/ - Diff - Metacat - Ecoinformatics Redmine

     import edu.ucsb.nceas.metacat.client.MetacatInaccessibleException;
     import edu.ucsb.nceas.metacat.properties.PropertyService;
     import edu.ucsb.nceas.metacat.shared.ServiceException;
     import edu.ucsb.nceas.metacat.util.DocumentUtil;
     import edu.ucsb.nceas.metacat.util.RequestUtil;
     import edu.ucsb.nceas.utilities.IOUtil;
     import edu.ucsb.nceas.utilities.PropertyNotFoundException;
-...
     		} catch (InterruptedException ie) {
     			debug("Could not sleep: " + ie.getMessage());
+    		}
     		StringBuffer docid = new StringBuffer(prefix);
     		docid.append(".");
     		// Create a calendar to get the date formatted properly
     		String[] ids = TimeZone.getAvailableIDs(-8 * 60 * 60 * 1000);
     		SimpleTimeZone pdt = new SimpleTimeZone(-8 * 60 * 60 * 1000, ids[0]);
     		pdt.setStartRule(Calendar.APRIL, 1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
     		pdt.setEndRule(Calendar.OCTOBER, -1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
     		Calendar calendar = new GregorianCalendar(pdt);
     		Date trialTime = new Date();
     		calendar.setTime(trialTime);
     		docid.append(calendar.get(Calendar.YEAR));
     		docid.append(calendar.get(Calendar.DAY_OF_YEAR));
     		docid.append(calendar.get(Calendar.HOUR_OF_DAY));
     		docid.append(calendar.get(Calendar.MINUTE));
     		docid.append(calendar.get(Calendar.SECOND));
     		return docid.toString();
     		return DocumentUtil.generateDocumentId(prefix, 0);
+    	}
     	/**
     	 * Insert a document into metacat. The expected result is passed as result
     	 */
     	protected String insertDocumentId(String docid, String docText, boolean result,
     			boolean expectKarmaException) {
     		debug("insertDocumentId() - docid=" + docid + " expectedResult=" + result

     import java.io.IOException;
     import java.io.Reader;
     import java.io.StringReader;
     import java.util.Calendar;
     import java.util.Date;
     import java.util.GregorianCalendar;
     import java.util.SimpleTimeZone;
     import java.util.TimeZone;
     import java.util.Vector;
     import junit.framework.Test;
-...
             debug("-------------------------------------------------------");
             try {
                 IdentifierManager im = IdentifierManager.getInstance();
                 String docid = insertTestDocument();
                 String guid = "test:"+docid;
                 im.createMapping(guid, docid);
                 String guid = insertTestDocument();
                 Reader r =  m.getObject(guid, null);
                 String doc = IOUtil.getAsString(r, true);
                 doc = doc +"\n";
-...
                         accessBlock, null, null,
                         null, null);
                 String docid = generateDocumentId();
                 debug("Generated id: " + docid);
         		StringReader sr = new StringReader(emldoc);
         		m.login(username,password);
-...
         		debug("response:\n"+response);
                 assertTrue(response.indexOf("success") != -1);
                 Thread.sleep(5000);
         		sr = new StringReader(emldoc);
         		debug("\nNow update the document...");
         		response = m.putObject(docid + ".2",sr,false);
-...
                 assertTrue(response.indexOf("success") != -1);
         		sr.close();
         		Thread.sleep(10000);
         		Thread.sleep(5000);
         		debug("\nFinally delete the document...");
         		response = m.deleteObject(docid + ".2");
-...
+              }
+        }
         /** Insert a test document, returning the docid that was used. */
         /** Insert a test document, returning the identifier that was used. */
         private String insertTestDocument()
+        {
             String accessBlock = getAccessBlock("public", true, true,
-...
                     null, "http://fake.example.com/somedata", null,
                     accessBlock, null, null,
                     null, null);
             String docid = generateDocumentId() + ".1";
             //String docid = generateDocumentId() + ".1";
             String guid = "testid:" + generateTimeString();
             StringReader sr = new StringReader(emldoc);
             String response;
             try {
                 m.login(username,password);
                 response = m.putObject(docid,sr,true);
                 response = m.putObject(guid, sr, true);
                 debug("response:\n"+response);
                 assertTrue(response.indexOf("success") != -1);
             } catch (InsufficientKarmaException e) {
-...
             } catch (MetacatAuthException e) {
                 fail(e.getMessage());
+            }
             return docid;
             return guid;
+        }
         /** Generate a timestamp for use in IDs. */
         private String generateTimeString()
+        {
             StringBuffer guid = new StringBuffer();
             // Create a calendar to get the date formatted properly
             String[] ids = TimeZone.getAvailableIDs(-8 * 60 * 60 * 1000);
             SimpleTimeZone pdt = new SimpleTimeZone(-8 * 60 * 60 * 1000, ids[0]);
             pdt.setStartRule(Calendar.APRIL, 1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
             pdt.setEndRule(Calendar.OCTOBER, -1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
             Calendar calendar = new GregorianCalendar(pdt);
             Date trialTime = new Date();
             calendar.setTime(trialTime);
             guid.append(calendar.get(Calendar.YEAR));
             guid.append(calendar.get(Calendar.DAY_OF_YEAR));
             guid.append(calendar.get(Calendar.HOUR_OF_DAY));
             guid.append(calendar.get(Calendar.MINUTE));
             guid.append(calendar.get(Calendar.SECOND));
             guid.append(calendar.get(Calendar.MILLISECOND));
             return guid.toString();
+        }
+    }

         private void loadSessionData() {
             SessionData sessionData = RequestUtil.getSessionData(request);
             // TODO: validate the session before allowing these values to be set
             username = sessionData.getUserName();
             password = sessionData.getPassword();
             groupNames = sessionData.getGroupNames();
             sessionId = sessionData.getId();
             if (username == null)
             if (username == null) {
                 username = "public";
+            }
+        }
         /**
-...
         /**
          *  Earthgrid API > Identifier Service > isRegistered Function : calls MetacatHandler > handleIdIsRegisteredAction
          * @param identifierId
          * @param guid
          * @throws IOException
          */
         private void isRegistered(String identifierId) throws IOException {
             params.put("docid", new String[] { identifierId });
         private void isRegistered(String guid) throws IOException
+        {
             // Look up the localId for this guid
             IdentifierManager im = IdentifierManager.getInstance();
             String localId = "";
             try {
                 localId = im.getLocalId(guid);
             } catch (McdbDocNotFoundException e) {
                 // TODO: Need to return the proper DataONE exception
+            }
             params.put("docid", new String[] { localId });
             PrintWriter out = response.getWriter();
             handler.handleIdIsRegisteredAction(out, params, response);
             out.close();
-...
         /**
          * Earthgrid API > Identifier Service > getNextRevision Function : calls MetacatHandler > handleGetRevisionAndDocTypeAction
          * @param identifierId
          * @param guid
          * @throws IOException
          */
         private void getNextRevision(String identifierId) throws IOException {
             params.put("docid", new String[] { identifierId });
         private void getNextRevision(String guid) throws IOException
+        {
             params.put("docid", new String[] { guid });
             PrintWriter out = response.getWriter();
             //handler.handleGetRevisionAndDocTypeAction(out, params);
             try {
                 // Make sure there is a docid
                 if (identifierId == null || identifierId.equals("")) {
                 if (guid == null || guid.equals("")) {
                     throw new Exception("User didn't specify docid!");
                 }//if
+                }
                 // Look up the localId for this guid
                 IdentifierManager im = IdentifierManager.getInstance();
                 String localId = "";
                 try {
                     localId = im.getLocalId(guid);
                 } catch (McdbDocNotFoundException e) {
                     // TODO: Need to return the proper DataONE exception
+                }
                 // Create a DBUtil object
                 DBUtil dbutil = new DBUtil();
                 // Get a rev and doctype
                 String revAndDocType = dbutil
                         .getCurrentRevisionAndDocTypeForGivenDocument(identifierId);
                         .getCurrentRevisionAndDocTypeForGivenDocument(localId);
                 int revision = Integer.parseInt(revAndDocType.split(";")[0]) + 1;
                 out.println("<?xml version=\"1.0\"?>");
-...
             try {
                 localId = im.getLocalId(guid);
             } catch (McdbDocNotFoundException e) {
                 // Need to return the proper DataONE exception
                 // TODO: Need to return the proper DataONE exception
+            }
             // Now use that localId to read the object and return it
-...
         private void query() throws Exception {
             /*  This block commented out because of the EcoGrid circular dependency.
              *  For now, query will not be supported until the circularity can be
              *  resolved, probably by movind the ecogrid query syntax transformers
              *  resolved, probably by moving the ecogrid query syntax transformers
              *  directly into the Metacat codebase.  MBJ 2010-02-03
             try {
-...
          */
         private void putObject(String objectId) throws IOException {
             // TODO: This function lacks proper handling of authz and authn, so it
             // seems that anyone can insert or update; interacts with
             // loadSessinData(), which doesn't validate the session
             String action = request.getParameter(FUNCTION_KEYWORD);
             if (action.equals(FUNCTION_NAME_UPDATE)
                     || action.equals(FUNCTION_NAME_INSERT)) {
                 //
                 // Check if the objectId exists
                 IdentifierManager im = IdentifierManager.getInstance();
                 if (im.identifierExists(objectId)) {
                     // TODO: return IdentifierNotUnique exception
+                }
                 // TODO: For updates, need to check if the old id exists, and if not throw an exception
                 // WARNING: This should not be a Reader if we are inserting data
                 // Nor should it be read into a String
                 // so this seems like a latent bug to me (MBJ; 16Mar2010)
-...
                     buffer.append(line);
+                }
                 params.put("docid", new String[] { objectId });
                 String localId = im.generateLocalId(objectId, 1);
                 params.put("docid", new String[] { localId });
                 params.put("doctext", new String[] { buffer.toString().trim() });
                 params.put("action", new String[] { action });
-...
                             params, username, groupNames);
                     out.close();
                 } else {
                     // TODO: throw exception to show lack of credentials
                     printError("Permission denied for user " + username, response);
+                }
             } else {
                 // TODO: throw the proper exception to indicate an invalid request
                 printError("Specifiy the operation type.(update or insert)",
                         response);
+            }

     import java.io.PrintWriter;
     import java.sql.SQLException;
     import java.util.Calendar;
     import java.util.Date;
     import java.util.GregorianCalendar;
     import java.util.Hashtable;
     import java.util.SimpleTimeZone;
     import java.util.Stack;
     import java.util.TimeZone;
     import java.util.Vector;
     import javax.servlet.http.HttpServletRequest;
-...
         private static Logger logMetacat = Logger.getLogger(DocumentUtil.class);
         private static char separator = '.';
         private static String prefix = "autogen";
         static {
             try {
             	separator = PropertyService.getProperty("document.accNumSeparator").charAt(0);
             	separator = PropertyService.getProperty("document.accNumSeparator").charAt(0);
             } catch (PropertyNotFoundException pnfe) {
             	logMetacat.error("DocumentUtil() - Could not retrieve account number separator. "
             	logMetacat.error("DocumentUtil() - Could not retrieve accession number separator. "
             			+ "Separator set to '.' : " + pnfe.getMessage());
+            }
             try {
                 prefix = PropertyService.getProperty("document.accNumPrefix");
             } catch (PropertyNotFoundException pnfe) {
                 logMetacat.error("DocumentUtil() - Could not retrieve accession number prefix. "
                         + "Prefix set to " + prefix + ": " + pnfe.getMessage());
+            }
+        }
         /**
-...
         	out.write(result);
+        }
         /**
          * Create a unique docid for use in inserts and updates using the default
          * prefix from the document.accNumPrefix property. Does not include the
          * 'revision' part of the id if revision is '0', otherwise sets the
          * revision number to 'revision'.
+         *
          * @param idPrefix the prefix to be used to construct the scope portion of the docid
          * @param revision the integer revision to use for this docid
          * @return a String docid based on the current date and time
          */
         public static String generateDocumentId(int revision) {
             return generateDocumentId(prefix, revision);
+        }
         /**
          * Create a unique docid for use in inserts and updates using the prefix
          * that is provided. Does not include the 'revision' part of the id if
          * revision is '0', otherwise sets the revision number to 'revision'.
+         *
          * @param idPrefix the prefix to be used to construct the scope portion of the docid
          * @param revision the integer revision to use for this docid
          * @return a String docid based on the current date and time
          */
         public static String generateDocumentId(String idPrefix, int revision)
+        {
             StringBuffer docid = new StringBuffer(idPrefix);
             docid.append(".");
             // Create a calendar to get the date formatted properly
             String[] ids = TimeZone.getAvailableIDs(-8 * 60 * 60 * 1000);
             SimpleTimeZone pdt = new SimpleTimeZone(-8 * 60 * 60 * 1000, ids[0]);
             pdt.setStartRule(Calendar.APRIL, 1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
             pdt.setEndRule(Calendar.OCTOBER, -1, Calendar.SUNDAY, 2 * 60 * 60 * 1000);
             Calendar calendar = new GregorianCalendar(pdt);
             Date trialTime = new Date();
             calendar.setTime(trialTime);
             docid.append(calendar.get(Calendar.YEAR));
             docid.append(calendar.get(Calendar.DAY_OF_YEAR));
             docid.append(calendar.get(Calendar.HOUR_OF_DAY));
             docid.append(calendar.get(Calendar.MINUTE));
             docid.append(calendar.get(Calendar.SECOND));
             docid.append(calendar.get(Calendar.MILLISECOND));
             if (revision > 0) {
                 docid.append(".").append(revision);
+            }
             return docid.toString();
+        }
+    }

     import edu.ucsb.nceas.metacat.database.DBConnection;
     import edu.ucsb.nceas.metacat.database.DBConnectionPool;
     import edu.ucsb.nceas.metacat.util.DocumentUtil;
     /**
      * Manage the relationship between Metacat local identifiers (LocalIDs) that are
-...
                 DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+            }
+        }
         /**
          * Given a global identifier (guid), create a suitable local identifier that
          * follows Metacat's docid semantics and format (scope.id.rev), and create
          * a mapping between these two identifiers.  This effectively reserves both
          * the global and the local identifier, as they will now be present in the
          * identifier mapping table.  If the incoming guid has the syntax of a
          * Metacat docid (scope.id.rev), then simply use it.
+         *
          * @param guid the global string identifier
          * @param rev the revision number to be used in the localId
          * @return String containing the localId to be used for Metacat operations
          */
         public String generateLocalId(String guid, int rev)
+        {
             String localId = "";
             boolean conformsToDocidFormat = false;
             // Check if the guid passed in is already in docid (scope.id.rev) format
             try {
                 AccessionNumber acc = new AccessionNumber(guid, "NONE");
                 if (new Integer(acc.getRev()).intValue() > 0) {
                     conformsToDocidFormat = true;
+                }
             } catch (NumberFormatException e) {
                 // No action needed, simply detecting invalid AccessionNumbers
             } catch (AccessionNumberException e) {
                 // No action needed, simply detecting invalid AccessionNumbers
             } catch (SQLException e) {
                 // No action needed, simply detecting invalid AccessionNumbers
+            }
             if (conformsToDocidFormat) {
                 // if it conforms, use it for both guid and localId
                 localId = guid;
             } else {
                 // if not, then generate a new unique localId
                 localId = DocumentUtil.generateDocumentId(rev);
+            }
             // Register this new pair in the identifier mapping table
             createMapping(guid, localId);
             return localId;
+        }
+    }

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Revision 5286

Added by Matt Jones about 14 years ago