Metacat

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

                    sysMeta = SystemMetadataFactory.createSystemMetadata(newdocid);

                            SystemMetadata sm = SystemMetadataFactory.createSystemMetadata(docid);

/**

 *  '$RCSfile$'

 *    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

 *

 *   '$Author$'

 *     '$Date$'

 * '$Revision$'

 *

 * 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

 */

package edu.ucsb.nceas.metacat.dataone;

import java.io.IOException;

import java.io.InputStream;

import java.math.BigInteger;

import java.security.NoSuchAlgorithmException;

import java.sql.SQLException;

import java.text.ParseException;

import java.text.SimpleDateFormat;

import java.util.Date;

import java.util.Hashtable;

import java.util.TimeZone;

import javax.xml.parsers.ParserConfigurationException;

import javax.xml.xpath.XPathExpressionException;

import org.apache.log4j.Logger;

import org.dataone.client.ObjectFormatCache;

import org.dataone.service.exceptions.BaseException;

import org.dataone.service.exceptions.NotFound;

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

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

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

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

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

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

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

import org.ecoinformatics.datamanager.DataManager;

import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface;

import org.ecoinformatics.datamanager.parser.DataPackage;

import org.jibx.runtime.JiBXException;

import org.xml.sax.SAXException;

import edu.ucsb.nceas.metacat.AccessionNumber;

import edu.ucsb.nceas.metacat.AccessionNumberException;

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.client.InsufficientKarmaException;

import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;

import edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory;

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

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

import edu.ucsb.nceas.utilities.ParseLSIDException;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

public class SystemMetadataFactory {

    private static Logger logMetacat = Logger.getLogger(SystemMetadataFactory.class);

	/**

     * Creates a system metadata object for insertion into metacat

     *

     * @param localId  The local document identifier

     * @param user  The user submitting the system metadata document

     * @param groups  The groups the user belongs to

     *

     * @return sysMeta  The system metadata object created

     */

    public static SystemMetadata createSystemMetadata(String localId) 

      throws McdbException, McdbDocNotFoundException, SQLException, 

      IOException, AccessionNumberException, ClassNotFoundException,

      InsufficientKarmaException, ParseLSIDException, PropertyNotFoundException,

      BaseException, NoSuchAlgorithmException, JiBXException

    {

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

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

      // create system metadata for the document

      SystemMetadata sysMeta = new SystemMetadata();

      sysMeta.setSerialVersion(BigInteger.valueOf(1));

      int rev = IdentifierManager.getInstance().getLatestRevForLocalId(localId);

      AccessionNumber accNum = new AccessionNumber(localId, "NONE");

      String guid = null;

      try {

    	  // get the guid if it exists

    	  guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);

      } catch ( McdbDocNotFoundException dnfe ) {

        // otherwise create the mapping

        logMetacat.debug("There was a problem getting the guid from " +

          "the given localId (docid and revision). The error message was: " + dnfe.getMessage());

        logMetacat.debug("No guid in the identifier table.  adding it for " + localId);

        IdentifierManager.getInstance().createMapping(localId, localId);

        logMetacat.debug("Mapping created for " + localId);

        logMetacat.debug("accessionNumber: " + accNum);

  	  	guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);

      }

      Identifier identifier = new Identifier();

      identifier.setValue(guid);

      //set the id

      sysMeta.setIdentifier(identifier);

      // get the data or metadata object

      InputStream inputStream;

      try {

          inputStream = MetacatHandler.read(localId);

      } catch ( ParseLSIDException ple ) {

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

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

        throw ple;

      } catch ( PropertyNotFoundException pnfe ) {

        logMetacat.debug("There was a problem finding a property. " +

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

        throw pnfe;

      } catch ( McdbException me ) {

        logMetacat.debug("There was a Metacat problem. " +

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

        throw me;

      } catch ( SQLException sqle ) {

        logMetacat.debug("There was a SQL problem. " +

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

        throw sqle;

      } catch ( ClassNotFoundException cnfe ) {

        logMetacat.debug("There was a problem finding a class. " +

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

        throw cnfe;

      } catch ( IOException ioe ) {

        logMetacat.debug("There was an I/O exception. " +

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

        throw ioe;

      } // end try()

      // get additional docinfo

      Hashtable<String, Object> docInfo = IdentifierManager.getInstance().getDocumentInfo(localId);

      //set the default object format

      String doctype = (String) docInfo.get("doctype");

      ObjectFormatIdentifier fmtid = null;

      // set the object format, fall back to defaults

      try {

	      fmtid = ObjectFormatCache.getInstance().getFormat(doctype).getFormatId();

      } catch (NotFound nfe) {

        try {

        	// format is not registered, use default

	        if (doctype.trim().equals("BIN")) {

	        	fmtid = ObjectFormatCache.getInstance().getFormat(

	        			"application/octet-stream").getFormatId();

	        } else {

	        	fmtid = ObjectFormatCache.getInstance().getFormat("text/plain").getFormatId();

	        }

        } catch (NotFound nf) {

          logMetacat.error("There was a problem getting the default format " +

          	"from the ObjectFormatCache: " + nf.getMessage());

          throw nf;

        }

      }

      sysMeta.setFormatId(fmtid);

      logMetacat.debug("The ObjectFormat for " + localId + " is " + fmtid.getValue());

      // further parse EML documents to get data object format,

      // describes and describedBy information

      if ( fmtid == ObjectFormatCache.getInstance().getFormat("eml://ecoinformatics.org/eml-2.0.0").getFormatId() ||

           fmtid == ObjectFormatCache.getInstance().getFormat("eml://ecoinformatics.org/eml-2.0.1").getFormatId() ||

           fmtid == ObjectFormatCache.getInstance().getFormat("eml://ecoinformatics.org/eml-2.1.0").getFormatId() ||

           fmtid == ObjectFormatCache.getInstance().getFormat("eml://ecoinformatics.org/eml-2.1.1").getFormatId() ) {

        try {

        	DatabaseConnectionPoolInterface connectionPool = MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();

        	DataManager dataManager = DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());

        	DataPackage dataPackage = dataManager.parseMetadata(inputStream);

          // iterate through the data objects in the EML doc and add sysmeta

          logMetacat.debug("In createSystemMetadata() the number of data " + 

            "entities is: " + dataPackage.getEntityNumber());

          // iterate through data objects described by the EML

          for (int j = 0; j < dataPackage.getEntityList().length; j++) {

            String dataDocUrl = dataPackage.getEntityList()[j].getURL();

            String dataDocMimeType = dataPackage.getEntityList()[j].getDataFormat();

            // default to binary

            if (dataDocMimeType == null) {

                dataDocMimeType = 

                	ObjectFormatCache.getInstance().getFormat("application/octet-stream").getFormatId().getValue();

            }

            String dataDocLocalId = "";

            logMetacat.debug("Data local ID: " + dataDocLocalId);

            logMetacat.debug("Data URL     : " + dataDocUrl);

            logMetacat.debug("Data mime    : " + dataDocMimeType);

            //we only handle ecogrid urls right now

            String ecogridPrefix = "ecogrid://knb/";

            if ( dataDocUrl.trim().startsWith(ecogridPrefix) ) {

              dataDocLocalId = 

                dataDocUrl.substring(dataDocUrl.indexOf(ecogridPrefix) + ecogridPrefix.length());

              // look up the guid for the data

              String dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);

              int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);

              SystemMetadata dataSysMeta = null;

              // check if data system metadata exists

              String dataGuidString = null;

              try {

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

            	  dataSysMeta = IdentifierManager.getInstance().getSystemMetadata(dataGuidString);

              } catch ( McdbDocNotFoundException nf ) {

            	  // System metadata for data doesn't exist yet, so create it

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

            	  try {

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

            		  dataSysMeta = createSystemMetadata(dataDocLocalId);

            		  // now look it up again

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

                	  //set the guid

                      Identifier dataGuid = new Identifier();

                      dataGuid.setValue(dataGuidString);

                      // set object format

                      logMetacat.debug("Updating system metadata for " + dataGuid.getValue() + " to " + dataDocMimeType);

                      try {

	                      ObjectFormatIdentifier fmt = 

	                      ObjectFormatCache.getInstance().getFormat(dataDocMimeType).getFormatId();

	                      dataSysMeta.setFormatId(fmt);

                      } catch (NotFound nfe) {

                      	logMetacat.debug("Couldn't find format identifier for: " +

                      			dataDocMimeType + ". Setting it to application/octet-stream.");

                        ObjectFormatIdentifier newFmtid = new ObjectFormatIdentifier();

                        newFmtid.setValue("application/octet-stream");

                      }

            		  // update the values

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

                } catch ( McdbDocNotFoundException mdnf) {

                  mdnf.printStackTrace();

                  throw mdnf;

                } catch ( NumberFormatException nfe) {

                  nfe.printStackTrace();

                  throw nfe;

                } catch ( AccessionNumberException ane) {

                  ane.printStackTrace();

                  throw ane;

                } catch ( SQLException sqle) {

                  sqle.printStackTrace();

                  throw sqle;

                } catch ( NoSuchAlgorithmException nsae) {

                  nsae.printStackTrace();

                  throw nsae;

                } catch ( IOException ioe) {

                  ioe.printStackTrace();

                  throw ioe;

                } catch ( PropertyNotFoundException pnfe) {

                  pnfe.printStackTrace();

                  throw pnfe;

                } catch ( BaseException be) {

                  be.printStackTrace();

                  throw be;

                }

              }

            } // end if()

          } // end for()

        } catch ( ParserConfigurationException pce ) {

          logMetacat.debug("There was a problem parsing the EML document. " +

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

        } catch ( SAXException saxe ) {

          logMetacat.debug("There was a problem traversing the EML document. " +

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

        } catch ( XPathExpressionException xpee ) {

          logMetacat.debug("There was a problem searching the EML document. " +

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

        } catch ( Exception e ) {

            logMetacat.debug("There was a problem creating System Metadata. " +

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

        } // end try()

      } // end if()

      //create the checksum

      inputStream = MetacatHandler.read(localId);

      String algorithm = "MD5";

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

      sysMeta.setChecksum(checksum);

      //set the size

      inputStream = MetacatHandler.read(localId);

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

      sysMeta.setSize(new BigInteger(sizeStr));

      //submitter

      Subject subject = new Subject();

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

      sysMeta.setSubmitter(subject);

      sysMeta.setRightsHolder(subject);

      try {

        SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-DD");

        dateFormat.setTimeZone(TimeZone.getDefault());

        Date dateCreated = dateFormat.parse((String) docInfo.get("date_created"));

        sysMeta.setDateUploaded(dateCreated);

        Date dateUpdated = dateFormat.parse((String) docInfo.get("date_updated"));

        sysMeta.setDateSysMetadataModified(dateUpdated);

      } catch (ParseException pe) {

        logMetacat.debug("There was a problem parsing a Metacat date. The " + 

          "error message was: " + pe.getMessage());

        Date dateCreated = new Date();

        sysMeta.setDateUploaded(dateCreated);

        Date dateUpdated = new Date();

        sysMeta.setDateSysMetadataModified(dateUpdated);

      }

      NodeReference nr = new NodeReference();

      nr.setValue(PropertyService.getProperty("dataone.memberNodeId"));

      sysMeta.setOriginMemberNode(nr);

      sysMeta.setAuthoritativeMemberNode(nr);

      return sysMeta;

    }

    /*

     * Find the size (in bytes) of a stream. Note: This needs to refactored out

     * of MetacatHandler and into a utility when stream i/o in Metacat is

     * evaluated.

     *

     * @param is  The InputStream of bytes

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

     * @throws IOException

     */

    private static long sizeOfStream(InputStream is)

      throws IOException {

      long size = 0;

      byte[] b = new byte[1024];

      int numread = is.read(b, 0, 1024);

      while(numread != -1)

      {

          size += numread;

          numread = is.read(b, 0, 1024);

      }

      return size;

    }

}

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

        	sm = SystemMetadataFactory.createSystemMetadata(localId);