)) {
|
412 |
|
|
dataDocLocalId = dataDocUrl.substring(dataDocUrl.indexOf(ecogridPrefix) + ecogridPrefix.length());
|
413 |
|
|
} else {
|
414 |
|
|
// should we try downloading the remote data?
|
415 |
|
|
if (downloadData) {
|
416 |
|
|
InputStream dataObject = null;
|
417 |
|
|
try {
|
418 |
|
|
// download the data from the URL
|
419 |
|
|
URL dataURL = new URL(dataDocUrl);
|
420 |
6873
|
leinfelder
|
URLConnection dataConnection = dataURL.openConnection();
|
421 |
|
|
|
422 |
|
|
// default is to download the data
|
423 |
|
|
dataObject = dataConnection.getInputStream();
|
424 |
|
|
|
425 |
|
|
String detectedContentType = dataConnection.getContentType();
|
426 |
|
|
logMetacat.info("Detected content type: " + detectedContentType);
|
427 |
|
|
|
428 |
|
|
if (detectedContentType != null) {
|
429 |
|
|
// seems to be HTML from the remote location
|
430 |
|
|
if (detectedContentType.contains("html")) {
|
431 |
|
|
// if we are not expecting it, we skip it
|
432 |
|
|
if (!dataDocMimeType.contains("html")) {
|
433 |
|
|
// set to null so we don't download it
|
434 |
|
|
dataObject = null;
|
435 |
|
|
logMetacat.warn("Skipping remote resource, unexpected HTML content type at: " + dataDocUrl);
|
436 |
|
|
}
|
437 |
|
|
}
|
438 |
|
|
|
439 |
|
|
} else {
|
440 |
|
|
// if we don't know what it is, should we skip it?
|
441 |
|
|
dataObject = null;
|
442 |
|
|
logMetacat.warn("Skipping remote resource, unknown content type at: " + dataDocUrl);
|
443 |
|
|
}
|
444 |
|
|
|
445 |
6852
|
leinfelder
|
} catch (Exception e) {
|
446 |
|
|
// error with the download
|
447 |
|
|
logMetacat.warn("Error downloading remote data. " + e.getMessage());
|
448 |
|
|
}
|
449 |
|
|
|
450 |
|
|
if (dataObject != null) {
|
451 |
|
|
// create the local version of it
|
452 |
|
|
dataDocLocalId = DocumentUtil.generateDocumentId(1);
|
453 |
|
|
IdentifierManager.getInstance().createMapping(dataDocLocalId, dataDocLocalId);
|
454 |
|
|
dataGuid.setValue(dataDocLocalId);
|
455 |
|
|
|
456 |
|
|
// save it locally
|
457 |
|
|
Session session = new Session();
|
458 |
|
|
session.setSubject(submitter);
|
459 |
|
|
MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
|
460 |
|
|
MNodeService.getInstance(request).insertDataObject(dataObject, dataGuid, session);
|
461 |
6855
|
leinfelder
|
|
462 |
|
|
remoteData = true;
|
463 |
6852
|
leinfelder
|
}
|
464 |
|
|
}
|
465 |
|
|
|
466 |
|
|
}
|
467 |
|
|
|
468 |
6744
|
leinfelder
|
logMetacat.debug("Data local ID: " + dataDocLocalId);
|
469 |
|
|
logMetacat.debug("Data URL : " + dataDocUrl);
|
470 |
|
|
logMetacat.debug("Data mime : " + dataDocMimeType);
|
471 |
6852
|
leinfelder
|
|
472 |
7112
|
leinfelder
|
// check for valid docid.rev
|
473 |
|
|
String dataDocid = null;
|
474 |
|
|
int dataRev = 0;
|
475 |
|
|
if (dataDocLocalId != null) {
|
476 |
|
|
// look up the guid for the data
|
477 |
|
|
try {
|
478 |
|
|
dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);
|
479 |
|
|
dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);
|
480 |
|
|
} catch (Exception e) {
|
481 |
|
|
logMetacat.warn(e.getClass().getName() + " - Problem parsing accession number for: " + dataDocLocalId + ". Message: " + e.getMessage());
|
482 |
|
|
dataDocLocalId = null;
|
483 |
|
|
}
|
484 |
|
|
}
|
485 |
|
|
|
486 |
6852
|
leinfelder
|
// now we have a local id for the data
|
487 |
|
|
if (dataDocLocalId != null) {
|
488 |
6744
|
leinfelder
|
|
489 |
|
|
// check if data system metadata exists already
|
490 |
|
|
SystemMetadata dataSysMeta = null;
|
491 |
|
|
String dataGuidString = null;
|
492 |
6706
|
leinfelder
|
try {
|
493 |
6744
|
leinfelder
|
// look for the identifier
|
494 |
6707
|
leinfelder
|
dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
|
495 |
6744
|
leinfelder
|
// set it
|
496 |
6706
|
leinfelder
|
dataGuid.setValue(dataGuidString);
|
497 |
6744
|
leinfelder
|
// look up the system metadata
|
498 |
6706
|
leinfelder
|
try {
|
499 |
6744
|
leinfelder
|
dataSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(dataGuid);
|
500 |
|
|
} catch (Exception e) {
|
501 |
|
|
// probably not in the system
|
502 |
|
|
dataSysMeta = null;
|
503 |
6706
|
leinfelder
|
}
|
504 |
6744
|
leinfelder
|
//dataSysMeta = IdentifierManager.getInstance().getSystemMetadata(dataGuidString);
|
505 |
|
|
} catch (McdbDocNotFoundException nf) {
|
506 |
|
|
// we didn't find it
|
507 |
|
|
dataSysMeta = null;
|
508 |
|
|
}
|
509 |
6712
|
leinfelder
|
|
510 |
6744
|
leinfelder
|
// we'll have to generate it
|
511 |
|
|
if (dataSysMeta == null) {
|
512 |
|
|
// System metadata for data doesn't exist yet, so create it
|
513 |
6964
|
leinfelder
|
logMetacat.debug("No exisiting SystemMetdata found, creating for: " + dataDocLocalId);
|
514 |
6961
|
leinfelder
|
dataSysMeta = createSystemMetadata(dataDocLocalId, includeORE, false);
|
515 |
|
|
|
516 |
|
|
// now look it up again
|
517 |
|
|
dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
|
518 |
|
|
|
519 |
|
|
// set the guid
|
520 |
|
|
dataGuid.setValue(dataGuidString);
|
521 |
|
|
|
522 |
|
|
// inherit access rules from metadata, if we don't have our own
|
523 |
|
|
if (remoteData) {
|
524 |
|
|
dataSysMeta.setAccessPolicy(sysMeta.getAccessPolicy());
|
525 |
|
|
// TODO: use access rules defined in EML, per data file
|
526 |
|
|
}
|
527 |
6744
|
leinfelder
|
|
528 |
|
|
}
|
529 |
6721
|
leinfelder
|
|
530 |
6961
|
leinfelder
|
// set object format for the data file
|
531 |
6964
|
leinfelder
|
logMetacat.debug("Updating system metadata for " + dataGuid.getValue() + " to " + dataDocMimeType);
|
532 |
6982
|
leinfelder
|
ObjectFormatIdentifier fmt = null;
|
533 |
6961
|
leinfelder
|
try {
|
534 |
6982
|
leinfelder
|
fmt = ObjectFormatCache.getInstance().getFormat(dataDocMimeType).getFormatId();
|
535 |
6961
|
leinfelder
|
} catch (NotFound nfe) {
|
536 |
|
|
logMetacat.debug("Couldn't find format identifier for: "
|
537 |
|
|
+ dataDocMimeType
|
538 |
|
|
+ ". Setting it to application/octet-stream.");
|
539 |
6982
|
leinfelder
|
fmt = new ObjectFormatIdentifier();
|
540 |
|
|
fmt.setValue("application/octet-stream");
|
541 |
6961
|
leinfelder
|
}
|
542 |
6982
|
leinfelder
|
dataSysMeta.setFormatId(fmt);
|
543 |
|
|
|
544 |
6961
|
leinfelder
|
// update the values
|
545 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().put(dataSysMeta.getIdentifier(), dataSysMeta);
|
546 |
|
|
|
547 |
8986
|
tao
|
// reindex data file if need it.
|
548 |
|
|
logMetacat.debug("do we need to reindex guid "+dataGuid.getValue()+"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~?"+indexDataFile);
|
549 |
|
|
if(indexDataFile) {
|
550 |
|
|
reindexDataFile(dataSysMeta.getIdentifier(), dataSysMeta);
|
551 |
|
|
}
|
552 |
|
|
|
553 |
6961
|
leinfelder
|
// include as part of the ORE package
|
554 |
6744
|
leinfelder
|
dataIds.add(dataGuid);
|
555 |
|
|
|
556 |
|
|
} // end if (EML package)
|
557 |
|
|
|
558 |
|
|
} // end for (data entities)
|
559 |
|
|
|
560 |
|
|
} // data entities not null
|
561 |
|
|
|
562 |
6712
|
leinfelder
|
// ORE map
|
563 |
6713
|
leinfelder
|
if (includeORE) {
|
564 |
6800
|
leinfelder
|
// can we generate them?
|
565 |
6713
|
leinfelder
|
if (!dataIds.isEmpty()) {
|
566 |
6800
|
leinfelder
|
// it doesn't exist in the system?
|
567 |
|
|
if (!oreExistsFor(sysMeta.getIdentifier())) {
|
568 |
|
|
|
569 |
|
|
// generate the ORE map for this datapackage
|
570 |
|
|
Identifier resourceMapId = new Identifier();
|
571 |
7001
|
leinfelder
|
// use the local id, not the guid in case we have DOIs for them already
|
572 |
7849
|
leinfelder
|
resourceMapId.setValue(RESOURCE_MAP_PREFIX + localId);
|
573 |
6800
|
leinfelder
|
idMap.put(sysMeta.getIdentifier(), dataIds);
|
574 |
|
|
ResourceMap rm = ResourceMapFactory.getInstance().createResourceMap(resourceMapId, idMap);
|
575 |
|
|
String resourceMapXML = ResourceMapFactory.getInstance().serializeResourceMap(rm);
|
576 |
|
|
// copy most of the same system metadata as the packaging metadata
|
577 |
|
|
SystemMetadata resourceMapSysMeta = new SystemMetadata();
|
578 |
|
|
BeanUtils.copyProperties(resourceMapSysMeta, sysMeta);
|
579 |
|
|
resourceMapSysMeta.setIdentifier(resourceMapId);
|
580 |
7222
|
leinfelder
|
Checksum oreChecksum = ChecksumUtil.checksum(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING), algorithm);
|
581 |
6800
|
leinfelder
|
resourceMapSysMeta.setChecksum(oreChecksum);
|
582 |
|
|
ObjectFormatIdentifier formatId = ObjectFormatCache.getInstance().getFormat("http://www.openarchives.org/ore/terms").getFormatId();
|
583 |
|
|
resourceMapSysMeta.setFormatId(formatId);
|
584 |
|
|
resourceMapSysMeta.setSize(BigInteger.valueOf(sizeOfStream(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING))));
|
585 |
|
|
|
586 |
|
|
// set the revision graph
|
587 |
|
|
resourceMapSysMeta.setObsoletes(null);
|
588 |
|
|
resourceMapSysMeta.setObsoletedBy(null);
|
589 |
|
|
// look up the resource map that this one obsoletes
|
590 |
|
|
if (sysMeta.getObsoletes() != null) {
|
591 |
7273
|
leinfelder
|
// use the localId in case we have a DOI
|
592 |
|
|
String obsoletesLocalId = IdentifierManager.getInstance().getLocalId(sysMeta.getObsoletes().getValue());
|
593 |
6800
|
leinfelder
|
Identifier resourceMapObsoletes = new Identifier();
|
594 |
7849
|
leinfelder
|
resourceMapObsoletes.setValue(RESOURCE_MAP_PREFIX + obsoletesLocalId );
|
595 |
6800
|
leinfelder
|
resourceMapSysMeta.setObsoletes(resourceMapObsoletes);
|
596 |
|
|
SystemMetadata resourceMapObsoletesSystemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(resourceMapObsoletes);
|
597 |
|
|
if (resourceMapObsoletesSystemMetadata != null) {
|
598 |
|
|
resourceMapObsoletesSystemMetadata.setObsoletedBy(resourceMapId);
|
599 |
7278
|
leinfelder
|
resourceMapObsoletesSystemMetadata.setArchived(true);
|
600 |
6800
|
leinfelder
|
HazelcastService.getInstance().getSystemMetadataMap().put(resourceMapObsoletes, resourceMapObsoletesSystemMetadata);
|
601 |
|
|
}
|
602 |
|
|
}
|
603 |
|
|
// look up the resource map that this one is obsoletedBy
|
604 |
|
|
if (sysMeta.getObsoletedBy() != null) {
|
605 |
7273
|
leinfelder
|
// use the localId in case we have a DOI
|
606 |
|
|
String obsoletedByLocalId = IdentifierManager.getInstance().getLocalId(sysMeta.getObsoletedBy().getValue());
|
607 |
6800
|
leinfelder
|
Identifier resourceMapObsoletedBy = new Identifier();
|
608 |
7849
|
leinfelder
|
resourceMapObsoletedBy.setValue(RESOURCE_MAP_PREFIX + obsoletedByLocalId);
|
609 |
6800
|
leinfelder
|
resourceMapSysMeta.setObsoletedBy(resourceMapObsoletedBy);
|
610 |
7278
|
leinfelder
|
resourceMapSysMeta.setArchived(true);
|
611 |
6800
|
leinfelder
|
SystemMetadata resourceMapObsoletedBySystemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(resourceMapObsoletedBy);
|
612 |
|
|
if (resourceMapObsoletedBySystemMetadata != null) {
|
613 |
|
|
resourceMapObsoletedBySystemMetadata.setObsoletes(resourceMapId);
|
614 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().put(resourceMapObsoletedBy, resourceMapObsoletedBySystemMetadata);
|
615 |
|
|
}
|
616 |
|
|
}
|
617 |
|
|
|
618 |
6907
|
leinfelder
|
// save it locally, if it doesn't already exist
|
619 |
|
|
if (!IdentifierManager.getInstance().identifierExists(resourceMapId.getValue())) {
|
620 |
|
|
Session session = new Session();
|
621 |
|
|
session.setSubject(submitter);
|
622 |
|
|
MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
|
623 |
|
|
MNodeService.getInstance(request).insertDataObject(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING), resourceMapId, session);
|
624 |
|
|
MNodeService.getInstance(request).insertSystemMetadata(resourceMapSysMeta);
|
625 |
|
|
logMetacat.info("Inserted ORE package: " + resourceMapId.getValue());
|
626 |
|
|
}
|
627 |
6800
|
leinfelder
|
}
|
628 |
6713
|
leinfelder
|
}
|
629 |
|
|
}
|
630 |
6706
|
leinfelder
|
|
631 |
|
|
} catch (ParserConfigurationException pce) {
|
632 |
6707
|
leinfelder
|
logMetacat.debug("There was a problem parsing the EML document. "
|
633 |
6706
|
leinfelder
|
+ "The error message was: " + pce.getMessage());
|
634 |
|
|
|
635 |
|
|
} catch (SAXException saxe) {
|
636 |
6707
|
leinfelder
|
logMetacat.debug("There was a problem traversing the EML document. "
|
637 |
6706
|
leinfelder
|
+ "The error message was: " + saxe.getMessage());
|
638 |
|
|
|
639 |
|
|
} catch (XPathExpressionException xpee) {
|
640 |
6707
|
leinfelder
|
logMetacat.debug("There was a problem searching the EML document. "
|
641 |
6706
|
leinfelder
|
+ "The error message was: " + xpee.getMessage());
|
642 |
|
|
} catch (Exception e) {
|
643 |
6707
|
leinfelder
|
logMetacat.debug("There was a problem creating System Metadata. "
|
644 |
6706
|
leinfelder
|
+ "The error message was: " + e.getMessage());
|
645 |
6721
|
leinfelder
|
e.printStackTrace();
|
646 |
6706
|
leinfelder
|
} // end try()
|
647 |
|
|
|
648 |
|
|
} // end if()
|
649 |
|
|
|
650 |
|
|
return sysMeta;
|
651 |
|
|
}
|
652 |
8986
|
tao
|
|
653 |
|
|
/*
|
654 |
|
|
* Re-index the data file since the access rule was changed during the inserting of the eml document.
|
655 |
|
|
* (During first time to index the data file in Metacat API, the eml hasn't been inserted)
|
656 |
|
|
*/
|
657 |
|
|
private static void reindexDataFile(Identifier id, SystemMetadata sysmeta) {
|
658 |
|
|
try {
|
659 |
|
|
logMetacat.debug("@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ reindex"+id.getValue());
|
660 |
8991
|
tao
|
if(sysmeta != null) {
|
661 |
|
|
if(!sysmeta.getArchived()) {
|
662 |
|
|
//set the archive to true to remove index.
|
663 |
|
|
sysmeta.setArchived(true);
|
664 |
|
|
MetacatSolrIndex.getInstance().submit(id, sysmeta, null, true);
|
665 |
|
|
//re-insert the index
|
666 |
|
|
sysmeta.setArchived(false);
|
667 |
|
|
MetacatSolrIndex.getInstance().submit(id, sysmeta, null, true);
|
668 |
|
|
} else {
|
669 |
|
|
MetacatSolrIndex.getInstance().submit(id, sysmeta, null, true);
|
670 |
|
|
}
|
671 |
|
|
}
|
672 |
|
|
|
673 |
8986
|
tao
|
} catch (Exception e) {
|
674 |
|
|
// TODO Auto-generated catch block
|
675 |
|
|
logMetacat.warn("Can't reindex the data object "+id.getValue()+" since "+e.getMessage());
|
676 |
|
|
//e.printStackTrace();
|
677 |
|
|
}
|
678 |
|
|
}
|
679 |
6988
|
jones
|
|
680 |
8190
|
leinfelder
|
/**
|
681 |
|
|
* Checks for potential ORE object existence
|
682 |
|
|
* @param identifier
|
683 |
|
|
* @return
|
684 |
|
|
*/
|
685 |
|
|
public static boolean oreExistsFor(Identifier identifier) {
|
686 |
|
|
MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
|
687 |
8200
|
leinfelder
|
List<Identifier> ids = MNodeService.getInstance(request).lookupOreFor(identifier, true);
|
688 |
8190
|
leinfelder
|
return (ids != null && ids.size() > 0);
|
689 |
|
|
}
|
690 |
|
|
|
691 |
|
|
/**
|
692 |
6911
|
leinfelder
|
* Generate SystemMetadata for any object in the object store that does
|
693 |
|
|
* not already have it. SystemMetadata documents themselves, are, of course,
|
694 |
|
|
* exempt. This is a utility method for migration of existing object
|
695 |
|
|
* stores to DataONE where SystemMetadata is required for all objects.
|
696 |
|
|
* @param idList
|
697 |
|
|
* @param includeOre
|
698 |
|
|
* @param downloadData
|
699 |
|
|
* @throws PropertyNotFoundException
|
700 |
|
|
* @throws NoSuchAlgorithmException
|
701 |
|
|
* @throws AccessionNumberException
|
702 |
|
|
* @throws SQLException
|
703 |
6964
|
leinfelder
|
* @throws SAXException
|
704 |
|
|
* @throws HandlerException
|
705 |
|
|
* @throws JiBXException
|
706 |
|
|
* @throws BaseException
|
707 |
|
|
* @throws ParseLSIDException
|
708 |
|
|
* @throws InsufficientKarmaException
|
709 |
|
|
* @throws ClassNotFoundException
|
710 |
|
|
* @throws IOException
|
711 |
|
|
* @throws McdbException
|
712 |
|
|
* @throws AccessException
|
713 |
|
|
* @throws AccessControlException
|
714 |
6911
|
leinfelder
|
*/
|
715 |
|
|
public static void generateSystemMetadata(List<String> idList, boolean includeOre, boolean downloadData)
|
716 |
6964
|
leinfelder
|
throws PropertyNotFoundException, NoSuchAlgorithmException, AccessionNumberException, SQLException, AccessControlException, AccessException, McdbException, IOException, ClassNotFoundException, InsufficientKarmaException, ParseLSIDException, BaseException, JiBXException, HandlerException, SAXException
|
717 |
6911
|
leinfelder
|
{
|
718 |
|
|
|
719 |
|
|
for (String localId : idList) {
|
720 |
6998
|
leinfelder
|
logMetacat.debug("Creating SystemMetadata for localId " + localId);
|
721 |
7178
|
leinfelder
|
logMetacat.trace("METRICS:\tGENERATE_SYSTEM_METADATA:\tBEGIN:\tLOCALID:\t" + localId);
|
722 |
|
|
|
723 |
6998
|
leinfelder
|
SystemMetadata sm = null;
|
724 |
|
|
|
725 |
|
|
//generate required system metadata fields from the document
|
726 |
7123
|
leinfelder
|
try {
|
727 |
|
|
sm = SystemMetadataFactory.createSystemMetadata(localId, includeOre, downloadData);
|
728 |
|
|
} catch (Exception e) {
|
729 |
|
|
logMetacat.error("Could not create/process system metadata for docid: " + localId, e);
|
730 |
|
|
continue;
|
731 |
|
|
}
|
732 |
|
|
|
733 |
6998
|
leinfelder
|
//insert the systemmetadata object or just update it as needed
|
734 |
7188
|
leinfelder
|
IdentifierManager.getInstance().insertOrUpdateSystemMetadata(sm);
|
735 |
|
|
logMetacat.info("Generated or Updated SystemMetadata for " + localId);
|
736 |
|
|
|
737 |
7178
|
leinfelder
|
logMetacat.trace("METRICS:\tGENERATE_SYSTEM_METADATA:\tEND:\tLOCALID:\t" + localId);
|
738 |
|
|
|
739 |
6911
|
leinfelder
|
}
|
740 |
6964
|
leinfelder
|
logMetacat.info("done generating system metadata for given list");
|
741 |
6911
|
leinfelder
|
}
|
742 |
6706
|
leinfelder
|
|
743 |
6707
|
leinfelder
|
/**
|
744 |
6706
|
leinfelder
|
* Find the size (in bytes) of a stream. Note: This needs to refactored out
|
745 |
|
|
* of MetacatHandler and into a utility when stream i/o in Metacat is
|
746 |
|
|
* evaluated.
|
747 |
|
|
*
|
748 |
|
|
* @param is The InputStream of bytes
|
749 |
|
|
*
|
750 |
|
|
* @return size The size in bytes of the input stream as a long
|
751 |
|
|
*
|
752 |
|
|
* @throws IOException
|
753 |
|
|
*/
|
754 |
7322
|
leinfelder
|
public static long sizeOfStream(InputStream is) throws IOException {
|
755 |
6706
|
leinfelder
|
|
756 |
|
|
long size = 0;
|
757 |
|
|
byte[] b = new byte[1024];
|
758 |
|
|
int numread = is.read(b, 0, 1024);
|
759 |
|
|
while (numread != -1) {
|
760 |
|
|
size += numread;
|
761 |
|
|
numread = is.read(b, 0, 1024);
|
762 |
|
|
}
|
763 |
|
|
return size;
|
764 |
|
|
|
765 |
|
|
}
|
766 |
6962
|
leinfelder
|
|
767 |
|
|
private static File getFileOnDisk(String docid) throws McdbException, PropertyNotFoundException {
|
768 |
|
|
|
769 |
|
|
DocumentImpl doc = new DocumentImpl(docid, false);
|
770 |
|
|
String filepath = null;
|
771 |
|
|
String filename = null;
|
772 |
|
|
|
773 |
|
|
// deal with data or metadata cases
|
774 |
|
|
if (doc.getRootNodeID() == 0) {
|
775 |
|
|
// this is a data file
|
776 |
|
|
filepath = PropertyService.getProperty("application.datafilepath");
|
777 |
|
|
} else {
|
778 |
|
|
filepath = PropertyService.getProperty("application.documentfilepath");
|
779 |
|
|
}
|
780 |
|
|
// ensure it is a directory path
|
781 |
|
|
if (!(filepath.endsWith("/"))) {
|
782 |
|
|
filepath += "/";
|
783 |
|
|
}
|
784 |
|
|
filename = filepath + docid;
|
785 |
|
|
File documentFile = new File(filename);
|
786 |
|
|
|
787 |
|
|
return documentFile;
|
788 |
|
|
}
|
789 |
6988
|
jones
|
|
790 |
|
|
/**
|
791 |
|
|
* Create a default ReplicationPolicy by reading properties from metacat's configuration
|
792 |
|
|
* and using those defaults. If the numReplicas property is not found, malformed, or less
|
793 |
|
|
* than or equal to zero, no policy needs to be set, so return null.
|
794 |
|
|
* @return ReplicationPolicy, or null if no replication policy is needed
|
795 |
|
|
*/
|
796 |
|
|
private static ReplicationPolicy getDefaultReplicationPolicy() {
|
797 |
|
|
ReplicationPolicy rp = null;
|
798 |
|
|
int numReplicas = -1;
|
799 |
|
|
try {
|
800 |
|
|
numReplicas = new Integer(PropertyService.getProperty("dataone.replicationpolicy.default.numreplicas"));
|
801 |
|
|
} catch (NumberFormatException e) {
|
802 |
|
|
// The property is not a valid integer, so return a null policy
|
803 |
|
|
return null;
|
804 |
|
|
} catch (PropertyNotFoundException e) {
|
805 |
|
|
// The property is not found, so return a null policy
|
806 |
|
|
return null;
|
807 |
|
|
}
|
808 |
|
|
|
809 |
|
|
if (numReplicas > 0) {
|
810 |
|
|
rp = new ReplicationPolicy();
|
811 |
|
|
rp.setReplicationAllowed(true);
|
812 |
|
|
rp.setNumberReplicas(numReplicas);
|
813 |
|
|
try {
|
814 |
|
|
String preferredNodeList = PropertyService.getProperty("dataone.replicationpolicy.default.preferredNodeList");
|
815 |
|
|
if (preferredNodeList != null) {
|
816 |
|
|
List<NodeReference> pNodes = extractNodeReferences(preferredNodeList);
|
817 |
|
|
if (pNodes != null && !pNodes.isEmpty()) {
|
818 |
|
|
rp.setPreferredMemberNodeList(pNodes);
|
819 |
|
|
}
|
820 |
|
|
}
|
821 |
|
|
} catch (PropertyNotFoundException e) {
|
822 |
|
|
// No preferred list found in properties, so just ignore it; no action needed
|
823 |
|
|
}
|
824 |
|
|
try {
|
825 |
|
|
String blockedNodeList = PropertyService.getProperty("dataone.replicationpolicy.default.blockedNodeList");
|
826 |
|
|
if (blockedNodeList != null) {
|
827 |
|
|
List<NodeReference> bNodes = extractNodeReferences(blockedNodeList);
|
828 |
|
|
if (bNodes != null && !bNodes.isEmpty()) {
|
829 |
7022
|
leinfelder
|
rp.setBlockedMemberNodeList(bNodes);
|
830 |
6988
|
jones
|
}
|
831 |
|
|
}
|
832 |
|
|
} catch (PropertyNotFoundException e) {
|
833 |
|
|
// No blocked list found in properties, so just ignore it; no action needed
|
834 |
|
|
}
|
835 |
|
|
}
|
836 |
|
|
return rp;
|
837 |
|
|
}
|
838 |
|
|
|
839 |
|
|
/**
|
840 |
7025
|
leinfelder
|
* Extract a List of NodeReferences from a String listing the node identifiers where
|
841 |
6988
|
jones
|
* each identifier is separated by whitespace, comma, or semicolon characters.
|
842 |
|
|
* @param nodeString the string containing the list of nodes
|
843 |
7025
|
leinfelder
|
* @return the List of NodeReference objects parsed from the input string
|
844 |
6988
|
jones
|
*/
|
845 |
|
|
private static List<NodeReference> extractNodeReferences(String nodeString) {
|
846 |
|
|
List<NodeReference> nodeList = new ArrayList<NodeReference>();
|
847 |
7022
|
leinfelder
|
String[] result = nodeString.split("[,;\\s]");
|
848 |
6988
|
jones
|
for (String r : result) {
|
849 |
7025
|
leinfelder
|
if (r != null && r.length() > 0) {
|
850 |
|
|
NodeReference noderef = new NodeReference();
|
851 |
|
|
noderef.setValue(r);
|
852 |
|
|
nodeList.add(noderef);
|
853 |
|
|
}
|
854 |
6988
|
jones
|
}
|
855 |
|
|
return nodeList;
|
856 |
|
|
}
|
857 |
6705
|
leinfelder
|
}
|