Metacat

	public static long sizeOfStream(InputStream is) throws IOException {

import java.io.InputStream;

import java.math.BigInteger;

import java.util.ArrayList;

import java.util.Calendar;

import java.util.Date;

import java.util.Map;

import org.apache.commons.beanutils.BeanUtils;

import org.apache.commons.io.IOUtils;

import org.dataone.client.D1Client;

import org.dataone.client.MNode;

import org.dataone.client.ObjectFormatCache;

import org.dataone.ore.ResourceMapFactory;

import org.dataone.service.types.v1.Checksum;

import org.dataone.service.types.v1.Identifier;

import org.dataone.service.types.v1.ObjectFormatIdentifier;

import org.dataone.service.types.v1.ObjectInfo;

import org.dataone.service.types.v1.ObjectList;

import org.dataone.service.types.v1.SystemMetadata;

import org.dataone.service.types.v1.util.ChecksumUtil;

import org.dspace.foresite.ResourceMap;

import edu.ucsb.nceas.metacat.MetaCatServlet;

	/**

	 * Need to update the existing ORE maps to have correct dateTime serializations

	 * see: https://redmine.dataone.org/issues/3046

	 * @param mnBaseUrl

	 */

	public static void updateOREdateFormat(String mnBaseUrl) {

		List<Identifier> orePids = getAllOREpids(mnBaseUrl);

		updateOREs(orePids, "b", mnBaseUrl);

	}

	/**

	 * Retrieves a list of all ORE objects on the given MN

	 * @param mnBaseUrl

	 * @return

	 */

	public static List<Identifier> getAllOREpids(String mnBaseUrl) {

		MNode mn = null;

		ObjectFormatIdentifier formatId = null;

		List<Identifier> pids = null;

		try {

			// get the MN

			mn = D1Client.getMN(mnBaseUrl);

			// get the ORE format id

	        formatId = ObjectFormatCache.getInstance().getFormat("http://www.openarchives.org/ore/terms").getFormatId();

	        // get the objects that match

			ObjectList objectList = mn.listObjects(null, null, null, formatId , null, 0, Integer.MAX_VALUE);

			pids = new ArrayList<Identifier>();

			for (ObjectInfo o: objectList.getObjectInfoList()) {

				pids.add(o.getIdentifier());

			}

		} catch (Exception e) {

			log.error("Could not get MN list of ORE pids", e);

		}

		return pids;

	}

	/**

	 * Updates the given OREs by regenerating and reserializing the RDF using the updated foresite library

	 * Only non-obsolete, non-archived ORE objects are updated and their SystemMetadata is based on the original version.

	 * see: https://redmine.dataone.org/issues/3046

	 * @param orePids

	 * @param pidSuffix

	 * @param mnBaseUrl

	 */

	public static void updateOREs(List<Identifier> orePids, String pidSuffix, String mnBaseUrl) {

		// get a MN client for this local node, or use the given baseUrl

		MNode mn = null;

		try {

			mn = D1Client.getMN(mnBaseUrl);

		} catch (Exception e) {

			log.error("Could not get MN client", e);

			// nothing more we can do here

			return;

		}

		// make sure we have something for the suffix

		if (pidSuffix == null) {

			pidSuffix = "b";

		}

		for (Identifier orePid: orePids) {

			try {

				log.debug("processing ORE pid: " + orePid.getValue());

				// get original SystemMetadata

				SystemMetadata originalOreSysMeta = mn.getSystemMetadata(orePid);

				// only update the CURRENT revision of the ORE

				if (originalOreSysMeta.getObsoletedBy() != null || originalOreSysMeta.getArchived()) {

					log.debug("ORE pid is obsolete or archived, skipping: " + orePid.getValue());

					continue;

				}

				// get the original ORE map

				InputStream originalOreStream = mn.get(orePid);

				Map<Identifier, Map<Identifier, List<Identifier>>> originalOre = ResourceMapFactory.getInstance().parseResourceMap(originalOreStream);

				// generate the updated ORE map, in this case we aren't changing any values, just altering the serialization using a newer foresite library

				Identifier updatedOrePid = new Identifier();

				updatedOrePid.setValue(orePid.getValue() + pidSuffix);

				ResourceMap updatedOre = ResourceMapFactory.getInstance().createResourceMap(updatedOrePid , originalOre.entrySet().iterator().next().getValue());

				String resourceMapXML = ResourceMapFactory.getInstance().serializeResourceMap(updatedOre);

	            Checksum oreChecksum = ChecksumUtil.checksum(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING), "MD5");

	            Date today = Calendar.getInstance().getTime();

				// copy the existing SystemMetada into the new SystemMetadata

				SystemMetadata updatedOreSysMeta = new SystemMetadata();

				BeanUtils.copyProperties(updatedOreSysMeta, originalOreSysMeta);

				// set the new SystemMetadata values

				updatedOreSysMeta.setIdentifier(updatedOrePid);

				updatedOreSysMeta.setObsoletes(orePid);

				updatedOreSysMeta.setObsoletedBy(null);

				updatedOreSysMeta.setArchived(false);

	            updatedOreSysMeta.setChecksum(oreChecksum);

	            updatedOreSysMeta.setSize(BigInteger.valueOf(SystemMetadataFactory.sizeOfStream(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING))));

	            updatedOreSysMeta.setDateSysMetadataModified(today);

	            updatedOreSysMeta.setDateUploaded(today);

	            updatedOreSysMeta.setReplicaList(null);

	            // save the updated ORE to the MN

				InputStream updatedOreStream = IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING);

				mn.update(null, orePid, updatedOreStream, updatedOrePid, updatedOreSysMeta);

			} catch (Exception e) {

				log.error("Could not update ORE map: " + orePid, e);

				// go to the next record, there's nothing else to do here

				continue;

			}

		}

	}