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Revision 5377

Added by berkley over 14 years ago

working on a function to create dataone system metadata docs for legacy metacat objects that do not have SM.

     	public static Test suite()
+    	{
     		TestSuite suite = new TestSuite();
     		suite.addTest(new CrudServiceTest("initialize"));
     		/*suite.addTest(new CrudServiceTest("initialize"));
     		suite.addTest(new CrudServiceTest("testSingletonAccessor"));
     		suite.addTest(new CrudServiceTest("testCreateAndGet"));
     		suite.addTest(new CrudServiceTest("testGetSystemMetadata"));
     		suite.addTest(new CrudServiceTest("testUpdate"));
     		suite.addTest(new CrudServiceTest("testListObjects"));
     		suite.addTest(new CrudServiceTest("testAccessControl"));
     		//suite.addTest(new CrudServiceTest(""));
     		suite.addTest(new CrudServiceTest("testAccessControl"));*/
     		suite.addTest(new CrudServiceTest("testGenerateMissingSystemMetadata"));
     		return suite;
+    	}
     	/**
     	 * test the generation of system metadata for docs that don't already
     	 * have it.  This will be used for migration of existing object stores
     	 * to dataone.
     	 */
     	public void testGenerateMissingSystemMetadata()
+    	{
     	    printTestHeader("testGenerateMissingSystemMetadata");
     	    try
+    	    {
     	        CrudService cs = CrudService.getInstance();
     	        cs.generateMissingSystemMetadata();
+    	    }
     	    catch(Exception e)
+    	    {
     	        fail("Unexpected error generating missing system metadata: " + e.getMessage());
+    	    }
+    	}
     	/**
     	 * make sure that only valid sessions can update/delete
     	 */
     	public void testAccessControl()
+    	{
     	    printTestHeader("testAccessControl");
             try
+            {
                 CrudService cs = CrudService.getInstance();

     package edu.ucsb.nceas.metacattest;
     import java.sql.SQLException;
     import java.util.*;
     import edu.ucsb.nceas.MCTestCase;
     import edu.ucsb.nceas.metacat.IdentifierManager;
-...
                 fail(e1.getMessage());
+            }
+        }
         /**
          * test getting a list of all local ids
          */
         public void testGetAllLocalIds()
+        {
             try
+            {
                 List l = IdentifierManager.getInstance().getAllLocalIds();
                 for(int i=0; i<l.size(); i++)
+                {
                     //System.out.println(l.get(i));
+                }
                 assertTrue(l.size() > 0);
+            }
             catch(Exception e)
+            {
                 fail("Error in testGetAllLocalIds: " + e.getMessage());
+            }
+        }
         /** Test that IM instances can be created. */
         public void testGetInstance() {

             params.put(name, value);
+        }
         /**
          * Generate SystemMetadata for any object in the object store that does
          * not already have it.  SystemMetadata documents themselves, are, of course,
          * exempt.  This is a utility method for migration of existing object
          * stores to DataONE where SystemMetadata is required for all objects.  See
          * https://trac.dataone.org/ticket/591
          */
         public void generateMissingSystemMetadata()
+        {
             //get the list of ids with no SM
             List<String> l = IdentifierManager.getInstance().getLocalIdsWithNoSystemMetadata();
             for(int i=0; i<l.size(); i++)
             { //for each id, add a system metadata doc
                 String id = l.get(i);
                 System.out.println("Creating SystemMetadata for localId " + id);
+            }
+        }
         public Identifier create(AuthToken token, Identifier guid,
                 InputStream object, SystemMetadata sysmeta) throws InvalidToken,
                 ServiceFailure, NotAuthorized, IdentifierNotUnique, UnsupportedType,
-...
          * insert a systemMetadata doc
          */
         private void insertSystemMetadata(SystemMetadata sysmeta, SessionData sessionData)
             throws ServiceFailure {
             throws ServiceFailure
+        {
             logMetacat.debug("Starting to insert SystemMetadata...");
             // generate guid/localId pair for sysmeta
-...
             String localId = insertDocument(xml, sysMetaGuid, sessionData);
             //insert the system metadata doc id into the identifiers table to
             //link it to the data or metadata document
             IdentifierManager.getInstance().createSystemMetadataMapping(sysmeta.getIdentifier().getValue(), sysMetaGuid.getValue());
             IdentifierManager.getInstance().createSystemMetadataMapping(
                     sysmeta.getIdentifier().getValue(), sysMetaGuid.getValue());
+        }
         /**

     package edu.ucsb.nceas.metacat;
     import java.util.*;
     import java.sql.PreparedStatement;
     import java.sql.ResultSet;
     import java.sql.SQLException;
-...
         public static final String TYPE_SYSTEM_METADATA = "systemmetadata";
         public static final String TYPE_IDENTIFIER = "identifier";
         public static final String DATAONE_SM_DOCTYPE = "http://dataone.org/service/types/SystemMetadata/0.1";
         /**
          * The single instance of the manager that is always returned.
-...
+        }
         /**
          * return all local ids in the object store that do not have associated
          * system metadata and are not themselves system metadata
          */
         public List<String> getLocalIdsWithNoSystemMetadata()
+        {
             Vector<String> ids = new Vector<String>();
             //String sql = "select docid from identifier where guid in (select guid from systemmetadata)";
             String sql = "select docid from xml_documents where docid not " +
                 "in (select docid from identifier where guid in (select guid from systemmetadata)) " +
                 "and doctype not like '" + DATAONE_SM_DOCTYPE + "'";
             DBConnection dbConn = null;
             int serialNumber = -1;
             try
+            {
                 // Get a database connection from the pool
                 dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getLocalIdsWithNoSystemMetadata");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
                 PreparedStatement stmt = dbConn.prepareStatement(sql);
                 ResultSet rs = stmt.executeQuery();
                 while (rs.next())
+                {
                     String localid = rs.getString(1);
                     ids.add(localid);
+                }
                 stmt.close();
+            }
             catch (SQLException e)
+            {
                 logMetacat.error("Error while looking up the guid: "
                         + e.getMessage());
+            }
             finally
+            {
                 // Return database connection to the pool
                 DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+            }
             return ids;
+        }
         /**
          * return a listing of all local ids in the object store
          * @return a list of all local ids in metacat
          */
         public List<String> getAllLocalIds()
            throws Exception
+        {
             Vector<String> ids = new Vector<String>();
             String sql = "select docid from xml_documents";
             DBConnection dbConn = null;
             int serialNumber = -1;
             try
+            {
                 // Get a database connection from the pool
                 dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getAllLocalIds");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
                 PreparedStatement stmt = dbConn.prepareStatement(sql);
                 ResultSet rs = stmt.executeQuery();
                 while (rs.next())
+                {
                     String localid = rs.getString(1);
                     ids.add(localid);
+                }
                 stmt.close();
+            }
             catch (SQLException e)
+            {
                 logMetacat.error("Error while looking up the guid: "
                         + e.getMessage());
+            }
             finally
+            {
                 // Return database connection to the pool
                 DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+            }
             return ids;
+        }
         /**
          * Lookup a GUID from the database, and return the associated LocalID. If
          * the identifier is not found, throw an exception.
+         *
-...
             int serialNumber = -1;
             try {
                 // Get a database connection from the pool
                 dbConn = DBConnectionPool.getDBConnection("Identifier.getGUID");
                 dbConn = DBConnectionPool.getDBConnection("IdentifierManager.getGUID");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
-...
             createGenericMapping(guid, localId, TYPE_SYSTEM_METADATA);
+        }
         /**
          * update a mapping
          * @param guid
          * @param localId
          */
         public void updateSystemMetadataMapping(String guid, String localId)
+        {
             int serialNumber = -1;
-...
                 // Get a database connection from the pool
                 dbConn =
                     DBConnectionPool.getDBConnection("Identifier.createMapping");
                     DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
-...
           return docid + "." + rev;
+        }
         /**
          * create a mapping in the systemmetadata or identifier table
          * @param guid
          * @param localId
          * @param type
          */
         private void createGenericMapping(String guid, String localId, String type)
+        {
             if(!type.equals(TYPE_IDENTIFIER) &&
-...
                 // Get a database connection from the pool
                 dbConn =
                     DBConnectionPool.getDBConnection("Identifier.createMapping");
                     DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement

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Revision 5377

Added by berkley over 14 years ago