/ - Diff - Metacat - Ecoinformatics Redmine

                       // handle inserts
                       try {
                     	// create the system metadata
                         sysMeta = SystemMetadataFactory.createSystemMetadata(newdocid, false);
                         sysMeta = SystemMetadataFactory.createSystemMetadata(newdocid, false, false);
                         // save it to the map
                         HazelcastService.getInstance().getSystemMetadataMap().put(sysMeta.getIdentifier(), sysMeta);
-...
                                         username, groupnames);
                                 // generate system metadata about the doc
                                 SystemMetadata sm = SystemMetadataFactory.createSystemMetadata(docid, false);
                                 SystemMetadata sm = SystemMetadataFactory.createSystemMetadata(docid, false, false);
     					        // manage it in the store
                                 HazelcastService.getInstance().getSystemMetadataMap().put(sm.getIdentifier(), sm);

      */
     package edu.ucsb.nceas.metacat.dataone;
     import java.io.BufferedInputStream;
     import java.io.IOException;
     import java.io.InputStream;
     import java.math.BigInteger;
     import java.net.URL;
     import java.security.NoSuchAlgorithmException;
     import java.sql.SQLException;
     import java.util.ArrayList;
-...
     	 * @throws AccessControlException
     	 * @throws AccessException
     	 */
     	public static SystemMetadata createSystemMetadata(String localId, boolean includeORE)
     	public static SystemMetadata createSystemMetadata(String localId, boolean includeORE, boolean downloadData)
     			throws McdbException, McdbDocNotFoundException, SQLException,
     			IOException, AccessionNumberException, ClassNotFoundException,
     			InsufficientKarmaException, ParseLSIDException,
-...
     									.getFormat("application/octet-stream")
     									.getFormatId().getValue();
+    						}
     						String dataDocLocalId = "";
     						// process the data
     						String dataDocLocalId = null;
     						Identifier dataGuid = new Identifier();
     						// handle ecogrid, or downloadable data
     						String ecogridPrefix = "ecogrid://knb/";
     						if (dataDocUrl.trim().startsWith(ecogridPrefix)) {
     							dataDocLocalId = dataDocUrl.substring(dataDocUrl.indexOf(ecogridPrefix) + ecogridPrefix.length());
     						} else {
     							// should we try downloading the remote data?
     							if (downloadData) {
     								InputStream dataObject = null;
     								try {
     									// download the data from the URL
     									URL dataURL = new URL(dataDocUrl);
     									dataObject = dataURL.openStream();
     									// TODO: check for valid content
     								} catch (Exception e) {
     									// error with the download
     									logMetacat.warn("Error downloading remote data. " + e.getMessage());
+    								}
     								if (dataObject != null) {
     									// create the local version of it
     									dataDocLocalId = DocumentUtil.generateDocumentId(1);
     									IdentifierManager.getInstance().createMapping(dataDocLocalId, dataDocLocalId);
     									dataGuid.setValue(dataDocLocalId);
     									// save it locally
     									Session session = new Session();
     									session.setSubject(submitter);
     									MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
     									MNodeService.getInstance(request).insertDataObject(dataObject, dataGuid, session);
+    								}
+    							}
+    						}
     						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());
     						// now we have a local id for the data
     						if (dataDocLocalId != null) {
     							// look up the guid for the data
     							String dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);
     							int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);
-...
     							// check if data system metadata exists already
     							SystemMetadata dataSysMeta = null;
     							String dataGuidString = null;
     							Identifier dataGuid = new Identifier();
     							try {
     								// look for the identifier
     								dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
-...
     								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, includeORE);
     									dataSysMeta = createSystemMetadata(dataDocLocalId, includeORE, false);
     									// now look it up again
     									dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);

             boolean success = true;
             // include ORE?
             boolean includeOre = true;
             boolean downloadData = true;
             try {
     			generateMissingSystemMetadata(includeOre);
     			generateMissingSystemMetadata(includeOre, downloadData);
     		} catch (Exception e) {
     			String msg = "Problem generating missing system metadata: " + e.getMessage();
     			log.error(msg, e);
-...
          * @throws McdbDocNotFoundException
          * @throws ServiceFailure
          */
         public void generateMissingSystemMetadata(boolean includeOre)
         public void generateMissingSystemMetadata(boolean includeOre, boolean downloadData)
         throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,
         NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException
+        {
-...
                 //for each id, add a system metadata doc
             	try {
             		log.debug("generating missing system metadata for " + localId);
             		generateMissingSystemMetadata(localId, includeOre);
             		generateMissingSystemMetadata(localId, includeOre, downloadData);
             	} catch (Exception e) {
     				log.error("Error generating system metadata for: " + localId, e);
+    			}
-...
          * @throws PropertyNotFoundException
          * @throws McdbDocNotFoundException
          */
         public void generateMissingSystemMetadata(String localId, boolean includeOre)
         public void generateMissingSystemMetadata(String localId, boolean includeOre, boolean downloadData)
         throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,
         NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException
+        {
-...
             //generate required system metadata fields from the document
             try {
             	sm = SystemMetadataFactory.createSystemMetadata(localId, includeOre);
             	sm = SystemMetadataFactory.createSystemMetadata(localId, includeOre, downloadData);
             } catch (Exception e1) {
             	e1.printStackTrace();
             	ServiceFailure sf = new ServiceFailure("00","Exception in generateMissingSystemMetadata: " +

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Metacat

Revision 6852

Added by ben leinfelder over 12 years ago