/src/edu/ucsb/nceas/metacat/IdentifierManager.java - Diff - Metacat - Ecoinformatics Redmine

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Revision 6099

Added by ben leinfelder almost 13 years ago

-remove system metadata guid -> local id mapping (there is no document for system metadata now)
-include system metadata elements when replicating data objects (TODO: transfer all system metadata structures with the docinfo request).
TODO: remove docid+rev from the systemMetadata table definition

     import edu.ucsb.nceas.metacat.database.DBConnection;
     import edu.ucsb.nceas.metacat.database.DBConnectionPool;
     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.utilities.PropertyNotFoundException;
     /**
      * Manage the relationship between Metacat local identifiers (LocalIDs) that are
      * codified as the (docid, rev) pair with globally uniqe string identifiers
      * codified as the (docid, rev) pair with globally unique string identifiers
      * (GUIDs) that are opaque strings.  This class provides methods to manage these
      * identifiers, and to search for and look up LocalIDs based on their GUID and
      * vice versa. IdentifierManager is a singleton.
-...
         public static final String TYPE_SYSTEM_METADATA = "systemmetadata";
         public static final String TYPE_IDENTIFIER = "identifier";
         public static String DATAONE_SM_DOCTYPE;
         /**
          * The single instance of the manager that is always returned.
          */
         private static IdentifierManager self = null;
         private Logger logMetacat = Logger.getLogger(EventLog.class);
         private Logger logMetacat = Logger.getLogger(IdentifierManager.class);
         /**
          * A private constructor that initializes the class when getInstance() is
          * called.
          */
         private IdentifierManager()
+        {
             try
+            {
                 DATAONE_SM_DOCTYPE = PropertyService.getProperty("crudService.listObjects.ReturnDoctype");
+            }
             catch(Exception e)
+            {
                 throw new RuntimeException("Error getting System Metadata doctype from " +
                         "the properties file.  Please make sure crudService.listObjects.ReturnDoctype " +
                         "exists in metacat.properties.");
+            }
+        }
         private IdentifierManager() {}
         /**
          * Return the single instance of the manager after initializing it if it
-...
         /**
          * return a hash of all of the info that is in the systemmetadata table
          * @param localId
          * @param guid
          * @return
          */
         public SystemMetadata getSystemMetadata(String localId)
         public SystemMetadata getSystemMetadata(String guid)
         	throws McdbDocNotFoundException
+        {
             try
+            {
                 AccessionNumber acc = new AccessionNumber(localId, "NONE");
                 localId = acc.getDocid();
+            }
             catch(Exception e)
+            {
                 //do nothing. just try the localId as it is
+            }
             SystemMetadata sysMeta = new SystemMetadata();
             String sql = "select guid, date_uploaded, rights_holder, checksum, checksum_algorithm, " +
               "origin_member_node, authoritive_member_node, date_modified, submitter, object_format, size " +
               "from systemmetadata where docid = ?";
               "from systemmetadata where guid = ?";
             DBConnection dbConn = null;
             int serialNumber = -1;
             try
-...
                 // Execute the statement
                 PreparedStatement stmt = dbConn.prepareStatement(sql);
                 stmt.setString(1, localId);
                 stmt.setString(1, guid);
                 ResultSet rs = stmt.executeQuery();
                 if (rs.next())
+                {
                     String guid = rs.getString(1);
                     Timestamp dateUploaded = rs.getTimestamp(2);
                     String rightsHolder = rs.getString(3);
                     String checksum = rs.getString(4);
-...
+                {
                     stmt.close();
                     DBConnectionPool.returnDBConnection(dbConn, serialNumber);
                     throw new McdbDocNotFoundException("Could not find " + localId);
                     throw new McdbDocNotFoundException("Could not find " + guid);
+                }
+            }
             catch (SQLException e)
+            {
                 e.printStackTrace();
                 logMetacat.error("Error while getting system metadata for localid " + localId + " : "
                 logMetacat.error("Error while getting system metadata for guid " + guid + " : "
                         + e.getMessage());
+            }
             finally
-...
                 String sql2 = "select principal_name, permission, perm_type, perm_order from xml_access " +
                 "where docid like '" + localId + "'";
                 System.out.println("executing sql: " + sql2);
                 logMetacat.debug("executing sql: " + sql2);
                 PreparedStatement stmt2 = dbConn.prepareStatement(sql2);
                 rs = stmt2.executeQuery();
                 Vector accessVector = new Vector();
-...
                     accessHash.put("permission", permission);
                     accessHash.put("permission_type", permissionType);
                     accessHash.put("permission_order", permissionOrder);
                     System.out.println("accessHash: " + accessHash.toString());
                     logMetacat.debug("accessHash: " + accessHash.toString());
                     accessVector.add(accessHash);
+                }
                 h.put("access", accessVector);
-...
         /**
          * return all local ids in the object store that do not have associated
          * system metadata and are not themselves system metadata
          * 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 + "'";
             String sql = "select docid, rev from xml_documents where docid not in " +
                 "(select docid from systemmetadata) and (docid not in " +
                 "(select docid from identifier where guid in (select guid from systemmetadata)))";
             String sql = "select docid, rev from xml_documents " +
             		"where docid not in " +
             		"(select docid from identifier where guid in (select guid from systemmetadata)))";
             DBConnection dbConn = null;
             int serialNumber = -1;
             try
-...
                     String localid = rs.getString(1);
                     String rev = rs.getString(2);
                     localid += "." + rev;
                     System.out.println("id to add SM for: " + localid);
                     logMetacat.debug("id to add SM for: " + localid);
                     ids.add(localid);
+                }
                 stmt.close();
-...
             return ids;
+        }
         /**
          * Lookup a GUID from the database, and return the associated LocalID. If
          * the identifier is not found, throw an exception.
+         *
          * @param guid the global identifier to look up
          * @return String containing the corresponding LocalId
          * @throws McdbDocNotFoundException if the identifier is not found
          */
         public String getLocalId(String guid) throws McdbDocNotFoundException
+        {
             return this.getLocalId(guid, TYPE_IDENTIFIER);
+        }
         /**
          * Determine if an identifier exists already, returning true if so.
-...
+        }
         /**
          * Create a mapping between two identifiers, one representing an
          * unconstrained, globally unique string (guid), and one a localId
          * in the Metacat docid format (scope.id.revision).
          * This mapping allows one to find the global id (guid) from the localId.
+         *
          * @param guid the global string identifier to be mapped
          * @param localId the local identifier to be mapped
          */
         public void createMapping(String guid, String localId)
+        {
             createGenericMapping(guid, localId, TYPE_IDENTIFIER);
+        }
         /**
+         *
          * @param guid
          * @param rev
          * @return
-...
+            }
             // Register this new pair in the identifier mapping table
             System.out.println("creating mapping in generateLocalId");
             logMetacat.debug("creating mapping in generateLocalId");
             if(!isSystemMetadata)
             { //don't do this if we're generating for system metadata
                 createMapping(guid, localId);
-...
         public String getGUID(String docid, int rev)
           throws McdbDocNotFoundException
+        {
             System.out.println("getting guid for " + docid);
             logMetacat.debug("getting guid for " + docid);
             String query = "select guid from identifier where docid = ? and rev = ?";
             String guid = null;
             boolean found = false;
             DBConnection dbConn = null;
             int serialNumber = -1;
-...
+        }
         /**
          * creates a mapping for a system metadata document, but DOES NOT add any
          * of the extra system metadata information to the table.  You must call
          * insertAdditionalSystemMetadataFields to complete the entry
+         *
          * @param guid the id to insert
          * @param localId the systemMetadata object to get the local id for
          */
         public void createSystemMetadataMapping(String guid, String localId)
+        {
             createGenericMapping(guid, localId, TYPE_SYSTEM_METADATA);
+        }
         /**
          * creates a system metadata mapping and adds additional fields from sysmeta
          * to the table for quick searching.
+         *
          * @param guid the id to insert
          * @param localId the systemMetadata object to get the local id for
          */
         public void createSystemMetadataMapping(SystemMetadata sysmeta, String localId)
         public void createSystemMetadata(SystemMetadata sysmeta)
+        {
             createGenericMapping(sysmeta.getIdentifier().getValue(), localId, TYPE_SYSTEM_METADATA);
             insertAdditionalSystemMetadataFields(sysmeta);
             insertSystemMetadata(sysmeta.getIdentifier().getValue());
             updateSystemMetadata(sysmeta);
+        }
         /**
          * update a system metadata mapping
          * @param guid
          * @param localId
          */
         public void updateSystemMetadataMapping(String guid, String localId)
+        {
         	updateMapping(guid, localId, TYPE_SYSTEM_METADATA);
+        }
         /**
          * update a mapping
          * @param guid
          * @param localId
          */
         public void updateMapping(String guid, String localId)
+        {
         	updateMapping(guid, localId, TYPE_IDENTIFIER);
+        }
         /**
          * update a mapping
          * @param guid
          * @param localId
          */
         private void updateMapping(String guid, String localId, String type)
+        {
         	if (!type.equals(TYPE_IDENTIFIER) && !type.equals(TYPE_SYSTEM_METADATA)) {
         		throw new RuntimeException("Cannot create mapping for type " + type +
         		            ".  Please choose 'identifier' or 'systemmetadata'.");
+        	}
             System.out.println("$$$$$$$$$$$$$$ updating mapping table");
             logMetacat.debug("$$$$$$$$$$$$$$ updating mapping table");
             int serialNumber = -1;
             DBConnection dbConn = null;
             try {
-...
                     DBConnectionPool.getDBConnection("IdentifierManager.updateMapping");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
                 String query = "update " + type + " set (docid, rev) = (?, ?) where guid='" + guid + "'";
                 //System.out.println("query: " + query + " for params: (guid:" + guid + ", docid=" + docid + ", rev=" + rev + ")");
                 // Execute the update statement
                 String query = "update " + TYPE_IDENTIFIER + " set (docid, rev) = (?, ?) where guid='" + guid + "'";
                 PreparedStatement stmt = dbConn.prepareStatement(query);
                 stmt.setString(1, docid);
                 stmt.setInt(2, rev);
-...
                 // Return database connection to the pool
                 DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+            }
             System.out.println("done updating mapping");
             logMetacat.debug("done updating mapping");
+        }
         /**
          * return the localId of a system metadata document based on its guid
          */
         public String getSystemMetadataLocalId(String guid)
           throws McdbDocNotFoundException
+        {
           return this.getLocalId(guid, TYPE_SYSTEM_METADATA);
+        }
         private void insertAdditionalSystemMetadataFields(long dateUploaded, String rightsHolder,
         private void updateSystemMetadataFields(long dateUploaded, String rightsHolder,
                 String checksum, String checksumAlgorithm, String originMemberNode,
                 String authoritativeMemberNode, long modifiedDate, String submitter,
                 String guid, String objectFormat, long size)
-...
                 stmt.setString(10, new Long(size).toString());
                 //where clause
                 stmt.setString(11, guid);
                 System.out.println("stmt: " + stmt.toString());
                 logMetacat.debug("stmt: " + stmt.toString());
                 //execute
                 int rows = stmt.executeUpdate();
-...
          * Insert the system metadata fields into the db
          * @param sm
          */
         public void insertAdditionalSystemMetadataFields(SystemMetadata sm)
         public void updateSystemMetadata(SystemMetadata sm)
+        {
             insertAdditionalSystemMetadataFields(
             updateSystemMetadataFields(
                     sm.getDateUploaded().getTime(),
                     sm.getRightsHolder().getValue(),
                     sm.getChecksum().getValue(),
-...
+        }
         /**
          * return a localId based on a guid.  The type can either be 'identifier'
          * to get an id from the identifier table or 'systemmetadata' to get
          * the identifier from the systemidentifier table
          * Lookup a localId given the GUID. If
          * the identifier is not found, throw an exception.
+         *
          * @param guid the global identifier to look up
          * @return String containing the corresponding LocalId
          * @throws McdbDocNotFoundException if the identifier is not found
          */
         private String getLocalId(String guid, String type)
           throws McdbDocNotFoundException
+        {
           if(!type.equals(TYPE_IDENTIFIER) &&
             !type.equals(TYPE_SYSTEM_METADATA))
+          {
             throw new RuntimeException("cannot lookup the identifier for type " + type +
               ".  Please choose 'identifier' or 'systemmetadata'.");
+          }
         public String getLocalId(String guid) throws McdbDocNotFoundException {
           String db_guid = "";
           String docid = "";
           int rev = 0;
           String query = "select guid, docid, rev from " + type + " where guid = ?";
           //System.out.println("query: " + query + " for params: (" + guid + ")");
           String query = "select guid, docid, rev from " + TYPE_IDENTIFIER + " where guid = ?";
           DBConnection dbConn = null;
           int serialNumber = -1;
-...
                     stmt.setTimestamp(1, new Timestamp(endTime.getTime()));
+                }
                 //System.out.println("LISTOBJECTS QUERY: " + stmt.toString());
                 //logMetacat.debug("LISTOBJECTS QUERY: " + stmt.toString());
                 ResultSet rs = stmt.executeQuery();
                 for(int i=0; i<start; i++)
-...
                         break;
+                    }
                     String guid = rs.getString(1);
                     //System.out.println("query found doc with guid " + guid);
                     //logMetacat.debug("query found doc with guid " + guid);
                     //Timestamp dateUploaded = rs.getTimestamp(2);
                     //String rightsHolder = rs.getString(3);
                     String checksum = rs.getString(4);
-...
             catch(Exception e)
+            {
                e.printStackTrace();
                System.out.println("Error querying system metadata: " + e.getMessage());
                logMetacat.error("Error querying system metadata: " + e.getMessage());
+            }
             finally
+            {
-...
+        }
         /**
          * create a mapping in the systemmetadata or identifier table
          * create a mapping in the identifier table
          * @param guid
          * @param localId
          * @param type
          */
         private void createGenericMapping(String guid, String localId, String type)
         public void createMapping(String guid, String localId)
+        {
             if(!type.equals(TYPE_IDENTIFIER) &&
             !type.equals(TYPE_SYSTEM_METADATA))
+            {
               throw new RuntimeException("Cannot create mapping for type " + type +
                 ".  Please choose 'identifier' or 'systemmetadata'.");
+            }
             int serialNumber = -1;
             DBConnection dbConn = null;
-...
                 AccessionNumber acc = new AccessionNumber(localId, "NOACTION");
                 String docid = acc.getDocid();
                 int rev = 1;
                 if(acc.getRev() != null)
+                {
                 if (acc.getRev() != null) {
                   rev = (new Integer(acc.getRev()).intValue());
+                }
                 // Get a database connection from the pool
                 dbConn =
                     DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
                 dbConn = DBConnectionPool.getDBConnection("IdentifierManager.createMapping");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
                 String query = "insert into " + type + " (guid, docid, rev) values (?, ?, ?)";
                 //System.out.println("query: " + query + " for params: (" + guid + ", " + docid + ", " + rev + ")");
                 String query = "insert into " + TYPE_IDENTIFIER + " (guid, docid, rev) values (?, ?, ?)";
                 PreparedStatement stmt = dbConn.prepareStatement(query);
                 stmt.setString(1, guid);
                 stmt.setString(2, docid);
                 stmt.setInt(3, rev);
                 System.out.println("generic mapping query: " + stmt.toString());
                 logMetacat.debug("mapping query: " + stmt.toString());
                 int rows = stmt.executeUpdate();
                 stmt.close();
             } catch (SQLException e) {
                 e.printStackTrace();
                 logMetacat.error("createGenericMapping: SQL error while creating a mapping to the " + type + " identifier: "
                 logMetacat.error("createGenericMapping: SQL error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
                         + e.getMessage());
             } catch (NumberFormatException e) {
                 e.printStackTrace();
                 logMetacat.error("createGenericMapping: NumberFormat error while creating a mapping to the " + type + " identifier: "
                 logMetacat.error("createGenericMapping: NumberFormat error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
                         + e.getMessage());
             } catch (AccessionNumberException e) {
                 e.printStackTrace();
                 logMetacat.error("createGenericMapping: AccessionNumber error while creating a mapping to the " + type + " identifier: "
                 logMetacat.error("createGenericMapping: AccessionNumber error while creating a mapping to the " + TYPE_IDENTIFIER + " identifier: "
                         + e.getMessage());
             } finally {
                 // Return database connection to the pool
                 DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+            }
+        }
         /**
          * create the systemmetadata record
          * @param guid
          */
         public void insertSystemMetadata(String guid)
+        {
             int serialNumber = -1;
             DBConnection dbConn = null;
             try {
                 // Get a database connection from the pool
                 dbConn = DBConnectionPool.getDBConnection("IdentifierManager.insertSystemMetadata");
                 serialNumber = dbConn.getCheckOutSerialNumber();
                 // Execute the insert statement
                 String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid) values (?)";
                 PreparedStatement stmt = dbConn.prepareStatement(query);
                 stmt.setString(1, guid);
                 logMetacat.debug("system metadata query: " + stmt.toString());
                 int rows = stmt.executeUpdate();
                 stmt.close();
             } catch (Exception e) {
                 e.printStackTrace();
                 logMetacat.error("Error while creating " + TYPE_SYSTEM_METADATA + " record: "
                         + e.getMessage());
             } finally {
                 // Return database connection to the pool
                 DBConnectionPool.returnDBConnection(dbConn, serialNumber);
+            }
+        }
+    }

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Revision 6099

Added by ben leinfelder almost 13 years ago