Metacat

package edu.ucsb.nceas.metacat.admin.upgrade;

/**

 *  '$RCSfile$'

 *    Purpose: A Class for upgrading the database to version 1.5

 *  Copyright: 2000 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Saurabh Garg

 *

 *   '$Author: leinfelder $'

 *     '$Date: 2011-03-29 18:23:38 +0000 (Tue, 29 Mar 2011) $'

 * '$Revision: 6025 $'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

import java.io.ByteArrayInputStream;

import java.io.IOException;

import java.io.InputStream;

import java.security.NoSuchAlgorithmException;

import java.sql.SQLException;

import java.util.Calendar;

import java.util.Date;

import java.util.Hashtable;

import java.util.List;

import java.util.TimeZone;

import java.util.Timer;

import javax.xml.parsers.ParserConfigurationException;

import javax.xml.xpath.XPathExpressionException;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.dataone.eml.DataoneEMLParser;

import org.dataone.eml.EMLDocument;

import org.dataone.eml.EMLDocument.DistributionMetadata;

import org.dataone.service.exceptions.InvalidRequest;

import org.dataone.service.exceptions.InvalidToken;

import org.dataone.service.exceptions.NotAuthorized;

import org.dataone.service.exceptions.NotFound;

import org.dataone.service.exceptions.NotImplemented;

import org.dataone.service.exceptions.ServiceFailure;

import org.dataone.service.types.AuthToken;

import org.dataone.service.types.Checksum;

import org.dataone.service.types.ChecksumAlgorithm;

import org.dataone.service.types.Identifier;

import org.dataone.service.types.NodeReference;

import org.dataone.service.types.ObjectFormat;

import org.dataone.service.types.Subject;

import org.dataone.service.types.SystemMetadata;

import org.xml.sax.SAXException;

import edu.ucsb.nceas.metacat.AccessionNumber;

import edu.ucsb.nceas.metacat.AccessionNumberException;

import edu.ucsb.nceas.metacat.DocumentImpl;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.McdbException;

import edu.ucsb.nceas.metacat.MetacatHandler;

import edu.ucsb.nceas.metacat.admin.AdminException;

import edu.ucsb.nceas.metacat.dataone.CrudService;

import edu.ucsb.nceas.metacat.properties.PropertyService;

import edu.ucsb.nceas.metacat.util.SessionData;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

import edu.ucsb.nceas.utilities.SortedProperties;

public class GenerateSystemMetadata implements UpgradeUtilityInterface {

	private static Log log = LogFactory.getLog(GenerateSystemMetadata.class);

	private MetacatHandler handler = new MetacatHandler(new Timer());

    public boolean upgrade() throws AdminException {

        boolean success = true;

        try {

			generateMissingSystemMetadata(null);

		} catch (Exception e) {

			String msg = "Problem generating missing system metadata: " + e.getMessage();

			log.error(msg, e);

			success = false;

			throw new AdminException(msg);

		}

    	return success;

    }

    /**

     * Generate SystemMetadata for any object in the object store that does

     * not already have it.  SystemMetadata documents themselves, are, of course,

     * exempt.  This is a utility method for migration of existing object 

     * stores to DataONE where SystemMetadata is required for all objects.  See 

     * https://trac.dataone.org/ticket/591

     * 

     * @param token an authtoken with appropriate permissions to read all 

     * documents in the object store.  To work correctly, this should probably

     * be an adminstrative credential.

     * @throws SQLException 

     * @throws AccessionNumberException 

     * @throws NoSuchAlgorithmException 

     * @throws InvalidRequest 

     * @throws NotImplemented 

     * @throws NotFound 

     * @throws NotAuthorized 

     * @throws InvalidToken 

     * @throws PropertyNotFoundException 

     * @throws McdbDocNotFoundException 

     * @throws ServiceFailure 

     */

    public void generateMissingSystemMetadata(AuthToken token) 

    throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized, 

    NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException 

    {

        IdentifierManager im = IdentifierManager.getInstance();

        //get the list of ids with no SM

        List<String> idList = im.getLocalIdsWithNoSystemMetadata();

        for (String localId : idList) { 

            //for each id, add a system metadata doc

        	try {

        		generateMissingSystemMetadata(token, localId);

        	} catch (Exception e) {

				log.error("Error generating system metadata for: " + localId, e);

			}

        }

        log.info("generateMissingSystemMetadata(token)");

    }

    /**

     * Generate SystemMetadata for a particular object with identifier localId.

     * This is a utility method for migration of existing objects 

     * to DataONE where SystemMetadata is required for all objects.

     * 

     * @param token an authtoken with appropriate permissions to read all 

     *        documents in the object store.  To work correctly, this should

     *        be an adminstrative credential.

     * @param localId the identifier of the object to be processed

     * @throws ServiceFailure 

     * @throws SQLException 

     * @throws AccessionNumberException 

     * @throws NoSuchAlgorithmException 

     * @throws InvalidRequest 

     * @throws NotImplemented 

     * @throws NotFound 

     * @throws NotAuthorized 

     * @throws InvalidToken 

     * @throws PropertyNotFoundException 

     * @throws McdbDocNotFoundException 

     */

    public void generateMissingSystemMetadata(AuthToken token, String localId) 

    throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,

    NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException 

    {

    	log.debug("CrudService.generateMissingSystemMetadata() called.");

    	log.debug("Creating SystemMetadata for localId " + localId);

        SystemMetadata sm = null;

        //generate required system metadata fields from the document

        try {

        	sm = handler.createSystemMetadata(localId, null, null);

        } catch (Exception e1) {

        	e1.printStackTrace();

        	ServiceFailure sf = new ServiceFailure("00","Exception in generateMissingSystemMetadata: " +

        			e1.getMessage());

        	sf.setStackTrace(e1.getStackTrace());

        	throw sf;

        }

        //insert the systemmetadata object

        String guid = null;

        try {

        	IdentifierManager.getInstance().getLocalId(sm.getIdentifier().getValue());

        } catch (Exception e) {

			guid = null;

		}

        if (guid == null) {

        	IdentifierManager.getInstance().createSystemMetadataMapping(sm, localId);

        }

        IdentifierManager.getInstance().insertAdditionalSystemMetadataFields(sm);

        log.info("generateMissingSystemMetadata(token, localId)");

    }

    public static void main(String [] ags){

        try {

        	// set up the properties based on the test/deployed configuration of the workspace

        	SortedProperties testProperties = 

				new SortedProperties("test/test.properties");

			testProperties.load();

			String metacatContextDir = testProperties.getProperty("metacat.contextDir");

			PropertyService.getInstance(metacatContextDir + "/WEB-INF");

			// now run it

            GenerateSystemMetadata upgrader = new GenerateSystemMetadata();

	        upgrader.upgrade();

        } catch (Exception ex) {

            System.out.println("Exception:" + ex.getMessage());

            ex.printStackTrace();

        }

    }

}