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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: leinfelder $'
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* '$Date: 2011-12-07 17:05:17 -0800 (Wed, 07 Dec 2011) $'
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* '$Revision: 6747 $'
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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.BufferedInputStream;
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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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import java.security.NoSuchAlgorithmException;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.Map;
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import java.util.Vector;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.xpath.XPathExpressionException;
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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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import org.apache.wicket.protocol.http.MockHttpServletRequest;
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import org.dataone.client.ObjectFormatCache;
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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.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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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import org.dataone.service.types.v1.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.ecoinformatics.datamanager.DataManager;
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import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface;
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import org.ecoinformatics.datamanager.parser.DataPackage;
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import org.jibx.runtime.JiBXException;
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import org.xml.sax.SAXException;
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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.DBUtil;
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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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import edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.replication.ReplicationService;
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import edu.ucsb.nceas.metacat.shared.AccessException;
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import edu.ucsb.nceas.metacat.shared.HandlerException;
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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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private static Logger logMetacat = Logger.getLogger(SystemMetadataFactory.class);
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/**
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* Creates a system metadata object for insertion into metacat
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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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* @throws SAXException
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* @throws HandlerException
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* @throws AccessControlException
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* @throws AccessException
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*/
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public static SystemMetadata createSystemMetadata(String localId, boolean includeORE)
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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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logMetacat.debug("MetacatHandler.createSystemMetadata() called.");
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logMetacat.debug("provided localId: " + localId);
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// create system metadata for the document
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SystemMetadata sysMeta = new SystemMetadata();
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sysMeta.setSerialVersion(BigInteger.valueOf(1));
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int rev = IdentifierManager.getInstance().getLatestRevForLocalId(localId);
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AccessionNumber accNum = new AccessionNumber(localId, "NONE");
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String guid = null;
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try {
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// get the guid if it exists
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guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);
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} catch (McdbDocNotFoundException dnfe) {
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// otherwise create the mapping
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logMetacat.debug("There was a problem getting the guid from "
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+ "the given localId (docid and revision). The error message was: "
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+ dnfe.getMessage());
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logMetacat.debug("No guid in the identifier table. adding it for " + localId);
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IdentifierManager.getInstance().createMapping(localId, localId);
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logMetacat.debug("Mapping created for " + localId);
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logMetacat.debug("accessionNumber: " + accNum);
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guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);
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}
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Identifier identifier = new Identifier();
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identifier.setValue(guid);
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// set the id
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sysMeta.setIdentifier(identifier);
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// get the data or metadata object
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InputStream inputStream;
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try {
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inputStream = MetacatHandler.read(localId);
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} catch (ParseLSIDException ple) {
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logMetacat.debug("There was a problem parsing the LSID from "
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+ localId + ". The error message was: " + ple.getMessage());
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throw ple;
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} catch (PropertyNotFoundException pnfe) {
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logMetacat.debug("There was a problem finding a property. "
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+ "The error message was: " + pnfe.getMessage());
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throw pnfe;
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} catch (McdbException me) {
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logMetacat.debug("There was a Metacat problem. "
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+ "The error message was: " + me.getMessage());
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throw me;
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} catch (SQLException sqle) {
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logMetacat.debug("There was a SQL problem. "
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+ "The error message was: " + sqle.getMessage());
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throw sqle;
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} catch (ClassNotFoundException cnfe) {
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logMetacat.debug("There was a problem finding a class. "
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+ "The error message was: " + cnfe.getMessage());
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throw cnfe;
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} catch (IOException ioe) {
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logMetacat.debug("There was an I/O exception. "
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+ "The error message was: " + ioe.getMessage());
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throw ioe;
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} // end try()
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// get additional docinfo
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Hashtable<String, String> docInfo = ReplicationService.getDocumentInfoMap(localId);
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// set the default object format
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String doctype = docInfo.get("doctype");
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ObjectFormatIdentifier fmtid = null;
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// set the object format, fall back to defaults
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try {
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fmtid = ObjectFormatCache.getInstance().getFormat(doctype).getFormatId();
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} catch (NotFound nfe) {
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try {
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// format is not registered, use default
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if (doctype.trim().equals("BIN")) {
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fmtid = ObjectFormatCache.getInstance().getFormat(
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"application/octet-stream").getFormatId();
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} else {
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fmtid = ObjectFormatCache.getInstance().getFormat(
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"text/plain").getFormatId();
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}
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} catch (NotFound nf) {
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logMetacat.error("There was a problem getting the default format "
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+ "from the ObjectFormatCache: "
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+ nf.getMessage());
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throw nf;
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}
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}
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sysMeta.setFormatId(fmtid);
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logMetacat.debug("The ObjectFormat for " + localId + " is " + fmtid.getValue());
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// create the checksum
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inputStream = MetacatHandler.read(localId);
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String algorithm = "MD5";
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Checksum checksum = ChecksumUtil.checksum(inputStream, algorithm);
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sysMeta.setChecksum(checksum);
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// set the size
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inputStream = MetacatHandler.read(localId);
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String sizeStr = new Long(sizeOfStream(inputStream)).toString();
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sysMeta.setSize(new BigInteger(sizeStr));
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// submitter
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Subject submitter = new Subject();
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submitter.setValue(docInfo.get("user_updated"));
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sysMeta.setSubmitter(submitter);
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// rights holder
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Subject owner = new Subject();
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owner.setValue(docInfo.get("user_owner"));
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sysMeta.setRightsHolder(owner);
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// dates
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String createdDateString = docInfo.get("date_created");
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String updatedDateString = docInfo.get("date_updated");
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Date createdDate = DateTimeMarshaller.deserializeDateToUTC(createdDateString);
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Date updatedDate = DateTimeMarshaller.deserializeDateToUTC(updatedDateString);
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sysMeta.setDateUploaded(createdDate);
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sysMeta.setDateSysMetadataModified(updatedDate);
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// set the revision history
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String docidWithoutRev = accNum.getDocid();
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Identifier obsoletedBy = null;
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Identifier obsoletes = null;
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Vector<Integer> revisions = DBUtil.getRevListFromRevisionTable(docidWithoutRev);
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// ensure this ordering since processing depends on it
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Collections.sort(revisions);
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for (int existingRev: revisions) {
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// use the docid+rev as the guid
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String existingPid = docidWithoutRev + "." + existingRev;
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if (existingRev < rev) {
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// it's the old docid, until it's not
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obsoletes = new Identifier();
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obsoletes.setValue(existingPid);
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}
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if (existingRev > rev) {
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// it's the newer docid
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obsoletedBy = new Identifier();
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obsoletedBy.setValue(existingPid);
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// only want the version just after it
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break;
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}
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}
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// set them on our object
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sysMeta.setObsoletedBy(obsoletedBy);
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sysMeta.setObsoletes(obsoletes);
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// update the system metadata for the object[s] we are revising
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if (obsoletedBy != null) {
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//SystemMetadata obsoletedBySysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletedBy);
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SystemMetadata obsoletedBySysMeta = IdentifierManager.getInstance().getSystemMetadata(obsoletedBy.getValue());
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if (obsoletedBySysMeta != null) {
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obsoletedBySysMeta.setObsoletes(identifier);
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HazelcastService.getInstance().getSystemMetadataMap().put(obsoletedBy, obsoletedBySysMeta);
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}
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}
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if (obsoletes != null) {
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//SystemMetadata obsoletesSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(obsoletes);
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SystemMetadata obsoletesSysMeta = IdentifierManager.getInstance().getSystemMetadata(obsoletes.getValue());
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if (obsoletesSysMeta != null) {
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obsoletesSysMeta.setObsoletedBy(identifier);
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HazelcastService.getInstance().getSystemMetadataMap().put(obsoletes, obsoletesSysMeta);
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}
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}
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290
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// look up the access control policy we have in metacat
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AccessPolicy accessPolicy = IdentifierManager.getInstance().getAccessPolicy(guid);
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sysMeta.setAccessPolicy(accessPolicy);
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// authoritative node
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NodeReference nr = new NodeReference();
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nr.setValue(PropertyService.getProperty("dataone.memberNodeId"));
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sysMeta.setOriginMemberNode(nr);
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sysMeta.setAuthoritativeMemberNode(nr);
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301
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// further parse EML documents to get data object format,
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// describes and describedBy information
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if (fmtid == ObjectFormatCache.getInstance().getFormat(
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"eml://ecoinformatics.org/eml-2.0.0").getFormatId()
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|| fmtid == ObjectFormatCache.getInstance().getFormat(
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"eml://ecoinformatics.org/eml-2.0.1").getFormatId()
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|| fmtid == ObjectFormatCache.getInstance().getFormat(
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308
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"eml://ecoinformatics.org/eml-2.1.0").getFormatId()
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309
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|| fmtid == ObjectFormatCache.getInstance().getFormat(
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310
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"eml://ecoinformatics.org/eml-2.1.1").getFormatId()) {
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311
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312
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try {
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313
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inputStream = MetacatHandler.read(localId);
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314
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DatabaseConnectionPoolInterface connectionPool =
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315
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MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();
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316
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DataManager dataManager =
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317
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DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());
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318
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DataPackage dataPackage = dataManager.parseMetadata(inputStream);
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319
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320
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// iterate through the data objects in the EML doc and add sysmeta
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321
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logMetacat.debug("In createSystemMetadata() the number of data "
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322
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+ "entities is: "
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323
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+ dataPackage.getEntityNumber());
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324
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|
325
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// for generating the ORE map
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326
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Map<Identifier, List<Identifier>> idMap = new HashMap<Identifier, List<Identifier>>();
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327
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List<Identifier> dataIds = new ArrayList<Identifier>();
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328
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|
329
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// iterate through data objects described by the EML
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330
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if (dataPackage.getEntityList() != null) {
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331
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for (int j = 0; j < dataPackage.getEntityList().length; j++) {
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332
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|
333
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String dataDocUrl = dataPackage.getEntityList()[j].getURL();
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334
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String dataDocMimeType = dataPackage.getEntityList()[j].getDataFormat();
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335
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// default to binary
|
336
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if (dataDocMimeType == null) {
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337
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dataDocMimeType = ObjectFormatCache.getInstance()
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338
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.getFormat("application/octet-stream")
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339
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.getFormatId().getValue();
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340
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}
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341
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String dataDocLocalId = "";
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342
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logMetacat.debug("Data local ID: " + dataDocLocalId);
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343
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logMetacat.debug("Data URL : " + dataDocUrl);
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344
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logMetacat.debug("Data mime : " + dataDocMimeType);
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345
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|
346
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// we only handle ecogrid urls right now
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347
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String ecogridPrefix = "ecogrid://knb/";
|
348
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if (dataDocUrl.trim().startsWith(ecogridPrefix)) {
|
349
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dataDocLocalId = dataDocUrl.substring(dataDocUrl
|
350
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.indexOf(ecogridPrefix)
|
351
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+ ecogridPrefix.length());
|
352
|
|
353
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// look up the guid for the data
|
354
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String dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);
|
355
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int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);
|
356
|
|
357
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// check if data system metadata exists already
|
358
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SystemMetadata dataSysMeta = null;
|
359
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String dataGuidString = null;
|
360
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Identifier dataGuid = new Identifier();
|
361
|
try {
|
362
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// look for the identifier
|
363
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dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
|
364
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// set it
|
365
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dataGuid.setValue(dataGuidString);
|
366
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// look up the system metadata
|
367
|
try {
|
368
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dataSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(dataGuid);
|
369
|
} catch (Exception e) {
|
370
|
// probably not in the system
|
371
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dataSysMeta = null;
|
372
|
}
|
373
|
//dataSysMeta = IdentifierManager.getInstance().getSystemMetadata(dataGuidString);
|
374
|
} catch (McdbDocNotFoundException nf) {
|
375
|
// we didn't find it
|
376
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dataSysMeta = null;
|
377
|
}
|
378
|
|
379
|
// we'll have to generate it
|
380
|
if (dataSysMeta == null) {
|
381
|
// System metadata for data doesn't exist yet, so create it
|
382
|
logMetacat.debug("There was not an existing system metadata document for " + dataDocLocalId);
|
383
|
try {
|
384
|
logMetacat.debug("Creating a system metadata " + "document for " + dataDocLocalId);
|
385
|
dataSysMeta = createSystemMetadata(dataDocLocalId, includeORE);
|
386
|
|
387
|
// now look it up again
|
388
|
dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
|
389
|
|
390
|
// set the guid
|
391
|
dataGuid.setValue(dataGuidString);
|
392
|
|
393
|
// set object format
|
394
|
logMetacat.debug("Updating system metadata for "
|
395
|
+ dataGuid.getValue() + " to "
|
396
|
+ dataDocMimeType);
|
397
|
try {
|
398
|
ObjectFormatIdentifier fmt =
|
399
|
ObjectFormatCache.getInstance().getFormat(dataDocMimeType).getFormatId();
|
400
|
dataSysMeta.setFormatId(fmt);
|
401
|
} catch (NotFound nfe) {
|
402
|
logMetacat.debug("Couldn't find format identifier for: "
|
403
|
+ dataDocMimeType
|
404
|
+ ". Setting it to application/octet-stream.");
|
405
|
ObjectFormatIdentifier newFmtid = new ObjectFormatIdentifier();
|
406
|
newFmtid.setValue("application/octet-stream");
|
407
|
}
|
408
|
|
409
|
// update the values
|
410
|
HazelcastService.getInstance().getSystemMetadataMap().put(dataSysMeta.getIdentifier(), dataSysMeta);
|
411
|
|
412
|
|
413
|
} catch (McdbDocNotFoundException mdnf) {
|
414
|
mdnf.printStackTrace();
|
415
|
throw mdnf;
|
416
|
} catch (NumberFormatException nfe) {
|
417
|
nfe.printStackTrace();
|
418
|
throw nfe;
|
419
|
} catch (AccessionNumberException ane) {
|
420
|
ane.printStackTrace();
|
421
|
throw ane;
|
422
|
} catch (SQLException sqle) {
|
423
|
sqle.printStackTrace();
|
424
|
throw sqle;
|
425
|
} catch (NoSuchAlgorithmException nsae) {
|
426
|
nsae.printStackTrace();
|
427
|
throw nsae;
|
428
|
} catch (IOException ioe) {
|
429
|
ioe.printStackTrace();
|
430
|
throw ioe;
|
431
|
} catch (PropertyNotFoundException pnfe) {
|
432
|
pnfe.printStackTrace();
|
433
|
throw pnfe;
|
434
|
} catch (BaseException be) {
|
435
|
be.printStackTrace();
|
436
|
throw be;
|
437
|
}
|
438
|
|
439
|
}
|
440
|
|
441
|
// part of the ORE package
|
442
|
dataIds.add(dataGuid);
|
443
|
|
444
|
} // end if (EML package)
|
445
|
|
446
|
} // end for (data entities)
|
447
|
|
448
|
} // data entities not null
|
449
|
|
450
|
// ORE map
|
451
|
if (includeORE) {
|
452
|
if (!dataIds.isEmpty()) {
|
453
|
// generate the ORE map for this datapackage
|
454
|
Identifier resourceMapId = new Identifier();
|
455
|
// want to be able to run this over and over again for now
|
456
|
resourceMapId.setValue("resourceMap_" + sysMeta.getIdentifier().getValue() + "_" + System.currentTimeMillis());
|
457
|
idMap.put(sysMeta.getIdentifier(), dataIds);
|
458
|
ResourceMap rm = ResourceMapFactory.getInstance().createResourceMap(resourceMapId, idMap);
|
459
|
String resourceMapXML = ResourceMapFactory.getInstance().serializeResourceMap(rm);
|
460
|
// copy most of the same system metadata as the packaging metadata
|
461
|
SystemMetadata resourceMapSysMeta = new SystemMetadata();
|
462
|
BeanUtils.copyProperties(resourceMapSysMeta, sysMeta);
|
463
|
resourceMapSysMeta.setIdentifier(resourceMapId);
|
464
|
Checksum oreChecksum = ChecksumUtil.checksum(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING), "MD5");
|
465
|
resourceMapSysMeta.setChecksum(oreChecksum);
|
466
|
ObjectFormatIdentifier formatId = ObjectFormatCache.getInstance().getFormat("http://www.openarchives.org/ore/terms").getFormatId();
|
467
|
resourceMapSysMeta.setFormatId(formatId);
|
468
|
// TODO: other fields to update?
|
469
|
resourceMapSysMeta.setObsoletes(null);
|
470
|
resourceMapSysMeta.setObsoletedBy(null);
|
471
|
resourceMapSysMeta.setSize(BigInteger.valueOf(sizeOfStream(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING))));
|
472
|
|
473
|
// save it locally
|
474
|
Session session = new Session();
|
475
|
session.setSubject(submitter);
|
476
|
MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
|
477
|
MNodeService.getInstance(request).create(
|
478
|
session,
|
479
|
resourceMapId,
|
480
|
IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING),
|
481
|
resourceMapSysMeta);
|
482
|
}
|
483
|
}
|
484
|
|
485
|
} catch (ParserConfigurationException pce) {
|
486
|
logMetacat.debug("There was a problem parsing the EML document. "
|
487
|
+ "The error message was: " + pce.getMessage());
|
488
|
|
489
|
} catch (SAXException saxe) {
|
490
|
logMetacat.debug("There was a problem traversing the EML document. "
|
491
|
+ "The error message was: " + saxe.getMessage());
|
492
|
|
493
|
} catch (XPathExpressionException xpee) {
|
494
|
logMetacat.debug("There was a problem searching the EML document. "
|
495
|
+ "The error message was: " + xpee.getMessage());
|
496
|
} catch (Exception e) {
|
497
|
logMetacat.debug("There was a problem creating System Metadata. "
|
498
|
+ "The error message was: " + e.getMessage());
|
499
|
e.printStackTrace();
|
500
|
} // end try()
|
501
|
|
502
|
} // end if()
|
503
|
|
504
|
return sysMeta;
|
505
|
}
|
506
|
|
507
|
/**
|
508
|
* Find the size (in bytes) of a stream. Note: This needs to refactored out
|
509
|
* of MetacatHandler and into a utility when stream i/o in Metacat is
|
510
|
* evaluated.
|
511
|
*
|
512
|
* @param is The InputStream of bytes
|
513
|
*
|
514
|
* @return size The size in bytes of the input stream as a long
|
515
|
*
|
516
|
* @throws IOException
|
517
|
*/
|
518
|
private static long sizeOfStream(InputStream is) throws IOException {
|
519
|
|
520
|
long size = 0;
|
521
|
byte[] b = new byte[1024];
|
522
|
int numread = is.read(b, 0, 1024);
|
523
|
while (numread != -1) {
|
524
|
size += numread;
|
525
|
numread = is.read(b, 0, 1024);
|
526
|
}
|
527
|
return size;
|
528
|
|
529
|
}
|
530
|
}
|