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6097
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leinfelder
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package edu.ucsb.nceas.metacat.admin.upgrade;
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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: 2011-03-29 18:23:38 +0000 (Tue, 29 Mar 2011) $'
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* '$Revision: 6025 $'
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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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import java.security.NoSuchAlgorithmException;
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import java.sql.SQLException;
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import java.util.List;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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6366
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leinfelder
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import org.dataone.service.types.v1.SystemMetadata;
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6097
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leinfelder
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6806
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leinfelder
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import edu.emory.mathcs.backport.java.util.Collections;
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6097
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leinfelder
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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6721
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leinfelder
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import edu.ucsb.nceas.metacat.DBUtil;
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import edu.ucsb.nceas.metacat.DocumentImpl;
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6097
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leinfelder
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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.admin.AdminException;
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6705
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leinfelder
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import edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory;
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6097
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leinfelder
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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6721
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leinfelder
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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6097
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leinfelder
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import edu.ucsb.nceas.utilities.SortedProperties;
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public class GenerateSystemMetadata implements UpgradeUtilityInterface {
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private static Log log = LogFactory.getLog(GenerateSystemMetadata.class);
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public boolean upgrade() throws AdminException {
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boolean success = true;
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6712
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leinfelder
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// include ORE?
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boolean includeOre = true;
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6852
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leinfelder
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boolean downloadData = true;
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6097
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leinfelder
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try {
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6852
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leinfelder
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generateMissingSystemMetadata(includeOre, downloadData);
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6097
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leinfelder
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} catch (Exception e) {
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String msg = "Problem generating missing system metadata: " + e.getMessage();
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log.error(msg, e);
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success = false;
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throw new AdminException(msg);
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}
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return success;
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}
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/**
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* Generate SystemMetadata for any object in the object store that does
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* not already have it. SystemMetadata documents themselves, are, of course,
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* exempt. This is a utility method for migration of existing object
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* stores to DataONE where SystemMetadata is required for all objects. See
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* https://trac.dataone.org/ticket/591
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6712
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leinfelder
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* @param includeOre
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6097
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leinfelder
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*
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* @param token an authtoken with appropriate permissions to read all
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* documents in the object store. To work correctly, this should probably
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* be an adminstrative credential.
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* @throws SQLException
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* @throws AccessionNumberException
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* @throws NoSuchAlgorithmException
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* @throws InvalidRequest
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* @throws NotImplemented
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* @throws NotFound
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* @throws NotAuthorized
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* @throws InvalidToken
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* @throws PropertyNotFoundException
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* @throws McdbDocNotFoundException
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* @throws ServiceFailure
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*/
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6852
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leinfelder
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public void generateMissingSystemMetadata(boolean includeOre, boolean downloadData)
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leinfelder
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throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,
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NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException
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{
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//get the list of ids with no SM
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6721
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leinfelder
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//List<String> idList = IdentifierManager.getInstance().getLocalIdsWithNoSystemMetadata(true);
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List<String> idList = DBUtil.getAllDocidsByType(null, true);
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leinfelder
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Collections.sort(idList);
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leinfelder
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for (String localId : idList) {
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//for each id, add a system metadata doc
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try {
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6721
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leinfelder
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log.debug("generating missing system metadata for " + localId);
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6852
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leinfelder
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generateMissingSystemMetadata(localId, includeOre, downloadData);
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6097
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leinfelder
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} catch (Exception e) {
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log.error("Error generating system metadata for: " + localId, e);
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}
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}
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6721
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leinfelder
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log.info("done generating missing system metadata");
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6097
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leinfelder
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}
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/**
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* Generate SystemMetadata for a particular object with identifier localId.
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* This is a utility method for migration of existing objects
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* to DataONE where SystemMetadata is required for all objects.
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*
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* @param token an authtoken with appropriate permissions to read all
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* documents in the object store. To work correctly, this should
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* be an adminstrative credential.
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* @param localId the identifier of the object to be processed
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6712
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leinfelder
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* @param includeOre
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6097
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leinfelder
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* @throws ServiceFailure
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* @throws SQLException
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* @throws AccessionNumberException
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* @throws NoSuchAlgorithmException
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* @throws InvalidRequest
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* @throws NotImplemented
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* @throws NotFound
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* @throws NotAuthorized
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* @throws InvalidToken
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* @throws PropertyNotFoundException
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* @throws McdbDocNotFoundException
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*/
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6852
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leinfelder
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public void generateMissingSystemMetadata(String localId, boolean includeOre, boolean downloadData)
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6097
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leinfelder
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throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,
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NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException
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{
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leinfelder
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log.debug("generateMissingSystemMetadata() called.");
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leinfelder
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log.debug("Creating SystemMetadata for localId " + localId);
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SystemMetadata sm = null;
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//generate required system metadata fields from the document
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try {
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6852
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leinfelder
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sm = SystemMetadataFactory.createSystemMetadata(localId, includeOre, downloadData);
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6097
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leinfelder
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} catch (Exception e1) {
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e1.printStackTrace();
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ServiceFailure sf = new ServiceFailure("00","Exception in generateMissingSystemMetadata: " +
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e1.getMessage());
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sf.setStackTrace(e1.getStackTrace());
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throw sf;
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}
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6721
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leinfelder
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//insert the systemmetadata object or just update it as needed
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boolean exists = IdentifierManager.getInstance().systemMetadataExists(sm.getIdentifier().getValue());
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leinfelder
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if (!exists) {
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IdentifierManager.getInstance().createSystemMetadata(sm);
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leinfelder
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}
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leinfelder
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IdentifierManager.getInstance().updateSystemMetadata(sm);
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leinfelder
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log.info("generateMissingSystemMetadata(token, localId)");
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}
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public static void main(String [] ags){
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try {
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// set up the properties based on the test/deployed configuration of the workspace
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SortedProperties testProperties =
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new SortedProperties("test/test.properties");
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testProperties.load();
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String metacatContextDir = testProperties.getProperty("metacat.contextDir");
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PropertyService.getInstance(metacatContextDir + "/WEB-INF");
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// now run it
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GenerateSystemMetadata upgrader = new GenerateSystemMetadata();
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upgrader.upgrade();
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} catch (Exception ex) {
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System.out.println("Exception:" + ex.getMessage());
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ex.printStackTrace();
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}
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}
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}
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