Metacat

import javax.xml.parsers.ParserConfigurationException;

import javax.xml.xpath.XPathExpressionException;

import org.apache.commons.io.input.XmlStreamReader;

import org.apache.log4j.Logger;

import org.dataone.client.ObjectFormatCache;

     * @throws ClassNotFoundException

     * @throws IOException

     */

        throws ParseLSIDException,

        PropertyNotFoundException, McdbException, SQLException, 

        ClassNotFoundException, IOException

     * 

     * @return fileInputStream  The file to read as a FileInputStream

     */

      throws FileNotFoundException {

        logMetacat.debug("MetacatHandler.readFromFilesystem() called.");

                  // handle inserts

                  try {

                	// create the system metadata  

                    // save it to the map

                    HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);

                                    username, groupnames);

                            // generate system metadata about the doc

					        // manage it in the store

                            HazelcastService.getInstance().getSystemMetadataMap().put(sm.getIdentifier(), sm);

     *

     * @return sysMeta  The system metadata object created

     */

      throws McdbException, McdbDocNotFoundException, SQLException, 

      IOException, AccessionNumberException, ClassNotFoundException,

      InsufficientKarmaException, ParseLSIDException, PropertyNotFoundException,

    {

      logMetacat.debug("MetacatHandler.createSystemMetadata() called.");

      logMetacat.debug("provided localId: " + localId);

      // create system metadata for the document

      SystemMetadata sysMeta = new SystemMetadata();

      // get the data or metadata object

      InputStream inputStream;

      try {

      } catch ( ParseLSIDException ple ) {

        logMetacat.debug("There was a problem parsing the LSID from " +

          localId + ". The error message was: " + ple.getMessage());

            	  logMetacat.debug("There was not an existing system metadata " + "document for " + dataDocLocalId);

            	  try {

            		  logMetacat.debug("Creating a system metadata " + "document for " + dataDocLocalId);

            		  // now look it up again

                	  dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);

      //create the checksum

      String algorithm = "MD5";

      Checksum checksum = ChecksumUtil.checksum(inputStream, algorithm);

      sysMeta.setChecksum(checksum);

      //set the size

      String sizeStr = new Long(sizeOfStream(inputStream)).toString();

      sysMeta.setSize(new BigInteger(sizeStr));

      //submitter

      Subject subject = new Subject();

      subject.setValue((String) docInfo.get("user_owner"));

     * @return size  The size in bytes of the input stream as a long

     * @throws IOException

     */

      throws IOException {

      long size = 0;

import java.security.NoSuchAlgorithmException;

import java.sql.SQLException;

import java.util.List;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

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

    public boolean upgrade() throws AdminException {

        boolean success = true;

        //generate required system metadata fields from the document

        try {

        } catch (Exception e1) {

        	e1.printStackTrace();

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